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\ No newline at end of file
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CONTROLS = {\n // Item types.\n ITEM_HISTORY: \"item_history\",\n ITEM_DATASET: \"item_dataset\",\n ITEM_WORKFLOW: \"item_workflow\",\n ITEM_PAGE: \"item_page\",\n ITEM_VISUALIZATION: \"item_visualization\",\n\n // Link dialogs.\n DIALOG_HISTORY_LINK: \"link_history\",\n DIALOG_DATASET_LINK: \"link_dataset\",\n DIALOG_WORKFLOW_LINK: \"link_workflow\",\n DIALOG_PAGE_LINK: \"link_page\",\n DIALOG_VISUALIZATION_LINK: \"link_visualization\",\n\n // Embed dialogs.\n DIALOG_EMBED_HISTORY: \"embed_history\",\n DIALOG_EMBED_DATASET: \"embed_dataset\",\n DIALOG_EMBED_WORKFLOW: \"embed_workflow\",\n DIALOG_EMBED_PAGE: \"embed_page\",\n DIALOG_EMBED_VISUALIZATION: \"embed_visualization\"\n};\n\n// Initialize Galaxy elements.\nfunction init_galaxy_elts(wym) {\n // Set up events to make annotation easy.\n $(\".annotation\", wym._doc.body).each(function() {\n $(this).click(function() {\n // Works in Safari, not in Firefox.\n var range = wym._doc.createRange();\n range.selectNodeContents(this);\n var selection = window.getSelection();\n selection.removeAllRanges();\n selection.addRange(range);\n var t = \"\";\n });\n });\n}\n\n// Based on the dialog type, return a dictionary of information about an item\nfunction get_item_info(dialog_type) {\n var item_singular, item_plural, item_controller;\n switch (dialog_type) {\n case CONTROLS.ITEM_HISTORY:\n item_singular = \"History\";\n item_plural = \"Histories\";\n item_controller = \"history\";\n item_class = \"History\";\n break;\n case CONTROLS.ITEM_DATASET:\n item_singular = \"Dataset\";\n item_plural = \"Datasets\";\n item_controller = \"dataset\";\n item_class = \"HistoryDatasetAssociation\";\n break;\n case CONTROLS.ITEM_WORKFLOW:\n item_singular = \"Workflow\";\n item_plural = \"Workflows\";\n item_controller = \"workflow\";\n item_class = \"StoredWorkflow\";\n break;\n case CONTROLS.ITEM_PAGE:\n item_singular = \"Page\";\n item_plural = \"Pages\";\n item_controller = \"page\";\n item_class = \"Page\";\n break;\n case CONTROLS.ITEM_VISUALIZATION:\n item_singular = \"Visualization\";\n item_plural = \"Visualizations\";\n item_controller = \"visualization\";\n item_class = \"Visualization\";\n break;\n }\n\n // Build ajax URL that lists items for selection.\n var item_list_action =\n \"list_\" + item_plural.toLowerCase() + \"_for_selection\";\n var ajax_url = list_objects_url.replace(\"LIST_ACTION\", item_list_action);\n\n // Set up and return dict.\n return {\n singular: item_singular,\n plural: item_plural,\n controller: item_controller,\n iclass: item_class,\n list_ajax_url: ajax_url\n };\n}\n\n// Make an item importable.\nfunction make_item_importable(item_controller, item_id, item_type) {\n var ajax_url = set_accessible_url.replace(\n \"ITEM_CONTROLLER\",\n item_controller\n );\n $.ajax({\n type: \"POST\",\n url: ajax_url,\n data: { id: item_id, accessible: \"True\" },\n error: function() {\n alert(\"Making \" + item_type + \" accessible failed\");\n }\n });\n}\n\n// Completely replace WYM's dialog handling\nWYMeditor.editor.prototype.dialog = function(\n dialogType,\n dialogFeatures,\n bodyHtml\n) {\n var wym = this;\n var sStamp = wym.uniqueStamp();\n var selected = wym.selected();\n\n // Swap out URL attribute for id/name attribute in link creation to enable anchor creation in page.\n function set_link_id() {\n // When \"set link id\" link clicked, update UI.\n $(\"#set_link_id\").click(function() {\n // Set label.\n $(\"#link_attribute_label\").text(\"ID/Name\");\n\n // Set input elt class, value.\n var attribute_input = $(\".wym_href\");\n attribute_input.addClass(\"wym_id\").removeClass(\"wym_href\");\n if (selected) attribute_input.val($(selected).attr(\"id\"));\n\n // Remove link.\n $(this).remove();\n });\n }\n\n // LINK DIALOG\n if (dialogType == WYMeditor.DIALOG_LINK) {\n if (selected) {\n $(wym._options.hrefSelector).val($(selected).attr(WYMeditor.HREF));\n $(wym._options.srcSelector).val($(selected).attr(WYMeditor.SRC));\n $(wym._options.titleSelector).val(\n 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\" +\n \"\" +\n \"\" +\n \"
\" +\n \"\" +\n \"\" +\n \"\" +\n \"
\",\n {\n Insert: function() {\n var iRows = $(wym._options.rowsSelector).val();\n var iCols = $(wym._options.colsSelector).val();\n\n if (iRows > 0 && iCols > 0) {\n var table = wym._doc.createElement(WYMeditor.TABLE);\n var newRow = null;\n var newCol = null;\n\n var sCaption = $(wym._options.captionSelector).val();\n\n //we create the caption\n var newCaption = table.createCaption();\n newCaption.innerHTML = sCaption;\n\n //we create the rows and cells\n for (var x = 0; x < iRows; x++) {\n newRow = table.insertRow(x);\n for (var y = 0; y < iCols; y++) {\n newRow.insertCell(y);\n }\n }\n\n //set the summary attr\n $(table).attr(\n \"summary\",\n $(wym._options.summarySelector).val()\n );\n\n //append the table after the selected container\n var node = $(\n wym.findUp(\n wym.container(),\n WYMeditor.MAIN_CONTAINERS\n )\n ).get(0);\n if (!node || !node.parentNode)\n $(wym._doc.body).append(table);\n else $(node).after(table);\n }\n hide_modal();\n },\n Cancel: function() {\n hide_modal();\n }\n }\n );\n }\n\n // INSERT \"GALAXY ITEM\" LINK DIALOG\n if (\n dialogType == CONTROLS.DIALOG_HISTORY_LINK ||\n dialogType == CONTROLS.DIALOG_DATASET_LINK ||\n dialogType == CONTROLS.DIALOG_WORKFLOW_LINK ||\n dialogType == CONTROLS.DIALOG_PAGE_LINK ||\n dialogType == CONTROLS.DIALOG_VISUALIZATION_LINK\n ) {\n // Based on item type, set useful vars.\n var item_info;\n switch (dialogType) {\n case CONTROLS.DIALOG_HISTORY_LINK:\n item_info = get_item_info(CONTROLS.ITEM_HISTORY);\n break;\n case CONTROLS.DIALOG_DATASET_LINK:\n item_info = get_item_info(CONTROLS.ITEM_DATASET);\n break;\n case CONTROLS.DIALOG_WORKFLOW_LINK:\n item_info = get_item_info(CONTROLS.ITEM_WORKFLOW);\n break;\n case CONTROLS.DIALOG_PAGE_LINK:\n item_info = get_item_info(CONTROLS.ITEM_PAGE);\n break;\n case CONTROLS.DIALOG_VISUALIZATION_LINK:\n item_info = get_item_info(CONTROLS.ITEM_VISUALIZATION);\n break;\n }\n\n require([\"mvc/grid/grid-view\"], function(GridView) {\n var grid = new GridView({\n url_base: item_info.list_ajax_url,\n dict_format: true,\n embedded: true\n });\n Galaxy.modal.show({\n title: \"Insert Link to \" + item_info.singular,\n body: $(\"\")\n .append(grid.$el)\n .append(\n $(\"\")\n .append(\n ''\n )\n .append(\n \"Make the selected \" +\n item_info.plural.toLowerCase() +\n \" accessible so that they can viewed by everyone.\"\n )\n ),\n closing_events: true,\n buttons: {\n Insert: function() {\n // Make selected items accessible (importable) ?\n var make_importable = false;\n if ($(\"#make-importable:checked\").val() != null)\n make_importable = true;\n\n // Insert links to history for each checked item.\n var item_ids = new Array();\n grid.$(\"input[name=id]:checked\").each(function() {\n var item_id = $(this).val();\n\n // Make item importable?\n if (make_importable)\n make_item_importable(\n item_info.controller,\n item_id,\n item_info.singular\n );\n\n // Insert link(s) to item(s). This is done by getting item info and then manipulating wym.\n var url_template = get_name_and_link_url + item_id;\n var ajax_url = url_template.replace(\n \"ITEM_CONTROLLER\",\n item_info.controller\n );\n $.getJSON(ajax_url, function(returned_item_info) {\n // Get link text.\n wym._exec(WYMeditor.CREATE_LINK, sStamp);\n var link_text = $(\n \"a[href=\" + sStamp + \"]\",\n wym._doc.body\n ).text();\n\n // Insert link: need to do different actions depending on link text.\n if (\n link_text == \"\" || // Firefox.\n link_text == sStamp // Safari\n ) {\n // User selected no text; create link from scratch and use default text.\n wym.insert(\n \"\" +\n item_info.singular +\n \" '\" +\n returned_item_info.name +\n \"'\"\n );\n } else {\n // Link created from selected text; add href and title.\n $(\"a[href=\" + sStamp + \"]\", wym._doc.body)\n .attr(\n WYMeditor.HREF,\n returned_item_info.link\n )\n .attr(\n WYMeditor.TITLE,\n item_info.singular + item_id\n );\n }\n });\n });\n Galaxy.modal.hide();\n },\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n });\n }\n // EMBED GALAXY OBJECT DIALOGS\n if (\n dialogType == CONTROLS.DIALOG_EMBED_HISTORY ||\n dialogType == CONTROLS.DIALOG_EMBED_DATASET ||\n dialogType == CONTROLS.DIALOG_EMBED_WORKFLOW ||\n dialogType == CONTROLS.DIALOG_EMBED_PAGE ||\n dialogType == CONTROLS.DIALOG_EMBED_VISUALIZATION\n ) {\n // Based on item type, set useful vars.\n var item_info;\n switch (dialogType) {\n case CONTROLS.DIALOG_EMBED_HISTORY:\n item_info = get_item_info(CONTROLS.ITEM_HISTORY);\n break;\n case CONTROLS.DIALOG_EMBED_DATASET:\n item_info = get_item_info(CONTROLS.ITEM_DATASET);\n break;\n case CONTROLS.DIALOG_EMBED_WORKFLOW:\n item_info = get_item_info(CONTROLS.ITEM_WORKFLOW);\n break;\n case CONTROLS.DIALOG_EMBED_PAGE:\n item_info = get_item_info(CONTROLS.ITEM_PAGE);\n break;\n case CONTROLS.DIALOG_EMBED_VISUALIZATION:\n item_info = get_item_info(CONTROLS.ITEM_VISUALIZATION);\n break;\n }\n\n require([\"mvc/grid/grid-view\"], function(GridView) {\n var grid = new GridView({\n url_base: item_info.list_ajax_url,\n dict_format: true,\n embedded: true\n });\n Galaxy.modal.show({\n title: \"Insert Link to \" + item_info.singular,\n body: $(\"\")\n .append(grid.$el)\n .append(\n $(\"\")\n .append(\n ''\n )\n .append(\n \"Make the selected \" +\n item_info.plural.toLowerCase() +\n \" accessible so that they can viewed by everyone.\"\n )\n ),\n closing_events: true,\n buttons: {\n Embed: function() {\n // Make selected items accessible (importable) ?\n var make_importable = false;\n if ($(\"#make-importable:checked\").val() != null)\n make_importable = true;\n\n grid.$(\"input[name=id]:checked\").each(function() {\n // Get item ID and name.\n var item_id = $(this).val();\n // Use ':first' because there are many labels in table; the first one is the item name.\n var item_name = $(\n \"label[for='\" + item_id + \"']:first\"\n ).text();\n\n if (make_importable)\n make_item_importable(\n item_info.controller,\n item_id,\n item_info.singular\n );\n\n // Embedded item HTML; item class is embedded in div container classes; this is necessary because the editor strips\n // all non-standard attributes when it returns its content (e.g. it will not return an element attribute of the form\n // item_class='History').\n var item_elt_id = item_info.iclass + \"-\" + item_id;\n var item_embed_html = [\n \"\"\n ].join(\"\");\n\n // Insert embedded item into document.\n wym.insert(item_embed_html);\n });\n Galaxy.modal.hide();\n },\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n });\n }\n};\n\n$(function() {\n // Generic error handling\n $(document).ajaxError(function(e, x) {\n // console.log( e, x );\n var message =\n x.responseText || x.statusText || \"Could not connect to server\";\n show_modal(\"Server error\", message, { \"Ignore error\": hide_modal });\n return false;\n });\n // Create editor\n $(\"[name=page_content]\").wymeditor({\n skin: \"galaxy\",\n basePath: editor_base_path,\n iframeBasePath: iframe_base_path,\n boxHtml:\n \"\" +\n WYMeditor.TOOLS +\n \" |
| \" +\n \" \" +\n // + WYMeditor.HTML\n WYMeditor.IFRAME +\n WYMeditor.STATUS +\n \" \" +\n \"\" +\n \" |
\",\n {\n \"Make link\": function() {\n // Get URL, name/title.\n var sUrl = $(wym._options.hrefSelector).val() || \"\",\n sId = $(\".wym_id\").val() || \"\",\n sName = $(wym._options.titleSelector).val() || \"\";\n\n if (sUrl || sId) {\n // Create link.\n wym._exec(WYMeditor.CREATE_LINK, sStamp);\n\n // Set link attributes.\n var link = $(\"a[href=\" + sStamp + \"]\", wym._doc.body);\n link\n .attr(WYMeditor.HREF, sUrl)\n .attr(WYMeditor.TITLE, sName)\n .attr(\"id\", sId);\n\n // If link's text is default (wym-...), change it to the title.\n if (link.text().indexOf(\"wym-\") === 0) {\n link.text(sName);\n }\n }\n hide_modal();\n },\n Cancel: function() {\n hide_modal();\n }\n },\n {},\n set_link_id\n );\n }\n\n // IMAGE DIALOG\n if (dialogType == WYMeditor.DIALOG_IMAGE) {\n if (wym._selected_image) {\n $(\n wym._options.dialogImageSelector +\n \" \" +\n wym._options.srcSelector\n ).val($(wym._selected_image).attr(WYMeditor.SRC));\n $(\n wym._options.dialogImageSelector +\n \" \" +\n wym._options.titleSelector\n ).val($(wym._selected_image).attr(WYMeditor.TITLE));\n $(\n wym._options.dialogImageSelector +\n \" \" +\n wym._options.altSelector\n ).val($(wym._selected_image).attr(WYMeditor.ALT));\n }\n show_modal(\n \"Image\",\n \"\" +\n \"
\",\n toolsItems: [\n { name: \"Bold\", title: \"Strong\", css: \"wym_tools_strong\" },\n { name: \"Italic\", title: \"Emphasis\", css: \"wym_tools_emphasis\" },\n {\n name: \"Superscript\",\n title: \"Superscript\",\n css: \"wym_tools_superscript\"\n },\n {\n name: \"Subscript\",\n title: \"Subscript\",\n css: \"wym_tools_subscript\"\n },\n {\n name: \"InsertOrderedList\",\n title: \"Ordered_List\",\n css: \"wym_tools_ordered_list\"\n },\n {\n name: \"InsertUnorderedList\",\n title: \"Unordered_List\",\n css: \"wym_tools_unordered_list\"\n },\n { name: \"Indent\", title: \"Indent\", css: \"wym_tools_indent\" },\n { name: \"Outdent\", title: \"Outdent\", css: \"wym_tools_outdent\" },\n { name: \"Undo\", title: \"Undo\", css: \"wym_tools_undo\" },\n { name: \"Redo\", title: \"Redo\", css: \"wym_tools_redo\" },\n { name: \"CreateLink\", title: \"Link\", css: \"wym_tools_link\" },\n { name: \"Unlink\", title: \"Unlink\", css: \"wym_tools_unlink\" },\n { name: \"InsertImage\", title: \"Image\", css: \"wym_tools_image\" },\n { name: \"InsertTable\", title: \"Table\", css: \"wym_tools_table\" }\n ]\n });\n // Get the editor object\n var editor = $.wymeditors(0);\n var save = function(callback) {\n show_modal(\"Saving page\", \"progress\");\n\n // Do save.\n $.ajax({\n url: save_url,\n type: \"POST\",\n data: {\n id: page_id,\n content: editor.xhtml(),\n annotations: JSON.stringify(new Object()),\n // annotations: JSON.stringify(annotations),\n _: \"true\"\n },\n success: function() {\n callback();\n }\n });\n };\n // Save button\n $(\"#save-button\").click(function() {\n save(function() {\n hide_modal();\n });\n });\n // Close button\n $(\"#close-button\").click(function() {\n // var new_content = editor.xhtml();\n // var changed = ( initial_content != new_content );\n var changed = false;\n if (changed) {\n var do_close = function() {\n window.onbeforeunload = undefined;\n window.document.location = page_list_url;\n };\n show_modal(\n \"Close editor\",\n \"There are unsaved changes to your page which will be lost.\",\n {\n Cancel: hide_modal,\n \"Save Changes\": function() {\n save(do_close);\n }\n },\n {\n \"Don't Save\": do_close\n }\n );\n } else {\n window.document.location = page_list_url;\n }\n });\n\n // Initialize galaxy elements.\n //init_galaxy_elts(editor);\n\n //\n // Containers, Galaxy style\n //\n var containers_menu = $(\n \"\"\n );\n $(\".wym_area_top\").append(containers_menu);\n\n // Add menu options.\n var items = {};\n $.each(editor._options.containersItems, function(k, v) {\n var tagname = v.name;\n items[v.title.replace(\"_\", \" \")] = function() {\n editor.container(tagname);\n };\n });\n make_popupmenu(containers_menu, items);\n\n //\n // Create 'Insert Link to Galaxy Object' menu.\n //\n\n // Add menu button.\n var insert_link_menu_button = $(\n \"\"\n ).addClass(\"galaxy-page-editor-button\");\n $(\".wym_area_top\").append(insert_link_menu_button);\n\n // Add menu options.\n make_popupmenu(insert_link_menu_button, {\n \"Insert History Link\": function() {\n editor.dialog(CONTROLS.DIALOG_HISTORY_LINK);\n },\n \"Insert Dataset Link\": function() {\n editor.dialog(CONTROLS.DIALOG_DATASET_LINK);\n },\n \"Insert Workflow Link\": function() {\n editor.dialog(CONTROLS.DIALOG_WORKFLOW_LINK);\n },\n \"Insert Page Link\": function() {\n editor.dialog(CONTROLS.DIALOG_PAGE_LINK);\n },\n \"Insert Visualization Link\": function() {\n editor.dialog(CONTROLS.DIALOG_VISUALIZATION_LINK);\n }\n });\n\n //\n // Create 'Embed Galaxy Object' menu.\n //\n\n // Add menu button.\n var embed_object_button = $(\n \"\"\n ).addClass(\"galaxy-page-editor-button\");\n $(\".wym_area_top\").append(embed_object_button);\n\n // Add menu options.\n make_popupmenu(embed_object_button, {\n \"Embed History\": function() {\n editor.dialog(CONTROLS.DIALOG_EMBED_HISTORY);\n },\n \"Embed Dataset\": function() {\n editor.dialog(CONTROLS.DIALOG_EMBED_DATASET);\n },\n \"Embed Workflow\": function() {\n editor.dialog(CONTROLS.DIALOG_EMBED_WORKFLOW);\n },\n \"Embed Visualization\": function() {\n editor.dialog(CONTROLS.DIALOG_EMBED_VISUALIZATION);\n }\n //\"Embed Page\": function() {\n // editor.dialog(CONTROLS.DIALOG_EMBED_PAGE);\n //}\n });\n});\n"]}
\ No newline at end of file
diff --git a/static/maps/i18n.js.map b/static/maps/i18n.js.map
index 71f56c3bc90..327dc0ed5ba 100644
--- a/static/maps/i18n.js.map
+++ b/static/maps/i18n.js.map
@@ -1 +1 @@
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It does the following:\n *\n * 1) A regular module can have a dependency on an i18n bundle, but the regular\n * module does not want to specify what locale to load. So it just specifies\n * the top-level bundle, like \"i18n!nls/colors\".\n *\n * This plugin will load the i18n bundle at nls/colors, see that it is a root/master\n * bundle since it does not have a locale in its name. It will then try to find\n * the best match locale available in that master bundle, then request all the\n * locale pieces for that best match locale. For instance, if the locale is \"en-us\",\n * then the plugin will ask for the \"en-us\", \"en\" and \"root\" bundles to be loaded\n * (but only if they are specified on the master bundle).\n *\n * Once all the bundles for the locale pieces load, then it mixes in all those\n * locale pieces into each other, then finally sets the context.defined value\n * for the nls/colors bundle to be that mixed in locale.\n *\n * 2) A regular module specifies a specific locale to load. For instance,\n * i18n!nls/fr-fr/colors. In this case, the plugin needs to load the master bundle\n * first, at nls/colors, then figure out what the best match locale is for fr-fr,\n * since maybe only fr or just root is defined for that locale. Once that best\n * fit is found, all of its locale pieces need to have their bundles loaded.\n *\n * Once all the bundles for the locale pieces load, then it mixes in all those\n * locale pieces into each other, then finally sets the context.defined value\n * for the nls/fr-fr/colors bundle to be that mixed in locale.\n */\n(function() {\n \"use strict\";\n\n //regexp for reconstructing the master bundle name from parts of the regexp match\n //nlsRegExp.exec(\"foo/bar/baz/nls/en-ca/foo\") gives:\n //[\"foo/bar/baz/nls/en-ca/foo\", \"foo/bar/baz/nls/\", \"/\", \"/\", \"en-ca\", \"foo\"]\n //nlsRegExp.exec(\"foo/bar/baz/nls/foo\") gives:\n //[\"foo/bar/baz/nls/foo\", \"foo/bar/baz/nls/\", \"/\", \"/\", \"foo\", \"\"]\n //so, if match[5] is blank, it means this is the top bundle definition.\n var nlsRegExp = /(^.*(^|\\/)nls(\\/|$))([^\\/]*)\\/?([^\\/]*)/;\n\n //Helper function to avoid repeating code. Lots of arguments in the\n //desire to stay functional and support RequireJS contexts without having\n //to know about the RequireJS contexts.\n function addPart(locale, master, needed, toLoad, prefix, suffix) {\n if (master[locale]) {\n needed.push(locale);\n if (master[locale] === true || master[locale] === 1) {\n toLoad.push(prefix + locale + \"/\" + suffix);\n }\n }\n }\n\n function addIfExists(req, locale, toLoad, prefix, suffix) {\n var fullName = prefix + locale + \"/\" + suffix;\n if (require._fileExists(req.toUrl(fullName + \".js\"))) {\n toLoad.push(fullName);\n }\n }\n\n /**\n * Simple function to mix in properties from source into target,\n * but only if target does not already have a property of the same name.\n * This is not robust in IE for transferring methods that match\n * Object.prototype names, but the uses of mixin here seem unlikely to\n * trigger a problem related to that.\n */\n function mixin(target, source, force) {\n var prop;\n for (prop in source) {\n if (\n source.hasOwnProperty(prop) &&\n (!target.hasOwnProperty(prop) || force)\n ) {\n target[prop] = source[prop];\n } else if (typeof source[prop] === \"object\") {\n if (!target[prop] && source[prop]) {\n target[prop] = {};\n }\n mixin(target[prop], source[prop], force);\n }\n }\n }\n\n define([\"module\"], function(module) {\n var masterConfig = module.config ? module.config() : {};\n\n return {\n version: \"2.0.4\",\n /**\n * Called when a dependency needs to be loaded.\n */\n load: function(name, req, onLoad, config) {\n config = config || {};\n\n if (config.locale) {\n masterConfig.locale = config.locale;\n }\n\n var masterName,\n match = nlsRegExp.exec(name),\n prefix = match[1],\n locale = match[4],\n suffix = match[5],\n parts = locale.split(\"-\"),\n toLoad = [],\n value = {},\n i,\n part,\n current = \"\";\n\n //If match[5] is blank, it means this is the top bundle definition,\n //so it does not have to be handled. Locale-specific requests\n //will have a match[4] value but no match[5]\n if (match[5]) {\n //locale-specific bundle\n prefix = match[1];\n masterName = prefix + suffix;\n } else {\n //Top-level bundle.\n masterName = name;\n suffix = match[4];\n locale = masterConfig.locale;\n if (!locale) {\n locale = masterConfig.locale =\n typeof navigator === \"undefined\"\n ? \"root\"\n : (navigator.language ||\n navigator.userLanguage ||\n \"root\"\n ).toLowerCase();\n }\n parts = locale.split(\"-\");\n }\n\n if (config.isBuild) {\n //Check for existence of all locale possible files and\n //require them if exist.\n toLoad.push(masterName);\n addIfExists(req, \"root\", toLoad, prefix, suffix);\n for (i = 0; i < parts.length; i++) {\n part = parts[i];\n current += (current ? \"-\" : \"\") + part;\n addIfExists(req, current, toLoad, prefix, suffix);\n }\n\n req(toLoad, function() {\n onLoad();\n });\n } else {\n //First, fetch the master bundle, it knows what locales are available.\n req([masterName], function(master) {\n //Figure out the best fit\n var needed = [],\n part;\n\n //Always allow for root, then do the rest of the locale parts.\n addPart(\"root\", master, needed, toLoad, prefix, suffix);\n for (i = 0; i < parts.length; i++) {\n part = parts[i];\n current += (current ? \"-\" : \"\") + part;\n addPart(\n current,\n master,\n needed,\n toLoad,\n prefix,\n suffix\n );\n }\n\n //Load all the parts missing.\n req(toLoad, function() {\n var i, partBundle, part;\n for (\n i = needed.length - 1;\n i > -1 && needed[i];\n i--\n ) {\n part = needed[i];\n partBundle = master[part];\n if (partBundle === true || partBundle === 1) {\n partBundle = req(\n prefix + part + \"/\" + suffix\n );\n }\n mixin(value, partBundle);\n }\n\n //All done, notify the loader.\n onLoad(value);\n });\n });\n }\n }\n };\n });\n})();\n"]}
\ No newline at end of file
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It does the following:\n *\n * 1) A regular module can have a dependency on an i18n bundle, but the regular\n * module does not want to specify what locale to load. So it just specifies\n * the top-level bundle, like \"i18n!nls/colors\".\n *\n * This plugin will load the i18n bundle at nls/colors, see that it is a root/master\n * bundle since it does not have a locale in its name. It will then try to find\n * the best match locale available in that master bundle, then request all the\n * locale pieces for that best match locale. For instance, if the locale is \"en-us\",\n * then the plugin will ask for the \"en-us\", \"en\" and \"root\" bundles to be loaded\n * (but only if they are specified on the master bundle).\n *\n * Once all the bundles for the locale pieces load, then it mixes in all those\n * locale pieces into each other, then finally sets the context.defined value\n * for the nls/colors bundle to be that mixed in locale.\n *\n * 2) A regular module specifies a specific locale to load. For instance,\n * i18n!nls/fr-fr/colors. In this case, the plugin needs to load the master bundle\n * first, at nls/colors, then figure out what the best match locale is for fr-fr,\n * since maybe only fr or just root is defined for that locale. Once that best\n * fit is found, all of its locale pieces need to have their bundles loaded.\n *\n * Once all the bundles for the locale pieces load, then it mixes in all those\n * locale pieces into each other, then finally sets the context.defined value\n * for the nls/fr-fr/colors bundle to be that mixed in locale.\n */\n(function() {\n \"use strict\";\n\n //regexp for reconstructing the master bundle name from parts of the regexp match\n //nlsRegExp.exec(\"foo/bar/baz/nls/en-ca/foo\") gives:\n //[\"foo/bar/baz/nls/en-ca/foo\", \"foo/bar/baz/nls/\", \"/\", \"/\", \"en-ca\", \"foo\"]\n //nlsRegExp.exec(\"foo/bar/baz/nls/foo\") gives:\n //[\"foo/bar/baz/nls/foo\", \"foo/bar/baz/nls/\", \"/\", \"/\", \"foo\", \"\"]\n //so, if match[5] is blank, it means this is the top bundle definition.\n var nlsRegExp = /(^.*(^|\\/)nls(\\/|$))([^\\/]*)\\/?([^\\/]*)/;\n\n //Helper function to avoid repeating code. Lots of arguments in the\n //desire to stay functional and support RequireJS contexts without having\n //to know about the RequireJS contexts.\n function addPart(locale, master, needed, toLoad, prefix, suffix) {\n if (master[locale]) {\n needed.push(locale);\n if (master[locale] === true || master[locale] === 1) {\n toLoad.push(prefix + locale + \"/\" + suffix);\n }\n }\n }\n\n function addIfExists(req, locale, toLoad, prefix, suffix) {\n var fullName = prefix + locale + \"/\" + suffix;\n if (require._fileExists(req.toUrl(fullName + \".js\"))) {\n toLoad.push(fullName);\n }\n }\n\n /**\n * Simple function to mix in properties from source into target,\n * but only if target does not already have a property of the same name.\n * This is not robust in IE for transferring methods that match\n * Object.prototype names, but the uses of mixin here seem unlikely to\n * trigger a problem related to that.\n */\n function mixin(target, source, force) {\n var prop;\n for (prop in source) {\n if (\n source.hasOwnProperty(prop) &&\n (!target.hasOwnProperty(prop) || force)\n ) {\n target[prop] = source[prop];\n } else if (typeof source[prop] === \"object\") {\n if (!target[prop] && source[prop]) {\n target[prop] = {};\n }\n mixin(target[prop], source[prop], force);\n }\n }\n }\n\n define([\"module\"], function(module) {\n var masterConfig = module.config ? module.config() : {};\n\n return {\n version: \"2.0.4\",\n /**\n * Called when a dependency needs to be loaded.\n */\n load: function(name, req, onLoad, config) {\n config = config || {};\n\n if (config.locale) {\n masterConfig.locale = config.locale;\n }\n\n var masterName,\n match = nlsRegExp.exec(name),\n prefix = match[1],\n locale = match[4],\n suffix = match[5],\n parts = locale.split(\"-\"),\n toLoad = [],\n value = {},\n i,\n part,\n current = \"\";\n\n //If match[5] is blank, it means this is the top bundle definition,\n //so it does not have to be handled. Locale-specific requests\n //will have a match[4] value but no match[5]\n if (match[5]) {\n //locale-specific bundle\n prefix = match[1];\n masterName = prefix + suffix;\n } else {\n //Top-level bundle.\n masterName = name;\n suffix = match[4];\n locale = masterConfig.locale;\n if (!locale) {\n locale = masterConfig.locale =\n typeof navigator === \"undefined\"\n ? \"root\"\n : (navigator.language ||\n navigator.userLanguage ||\n \"root\"\n ).toLowerCase();\n }\n parts = locale.split(\"-\");\n }\n\n if (config.isBuild) {\n //Check for existence of all locale possible files and\n //require them if exist.\n toLoad.push(masterName);\n addIfExists(req, \"root\", toLoad, prefix, suffix);\n for (i = 0; i < parts.length; i++) {\n part = parts[i];\n current += (current ? \"-\" : \"\") + part;\n addIfExists(req, current, toLoad, prefix, suffix);\n }\n\n req(toLoad, function() {\n onLoad();\n });\n } else {\n //First, fetch the master bundle, it knows what locales are available.\n req([masterName], function(master) {\n //Figure out the best fit\n var needed = [],\n part;\n\n //Always allow for root, then do the rest of the locale parts.\n addPart(\"root\", master, needed, toLoad, prefix, suffix);\n for (i = 0; i < parts.length; i++) {\n part = parts[i];\n current += (current ? \"-\" : \"\") + part;\n addPart(\n current,\n master,\n needed,\n toLoad,\n prefix,\n suffix\n );\n }\n\n //Load all the parts missing.\n req(toLoad, function() {\n var i, partBundle, part;\n for (\n i = needed.length - 1;\n i > -1 && needed[i];\n i--\n ) {\n part = needed[i];\n partBundle = master[part];\n if (partBundle === true || partBundle === 1) {\n partBundle = req(\n prefix + part + \"/\" + suffix\n );\n }\n mixin(value, partBundle);\n }\n\n //All done, notify the loader.\n onLoad(value);\n });\n });\n }\n }\n };\n });\n})();\n"]}
\ No newline at end of file
diff --git a/static/maps/layout/generic-nav-view.js.map b/static/maps/layout/generic-nav-view.js.map
index cac8c0af1a7..c565fc5c816 100644
--- a/static/maps/layout/generic-nav-view.js.map
+++ b/static/maps/layout/generic-nav-view.js.map
@@ -1 +1 @@
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\ No newline at end of file
+{"version":3,"sources":["layout/generic-nav-view.js"],"names":["define","Modal","GenericNavView","Backbone","View","extend","initialize","this","modal","makeModalIframe","e","$el_chat_modal_header","$el_chat_modal_body","iframe_template","class_names","window","Galaxy","config","communication_server_host","communication_server_port","query_string","escape","user","attributes","username","port","title_separator","cls","closing_events","frame_height","show","$","click","addClass","find","remove","removeAttr","append","css","height","hasClass","removeClass","width","attr","frame_width","self","navItem","icon","tooltip","render","id","visible","onclick"],"mappings":"kCACAA,QAAQ,mBAAoB,SAASC,GACjC,IAAIC,EAAiBC,SAASC,KAAKC,QAFvCC,WAAA,WACQC,KAAAC,MAAA,MAICC,gBAHqC,SAAAC,GAKtC,IAGIC,EAmBQ,KAnBRC,EAAA,KAAAC,EAwBIC,+DA3BRC,OAAAC,OAAAC,OAAAC,0BAiBQL,IAhBRJ,OAAiBO,OAAAC,OAAAE,2BAQTC,aAPJC,OAAAN,OAAAC,OAAAM,KAAAC,WAAAC,UAaIb,mCAZ4BO,OAC5BO,OAAOV,OAAOC,OAAOC,kCAyBzB,eAuDU,OA7CNS,EAAAA,eAAAA,OALkC,GAMlCC,EAAAA,eAAKb,SAGTZ,EAAAM,MAAA,IAAAP,EAAAG,MACAF,KAAAA,EACAS,OAXeH,IAYfI,MAXUC,IAYVe,gBAAA,EACAjB,iBAAAA,EACAC,IAbYiB,wBAiBZ3B,EAAAM,MAAAsB,OACAC,EAAkBC,EAAAA,6BACdD,EAAEA,EAAF,2BAEJpB,EAAAsB,SAAA,qBACAF,EAAEE,SAAA,qBACEtB,EAAMuB,KAAA,MAAAC,SACFJ,EAAEK,WAAA,6BACFL,EAAEM,OA9BNN,uPAkCIA,EAAAA,gBAAEC,MAAA,SAAAtB,GACFqB,EAAAA,eAAEO,IAAA,UAAA,UAGFP,EAAAA,0BAAEC,MAAA,SAA2BO,GAC7BR,EAAAA,0BAAES,SACGC,cAELV,EAAAA,6BAAAW,MAAiC,UACjCX,EAAAA,2BAAEQ,OAA8B,SACnCR,EAAA,0BAjBLU,YAAA,aAmBOR,SAAP,eAlFkCF,EAAA,0BAAAY,KAAA,QAAA,YAuE1BZ,EAAE,0BAA0BO,IAAI,cAAe,WAenDP,EAAA,6BAAWW,MAAAE,SACXC,EAAAA,2BAAJN,OAAAV,SACIiB,EAAAA,0BACJA,YAAU,eACFb,SAAA,aACJc,EAAAA,0BAFMJ,KAAA,QAAA,YAGNK,EAAAA,0BAHMV,IAAA,cAAA,YAAV/B,MAHJ0C,OAAQ,WAUJ,OAjGZC,GAAA,mBA4FgBH,KAAM,eACNC,QAAS,cACTG,SAAS,EACTC,QAML7C,KANmBE,oBAM1B,OACIP,eAAgBA","file":"../../scripts/layout/generic-nav-view.js","sourcesContent":["/** Real-time Communication feature **/\ndefine([\"mvc/ui/ui-modal\"], function(Modal) {\n var GenericNavView = Backbone.View.extend({\n initialize: function() {\n this.modal = null;\n },\n\n /** makes bootstrap modal and iframe inside it */\n makeModalIframe: function(e) {\n // make modal\n var host = window.Galaxy.config.communication_server_host,\n port = window.Galaxy.config.communication_server_port,\n username = escape(window.Galaxy.user.attributes.username),\n persistent_communication_rooms = escape(\n window.Galaxy.config.persistent_communication_rooms\n ),\n query_string =\n \"?username=\" +\n username +\n \"&persistent_communication_rooms=\" +\n persistent_communication_rooms,\n src = host + \":\" + port + query_string,\n $el_chat_modal_header = null,\n $el_chat_modal_body = null,\n iframe_template =\n '',\n header_template =\n '' +\n '' +\n '',\n frame_height = 350,\n frame_width = 600,\n class_names = \"ui-modal chat-modal\";\n\n // deletes the chat modal if already present and create one\n if ($(\".chat-modal\").length > 0) {\n $(\".chat-modal\").remove();\n }\n // creates a modal\n GenericNavView.modal = new Modal.View({\n body: iframe_template,\n height: frame_height,\n width: frame_width,\n closing_events: true,\n title_separator: false,\n cls: class_names\n });\n\n // shows modal\n GenericNavView.modal.show();\n $el_chat_modal_header = $(\".chat-modal .modal-header\");\n $el_chat_modal_body = $(\".chat-modal .modal-body\");\n // adjusts the css of bootstrap modal for chat\n $el_chat_modal_header.addClass(\"modal-header-body\");\n $el_chat_modal_body.addClass(\"modal-header-body\");\n $el_chat_modal_header.find(\"h4\").remove();\n $el_chat_modal_header.removeAttr(\"min-height padding border\");\n $el_chat_modal_header.append(header_template);\n // click event of the close button for chat\n $(\".close-modal\").click(function(e) {\n $(\".chat-modal\").css(\"display\", \"none\");\n });\n // click event of expand and compress icon\n $(\".expand-compress-modal\").click(function(e) {\n if ($(\".expand-compress-modal\").hasClass(\"fa-expand\")) {\n $(\".chat-modal .modal-dialog\").width(\"1000px\");\n $(\".chat-modal .modal-body\").height(\"575px\");\n $(\".expand-compress-modal\")\n .removeClass(\"fa-expand\")\n .addClass(\"fa-compress\");\n $(\".expand-compress-modal\").attr(\"title\", \"Minimize\");\n $(\".expand-compress-modal\").css(\"margin-left\", \"96.2%\");\n } else {\n $(\".chat-modal .modal-dialog\").width(frame_width + \"px\");\n $(\".chat-modal .modal-body\").height(frame_height + \"px\");\n $(\".expand-compress-modal\")\n .removeClass(\"fa-compress\")\n .addClass(\"fa-expand\");\n $(\".expand-compress-modal\").attr(\"title\", \"Maximize\");\n $(\".expand-compress-modal\").css(\"margin-left\", \"93.2%\");\n }\n });\n return this;\n },\n\n /**renders the chat icon as a nav item*/\n render: function() {\n var self = this,\n navItem = {};\n navItem = {\n id: \"show-chat-online\",\n icon: \"fa-comment-o\",\n tooltip: \"Chat online\",\n visible: false,\n onclick: self.makeModalIframe\n };\n return navItem;\n }\n });\n\n return {\n GenericNavView: GenericNavView\n };\n});\n"]}
\ No newline at end of file
diff --git a/static/maps/layout/masthead.js.map b/static/maps/layout/masthead.js.map
index 08ed87be94c..8e036baf488 100644
--- a/static/maps/layout/masthead.js.map
+++ b/static/maps/layout/masthead.js.map
@@ -1 +1 @@
-{"version":3,"sources":["layout/masthead.js"],"names":["define","View","initialize","Utils","options","Scratchbook","QuotaMeter","$navbarBrandLink","extend","$navbarBrandImage","$navbarBrandTitle","this","$navbarTabs","$quoteMeter","_template","$","collection","Collection","self","append","on","Menu","callback","model","Tab","render","$el","frame","each","m","fetch","Galaxy","quotaMeter","UserQuotaMeter","preventDefault","user","el","q","e","text","target","closest","length","attr","hide","$download_link","get","html","brand","logo_url","logo_src"],"mappings":"aAAAA,QAEQ,cAMA,cACIC,qBACAC,4BAEI,SAAAC,EAAKC,EAALC,EAAAC,GAyGR,OACIL,KAxGSM,SAAAA,KAALC,QACAN,WAAKO,SAAAA,GACL,IAAKC,EAAAA,KACLC,KAAKC,QAAcR,EACnBO,KAAKE,WAAcF,KAAAG,aAJnBH,KAAKJ,iBAAmBI,KAAKI,EAAE,sBAM/BJ,KAAAF,kBAAAE,KAAAI,EAAA,uBACAJ,KAAKK,kBAAsBC,KAAAA,EAAAA,uBAC3BN,KAAKK,YACGL,KAAOI,EAAA,gBACPG,KAAKN,YAAYO,KACbJ,EAAA,0BAMPK,KAAGJ,WAAY,IAAAK,EAASC,WACrBJ,KAAKF,WACDM,GAAAA,MAAA,SAAAC,GADJL,EAAAN,YAAAO,OAIQf,IAAAA,EAdhBoB,KAAAD,MAAAA,IAAAE,SAAAC,OAiBOC,GAAP,QAAoBA,WAChBX,EAAYJ,YAAKI,UAThBI,GAAG,WAAY,SAASE,GAY7BJ,EAAAF,WAAAY,KAAA,SAAAC,GACAP,EAAAO,OAIYC,MAAKjB,KAAAA,SAIjBkB,OAAAJ,MAAAhB,KAAAgB,MAAA,IAAAtB,GACAW,WAAAL,KACiBK,aASJe,OAAAC,WAAArB,KAAAqB,WAAA,IAAA1B,EAAA2B,gBAKCC,MAAAA,OAAFC,KACHC,GAAAzB,KAAAE,cAQGwB,EAAAA,QAJJjB,GAAA,QAAA,SAAAkB,GAMIC,IAAAA,EAAaxB,EAAAuB,EAAAE,QAAAC,QAAA,eACb,GAAOF,EAAPG,SACH,IAAA3B,EAAA,uBAAA2B,QA5BT3B,EAAA,QAAAI,OA5CwBJ,EAAA,aAmDC4B,KAAK,KAAM,YAyBrBC,QAOVnC,EAAAA,uBAAmCL,KACxBqB,MAChBoB,EAAAF,KAAA,SA1BYL,EAAEJ,oBAgCVd,GAAA,eAAA,WAcP,IAAAmB,EAAA,GAnCW,GAtEhBrB,EAAAF,WAAAY,KAAA,SAAAL,GAiEoB,IAAIc,EA2CjBd,EAAAuB,IAAA,mBACG7C,EAAAA,IAAAA,iBAAAA,GADVoC,IAAAE,GAAAF,EAAA,OAtC6B,KAATE,EACA,OAAOA,KAKvBd,OAAQ,WASJ,OARAd,KAAKD,kBAAkBqC,KACnB,WACMpC,KAAKP,QAAQ4C,OAAS,KAAOrC,KAAKP,QAAQ4C,OACxC,KAEZrC,KAAKJ,iBAAiBoC,KAAK,OAAQhC,KAAKP,QAAQ6C,UAChDtC,KAAKF,kBAAkBkC,KAAK,MAAOhC,KAAKP,QAAQ8C,UAChDvC,KAAKqB,WAAWP,SACTd,MAIXG,UAAW,WACP,MACI","file":"../../scripts/layout/masthead.js","sourcesContent":["define(\n [\n \"utils/utils\",\n \"layout/menu\",\n \"layout/scratchbook\",\n \"mvc/user/user-quotameter\"\n ],\n function(Utils, Menu, Scratchbook, QuotaMeter) {\n /** Masthead **/\n var View = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.options = options;\n this.setElement(this._template());\n this.$navbarBrandLink = this.$(\".navbar-brand-link\");\n this.$navbarBrandImage = this.$(\".navbar-brand-image\");\n this.$navbarBrandTitle = this.$(\".navbar-brand-title\");\n this.$navbarTabs = this.$(\".navbar-tabs\");\n this.$quoteMeter = this.$(\".quota-meter-container\");\n\n // build tabs\n this.collection = new Menu.Collection();\n this.collection\n .on(\"add\", function(model) {\n self.$navbarTabs.append(\n new Menu.Tab({ model: model }).render().$el\n );\n })\n .on(\"reset\", function() {\n self.$navbarTabs.empty();\n })\n .on(\"dispatch\", function(callback) {\n self.collection.each(function(m) {\n callback(m);\n });\n })\n .fetch(this.options);\n\n // scratchbook\n Galaxy.frame = this.frame = new Scratchbook({\n collection: this.collection\n });\n\n // set up the quota meter (And fetch the current user data from trans)\n // add quota meter to masthead\n Galaxy.quotaMeter = this.quotaMeter = new QuotaMeter.UserQuotaMeter(\n {\n model: Galaxy.user,\n el: this.$quoteMeter\n }\n );\n\n // loop through beforeunload functions if the user attempts to unload the page\n $(window)\n .on(\"click\", function(e) {\n var $download_link = $(e.target).closest(\"a[download]\");\n if ($download_link.length == 1) {\n if ($(\"iframe[id=download]\").length === 0) {\n $(\"body\").append(\n $(\"\")\n .attr(\"id\", \"download\")\n .hide()\n );\n }\n $(\"iframe[id=download]\").attr(\n \"src\",\n $download_link.attr(\"href\")\n );\n e.preventDefault();\n }\n })\n .on(\"beforeunload\", function() {\n var text = \"\";\n self.collection.each(function(model) {\n var q =\n model.get(\"onbeforeunload\") &&\n model.get(\"onbeforeunload\")();\n q && (text += q + \" \");\n });\n if (text !== \"\") {\n return text;\n }\n });\n },\n\n render: function() {\n this.$navbarBrandTitle.html(\n \"Galaxy \" +\n ((this.options.brand && \"/ \" + this.options.brand) ||\n \"\")\n );\n this.$navbarBrandLink.attr(\"href\", this.options.logo_url);\n this.$navbarBrandImage.attr(\"src\", this.options.logo_src);\n this.quotaMeter.render();\n return this;\n },\n\n /** body template */\n _template: function() {\n return (\n '
\" +\n \"
\" +\n \"\" +\n \"
\" +\n \"\" +\n \"\" +\n \"
\" +\n \"
\" +\n \"\" +\n \"
\" +\n \"\" +\n \"\" +\n \"
\" +\n \"
\" +\n \"\" +\n \"
\",\n {\n Insert: function() {\n var sUrl = $(wym._options.srcSelector).val();\n if (sUrl.length > 0) {\n wym._exec(WYMeditor.INSERT_IMAGE, sStamp);\n $(\"img[src$=\" + sStamp + \"]\", wym._doc.body)\n .attr(WYMeditor.SRC, sUrl)\n .attr(\n WYMeditor.TITLE,\n $(wym._options.titleSelector).val()\n )\n .attr(\n WYMeditor.ALT,\n $(wym._options.altSelector).val()\n );\n }\n hide_modal();\n },\n Cancel: function() {\n hide_modal();\n }\n }\n );\n return;\n }\n\n // TABLE DIALOG\n if (dialogType == WYMeditor.DIALOG_TABLE) {\n show_modal(\n \"Table\",\n \"\" +\n \"\" +\n \"
\" +\n \"
\" +\n \"\" +\n \"
\" +\n \"\" +\n \"\" +\n \"
\" +\n \"
\" +\n \"\" +\n \"
\" +\n \"\" +\n \"\" +\n \"
\" +\n \"\" +\n \"\" +\n \"
\" +\n \"\" +\n \"\" +\n \"\" +\n \"
\",\n {\n Insert: function() {\n var iRows = $(wym._options.rowsSelector).val();\n var iCols = $(wym._options.colsSelector).val();\n\n if (iRows > 0 && iCols > 0) {\n var table = wym._doc.createElement(WYMeditor.TABLE);\n var newRow = null;\n var newCol = null;\n\n var sCaption = $(wym._options.captionSelector).val();\n\n //we create the caption\n var newCaption = table.createCaption();\n newCaption.innerHTML = sCaption;\n\n //we create the rows and cells\n for (var x = 0; x < iRows; x++) {\n newRow = table.insertRow(x);\n for (var y = 0; y < iCols; y++) {\n newRow.insertCell(y);\n }\n }\n\n //set the summary attr\n $(table).attr(\n \"summary\",\n $(wym._options.summarySelector).val()\n );\n\n //append the table after the selected container\n var node = $(\n wym.findUp(\n wym.container(),\n WYMeditor.MAIN_CONTAINERS\n )\n ).get(0);\n if (!node || !node.parentNode)\n $(wym._doc.body).append(table);\n else $(node).after(table);\n }\n hide_modal();\n },\n Cancel: function() {\n hide_modal();\n }\n }\n );\n }\n\n // INSERT \"GALAXY ITEM\" LINK DIALOG\n if (\n dialogType == CONTROLS.DIALOG_HISTORY_LINK ||\n dialogType == CONTROLS.DIALOG_DATASET_LINK ||\n dialogType == CONTROLS.DIALOG_WORKFLOW_LINK ||\n dialogType == CONTROLS.DIALOG_PAGE_LINK ||\n dialogType == CONTROLS.DIALOG_VISUALIZATION_LINK\n ) {\n // Based on item type, set useful vars.\n var item_info;\n switch (dialogType) {\n case CONTROLS.DIALOG_HISTORY_LINK:\n item_info = get_item_info(CONTROLS.ITEM_HISTORY);\n break;\n case CONTROLS.DIALOG_DATASET_LINK:\n item_info = get_item_info(CONTROLS.ITEM_DATASET);\n break;\n case CONTROLS.DIALOG_WORKFLOW_LINK:\n item_info = get_item_info(CONTROLS.ITEM_WORKFLOW);\n break;\n case CONTROLS.DIALOG_PAGE_LINK:\n item_info = get_item_info(CONTROLS.ITEM_PAGE);\n break;\n case CONTROLS.DIALOG_VISUALIZATION_LINK:\n item_info = get_item_info(CONTROLS.ITEM_VISUALIZATION);\n break;\n }\n\n require([\"mvc/grid/grid-view\"], function(GridView) {\n var grid = new GridView({\n url_base: item_info.list_ajax_url,\n dict_format: true,\n embedded: true\n });\n Galaxy.modal.show({\n title: \"Insert Link to \" + item_info.singular,\n body: $(\"\")\n .append(grid.$el)\n .append(\n $(\"\")\n .append(\n ''\n )\n .append(\n \"Make the selected \" +\n item_info.plural.toLowerCase() +\n \" accessible so that they can viewed by everyone.\"\n )\n ),\n closing_events: true,\n buttons: {\n Insert: function() {\n // Make selected items accessible (importable) ?\n var make_importable = false;\n if ($(\"#make-importable:checked\").val() != null)\n make_importable = true;\n\n // Insert links to history for each checked item.\n var item_ids = new Array();\n grid.$(\"input[name=id]:checked\").each(function() {\n var item_id = $(this).val();\n\n // Make item importable?\n if (make_importable)\n make_item_importable(\n item_info.controller,\n item_id,\n item_info.singular\n );\n\n // Insert link(s) to item(s). This is done by getting item info and then manipulating wym.\n var url_template = get_name_and_link_url + item_id;\n var ajax_url = url_template.replace(\n \"ITEM_CONTROLLER\",\n item_info.controller\n );\n $.getJSON(ajax_url, function(returned_item_info) {\n // Get link text.\n wym._exec(WYMeditor.CREATE_LINK, sStamp);\n var link_text = $(\n \"a[href=\" + sStamp + \"]\",\n wym._doc.body\n ).text();\n\n // Insert link: need to do different actions depending on link text.\n if (\n link_text == \"\" || // Firefox.\n link_text == sStamp // Safari\n ) {\n // User selected no text; create link from scratch and use default text.\n wym.insert(\n \"\" +\n item_info.singular +\n \" '\" +\n returned_item_info.name +\n \"'\"\n );\n } else {\n // Link created from selected text; add href and title.\n $(\"a[href=\" + sStamp + \"]\", wym._doc.body)\n .attr(\n WYMeditor.HREF,\n returned_item_info.link\n )\n .attr(\n WYMeditor.TITLE,\n item_info.singular + item_id\n );\n }\n });\n });\n Galaxy.modal.hide();\n },\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n });\n }\n // EMBED GALAXY OBJECT DIALOGS\n if (\n dialogType == CONTROLS.DIALOG_EMBED_HISTORY ||\n dialogType == CONTROLS.DIALOG_EMBED_DATASET ||\n dialogType == CONTROLS.DIALOG_EMBED_WORKFLOW ||\n dialogType == CONTROLS.DIALOG_EMBED_PAGE ||\n dialogType == CONTROLS.DIALOG_EMBED_VISUALIZATION\n ) {\n // Based on item type, set useful vars.\n var item_info;\n switch (dialogType) {\n case CONTROLS.DIALOG_EMBED_HISTORY:\n item_info = get_item_info(CONTROLS.ITEM_HISTORY);\n break;\n case CONTROLS.DIALOG_EMBED_DATASET:\n item_info = get_item_info(CONTROLS.ITEM_DATASET);\n break;\n case CONTROLS.DIALOG_EMBED_WORKFLOW:\n item_info = get_item_info(CONTROLS.ITEM_WORKFLOW);\n break;\n case CONTROLS.DIALOG_EMBED_PAGE:\n item_info = get_item_info(CONTROLS.ITEM_PAGE);\n break;\n case CONTROLS.DIALOG_EMBED_VISUALIZATION:\n item_info = get_item_info(CONTROLS.ITEM_VISUALIZATION);\n break;\n }\n\n require([\"mvc/grid/grid-view\"], function(GridView) {\n var grid = new GridView({\n url_base: item_info.list_ajax_url,\n dict_format: true,\n embedded: true\n });\n Galaxy.modal.show({\n title: \"Insert Link to \" + item_info.singular,\n body: $(\"\")\n .append(grid.$el)\n .append(\n $(\"\")\n .append(\n ''\n )\n .append(\n \"Make the selected \" +\n item_info.plural.toLowerCase() +\n \" accessible so that they can viewed by everyone.\"\n )\n ),\n closing_events: true,\n buttons: {\n Embed: function() {\n // Make selected items accessible (importable) ?\n var make_importable = false;\n if ($(\"#make-importable:checked\").val() != null)\n make_importable = true;\n\n grid.$(\"input[name=id]:checked\").each(function() {\n // Get item ID and name.\n var item_id = $(this).val();\n // Use ':first' because there are many labels in table; the first one is the item name.\n var item_name = $(\n \"label[for='\" + item_id + \"']:first\"\n ).text();\n\n if (make_importable)\n make_item_importable(\n item_info.controller,\n item_id,\n item_info.singular\n );\n\n // Embedded item HTML; item class is embedded in div container classes; this is necessary because the editor strips\n // all non-standard attributes when it returns its content (e.g. it will not return an element attribute of the form\n // item_class='History').\n var item_elt_id = item_info.iclass + \"-\" + item_id;\n var item_embed_html = [\n \"\"\n ].join(\"\");\n\n // Insert embedded item into document.\n wym.insert(item_embed_html);\n });\n Galaxy.modal.hide();\n },\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n });\n }\n};\n\n$(function() {\n // Generic error handling\n $(document).ajaxError(function(e, x) {\n // console.log( e, x );\n var message =\n x.responseText || x.statusText || \"Could not connect to server\";\n show_modal(\"Server error\", message, { \"Ignore error\": hide_modal });\n return false;\n });\n // Create editor\n $(\"[name=page_content]\").wymeditor({\n skin: \"galaxy\",\n basePath: editor_base_path,\n iframeBasePath: iframe_base_path,\n boxHtml:\n \"\" +\n WYMeditor.TOOLS +\n \" |
| \" +\n \" \" +\n // + WYMeditor.HTML\n WYMeditor.IFRAME +\n WYMeditor.STATUS +\n \" \" +\n \"\" +\n \" |
' +\n '
' +\n '\" +\n '
' +\n '' +\n '![]()
' +\n '\" +\n \"
\" +\n '' +\n '\"\n );\n }\n });\n\n return {\n View: View\n };\n }\n);\n"]}
\ No newline at end of file
+{"version":3,"sources":["layout/masthead.js"],"names":["define","Utils","self","QuotaMeter","View","Backbone","setElement","extend","initialize","$navbarBrandLink","$navbarBrandImage","this","$navbarBrandTitle","$navbarTabs","_template","$quoteMeter","$","collection","Menu","empty","Collection","model","callback","append","Tab","render","$el","on","frame","each","m","Galaxy","Scratchbook","UserQuotaMeter","user","e","preventDefault","window","q","text","$download_link","target","closest","length","attr","hide","get","html","options","brand","logo_url","logo_src","quotaMeter"],"mappings":"kCAAAA,QAEQ,cAFRA,cAQQ,qBACA,4BAEQ,SAAAC,EAAIC,EAAAA,EAAJC,GA0GR,OACIC,KAzGIC,SAAKC,KAAWC,QAChBC,WAAKC,SAAAA,GACL,IAAAP,EAAKQ,KACLC,KAAKC,QAAAA,EACLD,KAAKE,WAALF,KAAmBG,aACnBH,KAAKI,iBAAmBC,KAAEA,EAAA,sBAH1BL,KAAKD,kBAAoBC,KAAKK,EAAE,uBAKhCL,KAAAC,kBAAAD,KAAAK,EAAA,uBACAL,KAAKM,YAAaN,KAAIO,EAAAA,gBACtBP,KAAKM,YACGN,KADRK,EACe,0BAMPd,KAAAA,WAAKW,IAAYM,EAAjBC,WACHT,KARLM,WAUQf,GAAAA,MAAKe,SAALI,GACIC,EAAAA,YAAAC,OADJ,IAAAL,EAAAM,KAAAH,MAAAA,IAAAI,SAAAC,OAMRC,GAAA,QAAA,WACOC,EAAPf,YAAeM,UAAfQ,GAAA,WAAA,SAAAL,GAPQpB,EAAKe,WAAWY,KAAK,SAASC,GAWtCR,EAAAQ,OAIQT,MAAOU,KAAAA,SARfA,OAAOH,MAAQjB,KAAKiB,MAAQ,IAAII,GAahCf,WAAAN,KAAAM,aAMgBD,OAAAA,WAAAL,KAAUY,WACJ,IAAFpB,EAAA8B,gBAKRjB,MAAEe,OAAAG,KAIFC,GAAEC,KAAAA,cAMFpB,EAAAqB,QAGAC,GAAAA,QAAMC,SAAYJ,GAJtB,IAAAK,EAAAxB,EAAAmB,EAAAM,QAAAC,QAAA,eAMiB,GAAbH,EAAaI,SACb,IAAOJ,EAAAA,uBAAPI,QACH3B,EAAA,QAAAO,OA5BTP,EAAA,aA5CwB4B,KAAA,KAAA,YAoDCC,QA8BpBpC,EAAAA,uBAA8BmC,KAC9BlC,MACWe,EAAhBmB,KAAA,SApFwBT,EAAAC,oBAyF5BtB,GAAW,eAAA,WAEH,IAAAyB,EAAA,GApGpB,GAkHarC,EAAAe,WAAAY,KAAA,SAAAR,GAzGL,IAAAiB,EAkEwBjB,EAAMyB,IAAI,mBA0C3BzB,EAAAyB,IAAA,iBAAAzB,GACGjB,IAAAA,GAAAA,EAAAA,OAtHlB,KAAAmC,EAgF4B,OAAOA,KAKvBd,OAAQ,WASJ,OARAd,KAAKC,kBAAkBmC,KACnB,WACMpC,KAAKqC,QAAQC,OAAS,KAAOtC,KAAKqC,QAAQC,OACxC,KAEZtC,KAAKF,iBAAiBmC,KAAK,OAAQjC,KAAKqC,QAAQE,UAChDvC,KAAKD,kBAAkBkC,KAAK,MAAOjC,KAAKqC,QAAQG,UAChDxC,KAAKyC,WAAW3B,SACTd,MAIXG,UAAW,WACP,MACI","file":"../../scripts/layout/masthead.js","sourcesContent":["define(\n [\n \"utils/utils\",\n \"layout/menu\",\n \"layout/scratchbook\",\n \"mvc/user/user-quotameter\"\n ],\n function(Utils, Menu, Scratchbook, QuotaMeter) {\n /** Masthead **/\n var View = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.options = options;\n this.setElement(this._template());\n this.$navbarBrandLink = this.$(\".navbar-brand-link\");\n this.$navbarBrandImage = this.$(\".navbar-brand-image\");\n this.$navbarBrandTitle = this.$(\".navbar-brand-title\");\n this.$navbarTabs = this.$(\".navbar-tabs\");\n this.$quoteMeter = this.$(\".quota-meter-container\");\n\n // build tabs\n this.collection = new Menu.Collection();\n this.collection\n .on(\"add\", function(model) {\n self.$navbarTabs.append(\n new Menu.Tab({ model: model }).render().$el\n );\n })\n .on(\"reset\", function() {\n self.$navbarTabs.empty();\n })\n .on(\"dispatch\", function(callback) {\n self.collection.each(function(m) {\n callback(m);\n });\n })\n .fetch(this.options);\n\n // scratchbook\n Galaxy.frame = this.frame = new Scratchbook({\n collection: this.collection\n });\n\n // set up the quota meter (And fetch the current user data from trans)\n // add quota meter to masthead\n Galaxy.quotaMeter = this.quotaMeter = new QuotaMeter.UserQuotaMeter(\n {\n model: Galaxy.user,\n el: this.$quoteMeter\n }\n );\n\n // loop through beforeunload functions if the user attempts to unload the page\n $(window)\n .on(\"click\", function(e) {\n var $download_link = $(e.target).closest(\"a[download]\");\n if ($download_link.length == 1) {\n if ($(\"iframe[id=download]\").length === 0) {\n $(\"body\").append(\n $(\"\")\n .attr(\"id\", \"download\")\n .hide()\n );\n }\n $(\"iframe[id=download]\").attr(\n \"src\",\n $download_link.attr(\"href\")\n );\n e.preventDefault();\n }\n })\n .on(\"beforeunload\", function() {\n var text = \"\";\n self.collection.each(function(model) {\n var q =\n model.get(\"onbeforeunload\") &&\n model.get(\"onbeforeunload\")();\n q && (text += q + \" \");\n });\n if (text !== \"\") {\n return text;\n }\n });\n },\n\n render: function() {\n this.$navbarBrandTitle.html(\n \"Galaxy \" +\n ((this.options.brand && \"/ \" + this.options.brand) ||\n \"\")\n );\n this.$navbarBrandLink.attr(\"href\", this.options.logo_url);\n this.$navbarBrandImage.attr(\"src\", this.options.logo_src);\n this.quotaMeter.render();\n return this;\n },\n\n /** body template */\n _template: function() {\n return (\n '
' +\n '
' +\n '\" +\n '
' +\n '' +\n '![]()
' +\n '\" +\n \"
\" +\n '' +\n '\"\n );\n }\n });\n\n return {\n View: View\n };\n }\n);\n"]}
\ No newline at end of file
diff --git a/static/maps/layout/menu.js.map b/static/maps/layout/menu.js.map
index e9dc300b675..9f6896d3c29 100644
--- a/static/maps/layout/menu.js.map
+++ b/static/maps/layout/menu.js.map
@@ -1 +1 @@
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Data\"),\n url: \"library/index\",\n tooltip: _l(\"Access published resources\"),\n menu: [\n {\n title: _l(\"Data Libraries\"),\n url: \"library/list\"\n },\n {\n title: _l(\"Histories\"),\n url: \"histories/list_published\"\n },\n {\n title: _l(\"Workflows\"),\n url: \"workflows/list_published\"\n },\n {\n title: _l(\"Visualizations\"),\n url: \"visualizations/list_published\"\n },\n {\n title: _l(\"Pages\"),\n url: \"pages/list_published\"\n }\n ]\n });\n\n //\n // Lab menu.\n //\n options.user_requests &&\n this.add({\n id: \"lab\",\n title: \"Lab\",\n menu: [\n {\n title: \"Sequencing Requests\",\n url: \"requests/index\"\n },\n {\n title: \"Find Samples\",\n url: \"requests/find_samples_index\"\n },\n {\n title: \"Help\",\n url: options.lims_doc_url\n }\n ]\n });\n\n //\n // Visualization tab.\n //\n this.add({\n id: \"visualization\",\n title: _l(\"Visualization\"),\n url: \"visualizations/list\",\n tooltip: _l(\"Visualize datasets\"),\n disabled: !Galaxy.user.id,\n menu: [\n {\n title: _l(\"New Track Browser\"),\n url: \"visualization/trackster\",\n target: \"_frame\"\n },\n {\n title: _l(\"Saved Visualizations\"),\n url: \"visualizations/list\",\n target: \"_frame\"\n },\n {\n title: _l(\"Interactive Environments\"),\n url: \"visualization/gie_list\",\n target: \"galaxy_main\"\n }\n ]\n });\n\n //\n // Webhooks\n //\n Webhooks.add({\n url: \"api/webhooks/masthead/all\",\n callback: function(webhooks) {\n $(document).ready(function() {\n $.each(webhooks.models, function(index, model) {\n var webhook = model.toJSON();\n if (webhook.activate) {\n var obj = {\n id: webhook.name,\n icon: webhook.config.icon,\n url: webhook.config.url,\n tooltip: webhook.config.tooltip,\n onclick:\n webhook.config.function &&\n new Function(\n webhook.config.function\n )\n };\n\n // Galaxy.page is undefined for data libraries, workflows pages\n if (Galaxy.page) {\n Galaxy.page.masthead.collection.add(\n obj\n );\n } else if (Galaxy.masthead) {\n Galaxy.masthead.collection.add(obj);\n }\n\n // Append masthead script and styles to Galaxy main\n Utils.appendScriptStyle(webhook);\n }\n });\n });\n }\n });\n\n //\n // Admin.\n //\n Galaxy.user.get(\"is_admin\") &&\n this.add({\n id: \"admin\",\n title: _l(\"Admin\"),\n url: \"admin\",\n tooltip: _l(\"Administer this Galaxy\"),\n cls: \"admin-only\"\n });\n\n //\n // Help tab.\n //\n var helpTab = {\n id: \"help\",\n title: _l(\"Help\"),\n tooltip: _l(\"Support, contact, and community\"),\n menu: [\n {\n title: _l(\"Support\"),\n url: options.support_url,\n target: \"_blank\"\n },\n {\n title: _l(\"Search\"),\n url: options.search_url,\n target: \"_blank\"\n },\n {\n title: _l(\"Mailing Lists\"),\n url: options.mailing_lists,\n target: \"_blank\"\n },\n {\n title: _l(\"Videos\"),\n url: options.screencasts_url,\n target: \"_blank\"\n },\n {\n title: _l(\"Wiki\"),\n url: options.wiki_url,\n target: \"_blank\"\n },\n {\n title: _l(\"How to Cite Galaxy\"),\n url: options.citation_url,\n target: \"_blank\"\n },\n {\n title: _l(\"Interactive Tours\"),\n url: \"tours\"\n }\n ]\n };\n options.terms_url &&\n helpTab.menu.push({\n title: _l(\"Terms and Conditions\"),\n url: options.terms_url,\n target: \"_blank\"\n });\n options.biostar_url &&\n helpTab.menu.unshift({\n title: _l(\"Ask a question\"),\n url: \"biostar/biostar_question_redirect\",\n target: \"_blank\"\n });\n options.biostar_url &&\n helpTab.menu.unshift({\n title: _l(\"Galaxy Biostar\"),\n url: options.biostar_url_redirect,\n target: \"_blank\"\n });\n this.add(helpTab);\n\n //\n // User tab.\n //\n var userTab = {};\n if (!Galaxy.user.id) {\n if (options.allow_user_creation) {\n userTab = {\n id: \"user\",\n title: _l(\"Login or Register\"),\n cls: \"loggedout-only\",\n tooltip: _l(\"Account registration or login\"),\n menu: [\n {\n title: _l(\"Login\"),\n url: \"user/login\",\n target: \"galaxy_main\",\n noscratchbook: true\n },\n {\n title: _l(\"Register\"),\n url: \"user/create\",\n target: \"galaxy_main\",\n noscratchbook: true\n }\n ]\n };\n } else {\n userTab = {\n id: \"user\",\n title: _l(\"Login\"),\n cls: \"loggedout-only\",\n tooltip: _l(\"Login\"),\n url: \"user/login\",\n target: \"galaxy_main\",\n noscratchbook: true\n };\n }\n } else {\n userTab = {\n id: \"user\",\n title: _l(\"User\"),\n cls: \"loggedin-only\",\n tooltip: _l(\"Account and saved data\"),\n menu: [\n {\n title:\n _l(\"Logged in as\") +\n \" \" +\n Galaxy.user.get(\"email\")\n },\n {\n title: _l(\"Preferences\"),\n url: \"user\"\n },\n {\n title: _l(\"Custom Builds\"),\n url: \"custom_builds\"\n },\n {\n title: _l(\"Logout\"),\n url:\n \"user/logout?session_csrf_token=\" +\n Galaxy.session_csrf_token,\n target: \"_top\",\n divider: true\n },\n {\n title: _l(\"Saved Histories\"),\n url: \"histories/list\",\n target: \"_top\"\n },\n {\n title: _l(\"Saved Datasets\"),\n url: \"datasets/list\",\n target: \"_top\"\n },\n {\n title: _l(\"Saved Pages\"),\n url: \"pages/list\",\n target: \"_top\"\n }\n ]\n };\n }\n this.add(userTab);\n var activeView = this.get(options.active_view);\n activeView && activeView.set(\"active\", true);\n return new jQuery.Deferred().resolve().promise();\n }\n });\n\n /** Masthead tab **/\n var Tab = Backbone.View.extend({\n initialize: function(options) {\n this.model = options.model;\n this.setElement(this._template());\n this.$dropdown = this.$(\".dropdown\");\n this.$toggle = this.$(\".dropdown-toggle\");\n this.$menu = this.$(\".dropdown-menu\");\n this.$note = this.$(\".dropdown-note\");\n this.listenTo(this.model, \"change\", this.render, this);\n },\n\n events: {\n \"click .dropdown-toggle\": \"_toggleClick\"\n },\n\n render: function() {\n var self = this;\n $(\".tooltip\").remove();\n this.$el.attr(\"id\", this.model.id).css({\n visibility:\n (this.model.get(\"visible\") && \"visible\") || \"hidden\"\n });\n this.model.set(\"url\", this._formatUrl(this.model.get(\"url\")));\n this.$note\n .html(this.model.get(\"note\") || \"\")\n .removeClass()\n .addClass(\"dropdown-note\")\n .addClass(this.model.get(\"note_cls\"))\n .css({\n display:\n (this.model.get(\"show_note\") && \"block\") || \"none\"\n });\n this.$toggle\n .html(this.model.get(\"title\") || \"\")\n .removeClass()\n .addClass(\"dropdown-toggle\")\n .addClass(this.model.get(\"cls\"))\n .addClass(\n this.model.get(\"icon\") &&\n \"dropdown-icon fa \" + this.model.get(\"icon\")\n )\n .addClass(this.model.get(\"toggle\") && \"toggle\")\n .attr(\"target\", this.model.get(\"target\"))\n .attr(\"href\", this.model.get(\"url\"))\n .attr(\"title\", this.model.get(\"tooltip\"))\n .tooltip(\"destroy\");\n this.model.get(\"tooltip\") &&\n this.$toggle.tooltip({ placement: \"bottom\" });\n this.$dropdown\n .removeClass()\n .addClass(\"dropdown\")\n .addClass(this.model.get(\"disabled\") && \"disabled\")\n .addClass(this.model.get(\"active\") && \"active\");\n if (this.model.get(\"menu\") && this.model.get(\"show_menu\")) {\n this.$menu.show();\n $(\"#dd-helper\")\n .show()\n .off()\n .on(\"click\", function() {\n $(\"#dd-helper\").hide();\n self.model.set(\"show_menu\", false);\n });\n } else {\n self.$menu.hide();\n $(\"#dd-helper\").hide();\n }\n this.$menu.empty().removeClass(\"dropdown-menu\");\n if (this.model.get(\"menu\")) {\n _.each(this.model.get(\"menu\"), function(menuItem) {\n self.$menu.append(self._buildMenuItem(menuItem));\n menuItem.divider &&\n self.$menu.append($(\"\").addClass(\"divider\"));\n });\n self.$menu.addClass(\"dropdown-menu\");\n self.$toggle.append($(\"\").addClass(\"caret\"));\n }\n return this;\n },\n\n /** Add new menu item */\n _buildMenuItem: function(options) {\n var self = this;\n options = _.defaults(options || {}, {\n title: \"\",\n url: \"\",\n target: \"_parent\",\n noscratchbook: false\n });\n options.url = self._formatUrl(options.url);\n return $(\"\").append(\n $(\"\")\n .attr(\"href\", options.url)\n .attr(\"target\", options.target)\n .html(options.title)\n .on(\"click\", function(e) {\n e.preventDefault();\n self.model.set(\"show_menu\", false);\n if (options.onclick) {\n options.onclick();\n } else {\n Galaxy.frame.add(options);\n }\n })\n );\n },\n\n /** Handle click event */\n _toggleClick: function(e) {\n var self = this;\n var model = this.model;\n e.preventDefault();\n $(\".tooltip\").hide();\n model.trigger(\"dispatch\", function(m) {\n model.id !== m.id &&\n m.get(\"menu\") &&\n m.set(\"show_menu\", false);\n });\n if (!model.get(\"disabled\")) {\n if (!model.get(\"menu\")) {\n model.get(\"onclick\")\n ? model.get(\"onclick\")()\n : Galaxy.frame.add(model.attributes);\n } else {\n model.set(\"show_menu\", true);\n }\n } else {\n function buildLink(label, url) {\n return $(\"\")\n .append(\n $(\"\")\n .attr(\"href\", Galaxy.root + url)\n .html(label)\n )\n .html();\n }\n this.$toggle.popover && this.$toggle.popover(\"destroy\");\n this.$toggle\n .popover({\n html: true,\n placement: \"bottom\",\n content:\n \"Please \" +\n buildLink(\n \"login\",\n \"user/login?use_panels=True\"\n ) +\n \" or \" +\n buildLink(\n \"register\",\n \"user/create?use_panels=True\"\n ) +\n \" to use this feature.\"\n })\n .popover(\"show\");\n setTimeout(function() {\n self.$toggle.popover(\"destroy\");\n }, 5000);\n }\n },\n\n /** Url formatting */\n _formatUrl: function(url) {\n return typeof url == \"string\" &&\n url.indexOf(\"//\") === -1 &&\n url.charAt(0) != \"/\"\n ? Galaxy.root + url\n : url;\n },\n\n /** body tempate */\n _template: function() {\n return (\n '
- ' +\n '
- ' +\n '' +\n '
- ' +\n '
- ' +\n '' +\n '
- ' +\n '
- \",\n _l(\n [\n \"Rename elements in the list by clicking on \",\n 'the existing name.'\n ].join(\"\")\n ),\n \" \",\n \"
- \",\n _l(\n [\n \"Discard elements from the final created list by clicking on the \",\n '\"Discard\" button.'\n ].join(\"\")\n ),\n \" \",\n \"
- \",\n _l(\n [\n \"Reorder the list by clicking and dragging elements. Select multiple elements by clicking on \",\n 'them and you can then move those selected by dragging the ',\n \"entire group. Deselect them by clicking them again or by clicking the \",\n 'the \"Clear selected\" link.'\n ].join(\"\")\n ),\n \" \",\n \"
- \",\n _l(\n [\n 'Click the \"Start over\" link to begin again as if you had just opened ',\n \"the interface.\"\n ].join(\"\")\n ),\n \" \",\n \"
- \",\n _l(\n [\n 'Click the \"Cancel\" button to exit the interface.'\n ].join(\"\")\n ),\n \" \",\n \"
- <%- problem.element.name %>: <%- problem.text %> \",\n \"<% }); %>
- \",\n _l(\n [\n \"Rename elements in the list by clicking on \",\n 'the existing name.'\n ].join(\"\")\n ),\n \" \",\n \"
- \",\n _l(\n [\n \"Discard elements from the final created list by clicking on the \",\n '\"Discard\" button.'\n ].join(\"\")\n ),\n \" \",\n \"
- \",\n _l(\n [\n \"Reorder the list by clicking and dragging elements. Select multiple elements by clicking on \",\n 'them and you can then move those selected by dragging the ',\n \"entire group. Deselect them by clicking them again or by clicking the \",\n 'the \"Clear selected\" link.'\n ].join(\"\")\n ),\n \" \",\n \"
- \",\n _l(\n [\n 'Click the \"Start over\" link to begin again as if you had just opened ',\n \"the interface.\"\n ].join(\"\")\n ),\n \" \",\n \"
- \",\n _l(\n [\n 'Click the \"Cancel\" button to exit the interface.'\n ].join(\"\")\n ),\n \" \",\n \"
- <%- problem.element.name %>: <%- problem.text %> \",\n \"<% }); %>
- Click a dataset in the \",\n 'forward column ',\n \"to select it then click a dataset in the \",\n 'reverse column.',\n \" \",\n '
- Click one of the \"Pair these datasets\" buttons in the ',\n 'middle column ',\n \"to pair the datasets in a particular row.\",\n \" \",\n '
- Click \"Auto-pair\" ',\n \"to have your datasets automatically paired based on name.\",\n \" \",\n \"
- Entering partial dataset names in either the \",\n 'forward filter or ',\n 'reverse filter.',\n \" \",\n \"
- Choosing from a list of preset filters by clicking the \",\n '\"Choose filters\" link.',\n \" \",\n \"
- Entering regular expressions to match dataset names. See: \",\n 'MDN\\'s JavaScript Regular Expression Tutorial. ',\n \"Note: forward slashes (\\\\) are not needed.\",\n \" \",\n \"
- Clearing the filters by clicking the \",\n '\"Clear filters\" link.',\n \" \",\n \"
- Click a dataset in the \",\n 'forward column ',\n \"to select it then click a dataset in the \",\n 'reverse column.',\n \" \",\n '
- Click one of the \"Pair these datasets\" buttons in the ',\n 'middle column ',\n \"to pair the datasets in a particular row.\",\n \" \",\n '
- Click \"Auto-pair\" ',\n \"to have your datasets automatically paired based on name.\",\n \" \",\n \"
- Entering partial dataset names in either the \",\n 'forward filter or ',\n 'reverse filter.',\n \" \",\n \"
- Choosing from a list of preset filters by clicking the \",\n '\"Choose filters\" link.',\n \" \",\n \"
- Entering regular expressions to match dataset names. See: \",\n 'MDN\\'s JavaScript Regular Expression Tutorial. ',\n \"Note: forward slashes (\\\\) are not needed.\",\n \" \",\n \"
- Clearing the filters by clicking the \",\n '\"Clear filters\" link.',\n \" \",\n \"
- \",\n _l(\n [\n 'Click the \"Swap\" link to make your forward dataset the reverse ',\n \"and the reverse dataset forward.\"\n ].join(\"\")\n ),\n \" \",\n \"
- \",\n _l(\n [\n 'Click the \"Cancel\" button to exit the interface.'\n ].join(\"\")\n ),\n \" \",\n \"
- \",\n _l(\n [\n 'Click the \"Swap\" link to make your forward dataset the reverse ',\n \"and the reverse dataset forward.\"\n ].join(\"\")\n ),\n \" \",\n \"
- \",\n _l(\n [\n 'Click the \"Cancel\" button to exit the interface.'\n ].join(\"\")\n ),\n \" \",\n \"
- Actions ' +\n '
- \" +\n '' +\n action.label +\n \"\" +\n \" \";\n }\n if (show_popup) {\n tmpl += \"
- Actions ' +\n '
- \" +\n '' +\n action.label +\n \"\" +\n \" \";\n }\n if (show_popup) {\n tmpl += \"
- /datasets/<%- item.id %>/versions/<%- version[0] %>\"><%- version[1] %> ',\n \"<% }) %>\",\n \"
- /datasets/<%- item.id %>/versions/<%- version[0] %>\"><%- version[1] %> ',\n \"<% }) %>\",\n \"
- \" data-name=\"<%= _.escape(history_item.get(\"type\")) %>\">',\n \" \",\n \"<% } else { %>\",\n '
- ',\n '',\n '<%= _.escape(history_item.get(\"hid\")) %>: ',\n '<%= item_name.length > 75 ? _.escape(\"...\".concat(item_name.substr(-75))) : _.escape(item_name) %> (Dataset Collection of type <%= _.escape(collection_type) %> not supported.)',\n \"\",\n \" \",\n \"<% } %>\",\n '<% } else if (history_item.get(\"visible\") === true && history_item.get(\"state\") === \"ok\") { %>',\n '
- \" data-name=\"<%= _.escape(history_item.get(\"type\")) %>\">',\n '\",\n \" \",\n \"<% } %>\",\n \"<% } %>\",\n \"<% }); %>\",\n \"
- /page/1\"> ',\n '
- /page/<% print( show_page ) %>\"><% print( show_page - 1 ) %> ',\n \"<% } else { %>\",\n '
- /page/1\"> ',\n '
- /page/<% print( show_page - 1 ) %>\"><% print( show_page - 1 ) %> ',\n \"<% } %>\",\n \"<% } else { %>\", // we are on the first page\n '
- /page/1\"> ',\n '
- /page/<% print( show_page ) %>\"><% print( show_page - 1 ) %> ',\n \"<% } %>\",\n '
- ',\n '/page/<% print( show_page ) %>\"><% print( show_page ) %>',\n \" \",\n \"<% if ( ( show_page ) < page_count ) { %>\",\n '
- /page/<% print( show_page + 1 ) %>\"><% print( show_page + 1 ) %> ',\n '
- /page/<% print( page_count ) %>\"> ',\n \"<% } else { %>\",\n '
- /page/<% print( show_page ) %>\"><% print( show_page + 1 ) %> ',\n '
- /page/<% print( page_count ) %>\"> ',\n \"<% } %>\",\n \"
- \" data-name=\"<%= _.escape(history_item.get(\"type\")) %>\">',\n \" \",\n \"<% } else { %>\",\n '
- ',\n '',\n '<%= _.escape(history_item.get(\"hid\")) %>: ',\n '<%= item_name.length > 75 ? _.escape(\"...\".concat(item_name.substr(-75))) : _.escape(item_name) %> (Dataset Collection of type <%= _.escape(collection_type) %> not supported.)',\n \"\",\n \" \",\n \"<% } %>\",\n '<% } else if (history_item.get(\"visible\") === true && history_item.get(\"state\") === \"ok\") { %>',\n '
- \" data-name=\"<%= _.escape(history_item.get(\"type\")) %>\">',\n '\",\n \" \",\n \"<% } %>\",\n \"<% } %>\",\n \"<% }); %>\",\n \"
- /page/1\"> ',\n '
- /page/<% print( show_page ) %>\"><% print( show_page - 1 ) %> ',\n \"<% } else { %>\",\n '
- /page/1\"> ',\n '
- /page/<% print( show_page - 1 ) %>\"><% print( show_page - 1 ) %> ',\n \"<% } %>\",\n \"<% } else { %>\", // we are on the first page\n '
- /page/1\"> ',\n '
- /page/<% print( show_page ) %>\"><% print( show_page - 1 ) %> ',\n \"<% } %>\",\n '
- ',\n '/page/<% print( show_page ) %>\"><% print( show_page ) %>',\n \" \",\n \"<% if ( ( show_page ) < page_count ) { %>\",\n '
- /page/<% print( show_page + 1 ) %>\"><% print( show_page + 1 ) %> ',\n '
- /page/<% print( page_count ) %>\"> ',\n \"<% } else { %>\",\n '
- /page/<% print( show_page ) %>\"><% print( show_page + 1 ) %> ',\n '
- /page/<% print( page_count ) %>\"> ',\n \"<% } %>\",\n \"
- ',\n '
- \"><% print( show_page - 1 ) %> ',\n \"<% } else { %>\",\n '
- ',\n '
- \"><% print( show_page - 1 ) %> ',\n \"<% } %>\",\n \"<% } else { %>\", // we are on the first page\n '
- ',\n '
- \"><% print( show_page - 1 ) %> ',\n \"<% } %>\",\n '
- ',\n '\"><% print( show_page ) %>',\n \" \",\n \"<% if ( ( show_page ) < page_count ) { %>\",\n '
- \"><% print( show_page + 1 ) %> ',\n '
- \"> ',\n \"<% } else { %>\",\n '
- \"><% print( show_page + 1 ) %> ',\n '
- \"> ',\n \"<% } %>\",\n \"
- ',\n '
- \"><% print( show_page - 1 ) %> ',\n \"<% } else { %>\",\n '
- ',\n '
- \"><% print( show_page - 1 ) %> ',\n \"<% } %>\",\n \"<% } else { %>\", // we are on the first page\n '
- ',\n '
- \"><% print( show_page - 1 ) %> ',\n \"<% } %>\",\n '
- ',\n '\"><% print( show_page ) %>',\n \" \",\n \"<% if ( ( show_page ) < page_count ) { %>\",\n '
- \"><% print( show_page + 1 ) %> ',\n '
- \"> ',\n \"<% } else { %>\",\n '
- \"><% print( show_page + 1 ) %> ',\n '
- \"> ',\n \"<% } %>\",\n \"
- ',\n action.html,\n \" \"\n ].join(\"\");\n return $(html).click(function(ev) {\n ev.preventDefault();\n return action.func(ev);\n });\n });\n $newMenu.find(\"ul\").append($actions);\n $menu.replaceWith($newMenu);\n return $newMenu;\n },\n\n /** return a list of plain objects used to render multiselect actions menu. Each object should have:\n * html: an html string used as the anchor contents\n * func: a function called when the anchor is clicked (passed the click event)\n */\n multiselectActions: function() {\n return [];\n },\n\n // ------------------------------------------------------------------------ sub-$element shortcuts\n /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */\n $scrollContainer: function($where) {\n // override or set via attributes.$scrollContainer\n return ($where || this.$el).parent().parent();\n },\n /** convenience selector for the section that displays the list controls */\n $controls: function($where) {\n return ($where || this.$el).find(\"> .controls\");\n },\n /** list-items: where the subviews are contained in the view's dom */\n $list: function($where) {\n return ($where || this.$el).find(\"> .list-items\");\n },\n /** container where list messages are attached */\n $messages: function($where) {\n //TODO: controls isn't really correct here (only for ModelListPanel)\n return ($where || this.$el).find(\"> .controls .messages\");\n },\n /** the message displayed when no views can be shown (no views, none matching search) */\n $emptyMessage: function($where) {\n return ($where || this.$el).find(\"> .empty-message\");\n },\n\n // ------------------------------------------------------------------------ hda sub-views\n /** render the subviews for the list's collection */\n renderItems: function($whereTo) {\n $whereTo = $whereTo || this.$el;\n var panel = this;\n panel.log(this + \".renderItems\", $whereTo);\n\n var $list = panel.$list($whereTo);\n panel.freeViews();\n // console.log( 'views freed' );\n //TODO:? cache and re-use views?\n var shownModels = panel._filterCollection();\n // console.log( 'models filtered:', shownModels );\n\n panel.views = shownModels.map(function(itemModel) {\n var view = panel._createItemView(itemModel);\n return view;\n });\n\n $list.empty();\n // console.log( 'list emptied' );\n if (panel.views.length) {\n panel._attachItems($whereTo);\n // console.log( 'items attached' );\n }\n panel._renderEmptyMessage($whereTo).toggle(!panel.views.length);\n panel.trigger(\"views:ready\", panel.views);\n\n // console.log( '------------------------------------------- rendering items' );\n return panel.views;\n },\n\n /** Filter the collection to only those models that should be currently viewed */\n _filterCollection: function() {\n // override this\n var panel = this;\n return panel.collection.filter(_.bind(panel._filterItem, panel));\n },\n\n /** Should the model be viewable in the current state?\n * Checks against this.filters and this.searchFor\n */\n _filterItem: function(model) {\n // override this\n var panel = this;\n return (\n _.every(\n panel.filters.map(function(fn) {\n return fn.call(model);\n })\n ) &&\n (!panel.searchFor || model.matchesAll(panel.searchFor))\n );\n },\n\n /** Create a view for a model and set up it's listeners */\n _createItemView: function(model) {\n var ViewClass = this._getItemViewClass(model);\n var options = _.extend(this._getItemViewOptions(model), {\n model: model\n });\n var view = new ViewClass(options);\n this._setUpItemViewListeners(view);\n return view;\n },\n\n /** Free a view for a model. Note: does not remove it from the DOM */\n _destroyItemView: function(view) {\n this.stopListening(view);\n this.views = _.without(this.views, view);\n },\n\n _destroyItemViews: function(view) {\n var self = this;\n self.views.forEach(function(v) {\n self.stopListening(v);\n });\n self.views = [];\n return self;\n },\n\n /** free any sub-views the list has */\n freeViews: function() {\n return this._destroyItemViews();\n },\n\n /** Get the bbone view class based on the model */\n _getItemViewClass: function(model) {\n // override this\n return this.viewClass;\n },\n\n /** Get the options passed to the new view based on the model */\n _getItemViewOptions: function(model) {\n // override this\n return {\n //logger : this.logger,\n fxSpeed: this.fxSpeed,\n expanded: false,\n selectable: this.selecting,\n selected: _.contains(this.selected, model.id),\n draggable: this.dragItems\n };\n },\n\n /** Set up listeners for new models */\n _setUpItemViewListeners: function(view) {\n var panel = this;\n // send all events to the panel, re-namspaceing them with the view prefix\n this.listenTo(view, \"all\", function() {\n var args = Array.prototype.slice.call(arguments, 0);\n args[0] = \"view:\" + args[0];\n panel.trigger.apply(panel, args);\n });\n\n // drag multiple - hijack ev.setData to add all selected items\n this.listenTo(\n view,\n \"draggable:dragstart\",\n function(ev, v) {\n //TODO: set multiple drag data here\n var json = {},\n selected = this.getSelectedModels();\n if (selected.length) {\n json = selected.toJSON();\n } else {\n json = [v.model.toJSON()];\n }\n ev.dataTransfer.setData(\"text\", JSON.stringify(json));\n //ev.dataTransfer.setDragImage( v.el, 60, 60 );\n },\n this\n );\n\n return panel;\n },\n\n /** Attach views in this.views to the model based on $whereTo */\n _attachItems: function($whereTo) {\n var self = this;\n // console.log( '_attachItems:', $whereTo, this.$list( $whereTo ) );\n //ASSUMES: $list has been emptied\n this.$list($whereTo).append(\n this.views.map(function(view) {\n return self._renderItemView$el(view);\n })\n );\n return this;\n },\n\n /** get a given subview's $el (or whatever may wrap it) and return it */\n _renderItemView$el: function(view) {\n // useful to wrap and override\n return view.render(0).$el;\n },\n\n /** render the empty/none-found message */\n _renderEmptyMessage: function($whereTo) {\n this.debug(\"_renderEmptyMessage\", $whereTo, this.searchFor);\n var text = this.searchFor ? this.noneFoundMsg : this.emptyMsg;\n return this.$emptyMessage($whereTo).text(text);\n },\n\n /** expand all item views */\n expandAll: function() {\n _.each(this.views, function(view) {\n view.expand();\n });\n },\n\n /** collapse all item views */\n collapseAll: function() {\n _.each(this.views, function(view) {\n view.collapse();\n });\n },\n\n // ------------------------------------------------------------------------ collection/views syncing\n /** Add a view (if the model should be viewable) to the panel */\n addItemView: function(model, collection, options) {\n // console.log( this + '.addItemView:', model );\n var panel = this;\n // get the index of the model in the list of filtered models shown by this list\n // in order to insert the view in the proper place\n //TODO:? potentially expensive\n var modelIndex = panel._filterCollection().indexOf(model);\n if (modelIndex === -1) {\n return undefined;\n }\n var view = panel._createItemView(model);\n // console.log( 'adding and rendering:', modelIndex, view.toString() );\n\n $(view).queue(\"fx\", [\n function(next) {\n // hide the empty message first if only view\n if (panel.$emptyMessage().is(\":visible\")) {\n panel.$emptyMessage().fadeOut(panel.fxSpeed, next);\n } else {\n next();\n }\n },\n function(next) {\n panel._attachView(view, modelIndex);\n next();\n }\n ]);\n return view;\n },\n\n /** internal fn to add view (to both panel.views and panel.$list) */\n _attachView: function(view, modelIndex, useFx) {\n // console.log( this + '._attachView:', view, modelIndex, useFx );\n useFx = _.isUndefined(useFx) ? true : useFx;\n modelIndex = modelIndex || 0;\n var panel = this;\n\n // use the modelIndex to splice into views and insert at the proper index in the DOM\n panel.views.splice(modelIndex, 0, view);\n panel._insertIntoListAt(\n modelIndex,\n panel._renderItemView$el(view).hide()\n );\n\n panel.trigger(\"view:attached\", view);\n if (useFx) {\n view.$el.slideDown(panel.fxSpeed, function() {\n panel.trigger(\"view:attached:rendered\");\n });\n } else {\n view.$el.show();\n panel.trigger(\"view:attached:rendered\");\n }\n return view;\n },\n\n /** insert a jq object as a child of list-items at the specified *DOM index* */\n _insertIntoListAt: function(index, $what) {\n // console.log( this + '._insertIntoListAt:', index, $what );\n var $list = this.$list();\n if (index === 0) {\n $list.prepend($what);\n } else {\n $list\n .children()\n .eq(index - 1)\n .after($what);\n }\n return $what;\n },\n\n /** Remove a view from the panel (if found) */\n removeItemView: function(model, collection, options) {\n var panel = this;\n var view = _.find(panel.views, function(v) {\n return v.model === model;\n });\n if (!view) {\n return undefined;\n }\n panel.views = _.without(panel.views, view);\n panel.trigger(\"view:removed\", view);\n\n // potentially show the empty message if no views left\n // use anonymous queue here - since remove can happen multiple times\n $({}).queue(\"fx\", [\n function(next) {\n view.$el.fadeOut(panel.fxSpeed, next);\n },\n function(next) {\n view.remove();\n panel.trigger(\"view:removed:rendered\");\n if (!panel.views.length) {\n panel._renderEmptyMessage().fadeIn(panel.fxSpeed, next);\n } else {\n next();\n }\n }\n ]);\n return view;\n },\n\n /** get views based on model.id */\n viewFromModelId: function(id) {\n return _.find(this.views, function(v) {\n return v.model.id === id;\n });\n },\n\n /** get views based on model */\n viewFromModel: function(model) {\n return model ? this.viewFromModelId(model.id) : undefined;\n },\n\n /** get views based on model properties */\n viewsWhereModel: function(properties) {\n return this.views.filter(function(view) {\n return _.isMatch(view.model.attributes, properties);\n });\n },\n\n /** A range of views between (and including) viewA and viewB */\n viewRange: function(viewA, viewB) {\n if (viewA === viewB) {\n return viewA ? [viewA] : [];\n }\n\n var indexA = this.views.indexOf(viewA),\n indexB = this.views.indexOf(viewB);\n\n // handle not found\n if (indexA === -1 || indexB === -1) {\n if (indexA === indexB) {\n return [];\n }\n return indexA === -1 ? [viewB] : [viewA];\n }\n // reverse if indeces are\n //note: end inclusive\n return indexA < indexB\n ? this.views.slice(indexA, indexB + 1)\n : this.views.slice(indexB, indexA + 1);\n },\n\n // ------------------------------------------------------------------------ searching\n /** render a search input for filtering datasets shown\n * (see SearchableMixin in base-mvc for implementation of the actual searching)\n * return will start the search\n * esc will clear the search\n * clicking the clear button will clear the search\n * uses searchInput in ui.js\n */\n _renderSearch: function($where) {\n $where.find(\".controls .search-input\").searchInput({\n placeholder: this.searchPlaceholder,\n initialVal: this.searchFor,\n onfirstsearch: _.bind(this._firstSearch, this),\n onsearch: _.bind(this.searchItems, this),\n onclear: _.bind(this.clearSearch, this)\n });\n return $where;\n },\n\n /** What to do on the first search entered */\n _firstSearch: function(searchFor) {\n // override to load model details if necc.\n this.log(\"onFirstSearch\", searchFor);\n return this.searchItems(searchFor);\n },\n\n /** filter view list to those that contain the searchFor terms */\n searchItems: function(searchFor, force) {\n this.log(\"searchItems\", searchFor, this.searchFor, force);\n if (!force && this.searchFor === searchFor) {\n return this;\n }\n this.searchFor = searchFor;\n this.renderItems();\n this.trigger(\"search:searching\", searchFor, this);\n var $search = this.$(\"> .controls .search-query\");\n if ($search.val() !== searchFor) {\n $search.val(searchFor);\n }\n return this;\n },\n\n /** clear the search filters and show all views that are normally shown */\n clearSearch: function(searchFor) {\n //this.log( 'onSearchClear', this );\n this.searchFor = \"\";\n this.trigger(\"search:clear\", this);\n this.$(\"> .controls .search-query\").val(\"\");\n this.renderItems();\n return this;\n },\n\n // ------------------------------------------------------------------------ selection\n /** @type Integer when the number of list item views is >= to this, don't animate selectors */\n THROTTLE_SELECTOR_FX_AT: 20,\n\n /** show selectors on all visible itemViews and associated controls */\n showSelectors: function(speed) {\n speed = speed !== undefined ? speed : this.fxSpeed;\n this.selecting = true;\n this.$(\".list-actions\").slideDown(speed);\n speed =\n this.views.length >= this.THROTTLE_SELECTOR_FX_AT ? 0 : speed;\n _.each(this.views, function(view) {\n view.showSelector(speed);\n });\n //this.selected = [];\n //this.lastSelected = null;\n },\n\n /** hide selectors on all visible itemViews and associated controls */\n hideSelectors: function(speed) {\n speed = speed !== undefined ? speed : this.fxSpeed;\n this.selecting = false;\n this.$(\".list-actions\").slideUp(speed);\n speed =\n this.views.length >= this.THROTTLE_SELECTOR_FX_AT ? 0 : speed;\n _.each(this.views, function(view) {\n view.hideSelector(speed);\n });\n this.selected = [];\n this.lastSelected = null;\n },\n\n /** show or hide selectors on all visible itemViews and associated controls */\n toggleSelectors: function() {\n if (!this.selecting) {\n this.showSelectors();\n } else {\n this.hideSelectors();\n }\n },\n\n /** select all visible items */\n selectAll: function(event) {\n _.each(this.views, function(view) {\n view.select(event);\n });\n },\n\n /** deselect all visible items */\n deselectAll: function(event) {\n this.lastSelected = null;\n _.each(this.views, function(view) {\n view.deselect(event);\n });\n },\n\n /** select a range of datasets between A and B */\n selectRange: function(viewA, viewB) {\n var range = this.viewRange(viewA, viewB);\n _.each(range, function(view) {\n view.select();\n });\n return range;\n },\n\n /** return an array of all currently selected itemViews */\n getSelectedViews: function() {\n return _.filter(this.views, function(v) {\n return v.selected;\n });\n },\n\n /** return a collection of the models of all currenly selected items */\n getSelectedModels: function() {\n // console.log( '(getSelectedModels)' );\n return new this.collection.constructor(\n _.map(this.getSelectedViews(), function(view) {\n return view.model;\n })\n );\n },\n\n // ------------------------------------------------------------------------ loading indicator\n /** hide the $el and display a loading indicator (in the $el's parent) when loading new data */\n _showLoadingIndicator: function(msg, speed, callback) {\n this.debug(\n \"_showLoadingIndicator\",\n this.indicator,\n msg,\n speed,\n callback\n );\n speed = speed !== undefined ? speed : this.fxSpeed;\n if (!this.indicator) {\n this.indicator = new LoadingIndicator(this.$el);\n this.debug(\"\\t created\", this.indicator);\n }\n if (!this.$el.is(\":visible\")) {\n this.indicator.show(0, callback);\n } else {\n this.$el.fadeOut(speed);\n this.indicator.show(msg, speed, callback);\n }\n },\n\n /** hide the loading indicator */\n _hideLoadingIndicator: function(speed, callback) {\n this.debug(\n \"_hideLoadingIndicator\",\n this.indicator,\n speed,\n callback\n );\n speed = speed !== undefined ? speed : this.fxSpeed;\n if (this.indicator) {\n this.indicator.hide(speed, callback);\n }\n },\n\n // ------------------------------------------------------------------------ scrolling\n /** get the current scroll position of the panel in its parent */\n scrollPosition: function() {\n return this.$scrollContainer().scrollTop();\n },\n\n /** set the current scroll position of the panel in its parent */\n scrollTo: function(pos, speed) {\n speed = speed || 0;\n this.$scrollContainer().animate({ scrollTop: pos }, speed);\n return this;\n },\n\n /** Scrolls the panel to the top. */\n scrollToTop: function(speed) {\n return this.scrollTo(0, speed);\n },\n\n /** scroll to the given view in list-items */\n scrollToItem: function(view, speed) {\n if (!view) {\n return this;\n }\n return this;\n },\n\n /** Scrolls the panel to show the content with the given id. */\n scrollToId: function(id, speed) {\n return this.scrollToItem(this.viewFromModelId(id), speed);\n },\n\n // ------------------------------------------------------------------------ panel events\n /** event map */\n events: {\n \"click .select-all\": \"selectAll\",\n \"click .deselect-all\": \"deselectAll\"\n },\n\n // ------------------------------------------------------------------------ misc\n /** Return a string rep of the panel */\n toString: function() {\n return \"ListPanel(\" + this.collection + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nListPanel.prototype.templates = (function() {\n var elTemplate = BASE_MVC.wrapTemplate([\n // temp container\n \"
- ',\n action.html,\n \" \"\n ].join(\"\");\n return $(html).click(function(ev) {\n ev.preventDefault();\n return action.func(ev);\n });\n });\n $newMenu.find(\"ul\").append($actions);\n $menu.replaceWith($newMenu);\n return $newMenu;\n },\n\n /** return a list of plain objects used to render multiselect actions menu. Each object should have:\n * html: an html string used as the anchor contents\n * func: a function called when the anchor is clicked (passed the click event)\n */\n multiselectActions: function() {\n return [];\n },\n\n // ------------------------------------------------------------------------ sub-$element shortcuts\n /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */\n $scrollContainer: function($where) {\n // override or set via attributes.$scrollContainer\n return ($where || this.$el).parent().parent();\n },\n /** convenience selector for the section that displays the list controls */\n $controls: function($where) {\n return ($where || this.$el).find(\"> .controls\");\n },\n /** list-items: where the subviews are contained in the view's dom */\n $list: function($where) {\n return ($where || this.$el).find(\"> .list-items\");\n },\n /** container where list messages are attached */\n $messages: function($where) {\n //TODO: controls isn't really correct here (only for ModelListPanel)\n return ($where || this.$el).find(\"> .controls .messages\");\n },\n /** the message displayed when no views can be shown (no views, none matching search) */\n $emptyMessage: function($where) {\n return ($where || this.$el).find(\"> .empty-message\");\n },\n\n // ------------------------------------------------------------------------ hda sub-views\n /** render the subviews for the list's collection */\n renderItems: function($whereTo) {\n $whereTo = $whereTo || this.$el;\n var panel = this;\n panel.log(this + \".renderItems\", $whereTo);\n\n var $list = panel.$list($whereTo);\n panel.freeViews();\n // console.log( 'views freed' );\n //TODO:? cache and re-use views?\n var shownModels = panel._filterCollection();\n // console.log( 'models filtered:', shownModels );\n\n panel.views = shownModels.map(function(itemModel) {\n var view = panel._createItemView(itemModel);\n return view;\n });\n\n $list.empty();\n // console.log( 'list emptied' );\n if (panel.views.length) {\n panel._attachItems($whereTo);\n // console.log( 'items attached' );\n }\n panel._renderEmptyMessage($whereTo).toggle(!panel.views.length);\n panel.trigger(\"views:ready\", panel.views);\n\n // console.log( '------------------------------------------- rendering items' );\n return panel.views;\n },\n\n /** Filter the collection to only those models that should be currently viewed */\n _filterCollection: function() {\n // override this\n var panel = this;\n return panel.collection.filter(_.bind(panel._filterItem, panel));\n },\n\n /** Should the model be viewable in the current state?\n * Checks against this.filters and this.searchFor\n */\n _filterItem: function(model) {\n // override this\n var panel = this;\n return (\n _.every(\n panel.filters.map(function(fn) {\n return fn.call(model);\n })\n ) &&\n (!panel.searchFor || model.matchesAll(panel.searchFor))\n );\n },\n\n /** Create a view for a model and set up it's listeners */\n _createItemView: function(model) {\n var ViewClass = this._getItemViewClass(model);\n var options = _.extend(this._getItemViewOptions(model), {\n model: model\n });\n var view = new ViewClass(options);\n this._setUpItemViewListeners(view);\n return view;\n },\n\n /** Free a view for a model. Note: does not remove it from the DOM */\n _destroyItemView: function(view) {\n this.stopListening(view);\n this.views = _.without(this.views, view);\n },\n\n _destroyItemViews: function(view) {\n var self = this;\n self.views.forEach(function(v) {\n self.stopListening(v);\n });\n self.views = [];\n return self;\n },\n\n /** free any sub-views the list has */\n freeViews: function() {\n return this._destroyItemViews();\n },\n\n /** Get the bbone view class based on the model */\n _getItemViewClass: function(model) {\n // override this\n return this.viewClass;\n },\n\n /** Get the options passed to the new view based on the model */\n _getItemViewOptions: function(model) {\n // override this\n return {\n //logger : this.logger,\n fxSpeed: this.fxSpeed,\n expanded: false,\n selectable: this.selecting,\n selected: _.contains(this.selected, model.id),\n draggable: this.dragItems\n };\n },\n\n /** Set up listeners for new models */\n _setUpItemViewListeners: function(view) {\n var panel = this;\n // send all events to the panel, re-namspaceing them with the view prefix\n this.listenTo(view, \"all\", function() {\n var args = Array.prototype.slice.call(arguments, 0);\n args[0] = \"view:\" + args[0];\n panel.trigger.apply(panel, args);\n });\n\n // drag multiple - hijack ev.setData to add all selected items\n this.listenTo(\n view,\n \"draggable:dragstart\",\n function(ev, v) {\n //TODO: set multiple drag data here\n var json = {},\n selected = this.getSelectedModels();\n if (selected.length) {\n json = selected.toJSON();\n } else {\n json = [v.model.toJSON()];\n }\n ev.dataTransfer.setData(\"text\", JSON.stringify(json));\n //ev.dataTransfer.setDragImage( v.el, 60, 60 );\n },\n this\n );\n\n return panel;\n },\n\n /** Attach views in this.views to the model based on $whereTo */\n _attachItems: function($whereTo) {\n var self = this;\n // console.log( '_attachItems:', $whereTo, this.$list( $whereTo ) );\n //ASSUMES: $list has been emptied\n this.$list($whereTo).append(\n this.views.map(function(view) {\n return self._renderItemView$el(view);\n })\n );\n return this;\n },\n\n /** get a given subview's $el (or whatever may wrap it) and return it */\n _renderItemView$el: function(view) {\n // useful to wrap and override\n return view.render(0).$el;\n },\n\n /** render the empty/none-found message */\n _renderEmptyMessage: function($whereTo) {\n this.debug(\"_renderEmptyMessage\", $whereTo, this.searchFor);\n var text = this.searchFor ? this.noneFoundMsg : this.emptyMsg;\n return this.$emptyMessage($whereTo).text(text);\n },\n\n /** expand all item views */\n expandAll: function() {\n _.each(this.views, function(view) {\n view.expand();\n });\n },\n\n /** collapse all item views */\n collapseAll: function() {\n _.each(this.views, function(view) {\n view.collapse();\n });\n },\n\n // ------------------------------------------------------------------------ collection/views syncing\n /** Add a view (if the model should be viewable) to the panel */\n addItemView: function(model, collection, options) {\n // console.log( this + '.addItemView:', model );\n var panel = this;\n // get the index of the model in the list of filtered models shown by this list\n // in order to insert the view in the proper place\n //TODO:? potentially expensive\n var modelIndex = panel._filterCollection().indexOf(model);\n if (modelIndex === -1) {\n return undefined;\n }\n var view = panel._createItemView(model);\n // console.log( 'adding and rendering:', modelIndex, view.toString() );\n\n $(view).queue(\"fx\", [\n function(next) {\n // hide the empty message first if only view\n if (panel.$emptyMessage().is(\":visible\")) {\n panel.$emptyMessage().fadeOut(panel.fxSpeed, next);\n } else {\n next();\n }\n },\n function(next) {\n panel._attachView(view, modelIndex);\n next();\n }\n ]);\n return view;\n },\n\n /** internal fn to add view (to both panel.views and panel.$list) */\n _attachView: function(view, modelIndex, useFx) {\n // console.log( this + '._attachView:', view, modelIndex, useFx );\n useFx = _.isUndefined(useFx) ? true : useFx;\n modelIndex = modelIndex || 0;\n var panel = this;\n\n // use the modelIndex to splice into views and insert at the proper index in the DOM\n panel.views.splice(modelIndex, 0, view);\n panel._insertIntoListAt(\n modelIndex,\n panel._renderItemView$el(view).hide()\n );\n\n panel.trigger(\"view:attached\", view);\n if (useFx) {\n view.$el.slideDown(panel.fxSpeed, function() {\n panel.trigger(\"view:attached:rendered\");\n });\n } else {\n view.$el.show();\n panel.trigger(\"view:attached:rendered\");\n }\n return view;\n },\n\n /** insert a jq object as a child of list-items at the specified *DOM index* */\n _insertIntoListAt: function(index, $what) {\n // console.log( this + '._insertIntoListAt:', index, $what );\n var $list = this.$list();\n if (index === 0) {\n $list.prepend($what);\n } else {\n $list\n .children()\n .eq(index - 1)\n .after($what);\n }\n return $what;\n },\n\n /** Remove a view from the panel (if found) */\n removeItemView: function(model, collection, options) {\n var panel = this;\n var view = _.find(panel.views, function(v) {\n return v.model === model;\n });\n if (!view) {\n return undefined;\n }\n panel.views = _.without(panel.views, view);\n panel.trigger(\"view:removed\", view);\n\n // potentially show the empty message if no views left\n // use anonymous queue here - since remove can happen multiple times\n $({}).queue(\"fx\", [\n function(next) {\n view.$el.fadeOut(panel.fxSpeed, next);\n },\n function(next) {\n view.remove();\n panel.trigger(\"view:removed:rendered\");\n if (!panel.views.length) {\n panel._renderEmptyMessage().fadeIn(panel.fxSpeed, next);\n } else {\n next();\n }\n }\n ]);\n return view;\n },\n\n /** get views based on model.id */\n viewFromModelId: function(id) {\n return _.find(this.views, function(v) {\n return v.model.id === id;\n });\n },\n\n /** get views based on model */\n viewFromModel: function(model) {\n return model ? this.viewFromModelId(model.id) : undefined;\n },\n\n /** get views based on model properties */\n viewsWhereModel: function(properties) {\n return this.views.filter(function(view) {\n return _.isMatch(view.model.attributes, properties);\n });\n },\n\n /** A range of views between (and including) viewA and viewB */\n viewRange: function(viewA, viewB) {\n if (viewA === viewB) {\n return viewA ? [viewA] : [];\n }\n\n var indexA = this.views.indexOf(viewA),\n indexB = this.views.indexOf(viewB);\n\n // handle not found\n if (indexA === -1 || indexB === -1) {\n if (indexA === indexB) {\n return [];\n }\n return indexA === -1 ? [viewB] : [viewA];\n }\n // reverse if indeces are\n //note: end inclusive\n return indexA < indexB\n ? this.views.slice(indexA, indexB + 1)\n : this.views.slice(indexB, indexA + 1);\n },\n\n // ------------------------------------------------------------------------ searching\n /** render a search input for filtering datasets shown\n * (see SearchableMixin in base-mvc for implementation of the actual searching)\n * return will start the search\n * esc will clear the search\n * clicking the clear button will clear the search\n * uses searchInput in ui.js\n */\n _renderSearch: function($where) {\n $where.find(\".controls .search-input\").searchInput({\n placeholder: this.searchPlaceholder,\n initialVal: this.searchFor,\n onfirstsearch: _.bind(this._firstSearch, this),\n onsearch: _.bind(this.searchItems, this),\n onclear: _.bind(this.clearSearch, this)\n });\n return $where;\n },\n\n /** What to do on the first search entered */\n _firstSearch: function(searchFor) {\n // override to load model details if necc.\n this.log(\"onFirstSearch\", searchFor);\n return this.searchItems(searchFor);\n },\n\n /** filter view list to those that contain the searchFor terms */\n searchItems: function(searchFor, force) {\n this.log(\"searchItems\", searchFor, this.searchFor, force);\n if (!force && this.searchFor === searchFor) {\n return this;\n }\n this.searchFor = searchFor;\n this.renderItems();\n this.trigger(\"search:searching\", searchFor, this);\n var $search = this.$(\"> .controls .search-query\");\n if ($search.val() !== searchFor) {\n $search.val(searchFor);\n }\n return this;\n },\n\n /** clear the search filters and show all views that are normally shown */\n clearSearch: function(searchFor) {\n //this.log( 'onSearchClear', this );\n this.searchFor = \"\";\n this.trigger(\"search:clear\", this);\n this.$(\"> .controls .search-query\").val(\"\");\n this.renderItems();\n return this;\n },\n\n // ------------------------------------------------------------------------ selection\n /** @type Integer when the number of list item views is >= to this, don't animate selectors */\n THROTTLE_SELECTOR_FX_AT: 20,\n\n /** show selectors on all visible itemViews and associated controls */\n showSelectors: function(speed) {\n speed = speed !== undefined ? speed : this.fxSpeed;\n this.selecting = true;\n this.$(\".list-actions\").slideDown(speed);\n speed =\n this.views.length >= this.THROTTLE_SELECTOR_FX_AT ? 0 : speed;\n _.each(this.views, function(view) {\n view.showSelector(speed);\n });\n //this.selected = [];\n //this.lastSelected = null;\n },\n\n /** hide selectors on all visible itemViews and associated controls */\n hideSelectors: function(speed) {\n speed = speed !== undefined ? speed : this.fxSpeed;\n this.selecting = false;\n this.$(\".list-actions\").slideUp(speed);\n speed =\n this.views.length >= this.THROTTLE_SELECTOR_FX_AT ? 0 : speed;\n _.each(this.views, function(view) {\n view.hideSelector(speed);\n });\n this.selected = [];\n this.lastSelected = null;\n },\n\n /** show or hide selectors on all visible itemViews and associated controls */\n toggleSelectors: function() {\n if (!this.selecting) {\n this.showSelectors();\n } else {\n this.hideSelectors();\n }\n },\n\n /** select all visible items */\n selectAll: function(event) {\n _.each(this.views, function(view) {\n view.select(event);\n });\n },\n\n /** deselect all visible items */\n deselectAll: function(event) {\n this.lastSelected = null;\n _.each(this.views, function(view) {\n view.deselect(event);\n });\n },\n\n /** select a range of datasets between A and B */\n selectRange: function(viewA, viewB) {\n var range = this.viewRange(viewA, viewB);\n _.each(range, function(view) {\n view.select();\n });\n return range;\n },\n\n /** return an array of all currently selected itemViews */\n getSelectedViews: function() {\n return _.filter(this.views, function(v) {\n return v.selected;\n });\n },\n\n /** return a collection of the models of all currenly selected items */\n getSelectedModels: function() {\n // console.log( '(getSelectedModels)' );\n return new this.collection.constructor(\n _.map(this.getSelectedViews(), function(view) {\n return view.model;\n })\n );\n },\n\n // ------------------------------------------------------------------------ loading indicator\n /** hide the $el and display a loading indicator (in the $el's parent) when loading new data */\n _showLoadingIndicator: function(msg, speed, callback) {\n this.debug(\n \"_showLoadingIndicator\",\n this.indicator,\n msg,\n speed,\n callback\n );\n speed = speed !== undefined ? speed : this.fxSpeed;\n if (!this.indicator) {\n this.indicator = new LoadingIndicator(this.$el);\n this.debug(\"\\t created\", this.indicator);\n }\n if (!this.$el.is(\":visible\")) {\n this.indicator.show(0, callback);\n } else {\n this.$el.fadeOut(speed);\n this.indicator.show(msg, speed, callback);\n }\n },\n\n /** hide the loading indicator */\n _hideLoadingIndicator: function(speed, callback) {\n this.debug(\n \"_hideLoadingIndicator\",\n this.indicator,\n speed,\n callback\n );\n speed = speed !== undefined ? speed : this.fxSpeed;\n if (this.indicator) {\n this.indicator.hide(speed, callback);\n }\n },\n\n // ------------------------------------------------------------------------ scrolling\n /** get the current scroll position of the panel in its parent */\n scrollPosition: function() {\n return this.$scrollContainer().scrollTop();\n },\n\n /** set the current scroll position of the panel in its parent */\n scrollTo: function(pos, speed) {\n speed = speed || 0;\n this.$scrollContainer().animate({ scrollTop: pos }, speed);\n return this;\n },\n\n /** Scrolls the panel to the top. */\n scrollToTop: function(speed) {\n return this.scrollTo(0, speed);\n },\n\n /** scroll to the given view in list-items */\n scrollToItem: function(view, speed) {\n if (!view) {\n return this;\n }\n return this;\n },\n\n /** Scrolls the panel to show the content with the given id. */\n scrollToId: function(id, speed) {\n return this.scrollToItem(this.viewFromModelId(id), speed);\n },\n\n // ------------------------------------------------------------------------ panel events\n /** event map */\n events: {\n \"click .select-all\": \"selectAll\",\n \"click .deselect-all\": \"deselectAll\"\n },\n\n // ------------------------------------------------------------------------ misc\n /** Return a string rep of the panel */\n toString: function() {\n return \"ListPanel(\" + this.collection + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nListPanel.prototype.templates = (function() {\n var elTemplate = BASE_MVC.wrapTemplate([\n // temp container\n \"
- ',\n 'Repository Installation Queue',\n \" \"\n ].join(\"\")\n ),\n\n templateRepoQueue: _.template(\n [\n '
- <%= wf %> ',\n \"<% }); %>\",\n \"
- <%= tool %> ',\n \"<% }); %>\",\n \"
- \" data-owner=\"<%= workflow_details[1] %>\" data-repo=\"<%= workflow_details[2] %>\" data-toolids=\"<%= workflow.tools.join(\",\") %>\" value=\"Preview\" /> ',\n '
- \" data-owner=\"<%= workflow_details[1] %>\" data-repo=\"<%= workflow_details[2] %>\" data-toolids=\"<%= workflow.tools.join(\",\") %>\" value=\"Add to queue\" /> ',\n \"
- ',\n 'Repository Installation Queue',\n \" \"\n ].join(\"\")\n ),\n\n templateRepoQueue: _.template(\n [\n '
- <%= wf %> ',\n \"<% }); %>\",\n \"
- <%= tool %> ',\n \"<% }); %>\",\n \"
- \" data-owner=\"<%= workflow_details[1] %>\" data-repo=\"<%= workflow_details[2] %>\" data-toolids=\"<%= workflow.tools.join(\",\") %>\" value=\"Preview\" /> ',\n '
- \" data-owner=\"<%= workflow_details[1] %>\" data-repo=\"<%= workflow_details[2] %>\" data-toolids=\"<%= workflow.tools.join(\",\") %>\" value=\"Add to queue\" /> ',\n \"
- Repository installation requires the following\",\n \"<% if (has_repository_dependencies) { %>\",\n \"<% _.each(repository_dependencies, function(dependency) { %>\",\n \"<% dependency.repository_dependency_template = repository_dependency_template; %>\",\n \"<%= repository_dependency_template(dependency) %>\",\n \"<% }); %>\",\n \"<% } %>\",\n \" \",\n \"
- \" class=\"datasetRow repository_dependency_row\">',\n \"Repository <%= repository.name %> revision <%= changeset_revision %> owned by <%= repository.owner %>\",\n \"<% if (has_repository_dependencies) { %>\",\n '
- ',\n \"<% _.each(repository_dependencies, function(dependency) { %>\",\n \"<% dependency.repository_dependency_template = repository_dependency_template; %>\",\n \"<%= repository_dependency_template(dependency) %>\",\n \"<% }); %>\",\n \"
\"\n ].join(\"\")\n ),\n\n templateShedToolConf: _.template(\n [\n ' - Repository installation requires the following\",\n \"<% if (has_repository_dependencies) { %>\",\n \"<% _.each(repository_dependencies, function(dependency) { %>\",\n \"<% dependency.repository_dependency_template = repository_dependency_template; %>\",\n \"<%= repository_dependency_template(dependency) %>\",\n \"<% }); %>\",\n \"<% } %>\",\n \" \",\n \"
- \" class=\"datasetRow repository_dependency_row\">',\n \"Repository <%= repository.name %> revision <%= changeset_revision %> owned by <%= repository.owner %>\",\n \"<% if (has_repository_dependencies) { %>\",\n '
- ',\n \"<% _.each(repository_dependencies, function(dependency) { %>\",\n \"<% dependency.repository_dependency_template = repository_dependency_template; %>\",\n \"<%= repository_dependency_template(dependency) %>\",\n \"<% }); %>\",\n \"
\"\n ].join(\"\")\n ),\n\n templateShedToolConf: _.template(\n [\n ' - <%= name %> ',\n \"<% }); %>\",\n \"
- <%= tool %> ',\n \"<% }); %>\",\n \"
- ',\n '\" data-owner=\"<%= workflow.get(\"owner\") %>\" data-repo=\"<%= workflow.get(\"repository\") %>\" data-toolids=\"<%= workflow.get(\"tools\").join(\",\") %>\" value=\"Show Repository\" /> ',\n \"
- <%= name %> ',\n \"<% }); %>\",\n \"
- <%= tool %> ',\n \"<% }); %>\",\n \"
- ',\n '\" data-owner=\"<%= workflow.get(\"owner\") %>\" data-repo=\"<%= workflow.get(\"repository\") %>\" data-toolids=\"<%= workflow.get(\"tools\").join(\",\") %>\" value=\"Show Repository\" /> ',\n \"
- \n \" class=\"tourItem\" data-tour.id=<%- tour.id %>>\n <%- tour.attributes.name || tour.id %>\n \n - <%- tour.attributes.description || \"No description given.\" %>\n \n<% }); %>\n
- \n \" class=\"tourItem\" data-tour.id=<%- tour.id %>>\n <%- tour.attributes.name || tour.id %>\n \n - <%- tour.attributes.description || \"No description given.\" %>\n \n<% }); %>\n
- (no options) \";\n }\n return _.map(options, function(option) {\n if (option.divider) {\n return '';\n } else if (option.header) {\n return [\n '
- ',\n option.html,\n \" \"\n ].join(\"\");\n }\n var href = option.href || \"javascript:void(0);\",\n target = option.target\n ? ' target=\"' + option.target + '\"'\n : \"\",\n check = option.checked\n ? ''\n : \"\";\n return [\n '
- \",\n check,\n option.html,\n \" \"\n ].join(\"\");\n }).join(\"\");\n },\n\n // get the absolute position/offset for the menu\n _getShownPosition: function(clickEvent) {\n // display menu horiz. centered on click...\n var menuWidth = this.$el.width();\n var x = clickEvent.pageX - menuWidth / 2;\n\n // adjust to handle horiz. scroll and window dimensions ( draw entirely on visible screen area )\n x = Math.min(\n x,\n $(document).scrollLeft() + $(window).width() - menuWidth - 5\n );\n x = Math.max(x, $(document).scrollLeft() + 5);\n return {\n top: clickEvent.pageY,\n left: x\n };\n },\n\n // bind an event handler to all available frames so that when anything is clicked\n // the menu is removed from the DOM and the event handler unbinds itself\n _setUpCloseBehavior: function() {\n var menu = this;\n //TODO: alternately: focus hack, blocking overlay, jquery.blockui\n\n // function to close popup and unbind itself\n function closePopup(event) {\n $(document).off(\"click.close_popup\");\n if (window && window.parent !== window) {\n try {\n $(window.parent.document).off(\"click.close_popup\");\n } catch (err) {}\n } else {\n try {\n $(\"iframe#galaxy_main\")\n .contents()\n .off(\"click.close_popup\");\n } catch (err) {}\n }\n menu.remove();\n }\n\n $(\"html\").one(\"click.close_popup\", closePopup);\n if (window && window.parent !== window) {\n try {\n $(window.parent.document)\n .find(\"html\")\n .one(\"click.close_popup\", closePopup);\n } catch (err) {}\n } else {\n try {\n $(\"iframe#galaxy_main\")\n .contents()\n .one(\"click.close_popup\", closePopup);\n } catch (err) {}\n }\n },\n\n // add a menu option/item at the given index\n addItem: function(item, index) {\n // append to end if no index\n index = index >= 0 ? index : this.options.length;\n this.options.splice(index, 0, item);\n return this;\n },\n\n // remove a menu option/item at the given index\n removeItem: function(index) {\n if (index >= 0) {\n this.options.splice(index, 1);\n }\n return this;\n },\n\n // search for a menu option by its html\n findIndexByHtml: function(html) {\n for (var i = 0; i < this.options.length; i++) {\n if (\n _.has(this.options[i], \"html\") &&\n this.options[i].html === html\n ) {\n return i;\n }\n }\n return null;\n },\n\n // search for a menu option by its html\n findItemByHtml: function(html) {\n return this.options[this.findIndexByHtml(html)];\n },\n\n // string representation\n toString: function() {\n return \"PopupMenu\";\n }\n });\n /** shortcut to new for when you don't need to preserve the ref */\n PopupMenu.create = function _create($button, options) {\n return new PopupMenu($button, options);\n };\n\n // -----------------------------------------------------------------------------\n // the following class functions are bridges from the original make_popupmenu and make_popup_menus\n // to the newer backbone.js PopupMenu\n\n /** Create a PopupMenu from simple map initial_options activated by clicking button_element.\n * Converts initial_options to object array used by PopupMenu.\n * @param {jQuery|DOMElement} button_element element which, when clicked, activates menu\n * @param {Object} initial_options map of key -> values, where\n * key is option text, value is fn to call when option is clicked\n * @returns {PopupMenu} the PopupMenu created\n */\n PopupMenu.make_popupmenu = function(button_element, initial_options) {\n var convertedOptions = [];\n _.each(initial_options, function(optionVal, optionKey) {\n var newOption = { html: optionKey };\n\n // keys with null values indicate: header\n if (optionVal === null) {\n // !optionVal? (null only?)\n newOption.header = true;\n\n // keys with function values indicate: a menu option\n } else if (jQuery.type(optionVal) === \"function\") {\n newOption.func = optionVal;\n }\n //TODO:?? any other special optionVals?\n // there was no divider option originally\n convertedOptions.push(newOption);\n });\n return new PopupMenu($(button_element), convertedOptions);\n };\n\n /** Find all anchors in $parent (using selector) and covert anchors into a PopupMenu options map.\n * @param {jQuery} $parent the element that contains the links to convert to options\n * @param {String} selector jq selector string to find links\n * @returns {Object[]} the options array to initialize a PopupMenu\n */\n //TODO: lose parent and selector, pass in array of links, use map to return options\n PopupMenu.convertLinksToOptions = function($parent, selector) {\n $parent = $($parent);\n selector = selector || \"a\";\n var options = [];\n $parent.find(selector).each(function(elem, i) {\n var option = {},\n $link = $(elem);\n\n // convert link text to the option text (html) and the href into the option func\n option.html = $link.text();\n if ($link.attr(\"href\")) {\n var linkHref = $link.attr(\"href\"),\n linkTarget = $link.attr(\"target\"),\n confirmText = $link.attr(\"confirm\");\n\n option.func = function() {\n // if there's a \"confirm\" attribute, throw up a confirmation dialog, and\n // if the user cancels - do nothing\n if (confirmText && !confirm(confirmText)) {\n return;\n }\n\n // if there's no confirm attribute, or the user accepted the confirm dialog:\n switch (linkTarget) {\n // relocate the center panel\n case \"_parent\":\n window.parent.location = linkHref;\n break;\n\n // relocate the entire window\n case \"_top\":\n window.top.location = linkHref;\n break;\n\n // relocate this panel\n default:\n window.location = linkHref;\n }\n };\n }\n options.push(option);\n });\n return options;\n };\n\n /** Create a single popupmenu from existing DOM button and anchor elements\n * @param {jQuery} $buttonElement the element that when clicked will open the menu\n * @param {jQuery} $menuElement the element that contains the anchors to convert into a menu\n * @param {String} menuElementLinkSelector jq selector string used to find anchors to be made into menu options\n * @returns {PopupMenu} the PopupMenu (Backbone View) that can render, control the menu\n */\n PopupMenu.fromExistingDom = function(\n $buttonElement,\n $menuElement,\n menuElementLinkSelector\n ) {\n $buttonElement = $($buttonElement);\n $menuElement = $($menuElement);\n var options = PopupMenu.convertLinksToOptions(\n $menuElement,\n menuElementLinkSelector\n );\n // we're done with the menu (having converted it to an options map)\n $menuElement.remove();\n return new PopupMenu($buttonElement, options);\n };\n\n /** Create all popupmenus within a document or a more specific element\n * @param {DOMElement} parent the DOM element in which to search for popupmenus to build (defaults to document)\n * @param {String} menuSelector jq selector string to find popupmenu menu elements (defaults to \"div[popupmenu]\")\n * @param {Function} buttonSelectorBuildFn the function to build the jq button selector.\n * Will be passed $menuElement, parent.\n * (Defaults to return '#' + $menuElement.attr( 'popupmenu' ); )\n * @returns {PopupMenu[]} array of popupmenus created\n */\n PopupMenu.make_popup_menus = function(\n parent,\n menuSelector,\n buttonSelectorBuildFn\n ) {\n parent = parent || document;\n // orig. Glx popupmenu menus have a (non-std) attribute 'popupmenu'\n // which contains the id of the button that activates the menu\n menuSelector = menuSelector || \"div[popupmenu]\";\n // default to (orig. Glx) matching button to menu by using the popupmenu attr of the menu as the id of the button\n buttonSelectorBuildFn =\n buttonSelectorBuildFn ||\n function($menuElement, parent) {\n return \"#\" + $menuElement.attr(\"popupmenu\");\n };\n\n // aggregate and return all PopupMenus\n var popupMenusCreated = [];\n $(parent)\n .find(menuSelector)\n .each(function() {\n var $menuElement = $(this),\n $buttonElement = $(parent).find(\n buttonSelectorBuildFn($menuElement, parent)\n );\n popupMenusCreated.push(\n PopupMenu.fromDom($buttonElement, $menuElement)\n );\n $buttonElement.addClass(\"popup\");\n });\n return popupMenusCreated;\n };\n\n // =============================================================================\n return PopupMenu;\n }\n);\n"]} \ No newline at end of file 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[\n //jquery\n //backbone\n ],\n function() {\n // =============================================================================\n /**\n * view for a popup menu\n */\n var PopupMenu = Backbone.View.extend({\n //TODO: maybe better as singleton off the Galaxy obj\n /** Cache the desired button element and options, set up the button click handler\n * NOTE: attaches this view as HTML/jQ data on the button for later use.\n */\n initialize: function($button, options) {\n // default settings\n this.$button = $button;\n if (!this.$button.length) {\n this.$button = $(\"\");\n }\n this.options = options || [];\n this.$button.data(\"popupmenu\", this);\n\n // set up button click -> open menu behavior\n var menu = this;\n this.$button.click(function(event) {\n // if there's already a menu open, remove it\n $(\".popmenu-wrapper\").remove();\n menu._renderAndShow(event);\n return false;\n });\n },\n\n // render the menu, append to the page body at the click position, and set up the 'click-away' handlers, show\n _renderAndShow: function(clickEvent) {\n this.render();\n this.$el\n .appendTo(\"body\")\n .css(this._getShownPosition(clickEvent))\n .show();\n this._setUpCloseBehavior();\n },\n\n // render the menu\n // this menu doesn't attach itself to the DOM ( see _renderAndShow )\n render: function() {\n // render the menu body absolute and hidden, fill with template\n this.$el\n .addClass(\"popmenu-wrapper\")\n .hide()\n .css({ position: \"absolute\" })\n .html(this.template(this.$button.attr(\"id\"), this.options));\n\n // set up behavior on each link/anchor elem\n if (this.options.length) {\n var menu = this;\n //precondition: there should be one option per li\n this.$el.find(\"li\").each(function(i, li) {\n var option = menu.options[i];\n\n // if the option has 'func', call that function when the anchor is clicked\n if (option.func) {\n $(this)\n .children(\"a.popupmenu-option\")\n .click(function(event) {\n option.func.call(menu, event, option);\n // We must preventDefault otherwise clicking \"cancel\"\n // on a purge or something still navigates and causes\n // the action.\n event.preventDefault();\n // bubble up so that an option click will call the close behavior\n });\n }\n });\n }\n return this;\n },\n\n template: function(id, options) {\n return [\n '\"\n ].join(\"\");\n },\n\n _templateOptions: function(options) {\n if (!options.length) {\n return \"
- (no options) \";\n }\n return _.map(options, function(option) {\n if (option.divider) {\n return '';\n } else if (option.header) {\n return [\n '
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this.$icon.addClass(\"ui-margin-right\");\n }\n },\n\n /** Show button */\n show: function() {\n this.$el.show();\n },\n\n /** Hide button */\n hide: function() {\n this.$el.hide();\n },\n\n /** Disable button */\n disable: function() {\n this.model.set(\"disabled\", true);\n },\n\n /** Enable button */\n enable: function() {\n this.model.set(\"disabled\", false);\n },\n\n /** Show spinner to indicate that the button is not ready to be clicked */\n wait: function() {\n this.model.set(\"wait\", true);\n },\n\n /** Hide spinner to indicate that the button is ready to be clicked */\n unwait: function() {\n this.model.set(\"wait\", false);\n },\n\n /** Change icon */\n setIcon: function(icon) {\n this.model.set(\"icon\", icon);\n }\n });\n\n /** This button allows the right-click/open-in-new-tab feature, its used e.g. for panel buttons. */\n var ButtonLink = ButtonDefault.extend({\n initialize: function(options) {\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n id: Utils.uid(),\n title: \"\",\n icon: \"\",\n cls: \"\"\n }).set(options);\n this.setElement($(\"\").append((this.$icon = $(\"\"))));\n this.listenTo(this.model, \"change\", this.render, this);\n this.render();\n },\n\n render: function() {\n var options = this.model.attributes;\n this.$el\n .removeClass()\n .addClass(options.cls)\n .attr({\n id: options.id,\n href: options.href || \"javascript:void(0)\",\n title: options.title,\n target: options.target || \"_top\",\n disabled: options.disabled\n })\n .tooltip({ placement: \"bottom\" })\n .off(\"click\")\n .on(\"click\", function() {\n options.onclick && !options.disabled && options.onclick();\n });\n this.$icon.removeClass().addClass(options.icon);\n }\n });\n\n /** The check button is used in the tool form and allows to distinguish between multiple states e.g. all, partially and nothing selected. */\n var ButtonCheck = Backbone.View.extend({\n initialize: function(options) {\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n id: Utils.uid(),\n title: \"Select/Unselect all\",\n icons: [\n \"fa-square-o\",\n \"fa-minus-square-o\",\n \"fa-check-square-o\"\n ],\n value: 0,\n onchange: function() {}\n }).set(options);\n this.setElement(\n $(\"\")\n .append((this.$icon = $(\"\")))\n .append((this.$title = $(\"\")))\n );\n this.listenTo(this.model, \"change\", this.render, this);\n this.render();\n },\n\n render: function(options) {\n var self = this;\n var options = this.model.attributes;\n this.$el\n .addClass(\"ui-button-check\")\n .off(\"click\")\n .on(\"click\", function() {\n self.model.set(\n \"value\",\n (self.model.get(\"value\") === 0 && 2) || 0\n );\n options.onclick && options.onclick();\n });\n this.$title.html(options.title);\n this.$icon\n .removeClass()\n .addClass(\"icon fa ui-margin-right\")\n .addClass(options.icons[options.value]);\n },\n\n /* Sets a new value and/or returns the value.\n * @param{Integer} new_val - Set a new value 0=unchecked, 1=partial and 2=checked.\n * OR:\n * @param{Integer} new_val - Number of selected options.\n * @param{Integer} total - Total number of available options.\n */\n value: function(new_val, total) {\n if (new_val !== undefined) {\n if (total && new_val !== 0) {\n new_val = (new_val !== total && 1) || 2;\n }\n this.model.set(\"value\", new_val);\n this.model.get(\"onchange\")(this.model.get(\"value\"));\n }\n return this.model.get(\"value\");\n }\n });\n\n /** This renders a differently styled, more compact button version. */\n var ButtonIcon = ButtonDefault.extend({\n initialize: function(options) {\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n id: Utils.uid(),\n title: \"\",\n icon: \"\",\n cls: \"ui-button-icon\",\n disabled: false\n }).set(options);\n this.setElement(\n $(\"\").append(\n (this.$button = $(\"\")\n .append((this.$icon = $(\"\")))\n .append((this.$title = $(\"\"))))\n )\n );\n this.listenTo(this.model, \"change\", this.render, this);\n this.render();\n },\n\n render: function(options) {\n var self = this;\n var options = this.model.attributes;\n this.$el\n .removeClass()\n .addClass(options.cls)\n .addClass(options.disabled && \"disabled\")\n .attr(\"disabled\", options.disabled)\n .attr(\"id\", options.id)\n .off(\"click\")\n .on(\"click\", function() {\n $(\".tooltip\").hide();\n !options.disabled && options.onclick && options.onclick();\n });\n this.$button\n .addClass(\"button\")\n .tooltip({ title: options.tooltip, placement: \"bottom\" });\n this.$icon\n .removeClass()\n .addClass(\"icon fa\")\n .addClass(options.icon);\n this.$title.addClass(\"title\").html(options.title);\n options.icon &&\n options.title &&\n this.$icon.addClass(\"ui-margin-right\");\n }\n });\n\n /** This class creates a button with dropdown menu. */\n var ButtonMenu = ButtonDefault.extend({\n $menu: null,\n initialize: function(options) {\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n id: \"\",\n title: \"\",\n pull: \"right\",\n icon: null,\n onclick: null,\n cls: \"ui-button-icon ui-button-menu\",\n tooltip: \"\",\n target: \"\",\n href: \"\",\n onunload: null,\n visible: true,\n tag: \"\"\n }).set(options);\n this.collection = new Backbone.Collection();\n this.setElement(\n $(\"\").append(\n (this.$root = $(\"\")\n .append((this.$icon = $(\"\")))\n .append((this.$title = $(\"\"))))\n )\n );\n this.listenTo(this.model, \"change\", this.render, this);\n this.listenTo(\n this.collection,\n \"change add remove reset\",\n this.render,\n this\n );\n this.render();\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el\n .removeClass()\n .addClass(\"dropdown\")\n .addClass(options.cls)\n .attr(\"id\", options.id)\n .css({\n display:\n options.visible &&\n this.collection.where({ visible: true }).length > 0\n ? \"block\"\n : \"none\"\n });\n this.$root\n .addClass(\"root button dropdown-toggle\")\n .attr(\"data-toggle\", \"dropdown\")\n .tooltip({ title: options.tooltip, placement: \"bottom\" })\n .off(\"click\")\n .on(\"click\", function(e) {\n $(\".tooltip\").hide();\n e.preventDefault();\n options.onclick && options.onclick();\n });\n this.$icon\n .removeClass()\n .addClass(\"icon fa\")\n .addClass(options.icon);\n this.$title\n .removeClass()\n .addClass(\"title\")\n .html(options.title);\n options.icon &&\n options.title &&\n this.$icon.addClass(\"ui-margin-right\");\n this.$menu && this.$menu.remove();\n if (this.collection.length > 0) {\n this.$menu = $(\"
- \" + step.errors + \" \";\n }\n _.each(data.upgrade_messages[step_id], function(m) {\n details += \"
- \" + m + \" \";\n });\n if (details) {\n upgrade_message +=\n \"
- Step \" +\n (parseInt(step_id, 10) + 1) +\n \": \" +\n self.workflow.nodes[step_id].name +\n \"
- \" +\n details +\n \"
\";\n }\n });\n if (upgrade_message) {\n window.show_modal(\n \"Issues loading this workflow\",\n \"Please review the following issues, possibly resulting from tool upgrades or changes. - Step \" +\n (parseInt(k, 10) + 1) +\n \": \" +\n self.workflow.nodes[k].name +\n \"
- \";\n $.each(v, function(i, vv) {\n upgrade_message += \"
- \" + vv + \" \";\n });\n upgrade_message += \"
\";\n });\n if (upgrade_message) {\n window.show_modal(\n \"Subworkflow embedded with changes\",\n \"Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save. - \" + step.errors + \" \";\n }\n _.each(data.upgrade_messages[step_id], function(m) {\n details += \"
- \" + m + \" \";\n });\n if (details) {\n upgrade_message +=\n \"
- Step \" +\n (parseInt(step_id, 10) + 1) +\n \": \" +\n self.workflow.nodes[step_id].name +\n \"
- \" +\n details +\n \"
\";\n }\n });\n if (upgrade_message) {\n window.show_modal(\n \"Issues loading this workflow\",\n \"Please review the following issues, possibly resulting from tool upgrades or changes. - Step \" +\n (parseInt(k, 10) + 1) +\n \": \" +\n self.workflow.nodes[k].name +\n \"
- \";\n $.each(v, function(i, vv) {\n upgrade_message += \"
- \" + vv + \" \";\n });\n upgrade_message += \"
\";\n });\n if (upgrade_message) {\n window.show_modal(\n \"Subworkflow embedded with changes\",\n \"Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save. - \" +\n '' +\n \" \" +\n \"
- \" +\n '' +\n \"\" +\n \" \" +\n \"
- \" +\n '' +\n \"\" +\n \" \" +\n \"
- \" +\n '' +\n \" \" +\n \"
- \" +\n '' +\n \"\" +\n \" \" +\n \"
- \" +\n '' +\n \"\" +\n \" \" +\n \"
- ', contents, \" \"].join(\n \"\"\n )\n );\n }\n\n /** render previous and next pagination buttons */\n Pagination.prototype._render = function __render() {\n // no data - no pagination\n if (this.options.totalDataSize === 0) {\n return this;\n }\n // only one page\n if (this.numPages === 1) {\n return this;\n }\n\n // when the number of pages are known, render each page as a link\n if (this.numPages > 0) {\n this._renderPages();\n this._scrollToActivePage();\n\n // when the number of pages is not known, render previous or next\n } else {\n this._renderPrevNext();\n }\n return this;\n };\n\n /** render previous and next pagination buttons */\n Pagination.prototype._renderPrevNext = function __renderPrevNext() {\n var pagination = this,\n $prev = _make$Li(\"Prev\"),\n $next = _make$Li(\"Next\"),\n $paginationContainer = $(\"
- ', contents, \" \"].join(\n \"\"\n )\n );\n }\n\n /** render previous and next pagination buttons */\n Pagination.prototype._render = function __render() {\n // no data - no pagination\n if (this.options.totalDataSize === 0) {\n return this;\n }\n // only one page\n if (this.numPages === 1) {\n return this;\n }\n\n // when the number of pages are known, render each page as a link\n if (this.numPages > 0) {\n this._renderPages();\n this._scrollToActivePage();\n\n // when the number of pages is not known, render previous or next\n } else {\n this._renderPrevNext();\n }\n return this;\n };\n\n /** render previous and next pagination buttons */\n Pagination.prototype._renderPrevNext = function __renderPrevNext() {\n var pagination = this,\n $prev = _make$Li(\"Prev\"),\n $next = _make$Li(\"Next\"),\n $paginationContainer = $(\"
- No Options. \").appendTo(menu_element);\n }\n $.each(options, function(k, v) {\n if (v) {\n // Action can be either an anonymous function and a mapped dict.\n var action = v.action || v;\n menu_element.append(\n $(\"\").append(\n $(\"\")\n .attr(\"href\", v.url)\n .html(k)\n .click(action)\n )\n );\n } else {\n menu_element.append(\n $(\"\")\n .addClass(\"head\")\n .append($(\"\").html(k))\n );\n }\n });\n var wrapper = $(\n \"\"\n )\n .append(menu_element)\n .appendTo(\"body\");\n\n var x = e.pageX - wrapper.width() / 2;\n x = Math.min(\n x,\n $(document).scrollLeft() +\n $(window).width() -\n $(wrapper).width() -\n 5\n );\n x = Math.max(x, $(document).scrollLeft() + 5);\n\n wrapper.css({\n top: e.pageY,\n left: x\n });\n }, 10);\n\n setTimeout(function() {\n // Bind click event to current window and all frames to remove any visible menus\n // Bind to document object instead of window object for IE compat\n var close_popup = function(el) {\n $(el).bind(\"click.close_popup\", function() {\n $(\".popmenu-wrapper\").remove();\n el.unbind(\"click.close_popup\");\n });\n };\n close_popup($(window.document)); // Current frame\n close_popup($(window.top.document)); // Parent frame\n for (var frame_id = window.top.frames.length; frame_id--; ) {\n // Sibling frames\n var frame = $(window.top.frames[frame_id].document);\n close_popup(frame);\n }\n }, 50);\n\n return false;\n });\n }\n\n /**\n * Convert two seperate (often adjacent) divs into galaxy popupmenu\n * - div 1 contains a number of anchors which become the menu options\n * - div 1 should have a 'popupmenu' attribute\n * - this popupmenu attribute contains the id of div 2\n * - div 2 becomes the 'face' of the popupmenu\n *\n * NOTE: make_popup_menus finds and operates on all divs with a popupmenu attr (no need to point it at something)\n * but (since that selector searches the dom on the page), you can send a parent in\n * NOTE: make_popup_menus, and make_popupmenu are horrible names\n */\n function make_popup_menus(parent) {\n // find all popupmenu menu divs (divs that contains anchors to be converted to menu options)\n // either in the parent or the document if no parent passed\n parent = parent || document;\n $(parent)\n .find(\"div[popupmenu]\")\n .each(function() {\n var options = {};\n var menu = $(this);\n\n // find each anchor in the menu, convert them into an options map: { a.text : click_function }\n menu.find(\"a\").each(function() {\n var link = $(this),\n link_dom = link.get(0),\n confirmtext = link_dom.getAttribute(\"confirm\"),\n href = link_dom.getAttribute(\"href\"),\n target = link_dom.getAttribute(\"target\");\n\n // no href - no function (gen. a label)\n if (!href) {\n options[link.text()] = null;\n } else {\n options[link.text()] = {\n url: href,\n action: function(event) {\n // if theres confirm text, send the dialog\n if (!confirmtext || confirm(confirmtext)) {\n // link.click() doesn't use target for some reason,\n // so manually do it here.\n if (target) {\n window.open(href, target);\n return false;\n } else {\n // For all other links, do the default action.\n link.click();\n }\n } else {\n event.preventDefault();\n }\n }\n };\n }\n });\n // locate the element with the id corresponding to the menu's popupmenu attr\n var box = $(parent).find(\"#\" + menu.attr(\"popupmenu\"));\n\n // For menus with clickable link text, make clicking on the link go through instead\n // of activating the popup menu\n box.find(\"a\").bind(\"click\", function(e) {\n e.stopPropagation(); // Stop bubbling so clicking on the link goes through\n return true;\n });\n\n // attach the click events and menu box building to the box element\n make_popupmenu(box, options);\n box.addClass(\"popup\");\n menu.remove();\n });\n }\n\n // ============================================================================\n return {\n make_popupmenu: make_popupmenu,\n make_popup_menus: make_popup_menus\n };\n});\n"]} \ No newline at end of file +{"version":3,"sources":["ui/popupmenu.js"],"names":["define","jQuery","make_popupmenu","button_element","initial_options","element_menu_exists","data","bind","e","$","remove","menu_element","setTimeout","attr","options","appendTo","each","k","v","append","url","html","click","action","css","pageY","x","close_popup","el","unbind","width","Math","min","window","wrapper","frame_id","scrollLeft","top","left","document","make_popup_menus","parent","frames","length","find","menu","this","link","event","preventDefault","confirmtext","link_dom","getAttribute","href","target","text","confirm","open","box","stopPropagation","addClass"],"mappings":"kCAAAA,QAAQ,UAAW,SAASC,GACxB,aAYA,SAASC,EAAeC,EAAgBC,GACpC,IAAAC,EAAAF,EAAAG,KAAA,gBAIAH,EAAeG,KAAK,eAAgBF,GAApCD,GAIIA,EAAAI,KAAA,mBAAA,SAAAC,GA+EA,OA1EAC,EAAE,oBAAoBC,SAAtBD,WAAE,WAEF,IAAAE,EAAAF,EACAG,iCACIT,EAAAU,KAAA,MACIF,gBAMJG,EAAIX,EAAJG,KAA0B,gBACtBG,EAAAA,KAAEK,IAAA,GACLL,EAAA,wBAAAM,SAAAJ,GAEGF,EAAAO,KAAAF,EAAO,SAAAG,EAAAC,GACH,GAAAA,EAAA,CAEAP,IAAAA,EAAAA,EAAAA,QACIF,EAOPE,EAAMQ,OACHR,EAAAA,aAAaQ,OAKhBV,EAAA,OAlBLI,KAAA,OAAAK,EAAAE,KAqBIC,KAAAJ,GAZiBK,MAAMC,UAInBZ,EAAaQ,OAuBbK,EAAAA,aACGC,SADC,QAEFC,OAAAA,EAAAA,oBAAAA,KAAAA,OAIdd,IAAAA,EAAWH,EACP,uFAEAU,OAAIQ,GACAlB,SAAMF,QAEFqB,EAAAA,EAAAA,MAAGC,EAAOC,QAAA,EACbJ,EAAAK,KAHDC,IAIHN,EACDC,EAAAA,UAAYlB,aACZkB,EAAAA,QAAcM,QACdxB,EAAKyB,GAAIC,QACL,GAEAR,EAAAA,KAAAA,IAAAA,EAAAA,EAAAA,UAAAS,aAAA,GAEPF,EAhBDV,KALQa,IAAK7B,EAAEiB,MAuBfa,KAAOZ,KAEd,IAEDd,WAAA,WAnBY,IAAIe,EAAc,SAASC,GACvBnB,EAAEmB,GAAIrB,KAAK,oBAAqB,WAC5BE,EAAE,oBAAoBC,SACtBkB,EAAGC,OAAO,wBAGlBF,EAAYlB,EAAEwB,OAAOM,WACrBZ,EAAYlB,EAAEwB,OAAOI,IAAIE,WAuBrC,IAASC,IAAAA,EAAiBC,OAAQJ,IAAAK,OAAAC,OAAAR,KAG9BM,EADAhC,EAAAwB,OAAAI,IAAAK,OAAAP,GAAAI,YAKQ,KAtBG,IArGnBvC,IAAAA,EAAQC,EAiLJ,OACIC,eAAgBA,EAChBsC,iBAvCoBjB,SAAAA,GAGQkB,EAAAA,GAAAF,SACA9B,EAAAgC,GACAG,KAAA,kBACIX,KAAAA,WACA,IAAAnB,KACH+B,EAAApC,EAAAqC,MAGAD,EAAAD,KAAA,KAAA5B,KAAA,WACJ,IAAA+B,EAAAtC,EAVDqC,MAWIE,EAAAA,EAAAA,IAAMC,GACTC,EAAAC,EAAAC,aAAA,WACJC,EAAAF,EAAAC,aAAA,QAjBkBE,EAAvBH,EAAAC,aAAA,UAwBRtC,EAAAiC,EAAAQ,QAHAF,GAIAjC,IAAAiC,EACA9B,OAAmB,SAASyB,GAExB,IAAAE,GAAAM,QAAAN,GAAA,CAGJ,GAAAI,EAEA,OADoBxC,OAApB2C,KAAAJ,EAAAC,IACA,EAGXP,EAAAzB,aAGM0B,EAAAC,mBAjBoCJ,OAA/B,IAAIa,EAAMjD,EAAEgC,GAAQG,KAAK,IAAMC,EAAKhC,KAAK,cAIzC6C,EAAId,KAAK,KAAKrC,KAAK,QAAS,SAASC,GAEjC,OADAA,EAAEmD,mBACK,IAIXzD,EAAewD,EAAK5C,GACpB4C,EAAIE,SAAS,SACbf,EAAKnC","file":"../../scripts/ui/popupmenu.js","sourcesContent":["define([\"jquery\"], function(jQuery) {\n \"use_strict\";\n\n var $ = jQuery;\n\n // ============================================================================\n // TODO: unify popup menus and/or eliminate this\n /**\n * Sets up popupmenu rendering and binds options functions to the appropriate links.\n * initial_options is a dict with text describing the option pointing to either (a) a\n * function to perform; or (b) another dict with two required keys, 'url' and 'action' (the\n * function to perform. (b) is useful for exposing the underlying URL of the option.\n */\n function make_popupmenu(button_element, initial_options) {\n /* Use the $.data feature to store options with the link element.\n This allows options to be changed at a later time\n */\n var element_menu_exists = button_element.data(\"menu_options\");\n button_element.data(\"menu_options\", initial_options);\n\n // If element already has menu, nothing else to do since HTML and actions are already set.\n if (element_menu_exists) {\n return;\n }\n\n button_element.bind(\"click.show_popup\", function(e) {\n // Close existing visible menus\n $(\".popmenu-wrapper\").remove();\n\n // Need setTimeouts so clicks don't interfere with each other\n setTimeout(function() {\n // Dynamically generate the wrapper holding all the selectable options of the menu.\n var menu_element = $(\n \"\"\n );\n var options = button_element.data(\"menu_options\");\n if (_.size(options) <= 0) {\n $(\"
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from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js\n// Uses AMD or browser globals to create a jQuery plugin.\n(function(factory) {\n if (typeof define === \"function\" && define.amd) {\n //TODO: So...this turns out to be an all or nothing thing. 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searchTerms) {\n if (!searchTerms) {\n return clearSearchInput();\n }\n $(this).trigger(\"search.search\", searchTerms);\n if (typeof options.onfirstsearch === \"function\" && firstSearch) {\n firstSearch = false;\n options.onfirstsearch(searchTerms);\n } else {\n options.onsearch(searchTerms);\n }\n }\n\n // .................................................................... input rendering and events\n function inputTemplate() {\n // class search-query is bootstrap 2.3 style that now lives in base.less\n return [\n '\"\n ].join(\"\");\n }\n\n // the search input that responds to keyboard events and displays the search value\n function $input() {\n return ($(inputTemplate())\n // select all text on a focus\n .focus(function(event) {\n $(this).select();\n })\n // attach behaviors to esc, return if desired, search on some min len string\n .keyup(function(event) {\n event.preventDefault();\n event.stopPropagation();\n\n // esc key will clear if desired\n if (\n event.which === KEYCODE_ESC &&\n options.escWillClear\n ) {\n clearSearchInput.call(this, event);\n } else {\n var searchTerms = $(this).val();\n // return key or the search string len > minSearchLen (if not 0) triggers search\n if (\n event.which === KEYCODE_RETURN ||\n (options.minSearchLen &&\n searchTerms.length >= options.minSearchLen)\n ) {\n search.call(this, event, searchTerms);\n }\n }\n })\n .val(options.initialVal) );\n }\n\n // .................................................................... clear button rendering and events\n // a button for clearing the search bar, placed on the right hand side\n function $clearBtn() {\n return $(\n [\n ''\n ].join(\"\")\n )\n .tooltip({ placement: \"bottom\" })\n .click(function(event) {\n clearSearchInput.call(this, event);\n });\n }\n\n // .................................................................... loadingIndicator rendering\n // a button for clearing the search bar, placed on the right hand side\n function $loadingIndicator() {\n return $(\n [\n ''\n ].join(\"\")\n )\n .hide()\n .tooltip({ placement: \"bottom\" });\n }\n\n // .................................................................... commands\n // visually swap the load, clear buttons\n function toggleLoadingIndicator() {\n $parentNode.find(\".search-loading\").toggle();\n $parentNode.find(\".search-clear\").toggle();\n }\n\n // .................................................................... init\n // string command (not constructor)\n if (jQuery.type(options) === \"string\") {\n if (options === \"toggle-loading\") {\n toggleLoadingIndicator();\n }\n return $parentNode;\n }\n\n // initial render\n if (jQuery.type(options) === \"object\") {\n options = jQuery.extend(true, {}, defaults, options);\n }\n //NOTE: prepended\n return $parentNode\n .addClass(\"search-input\")\n .prepend([$input(), $clearBtn(), $loadingIndicator()]);\n }\n\n // as jq plugin\n jQuery.fn.extend({\n searchInput: function $searchInput(options) {\n return this.each(function() {\n return searchInput(this, options);\n });\n }\n });\n});\n"]} \ No newline at end of file diff --git a/static/maps/utils/add-logging.js.map b/static/maps/utils/add-logging.js.map index 351337c657d..4e311830589 100644 --- a/static/maps/utils/add-logging.js.map +++ b/static/maps/utils/add-logging.js.map @@ -1 +1 @@ -{"version":3,"sources":["utils/add-logging.js"],"names":["define","LOGGING_FNS","obj","namespace","addTo","undefined","prototype","forEach","logFn","this","logger","emit","_logNamespace","arguments","apply"],"mappings":"aAAAA,UAAW,WAAXA,IAAOC,GAAe,MAAA,QAAA,OAAA,OAAA,QAAA,UA2ClB,OApCA,SAAoBC,EAAKC,GACrB,IAAIC,OAA0BC,IAAlBH,EAAII,UAA0BJ,EAAII,UAAYJ,EA+B1D,YAhCgBA,IAApBC,IACQC,EAAAA,cAAQD,GAUZF,EAAYM,QAAQ,SAASC,GAD7BJ,EAAAI,GAAA,WACAP,GAAYM,KAAAA,OAGA,OAAAE,KAAAC,OAAOL,KACVI,KAAAC,OAAAC,KACGH,EACAC,KAAOG,cAKVC,WAGGJ,KAAAC,OAAAF,GAIGH,KAAPK,OAAAF,GAAAM,MAAAL,KAAAC,OAAAG,gBAJI,KAOLX","file":"../../scripts/utils/add-logging.js","sourcesContent":["define([], function() {\n //==============================================================================\n var LOGGING_FNS = [\"log\", \"debug\", \"info\", \"warn\", \"error\", \"metric\"];\n /** adds logging functions to an obj.prototype (or obj directly) adding a namespace for filtering\n * @param {Object} obj\n * @param {String} namespace\n */\n function addLogging(obj, namespace) {\n var addTo = obj.prototype !== undefined ? obj.prototype : obj;\n if (namespace !== undefined) {\n addTo._logNamespace = namespace;\n }\n //yagni?: without this, may not capture Galaxy.config.debug and add Galaxy.logger properly\n // if( window.Galaxy && window.Galaxy.config && window.Galaxy.config.debug ){\n // addTo.logger = window.Galaxy.logger;\n // }\n\n // give the object each\n LOGGING_FNS.forEach(function(logFn) {\n addTo[logFn] = function() {\n if (!this.logger) {\n return undefined;\n }\n if (this.logger.emit) {\n return this.logger.emit(\n logFn,\n this._logNamespace,\n arguments\n );\n }\n if (this.logger[logFn]) {\n //TODO:! there has to be a way to get the lineno/file into this\n // http://stackoverflow.com/questions/13815640/a-proper-wrapper-for-console-log-with-correct-line-number\n // http://www.paulirish.com/2009/log-a-lightweight-wrapper-for-consolelog/\n return this.logger[logFn].apply(this.logger, arguments);\n }\n return undefined;\n };\n });\n return obj;\n }\n\n //==============================================================================\n return addLogging;\n});\n"]} \ No newline at end of file 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function addLogging(obj, namespace) {\n var addTo = obj.prototype !== undefined ? obj.prototype : obj;\n if (namespace !== undefined) {\n addTo._logNamespace = namespace;\n }\n //yagni?: without this, may not capture Galaxy.config.debug and add Galaxy.logger properly\n // if( window.Galaxy && window.Galaxy.config && window.Galaxy.config.debug ){\n // addTo.logger = window.Galaxy.logger;\n // }\n\n // give the object each\n LOGGING_FNS.forEach(function(logFn) {\n addTo[logFn] = function() {\n if (!this.logger) {\n return undefined;\n }\n if (this.logger.emit) {\n return this.logger.emit(\n logFn,\n this._logNamespace,\n arguments\n );\n }\n if (this.logger[logFn]) {\n //TODO:! there has to be a way to get the lineno/file into this\n // http://stackoverflow.com/questions/13815640/a-proper-wrapper-for-console-log-with-correct-line-number\n // http://www.paulirish.com/2009/log-a-lightweight-wrapper-for-consolelog/\n return this.logger[logFn].apply(this.logger, arguments);\n }\n return undefined;\n };\n });\n return obj;\n }\n\n //==============================================================================\n return addLogging;\n});\n"]} \ No newline at end of file diff --git a/static/maps/utils/ajax-queue.js.map b/static/maps/utils/ajax-queue.js.map index ba806b76c31..8905afe9cca 100644 --- a/static/maps/utils/ajax-queue.js.map +++ b/static/maps/utils/ajax-queue.js.map @@ -1 +1 @@ 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top:\n $(this).position().top -\n $(tip).height() / 2 +\n $(this).height() / 2\n })\n .show();\n\n // Click management:\n\n // Keep showing tip if clicking in tip.\n tip.click(function(e) {\n e.stopPropagation();\n });\n\n // Hide tip if clicking outside of tip.\n $(document).bind(\n \"click.color-picker\",\n function() {\n tip.hide();\n $(document).unbind(\n \"click.color-picker\"\n );\n }\n );\n\n // No propagation to avoid triggering document click (and tip hiding) above.\n e.stopPropagation();\n }),\n // Icon for setting a new random color; behavior set below.\n new_color_icon = $(\"\")\n .addClass(\"icon-button arrow-circle\")\n .appendTo(container_div)\n .attr(\"title\", \"Set new random color\")\n .tooltip(),\n // Color picker in tool tip style.\n tip = $(\n \"\"\n )\n .appendTo(container_div)\n .hide(),\n // Inner div for padding purposes\n tip_inner = $(\n \"\"\n ).appendTo(tip),\n tip_arrow = $(\n \"\"\n ).appendTo(tip),\n farb_obj = $.farbtastic(tip_inner, {\n width: 100,\n height: 100,\n callback: input,\n color: value\n });\n\n // Clear floating.\n container_div.append($(\"\").css(\"clear\", \"both\"));\n\n // Use function to fix farb_obj value.\n (function(fixed_farb_obj) {\n new_color_icon.click(function() {\n fixed_farb_obj.setColor(\n util_mod.get_random_color()\n );\n });\n })(farb_obj);\n } else {\n row.append(\n $(\"\")\n .attr(\"id\", id)\n .attr(\"name\", id)\n .val(value)\n );\n }\n // Help text\n if (param.help) {\n row.append($(\"\").text(param.help));\n }\n });\n\n return this;\n },\n\n /**\n * Render view in modal.\n */\n render_in_modal: function(title) {\n // Set up handlers for cancel, ok button and for handling esc key.\n var self = this,\n cancel_fn = function() {\n Galaxy.modal.hide();\n $(window).unbind(\"keypress.check_enter_esc\");\n },\n ok_fn = function() {\n Galaxy.modal.hide();\n $(window).unbind(\"keypress.check_enter_esc\");\n self.update_from_form();\n },\n check_enter_esc = function(e) {\n if ((e.keyCode || e.which) === 27) {\n // Escape key\n cancel_fn();\n } else if ((e.keyCode || e.which) === 13) {\n // Enter key\n ok_fn();\n }\n };\n\n // Set keypress handler.\n $(window).bind(\"keypress.check_enter_esc\", check_enter_esc);\n\n // Show modal.\n if (this.$el.children().length === 0) {\n this.render();\n }\n Galaxy.modal.show({\n title: title || \"Configure\",\n body: this.$el,\n buttons: {\n Cancel: cancel_fn,\n OK: ok_fn\n }\n });\n },\n\n /**\n * Update settings with new values entered via form.\n */\n update_from_form: function() {\n var self = this;\n this.collection.each(function(setting, index) {\n if (!setting.get(\"hidden\")) {\n // Set value from view.\n var id = \"param_\" + index;\n var value = self.$el.find(\"#\" + id).val();\n if (setting.get(\"type\") === \"bool\") {\n value = self.$el.find(\"#\" + id).is(\":checked\");\n }\n setting.set_value(value);\n }\n });\n }\n });\n\n return {\n ConfigSetting: ConfigSetting,\n ConfigSettingCollection: ConfigSettingCollection,\n ConfigSettingCollectionView: ConfigSettingCollectionView\n };\n});\n"]} \ No newline at end of file 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results */\n GraphSearch.prototype.searchTree = function _searchTree(start) {\n return this._searchTree(this.search(start));\n };\n\n /** Helper fn that returns a graph (a search tree) based on the search object passed in (does not actually search) */\n GraphSearch.prototype._searchTree = function __searchTree(search) {\n var self = this;\n return new Graph(true, {\n edges: search.edges,\n vertices: Object.keys(search.discovered).map(function(key) {\n return self.graph.vertices[key].toJSON();\n })\n });\n };\n\n // ============================================================================\n /** Breadth first search algo.\n */\n var BreadthFirstSearch = function(graph, processFns) {\n var self = this;\n GraphSearch.call(this, graph, processFns);\n return self;\n };\n BreadthFirstSearch.prototype = new GraphSearch();\n BreadthFirstSearch.prototype.constructor = BreadthFirstSearch;\n\n /** (Private) implementation of BFS */\n BreadthFirstSearch.prototype._search = function __search(start, search) {\n search = search || {\n discovered: {},\n //parents : {},\n edges: []\n };\n\n var self = this,\n queue = [];\n\n function discoverAdjacent(adj, edge) {\n var source = this;\n if (self.processFns.edge) {\n self.processFns.edge.call(self, source, edge, search);\n }\n if (!search.discovered[adj.name]) {\n //console.debug( '\\t\\t\\t', adj.name, 'is undiscovered:', search.discovered[ adj.name ] );\n search.discovered[adj.name] = true;\n //search.parents[ adj.name ] = source;\n search.edges.push({ source: source.name, target: adj.name });\n //console.debug( '\\t\\t\\t queuing undiscovered: ', adj );\n queue.push(adj);\n }\n }\n\n //console.debug( 'BFS starting. start:', start );\n search.discovered[start.name] = true;\n queue.push(start);\n while (queue.length) {\n var vertex = queue.shift();\n //console.debug( '\\t Queue is shifting. Current:', vertex, 'queue:', queue );\n if (self.processFns.vertexEarly) {\n self.processFns.vertexEarly.call(self, vertex, search);\n }\n self.graph.eachAdjacent(vertex, discoverAdjacent);\n if (self.processFns.vertexLate) {\n self.processFns.vertexLate.call(self, vertex, search);\n }\n }\n //console.debug( 'search.edges:', JSON.stringify( search.edges ) );\n return search;\n };\n\n // ============================================================================\n /** Depth first search algorithm.\n */\n var DepthFirstSearch = function(graph, processFns) {\n var self = this;\n GraphSearch.call(this, graph, processFns);\n return self;\n };\n DepthFirstSearch.prototype = new GraphSearch();\n DepthFirstSearch.prototype.constructor = DepthFirstSearch;\n\n /** (Private) implementation of DFS */\n DepthFirstSearch.prototype._search = function(start, search) {\n //console.debug( 'depthFirstSearch:', start );\n search = search || {\n discovered: {},\n //parents : {},\n edges: [],\n entryTimes: {},\n exitTimes: {}\n };\n var self = this,\n time = 0;\n\n // discover verts adjacent to the source (this):\n // processing each edge, saving the edge to the tree, and caching the reverse path with parents\n function discoverAdjacentVertices(adjacent, edge) {\n //console.debug( '\\t\\t adjacent:', adjacent, 'edge:', edge );\n var sourceVertex = this;\n if (self.processFns.edge) {\n self.processFns.edge.call(self, sourceVertex, edge, search);\n }\n if (!search.discovered[adjacent.name]) {\n //search.parents[ adjacent.name ] = sourceVertex;\n search.edges.push({\n source: sourceVertex.name,\n target: adjacent.name\n });\n recurse(adjacent);\n }\n }\n\n // use function stack for DFS stack process verts, times, and discover adjacent verts (recursing into them)\n function recurse(vertex) {\n //console.debug( '\\t recursing into: ', vertex );\n search.discovered[vertex.name] = true;\n if (self.processFns.vertexEarly) {\n self.processFns.vertexEarly.call(self, vertex, search);\n }\n search.entryTimes[vertex.name] = time++;\n\n self.graph.eachAdjacent(vertex, discoverAdjacentVertices);\n\n if (self.processFns.vertexLate) {\n self.processFns.vertexLate.call(self, vertex, search);\n }\n search.exitTimes[vertex.name] = time++;\n }\n // begin recursion with the desired start\n recurse(start);\n\n return search;\n };\n\n // ============================================================================\n /** A directed/non-directed graph object.\n */\n function Graph(directed, data, options) {\n //TODO: move directed to options\n this.directed = directed || false;\n return this.init(options).read(data);\n }\n window.Graph = Graph;\n\n /** Set up options and instance variables */\n Graph.prototype.init = function(options) {\n options = options || {};\n var self = this;\n\n self.allowReflexiveEdges = options.allowReflexiveEdges || false;\n\n self.vertices = {};\n self.numEdges = 0;\n return self;\n };\n\n /** Read data from the plain object data - both in d3 form (nodes and links) or vertices and edges */\n Graph.prototype.read = function(data) {\n if (!data) {\n return this;\n }\n var self = this;\n if (data.hasOwnProperty(\"nodes\")) {\n return self.readNodesAndLinks(data);\n }\n if (data.hasOwnProperty(\"vertices\")) {\n return self.readVerticesAndEdges(data);\n }\n return self;\n };\n\n //TODO: the next two could be combined\n /** Create the graph using a list of nodes and a list of edges (where source and target are indeces into nodes) */\n Graph.prototype.readNodesAndLinks = function(data) {\n if (!(data && data.hasOwnProperty(\"nodes\"))) {\n return this;\n }\n //console.debug( 'readNodesAndLinks:', data );\n //console.debug( 'data:\\n' + JSON.stringify( data, null, ' ' ) );\n var self = this;\n data.nodes.forEach(function(node) {\n self.createVertex(node.name, node.data);\n });\n //console.debug( JSON.stringify( self.vertices, null, ' ' ) );\n\n (data.links || []).forEach(function(edge, i) {\n var sourceName = data.nodes[edge.source].name,\n targetName = data.nodes[edge.target].name;\n self.createEdge(sourceName, targetName, self.directed);\n });\n //self.print();\n //console.debug( JSON.stringify( self.toNodesAndLinks(), null, ' ' ) );\n return self;\n };\n\n /** Create the graph using a list of nodes and a list of edges (where source and target are names of nodes) */\n Graph.prototype.readVerticesAndEdges = function(data) {\n if (!(data && data.hasOwnProperty(\"vertices\"))) {\n return this;\n }\n //console.debug( 'readVerticesAndEdges:', data );\n //console.debug( 'data:\\n' + JSON.stringify( data, null, ' ' ) );\n var self = this;\n data.vertices.forEach(function(node) {\n self.createVertex(node.name, node.data);\n });\n //console.debug( JSON.stringify( self.vertices, null, ' ' ) );\n\n (data.edges || []).forEach(function(edge, i) {\n self.createEdge(edge.source, edge.target, self.directed);\n });\n //self.print();\n //console.debug( JSON.stringify( self.toNodesAndLinks(), null, ' ' ) );\n return self;\n };\n\n /** Return the vertex with name, creating it if necessary */\n Graph.prototype.createVertex = function(name, data) {\n //console.debug( 'createVertex:', name, data );\n if (this.vertices[name]) {\n return this.vertices[name];\n }\n return (this.vertices[name] = new Vertex(name, data));\n };\n\n /** Create an edge in vertex named sourceName to targetName (optionally adding data to it)\n * If directed is false, create a second edge from targetName to sourceName.\n */\n Graph.prototype.createEdge = function(\n sourceName,\n targetName,\n directed,\n data\n ) {\n //note: allows multiple 'equivalent' edges (to/from same source/target)\n //console.debug( 'createEdge:', source, target, directed );\n var isReflexive = sourceName === targetName;\n if (!this.allowReflexiveEdges && isReflexive) {\n return null;\n }\n\n var sourceVertex = this.vertices[sourceName];\n var targetVertex = this.vertices[targetName];\n //note: silently ignores edges from/to unknown vertices\n if (!(sourceVertex && targetVertex)) {\n return null;\n }\n\n //TODO: prob. move to vertex\n var self = this,\n edge = new Edge(sourceName, targetName, data);\n sourceVertex.edges[targetName] = edge;\n sourceVertex.degree += 1;\n self.numEdges += 1;\n\n //TODO:! don't like having duplicate edges for non-directed graphs\n // mirror edges (reversing source and target) in non-directed graphs\n // but only if not reflexive\n if (!isReflexive && !directed) {\n // flip directed to prevent recursion loop\n self.createEdge(targetName, sourceName, true);\n }\n\n return edge;\n };\n\n /** Walk over all the edges of the graph using the vertex.eachEdge iterator */\n Graph.prototype.edges = function(propsOrFn) {\n return Array.prototype.concat.apply(\n [],\n this.eachVertex(function(vertex) {\n return vertex.eachEdge(propsOrFn);\n })\n );\n };\n\n /** Iterate over all the vertices in the graph */\n Graph.prototype.eachVertex = function(propsOrFn) {\n return iterate(this.vertices, propsOrFn);\n };\n\n /** Return a list of the vertices adjacent to vertex */\n Graph.prototype.adjacent = function(vertex) {\n var self = this;\n return iterate(vertex.edges, function(edge) {\n return self.vertices[edge.target];\n });\n };\n\n /** Call fn on each vertex adjacent to vertex */\n Graph.prototype.eachAdjacent = function(vertex, fn) {\n var self = this;\n return iterate(vertex.edges, function(edge) {\n var adj = self.vertices[edge.target];\n return fn.call(vertex, adj, edge);\n });\n };\n\n /** Print the graph to the console (debugging) */\n Graph.prototype.print = function() {\n var self = this;\n console.log(\n \"Graph has \" + Object.keys(self.vertices).length + \" vertices\"\n );\n self.eachVertex(function(vertex) {\n console.log(vertex.toString());\n vertex.eachEdge(function(edge) {\n console.log(\"\\t \" + edge);\n });\n });\n return self;\n };\n\n /** Return a DOT format string of this graph */\n Graph.prototype.toDOT = function() {\n var self = this,\n strings = [];\n strings.push(\"graph bler {\");\n self.edges(function(edge) {\n strings.push(\"\\t\" + edge.from + \" -- \" + edge.to + \";\");\n });\n strings.push(\"}\");\n return strings.join(\"\\n\");\n };\n\n /** Return vertices and edges of this graph in d3 node/link format */\n Graph.prototype.toNodesAndLinks = function() {\n var self = this,\n indeces = {};\n return {\n nodes: self.eachVertex(function(vertex, key, i) {\n indeces[vertex.name] = i;\n return vertex.toJSON();\n }),\n links: self.edges(function(edge) {\n var json = edge.toJSON();\n json.source = indeces[edge.source];\n json.target = indeces[edge.target];\n return json;\n })\n };\n };\n\n /** Return vertices and edges of this graph where edges use the name/id as source and target */\n Graph.prototype.toVerticesAndEdges = function() {\n var self = this;\n return {\n vertices: self.eachVertex(function(vertex, key) {\n return vertex.toJSON();\n }),\n edges: self.edges(function(edge) {\n return edge.toJSON();\n })\n };\n };\n\n /** Search this graph using BFS */\n Graph.prototype.breadthFirstSearch = function(start, processFns) {\n return new BreadthFirstSearch(this).search(start);\n };\n\n /** Return a searchtree of this graph using BFS */\n Graph.prototype.breadthFirstSearchTree = function(start, processFns) {\n return new BreadthFirstSearch(this).searchTree(start);\n };\n\n /** Search this graph using DFS */\n Graph.prototype.depthFirstSearch = function(start, processFns) {\n return new DepthFirstSearch(this).search(start);\n };\n\n /** Return a searchtree of this graph using DFS */\n Graph.prototype.depthFirstSearchTree = function(start, processFns) {\n return new DepthFirstSearch(this).searchTree(start);\n };\n\n //Graph.prototype.shortestPath = function( start, end ){\n //};\n //\n //Graph.prototype.articulationVertices = function(){\n //};\n //\n //Graph.prototype.isAcyclic = function(){\n //};\n //\n //Graph.prototype.isBipartite = function(){\n //};\n\n /** Return an array of weakly connected (no edges between) sub-graphs in this graph */\n Graph.prototype.weakComponents = function() {\n //TODO: alternately, instead of returning graph-like objects:\n // - could simply decorate the vertices (vertex.component = componentIndex), or clone the graph and do that\n var self = this,\n searchGraph = this,\n undiscovered,\n components = [];\n\n function getComponent(undiscoveredVertex) {\n //TODO: better interface on dfs (search v. searchTree)\n var search = new DepthFirstSearch(searchGraph)._search(\n undiscoveredVertex\n );\n\n // remove curr discovered from undiscovered\n undiscovered = undiscovered.filter(function(name) {\n return !(name in search.discovered);\n });\n\n return {\n vertices: Object.keys(search.discovered).map(function(\n vertexName\n ) {\n return self.vertices[vertexName].toJSON();\n }),\n edges: search.edges.map(function(edge) {\n // restore any reversed edges\n var hasBeenReversed =\n self.vertices[edge.target].edges[edge.source] !==\n undefined;\n if (self.directed && hasBeenReversed) {\n var swap = edge.source;\n edge.source = edge.target;\n edge.target = swap;\n }\n return edge;\n })\n };\n }\n\n if (self.directed) {\n // if directed - convert to undirected for search\n searchGraph = new Graph(false, self.toNodesAndLinks());\n }\n undiscovered = Object.keys(searchGraph.vertices);\n //console.debug( '(initial) undiscovered:', undiscovered );\n while (undiscovered.length) {\n var undiscoveredVertex = searchGraph.vertices[undiscovered.shift()];\n components.push(getComponent(undiscoveredVertex));\n //console.debug( 'undiscovered now:', undiscovered );\n }\n\n //console.debug( 'components:\\n', JSON.stringify( components, null, ' ' ) );\n return components;\n };\n\n /** Return a single graph containing the weakly connected components in this graph */\n Graph.prototype.weakComponentGraph = function() {\n //note: although this can often look like the original graph - edges can be lost\n var components = this.weakComponents();\n return new Graph(this.directed, {\n vertices: components.reduce(function(reduction, curr) {\n return reduction.concat(curr.vertices);\n }, []),\n edges: components.reduce(function(reduction, curr) {\n return reduction.concat(curr.edges);\n }, [])\n });\n };\n\n /** Return an array of graphs of the weakly connected components in this graph */\n Graph.prototype.weakComponentGraphArray = function() {\n //note: although this can often look like the original graph - edges can be lost\n var graph = this;\n return this.weakComponents().map(function(component) {\n return new Graph(graph.directed, component);\n });\n };\n\n // ============================================================================\n /** Create a random graph with numVerts vertices and numEdges edges (for testing)\n */\n function randGraph(directed, numVerts, numEdges) {\n //console.debug( 'randGraph', directed, numVerts, numEdges );\n var data = { nodes: [], links: [] };\n function randRange(range) {\n return Math.floor(Math.random() * range);\n }\n for (var i = 0; i 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results */\n GraphSearch.prototype.searchTree = function _searchTree(start) {\n return this._searchTree(this.search(start));\n };\n\n /** Helper fn that returns a graph (a search tree) based on the search object passed in (does not actually search) */\n GraphSearch.prototype._searchTree = function __searchTree(search) {\n var self = this;\n return new Graph(true, {\n edges: search.edges,\n vertices: Object.keys(search.discovered).map(function(key) {\n return self.graph.vertices[key].toJSON();\n })\n });\n };\n\n // ============================================================================\n /** Breadth first search algo.\n */\n var BreadthFirstSearch = function(graph, processFns) {\n var self = this;\n GraphSearch.call(this, graph, processFns);\n return self;\n };\n BreadthFirstSearch.prototype = new GraphSearch();\n BreadthFirstSearch.prototype.constructor = BreadthFirstSearch;\n\n /** (Private) implementation of BFS */\n BreadthFirstSearch.prototype._search = function 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Current:', vertex, 'queue:', queue );\n if (self.processFns.vertexEarly) {\n self.processFns.vertexEarly.call(self, vertex, search);\n }\n self.graph.eachAdjacent(vertex, discoverAdjacent);\n if (self.processFns.vertexLate) {\n self.processFns.vertexLate.call(self, vertex, search);\n }\n }\n //console.debug( 'search.edges:', JSON.stringify( search.edges ) );\n return search;\n };\n\n // ============================================================================\n /** Depth first search algorithm.\n */\n var DepthFirstSearch = function(graph, processFns) {\n var self = this;\n GraphSearch.call(this, graph, processFns);\n return self;\n };\n DepthFirstSearch.prototype = new GraphSearch();\n DepthFirstSearch.prototype.constructor = DepthFirstSearch;\n\n /** (Private) implementation of DFS */\n DepthFirstSearch.prototype._search = function(start, search) {\n //console.debug( 'depthFirstSearch:', start );\n search = search || {\n discovered: {},\n //parents : {},\n edges: [],\n entryTimes: {},\n exitTimes: {}\n };\n var self = this,\n time = 0;\n\n // discover verts adjacent to the source (this):\n // processing each edge, saving the edge to the tree, and caching the reverse path with parents\n function discoverAdjacentVertices(adjacent, edge) {\n //console.debug( '\\t\\t adjacent:', adjacent, 'edge:', edge );\n var sourceVertex = this;\n if (self.processFns.edge) {\n self.processFns.edge.call(self, sourceVertex, edge, search);\n }\n if (!search.discovered[adjacent.name]) {\n //search.parents[ adjacent.name ] = sourceVertex;\n search.edges.push({\n source: sourceVertex.name,\n target: adjacent.name\n });\n recurse(adjacent);\n }\n }\n\n // use function stack for DFS stack process verts, times, and discover adjacent verts (recursing into them)\n function recurse(vertex) {\n //console.debug( '\\t recursing into: ', vertex );\n search.discovered[vertex.name] = true;\n if (self.processFns.vertexEarly) {\n self.processFns.vertexEarly.call(self, vertex, search);\n }\n search.entryTimes[vertex.name] = time++;\n\n self.graph.eachAdjacent(vertex, discoverAdjacentVertices);\n\n if (self.processFns.vertexLate) {\n self.processFns.vertexLate.call(self, vertex, search);\n }\n search.exitTimes[vertex.name] = time++;\n }\n // begin recursion with the desired start\n recurse(start);\n\n return search;\n };\n\n // ============================================================================\n /** A directed/non-directed graph object.\n */\n function Graph(directed, data, options) {\n //TODO: move directed to options\n this.directed = directed || false;\n return this.init(options).read(data);\n }\n window.Graph = Graph;\n\n /** Set up options and instance variables */\n Graph.prototype.init = function(options) {\n options = options || {};\n var self = this;\n\n self.allowReflexiveEdges = options.allowReflexiveEdges || false;\n\n self.vertices = {};\n self.numEdges = 0;\n return self;\n };\n\n /** Read data from the plain object data - both in d3 form (nodes and links) or vertices and edges */\n Graph.prototype.read = function(data) {\n if (!data) {\n return this;\n }\n var self = this;\n if (data.hasOwnProperty(\"nodes\")) {\n return self.readNodesAndLinks(data);\n }\n if (data.hasOwnProperty(\"vertices\")) {\n return self.readVerticesAndEdges(data);\n }\n return self;\n };\n\n //TODO: the next two could be combined\n /** Create the graph using a list of nodes and a list of edges (where source and target are indeces into nodes) */\n Graph.prototype.readNodesAndLinks = function(data) {\n if (!(data && data.hasOwnProperty(\"nodes\"))) {\n return this;\n }\n //console.debug( 'readNodesAndLinks:', data );\n //console.debug( 'data:\\n' + JSON.stringify( data, null, ' ' ) );\n var self = this;\n data.nodes.forEach(function(node) {\n self.createVertex(node.name, node.data);\n });\n //console.debug( JSON.stringify( self.vertices, null, ' ' ) );\n\n (data.links || []).forEach(function(edge, i) {\n var sourceName = data.nodes[edge.source].name,\n targetName = data.nodes[edge.target].name;\n self.createEdge(sourceName, targetName, self.directed);\n });\n //self.print();\n //console.debug( JSON.stringify( self.toNodesAndLinks(), null, ' ' ) );\n return self;\n };\n\n /** Create the graph using a list of nodes and a list of edges (where source and target are names of nodes) */\n Graph.prototype.readVerticesAndEdges = function(data) {\n if (!(data && data.hasOwnProperty(\"vertices\"))) {\n return this;\n }\n //console.debug( 'readVerticesAndEdges:', data );\n //console.debug( 'data:\\n' + JSON.stringify( data, null, ' ' ) );\n var self = this;\n data.vertices.forEach(function(node) {\n self.createVertex(node.name, node.data);\n });\n //console.debug( JSON.stringify( self.vertices, null, ' ' ) );\n\n (data.edges || []).forEach(function(edge, i) {\n self.createEdge(edge.source, edge.target, self.directed);\n });\n //self.print();\n //console.debug( JSON.stringify( self.toNodesAndLinks(), null, ' ' ) );\n return self;\n };\n\n /** Return the vertex with name, creating it if necessary */\n Graph.prototype.createVertex = function(name, data) {\n //console.debug( 'createVertex:', name, data );\n if (this.vertices[name]) {\n return this.vertices[name];\n }\n return (this.vertices[name] = new Vertex(name, data));\n };\n\n /** Create an edge in vertex named sourceName to targetName (optionally adding data to it)\n * If directed is false, create a second edge from targetName to sourceName.\n */\n Graph.prototype.createEdge = function(\n sourceName,\n targetName,\n directed,\n data\n ) {\n //note: allows multiple 'equivalent' edges (to/from same source/target)\n //console.debug( 'createEdge:', source, target, directed );\n var isReflexive = sourceName === targetName;\n if (!this.allowReflexiveEdges && isReflexive) {\n return null;\n }\n\n var sourceVertex = this.vertices[sourceName];\n var targetVertex = this.vertices[targetName];\n //note: silently ignores edges from/to unknown vertices\n if (!(sourceVertex && targetVertex)) {\n return null;\n }\n\n //TODO: prob. move to vertex\n var self = this,\n edge = new Edge(sourceName, targetName, data);\n sourceVertex.edges[targetName] = edge;\n sourceVertex.degree += 1;\n self.numEdges += 1;\n\n //TODO:! don't like having duplicate edges for non-directed graphs\n // mirror edges (reversing source and target) in non-directed graphs\n // but only if not reflexive\n if (!isReflexive && !directed) {\n // flip directed to prevent recursion loop\n self.createEdge(targetName, sourceName, true);\n }\n\n return edge;\n };\n\n /** Walk over all the edges of the graph using the vertex.eachEdge iterator */\n Graph.prototype.edges = function(propsOrFn) {\n return Array.prototype.concat.apply(\n [],\n this.eachVertex(function(vertex) {\n return vertex.eachEdge(propsOrFn);\n })\n );\n };\n\n /** Iterate over all the vertices in the graph */\n Graph.prototype.eachVertex = function(propsOrFn) {\n return iterate(this.vertices, propsOrFn);\n };\n\n /** Return a list of the vertices adjacent to vertex */\n Graph.prototype.adjacent = function(vertex) {\n var self = this;\n return iterate(vertex.edges, function(edge) {\n return self.vertices[edge.target];\n });\n };\n\n /** Call fn on each vertex adjacent to vertex */\n Graph.prototype.eachAdjacent = function(vertex, fn) {\n var self = this;\n return iterate(vertex.edges, function(edge) {\n var adj = self.vertices[edge.target];\n return fn.call(vertex, adj, edge);\n });\n };\n\n /** Print the graph to the console (debugging) */\n Graph.prototype.print = function() {\n var self = this;\n console.log(\n \"Graph has \" + Object.keys(self.vertices).length + \" vertices\"\n );\n self.eachVertex(function(vertex) {\n console.log(vertex.toString());\n vertex.eachEdge(function(edge) {\n console.log(\"\\t \" + edge);\n });\n });\n return self;\n };\n\n /** Return a DOT format string of this graph */\n Graph.prototype.toDOT = function() {\n var self = this,\n strings = [];\n strings.push(\"graph bler {\");\n self.edges(function(edge) {\n strings.push(\"\\t\" + edge.from + \" -- \" + edge.to + \";\");\n });\n strings.push(\"}\");\n return strings.join(\"\\n\");\n };\n\n /** Return vertices and edges of this graph in d3 node/link format */\n Graph.prototype.toNodesAndLinks = function() {\n var self = this,\n indeces = {};\n return {\n nodes: self.eachVertex(function(vertex, key, i) {\n indeces[vertex.name] = i;\n return vertex.toJSON();\n }),\n links: self.edges(function(edge) {\n var json = edge.toJSON();\n json.source = indeces[edge.source];\n json.target = indeces[edge.target];\n return json;\n })\n };\n };\n\n /** Return vertices and edges of this graph where edges use the name/id as source and target */\n Graph.prototype.toVerticesAndEdges = function() {\n var self = this;\n return {\n vertices: self.eachVertex(function(vertex, key) {\n return vertex.toJSON();\n }),\n edges: self.edges(function(edge) {\n return edge.toJSON();\n })\n };\n };\n\n /** Search this graph using BFS */\n Graph.prototype.breadthFirstSearch = function(start, processFns) {\n return new BreadthFirstSearch(this).search(start);\n };\n\n /** Return a searchtree of this graph using BFS */\n Graph.prototype.breadthFirstSearchTree = function(start, processFns) {\n return new BreadthFirstSearch(this).searchTree(start);\n };\n\n /** Search this graph using DFS */\n Graph.prototype.depthFirstSearch = function(start, processFns) {\n return new DepthFirstSearch(this).search(start);\n };\n\n /** Return a searchtree of this graph using DFS */\n Graph.prototype.depthFirstSearchTree = function(start, processFns) {\n return new DepthFirstSearch(this).searchTree(start);\n };\n\n //Graph.prototype.shortestPath = function( start, end ){\n //};\n //\n //Graph.prototype.articulationVertices = function(){\n //};\n //\n //Graph.prototype.isAcyclic = function(){\n //};\n //\n //Graph.prototype.isBipartite = function(){\n //};\n\n /** Return an array of weakly connected (no edges between) sub-graphs in this graph */\n Graph.prototype.weakComponents = function() {\n //TODO: alternately, instead of returning graph-like objects:\n // - could simply decorate the vertices (vertex.component = componentIndex), or clone the graph and do that\n var self = this,\n searchGraph = this,\n undiscovered,\n components = [];\n\n function getComponent(undiscoveredVertex) {\n //TODO: better interface on dfs (search v. searchTree)\n var search = new DepthFirstSearch(searchGraph)._search(\n undiscoveredVertex\n );\n\n // remove curr discovered from undiscovered\n undiscovered = undiscovered.filter(function(name) {\n return !(name in search.discovered);\n });\n\n return {\n vertices: Object.keys(search.discovered).map(function(\n vertexName\n ) {\n return self.vertices[vertexName].toJSON();\n }),\n edges: search.edges.map(function(edge) {\n // restore any reversed edges\n var hasBeenReversed =\n self.vertices[edge.target].edges[edge.source] !==\n undefined;\n if (self.directed && hasBeenReversed) {\n var swap = edge.source;\n edge.source = edge.target;\n edge.target = swap;\n }\n return edge;\n })\n };\n }\n\n if (self.directed) {\n // if directed - convert to undirected for search\n searchGraph = new Graph(false, self.toNodesAndLinks());\n }\n undiscovered = Object.keys(searchGraph.vertices);\n //console.debug( '(initial) undiscovered:', undiscovered );\n while (undiscovered.length) {\n var undiscoveredVertex = searchGraph.vertices[undiscovered.shift()];\n components.push(getComponent(undiscoveredVertex));\n //console.debug( 'undiscovered now:', undiscovered );\n }\n\n //console.debug( 'components:\\n', JSON.stringify( components, null, ' ' ) );\n return components;\n };\n\n /** Return a single graph containing the weakly connected components in this graph */\n Graph.prototype.weakComponentGraph = function() {\n //note: although this can often look like the original graph - edges can be lost\n var components = this.weakComponents();\n return new Graph(this.directed, {\n vertices: components.reduce(function(reduction, curr) {\n return reduction.concat(curr.vertices);\n }, []),\n edges: components.reduce(function(reduction, curr) {\n return reduction.concat(curr.edges);\n }, [])\n });\n };\n\n /** Return an array of graphs of the weakly connected components in this graph */\n Graph.prototype.weakComponentGraphArray = function() {\n //note: although this can often look like the original graph - edges can be lost\n var graph = this;\n return this.weakComponents().map(function(component) {\n return new Graph(graph.directed, component);\n });\n };\n\n // ============================================================================\n /** Create a random graph with numVerts vertices and numEdges edges (for testing)\n */\n function randGraph(directed, numVerts, numEdges) {\n //console.debug( 'randGraph', directed, numVerts, numEdges );\n var data = { nodes: [], links: [] };\n function randRange(range) {\n return Math.floor(Math.random() * range);\n }\n for (var i = 0; i < numVerts; i++) {\n data.nodes.push({ name: i });\n }\n for (i = 0; i < numEdges; i++) {\n data.links.push({\n source: randRange(numVerts),\n target: randRange(numVerts)\n });\n }\n //console.debug( JSON.stringify( data, null, ' ' ) );\n return new Graph(directed, data);\n }\n\n // ============================================================================\n return {\n Vertex: Vertex,\n Edge: Edge,\n BreadthFirstSearch: BreadthFirstSearch,\n DepthFirstSearch: DepthFirstSearch,\n Graph: Graph,\n randGraph: randGraph\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/utils/levenshtein.js.map b/static/maps/utils/levenshtein.js.map index aae93339b94..d9d99ca649a 100644 --- a/static/maps/utils/levenshtein.js.map +++ b/static/maps/utils/levenshtein.js.map @@ -1 +1 @@ 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From: https://gist.github.com/andrei-m/982927)\nCopyright (c) 2011 Andrei Mackenzie\n\nPermission is hereby granted, free of charge, to any person obtaining a copy of this software and associated\ndocumentation files (the \"Software\"), to deal in the Software without restriction, including without limitation the\nrights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit\npersons to whom the Software is furnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all copies or substantial portions of the\nSoftware.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE\nWARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR\nCOPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR\nOTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.\n*/\n // Compute the edit distance between the two given strings\n //exports.getEditDistance = function(a, b){\n function levenshteinDistance(a, b) {\n if (a.length === 0) {\n return b.length;\n }\n if (b.length === 0) {\n return a.length;\n }\n\n var matrix = [];\n\n // increment along the first column of each row\n var i;\n for (i = 0; i <= b.length; i++) {\n matrix[i] = [i];\n }\n\n // increment each column in the first row\n var j;\n for (j = 0; j <= a.length; j++) {\n matrix[0][j] = j;\n }\n\n // Fill in the rest of the matrix\n for (i = 1; i <= b.length; i++) {\n for (j = 1; j <= a.length; j++) {\n if (b.charAt(i - 1) === a.charAt(j - 1)) {\n matrix[i][j] = matrix[i - 1][j - 1];\n } else {\n matrix[i][j] = Math.min(\n matrix[i - 1][j - 1] + 1, // substitution\n Math.min(\n matrix[i][j - 1] + 1, // insertion\n matrix[i - 1][j] + 1\n )\n ); // deletion\n }\n }\n }\n\n //console.debug( '\\t\\t levenshteinDistance', a, b, matrix[b.length][a.length] );\n return matrix[b.length][a.length];\n }\n\n //=============================================================================\n return levenshteinDistance;\n});\n"]} \ No newline at end of file +{"version":3,"sources":["utils/levenshtein.js"],"names":["define","levenshteinDistance","b","a","length","i","matrix","j","charAt","Math","min"],"mappings":"kCAAAA,UAAW,WAiEP,OA5CA,SAASC,EAATC,GACI,GAAI,IAAJC,EAAAC,OACI,OAAAF,EAAAE,OAEJ,GAAI,IAAJF,EAAAE,OACI,OAAAD,EAAAC,OAGJ,IAGAC,EAHAC,KAIA,IAAAD,EAAKA,EAAAA,GAAOA,EAAAA,OAAOD,IACfE,EAAAA,IAAAD,GAIJ,IAAAE,EACA,IAAAA,EAAKA,EAAAA,GAAOA,EAAAA,OAAOH,IACfE,EAAAA,GAAAA,GAAAC,EAIJ,IAAAF,EAAKA,EAAAA,GAAOA,EAAAA,OAAOD,IACf,IAAAG,EAAKA,EAAAA,GAAOA,EAAAA,OAAOH,IACfF,EAAAM,OAAMA,EAAOH,KAATF,EAAAK,OAAsBA,EAAOD,GAC7BD,EAAAA,GAAAA,GAAAA,EAAeA,EAAOD,GAAAA,EAAOE,GAE7BD,EAAAA,GAAAA,GAAAG,KAAeA,IAEXA,EAAKC,EACDJ,GAAAA,EAAA,GAAc,EACdA,KAAAA,IAGXA,EAAAD,GAAAE,EAAA,GAAA,EACJD,EAAAD,EAAA,GAAAE,GAAA,IAQT,OAAON,EAAAA,EAAAA,QAAAA,EAAPG","file":"../../scripts/utils/levenshtein.js","sourcesContent":["define([], function() {\n //=============================================================================\n /**\n(Imported for edit distance algorith. From: https://gist.github.com/andrei-m/982927)\nCopyright (c) 2011 Andrei Mackenzie\n\nPermission is hereby granted, free of charge, to any person obtaining a copy of this software and associated\ndocumentation files (the \"Software\"), to deal in the Software without restriction, including without limitation the\nrights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit\npersons to whom the Software is furnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all copies or substantial portions of the\nSoftware.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE\nWARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR\nCOPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR\nOTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.\n*/\n // Compute the edit distance between the two given strings\n //exports.getEditDistance = function(a, b){\n function levenshteinDistance(a, b) {\n if (a.length === 0) {\n return b.length;\n }\n if (b.length === 0) {\n return a.length;\n }\n\n var matrix = [];\n\n // increment along the first column of each row\n var i;\n for (i = 0; i <= b.length; i++) {\n matrix[i] = [i];\n }\n\n // increment each column in the first row\n var j;\n for (j = 0; j <= a.length; j++) {\n matrix[0][j] = j;\n }\n\n // Fill in the rest of the matrix\n for (i = 1; i <= b.length; i++) {\n for (j = 1; j <= a.length; j++) {\n if (b.charAt(i - 1) === a.charAt(j - 1)) {\n matrix[i][j] = matrix[i - 1][j - 1];\n } else {\n matrix[i][j] = Math.min(\n matrix[i - 1][j - 1] + 1, // substitution\n Math.min(\n matrix[i][j - 1] + 1, // insertion\n matrix[i - 1][j] + 1\n )\n ); // deletion\n }\n }\n }\n\n //console.debug( '\\t\\t levenshteinDistance', a, b, matrix[b.length][a.length] );\n return matrix[b.length][a.length];\n }\n\n //=============================================================================\n return levenshteinDistance;\n});\n"]} \ No newline at end of file diff --git a/static/maps/utils/localization.js.map b/static/maps/utils/localization.js.map index 92b6b5c5b12..3c0a224107f 100644 --- a/static/maps/utils/localization.js.map +++ b/static/maps/utils/localization.js.map @@ -1 +1 @@ -{"version":3,"sources":["utils/localization.js"],"names":["define","localeStrings","hasOwnProperty","navigator","locale","userLanguage","toLowerCase","split","__root","localize","strToLocalize","cacheNonLocalized"],"mappings":"aAAAA,QAAQ,mBAAoB,SAASC,GAIjC,GAAAA,EAAAC,eAAA,UAAA,CAEID,IAAAA,EACA,oBAAAE,UACIC,UAOJH,UACIA,UAJUE,UAAUE,cAQxB,UACAC,cACHL,EACDA,EAAA,KAAAG,IANQH,EAAc,KAAOG,EAAOG,MAAM,KAAK,KAQ/CN,EAAAO,OAaI,IAAAC,EAAA,SAAAC,GAOA,OAAOT,EAAcS,IAAkBA,GAK3C,OAHAD,EAASE,mBAAoB,EAGtBF","file":"../../scripts/utils/localization.js","sourcesContent":["define([\"i18n!nls/locale\"], function(localeStrings) {\n // =============================================================================\n /** Simple string replacement localization. Language data from galaxy/scripts/nls */\n\n // support both requirejs and webpack from the same file\n // if loaded via webpack, it will be a different format than via requirejs - convert\n if (localeStrings.hasOwnProperty(\"__root\")) {\n //console.debug( 'amdi18n+webpack localization for ' + locale + ' loaded' );\n var locale =\n typeof navigator === \"undefined\"\n ? \"__root\"\n : (navigator.language ||\n navigator.userLanguage ||\n \"__root\"\n ).toLowerCase();\n localeStrings =\n localeStrings[\"__\" + locale] ||\n localeStrings[\"__\" + locale.split(\"-\")[0]] ||\n localeStrings.__root;\n\n // } else {\n // console.debug( 'i18n+requirejs localization for ' + locale + ' loaded' );\n }\n // TODO: when this is no longer necessary remove this, i18n.js, and the resolveModule in config\n\n // -----------------------------------------------------------------------------\n /** Attempt to get a localized string for strToLocalize. 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up instance vars and cache, and add onpageunload to window */\n MetricsLogger.prototype._init = function _init(options) {\n var self = this;\n self.options = {};\n for (var k in MetricsLogger.defaultOptions) {\n if (MetricsLogger.defaultOptions.hasOwnProperty(k)) {\n self.options[k] = options.hasOwnProperty(k)\n ? options[k]\n : MetricsLogger.defaultOptions[k];\n }\n }\n self.options.logLevel = self._parseLevel(self.options.logLevel);\n self.options.consoleLevel = self._parseLevel(self.options.consoleLevel);\n //self._emitToConsole( 'debug', 'MetricsLogger', 'MetricsLogger.options:', self.options );\n\n /** is the logger currently sending? */\n self._sending = false;\n /** the setTimeout id if the logger POST has failed more than once */\n self._waiting = null;\n /** the current number of entries to send in a POST */\n self._postSize = self.options.postSize;\n\n self._initCache();\n\n return self;\n };\n\n /** initialize the cache */\n MetricsLogger.prototype._initCache = function _initCache() {\n try {\n this.cache = new LoggingCache({\n maxSize: this.options.maxCacheSize,\n key: this.options.cacheKeyPrefix + this.userId\n });\n } catch (err) {\n this._emitToConsole(\"warn\", \"MetricsLogger\", [\n \"Could not intitialize logging cache:\",\n err\n ]);\n this.options.logLevel = MetricsLogger.NONE;\n }\n };\n\n /** return the numeric log level if level in 'none, debug, log, info, warn, error' */\n MetricsLogger.prototype._parseLevel = function _parseLevel(level) {\n var type = typeof level;\n if (type === \"number\") {\n return level;\n }\n if (type === \"string\") {\n var upper = level.toUpperCase();\n if (MetricsLogger.hasOwnProperty(upper)) {\n return MetricsLogger[upper];\n }\n }\n throw new Error(\"Unknown log level: \" + level);\n };\n\n //----------------------------------------------------------------------------- main entry point\n /** record a log/message's arguments to the cache and/or the console based on level and namespace */\n MetricsLogger.prototype.emit = function emit(\n level,\n namespace,\n logArguments\n ) {\n //this._emitToConsole( 'debug', 'MetricsLogger', [ 'emit:', level, namespace, logArguments ]);\n var self = this;\n namespace = namespace || self.options.defaultNamespace;\n if (!level || !logArguments) {\n return self;\n }\n // add to cache if proper level\n //TODO: respect do not track?\n //if( !navigator.doNotTrack && level >= self.options.logLevel ){\n level = self._parseLevel(level);\n if (level >= self.options.logLevel) {\n self._addToCache(level, namespace, logArguments);\n }\n // also emit to consoleLogger if proper level for that\n if (self.consoleLogger && level >= self.options.consoleLevel) {\n self._emitToConsole(level, namespace, logArguments);\n }\n return self;\n };\n\n //----------------------------------------------------------------------------- cache\n /** add a message to the cache and if messages.length is high enough post them to the server */\n MetricsLogger.prototype._addToCache = function _addToCache(\n level,\n namespace,\n logArguments\n ) {\n this._emitToConsole(\"debug\", \"MetricsLogger\", [\n \"_addToCache:\",\n arguments,\n this.options.addTime,\n this.cache.length()\n ]);\n //this._emitToConsole( 'debug', 'MetricsLogger', [ '\\t logArguments:', logArguments ]);\n var self = this;\n // try add to the cache and if we've got _postSize number of entries, attempt to post them to the server\n try {\n var newLength = self.cache.add(\n self._buildEntry(level, namespace, logArguments)\n );\n if (newLength >= self._postSize) {\n self._postCache();\n }\n // discard entry if an error occurs, but warn if level set to do so\n } catch (err) {\n self._emitToConsole(\"warn\", \"MetricsLogger\", [\n \"Metrics logger could not stringify logArguments:\",\n namespace,\n logArguments\n ]);\n self._emitToConsole(\"error\", \"MetricsLogger\", [err]);\n }\n return self;\n };\n\n /** build a log cache entry object from the given level, namespace, and arguments (optionally adding timestamp */\n MetricsLogger.prototype._buildEntry = function _buildEntry(\n level,\n namespace,\n logArguments\n ) {\n this._emitToConsole(\"debug\", \"MetricsLogger\", [\n \"_buildEntry:\",\n arguments\n ]);\n var entry = {\n level: level,\n namespace: this.options.clientPrefix + namespace,\n args: logArguments\n };\n if (this.options.addTime) {\n entry.time = new Date().toISOString();\n }\n return entry;\n };\n\n /** post _postSize messages from the cache to the server, removing them if successful\n * if the post fails, wait until maxCacheSize is accumulated instead and try again then\n * in addition to the messages from the cache ('metrics'), any info from getPingData (if set) will be sent\n * onServerResponse will be called (if set) with any response from the server\n */\n MetricsLogger.prototype._postCache = function _postCache(options) {\n options = options || {};\n this._emitToConsole(\"info\", \"MetricsLogger\", [\n \"_postCache\",\n options,\n this._postSize\n ]);\n\n // short circuit if we're already sending\n if (!this.options.postUrl || this._sending) {\n return jQuery.when({});\n }\n\n var self = this,\n postSize = options.count || self._postSize,\n // do not splice - remove after *successful* post\n entries = self.cache.get(postSize),\n entriesLength = entries.length,\n // use the optional getPingData to add any extra info we may want to send\n postData =\n typeof self.options.getPingData === \"function\"\n ? self.options.getPingData()\n : {};\n //console.debug( postSize, entriesLength );\n\n // add the metrics and send\n postData.metrics = JSON.stringify(entries);\n //console.debug( postData.metrics );\n self._sending = true;\n return jQuery\n .post(self.options.postUrl, postData)\n .always(function() {\n self._sending = false;\n })\n .fail(function(xhr, status, message) {\n // if we failed the previous time, set the next post target to the max num of entries\n self._postSize = self.options.maxCacheSize;\n //TODO:??\n // log this failure to explain any gap in metrics\n self.emit(\"error\", \"MetricsLogger\", [\n \"_postCache error:\",\n xhr.readyState,\n xhr.status,\n xhr.responseJSON || xhr.responseText\n ]);\n //TODO: still doesn't solve the problem that when cache == max, post will be tried on every emit\n //TODO: see _delayPost\n })\n .done(function(response) {\n if (typeof self.options.onServerResponse === \"function\") {\n self.options.onServerResponse(response);\n }\n // only remove if post successful\n self.cache.remove(entriesLength);\n //console.debug( 'removed entries:', entriesLength, 'size now:', self.cache.length() );\n // if we succeeded, reset the post target to the normal num of entries\n self._postSize = self.options.postSize;\n });\n // return the xhr promise\n };\n\n /** set _waiting to true and, after delayPostInMs, set it back to false */\n MetricsLogger.prototype._delayPost = function _delayPost() {\n //TODO: this won't work between pages\n var self = this;\n self._waiting = setTimeout(function() {\n self._waiting = null;\n }, self.options.delayPostInMs);\n };\n\n //----------------------------------------------------------------------------- console\n /** output message to console based on level and consoleLogger type */\n MetricsLogger.prototype._emitToConsole = function _emitToConsole(\n level,\n namespace,\n logArguments\n ) {\n //console.debug( '_emitToConsole:', level, namespace, logArguments );\n var self = this,\n whitelist = self.options.consoleNamespaceWhitelist;\n if (!self.consoleLogger) {\n return self;\n }\n // if a whitelist for namespaces is set, bail if this namespace is not in the list\n if (whitelist && whitelist.indexOf(namespace) === -1) {\n return self;\n }\n\n var args = Array.prototype.slice.call(logArguments, 0);\n args.unshift(namespace);\n //TODO: script location and/or source maps?\n //TODO: branch on navigator.userAgent == AIIEEE - it only has log\n if (\n level >= MetricsLogger.METRIC &&\n typeof self.consoleLogger.info === \"function\"\n ) {\n return self.consoleLogger.info.apply(self.consoleLogger, args);\n } else if (\n level >= MetricsLogger.ERROR &&\n typeof self.consoleLogger.error === \"function\"\n ) {\n return self.consoleLogger.error.apply(self.consoleLogger, args);\n } else if (\n level >= MetricsLogger.WARN &&\n typeof self.consoleLogger.warn === \"function\"\n ) {\n self.consoleLogger.warn.apply(self.consoleLogger, args);\n } else if (\n level >= MetricsLogger.INFO &&\n typeof self.consoleLogger.info === \"function\"\n ) {\n self.consoleLogger.info.apply(self.consoleLogger, args);\n } else if (\n level >= MetricsLogger.DEBUG &&\n typeof self.consoleLogger.debug === \"function\"\n ) {\n self.consoleLogger.debug.apply(self.consoleLogger, args);\n } else if (typeof self.consoleLogger.log === \"function\") {\n self.consoleLogger.log.apply(self.consoleLogger, args);\n }\n return self;\n };\n\n //----------------------------------------------------------------------------- shortcuts\n // generic functions when logging from non-namespaced object (e.g. templates)\n /** log to default namespace */\n MetricsLogger.prototype.log = function log() {\n this.emit(\n 1,\n this.options.defaultNamespace,\n Array.prototype.slice.call(arguments, 0)\n );\n };\n\n /** debug to default namespace */\n MetricsLogger.prototype.debug = function debug() {\n this.emit(\n MetricsLogger.DEBUG,\n this.options.defaultNamespace,\n Array.prototype.slice.call(arguments, 0)\n );\n };\n\n /** info to default namespace */\n MetricsLogger.prototype.info = function info() {\n this.emit(\n MetricsLogger.INFO,\n this.options.defaultNamespace,\n Array.prototype.slice.call(arguments, 0)\n );\n };\n\n /** warn to default namespace */\n MetricsLogger.prototype.warn = function warn() {\n this.emit(\n MetricsLogger.WARN,\n this.options.defaultNamespace,\n Array.prototype.slice.call(arguments, 0)\n );\n };\n\n /** error to default namespace */\n MetricsLogger.prototype.error = function error() {\n this.emit(\n MetricsLogger.ERROR,\n this.options.defaultNamespace,\n Array.prototype.slice.call(arguments, 0)\n );\n };\n\n /** metric to default namespace */\n MetricsLogger.prototype.metric = function metric() {\n this.emit(\n MetricsLogger.METRIC,\n this.options.defaultNamespace,\n Array.prototype.slice.call(arguments, 0)\n );\n };\n\n /* ============================================================================\nTODO:\n need a performance pass - the JSON un/parsing is a bit much\n\n============================================================================ */\n /** @class LoggingCache\n * Simple implementation of cache wrapping an array.\n *\n * Formats an entry before it's cached and only keeps options.maxSize number\n * of entries. 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function() {\n /*global window, jQuery, console */\n /*=============================================================================\nTODO:\n while anon: logs saved to 'logs-null' - this will never post\n unless we manually do so at/after login\n OR prepend when userId and localStorage has 'logs-null'\n wire up _delayPost and test\n\n=============================================================================*/\n /** @class MetricsLogger\n *\n * Object to cache, output, and post log/metric messages to the server.\n * Meant to be attached to the Galaxy object.\n *\n * Log from objects by either attaching logger directly:\n * panel.logger.metric( 'user dataset deletion', panel.user.id, hda.toJSON() )\n * or using the LoggableMixin or addLogging function:\n * MyBackboneModel.extend( LoggableMixin ).extend({ ... })\n * addLogging( MyBackboneModel, 'my-backbone-model' )\n *\n * Log from templates by calling directly from Galaxy object:\n * Galaxy.logger.metric( 'template loaded', { ownedByUser : true });\n *\n * If you attempt to log an un-serializable object (circular reference, window, etc.),\n * that entry will not be cached (or sent). 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self._waiting = setTimeout(function() {\n self._waiting = null;\n }, self.options.delayPostInMs);\n };\n\n //----------------------------------------------------------------------------- console\n /** output message to console based on level and consoleLogger type */\n MetricsLogger.prototype._emitToConsole = function _emitToConsole(\n level,\n namespace,\n logArguments\n ) {\n //console.debug( '_emitToConsole:', level, namespace, logArguments );\n var self = this,\n whitelist = self.options.consoleNamespaceWhitelist;\n if (!self.consoleLogger) {\n return self;\n }\n // if a whitelist for namespaces is set, bail if this namespace is not in the list\n if (whitelist && whitelist.indexOf(namespace) === -1) {\n return self;\n }\n\n var args = Array.prototype.slice.call(logArguments, 0);\n args.unshift(namespace);\n //TODO: script location and/or source maps?\n //TODO: branch on navigator.userAgent == AIIEEE - it only has log\n if (\n level >= MetricsLogger.METRIC &&\n typeof self.consoleLogger.info === \"function\"\n ) {\n return self.consoleLogger.info.apply(self.consoleLogger, args);\n } else if (\n level >= MetricsLogger.ERROR &&\n typeof self.consoleLogger.error === \"function\"\n ) {\n return self.consoleLogger.error.apply(self.consoleLogger, args);\n } else if (\n level >= MetricsLogger.WARN &&\n typeof self.consoleLogger.warn === \"function\"\n ) {\n self.consoleLogger.warn.apply(self.consoleLogger, args);\n } else if (\n level >= MetricsLogger.INFO &&\n typeof self.consoleLogger.info === \"function\"\n ) {\n self.consoleLogger.info.apply(self.consoleLogger, args);\n } else if (\n level >= MetricsLogger.DEBUG &&\n typeof self.consoleLogger.debug === \"function\"\n ) {\n self.consoleLogger.debug.apply(self.consoleLogger, args);\n } else if (typeof self.consoleLogger.log === \"function\") {\n self.consoleLogger.log.apply(self.consoleLogger, args);\n }\n return self;\n };\n\n //----------------------------------------------------------------------------- shortcuts\n // generic functions when logging from non-namespaced object (e.g. templates)\n /** log to default namespace */\n MetricsLogger.prototype.log = function log() {\n this.emit(\n 1,\n this.options.defaultNamespace,\n Array.prototype.slice.call(arguments, 0)\n );\n };\n\n /** debug to default namespace */\n MetricsLogger.prototype.debug = function debug() {\n this.emit(\n MetricsLogger.DEBUG,\n this.options.defaultNamespace,\n Array.prototype.slice.call(arguments, 0)\n );\n };\n\n /** info to default namespace */\n MetricsLogger.prototype.info = function info() {\n this.emit(\n MetricsLogger.INFO,\n this.options.defaultNamespace,\n Array.prototype.slice.call(arguments, 0)\n );\n };\n\n /** warn to default namespace */\n MetricsLogger.prototype.warn = function warn() {\n this.emit(\n MetricsLogger.WARN,\n this.options.defaultNamespace,\n Array.prototype.slice.call(arguments, 0)\n );\n };\n\n /** error to default namespace */\n MetricsLogger.prototype.error = function error() {\n this.emit(\n MetricsLogger.ERROR,\n this.options.defaultNamespace,\n Array.prototype.slice.call(arguments, 0)\n );\n };\n\n /** metric to default namespace */\n MetricsLogger.prototype.metric = function metric() {\n this.emit(\n MetricsLogger.METRIC,\n this.options.defaultNamespace,\n Array.prototype.slice.call(arguments, 0)\n );\n };\n\n /* ============================================================================\nTODO:\n need a performance pass - the JSON un/parsing is a bit much\n\n============================================================================ */\n /** @class LoggingCache\n * Simple implementation of cache wrapping an array.\n *\n * Formats an entry before it's cached and only keeps options.maxSize number\n * of entries. Older entries are deleted first.\n */\n function LoggingCache(options) {\n var self = this;\n return self._init(options || {});\n }\n\n /** default options */\n LoggingCache.defaultOptions = {\n /** maximum number of entries to keep before discarding oldest */\n maxSize: 5000\n };\n\n /** initialize with options */\n LoggingCache.prototype._init = function _init(options) {\n if (!this._hasStorage()) {\n //TODO: fall back to jstorage\n throw new Error(\"LoggingCache needs localStorage\");\n }\n if (!options.key) {\n throw new Error(\"LoggingCache needs key for localStorage\");\n }\n this.key = options.key;\n this._initStorage();\n\n this.maxSize = options.maxSize || LoggingCache.defaultOptions.maxSize;\n return this;\n };\n\n /** tests for localStorage fns */\n LoggingCache.prototype._hasStorage = function _hasStorage() {\n //TODO: modernizr\n var test = \"test\";\n try {\n localStorage.setItem(test, test);\n localStorage.removeItem(test);\n return true;\n } catch (e) {\n return false;\n }\n };\n\n /** if no localStorage set for key, initialize to empty array */\n LoggingCache.prototype._initStorage = function _initStorage() {\n if (localStorage.getItem(this.key) === null) {\n return this.empty();\n }\n return this;\n };\n\n /** add an entry to the cache, removing the oldest beforehand if size >= maxSize */\n LoggingCache.prototype.add = function add(entry) {\n var self = this,\n _cache = self._fetchAndParse(),\n overage = _cache.length + 1 - self.maxSize;\n if (overage > 0) {\n _cache.splice(0, overage);\n }\n _cache.push(entry);\n self._unparseAndStore(_cache);\n return _cache.length;\n };\n\n /** get the entries from localStorage and parse them */\n LoggingCache.prototype._fetchAndParse = function _fetchAndParse() {\n var self = this;\n return JSON.parse(localStorage.getItem(self.key));\n };\n\n /** stringify the entries and put them in localStorage */\n LoggingCache.prototype._unparseAndStore = function _unparseAndStore(\n entries\n ) {\n var self = this;\n return localStorage.setItem(self.key, JSON.stringify(entries));\n };\n\n ///** process the entry before caching */\n //LoggingCache.prototype._preprocessEntry = function _preprocessEntry( entry ){\n // return JSON.stringify( entry );\n //};\n\n /** return the length --- oh, getters where are you? */\n LoggingCache.prototype.length = function length() {\n return this._fetchAndParse().length;\n };\n\n /** get count number of entries starting with the oldest */\n LoggingCache.prototype.get = function get(count) {\n return this._fetchAndParse().slice(0, count);\n };\n\n /** remove count number of entries starting with the oldest */\n LoggingCache.prototype.remove = function remove(count) {\n var _cache = this._fetchAndParse(),\n removed = _cache.splice(0, count);\n this._unparseAndStore(_cache);\n return removed;\n };\n\n /** empty/clear the entire cache */\n LoggingCache.prototype.empty = function empty() {\n localStorage.setItem(this.key, \"[]\");\n return this;\n };\n\n /** stringify count number of entries (but do not remove) */\n LoggingCache.prototype.stringify = function stringify(count) {\n return JSON.stringify(this.get(count));\n };\n\n /** outputs entire cache to console */\n LoggingCache.prototype.print = function print() {\n // popup? (really, carl? a popup?) - easier to copy/paste\n console.log(JSON.stringify(this._fetchAndParse(), null, \" \"));\n };\n\n //=============================================================================\n return {\n MetricsLogger: MetricsLogger,\n LoggingCache: LoggingCache\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/utils/natural-sort.js.map b/static/maps/utils/natural-sort.js.map index 9383deae0c8..6f83abd1b82 100644 --- a/static/maps/utils/natural-sort.js.map +++ b/static/maps/utils/natural-sort.js.map @@ -1 +1 @@ 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function() {\n // Alphanumeric/natural sort fn\n function naturalSort(a, b) {\n // setup temp-scope variables for comparison evauluation\n var re = /(-?[0-9\\.]+)/g,\n x = a.toString().toLowerCase() || \"\",\n y = b.toString().toLowerCase() || \"\",\n nC = String.fromCharCode(0),\n xN = x.replace(re, nC + \"$1\" + nC).split(nC),\n yN = y.replace(re, nC + \"$1\" + nC).split(nC),\n xD = new Date(x).getTime(),\n yD = xD ? new Date(y).getTime() : null;\n // natural sorting of dates\n if (yD) {\n if (xD < yD) {\n return -1;\n } else if (xD > yD) {\n return 1;\n }\n }\n // natural sorting through split numeric strings and default strings\n var oFxNcL, oFyNcL;\n for (\n var cLoc = 0, numS = Math.max(xN.length, yN.length);\n cLoc < numS;\n cLoc++\n ) {\n oFxNcL = parseFloat(xN[cLoc]) || xN[cLoc];\n oFyNcL = parseFloat(yN[cLoc]) || yN[cLoc];\n if (oFxNcL < oFyNcL) {\n return -1;\n } else if (oFxNcL > oFyNcL) {\n return 1;\n }\n }\n return 0;\n }\n\n return naturalSort;\n});\n"]} \ No newline at end of file +{"version":3,"sources":["utils/natural-sort.js"],"names":["define","a","b","re","x","naturalSort","y","toString","toLowerCase","nC","fromCharCode","xN","split","yN","xD","String","yD","replace","getTime","oFxNcL","oFyNcL","cLoc","numS","Math","max","length","parseFloat"],"mappings":"kCAAAA,UAAW,WAuCV,OArCG,SAAqBC,EAAGC,GADxB,IAAAC,EAAA,gBACAC,EAAAH,EAASI,WAAYJ,eAAM,GACvBK,EAAAJ,EAAAK,WAAAC,eAAA,GACAC,EAAIN,OAAKO,aAAT,GAAAC,EACIP,EAAAA,QAAMG,EAAFE,EAAaD,KAAAA,GAAbI,MADRH,GAAAI,EAEIP,EAAAA,QAAMC,EAAFE,EAAaD,KAAAA,GAAbI,MAFRH,GAAAK,EAGIL,IAAKM,KAAAA,GAAOL,UAHhBM,EAIIL,EAAKP,IAAEa,KAAQd,GAAVe,UAAc,KAJvB,GAAAF,EAMIF,CANJ,GAOIE,EAAKF,EACT,OAAA,EACA,GAAQA,EAAAE,EACJ,OAAIF,EAKP,IACD,IAFKK,EAAAC,EAELC,EAAA,EAAAC,EAAAC,KAAAC,IAAAb,EAAAc,OAAAZ,EAAAY,QACAJ,EAAIF,EACJE,IAKIF,CAGI,GAFJC,EAAAA,WAASM,EAAAA,KAAAf,EAAAU,GACTD,EAAID,WAASC,EAAbC,KAAqBR,EAAAQ,GACjBF,EAAAC,EACH,OAAM,EACH,GAAAD,EAAAC,EACH,OAAA,EAGR,OAAA","file":"../../scripts/utils/natural-sort.js","sourcesContent":["define([], function() {\n // Alphanumeric/natural sort fn\n function naturalSort(a, b) {\n // setup temp-scope variables for comparison evauluation\n var re = /(-?[0-9\\.]+)/g,\n x = a.toString().toLowerCase() || \"\",\n y = b.toString().toLowerCase() || \"\",\n nC = String.fromCharCode(0),\n xN = x.replace(re, nC + \"$1\" + nC).split(nC),\n yN = y.replace(re, nC + \"$1\" + nC).split(nC),\n xD = new Date(x).getTime(),\n yD = xD ? new Date(y).getTime() : null;\n // natural sorting of dates\n if (yD) {\n if (xD < yD) {\n return -1;\n } else if (xD > yD) {\n return 1;\n }\n }\n // natural sorting through split numeric strings and default strings\n var oFxNcL, oFyNcL;\n for (\n var cLoc = 0, numS = Math.max(xN.length, yN.length);\n cLoc < numS;\n cLoc++\n ) {\n oFxNcL = parseFloat(xN[cLoc]) || xN[cLoc];\n oFyNcL = parseFloat(yN[cLoc]) || yN[cLoc];\n if (oFxNcL < oFyNcL) {\n return -1;\n } else if (oFxNcL > oFyNcL) {\n return 1;\n }\n }\n return 0;\n }\n\n return naturalSort;\n});\n"]} \ No newline at end of file diff --git a/static/maps/utils/query-string-parsing.js.map b/static/maps/utils/query-string-parsing.js.map index 910b88e15a2..a99f4dab9f8 100644 --- a/static/maps/utils/query-string-parsing.js.map +++ b/static/maps/utils/query-string-parsing.js.map @@ -1 +1 @@ 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|| window.location.search.substr(1);\n var keyRegex = new RegExp(key + \"=([^&#$]+)\", \"g\");\n var matches = queryString.match(keyRegex);\n if (!matches || !matches.length) {\n return undefined;\n }\n matches = _.map(matches, function(match) {\n return decodeURIComponent(\n match.substr(key.length + 1).replace(/\\+/g, \" \")\n );\n });\n if (matches.length === 1) {\n return matches[0];\n }\n return matches;\n }\n\n function parse(queryString) {\n if (!queryString) {\n return {};\n }\n var parsed = {},\n split = queryString.split(\"&\");\n split.forEach(function(pairString) {\n var pair = pairString.split(\"=\");\n parsed[pair[0]] = decodeURI(pair[1]);\n });\n return parsed;\n }\n\n // ============================================================================\n return {\n get: get,\n parse: parse\n };\n});\n"]} \ No newline at end of file +{"version":3,"sources":["utils/query-string-parsing.js"],"names":["define","get","key","queryString","window","location","search","substr","keyRegex","RegExp","matches","length","decodeURIComponent","match","replace","parsed","split","forEach","pairString","pair"],"mappings":"kCAAAA,UAAW,WAiCP,OACAC,IAhCA,SAAaC,EAAKC,GAFtBH,EAAWG,GAAWC,OAAAC,SAAAC,OAAAC,OAAA,GAClB,IAAAC,EAAA,IAAAC,OAAAP,EAAA,aAAA,KACAQ,EAAaR,EAAKC,MAAaK,GAC3BL,GAAAA,GAAAA,EAAcA,OAUb,OAJD,KAHAO,EAAKA,EAAAA,IAADA,EAAaA,SAAQC,GACrB,OAAAC,mBACHC,EAAAN,OAAAL,EAAAS,OAAA,GAAAG,QAAA,MAAA,SACDH,OAKID,EAAQC,GAEXD,GAmBDT,MAfJ,SAAeE,GAAf,IAAAA,EACI,SAEC,IAAAY,KAMA,OALGA,EAAJC,MAAA,KAAAC,QACID,SAAQb,GACZa,IAAAA,EAAMC,EAAQD,MAASE,KACnBH,EAAAI,EAAIA,IAAOD,UAAWF,EAAM,MADhCD","file":"../../scripts/utils/query-string-parsing.js","sourcesContent":["define([], function() {\n // ============================================================================\n function get(key, queryString) {\n queryString = queryString || 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a/static/maps/utils/uploadbox.js.map +++ b/static/maps/utils/uploadbox.js.map @@ -1 +1 @@ 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load required libraries\nrequire([\"utils/utils\"], function(mod_utils) {\n // load css\n mod_utils.cssLoadFile(\"static/style/circster.css\");\n});\n\ndefine(\n [\n \"libs/underscore\",\n \"libs/d3\",\n \"viz/visualization\",\n \"utils/config\",\n \"mvc/ui/icon-button\",\n \"libs/farbtastic\"\n ],\n function(_, d3, visualization, config, mod_icon_btn) {\n /**\n * Utility class for working with SVG.\n */\n var SVGUtils = Backbone.Model.extend({\n /**\n * Returns true if element is visible.\n */\n is_visible: function(svg_elt, svg) {\n var eltBRect = svg_elt.getBoundingClientRect(),\n svgBRect = $(\"svg\")[0].getBoundingClientRect();\n\n if (\n // To the left of screen?\n eltBRect.right < 0 ||\n // To the right of screen?\n eltBRect.left > svgBRect.right ||\n // Above screen?\n eltBRect.bottom < 0 ||\n // Below screen?\n eltBRect.top > svgBRect.bottom\n ) {\n return false;\n }\n return true;\n }\n });\n\n /**\n * Mixin for using ticks.\n */\n var UsesTicks = {\n drawTicks: function(\n parent_elt,\n data,\n dataHandler,\n textTransform,\n horizontal\n ) {\n // Set up group elements for chroms and for each tick.\n var ticks = parent_elt\n .append(\"g\")\n .selectAll(\"g\")\n .data(data)\n .enter()\n .append(\"g\")\n .selectAll(\"g\")\n .data(dataHandler)\n .enter()\n .append(\"g\")\n .attr(\"class\", \"tick\")\n .attr(\"transform\", function(d) {\n return (\n \"rotate(\" +\n (d.angle * 180 / Math.PI - 90) +\n \")\" +\n \"translate(\" +\n d.radius +\n \",0)\"\n );\n });\n\n // Add line + text for ticks.\n var tick_coords = [],\n text_coords = [],\n text_anchor = function(d) {\n return d.angle > Math.PI ? \"end\" : null;\n };\n if (horizontal) {\n tick_coords = [0, 0, 0, -4];\n text_coords = [4, 0, \"\", \".35em\"];\n text_anchor = null;\n } else {\n tick_coords = [1, 0, 4, 0];\n text_coords = [0, 4, \".35em\", \"\"];\n }\n\n ticks\n .append(\"line\")\n .attr(\"x1\", tick_coords[0])\n .attr(\"y1\", tick_coords[1])\n .attr(\"x2\", tick_coords[2])\n .attr(\"y1\", tick_coords[3])\n .style(\"stroke\", \"#000\");\n\n return ticks\n .append(\"text\")\n .attr(\"x\", text_coords[0])\n .attr(\"y\", text_coords[1])\n .attr(\"dx\", text_coords[2])\n .attr(\"dy\", text_coords[3])\n .attr(\"text-anchor\", text_anchor)\n .attr(\"transform\", textTransform)\n .text(function(d) {\n return d.label;\n });\n },\n\n /**\n * Format number for display at a tick.\n */\n formatNum: function(num, sigDigits) {\n // Use default of 2 sig. digits.\n if (sigDigits === undefined) sigDigits = 2;\n\n // Verify input number\n if (num === null) return null;\n\n // Calculate return value\n var rval = null;\n if (Math.abs(num) < 1) {\n rval = num.toPrecision(sigDigits);\n } else {\n // Use round to turn string from toPrecision() back into a number.\n var roundedNum = Math.round(num.toPrecision(sigDigits));\n\n // Use abbreviations.\n num = Math.abs(num);\n if (num < 1000) {\n rval = roundedNum;\n } else if (num < 1000000) {\n // Use K.\n rval =\n Math.round(\n (roundedNum / 1000).toPrecision(3)\n ).toFixed(0) + \"K\";\n } else if (num < 1000000000) {\n // Use M.\n rval =\n Math.round(\n (roundedNum / 1000000).toPrecision(3)\n ).toFixed(0) + \"M\";\n }\n }\n\n return rval;\n }\n };\n\n /**\n * A label track.\n */\n var CircsterLabelTrack = Backbone.Model.extend({});\n\n /**\n * Renders a full circster visualization.\n */\n var CircsterView = Backbone.View.extend({\n className: \"circster\",\n\n initialize: function(options) {\n this.genome = options.genome;\n this.label_arc_height = 50;\n this.scale = 1;\n this.circular_views = null;\n this.chords_views = null;\n\n // When tracks added to/removed from model, update view.\n this.model.get(\"drawables\").on(\"add\", this.add_track, this);\n this.model\n .get(\"drawables\")\n .on(\"remove\", this.remove_track, this);\n\n // When config settings change, update view.\n var vis_config = this.model.get(\"config\");\n vis_config\n .get(\"arc_dataset_height\")\n .on(\"change:value\", this.update_track_bounds, this);\n vis_config\n .get(\"track_gap\")\n .on(\"change:value\", this.update_track_bounds, this);\n },\n\n // HACKs: using track_type for circular/chord distinction in the functions below for now.\n\n /**\n * Returns tracks to be rendered using circular view.\n */\n get_circular_tracks: function() {\n return this.model.get(\"drawables\").filter(function(track) {\n return track.get(\"track_type\") !== \"DiagonalHeatmapTrack\";\n });\n },\n\n /**\n * Returns tracks to be rendered using chords view.\n */\n get_chord_tracks: function() {\n return this.model.get(\"drawables\").filter(function(track) {\n return track.get(\"track_type\") === \"DiagonalHeatmapTrack\";\n });\n },\n\n /**\n * Returns a list of circular tracks' radius bounds.\n */\n get_tracks_bounds: function() {\n var circular_tracks = this.get_circular_tracks(),\n dataset_arc_height = this.model\n .get(\"config\")\n .get_value(\"arc_dataset_height\"),\n track_gap = this.model.get(\"config\").get_value(\"track_gap\"),\n // Subtract 20 to make sure chrom labels are on screen.\n min_dimension =\n Math.min(this.$el.width(), this.$el.height()) - 20,\n // Compute radius start based on model, will be centered\n // and fit entirely inside element by default.\n radius_start =\n min_dimension / 2 -\n circular_tracks.length *\n (dataset_arc_height + track_gap) +\n // Add track_gap back in because no gap is needed for last track.\n track_gap -\n this.label_arc_height,\n // Compute range of track starting radii.\n tracks_start_radii = d3.range(\n radius_start,\n min_dimension / 2,\n dataset_arc_height + track_gap\n );\n\n // Map from track start to bounds.\n var self = this;\n return _.map(tracks_start_radii, function(radius) {\n return [radius, radius + dataset_arc_height];\n });\n },\n\n /**\n * Renders circular tracks, chord tracks, and label tracks.\n */\n render: function() {\n var self = this,\n width = self.$el.width(),\n height = self.$el.height(),\n circular_tracks = this.get_circular_tracks(),\n chords_tracks = this.get_chord_tracks(),\n total_gap = self.model.get(\"config\").get_value(\"total_gap\"),\n tracks_bounds = this.get_tracks_bounds(),\n // Set up SVG element.\n svg = d3\n .select(self.$el[0])\n .append(\"svg\")\n .attr(\"width\", width)\n .attr(\"height\", height)\n .attr(\"pointer-events\", \"all\")\n // Set up zooming, dragging.\n .append(\"svg:g\")\n .call(\n d3.behavior.zoom().on(\"zoom\", function() {\n // Do zoom, drag.\n var scale = d3.event.scale;\n svg.attr(\n \"transform\",\n \"translate(\" +\n d3.event.translate +\n \")\" +\n \" scale(\" +\n scale +\n \")\"\n );\n\n // Propagate scale changes to views.\n if (self.scale !== scale) {\n // Use timeout to wait for zooming/dragging to stop before rendering more detail.\n if (self.zoom_drag_timeout) {\n clearTimeout(self.zoom_drag_timeout);\n }\n self.zoom_drag_timeout = setTimeout(\n function() {\n // Render more detail in tracks' visible elements.\n // FIXME: do not do this right now; it is not fully implemented--e.g. data bounds\n // are not updated when new data is fetched--and fetching more detailed quantitative\n // data is not that useful.\n /*\n _.each(self.circular_views, function(view) {\n view.update_scale(scale);\n });\n */\n },\n 400\n );\n }\n })\n )\n .attr(\n \"transform\",\n \"translate(\" + width / 2 + \",\" + height / 2 + \")\"\n )\n .append(\"svg:g\")\n .attr(\"class\", \"tracks\");\n\n // -- Render circular tracks. --\n\n // Create a view for each track in the visualization and render.\n this.circular_views = circular_tracks.map(function(\n track,\n index\n ) {\n var view = new CircsterBigWigTrackView({\n el: svg.append(\"g\")[0],\n track: track,\n radius_bounds: tracks_bounds[index],\n genome: self.genome,\n total_gap: total_gap\n });\n\n view.render();\n\n return view;\n });\n\n // -- Render chords tracks. --\n\n this.chords_views = chords_tracks.map(function(track) {\n var view = new CircsterChromInteractionsTrackView({\n el: svg.append(\"g\")[0],\n track: track,\n radius_bounds: tracks_bounds[0],\n genome: self.genome,\n total_gap: total_gap\n });\n\n view.render();\n\n return view;\n });\n\n // -- Render label track. --\n\n // Track bounds are:\n // (a) outer radius of last circular track;\n // (b)\n var outermost_radius = this.circular_views[\n this.circular_views.length - 1\n ].radius_bounds[1],\n track_bounds = [\n outermost_radius,\n outermost_radius + this.label_arc_height\n ];\n this.label_track_view = new CircsterChromLabelTrackView({\n el: svg.append(\"g\")[0],\n track: new CircsterLabelTrack(),\n radius_bounds: track_bounds,\n genome: self.genome,\n total_gap: total_gap\n });\n\n this.label_track_view.render();\n },\n\n /**\n * Render a single track on the outside of the current visualization.\n */\n add_track: function(new_track) {\n var total_gap = this.model.get(\"config\").get_value(\"total_gap\");\n\n if (new_track.get(\"track_type\") === \"DiagonalHeatmapTrack\") {\n // Added chords track.\n var innermost_radius_bounds = this.circular_views[0]\n .radius_bounds,\n new_view = new CircsterChromInteractionsTrackView({\n el: d3.select(\"g.tracks\").append(\"g\")[0],\n track: new_track,\n radius_bounds: innermost_radius_bounds,\n genome: this.genome,\n total_gap: total_gap\n });\n new_view.render();\n this.chords_views.push(new_view);\n } else {\n // Added circular track.\n\n // Recompute and update circular track bounds.\n var new_track_bounds = this.get_tracks_bounds();\n _.each(this.circular_views, function(track_view, i) {\n track_view.update_radius_bounds(new_track_bounds[i]);\n });\n\n // Update chords tracks.\n _.each(this.chords_views, function(track_view) {\n track_view.update_radius_bounds(new_track_bounds[0]);\n });\n\n // Render new track.\n var track_index = this.circular_views.length,\n track_view = new CircsterBigWigTrackView({\n el: d3.select(\"g.tracks\").append(\"g\")[0],\n track: new_track,\n radius_bounds: new_track_bounds[track_index],\n genome: this.genome,\n total_gap: total_gap\n });\n track_view.render();\n this.circular_views.push(track_view);\n\n // Update label track.\n /*\n FIXME: should never have to update label track because vis always expands to fit area\n within label track.\n var track_bounds = new_track_bounds[ new_track_bounds.length-1 ];\n track_bounds[1] = track_bounds[0];\n this.label_track_view.update_radius_bounds(track_bounds);\n */\n }\n },\n\n /**\n * Remove a track from the view.\n */\n remove_track: function(track, tracks, options) {\n // -- Remove track from view. --\n var track_view = this.circular_views[options.index];\n this.circular_views.splice(options.index, 1);\n track_view.$el.remove();\n\n // Recompute and update track bounds.\n var new_track_bounds = this.get_tracks_bounds();\n _.each(this.circular_views, function(track_view, i) {\n track_view.update_radius_bounds(new_track_bounds[i]);\n });\n },\n\n update_track_bounds: function() {\n // Recompute and update track bounds.\n var new_track_bounds = this.get_tracks_bounds();\n _.each(this.circular_views, function(track_view, i) {\n track_view.update_radius_bounds(new_track_bounds[i]);\n });\n\n // Update chords tracks.\n _.each(this.chords_views, function(track_view) {\n track_view.update_radius_bounds(new_track_bounds[0]);\n });\n }\n });\n\n /**\n * Renders a track in a Circster visualization.\n */\n var CircsterTrackView = Backbone.View.extend({\n tagName: \"g\",\n\n /* ----------------------- Public Methods ------------------------- */\n\n initialize: function(options) {\n this.bg_stroke = \"#ddd\";\n // Fill color when loading data.\n this.loading_bg_fill = \"#ffc\";\n // Fill color when data has been loaded.\n this.bg_fill = \"#ddd\";\n this.total_gap = options.total_gap;\n this.track = options.track;\n this.radius_bounds = options.radius_bounds;\n this.genome = options.genome;\n this.chroms_layout = this._chroms_layout();\n this.data_bounds = [];\n this.scale = 1;\n this.parent_elt = d3.select(this.$el[0]);\n },\n\n /**\n * Get fill color from config.\n */\n get_fill_color: function() {\n var color = this.track.get(\"config\").get_value(\"block_color\");\n if (!color) {\n color = this.track.get(\"config\").get_value(\"color\");\n }\n return color;\n },\n\n /**\n * Render track's data by adding SVG elements to parent.\n */\n render: function() {\n // -- Create track group element. --\n var track_parent_elt = this.parent_elt;\n\n // -- Render background arcs. --\n var genome_arcs = this.chroms_layout,\n arc_gen = d3.svg\n .arc()\n .innerRadius(this.radius_bounds[0])\n .outerRadius(this.radius_bounds[1]),\n // Attach data to group element.\n chroms_elts = track_parent_elt\n .selectAll(\"g\")\n .data(genome_arcs)\n .enter()\n .append(\"svg:g\"),\n // Draw chrom arcs/paths.\n chroms_paths = chroms_elts\n .append(\"path\")\n .attr(\"d\", arc_gen)\n .attr(\"class\", \"chrom-background\")\n .style(\"stroke\", this.bg_stroke)\n .style(\"fill\", this.loading_bg_fill);\n\n // Append titles to paths.\n chroms_paths.append(\"title\").text(function(d) {\n return d.data.chrom;\n });\n\n // -- Render track data and, when track data is rendered, apply preferences and update chrom_elts fill. --\n\n var self = this,\n data_manager = self.track.get(\"data_manager\"),\n // If track has a data manager, get deferred that resolves when data is ready.\n data_ready_deferred = data_manager\n ? data_manager.data_is_ready()\n : true;\n\n // When data is ready, render track.\n $.when(data_ready_deferred).then(function() {\n $.when(\n self._render_data(track_parent_elt)\n ).then(function() {\n chroms_paths.style(\"fill\", self.bg_fill);\n\n // Render labels after data is available so that data attributes are available.\n self.render_labels();\n });\n });\n },\n\n /**\n * Render track labels.\n */\n render_labels: function() {},\n\n /**\n * Update radius bounds.\n */\n update_radius_bounds: function(radius_bounds) {\n // Update bounds.\n this.radius_bounds = radius_bounds;\n\n // -- Update background arcs. --\n var new_d = d3.svg\n .arc()\n .innerRadius(this.radius_bounds[0])\n .outerRadius(this.radius_bounds[1]);\n\n this.parent_elt\n .selectAll(\"g>path.chrom-background\")\n .transition()\n .duration(1000)\n .attr(\"d\", new_d);\n\n this._transition_chrom_data();\n\n this._transition_labels();\n },\n\n /**\n * Update view scale. This fetches more data if scale is increased.\n */\n update_scale: function(new_scale) {\n // -- Update scale and return if new scale is less than old scale. --\n\n var old_scale = this.scale;\n this.scale = new_scale;\n if (new_scale <= old_scale) {\n return;\n }\n\n // -- Scale increased, so render visible data with more detail. --\n\n var self = this,\n utils = new SVGUtils();\n\n // Select all chrom data and filter to operate on those that are visible.\n this.parent_elt\n .selectAll(\"path.chrom-data\")\n .filter(function(d, i) {\n return utils.is_visible(this);\n })\n .each(function(d, i) {\n // -- Now operating on a single path element representing chromosome data. --\n\n var path_elt = d3.select(this),\n chrom = path_elt.attr(\"chrom\"),\n chrom_region = self.genome.get_chrom_region(chrom),\n data_manager = self.track.get(\"data_manager\"),\n data_deferred;\n\n // If can't get more detailed data, return.\n if (\n !data_manager.can_get_more_detailed_data(\n chrom_region\n )\n ) {\n return;\n }\n\n // -- Get more detailed data. --\n data_deferred = self.track\n .get(\"data_manager\")\n .get_more_detailed_data(\n chrom_region,\n \"Coverage\",\n 0,\n new_scale\n );\n\n // When more data is available, use new data to redraw path.\n $.when(data_deferred).then(function(data) {\n // Remove current data path.\n path_elt.remove();\n\n // Update data bounds with new data.\n self._update_data_bounds();\n\n // Find chromosome arc to draw data on.\n var chrom_arc = _.find(self.chroms_layout, function(\n layout\n ) {\n return layout.data.chrom === chrom;\n });\n\n // Add new data path and apply preferences.\n var color = self.get_fill_color();\n self\n ._render_chrom_data(\n self.parent_elt,\n chrom_arc,\n data\n )\n .style(\"stroke\", color)\n .style(\"fill\", color);\n });\n });\n\n return self;\n },\n\n /* ----------------------- Internal Methods ------------------------- */\n\n /**\n * Transitions chrom data to new values (e.g new radius or data bounds).\n */\n _transition_chrom_data: function() {\n var track = this.track,\n chrom_arcs = this.chroms_layout,\n chrom_data_paths = this.parent_elt.selectAll(\n \"g>path.chrom-data\"\n ),\n num_paths = chrom_data_paths[0].length;\n\n if (num_paths > 0) {\n var self = this;\n $.when(\n track\n .get(\"data_manager\")\n .get_genome_wide_data(this.genome)\n ).then(function(genome_wide_data) {\n // Map chrom data to path data, filtering out null values.\n var path_data = _.reject(\n _.map(genome_wide_data, function(chrom_data, i) {\n var rval = null,\n path_fn = self._get_path_function(\n chrom_arcs[i],\n chrom_data\n );\n if (path_fn) {\n rval = path_fn(chrom_data.data);\n }\n return rval;\n }),\n function(p_data) {\n return p_data === null;\n }\n );\n\n // Transition each path for data and color.\n var color = track.get(\"config\").get_value(\"color\");\n chrom_data_paths.each(function(path, index) {\n d3\n .select(this)\n .transition()\n .duration(1000)\n .style(\"stroke\", color)\n .style(\"fill\", color)\n .attr(\"d\", path_data[index]);\n });\n });\n }\n },\n\n /**\n * Transition labels to new values (e.g new radius or data bounds).\n */\n _transition_labels: function() {},\n\n /**\n * Update data bounds. If there are new_bounds, use them; otherwise use\n * default data bounds.\n */\n _update_data_bounds: function(new_bounds) {\n var old_bounds = this.data_bounds;\n this.data_bounds =\n new_bounds ||\n this.get_data_bounds(\n this.track\n .get(\"data_manager\")\n .get_genome_wide_data(this.genome)\n );\n this._transition_chrom_data();\n },\n\n /**\n * Render data as elements attached to svg.\n */\n _render_data: function(svg) {\n var self = this,\n chrom_arcs = this.chroms_layout,\n track = this.track,\n rendered_deferred = $.Deferred();\n\n // When genome-wide data is available, render data.\n $.when(\n track.get(\"data_manager\").get_genome_wide_data(this.genome)\n ).then(function(genome_wide_data) {\n // Set bounds.\n self.data_bounds = self.get_data_bounds(genome_wide_data);\n\n // Set min, max value in config so that they can be adjusted. Make this silent\n // because these attributes are watched for changes and the viz is updated\n // accordingly (set up in initialize). Because we are setting up, we don't want\n // the watch to trigger events here.\n track\n .get(\"config\")\n .set_value(\"min_value\", self.data_bounds[0], {\n silent: true\n });\n track\n .get(\"config\")\n .set_value(\"max_value\", self.data_bounds[1], {\n silent: true\n });\n\n // Merge chroms layout with data.\n var layout_and_data = _.zip(chrom_arcs, genome_wide_data);\n\n // Render each chromosome's data.\n _.each(layout_and_data, function(chrom_info) {\n var chrom_arc = chrom_info[0],\n data = chrom_info[1];\n return self._render_chrom_data(svg, chrom_arc, data);\n });\n\n // Apply prefs to all track data.\n var color = self.get_fill_color();\n self.parent_elt\n .selectAll(\"path.chrom-data\")\n .style(\"stroke\", color)\n .style(\"fill\", color);\n\n rendered_deferred.resolve(svg);\n });\n\n return rendered_deferred;\n },\n\n /**\n * Render a chromosome data and attach elements to svg.\n */\n _render_chrom_data: function(svg, chrom_arc, data) {},\n\n /**\n * Returns data for creating a path for the given data using chrom_arc and data bounds.\n */\n _get_path_function: function(chrom_arc, chrom_data) {},\n\n /**\n * Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle\n * separated by gaps.\n */\n _chroms_layout: function() {\n // Setup chroms layout using pie.\n var chroms_info = this.genome.get_chroms_info(),\n pie_layout = d3.layout\n .pie()\n .value(function(d) {\n return d.len;\n })\n .sort(null),\n init_arcs = pie_layout(chroms_info),\n gap_per_chrom =\n 2 * Math.PI * this.total_gap / chroms_info.length,\n chrom_arcs = _.map(init_arcs, function(arc, index) {\n // For short chroms, endAngle === startAngle.\n var new_endAngle = arc.endAngle - gap_per_chrom;\n arc.endAngle =\n new_endAngle > arc.startAngle\n ? new_endAngle\n : arc.startAngle;\n return arc;\n });\n return chrom_arcs;\n }\n });\n\n /**\n * Render chromosome labels.\n */\n var CircsterChromLabelTrackView = CircsterTrackView.extend({\n initialize: function(options) {\n CircsterTrackView.prototype.initialize.call(this, options);\n // Use a single arc for rendering data.\n this.innerRadius = this.radius_bounds[0];\n this.radius_bounds[0] = this.radius_bounds[1];\n this.bg_stroke = \"#fff\";\n this.bg_fill = \"#fff\";\n\n // Minimum arc distance for labels to be applied.\n this.min_arc_len = 0.05;\n },\n\n /**\n * Render labels.\n */\n _render_data: function(svg) {\n // -- Add chromosome label where it will fit; an alternative labeling mechanism\n // would be nice for small chromosomes. --\n var self = this,\n chrom_arcs = svg.selectAll(\"g\");\n\n chrom_arcs.selectAll(\"path\").attr(\"id\", function(d) {\n return \"label-\" + d.data.chrom;\n });\n\n chrom_arcs\n .append(\"svg:text\")\n .filter(function(d) {\n return d.endAngle - d.startAngle > self.min_arc_len;\n })\n .attr(\"text-anchor\", \"middle\")\n .append(\"svg:textPath\")\n .attr(\"class\", \"chrom-label\")\n .attr(\"xlink:href\", function(d) {\n return \"#label-\" + d.data.chrom;\n })\n .attr(\"startOffset\", \"25%\")\n .text(function(d) {\n return d.data.chrom;\n });\n\n // -- Add ticks to denote chromosome length. --\n\n /** Returns an array of tick angles and labels, given a chrom arc. */\n var chromArcTicks = function(d) {\n var k = (d.endAngle - d.startAngle) / d.value,\n ticks = d3\n .range(0, d.value, 25000000)\n .map(function(v, i) {\n return {\n radius: self.innerRadius,\n angle: v * k + d.startAngle,\n label:\n i === 0\n ? 0\n : i % 3 ? null : self.formatNum(v)\n };\n });\n\n // If there are fewer that 4 ticks, label last tick so that at least one non-zero tick is labeled.\n if (ticks.length < 4) {\n ticks[ticks.length - 1].label = self.formatNum(\n Math.round(\n (ticks[ticks.length - 1].angle - d.startAngle) /\n k\n )\n );\n }\n\n return ticks;\n };\n\n /** Rotate and move text as needed. */\n var textTransform = function(d) {\n return d.angle > Math.PI\n ? \"rotate(180)translate(-16)\"\n : null;\n };\n\n // Filter chroms for only those large enough for display.\n var visibleChroms = _.filter(this.chroms_layout, function(c) {\n return c.endAngle - c.startAngle > self.min_arc_len;\n });\n\n this.drawTicks(\n this.parent_elt,\n visibleChroms,\n chromArcTicks,\n textTransform\n );\n }\n });\n _.extend(CircsterChromLabelTrackView.prototype, UsesTicks);\n\n /**\n * View for quantitative track in Circster.\n */\n var CircsterQuantitativeTrackView = CircsterTrackView.extend({\n initialize: function(options) {\n CircsterTrackView.prototype.initialize.call(this, options);\n\n // When config settings change, update view.\n var track_config = this.track.get(\"config\");\n track_config\n .get(\"min_value\")\n .on(\"change:value\", this._update_min_max, this);\n track_config\n .get(\"max_value\")\n .on(\"change:value\", this._update_min_max, this);\n track_config\n .get(\"color\")\n .on(\"change:value\", this._transition_chrom_data, this);\n },\n\n /**\n * Update track when min and/or max are changed.\n */\n _update_min_max: function() {\n var track_config = this.track.get(\"config\"),\n new_bounds = [\n track_config.get_value(\"min_value\"),\n track_config.get_value(\"max_value\")\n ];\n this._update_data_bounds(new_bounds);\n\n // FIXME: this works to update tick/text bounds, but there's probably a better way to do this\n // by updating the data itself.\n this.parent_elt.selectAll(\".min_max\").text(function(d, i) {\n return new_bounds[i];\n });\n },\n\n /**\n * Returns quantile for an array of numbers.\n */\n _quantile: function(numbers, quantile) {\n numbers.sort(d3.ascending);\n return d3.quantile(numbers, quantile);\n },\n\n /**\n * Renders quantitative data with the form [x, value] and assumes data is equally spaced across\n * chromosome. Attachs a dict with track and chrom name information to DOM element.\n */\n _render_chrom_data: function(svg, chrom_arc, chrom_data) {\n var path_data = this._get_path_function(chrom_arc, chrom_data);\n\n if (!path_data) {\n return null;\n }\n\n // There is path data, so render as path.\n var parent = svg.datum(chrom_data.data),\n path = parent\n .append(\"path\")\n .attr(\"class\", \"chrom-data\")\n .attr(\"chrom\", chrom_arc.data.chrom)\n .attr(\"d\", path_data);\n\n return path;\n },\n\n /**\n * Returns function for creating a path across the chrom arc.\n */\n _get_path_function: function(chrom_arc, chrom_data) {\n // If no chrom data, return null.\n if (\n typeof chrom_data === \"string\" ||\n !chrom_data.data ||\n chrom_data.data.length === 0\n ) {\n return null;\n }\n\n // Radius scaler.\n var radius = d3.scale\n .linear()\n .domain(this.data_bounds)\n .range(this.radius_bounds)\n .clamp(true);\n\n // Scaler for placing data points across arc.\n var angle = d3.scale\n .linear()\n .domain([0, chrom_data.data.length])\n .range([chrom_arc.startAngle, chrom_arc.endAngle]);\n\n // Use line generator to create area.\n var line = d3.svg.line\n .radial()\n .interpolate(\"linear\")\n .radius(function(d) {\n return radius(d[1]);\n })\n .angle(function(d, i) {\n return angle(i);\n });\n\n return d3.svg.area\n .radial()\n .interpolate(line.interpolate())\n .innerRadius(radius(0))\n .outerRadius(line.radius())\n .angle(line.angle());\n },\n\n /**\n * Render track min, max using ticks.\n */\n render_labels: function() {\n var self = this,\n // Keep counter of visible chroms.\n textTransform = function() {\n return \"rotate(90)\";\n };\n\n // FIXME:\n // (1) using min_max class below is needed for _update_min_max, which could be improved.\n // (2) showing config on tick click should be replaced by proper track config icon.\n\n // Draw min, max on first chrom only.\n var ticks = this.drawTicks(\n this.parent_elt,\n [this.chroms_layout[0]],\n this._data_bounds_ticks_fn(),\n textTransform,\n true\n ).classed(\"min_max\", true);\n\n // Show config when ticks are clicked on.\n _.each(ticks, function(tick) {\n $(tick).click(function() {\n var view = new config.ConfigSettingCollectionView({\n collection: self.track.get(\"config\")\n });\n view.render_in_modal(\"Configure Track\");\n });\n });\n\n /*\n // Filter for visible chroms, then for every third chrom so that labels attached to only every\n // third chrom.\n var visibleChroms = _.filter(this.chroms_layout, function(c) { return c.endAngle - c.startAngle > 0.08; }),\n labeledChroms = _.filter(visibleChroms, function(c, i) { return i % 3 === 0; });\n this.drawTicks(this.parent_elt, labeledChroms, this._data_bounds_ticks_fn(), textTransform, true);\n */\n },\n\n /**\n * Transition labels to new values (e.g new radius or data bounds).\n */\n _transition_labels: function() {\n // FIXME: (a) pull out function for getting labeled chroms? and (b) function used in transition below\n // is copied from UseTicks mixin, so pull out and make generally available.\n\n // If there are no data bounds, nothing to transition.\n if (this.data_bounds.length === 0) {\n return;\n }\n\n // Transition labels to new radius bounds.\n var self = this,\n visibleChroms = _.filter(this.chroms_layout, function(c) {\n return c.endAngle - c.startAngle > 0.08;\n }),\n labeledChroms = _.filter(visibleChroms, function(c, i) {\n return i % 3 === 0;\n }),\n new_data = _.flatten(\n _.map(labeledChroms, function(c) {\n return self._data_bounds_ticks_fn()(c);\n })\n );\n this.parent_elt\n .selectAll(\"g.tick\")\n .data(new_data)\n .transition()\n .attr(\"transform\", function(d) {\n return (\n \"rotate(\" +\n (d.angle * 180 / Math.PI - 90) +\n \")\" +\n \"translate(\" +\n d.radius +\n \",0)\"\n );\n });\n },\n\n /**\n * Get function for locating data bounds ticks.\n */\n _data_bounds_ticks_fn: function() {\n // Closure vars.\n var self = this;\n visibleChroms = 0;\n\n // Return function for locating ticks based on chrom arc data.\n return function(d) {\n // Set up data to display min, max ticks.\n return [\n {\n radius: self.radius_bounds[0],\n angle: d.startAngle,\n label: self.formatNum(self.data_bounds[0])\n },\n {\n radius: self.radius_bounds[1],\n angle: d.startAngle,\n label: self.formatNum(self.data_bounds[1])\n }\n ];\n };\n },\n\n /**\n * Returns an array with two values denoting the minimum and maximum\n * values for the track.\n */\n get_data_bounds: function(data) {}\n });\n _.extend(CircsterQuantitativeTrackView.prototype, UsesTicks);\n\n /**\n * Bigwig track view in Circster.\n */\n var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({\n get_data_bounds: function(data) {\n // Set max across dataset by extracting all values, flattening them into a\n // single array, and getting third quartile.\n var values = _.flatten(\n _.map(data, function(d) {\n if (d) {\n // Each data point has the form [position, value], so return all values.\n return _.map(d.data, function(p) {\n // Null is used for a lack of data; resolve null to 0 for comparison.\n return parseInt(p[1], 10) || 0;\n });\n } else {\n return 0;\n }\n })\n );\n\n // For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0\n // for sparsely populated data, so use max in that case.\n return [\n _.min(values),\n this._quantile(values, 0.98) || _.max(values)\n ];\n }\n });\n\n /**\n * Chromosome interactions track view in Circster.\n */\n var CircsterChromInteractionsTrackView = CircsterTrackView.extend({\n render: function() {\n var self = this;\n\n // When data is ready, render track.\n $.when(\n self.track.get(\"data_manager\").data_is_ready()\n ).then(function() {\n // When data has been fetched, render track.\n $.when(\n self.track\n .get(\"data_manager\")\n .get_genome_wide_data(self.genome)\n ).then(function(genome_wide_data) {\n var chord_data = [],\n chroms_info = self.genome.get_chroms_info();\n // Convert chromosome data into chord data.\n _.each(genome_wide_data, function(chrom_data, index) {\n // Map each interaction into chord data.\n var cur_chrom = chroms_info[index].chrom;\n var chrom_chord_data = _.map(\n chrom_data.data,\n function(datum) {\n // Each datum is an interaction/chord.\n var source_angle = self._get_region_angle(\n cur_chrom,\n datum[1]\n ),\n target_angle = self._get_region_angle(\n datum[3],\n datum[4]\n );\n return {\n source: {\n startAngle: source_angle,\n endAngle: source_angle + 0.01\n },\n target: {\n startAngle: target_angle,\n endAngle: target_angle + 0.01\n }\n };\n }\n );\n\n chord_data = chord_data.concat(chrom_chord_data);\n });\n\n self.parent_elt\n .append(\"g\")\n .attr(\"class\", \"chord\")\n .selectAll(\"path\")\n .data(chord_data)\n .enter()\n .append(\"path\")\n .style(\"fill\", self.get_fill_color())\n .attr(\n \"d\",\n d3.svg.chord().radius(self.radius_bounds[0])\n )\n .style(\"opacity\", 1);\n });\n });\n },\n\n update_radius_bounds: function(radius_bounds) {\n this.radius_bounds = radius_bounds;\n this.parent_elt\n .selectAll(\"path\")\n .transition()\n .attr(\"d\", d3.svg.chord().radius(this.radius_bounds[0]));\n },\n\n /**\n * Returns radians for a genomic position.\n */\n _get_region_angle: function(chrom, position) {\n // Find chrom angle data\n var chrom_angle_data = _.find(this.chroms_layout, function(\n chrom_layout\n ) {\n return chrom_layout.data.chrom === chrom;\n });\n\n // Return angle at position.\n return (\n chrom_angle_data.endAngle -\n (chrom_angle_data.endAngle - chrom_angle_data.startAngle) *\n (chrom_angle_data.data.len - position) /\n chrom_angle_data.data.len\n );\n }\n });\n\n // circster app loader\n var Circster = Backbone.View.extend({\n initialize: function() {\n // -- Configure visualization --\n var genome = new visualization.Genome(galaxy_config.app.genome),\n vis = new visualization.GenomeVisualization(\n galaxy_config.app.viz_config\n );\n\n // Add Circster-specific config options.\n vis.get(\"config\").add([\n {\n key: \"arc_dataset_height\",\n label: \"Arc Dataset Height\",\n type: \"int\",\n value: 25,\n view: \"circster\"\n },\n {\n key: \"track_gap\",\n label: \"Gap Between Tracks\",\n type: \"int\",\n value: 5,\n view: \"circster\"\n },\n {\n key: \"total_gap\",\n label: \"Gap [0-1]\",\n type: \"float\",\n value: 0.4,\n view: \"circster\",\n hidden: true\n }\n ]);\n\n var viz_view = new CircsterView({\n // view pane\n el: $(\"#center .unified-panel-body\"),\n genome: genome,\n model: vis\n });\n\n // Render vizualization\n viz_view.render();\n\n // setup title\n $(\"#center .unified-panel-header-inner\").append(\n galaxy_config.app.viz_config.title +\n \" \" +\n galaxy_config.app.viz_config.dbkey\n );\n\n // setup menu\n var menu = mod_icon_btn.create_icon_buttons_menu(\n [\n {\n icon_class: \"plus-button\",\n title: \"Add tracks\",\n on_click: function() {\n visualization.select_datasets(\n { dbkey: vis.get(\"dbkey\") },\n function(tracks) {\n vis.add_tracks(tracks);\n }\n );\n }\n },\n {\n icon_class: \"gear\",\n title: \"Settings\",\n on_click: function() {\n var view = new config.ConfigSettingCollectionView(\n {\n collection: vis.get(\"config\")\n }\n );\n view.render_in_modal(\"Configure Visualization\");\n }\n },\n {\n icon_class: \"disk--arrow\",\n title: \"Save\",\n on_click: function() {\n // show saving dialog box\n Galaxy.modal.show({\n title: \"Saving...\",\n body: \"progress\"\n });\n\n // send to server\n $.ajax({\n url: Galaxy.root + \"visualization/save\",\n type: \"POST\",\n dataType: \"json\",\n data: {\n id: vis.get(\"vis_id\"),\n title: vis.get(\"title\"),\n dbkey: vis.get(\"dbkey\"),\n type: \"trackster\",\n vis_json: JSON.stringify(vis)\n }\n })\n .success(function(vis_info) {\n Galaxy.modal.hide();\n vis.set(\"vis_id\", vis_info.vis_id);\n })\n .error(function() {\n // show dialog\n Galaxy.modal.show({\n title: \"Could Not Save\",\n body:\n \"Could not save visualization. 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load required libraries\nrequire([\"utils/utils\"], function(mod_utils) {\n // load css\n mod_utils.cssLoadFile(\"static/style/circster.css\");\n});\n\ndefine(\n [\n \"libs/underscore\",\n \"libs/d3\",\n \"viz/visualization\",\n \"utils/config\",\n \"mvc/ui/icon-button\",\n \"libs/farbtastic\"\n ],\n function(_, d3, visualization, config, mod_icon_btn) {\n /**\n * Utility class for working with SVG.\n */\n var SVGUtils = Backbone.Model.extend({\n /**\n * Returns true if element is visible.\n */\n is_visible: function(svg_elt, svg) {\n var eltBRect = svg_elt.getBoundingClientRect(),\n svgBRect = $(\"svg\")[0].getBoundingClientRect();\n\n if (\n // To the left of screen?\n eltBRect.right < 0 ||\n // To the right of screen?\n eltBRect.left > svgBRect.right ||\n // Above screen?\n eltBRect.bottom < 0 ||\n // Below screen?\n eltBRect.top > svgBRect.bottom\n ) {\n return false;\n }\n return true;\n }\n });\n\n /**\n * Mixin for using ticks.\n */\n var UsesTicks = {\n drawTicks: function(\n parent_elt,\n data,\n dataHandler,\n textTransform,\n horizontal\n ) {\n // Set up group elements for chroms and for each tick.\n var ticks = parent_elt\n .append(\"g\")\n .selectAll(\"g\")\n .data(data)\n .enter()\n .append(\"g\")\n .selectAll(\"g\")\n .data(dataHandler)\n .enter()\n .append(\"g\")\n .attr(\"class\", \"tick\")\n .attr(\"transform\", function(d) {\n return (\n \"rotate(\" +\n (d.angle * 180 / Math.PI - 90) +\n \")\" +\n \"translate(\" +\n d.radius +\n \",0)\"\n );\n });\n\n // Add line + text for ticks.\n var tick_coords = [],\n text_coords = [],\n text_anchor = function(d) {\n return d.angle > Math.PI ? \"end\" : null;\n };\n if (horizontal) {\n tick_coords = [0, 0, 0, -4];\n text_coords = [4, 0, \"\", \".35em\"];\n text_anchor = null;\n } else {\n tick_coords = [1, 0, 4, 0];\n text_coords = [0, 4, \".35em\", \"\"];\n }\n\n ticks\n .append(\"line\")\n .attr(\"x1\", tick_coords[0])\n .attr(\"y1\", tick_coords[1])\n .attr(\"x2\", tick_coords[2])\n .attr(\"y1\", tick_coords[3])\n .style(\"stroke\", \"#000\");\n\n return ticks\n .append(\"text\")\n .attr(\"x\", text_coords[0])\n .attr(\"y\", text_coords[1])\n .attr(\"dx\", text_coords[2])\n .attr(\"dy\", text_coords[3])\n .attr(\"text-anchor\", text_anchor)\n .attr(\"transform\", textTransform)\n .text(function(d) {\n return d.label;\n });\n },\n\n /**\n * Format number for display at a tick.\n */\n formatNum: function(num, sigDigits) {\n // Use default of 2 sig. digits.\n if (sigDigits === undefined) sigDigits = 2;\n\n // Verify input number\n if (num === null) return null;\n\n // Calculate return value\n var rval = null;\n if (Math.abs(num) < 1) {\n rval = num.toPrecision(sigDigits);\n } else {\n // Use round to turn string from toPrecision() back into a number.\n var roundedNum = Math.round(num.toPrecision(sigDigits));\n\n // Use abbreviations.\n num = Math.abs(num);\n if (num < 1000) {\n rval = roundedNum;\n } else if (num < 1000000) {\n // Use K.\n rval =\n Math.round(\n (roundedNum / 1000).toPrecision(3)\n ).toFixed(0) + \"K\";\n } else if (num < 1000000000) {\n // Use M.\n rval =\n Math.round(\n (roundedNum / 1000000).toPrecision(3)\n ).toFixed(0) + \"M\";\n }\n }\n\n return rval;\n }\n };\n\n /**\n * A label track.\n */\n var CircsterLabelTrack = Backbone.Model.extend({});\n\n /**\n * Renders a full circster visualization.\n */\n var CircsterView = Backbone.View.extend({\n className: \"circster\",\n\n initialize: function(options) {\n this.genome = options.genome;\n this.label_arc_height = 50;\n this.scale = 1;\n this.circular_views = null;\n this.chords_views = null;\n\n // When tracks added to/removed from model, update view.\n this.model.get(\"drawables\").on(\"add\", this.add_track, this);\n this.model\n .get(\"drawables\")\n .on(\"remove\", this.remove_track, this);\n\n // When config settings change, update view.\n var vis_config = this.model.get(\"config\");\n vis_config\n .get(\"arc_dataset_height\")\n .on(\"change:value\", this.update_track_bounds, this);\n vis_config\n .get(\"track_gap\")\n .on(\"change:value\", this.update_track_bounds, this);\n },\n\n // HACKs: using track_type for circular/chord distinction in the functions below for now.\n\n /**\n * Returns tracks to be rendered using circular view.\n */\n get_circular_tracks: function() {\n return this.model.get(\"drawables\").filter(function(track) {\n return track.get(\"track_type\") !== \"DiagonalHeatmapTrack\";\n });\n },\n\n /**\n * Returns tracks to be rendered using chords view.\n */\n get_chord_tracks: function() {\n return this.model.get(\"drawables\").filter(function(track) {\n return track.get(\"track_type\") === \"DiagonalHeatmapTrack\";\n });\n },\n\n /**\n * Returns a list of circular tracks' radius bounds.\n */\n get_tracks_bounds: function() {\n var circular_tracks = this.get_circular_tracks(),\n dataset_arc_height = this.model\n .get(\"config\")\n .get_value(\"arc_dataset_height\"),\n track_gap = this.model.get(\"config\").get_value(\"track_gap\"),\n // Subtract 20 to make sure chrom labels are on screen.\n min_dimension =\n Math.min(this.$el.width(), this.$el.height()) - 20,\n // Compute radius start based on model, will be centered\n // and fit entirely inside element by default.\n radius_start =\n min_dimension / 2 -\n circular_tracks.length *\n (dataset_arc_height + track_gap) +\n // Add track_gap back in because no gap is needed for last track.\n track_gap -\n this.label_arc_height,\n // Compute range of track starting radii.\n tracks_start_radii = d3.range(\n radius_start,\n min_dimension / 2,\n dataset_arc_height + track_gap\n );\n\n // Map from track start to bounds.\n var self = this;\n return _.map(tracks_start_radii, function(radius) {\n return [radius, radius + dataset_arc_height];\n });\n },\n\n /**\n * Renders circular tracks, chord tracks, and label tracks.\n */\n render: function() {\n var self = this,\n width = self.$el.width(),\n height = self.$el.height(),\n circular_tracks = this.get_circular_tracks(),\n chords_tracks = this.get_chord_tracks(),\n total_gap = self.model.get(\"config\").get_value(\"total_gap\"),\n tracks_bounds = this.get_tracks_bounds(),\n // Set up SVG element.\n svg = d3\n .select(self.$el[0])\n .append(\"svg\")\n .attr(\"width\", width)\n .attr(\"height\", height)\n .attr(\"pointer-events\", \"all\")\n // Set up zooming, dragging.\n .append(\"svg:g\")\n .call(\n d3.behavior.zoom().on(\"zoom\", function() {\n // Do zoom, drag.\n var scale = d3.event.scale;\n svg.attr(\n \"transform\",\n \"translate(\" +\n d3.event.translate +\n \")\" +\n \" scale(\" +\n scale +\n \")\"\n );\n\n // Propagate scale changes to views.\n if (self.scale !== scale) {\n // Use timeout to wait for zooming/dragging to stop before rendering more detail.\n if (self.zoom_drag_timeout) {\n clearTimeout(self.zoom_drag_timeout);\n }\n self.zoom_drag_timeout = setTimeout(\n function() {\n // Render more detail in tracks' visible elements.\n // FIXME: do not do this right now; it is not fully implemented--e.g. data bounds\n // are not updated when new data is fetched--and fetching more detailed quantitative\n // data is not that useful.\n /*\n _.each(self.circular_views, function(view) {\n view.update_scale(scale);\n });\n */\n },\n 400\n );\n }\n })\n )\n .attr(\n \"transform\",\n \"translate(\" + width / 2 + \",\" + height / 2 + \")\"\n )\n .append(\"svg:g\")\n .attr(\"class\", \"tracks\");\n\n // -- Render circular tracks. --\n\n // Create a view for each track in the visualization and render.\n this.circular_views = circular_tracks.map(function(\n track,\n index\n ) {\n var view = new CircsterBigWigTrackView({\n el: svg.append(\"g\")[0],\n track: track,\n radius_bounds: tracks_bounds[index],\n genome: self.genome,\n total_gap: total_gap\n });\n\n view.render();\n\n return view;\n });\n\n // -- Render chords tracks. --\n\n this.chords_views = chords_tracks.map(function(track) {\n var view = new CircsterChromInteractionsTrackView({\n el: svg.append(\"g\")[0],\n track: track,\n radius_bounds: tracks_bounds[0],\n genome: self.genome,\n total_gap: total_gap\n });\n\n view.render();\n\n return view;\n });\n\n // -- Render label track. --\n\n // Track bounds are:\n // (a) outer radius of last circular track;\n // (b)\n var outermost_radius = this.circular_views[\n this.circular_views.length - 1\n ].radius_bounds[1],\n track_bounds = [\n outermost_radius,\n outermost_radius + this.label_arc_height\n ];\n this.label_track_view = new CircsterChromLabelTrackView({\n el: svg.append(\"g\")[0],\n track: new CircsterLabelTrack(),\n radius_bounds: track_bounds,\n genome: self.genome,\n total_gap: total_gap\n });\n\n this.label_track_view.render();\n },\n\n /**\n * Render a single track on the outside of the current visualization.\n */\n add_track: function(new_track) {\n var total_gap = this.model.get(\"config\").get_value(\"total_gap\");\n\n if (new_track.get(\"track_type\") === \"DiagonalHeatmapTrack\") {\n // Added chords track.\n var innermost_radius_bounds = this.circular_views[0]\n .radius_bounds,\n new_view = new CircsterChromInteractionsTrackView({\n el: d3.select(\"g.tracks\").append(\"g\")[0],\n track: new_track,\n radius_bounds: innermost_radius_bounds,\n genome: this.genome,\n total_gap: total_gap\n });\n new_view.render();\n this.chords_views.push(new_view);\n } else {\n // Added circular track.\n\n // Recompute and update circular track bounds.\n var new_track_bounds = this.get_tracks_bounds();\n _.each(this.circular_views, function(track_view, i) {\n track_view.update_radius_bounds(new_track_bounds[i]);\n });\n\n // Update chords tracks.\n _.each(this.chords_views, function(track_view) {\n track_view.update_radius_bounds(new_track_bounds[0]);\n });\n\n // Render new track.\n var track_index = this.circular_views.length,\n track_view = new CircsterBigWigTrackView({\n el: d3.select(\"g.tracks\").append(\"g\")[0],\n track: new_track,\n radius_bounds: new_track_bounds[track_index],\n genome: this.genome,\n total_gap: total_gap\n });\n track_view.render();\n this.circular_views.push(track_view);\n\n // Update label track.\n /*\n FIXME: should never have to update label track because vis always expands to fit area\n within label track.\n var track_bounds = new_track_bounds[ new_track_bounds.length-1 ];\n track_bounds[1] = track_bounds[0];\n this.label_track_view.update_radius_bounds(track_bounds);\n */\n }\n },\n\n /**\n * Remove a track from the view.\n */\n remove_track: function(track, tracks, options) {\n // -- Remove track from view. --\n var track_view = this.circular_views[options.index];\n this.circular_views.splice(options.index, 1);\n track_view.$el.remove();\n\n // Recompute and update track bounds.\n var new_track_bounds = this.get_tracks_bounds();\n _.each(this.circular_views, function(track_view, i) {\n track_view.update_radius_bounds(new_track_bounds[i]);\n });\n },\n\n update_track_bounds: function() {\n // Recompute and update track bounds.\n var new_track_bounds = this.get_tracks_bounds();\n _.each(this.circular_views, function(track_view, i) {\n track_view.update_radius_bounds(new_track_bounds[i]);\n });\n\n // Update chords tracks.\n _.each(this.chords_views, function(track_view) {\n track_view.update_radius_bounds(new_track_bounds[0]);\n });\n }\n });\n\n /**\n * Renders a track in a Circster visualization.\n */\n var CircsterTrackView = Backbone.View.extend({\n tagName: \"g\",\n\n /* ----------------------- Public Methods ------------------------- */\n\n initialize: function(options) {\n this.bg_stroke = \"#ddd\";\n // Fill color when loading data.\n this.loading_bg_fill = \"#ffc\";\n // Fill color when data has been loaded.\n this.bg_fill = \"#ddd\";\n this.total_gap = options.total_gap;\n this.track = options.track;\n this.radius_bounds = options.radius_bounds;\n this.genome = options.genome;\n this.chroms_layout = this._chroms_layout();\n this.data_bounds = [];\n this.scale = 1;\n this.parent_elt = d3.select(this.$el[0]);\n },\n\n /**\n * Get fill color from config.\n */\n get_fill_color: function() {\n var color = this.track.get(\"config\").get_value(\"block_color\");\n if (!color) {\n color = this.track.get(\"config\").get_value(\"color\");\n }\n return color;\n },\n\n /**\n * Render track's data by adding SVG elements to parent.\n */\n render: function() {\n // -- Create track group element. --\n var track_parent_elt = this.parent_elt;\n\n // -- Render background arcs. --\n var genome_arcs = this.chroms_layout,\n arc_gen = d3.svg\n .arc()\n .innerRadius(this.radius_bounds[0])\n .outerRadius(this.radius_bounds[1]),\n // Attach data to group element.\n chroms_elts = track_parent_elt\n .selectAll(\"g\")\n .data(genome_arcs)\n .enter()\n .append(\"svg:g\"),\n // Draw chrom arcs/paths.\n chroms_paths = chroms_elts\n .append(\"path\")\n .attr(\"d\", arc_gen)\n .attr(\"class\", \"chrom-background\")\n .style(\"stroke\", this.bg_stroke)\n .style(\"fill\", this.loading_bg_fill);\n\n // Append titles to paths.\n chroms_paths.append(\"title\").text(function(d) {\n return d.data.chrom;\n });\n\n // -- Render track data and, when track data is rendered, apply preferences and update chrom_elts fill. --\n\n var self = this,\n data_manager = self.track.get(\"data_manager\"),\n // If track has a data manager, get deferred that resolves when data is ready.\n data_ready_deferred = data_manager\n ? data_manager.data_is_ready()\n : true;\n\n // When data is ready, render track.\n $.when(data_ready_deferred).then(function() {\n $.when(\n self._render_data(track_parent_elt)\n ).then(function() {\n chroms_paths.style(\"fill\", self.bg_fill);\n\n // Render labels after data is available so that data attributes are available.\n self.render_labels();\n });\n });\n },\n\n /**\n * Render track labels.\n */\n render_labels: function() {},\n\n /**\n * Update radius bounds.\n */\n update_radius_bounds: function(radius_bounds) {\n // Update bounds.\n this.radius_bounds = radius_bounds;\n\n // -- Update background arcs. --\n var new_d = d3.svg\n .arc()\n .innerRadius(this.radius_bounds[0])\n .outerRadius(this.radius_bounds[1]);\n\n this.parent_elt\n .selectAll(\"g>path.chrom-background\")\n .transition()\n .duration(1000)\n .attr(\"d\", new_d);\n\n this._transition_chrom_data();\n\n this._transition_labels();\n },\n\n /**\n * Update view scale. This fetches more data if scale is increased.\n */\n update_scale: function(new_scale) {\n // -- Update scale and return if new scale is less than old scale. --\n\n var old_scale = this.scale;\n this.scale = new_scale;\n if (new_scale <= old_scale) {\n return;\n }\n\n // -- Scale increased, so render visible data with more detail. --\n\n var self = this,\n utils = new SVGUtils();\n\n // Select all chrom data and filter to operate on those that are visible.\n this.parent_elt\n .selectAll(\"path.chrom-data\")\n .filter(function(d, i) {\n return utils.is_visible(this);\n })\n .each(function(d, i) {\n // -- Now operating on a single path element representing chromosome data. --\n\n var path_elt = d3.select(this),\n chrom = path_elt.attr(\"chrom\"),\n chrom_region = self.genome.get_chrom_region(chrom),\n data_manager = self.track.get(\"data_manager\"),\n data_deferred;\n\n // If can't get more detailed data, return.\n if (\n !data_manager.can_get_more_detailed_data(\n chrom_region\n )\n ) {\n return;\n }\n\n // -- Get more detailed data. --\n data_deferred = self.track\n .get(\"data_manager\")\n .get_more_detailed_data(\n chrom_region,\n \"Coverage\",\n 0,\n new_scale\n );\n\n // When more data is available, use new data to redraw path.\n $.when(data_deferred).then(function(data) {\n // Remove current data path.\n path_elt.remove();\n\n // Update data bounds with new data.\n self._update_data_bounds();\n\n // Find chromosome arc to draw data on.\n var chrom_arc = _.find(self.chroms_layout, function(\n layout\n ) {\n return layout.data.chrom === chrom;\n });\n\n // Add new data path and apply preferences.\n var color = self.get_fill_color();\n self\n ._render_chrom_data(\n self.parent_elt,\n chrom_arc,\n data\n )\n .style(\"stroke\", color)\n .style(\"fill\", color);\n });\n });\n\n return self;\n },\n\n /* ----------------------- Internal Methods ------------------------- */\n\n /**\n * Transitions chrom data to new values (e.g new radius or data bounds).\n */\n _transition_chrom_data: function() {\n var track = this.track,\n chrom_arcs = this.chroms_layout,\n chrom_data_paths = this.parent_elt.selectAll(\n \"g>path.chrom-data\"\n ),\n num_paths = chrom_data_paths[0].length;\n\n if (num_paths > 0) {\n var self = this;\n $.when(\n track\n .get(\"data_manager\")\n .get_genome_wide_data(this.genome)\n ).then(function(genome_wide_data) {\n // Map chrom data to path data, filtering out null values.\n var path_data = _.reject(\n _.map(genome_wide_data, function(chrom_data, i) {\n var rval = null,\n path_fn = self._get_path_function(\n chrom_arcs[i],\n chrom_data\n );\n if (path_fn) {\n rval = path_fn(chrom_data.data);\n }\n return rval;\n }),\n function(p_data) {\n return p_data === null;\n }\n );\n\n // Transition each path for data and color.\n var color = track.get(\"config\").get_value(\"color\");\n chrom_data_paths.each(function(path, index) {\n d3\n .select(this)\n .transition()\n .duration(1000)\n .style(\"stroke\", color)\n .style(\"fill\", color)\n .attr(\"d\", path_data[index]);\n });\n });\n }\n },\n\n /**\n * Transition labels to new values (e.g new radius or data bounds).\n */\n _transition_labels: function() {},\n\n /**\n * Update data bounds. If there are new_bounds, use them; otherwise use\n * default data bounds.\n */\n _update_data_bounds: function(new_bounds) {\n var old_bounds = this.data_bounds;\n this.data_bounds =\n new_bounds ||\n this.get_data_bounds(\n this.track\n .get(\"data_manager\")\n .get_genome_wide_data(this.genome)\n );\n this._transition_chrom_data();\n },\n\n /**\n * Render data as elements attached to svg.\n */\n _render_data: function(svg) {\n var self = this,\n chrom_arcs = this.chroms_layout,\n track = this.track,\n rendered_deferred = $.Deferred();\n\n // When genome-wide data is available, render data.\n $.when(\n track.get(\"data_manager\").get_genome_wide_data(this.genome)\n ).then(function(genome_wide_data) {\n // Set bounds.\n self.data_bounds = self.get_data_bounds(genome_wide_data);\n\n // Set min, max value in config so that they can be adjusted. Make this silent\n // because these attributes are watched for changes and the viz is updated\n // accordingly (set up in initialize). Because we are setting up, we don't want\n // the watch to trigger events here.\n track\n .get(\"config\")\n .set_value(\"min_value\", self.data_bounds[0], {\n silent: true\n });\n track\n .get(\"config\")\n .set_value(\"max_value\", self.data_bounds[1], {\n silent: true\n });\n\n // Merge chroms layout with data.\n var layout_and_data = _.zip(chrom_arcs, genome_wide_data);\n\n // Render each chromosome's data.\n _.each(layout_and_data, function(chrom_info) {\n var chrom_arc = chrom_info[0],\n data = chrom_info[1];\n return self._render_chrom_data(svg, chrom_arc, data);\n });\n\n // Apply prefs to all track data.\n var color = self.get_fill_color();\n self.parent_elt\n .selectAll(\"path.chrom-data\")\n .style(\"stroke\", color)\n .style(\"fill\", color);\n\n rendered_deferred.resolve(svg);\n });\n\n return rendered_deferred;\n },\n\n /**\n * Render a chromosome data and attach elements to svg.\n */\n _render_chrom_data: function(svg, chrom_arc, data) {},\n\n /**\n * Returns data for creating a path for the given data using chrom_arc and data bounds.\n */\n _get_path_function: function(chrom_arc, chrom_data) {},\n\n /**\n * Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle\n * separated by gaps.\n */\n _chroms_layout: function() {\n // Setup chroms layout using pie.\n var chroms_info = this.genome.get_chroms_info(),\n pie_layout = d3.layout\n .pie()\n .value(function(d) {\n return d.len;\n })\n .sort(null),\n init_arcs = pie_layout(chroms_info),\n gap_per_chrom =\n 2 * Math.PI * this.total_gap / chroms_info.length,\n chrom_arcs = _.map(init_arcs, function(arc, index) {\n // For short chroms, endAngle === startAngle.\n var new_endAngle = arc.endAngle - gap_per_chrom;\n arc.endAngle =\n new_endAngle > arc.startAngle\n ? new_endAngle\n : arc.startAngle;\n return arc;\n });\n return chrom_arcs;\n }\n });\n\n /**\n * Render chromosome labels.\n */\n var CircsterChromLabelTrackView = CircsterTrackView.extend({\n initialize: function(options) {\n CircsterTrackView.prototype.initialize.call(this, options);\n // Use a single arc for rendering data.\n this.innerRadius = this.radius_bounds[0];\n this.radius_bounds[0] = this.radius_bounds[1];\n this.bg_stroke = \"#fff\";\n this.bg_fill = \"#fff\";\n\n // Minimum arc distance for labels to be applied.\n this.min_arc_len = 0.05;\n },\n\n /**\n * Render labels.\n */\n _render_data: function(svg) {\n // -- Add chromosome label where it will fit; an alternative labeling mechanism\n // would be nice for small chromosomes. --\n var self = this,\n chrom_arcs = svg.selectAll(\"g\");\n\n chrom_arcs.selectAll(\"path\").attr(\"id\", function(d) {\n return \"label-\" + d.data.chrom;\n });\n\n chrom_arcs\n .append(\"svg:text\")\n .filter(function(d) {\n return d.endAngle - d.startAngle > self.min_arc_len;\n })\n .attr(\"text-anchor\", \"middle\")\n .append(\"svg:textPath\")\n .attr(\"class\", \"chrom-label\")\n .attr(\"xlink:href\", function(d) {\n return \"#label-\" + d.data.chrom;\n })\n .attr(\"startOffset\", \"25%\")\n .text(function(d) {\n return d.data.chrom;\n });\n\n // -- Add ticks to denote chromosome length. --\n\n /** Returns an array of tick angles and labels, given a chrom arc. */\n var chromArcTicks = function(d) {\n var k = (d.endAngle - d.startAngle) / d.value,\n ticks = d3\n .range(0, d.value, 25000000)\n .map(function(v, i) {\n return {\n radius: self.innerRadius,\n angle: v * k + d.startAngle,\n label:\n i === 0\n ? 0\n : i % 3 ? null : self.formatNum(v)\n };\n });\n\n // If there are fewer that 4 ticks, label last tick so that at least one non-zero tick is labeled.\n if (ticks.length < 4) {\n ticks[ticks.length - 1].label = self.formatNum(\n Math.round(\n (ticks[ticks.length - 1].angle - d.startAngle) /\n k\n )\n );\n }\n\n return ticks;\n };\n\n /** Rotate and move text as needed. */\n var textTransform = function(d) {\n return d.angle > Math.PI\n ? \"rotate(180)translate(-16)\"\n : null;\n };\n\n // Filter chroms for only those large enough for display.\n var visibleChroms = _.filter(this.chroms_layout, function(c) {\n return c.endAngle - c.startAngle > self.min_arc_len;\n });\n\n this.drawTicks(\n this.parent_elt,\n visibleChroms,\n chromArcTicks,\n textTransform\n );\n }\n });\n _.extend(CircsterChromLabelTrackView.prototype, UsesTicks);\n\n /**\n * View for quantitative track in Circster.\n */\n var CircsterQuantitativeTrackView = CircsterTrackView.extend({\n initialize: function(options) {\n CircsterTrackView.prototype.initialize.call(this, options);\n\n // When config settings change, update view.\n var track_config = this.track.get(\"config\");\n track_config\n .get(\"min_value\")\n .on(\"change:value\", this._update_min_max, this);\n track_config\n .get(\"max_value\")\n .on(\"change:value\", this._update_min_max, this);\n track_config\n .get(\"color\")\n .on(\"change:value\", this._transition_chrom_data, this);\n },\n\n /**\n * Update track when min and/or max are changed.\n */\n _update_min_max: function() {\n var track_config = this.track.get(\"config\"),\n new_bounds = [\n track_config.get_value(\"min_value\"),\n track_config.get_value(\"max_value\")\n ];\n this._update_data_bounds(new_bounds);\n\n // FIXME: this works to update tick/text bounds, but there's probably a better way to do this\n // by updating the data itself.\n this.parent_elt.selectAll(\".min_max\").text(function(d, i) {\n return new_bounds[i];\n });\n },\n\n /**\n * Returns quantile for an array of numbers.\n */\n _quantile: function(numbers, quantile) {\n numbers.sort(d3.ascending);\n return d3.quantile(numbers, quantile);\n },\n\n /**\n * Renders quantitative data with the form [x, value] and assumes data is equally spaced across\n * chromosome. Attachs a dict with track and chrom name information to DOM element.\n */\n _render_chrom_data: function(svg, chrom_arc, chrom_data) {\n var path_data = this._get_path_function(chrom_arc, chrom_data);\n\n if (!path_data) {\n return null;\n }\n\n // There is path data, so render as path.\n var parent = svg.datum(chrom_data.data),\n path = parent\n .append(\"path\")\n .attr(\"class\", \"chrom-data\")\n .attr(\"chrom\", chrom_arc.data.chrom)\n .attr(\"d\", path_data);\n\n return path;\n },\n\n /**\n * Returns function for creating a path across the chrom arc.\n */\n _get_path_function: function(chrom_arc, chrom_data) {\n // If no chrom data, return null.\n if (\n typeof chrom_data === \"string\" ||\n !chrom_data.data ||\n chrom_data.data.length === 0\n ) {\n return null;\n }\n\n // Radius scaler.\n var radius = d3.scale\n .linear()\n .domain(this.data_bounds)\n .range(this.radius_bounds)\n .clamp(true);\n\n // Scaler for placing data points across arc.\n var angle = d3.scale\n .linear()\n .domain([0, chrom_data.data.length])\n .range([chrom_arc.startAngle, chrom_arc.endAngle]);\n\n // Use line generator to create area.\n var line = d3.svg.line\n .radial()\n .interpolate(\"linear\")\n .radius(function(d) {\n return radius(d[1]);\n })\n .angle(function(d, i) {\n return angle(i);\n });\n\n return d3.svg.area\n .radial()\n .interpolate(line.interpolate())\n .innerRadius(radius(0))\n .outerRadius(line.radius())\n .angle(line.angle());\n },\n\n /**\n * Render track min, max using ticks.\n */\n render_labels: function() {\n var self = this,\n // Keep counter of visible chroms.\n textTransform = function() {\n return \"rotate(90)\";\n };\n\n // FIXME:\n // (1) using min_max class below is needed for _update_min_max, which could be improved.\n // (2) showing config on tick click should be replaced by proper track config icon.\n\n // Draw min, max on first chrom only.\n var ticks = this.drawTicks(\n this.parent_elt,\n [this.chroms_layout[0]],\n this._data_bounds_ticks_fn(),\n textTransform,\n true\n ).classed(\"min_max\", true);\n\n // Show config when ticks are clicked on.\n _.each(ticks, function(tick) {\n $(tick).click(function() {\n var view = new config.ConfigSettingCollectionView({\n collection: self.track.get(\"config\")\n });\n view.render_in_modal(\"Configure Track\");\n });\n });\n\n /*\n // Filter for visible chroms, then for every third chrom so that labels attached to only every\n // third chrom.\n var visibleChroms = _.filter(this.chroms_layout, function(c) { return c.endAngle - c.startAngle > 0.08; }),\n labeledChroms = _.filter(visibleChroms, function(c, i) { return i % 3 === 0; });\n this.drawTicks(this.parent_elt, labeledChroms, this._data_bounds_ticks_fn(), textTransform, true);\n */\n },\n\n /**\n * Transition labels to new values (e.g new radius or data bounds).\n */\n _transition_labels: function() {\n // FIXME: (a) pull out function for getting labeled chroms? and (b) function used in transition below\n // is copied from UseTicks mixin, so pull out and make generally available.\n\n // If there are no data bounds, nothing to transition.\n if (this.data_bounds.length === 0) {\n return;\n }\n\n // Transition labels to new radius bounds.\n var self = this,\n visibleChroms = _.filter(this.chroms_layout, function(c) {\n return c.endAngle - c.startAngle > 0.08;\n }),\n labeledChroms = _.filter(visibleChroms, function(c, i) {\n return i % 3 === 0;\n }),\n new_data = _.flatten(\n _.map(labeledChroms, function(c) {\n return self._data_bounds_ticks_fn()(c);\n })\n );\n this.parent_elt\n .selectAll(\"g.tick\")\n .data(new_data)\n .transition()\n .attr(\"transform\", function(d) {\n return (\n \"rotate(\" +\n (d.angle * 180 / Math.PI - 90) +\n \")\" +\n \"translate(\" +\n d.radius +\n \",0)\"\n );\n });\n },\n\n /**\n * Get function for locating data bounds ticks.\n */\n _data_bounds_ticks_fn: function() {\n // Closure vars.\n var self = this;\n visibleChroms = 0;\n\n // Return function for locating ticks based on chrom arc data.\n return function(d) {\n // Set up data to display min, max ticks.\n return [\n {\n radius: self.radius_bounds[0],\n angle: d.startAngle,\n label: self.formatNum(self.data_bounds[0])\n },\n {\n radius: self.radius_bounds[1],\n angle: d.startAngle,\n label: self.formatNum(self.data_bounds[1])\n }\n ];\n };\n },\n\n /**\n * Returns an array with two values denoting the minimum and maximum\n * values for the track.\n */\n get_data_bounds: function(data) {}\n });\n _.extend(CircsterQuantitativeTrackView.prototype, UsesTicks);\n\n /**\n * Bigwig track view in Circster.\n */\n var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({\n get_data_bounds: function(data) {\n // Set max across dataset by extracting all values, flattening them into a\n // single array, and getting third quartile.\n var values = _.flatten(\n _.map(data, function(d) {\n if (d) {\n // Each data point has the form [position, value], so return all values.\n return _.map(d.data, function(p) {\n // Null is used for a lack of data; resolve null to 0 for comparison.\n return parseInt(p[1], 10) || 0;\n });\n } else {\n return 0;\n }\n })\n );\n\n // For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0\n // for sparsely populated data, so use max in that case.\n return [\n _.min(values),\n this._quantile(values, 0.98) || _.max(values)\n ];\n }\n });\n\n /**\n * Chromosome interactions track view in Circster.\n */\n var CircsterChromInteractionsTrackView = CircsterTrackView.extend({\n render: function() {\n var self = this;\n\n // When data is ready, render track.\n $.when(\n self.track.get(\"data_manager\").data_is_ready()\n ).then(function() {\n // When data has been fetched, render track.\n $.when(\n self.track\n .get(\"data_manager\")\n .get_genome_wide_data(self.genome)\n ).then(function(genome_wide_data) {\n var chord_data = [],\n chroms_info = self.genome.get_chroms_info();\n // Convert chromosome data into chord data.\n _.each(genome_wide_data, function(chrom_data, index) {\n // Map each interaction into chord data.\n var cur_chrom = chroms_info[index].chrom;\n var chrom_chord_data = _.map(\n chrom_data.data,\n function(datum) {\n // Each datum is an interaction/chord.\n var source_angle = self._get_region_angle(\n cur_chrom,\n datum[1]\n ),\n target_angle = self._get_region_angle(\n datum[3],\n datum[4]\n );\n return {\n source: {\n startAngle: source_angle,\n endAngle: source_angle + 0.01\n },\n target: {\n startAngle: target_angle,\n endAngle: target_angle + 0.01\n }\n };\n }\n );\n\n chord_data = chord_data.concat(chrom_chord_data);\n });\n\n self.parent_elt\n .append(\"g\")\n .attr(\"class\", \"chord\")\n .selectAll(\"path\")\n .data(chord_data)\n .enter()\n .append(\"path\")\n .style(\"fill\", self.get_fill_color())\n .attr(\n \"d\",\n d3.svg.chord().radius(self.radius_bounds[0])\n )\n .style(\"opacity\", 1);\n });\n });\n },\n\n update_radius_bounds: function(radius_bounds) {\n this.radius_bounds = radius_bounds;\n this.parent_elt\n .selectAll(\"path\")\n .transition()\n .attr(\"d\", d3.svg.chord().radius(this.radius_bounds[0]));\n },\n\n /**\n * Returns radians for a genomic position.\n */\n _get_region_angle: function(chrom, position) {\n // Find chrom angle data\n var chrom_angle_data = _.find(this.chroms_layout, function(\n chrom_layout\n ) {\n return chrom_layout.data.chrom === chrom;\n });\n\n // Return angle at position.\n return (\n chrom_angle_data.endAngle -\n (chrom_angle_data.endAngle - chrom_angle_data.startAngle) *\n (chrom_angle_data.data.len - position) /\n chrom_angle_data.data.len\n );\n }\n });\n\n // circster app loader\n var Circster = Backbone.View.extend({\n initialize: function() {\n // -- Configure visualization --\n var genome = new visualization.Genome(galaxy_config.app.genome),\n vis = new visualization.GenomeVisualization(\n galaxy_config.app.viz_config\n );\n\n // Add Circster-specific config options.\n vis.get(\"config\").add([\n {\n key: \"arc_dataset_height\",\n label: \"Arc Dataset Height\",\n type: \"int\",\n value: 25,\n view: \"circster\"\n },\n {\n key: \"track_gap\",\n label: \"Gap Between Tracks\",\n type: \"int\",\n value: 5,\n view: \"circster\"\n },\n {\n key: \"total_gap\",\n label: \"Gap [0-1]\",\n type: \"float\",\n value: 0.4,\n view: \"circster\",\n hidden: true\n }\n ]);\n\n var viz_view = new CircsterView({\n // view pane\n el: $(\"#center .unified-panel-body\"),\n genome: genome,\n model: vis\n });\n\n // Render vizualization\n viz_view.render();\n\n // setup title\n $(\"#center .unified-panel-header-inner\").append(\n galaxy_config.app.viz_config.title +\n \" \" +\n galaxy_config.app.viz_config.dbkey\n );\n\n // setup menu\n var menu = mod_icon_btn.create_icon_buttons_menu(\n [\n {\n icon_class: \"plus-button\",\n title: \"Add tracks\",\n on_click: function() {\n visualization.select_datasets(\n { dbkey: vis.get(\"dbkey\") },\n function(tracks) {\n vis.add_tracks(tracks);\n }\n );\n }\n },\n {\n icon_class: \"gear\",\n title: \"Settings\",\n on_click: function() {\n var view = new config.ConfigSettingCollectionView(\n {\n collection: vis.get(\"config\")\n }\n );\n view.render_in_modal(\"Configure Visualization\");\n }\n },\n {\n icon_class: \"disk--arrow\",\n title: \"Save\",\n on_click: function() {\n // show saving dialog box\n Galaxy.modal.show({\n title: \"Saving...\",\n body: \"progress\"\n });\n\n // send to server\n $.ajax({\n url: Galaxy.root + \"visualization/save\",\n type: \"POST\",\n dataType: \"json\",\n data: {\n id: vis.get(\"vis_id\"),\n title: vis.get(\"title\"),\n dbkey: vis.get(\"dbkey\"),\n type: \"trackster\",\n vis_json: JSON.stringify(vis)\n }\n })\n .success(function(vis_info) {\n Galaxy.modal.hide();\n vis.set(\"vis_id\", vis_info.vis_id);\n })\n .error(function() {\n // show dialog\n Galaxy.modal.show({\n title: \"Could Not Save\",\n body:\n \"Could not save visualization. Please try again later.\",\n buttons: {\n Cancel: function() {\n Galaxy.modal.hide();\n }\n }\n });\n });\n }\n },\n {\n icon_class: \"cross-circle\",\n title: \"Close\",\n on_click: function() {\n window.location =\n Galaxy.root + \"visualizations/list\";\n }\n }\n ],\n { tooltip_config: { placement: \"bottom\" } }\n );\n\n // add menu\n menu.$el.attr(\"style\", \"float: right\");\n $(\"#center .unified-panel-header-inner\").append(menu.$el);\n\n // manual tooltip config because default gravity is S and cannot be changed\n $(\".menu-button\").tooltip({ placement: \"bottom\" });\n }\n });\n\n // Module exports.\n return {\n GalaxyApp: Circster\n };\n }\n);\n"]} \ No newline at end of file diff --git a/static/maps/viz/phyloviz.js.map b/static/maps/viz/phyloviz.js.map index 47787d354e2..09adfa23cf1 100644 --- a/static/maps/viz/phyloviz.js.map +++ b/static/maps/viz/phyloviz.js.map @@ -1 +1 @@ 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[\"libs/d3\", \"viz/visualization\", \"mvc/dataset/data\", \"mvc/ui/icon-button\"],\n function(d3, visualization_mod, data_mod, mod_icon_btn) {\n /**\n * Base class of any menus that takes in user interaction. Contains checking methods.\n */\n var UserMenuBase = Backbone.View.extend({\n className: \"UserMenuBase\",\n\n /**\n * Check if an input value is a number and falls within max min.\n */\n isAcceptableValue: function($inputKey, min, max) {\n //TODO: use better feedback than alert\n var value = $inputKey.val(),\n fieldName =\n $inputKey.attr(\"displayLabel\") ||\n $inputKey.attr(\"id\").replace(\"phyloViz\", \"\");\n\n function isNumeric(n) {\n return !isNaN(parseFloat(n)) && isFinite(n);\n }\n\n if (!isNumeric(value)) {\n alert(fieldName + \" is not a number!\");\n return false;\n }\n\n if (value > max) {\n alert(fieldName + \" is too large.\");\n return false;\n } else if (value < min) {\n alert(fieldName + \" is too small.\");\n return false;\n }\n return true;\n },\n\n /**\n * Check if any user string inputs has illegal characters that json cannot accept\n */\n hasIllegalJsonCharacters: function($inputKey) {\n if ($inputKey.val().search(/\"|'|\\\\/) !== -1) {\n alert(\n \"Named fields cannot contain these illegal characters: \" +\n \"double quote(\\\"), single guote('), or back slash(\\\\). \"\n );\n return true;\n }\n return false;\n }\n });\n\n /**\n * -- Custom Layout call for phyloViz to suit the needs of a phylogenetic tree.\n * -- Specifically: 1) Nodes have a display display of (= evo dist X depth separation) from their parent\n * 2) Nodes must appear in other after they have expand and contracted\n */\n function PhyloTreeLayout() {\n var self = this,\n hierarchy = d3.layout\n .hierarchy()\n .sort(null)\n .value(null),\n height = 360, // ! represents both the layout angle and the height of the layout, in px\n layoutMode = \"Linear\",\n leafHeight = 18, // height of each individual leaf node\n depthSeparation = 200, // separation between nodes of different depth, in px\n leafIndex = 0, // change to recurssive call\n defaultDist = 0.5, // tree defaults to 0.5 dist if no dist is specified\n maxTextWidth = 50; // maximum length of the text labels\n\n self.leafHeight = function(inputLeafHeight) {\n if (typeof inputLeafHeight === \"undefined\") {\n return leafHeight;\n } else {\n leafHeight = inputLeafHeight;\n return self;\n }\n };\n\n self.layoutMode = function(mode) {\n if (typeof mode === \"undefined\") {\n return layoutMode;\n } else {\n layoutMode = mode;\n return self;\n }\n };\n\n // changes the layout angle of the display, which is really changing the height\n self.layoutAngle = function(angle) {\n if (typeof angle === \"undefined\") {\n return height;\n }\n // to use default if the user puts in strange values\n if (isNaN(angle) || angle < 0 || angle > 360) {\n return self;\n } else {\n height = angle;\n return self;\n }\n };\n\n self.separation = function(dist) {\n // changes the dist between the nodes of different depth\n if (typeof dist === \"undefined\") {\n return depthSeparation;\n } else {\n depthSeparation = dist;\n return self;\n }\n };\n\n self.links = function(nodes) {\n // uses d3 native method to generate links. Done.\n return d3.layout.tree().links(nodes);\n };\n\n // -- Custom method for laying out phylogeny tree in a linear fashion\n self.nodes = function(d, i) {\n //TODO: newick and phyloxml return arrays. where should this go (client (here, else), server)?\n if (toString.call(d) === \"[object Array]\") {\n // if d is an array, replate with the first object (newick, phyloxml)\n d = d[0];\n }\n // self is to find the depth of all the nodes, assumes root is passed in\n var _nodes = hierarchy.call(self, d, i),\n nodes = [],\n maxDepth = 0,\n numLeaves = 0;\n //console.debug( JSON.stringify( _nodes, null, 2 ) )\n window._d = d;\n window._nodes = _nodes;\n\n //TODO: remove dbl-touch loop\n // changing from hierarchy's custom format for data to usable format\n _nodes.forEach(function(node) {\n maxDepth = node.depth > maxDepth ? node.depth : maxDepth; //finding max depth of tree\n nodes.push(node);\n });\n // counting the number of leaf nodes and assigning max depth\n // to nodes that do not have children to flush all the leave nodes\n nodes.forEach(function(node) {\n if (!node.children) {\n //&& !node._children\n numLeaves += 1;\n node.depth = maxDepth; // if a leaf has no child it would be assigned max depth\n }\n });\n\n leafHeight =\n layoutMode === \"Circular\" ? height / numLeaves : leafHeight;\n leafIndex = 0;\n layout(nodes[0], maxDepth, leafHeight, null);\n\n return nodes;\n };\n\n /**\n * -- Function with side effect of adding x0, y0 to all child; take in the root as starting point\n * assuming that the leave nodes would be sorted in presented order\n * horizontal(y0) is calculated according to (= evo dist X depth separation) from their parent\n * vertical (x0) - if leave node: find its order in all of the leave node === node.id,\n * then multiply by verticalSeparation\n * - if parent node: is place in the mid point all of its children nodes\n * -- The layout will first calculate the y0 field going towards the leaves, and x0 when returning\n */\n function layout(node, maxDepth, vertSeparation, parent) {\n var children = node.children,\n sumChildVertSeparation = 0;\n\n // calculation of node's dist from parents, going down.\n var dist = node.dist || defaultDist;\n dist = dist > 1 ? 1 : dist; // We constrain all dist to be less than one\n node.dist = dist;\n if (parent !== null) {\n node.y0 = parent.y0 + dist * depthSeparation;\n } else {\n //root node\n node.y0 = maxTextWidth;\n }\n\n // if a node have no children, we will treat it as a leaf and start laying it out first\n if (!children) {\n node.x0 = leafIndex * vertSeparation;\n leafIndex += 1;\n } else {\n // if it has children, we will visit all its children and calculate its position from its children\n children.forEach(function(child) {\n child.parent = node;\n sumChildVertSeparation += layout(\n child,\n maxDepth,\n vertSeparation,\n node\n );\n });\n node.x0 = sumChildVertSeparation / children.length;\n }\n\n // adding properties to the newly created node\n node.x = node.x0;\n node.y = node.y0;\n return node.x0;\n }\n return self;\n }\n\n /**\n * -- PhyloTree Model --\n */\n var PhyloTree = visualization_mod.Visualization.extend({\n defaults: {\n layout: \"Linear\",\n separation: 250, // px dist between nodes of different depth to represent 1 evolutionary until\n leafHeight: 18,\n type: \"phyloviz\", // visualization type\n title: \"Title\",\n scaleFactor: 1,\n translate: [0, 0],\n fontSize: 12, //fontSize of node label\n selectedNode: null,\n nodeAttrChangedTime: 0\n },\n\n initialize: function(options) {\n this.set(\n \"dataset\",\n new data_mod.Dataset({\n id: options.dataset_id\n })\n );\n },\n\n root: {}, // Root has to be its own independent object because it is not part of the viz_config\n\n /**\n * Mechanism to expand or contract a single node. Expanded nodes have a children list, while for\n * contracted nodes the list is stored in _children. Nodes with their children data stored in _children will not\n * have their children rendered.\n */\n toggle: function(d) {\n if (typeof d === \"undefined\") {\n return;\n }\n if (d.children) {\n d._children = d.children;\n d.children = null;\n } else {\n d.children = d._children;\n d._children = null;\n }\n },\n\n /**\n * Contracts the phylotree to a single node by repeatedly calling itself to place all the list\n * of children under _children.\n */\n toggleAll: function(d) {\n if (d.children && d.children.length !== 0) {\n d.children.forEach(this.toggleAll);\n toggle(d);\n }\n },\n\n /**\n * Return the data of the tree. Used for preserving state.\n */\n getData: function() {\n return this.root;\n },\n\n /**\n * Overriding the default save mechanism to do some clean of circular reference of the\n * phyloTree and to include phyloTree in the saved json\n */\n save: function() {\n var root = this.root;\n cleanTree(root);\n //this.set(\"root\", root);\n\n function cleanTree(node) {\n // we need to remove parent to delete circular reference\n delete node.parent;\n\n // removing unnecessary attributes\n if (node._selected) {\n delete node._selected;\n }\n\n if (node.children) {\n node.children.forEach(cleanTree);\n }\n if (node._children) {\n node._children.forEach(cleanTree);\n }\n }\n\n var config = jQuery.extend(true, {}, this.attributes);\n config.selectedNode = null;\n\n show_message(\"Saving to Galaxy\", \"progress\");\n\n return $.ajax({\n url: this.url(),\n type: \"POST\",\n dataType: \"json\",\n data: {\n config: JSON.stringify(config),\n type: \"phyloviz\"\n },\n success: function(res) {\n hide_modal();\n }\n });\n }\n });\n\n // -- Views --\n /**\n * Stores the default variable for setting up the visualization\n */\n var PhylovizLayoutBase = Backbone.View.extend({\n defaults: {\n nodeRadius: 4.5 // radius of each node in the diagram\n },\n\n /**\n * Common initialization in layouts\n */\n stdInit: function(options) {\n var self = this;\n self.model.on(\n \"change:separation change:leafHeight change:fontSize change:nodeAttrChangedTime\",\n self.updateAndRender,\n self\n );\n\n self.vis = options.vis;\n self.i = 0;\n self.maxDepth = -1; // stores the max depth of the tree\n\n self.width = options.width;\n self.height = options.height;\n },\n\n /**\n * Updates the visualization whenever there are changes in the expansion and contraction of nodes\n * AND possibly when the tree is edited.\n */\n updateAndRender: function(source) {\n var vis = d3.select(\".vis\"),\n self = this;\n source = source || self.model.root;\n\n self.renderNodes(source);\n self.renderLinks(source);\n self.addTooltips();\n },\n\n /**\n * Renders the links for the visualization.\n */\n renderLinks: function(source) {\n var self = this;\n var diagonal = self.diagonal;\n var duration = self.duration;\n var layoutMode = self.layoutMode;\n var link = self.vis\n .selectAll(\"g.completeLink\")\n .data(self.tree.links(self.nodes), function(d) {\n return d.target.id;\n });\n\n var calcalateLinePos = function(d) {\n // position of the source node <=> starting location of the line drawn\n d.pos0 = d.source.y0 + \" \" + d.source.x0;\n // position where the line makes a right angle bend\n d.pos1 = d.source.y0 + \" \" + d.target.x0;\n // point where the horizontal line becomes a dotted line\n d.pos2 = d.target.y0 + \" \" + d.target.x0;\n };\n\n var linkEnter = link\n .enter()\n .insert(\"svg:g\", \"g.node\")\n .attr(\"class\", \"completeLink\");\n\n linkEnter\n .append(\"svg:path\")\n .attr(\"class\", \"link\")\n .attr(\"d\", function(d) {\n calcalateLinePos(d);\n return \"M \" + d.pos0 + \" L \" + d.pos1;\n });\n\n var linkUpdate = link.transition().duration(500);\n\n linkUpdate.select(\"path.link\").attr(\"d\", function(d) {\n calcalateLinePos(d);\n return \"M \" + d.pos0 + \" L \" + d.pos1 + \" L \" + d.pos2;\n });\n\n var linkExit = link.exit().remove();\n },\n\n // User Interaction methods below\n\n /**\n * Displays the information for editing\n */\n selectNode: function(node) {\n var self = this;\n d3\n .selectAll(\"g.node\")\n .classed(\"selectedHighlight\", function(d) {\n if (node.id === d.id) {\n if (node._selected) {\n // for de=selecting node.\n delete node._selected;\n return false;\n } else {\n node._selected = true;\n return true;\n }\n }\n return false;\n });\n\n self.model.set(\"selectedNode\", node);\n $(\"#phyloVizSelectedNodeName\").val(node.name);\n $(\"#phyloVizSelectedNodeDist\").val(node.dist);\n $(\"#phyloVizSelectedNodeAnnotation\").val(node.annotation || \"\");\n },\n\n /**\n * Creates bootstrap tooltip for the visualization. Has to be called repeatedly due to newly generated\n * enterNodes\n */\n addTooltips: function() {\n $(\".tooltip\").remove(); //clean up tooltip, just in case its listeners are removed by d3\n $(\".node\")\n .attr(\"data-original-title\", function() {\n var d = this.__data__,\n annotation = d.annotation || \"None\";\n return d\n ? (d.name ? d.name + \"
- Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.\" +\n \"
- Adjust the tree by using parameter inputs to select min, max, and number of samples\" +\n \"
- Run the tool with different settings by clicking on tree nodes\" +\n \"
- Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.\" +\n \"
- Adjust the tree by using parameter inputs to select min, max, and number of samples\" +\n \"
- Run the tool with different settings by clicking on tree nodes\" +\n \"
- a new track to one of your existing, saved Trackster \" +\n \"sessions if they share the genome build: \" +\n (dbkey || \"Not available.\") +\n \" \" +\n \"
- or create a new session with this dataset as the only track \" +\n \"
- a new track to one of your existing, saved Trackster \" +\n \"sessions if they share the genome build: \" +\n (dbkey || \"Not available.\") +\n \" \" +\n \"
- or create a new session with this dataset as the only track \" +\n \"
- No Options. 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Are you sure?":!1,Dataset:!1,Annotation:!1,"This history is empty. Click 'Get Data' on the left tool menu to start":!1,"You must be logged in to create histories":!1,"Unable to purge dataset":!1,"Cannot display datasets removed from disk":!1,"This dataset must finish uploading before it can be viewed":!1,"This dataset is not yet viewable":!1,"View data":!1,Download:!1,"Download dataset":!1,"Additional files":!1,"View details":!1,"This is a new dataset and not all of its data are available yet":!1,"You do not have permission to view this dataset":!1,"The job creating this dataset was cancelled before completion":!1,"This job is waiting to run":!1,"This dataset is currently uploading":!1,"Metadata is being auto-detected":!1,"This job is currently running":!1,'This job is paused. Use the "Resume Paused Jobs" in the history menu to resume':!1,"An error occurred with this dataset":!1,"No data":!1,"An error occurred setting the metadata for this dataset":!1,"There was an error getting the data for this dataset":!1,"This dataset has been deleted and removed from disk":!1,"This dataset has been deleted":!1,"This dataset has been hidden":!1,format:!1,database:!1,"Edit attributes":!1,"Cannot edit attributes of datasets removed from disk":!1,"Undelete dataset to edit attributes":!1,"This dataset must finish uploading before it can be edited":!1,"This dataset is not yet editable":!1,Delete:!1,"Dataset is already deleted":!1,"View or report this error":!1,"Run this job again":!1,Visualize:!1,"Visualize in":!1,"Undelete it":!1,"Permanently remove it from disk":!1,"Unhide it":!1,"You may be able to":!1,"set it manually or retry auto-detection":!1,"Edit dataset tags":!1,"Edit dataset annotation":!1,"Tool Help":!1,"Search Tool Shed":!1,"Monitor installing repositories":!1,"Manage installed tools":!1,"Reset metadata":!1,"Download local tool":!1,"Tool lineage":!1,"Reload a tool's configuration":!1,"Review tool migration stages":!1,"View Tool Error Logs":!1,"Manage Display Whitelist":!1,"Manage Tool Dependencies":!1,Users:!1,Groups:!1,"API keys":!1,"Impersonate a user":!1,Data:!1,Quotas:!1,Roles:!1,"Local data":!1,"Form Definitions":!1,"Enable/Disable Scratchbook":!1,"Show/Hide Scratchbook":!1,Tags:!1,"Edit annotation":!1},__ja:{"Analyze Data":"データ解析",Workflow:"ワークフロー","Shared Data":"共有データ","Data Libraries":"データライブラリ",Histories:"ヒストリー",Workflows:"ワークフロー",Visualizations:"可視化",Pages:"ページ",Visualization:"可視化","New Track Browser":"新しい Track Browser","Saved Visualizations":"保存された可視化","Interactive Environments":"インタラクティブ環境",Admin:"管理者",Help:"ヘルプ",Support:"サポート",Search:"検索","Mailing Lists":"メーリングリスト",Videos:"動画","How to Cite Galaxy":"Galaxy を引用する方法","Interactive Tours":"インタラクティブツアー",User:"ユーザー",Login:"ログイン",Register:"登録","Login or Register":"ログイン/登録",Preferences:"設定","Custom Builds":"カスタムビルド",Logout:"ログアウト","Saved Histories":"保存されたヒストリ","Saved Datasets":"保存されたデータセット","Saved Pages":"保存されたページ","Account and saved data":"アカウントと保存されたデータ","Account registration or login":"アカウントの登録またはログイン","Support, contact, and community":"サポート、コンタクト、コミュニティ","Administer this Galaxy":"この Galaxy の管理者","Visualize datasets":"データセットの可視化","Access published resources":"パブリッシュされたリソースへアクセス","Chain tools into workflows":"ツールとワークフローの連携","Analysis home view":"解析ホーム","History Lists":"ヒストリーリスト","Histories Shared with Me":"私と共有されているヒストリー","Current History":"現在のヒストリー","Create New":"新しく作成","Copy History":"ヒストリーをコピーする","Share or Publish":"共有またはパブリッシュ","Show Structure":"構造を見る","Extract Workflow":"ワークフローを抽出","Delete Permanently":"永久に削除","Dataset Actions":"データセットの操作","Copy Datasets":"データセットをコピー","Dataset Security":"データセットのセキュリティ","Resume Paused Jobs":"一時停止したジョブの再開","Collapse Expanded Datasets":"展開されたデータセットを畳む","Unhide Hidden Datasets":"隠されたデータセットを表示する","Delete Hidden Datasets":"隠されたデータセットを削除する","Purge Deleted Datasets":"削除されたデータセットを永久に削除",Downloads:"ダウンロード","Export Tool Citations":"ツールの引用をエクスポート","Export History to File":"ヒストリーをファイルへエクスポート","Other Actions":"その他のアクション","Import from File":"ファイルからの読み込み",Webhooks:"Webhooks","This history is empty":"ヒストリーは空です","No matching datasets found":"一致するデータセットが見つかりませんでした","Search datasets":"データセットを検索する","You are currently viewing a deleted history!":"消去したヒストリーをみています。","You are over your disk quota":"あなたはディスククォータを超えている",All:"一式",None:"なし","For all selected":"各項目を","Edit history tags":"ヒストリーのタグを編集","Edit history annotation":"ヒストリーのアノテーションを編集","Click to rename history":"ヒストリーの名前を変更するにはクリック","Operations on multiple datasets":"複数のデータセットに対する操作","Permanently delete datasets":"永久にデータセットを削除","This will permanently remove the data in your datasets. Are you sure?":"これは永久にあなたのデータセット内のデータを削除します。本当に？",Dataset:"データセット","This history is empty. Click 'Get Data' on the left tool menu to start":"ヒストリーは空です。解析をはじめるには、左パネルの 'データ取得' をクリック","You must be logged in to create histories":"ヒストリーを作成するためにはログインする必要があります","View data":"データを表示",Download:"ダウンロード","Download dataset":"データセットをダウンロード","View details":"細部を表示","This job is waiting to run":"ジョブは実行待ちです","This job is currently running":"ジョブは実行中です","An error occurred with this dataset":"このジョブの実行中に発生したエラー","No data":"データ無し","This dataset has been deleted and removed from disk":"このデータセットは、永続的にディスクから削除されました","This dataset has been deleted":"このデータセットは削除されました","This dataset has been hidden":"このデータセットは、非表示にされた",format:"フォーマット",database:"データベース","Edit attributes":"変数を編集する",Delete:"削除する","View or report this error":"このエラーを届け出る","Run this job again":"もう一度このジョブを実行する",Visualize:"可視化する","Undelete it":"復元する","Permanently remove it from disk":"永久にディスクから削除","Unhide it":"非表示解除する","Search Tool Shed":"Tool Shed で探す","Search Tool Shed (Beta)":"Tool Shed (Beta) で探す","Monitor installing repositories":"インストールレポジトリのモニタ","Manage installed tools":"インストールしたツールの管理","Reset metadata":"メタデータのリセット","Download local tool":"ローカルツールのダウンロード","Tool lineage":"ツール系統","Reload a tool's configuration":"ツールのコンフィグのリロード","Review tool migration stages":"ツール移行ステージのレビュー","View Tool Error Logs":"ツールのエラーログ","Manage Display Whitelist":"表示ホワイトリストの管理","Manage Tool Dependencies":"ツール依存関係の管理",Users:"ユーザー",Groups:"グループ","API keys":"API キー","Impersonate a user":"ユーザー偽装",Data:"データ",Quotas:"クォータ",Roles:"ロール","Local data":"ローカルデータ","Form definitions":"フォーム定義",Administration:"管理",Server:"サーバー","Tools and Tool Shed":"ツールと Tool Shed","User Management":"ユーザ管理","Form Definitions":"フォーム定義"},__fr:{"Analyze Data":"Analyse de données",Workflow:"Workflow","Shared Data":"Données partagées","Data Libraries":"Bibliothèque de données",Histories:"Historiques",Workflows:"Workflows",Visualizations:"Visualisations",Pages:"Pages",Visualization:"Visualisation","New Track Browser":"Nouveau Navigateur de Tracks/Pistes","Saved Visualizations":"Visualisations sauvegardées","Interactive Environments":"Environnements interactifs",Admin:"Admin",Help:"Aide",Support:"Assistance",Search:"Recherche","Mailing Lists":"Liste de diffusion",Videos:"Vidéos",Wiki:"Documentations","How to Cite Galaxy":"Comment citer Galaxy","Interactive Tours":"Guides interactifs",User:"Utilisateur",Login:"Authentification",Register:"Enregistrement","Login or Register":"Authentification et Enregistrement","Logged in as":"Authentifié en tant que",Preferences:"Préférences","Custom Builds":"Mes génomes Builds de référence",Logout:"Déconnexion","Saved Histories":"Historiques sauvegardés","Saved Datasets":"Jeux de données sauvegardés","Saved Pages":"Pages sauvegardées","Account and saved data":"Compte et données sauvegardées","Account registration or login":"Enregistrement ou authentification","Support, contact, and community":"Support,contact et communauté","Administer this Galaxy":"Outils Admin","Visualize datasets":"Visualiser les jeux de données","Access published resources":"Accéder aux données partagées","Chain tools into workflows":"Relier outils dans un workflow","Analysis home view":"Accueil analyse de données","History Lists":"Tableaux des historiques","Histories Shared with Me":"Historiques partagés avec moi","Current History":"Cet Historique","Create New":"Créer un nouveau","Copy History":"Copier l'Historique","Share or Publish":"Partager et publier","Show Structure":"Montrer la structure","Extract Workflow":"Extraire un Workflow","Delete Permanently":"Supprimer définitivement","Dataset Actions":"Actions sur les jeux de données","Copy Datasets":"Copier des jeux de données","Dataset Security":"Permissions/Sécurité","Resume Paused Jobs":"Reprendre les processus en pause","Collapse Expanded Datasets":"Réduire les données étendues","Unhide Hidden Datasets":"Afficher les données cachées","Delete Hidden Datasets":"Supprimer les données cachées","Purge Deleted Datasets":"Purger les données supprimées",Downloads:"Télécharger","Export Tool Citations":"Exporter les citations des outils","Export History to File":"Exporter l'Historique dans un fichier","Other Actions":"Autres actions","Import from File":"Importer depuis un fichier",Webhooks:"Webhooks","This history is empty":"Cet historique est vide","No matching datasets found":"Aucunes données correspondantes n'ont été trouvées","An error occurred while getting updates from the server":"Une erreur s'est produite lors de la réception des données depuis le serveur","Please contact a Galaxy administrator if the problem persists":"Veuillez contacter un administrateur de l'instance Galaxy si ce problème persiste","search datasets":"Rechercher des données","You are currently viewing a deleted history!":"Vous consultez actuellement un historique supprimé!","You are over your disk quota":"Vous avez dépassé votre quota d'espace disque","Tool execution is on hold until your disk usage drops below your allocated quota":"L'exécution de l'outil est en attente tant que votre utilisation d'espace disque dépasse le quota attribué",All:"Tout",None:"Aucun","For all selected":"Pour toute la sélection","Edit history tags":"Editer les mots-clés de l'historique","Edit history Annotation":"Editer l'annotation de l'historique","Click to rename history":"Cliquer pour renommer l'historique","Operations on multiple datasets":"Opérer sur plusieurs jeux de données en même temps","Hide datasets":"Cacher les jeux de données","Unhide datasets":"Afficher les jeux de données cachés","Delete datasets":"Supprimer les jeux de données","Undelete datasets":"Restaurer les jeux de données supprimés","Permanently delete datasets":"Supprimer définitivement les jeux de données","This will permanently remove the data in your datasets. Are you sure?":"Cela supprimera de manière permanente les données de votre historique. Êtes-vous certain?",Dataset:"Jeu de données",Annotation:"Annotation","This history is empty. Click 'Get Data' on the left tool menu to start":"Cet historique est vide. Cliquer sur 'Get Data' au niveau du menu d'outils à gauche pour démarrer","You must be logged in to create histories":"Vous devez être connecté pour créer un historique","load your own data":"Charger vos propres données","get data from an external source":"Charger des données depuis une source externe","Include Deleted Datasets":"Inclure les jeux de données supprimés","Include Hidden Datasets":"Inclure les jeux de données cachés","Unable to purge dataset":"Impossible de purger le jeu de données","Cannot display datasets removed from disk":"Impossible de visualiser les jeux de données supprimés du disque","This dataset must finish uploading before it can be viewed":"Le jeu de données doit être totalement téléversé avant de pouvoir être visualiser","This dataset is not yet viewable":"Ce jeu de données n'est pas visualisable","View data":"Voir les données",Download:"Télécharger","Download dataset":"Télécharger le jeu de données","Additional files":"Fichiers additionnels","View details":"Voir les détails","This is a new dataset and not all of its data are available yet":"Il s'agit d'un nouveau jeu de données et seule une partie des données est accessible pour le moment","You do not have permission to view this dataset":"Vous n'avez pas la permission de voir ce jeu de données","The job creating this dataset was cancelled before completion":"Le processus à l'origine de ce jeu de données a été annulé prématurément","This job is waiting to run":"Ce calcul est en attente de traitement","This dataset is currently uploading":"Ce jeu de données est en cours de téléversement","Metadata is being auto-detected":"Les métadonnées sont auto-détectées","This job is currently running":"Le traitement est en cours",'This job is paused. Use the "Resume Paused Jobs" in the history menu to resume':'Ce traitement est en pause. 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Are you sure?":"これは永久にあなたのデータセット内のデータを削除します。本当に？",Dataset:"データセット","This history is empty. Click 'Get Data' on the left tool menu to start":"ヒストリーは空です。解析をはじめるには、左パネルの 'データ取得' をクリック","You must be logged in to create histories":"ヒストリーを作成するためにはログインする必要があります","View data":"データを表示",Download:"ダウンロード","Download dataset":"データセットをダウンロード","View details":"細部を表示","This job is waiting to run":"ジョブは実行待ちです","This job is currently running":"ジョブは実行中です","An error occurred with this dataset":"このジョブの実行中に発生したエラー","No data":"データ無し","This dataset has been deleted and removed from disk":"このデータセットは、永続的にディスクから削除されました","This dataset has been deleted":"このデータセットは削除されました","This dataset has been hidden":"このデータセットは、非表示にされた",format:"フォーマット",database:"データベース","Edit attributes":"変数を編集する",Delete:"削除する","View or report this error":"このエラーを届け出る","Run this job again":"もう一度このジョブを実行する",Visualize:"可視化する","Undelete it":"復元する","Permanently remove it from disk":"永久にディスクから削除","Unhide it":"非表示解除する","Search Tool Shed":"Tool Shed で探す","Search Tool Shed (Beta)":"Tool Shed (Beta) で探す","Monitor installing 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function(jQuery) {\n \"use strict\";\n // ============================================================================\n //TODO: (the older version) unify with ui-modal (the newer version)\n var $ = jQuery;\n\n // Modal dialog boxes\n var Modal = function(options) {\n this.$overlay = options.overlay;\n this.$dialog = options.dialog;\n this.$header = this.$dialog.find(\".modal-header\");\n this.$body = this.$dialog.find(\".modal-body\");\n this.$footer = this.$dialog.find(\".modal-footer\");\n this.$backdrop = options.backdrop;\n // Close button\n this.$header.find(\".close\").on(\"click\", $.proxy(this.hide, this));\n };\n\n $.extend(Modal.prototype, {\n setContent: function(options) {\n this.$header.hide();\n // Title\n if (options.title) {\n this.$header.find(\".title\").html(options.title);\n this.$header.show();\n }\n if (options.closeButton) {\n this.$header.find(\".close\").show();\n this.$header.show();\n } else {\n this.$header.find(\".close\").hide();\n }\n // Buttons\n 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function(jQuery) {\n \"use strict\";\n // ============================================================================\n //TODO: (the older version) unify with ui-modal (the newer version)\n var $ = jQuery;\n\n // Modal dialog boxes\n var Modal = function(options) {\n this.$overlay = options.overlay;\n this.$dialog = options.dialog;\n this.$header = this.$dialog.find(\".modal-header\");\n this.$body = this.$dialog.find(\".modal-body\");\n this.$footer = this.$dialog.find(\".modal-footer\");\n this.$backdrop = options.backdrop;\n // Close button\n this.$header.find(\".close\").on(\"click\", $.proxy(this.hide, this));\n };\n\n $.extend(Modal.prototype, {\n setContent: function(options) {\n this.$header.hide();\n // Title\n if (options.title) {\n this.$header.find(\".title\").html(options.title);\n this.$header.show();\n }\n if (options.closeButton) {\n this.$header.find(\".close\").show();\n this.$header.show();\n } else {\n this.$header.find(\".close\").hide();\n }\n // Buttons\n this.$footer.hide();\n var $buttons = this.$footer.find(\".buttons\").html(\"\");\n if (options.buttons) {\n $.each(options.buttons, function(name, value) {\n $buttons\n .append(\n $(\" \")\n .text(name)\n .click(value)\n )\n .append(\" \");\n });\n this.$footer.show();\n }\n var $extraButtons = this.$footer.find(\".extra_buttons\").html(\"\");\n if (options.extra_buttons) {\n $.each(options.extra_buttons, function(name, value) {\n $extraButtons\n .append(\n $(\"\")\n .text(name)\n .click(value)\n )\n .append(\" \");\n });\n this.$footer.show();\n }\n // Body\n var body = options.body;\n if (body == \"progress\") {\n body = $(\n \"\"\n );\n }\n this.$body.html(body);\n },\n show: function(options, callback) {\n if (!this.$dialog.is(\":visible\")) {\n if (options.backdrop) {\n this.$backdrop.addClass(\"in\");\n } else {\n this.$backdrop.removeClass(\"in\");\n }\n this.$overlay.show();\n this.$dialog.show();\n this.$overlay.addClass(\"in\");\n // Fix min-width so that modal cannot shrink considerably if new content is loaded.\n this.$body.css(\"min-width\", this.$body.width());\n // Set max-height so that modal does not exceed window size and is in middle of page.\n // TODO: this could perhaps be handled better using CSS.\n this.$body.css(\n \"max-height\",\n $(window).height() -\n this.$footer.outerHeight() -\n this.$header.outerHeight() -\n parseInt(this.$dialog.css(\"padding-top\"), 10) -\n parseInt(this.$dialog.css(\"padding-bottom\"), 10)\n );\n }\n // Callback on init\n if (callback) {\n callback();\n }\n },\n hide: function() {\n var modal = this;\n modal.$dialog.fadeOut(function() {\n modal.$overlay.hide();\n modal.$backdrop.removeClass(\"in\");\n modal.$body.children().remove();\n // Clear min-width to allow for modal to take size of new body.\n modal.$body.css(\"min-width\", undefined);\n });\n }\n });\n\n var modal;\n\n $(function() {\n modal = new Modal({\n overlay: $(\"#top-modal\"),\n dialog: $(\"#top-modal-dialog\"),\n backdrop: $(\"#top-modal-backdrop\")\n });\n });\n\n // Backward compatibility\n function hide_modal() {\n modal.hide();\n }\n\n function show_modal(title, body, buttons, extra_buttons, init_fn) {\n modal.setContent({\n title: title,\n body: body,\n buttons: buttons,\n extra_buttons: extra_buttons\n });\n modal.show({ backdrop: true }, init_fn);\n }\n\n function show_message(title, body, buttons, extra_buttons, init_fn) {\n modal.setContent({\n title: title,\n body: body,\n buttons: buttons,\n extra_buttons: extra_buttons\n });\n modal.show({ backdrop: false }, init_fn);\n }\n\n function show_in_overlay(options) {\n var width = options.width || \"600\";\n var height = options.height || \"400\";\n var scroll = options.scroll || \"auto\";\n $(\"#overlay-background\").bind(\"click.overlay\", function() {\n hide_modal();\n $(\"#overlay-background\").unbind(\"click.overlay\");\n });\n modal.setContent({\n closeButton: true,\n title: \" \",\n body: $(\n \"\"\n )\n });\n modal.show({ backdrop: true 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[\"layout/masthead\", \"layout/panel\", \"mvc/ui/ui-modal\", \"utils/utils\"],\n function(Masthead, Panel, Modal, Utils) {\n var View = Backbone.View.extend({\n el: \"body\",\n className: \"full-content\",\n _panelids: [\"left\", \"right\"],\n\n initialize: function(options) {\n var self = this;\n this.config = _.defaults(options.config || {}, {\n message_box_visible: false,\n message_box_content: \"\",\n message_box_class: \"info\",\n show_inactivity_warning: false,\n inactivity_box_content: \"\"\n });\n\n // attach global objects, build mastheads\n Galaxy.modal = this.modal = new Modal.View();\n Galaxy.display = this.display = function(view) {\n if (view.title) {\n Utils.setWindowTitle(view.title);\n view.allow_title_display = false;\n } else {\n Utils.setWindowTitle();\n view.allow_title_display = true;\n }\n self.center.display(view);\n };\n Galaxy.router = this.router =\n options.Router && new options.Router(self, options);\n this.masthead = new Masthead.View(this.config);\n this.center = new Panel.CenterPanel();\n\n // build page template\n this.$el.attr(\"scroll\", \"no\");\n this.$el.html(this._template());\n this.$(\"#masthead\").replaceWith(this.masthead.$el);\n this.$(\"#center\").append(this.center.$el);\n this.$el.append(this.masthead.frame.$el);\n this.$el.append(this.modal.$el);\n this.$messagebox = this.$(\"#messagebox\");\n this.$inactivebox = this.$(\"#inactivebox\");\n\n // build panels\n this.panels = {};\n _.each(this._panelids, function(panel_id) {\n var panel_class_name =\n panel_id.charAt(0).toUpperCase() + panel_id.slice(1);\n var panel_class = options[panel_class_name];\n if (panel_class) {\n var panel_instance = new panel_class(self, options);\n self[panel_instance.toString()] = panel_instance;\n self.panels[panel_id] = new Panel.SidePanel({\n id: panel_id,\n el: self.$(\"#\" + panel_id),\n view: panel_instance\n });\n }\n });\n this.render();\n\n // start the router\n this.router &&\n Backbone.history.start({\n root: Galaxy.root,\n 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[\"layout/masthead\", \"layout/panel\", \"mvc/ui/ui-modal\", \"utils/utils\"],\n function(Masthead, Panel, Modal, Utils) {\n var View = Backbone.View.extend({\n el: \"body\",\n className: \"full-content\",\n _panelids: [\"left\", \"right\"],\n\n initialize: function(options) {\n var self = this;\n this.config = _.defaults(options.config || {}, {\n message_box_visible: false,\n message_box_content: \"\",\n message_box_class: \"info\",\n show_inactivity_warning: false,\n inactivity_box_content: \"\"\n });\n\n // attach global objects, build mastheads\n Galaxy.modal = this.modal = new Modal.View();\n Galaxy.display = this.display = function(view) {\n if (view.title) {\n Utils.setWindowTitle(view.title);\n view.allow_title_display = false;\n } else {\n Utils.setWindowTitle();\n view.allow_title_display = true;\n }\n self.center.display(view);\n };\n Galaxy.router = this.router =\n options.Router && new options.Router(self, options);\n this.masthead = new Masthead.View(this.config);\n this.center = new Panel.CenterPanel();\n\n // build page template\n this.$el.attr(\"scroll\", \"no\");\n this.$el.html(this._template());\n this.$(\"#masthead\").replaceWith(this.masthead.$el);\n this.$(\"#center\").append(this.center.$el);\n this.$el.append(this.masthead.frame.$el);\n this.$el.append(this.modal.$el);\n this.$messagebox = this.$(\"#messagebox\");\n this.$inactivebox = this.$(\"#inactivebox\");\n\n // build panels\n this.panels = {};\n _.each(this._panelids, function(panel_id) {\n var panel_class_name =\n panel_id.charAt(0).toUpperCase() + panel_id.slice(1);\n var panel_class = options[panel_class_name];\n if (panel_class) {\n var panel_instance = new panel_class(self, options);\n self[panel_instance.toString()] = panel_instance;\n self.panels[panel_id] = new Panel.SidePanel({\n id: panel_id,\n el: self.$(\"#\" + panel_id),\n view: panel_instance\n });\n }\n });\n this.render();\n\n // start the router\n this.router &&\n Backbone.history.start({\n root: Galaxy.root,\n pushState: true\n });\n },\n\n render: function() {\n // TODO: Remove this line after select2 update\n $(\".select2-hidden-accessible\").remove();\n this.masthead.render();\n this.renderMessageBox();\n this.renderInactivityBox();\n this.renderPanels();\n this._checkCommunicationServerOnline();\n return this;\n },\n\n /** Render message box */\n renderMessageBox: function() {\n if (this.config.message_box_visible) {\n var content = this.config.message_box_content || \"\";\n var level = this.config.message_box_class || \"info\";\n this.$el.addClass(\"has-message-box\");\n this.$messagebox\n .attr(\"class\", \"panel-\" + level + \"-message\")\n .html(content)\n .toggle(!!content)\n .show();\n } else {\n this.$el.removeClass(\"has-message-box\");\n this.$messagebox.hide();\n }\n return this;\n },\n\n /** Render inactivity warning */\n renderInactivityBox: function() {\n if (this.config.show_inactivity_warning) {\n var content = this.config.inactivity_box_content || \"\";\n var 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\"libs/underscore\", \"libs/backbone\"], function(\n $,\n _,\n Backbone\n) {\n \"use strict\";\n\n var MIN_PANEL_WIDTH = 160,\n MAX_PANEL_WIDTH = 800;\n\n /** View for left/right panels used by Page view */\n var SidePanel = Backbone.View.extend({\n initialize: function(options) {\n this.view = options.view;\n this.hidden = false;\n this.saved_size = null;\n this.hiddenByTool = false;\n },\n\n $center: function() {\n return this.$el.siblings(\"#center\");\n },\n\n $toggleButton: function() {\n return this.$(\".unified-panel-footer > .panel-collapse\");\n },\n\n render: function() {\n var self = this;\n var panel = this.view;\n var components = this.view.model.attributes || {};\n this.$el.html(this._templatePanel(this.id));\n _.each(components.buttons, function(button) {\n self.$(\".panel-header-buttons\").append(button.$el);\n });\n this.$el.addClass(components.cls);\n this.$(\".panel-header-text\").html(_.escape(components.title));\n this.$(\".unified-panel-body\").append(panel.$el);\n panel.render();\n },\n\n /** panel dom template. id is 'right' or 'left' */\n _templatePanel: function() {\n return [\n this._templateHeader(),\n this._templateBody(),\n this._templateFooter()\n ].join(\"\");\n },\n\n /** panel dom template. id is 'right' or 'left' */\n _templateHeader: function(data) {\n return [\n '',\n '',\n '',\n '\"\n ].join(\"\");\n },\n\n /** panel dom template. id is 'right' or 'left' */\n _templateBody: function(data) {\n return '',\n \"\",\n \"';\n },\n\n /** panel dom template. id is 'right' or 'left' */\n _templateFooter: function(data) {\n return [\n '',\n '',\n '',\n \"\"\n ].join(\"\");\n },\n\n events: {\n \"mousedown .unified-panel-footer > .drag\": \"_mousedownDragHandler\",\n \"click .unified-panel-footer > .panel-collapse\": \"toggle\"\n },\n\n _mousedownDragHandler: function(ev) {\n var self = this,\n draggingLeft = this.id === \"left\",\n prevX = ev.pageX;\n\n function move(e) {\n var delta = e.pageX - prevX;\n prevX = e.pageX;\n var oldWidth = self.$el.width(),\n newWidth = draggingLeft\n ? oldWidth + delta\n : oldWidth - delta;\n // Limit range\n newWidth = Math.min(\n MAX_PANEL_WIDTH,\n Math.max(MIN_PANEL_WIDTH, newWidth)\n );\n self.resize(newWidth);\n }\n\n // this is a page wide overlay that assists in capturing the move and release of the mouse\n // if not provided, progress and end wouldn't fire if the mouse moved out of the drag button area\n $(\"#dd-helper\")\n .show()\n .on(\"mousemove\", move)\n .one(\"mouseup\", function(e) {\n $(this)\n .hide()\n .off(\"mousemove\", move);\n });\n },\n\n // TODO: the following three could be simplified I think\n // if panel is 'right' (this.id), move center right newSize number of pixels\n resize: function(newSize) {\n this.$el.css(\"width\", newSize);\n this.$center().css(this.id, newSize);\n return this;\n },\n\n show: function() {\n if (!this.hidden) {\n return;\n }\n var self = this,\n animation = {},\n whichSide = this.id;\n animation[whichSide] = 0;\n self.$el\n .css(whichSide, -this.saved_size)\n .show()\n .animate(animation, \"fast\", function() {\n self.resize(self.saved_size);\n });\n self.hidden = false;\n self.$toggleButton().removeClass(\"hidden\");\n return this;\n },\n\n hide: function() {\n if (this.hidden) {\n return;\n }\n var animation = {},\n whichSide = this.id;\n this.saved_size = this.$el.width();\n animation[whichSide] = -this.saved_size;\n this.$el.animate(animation, \"fast\");\n this.$center().css(whichSide, 0);\n this.hidden = true;\n this.$toggleButton().addClass(\"hidden\");\n return this;\n },\n\n toggle: function(ev) {\n this.hidden ? this.show() : this.hide();\n this.hiddenByTool = false;\n return this;\n },\n\n // ..............................................................\n //TODO: only used in message.mako?\n /** */\n handle_minwidth_hint: function(hint) {\n var space =\n this.$center().width() - (this.hidden ? this.saved_size : 0);\n if (space < hint) {\n if (!this.hidden) {\n this.toggle();\n this.hiddenByTool = true;\n }\n } else {\n if (this.hiddenByTool) {\n this.toggle();\n this.hiddenByTool = false;\n }\n }\n return self;\n },\n\n /** */\n force_panel: function(op) {\n if (op == \"show\") {\n return this.show();\n }\n if (op == \"hide\") {\n return this.hide();\n }\n return self;\n },\n\n toString: function() {\n return \"SidePanel(\" + this.id + \")\";\n }\n });\n\n // ----------------------------------------------------------------------------\n // TODO: side should be defined by page - not here\n var LeftPanel = SidePanel.extend({\n id: \"left\"\n });\n\n var RightPanel = SidePanel.extend({\n id: \"right\"\n });\n\n /** Center panel with the ability to switch between iframe and view */\n var CenterPanel = Backbone.View.extend({\n initialize: function(options) {\n this.setElement($(this.template()));\n this.$frame = this.$(\".center-frame\");\n this.$panel = this.$(\".center-panel\");\n this.$frame.on(\"load\", 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\"libs/underscore\", \"libs/backbone\"], function(\n $,\n _,\n Backbone\n) {\n \"use strict\";\n\n var MIN_PANEL_WIDTH = 160,\n MAX_PANEL_WIDTH = 800;\n\n /** View for left/right panels used by Page view */\n var SidePanel = Backbone.View.extend({\n initialize: function(options) {\n this.view = options.view;\n this.hidden = false;\n this.saved_size = null;\n this.hiddenByTool = false;\n },\n\n $center: function() {\n return this.$el.siblings(\"#center\");\n },\n\n $toggleButton: function() {\n return this.$(\".unified-panel-footer > .panel-collapse\");\n },\n\n render: function() {\n var self = this;\n var panel = this.view;\n var components = this.view.model.attributes || {};\n this.$el.html(this._templatePanel(this.id));\n _.each(components.buttons, function(button) {\n self.$(\".panel-header-buttons\").append(button.$el);\n });\n this.$el.addClass(components.cls);\n this.$(\".panel-header-text\").html(_.escape(components.title));\n this.$(\".unified-panel-body\").append(panel.$el);\n panel.render();\n },\n\n /** panel dom template. id is 'right' or 'left' */\n _templatePanel: function() {\n return [\n this._templateHeader(),\n this._templateBody(),\n this._templateFooter()\n ].join(\"\");\n },\n\n /** panel dom template. id is 'right' or 'left' */\n _templateHeader: function(data) {\n return [\n '',\n '',\n '',\n '\"\n ].join(\"\");\n },\n\n /** panel dom template. id is 'right' or 'left' */\n _templateBody: function(data) {\n return '',\n \"\",\n \"';\n },\n\n /** panel dom template. id is 'right' or 'left' */\n _templateFooter: function(data) {\n return [\n '',\n '',\n '',\n \"\"\n ].join(\"\");\n },\n\n events: {\n \"mousedown .unified-panel-footer > .drag\": \"_mousedownDragHandler\",\n \"click .unified-panel-footer > .panel-collapse\": \"toggle\"\n },\n\n _mousedownDragHandler: function(ev) {\n var self = this,\n draggingLeft = this.id === \"left\",\n prevX = ev.pageX;\n\n function move(e) {\n var delta = e.pageX - prevX;\n prevX = e.pageX;\n var oldWidth = self.$el.width(),\n newWidth = draggingLeft\n ? oldWidth + delta\n : oldWidth - delta;\n // Limit range\n newWidth = Math.min(\n MAX_PANEL_WIDTH,\n Math.max(MIN_PANEL_WIDTH, newWidth)\n );\n self.resize(newWidth);\n }\n\n // this is a page wide overlay that assists in capturing the move and release of the mouse\n // if not provided, progress and end wouldn't fire if the mouse moved out of the drag button area\n $(\"#dd-helper\")\n .show()\n .on(\"mousemove\", move)\n .one(\"mouseup\", function(e) {\n $(this)\n .hide()\n .off(\"mousemove\", move);\n });\n },\n\n // TODO: the following three could be simplified I think\n // if panel is 'right' (this.id), move center right newSize number of pixels\n resize: function(newSize) {\n this.$el.css(\"width\", newSize);\n this.$center().css(this.id, newSize);\n return this;\n },\n\n show: function() {\n if (!this.hidden) {\n return;\n }\n var self = this,\n animation = {},\n whichSide = this.id;\n animation[whichSide] = 0;\n self.$el\n .css(whichSide, -this.saved_size)\n .show()\n .animate(animation, \"fast\", function() {\n self.resize(self.saved_size);\n });\n self.hidden = false;\n self.$toggleButton().removeClass(\"hidden\");\n return this;\n },\n\n hide: function() {\n if (this.hidden) {\n return;\n }\n var animation = {},\n whichSide = this.id;\n this.saved_size = this.$el.width();\n animation[whichSide] = -this.saved_size;\n this.$el.animate(animation, \"fast\");\n this.$center().css(whichSide, 0);\n this.hidden = true;\n this.$toggleButton().addClass(\"hidden\");\n return this;\n },\n\n toggle: function(ev) {\n this.hidden ? this.show() : this.hide();\n this.hiddenByTool = false;\n return this;\n },\n\n // ..............................................................\n //TODO: only used in message.mako?\n /** */\n handle_minwidth_hint: function(hint) {\n var space =\n this.$center().width() - (this.hidden ? this.saved_size : 0);\n if (space < hint) {\n if (!this.hidden) {\n this.toggle();\n this.hiddenByTool = true;\n }\n } else {\n if (this.hiddenByTool) {\n this.toggle();\n this.hiddenByTool = false;\n }\n }\n return self;\n },\n\n /** */\n force_panel: function(op) {\n if (op == \"show\") {\n return this.show();\n }\n if (op == \"hide\") {\n return this.hide();\n }\n return self;\n },\n\n toString: function() {\n return \"SidePanel(\" + this.id + \")\";\n }\n });\n\n // ----------------------------------------------------------------------------\n // TODO: side should be defined by page - not here\n var LeftPanel = SidePanel.extend({\n id: \"left\"\n });\n\n var RightPanel = SidePanel.extend({\n id: \"right\"\n });\n\n /** Center panel with the ability to switch between iframe and view */\n var CenterPanel = Backbone.View.extend({\n initialize: function(options) {\n this.setElement($(this.template()));\n this.$frame = this.$(\".center-frame\");\n this.$panel = this.$(\".center-panel\");\n this.$frame.on(\"load\", _.bind(this._iframeChangeHandler, this));\n },\n\n /** Display iframe if its target url changes, hide center panel */\n _iframeChangeHandler: function(ev) {\n var iframe = ev.currentTarget;\n var location =\n iframe.contentWindow && iframe.contentWindow.location;\n if (location && location.host) {\n $(iframe).show();\n this.$panel.empty().hide();\n Galaxy.trigger(\"center-frame:load\", {\n fullpath:\n location.pathname + location.search + location.hash,\n pathname: location.pathname,\n search: location.search,\n hash: location.hash\n });\n }\n },\n\n /** Display a view in the center panel, hide iframe */\n display: function(view) {\n var contentWindow = this.$frame[0].contentWindow || {};\n var message =\n contentWindow.onbeforeunload && contentWindow.onbeforeunload();\n if (!message || confirm(message)) {\n contentWindow.onbeforeunload = undefined;\n this.$frame.attr(\"src\", \"about:blank\").hide();\n this.$panel\n .empty()\n .scrollTop(0)\n .append(view.$el)\n .show();\n Galaxy.trigger(\"center-panel:load\", view);\n }\n },\n\n template: function() {\n return (\n '' +\n '' +\n '' +\n \"\"\n );\n },\n\n toString: function() {\n return \"CenterPanel\";\n }\n });\n\n return {\n SidePanel: SidePanel,\n LeftPanel: LeftPanel,\n RightPanel: RightPanel,\n CenterPanel: CenterPanel\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/layout/router.js.map b/static/maps/layout/router.js.map index 6a1eced92af..aba4d1f7793 100644 --- a/static/maps/layout/router.js.map +++ b/static/maps/layout/router.js.map @@ -1 +1 @@ -{"version":3,"sources":["layout/router.js"],"names":["_jquery","require","_queryStringParsing","_uiMisc","$","Router","Backbone","extend","initialize","page","options","this","push","url","data","__identifer","Math","random","toString","substr","isEmptyObject","param","navigate","trigger","execute","callback","args","name","Galaxy","debug","queryObj","_queryStringParsing2","default","parse","pop","apply","authenticate","message","persistent"],"mappings":"4IAAA,IAAAA,QAAAC,QAAA,mDAEAC,oBAAAD,QAAA,+FACAE,QAAAF,QAAA,2DAFIG,EAAAA,SAAAA,QAIAC,OAASC,SAASD,OAAOE,QAGzBC,WAAY,SAASC,EAAMC,GACvBC,KAAKF,KAAOA,EAPpBE,KAAAD,QAAAA,GACAE,KAAA,SAAAC,EAAAC,IAYQA,EAAOA,OACFC,YAAcC,KAAKC,SACnBC,SAAS,IACTC,OAAO,GACPf,EAAEgB,cAAcN,KAlBzBV,IAAJ,GAAIA,EAAAA,QAAJ,KAAA,IAAA,IAoBYS,GAAOT,EAAEiB,MAAMP,GAAM,IAhB7BT,OAASC,OAASD,EAClBM,KAAAW,SAAAT,GAAAU,SAAA,KAIIC,QAAKd,SAALe,EAAAC,EAAAC,GAL4BC,OAAAC,MAAA,kBAAAJ,EAAAC,EAAAC,GAyB5B,IAAIG,EAAWC,qBAAAC,QAAaC,MAAMP,EAAKQ,OAjB3CR,EAAAd,KAAAkB,GACML,IACKX,KAAAA,aAAPY,EAAAC,GACKZ,EAALoB,MAAmBnB,KAAKC,GAIpBJ,KAAOA,kBAKduB,aApB+B,SAAAV,EAAAC,GAqC5B,OAAO,GAbPC,cAAOC,WACPlB,KAAImB,KAAAA,QACJJ,IAAKd,SAAAA,QAAKkB,SACNL,OAAU,SACNY,QACAZ,sEADJa,YAEO,wBAMfF","file":"../../scripts/layout/router.js","sourcesContent":["import jQuery from \"jquery\";\nvar $ = jQuery;\nimport QUERY_STRING from \"utils/query-string-parsing\";\nimport Ui from \"mvc/ui/ui-misc\";\n\nvar Router = Backbone.Router.extend({\n // TODO: not many client routes at this point - fill and remove from server.\n // since we're at root here, this may be the last to be routed entirely on the client.\n initialize: function(page, options) {\n this.page = page;\n this.options = options;\n },\n\n /** helper to push a new navigation state */\n push: function(url, data) {\n data = data || {};\n data.__identifer = Math.random()\n .toString(36)\n .substr(2);\n if (!$.isEmptyObject(data)) {\n url += url.indexOf(\"?\") == -1 ? \"?\" : \"&\";\n url += $.param(data, true);\n }\n Galaxy.params = data;\n this.navigate(url, { trigger: true });\n },\n\n /** override to parse query string into obj and send to each route */\n execute: function(callback, args, name) {\n Galaxy.debug(\"router execute:\", callback, args, name);\n var queryObj = QUERY_STRING.parse(args.pop());\n args.push(queryObj);\n if (callback) {\n if (this.authenticate(args, name)) {\n callback.apply(this, args);\n } else {\n this.access_denied();\n }\n }\n },\n\n authenticate: function(args, name) {\n return true;\n },\n\n access_denied: function() {\n this.page.display(\n new Ui.Message({\n status: \"danger\",\n message:\n \"You must be logged in with proper credentials to make this request.\",\n persistent: true\n })\n );\n }\n});\n\nexport default Router;\n"]} \ No newline at end of file +{"version":3,"sources":["layout/router.js"],"names":["$","Router","Backbone","extend","initialize","page","options","this","push","url","data","__identifer","Math","random","toString","substr","indexOf","param","Galaxy","params","navigate","trigger","execute","callback","args","name","debug","queryObj","_queryStringParsing2","default","parse","pop","isEmptyObject","authenticate","access_denied","status","persistent"],"mappings":"sOACIA,EAAAA,EAAAA,QAIAC,EAASC,SAASD,OAAOE,QAGzBC,WAAY,SAASC,EAAMC,GACvBC,KAAKF,KAAOA,EACZE,KAAKD,QAAUA,GAInBE,KAAM,SAASC,EAAKC,IAChBA,EAAOA,OACFC,YAAcC,KAAKC,SACnBC,SAAS,IACTC,OAAO,GAjBhBf,EAAAA,cAAJU,KAmBYD,IAA4B,GAArBA,EAAIO,QAAQ,KAAa,IAAM,IACtCP,GAAOT,EAAEiB,MAAMP,GAAM,IAf7BQ,OAAAC,OAAAT,EACAH,KAAAa,SAAAX,GAAAY,SAAA,KAICC,QAN+B,SAAAC,EAAAC,EAAAC,GAwB5BP,OAAOQ,MAAM,kBAAmBH,EAAUC,EAAMC,GAhBpD,IAAAE,EAAAC,EAAAC,QAAAC,MAAAN,EAAAO,OACAvB,EAAAA,KAAMmB,GACFjB,IACAA,KAAKC,aAAcC,EAAKC,GAGpBU,EAAGS,MAAAA,KAAFR,GAEDf,KAAAA,kBAoBRwB,aAAc,SAAST,EAAMC,GAd7B,OAAA,GAGIS,cAAIP,WACJH,KAAAA,KAAKhB,QACL,IAAIe,EAAAA,QAAAA,SACAY,OAAI,SACAZ,QADJ,sEAGIa,YAAKF,kBAMbjC","file":"../../scripts/layout/router.js","sourcesContent":["import jQuery from \"jquery\";\nvar $ = jQuery;\nimport QUERY_STRING from \"utils/query-string-parsing\";\nimport Ui from \"mvc/ui/ui-misc\";\n\nvar Router = Backbone.Router.extend({\n // TODO: not many client routes at this point - fill and remove from server.\n // since we're at root here, this may be the last to be routed entirely on the client.\n initialize: function(page, options) {\n this.page = page;\n this.options = options;\n },\n\n /** helper to push a new navigation state */\n push: function(url, data) {\n data = data || {};\n data.__identifer = Math.random()\n .toString(36)\n .substr(2);\n if (!$.isEmptyObject(data)) {\n url += url.indexOf(\"?\") == -1 ? \"?\" : \"&\";\n url += $.param(data, true);\n }\n Galaxy.params = data;\n this.navigate(url, { trigger: true });\n },\n\n /** override to parse query string into obj and send to each route */\n execute: function(callback, args, name) {\n Galaxy.debug(\"router execute:\", callback, args, name);\n var queryObj = QUERY_STRING.parse(args.pop());\n args.push(queryObj);\n if (callback) {\n if (this.authenticate(args, name)) {\n callback.apply(this, args);\n } else {\n this.access_denied();\n }\n }\n },\n\n authenticate: function(args, name) {\n return true;\n },\n\n access_denied: function() {\n this.page.display(\n new Ui.Message({\n status: \"danger\",\n message:\n \"You must be logged in with proper credentials to make this request.\",\n persistent: true\n })\n );\n }\n});\n\nexport default Router;\n"]} \ No newline at end of file diff --git a/static/maps/layout/scratchbook.js.map b/static/maps/layout/scratchbook.js.map index 00b4689b411..6a0a01f1a6c 100644 --- a/static/maps/layout/scratchbook.js.map +++ b/static/maps/layout/scratchbook.js.map @@ -1 +1 @@ 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Frame manager uses the ui-frames to create the scratch book masthead icon and functionality **/\ndefine([\"mvc/ui/ui-frames\"], function(Frames) {\n return Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n options = options || {};\n this.frames = new Frames.View({ visible: false });\n this.setElement(this.frames.$el);\n this.buttonActive = options.collection.add({\n id: \"enable-scratchbook\",\n icon: \"fa-th\",\n tooltip: _l(\"Enable/Disable Scratchbook\"),\n onclick: function() {\n self.active = !self.active;\n self.buttonActive.set({\n toggle: self.active,\n show_note: self.active,\n note_cls: self.active && \"fa fa-check\"\n });\n !self.active && self.frames.hide();\n },\n onbeforeunload: function() {\n if (self.frames.length() > 0) {\n return (\n \"You opened \" +\n self.frames.length() +\n \" frame(s) which will be lost.\"\n );\n }\n }\n });\n this.buttonLoad = options.collection.add({\n id: \"show-scratchbook\",\n icon: \"fa-eye\",\n tooltip: _l(\"Show/Hide Scratchbook\"),\n show_note: true,\n visible: false,\n onclick: function(e) {\n self.frames.visible\n ? self.frames.hide()\n : self.frames.show();\n }\n });\n this.frames\n .on(\"add remove\", function() {\n this.visible && this.length() == 0 && this.hide();\n self.buttonLoad.set({\n note: this.length(),\n visible: this.length() > 0\n });\n })\n .on(\"show hide \", function() {\n self.buttonLoad.set({\n toggle: this.visible,\n icon: (this.visible && \"fa-eye\") || \"fa-eye-slash\"\n });\n });\n this.history_cache = {};\n },\n\n /** Add a dataset to the frames */\n addDataset: function(dataset_id) {\n var self = this;\n var current_dataset = null;\n if (Galaxy && Galaxy.currHistoryPanel) {\n var history_id = Galaxy.currHistoryPanel.collection.historyId;\n this.history_cache[history_id] = {\n name: Galaxy.currHistoryPanel.model.get(\"name\"),\n dataset_ids: []\n };\n Galaxy.currHistoryPanel.collection.each(function(model) {\n !model.get(\"deleted\") &&\n model.get(\"visible\") &&\n self.history_cache[history_id].dataset_ids.push(\n model.get(\"id\")\n );\n });\n }\n var _findDataset = function(dataset, offset) {\n if (dataset) {\n var history_details =\n self.history_cache[dataset.get(\"history_id\")];\n if (history_details && history_details.dataset_ids) {\n var dataset_list = history_details.dataset_ids;\n var pos = dataset_list.indexOf(dataset.get(\"id\"));\n if (\n pos !== -1 &&\n pos + offset >= 0 &&\n pos + offset < dataset_list.length\n ) {\n return dataset_list[pos + offset];\n }\n }\n }\n };\n var _loadDatasetOffset = function(dataset, offset, frame) {\n var new_dataset_id = _findDataset(dataset, offset);\n if (new_dataset_id) {\n self._loadDataset(new_dataset_id, function(\n new_dataset,\n config\n ) {\n current_dataset = new_dataset;\n frame.model.set(config);\n });\n } else {\n frame.model.trigger(\"change\");\n }\n };\n this._loadDataset(dataset_id, function(dataset, config) {\n current_dataset = dataset;\n self.add(\n _.extend(\n {\n menu: [\n {\n icon: \"fa fa-chevron-circle-left\",\n tooltip: \"Previous in History\",\n onclick: function(frame) {\n _loadDatasetOffset(\n current_dataset,\n -1,\n frame\n );\n },\n disabled: function() {\n return !_findDataset(\n current_dataset,\n -1\n );\n }\n },\n {\n icon: \"fa fa-chevron-circle-right\",\n tooltip: \"Next in History\",\n onclick: function(frame) {\n _loadDatasetOffset(\n current_dataset,\n 1,\n frame\n );\n },\n disabled: function() {\n return !_findDataset(\n current_dataset,\n 1\n );\n }\n }\n ]\n },\n config\n )\n );\n });\n },\n\n _loadDataset: function(dataset_id, callback) {\n var self = this;\n require([\"mvc/dataset/data\"], function(DATA) {\n var dataset = new DATA.Dataset({ id: dataset_id });\n $.when(dataset.fetch()).then(function() {\n var is_tabular = _.find([\"tabular\", \"interval\"], function(\n data_type\n ) {\n return (\n dataset.get(\"data_type\").indexOf(data_type) !== -1\n );\n });\n var title = dataset.get(\"name\");\n var history_details =\n self.history_cache[dataset.get(\"history_id\")];\n if (history_details) {\n title = history_details.name + \": \" + title;\n }\n callback(\n dataset,\n is_tabular\n ? {\n title: title,\n url: null,\n content: DATA.createTabularDatasetChunkedView(\n {\n model: new DATA.TabularDataset(\n dataset.toJSON()\n ),\n embedded: true,\n height: \"100%\"\n }\n ).$el\n }\n : {\n title: title,\n url:\n Galaxy.root +\n \"datasets/\" +\n dataset_id +\n \"/display/?preview=True\",\n content: null\n }\n );\n });\n });\n },\n\n /** Add a trackster visualization to the frames. */\n addTrackster: function(viz_id) {\n var self = this;\n require([\"viz/visualization\", \"viz/trackster\"], function(\n visualization,\n trackster\n ) {\n var viz = new visualization.Visualization({ id: viz_id });\n $.when(viz.fetch()).then(function() {\n var ui = new trackster.TracksterUI(Galaxy.root);\n\n // Construct frame config based on dataset's type.\n var frame_config = {\n title: viz.get(\"name\"),\n type: \"other\",\n content: function(parent_elt) {\n // Create view config.\n var view_config = {\n container: parent_elt,\n name: viz.get(\"title\"),\n id: viz.id,\n // FIXME: this will not work with custom builds b/c the dbkey needed to be encoded.\n dbkey: viz.get(\"dbkey\"),\n stand_alone: false\n },\n latest_revision = viz.get(\"latest_revision\"),\n drawables =\n latest_revision.config.view.drawables;\n\n // Set up datasets in drawables.\n _.each(drawables, function(d) {\n d.dataset = {\n hda_ldda: d.hda_ldda,\n id: d.dataset_id\n };\n });\n view = ui.create_visualization(\n view_config,\n latest_revision.config.viewport,\n latest_revision.config.view.drawables,\n latest_revision.config.bookmarks,\n false\n );\n }\n };\n self.add(frame_config);\n });\n });\n },\n\n /** Add and display a new frame/window based on options. */\n add: function(options) {\n if (options.target == \"_blank\") {\n window.open(options.url);\n } else if (\n options.target == \"_top\" ||\n options.target == 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Frame manager uses the ui-frames to create the scratch book masthead icon and functionality **/\ndefine([\"mvc/ui/ui-frames\"], function(Frames) {\n return Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n options = options || {};\n this.frames = new Frames.View({ visible: false });\n this.setElement(this.frames.$el);\n this.buttonActive = options.collection.add({\n id: \"enable-scratchbook\",\n icon: \"fa-th\",\n tooltip: _l(\"Enable/Disable Scratchbook\"),\n onclick: function() {\n self.active = !self.active;\n self.buttonActive.set({\n toggle: self.active,\n show_note: self.active,\n note_cls: self.active && \"fa fa-check\"\n });\n !self.active && self.frames.hide();\n },\n onbeforeunload: function() {\n if (self.frames.length() > 0) {\n return (\n \"You opened \" +\n self.frames.length() +\n \" frame(s) which will be lost.\"\n );\n }\n }\n });\n this.buttonLoad = options.collection.add({\n id: \"show-scratchbook\",\n icon: \"fa-eye\",\n tooltip: 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_.extend(\n {\n menu: [\n {\n icon: \"fa fa-chevron-circle-left\",\n tooltip: \"Previous in History\",\n onclick: function(frame) {\n _loadDatasetOffset(\n current_dataset,\n -1,\n frame\n );\n },\n disabled: function() {\n return !_findDataset(\n current_dataset,\n -1\n );\n }\n },\n {\n icon: \"fa fa-chevron-circle-right\",\n tooltip: \"Next in History\",\n onclick: function(frame) {\n _loadDatasetOffset(\n current_dataset,\n 1,\n frame\n );\n },\n disabled: function() {\n return !_findDataset(\n current_dataset,\n 1\n );\n }\n }\n ]\n },\n config\n )\n );\n });\n },\n\n _loadDataset: function(dataset_id, callback) {\n var self = this;\n require([\"mvc/dataset/data\"], function(DATA) {\n var dataset = new DATA.Dataset({ id: dataset_id });\n $.when(dataset.fetch()).then(function() {\n var is_tabular = _.find([\"tabular\", \"interval\"], function(\n data_type\n ) {\n return (\n dataset.get(\"data_type\").indexOf(data_type) !== -1\n );\n });\n var title = dataset.get(\"name\");\n var history_details =\n self.history_cache[dataset.get(\"history_id\")];\n if (history_details) {\n title = history_details.name + \": \" + title;\n }\n callback(\n dataset,\n is_tabular\n ? {\n title: title,\n url: null,\n content: DATA.createTabularDatasetChunkedView(\n {\n model: new DATA.TabularDataset(\n dataset.toJSON()\n ),\n embedded: true,\n height: \"100%\"\n }\n ).$el\n }\n : {\n title: title,\n url:\n Galaxy.root +\n \"datasets/\" +\n dataset_id +\n \"/display/?preview=True\",\n content: null\n }\n );\n });\n });\n },\n\n /** Add a trackster visualization to the frames. */\n addTrackster: function(viz_id) {\n var self = this;\n require([\"viz/visualization\", \"viz/trackster\"], function(\n visualization,\n trackster\n ) {\n var viz = new visualization.Visualization({ id: viz_id });\n $.when(viz.fetch()).then(function() {\n var ui = new trackster.TracksterUI(Galaxy.root);\n\n // Construct frame config based on dataset's type.\n var frame_config = {\n title: viz.get(\"name\"),\n 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baseMVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\nimport \"ui/editable-text\";\n// =============================================================================\n/** A view on any model that has a 'annotation' attribute\n */\nvar AnnotationEditor = Backbone.View\n .extend(baseMVC.LoggableMixin)\n .extend(baseMVC.HiddenUntilActivatedViewMixin)\n .extend({\n tagName: \"div\",\n className: \"annotation-display\",\n\n /** Set up listeners, parse options */\n initialize: function(options) {\n options = options || {};\n this.tooltipConfig = options.tooltipConfig || {\n placement: \"bottom\"\n };\n //console.debug( this, options );\n // only listen to the model only for changes to annotations\n this.listenTo(this.model, \"change:annotation\", function() {\n this.render();\n });\n this.hiddenUntilActivated(options.$activator, options);\n },\n\n /** Build the DOM elements, call select to on the created input, and set up behaviors */\n render: function() {\n var view = 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'_searchArrayAttribute', array, searchFor );\n searchFor = searchFor.toLowerCase();\n //precondition: searchFor has already been validated as non-empty string\n //precondition: assumes only 1 level array\n //TODO: could possibly break up searchFor more (CSV...)\n return _.any(array, function(elem) {\n return (\n elem\n .toString()\n .toLowerCase()\n .indexOf(searchFor.toLowerCase()) !== -1\n );\n });\n },\n\n /** search all searchAttributes for the string searchFor,\n * returning a list of keys of attributes that contain searchFor\n */\n search: function(searchFor) {\n var model = this;\n return _.filter(this.searchAttributes, function(key) {\n return model.searchAttribute(key, searchFor);\n });\n },\n\n /** alias of search, but returns a boolean; accepts attribute specifiers where\n * the attributes searched can be narrowed to a single attribute using\n * the form: matches( 'genome_build=hg19' )\n * (the attribute keys allowed can also be aliases to the true attribute key;\n * see searchAliases above)\n * @param {String} term plain text or ATTR_SPECIFIER sep. key=val pair\n * @returns {Boolean} was term found in (any) attribute(s)\n */\n matches: function(term) {\n var ATTR_SPECIFIER = \"=\",\n split = term.split(ATTR_SPECIFIER);\n // attribute is specified - search only that\n if (split.length >= 2) {\n var attrKey = split[0];\n attrKey = this.searchAliases[attrKey] || attrKey;\n return this.searchAttribute(attrKey, split[1]);\n }\n // no attribute is specified - search all attributes in searchAttributes\n return !!this.search(term).length;\n },\n\n /** an implicit AND search for all terms; IOW, a model must match all terms given\n * where terms is a whitespace separated value string.\n * e.g. given terms of: 'blah bler database=hg19'\n * an HDA would have to have attributes containing blah AND bler AND a genome_build == hg19\n * To include whitespace in terms: wrap the term in double quotations (name=\"blah bler\").\n */\n matchesAll: function(terms) {\n var model = this;\n // break the terms up by whitespace and filter out the empty strings\n terms = terms.match(/(\".*\"|\\w*=\".*\"|\\S*)/g).filter(function(s) {\n return !!s;\n });\n return _.all(terms, function(term) {\n term = term.replace(/\"/g, \"\");\n return model.matches(term);\n });\n }\n};\n\n//==============================================================================\n/** A view that renders hidden and shows when some activator is clicked.\n * options:\n * showFn: the effect used to show/hide the View (defaults to jq.toggle)\n * $elementShown: some jqObject (defaults to this.$el) to be shown/hidden\n * onShowFirstTime: fn called the first time the view is shown\n * onshow: fn called every time the view is shown\n * onhide: fn called every time the view is hidden\n * events:\n * hiddenUntilActivated:shown (the view is passed as an arg)\n * hiddenUntilActivated:hidden (the view is passed as an arg)\n * instance vars:\n * view.hidden {boolean} is the view in the hidden state\n */\nvar HiddenUntilActivatedViewMixin = /** @lends hiddenUntilActivatedMixin# */ {\n //TODO: since this is a mixin, consider moving toggle, hidden into HUAVOptions\n\n /** call this in your initialize to set up the mixin\n * @param {jQuery} $activator the 'button' that's clicked to show/hide the view\n * @param {Object} hash with mixin options\n */\n hiddenUntilActivated: function($activator, options) {\n // call this in your view's initialize fn\n options = options || {};\n //TODO: flesh out options - show them all here\n this.HUAVOptions = {\n $elementShown: this.$el,\n showFn: jQuery.prototype.toggle,\n showSpeed: \"fast\"\n };\n _.extend(this.HUAVOptions, options || {});\n /** has this been shown already (and onshowFirstTime called)? */\n this.HUAVOptions.hasBeenShown = this.HUAVOptions.$elementShown.is(\n \":visible\"\n );\n this.hidden = this.isHidden();\n\n if ($activator) {\n var mixin = this;\n $activator.on(\"click\", function(ev) {\n mixin.toggle(mixin.HUAVOptions.showSpeed);\n });\n }\n },\n\n //TODO:?? remove? use .hidden?\n /** returns T/F if the view is hidden */\n isHidden: function() {\n return this.HUAVOptions.$elementShown.is(\":hidden\");\n },\n\n /** toggle the hidden state, show/hide $elementShown, call onshow/hide, trigger events */\n toggle: function() {\n //TODO: more specific name - toggle is too general\n // can be called manually as well with normal toggle arguments\n //TODO: better as a callback (when the show/hide is actually done)\n // show\n if (this.hidden) {\n // fire the optional fns on the first/each showing - good for render()\n if (!this.HUAVOptions.hasBeenShown) {\n if (_.isFunction(this.HUAVOptions.onshowFirstTime)) {\n this.HUAVOptions.hasBeenShown = true;\n this.HUAVOptions.onshowFirstTime.call(this);\n }\n }\n if (_.isFunction(this.HUAVOptions.onshow)) {\n this.HUAVOptions.onshow.call(this);\n this.trigger(\"hiddenUntilActivated:shown\", this);\n }\n this.hidden = false;\n\n // hide\n } else {\n if (_.isFunction(this.HUAVOptions.onhide)) {\n this.HUAVOptions.onhide.call(this);\n this.trigger(\"hiddenUntilActivated:hidden\", this);\n }\n this.hidden = true;\n }\n return this.HUAVOptions.showFn.apply(\n this.HUAVOptions.$elementShown,\n arguments\n );\n }\n};\n\n//==============================================================================\n/** Mixin for views that can be dragged and dropped\n * Allows for the drag behavior to be turned on/off, setting/removing jQuery event\n * handlers each time.\n * dataTransfer data is set to the JSON string of the view's model.toJSON\n * Override '$dragHandle' to define the draggable DOM sub-element.\n */\nvar DraggableViewMixin = {\n /** set up instance vars to track whether this view is currently draggable */\n initialize: function(attributes) {\n /** is the body of this hda view expanded/not? */\n this.draggable = attributes.draggable || false;\n },\n\n /** what part of the view's DOM triggers the dragging */\n $dragHandle: function() {\n //TODO: make abstract/general - move this to listItem\n // override to the element you want to be your view's handle\n return this.$(\".title-bar\");\n },\n\n /** toggle whether this view is draggable */\n toggleDraggable: function() {\n if (this.draggable) {\n this.draggableOff();\n } else {\n this.draggableOn();\n }\n },\n\n /** allow the view to be dragged, set up event handlers */\n draggableOn: function() {\n this.draggable = true;\n this.dragStartHandler = _.bind(this._dragStartHandler, this);\n this.dragEndHandler = _.bind(this._dragEndHandler, this);\n\n var handle = this.$dragHandle()\n .attr(\"draggable\", true)\n .get(0);\n handle.addEventListener(\"dragstart\", this.dragStartHandler, false);\n handle.addEventListener(\"dragend\", this.dragEndHandler, false);\n },\n\n /** turn of view dragging and remove event listeners */\n draggableOff: function() {\n this.draggable = false;\n var handle = this.$dragHandle()\n .attr(\"draggable\", false)\n .get(0);\n handle.removeEventListener(\"dragstart\", this.dragStartHandler, false);\n handle.removeEventListener(\"dragend\", this.dragEndHandler, false);\n },\n\n /** sets the dataTransfer data to the model's toJSON\n * @fires draggable:dragstart (bbone event) which is passed the event and this view\n */\n _dragStartHandler: function(event) {\n event.dataTransfer.effectAllowed = \"move\";\n //ASSUMES: this.model\n //TODO: all except IE: should be 'application/json', IE: must be 'text'\n event.dataTransfer.setData(\"text\", JSON.stringify(this.model.toJSON()));\n this.trigger(\"draggable:dragstart\", event, this);\n return false;\n },\n\n /** handle the dragend\n * @fires draggable:dragend (bbone event) which is passed the event and this view\n */\n _dragEndHandler: function(event) {\n this.trigger(\"draggable:dragend\", event, this);\n return false;\n }\n};\n\n//==============================================================================\n/** Mixin that allows a view to be selected (gen. from a list).\n * Selection controls ($selector) may be hidden/shown/toggled.\n * The bbone event 'selectable' is fired when the controls are shown/hidden (passed T/F).\n * Default rendering is a font-awesome checkbox.\n * Default selector is '.selector' within the view's $el.\n * The bbone events 'selected' and 'de-selected' are fired when the $selector is clicked.\n * Both events are passed the view and the (jQuery) event.\n */\nvar SelectableViewMixin = {\n /** Set up instance state vars for whether the selector is shown and whether the view has been selected */\n initialize: function(attributes) {\n /** is the view currently in selection mode? */\n this.selectable = attributes.selectable || false;\n /** is the view currently selected? */\n this.selected = attributes.selected || false;\n },\n\n /** $el sub-element where the selector is rendered and what can be clicked to select. */\n $selector: function() {\n return this.$(\".selector\");\n },\n\n /** How the selector is rendered - defaults to font-awesome checkbox */\n _renderSelected: function() {\n // override\n this.$selector()\n .find(\"span\")\n .toggleClass(\"fa-check-square-o\", this.selected)\n .toggleClass(\"fa-square-o\", !this.selected);\n },\n\n /** Toggle whether the selector is shown */\n toggleSelector: function() {\n //TODO: use this.selectable\n if (!this.$selector().is(\":visible\")) {\n this.showSelector();\n } else {\n this.hideSelector();\n }\n },\n\n /** Display the selector control.\n * @param {Number} a jQuery fx speed\n * @fires: selectable which is passed true (IOW, the selector is shown) and the view\n */\n showSelector: function(speed) {\n speed = speed !== undefined ? speed : this.fxSpeed;\n // make sure selected state is represented properly\n this.selectable = true;\n this.trigger(\"selectable\", true, this);\n this._renderSelected();\n if (speed) {\n this.$selector().show(speed);\n } else {\n this.$selector().show();\n }\n },\n\n /** remove the selector control\n * @param {Number} a jQuery fx speed\n * @fires: selectable which is passed false (IOW, the selector is not shown) and the view\n */\n hideSelector: function(speed) {\n speed = speed !== undefined ? speed : this.fxSpeed;\n // reverse the process from showSelect\n this.selectable = false;\n this.trigger(\"selectable\", false, this);\n if (speed) {\n this.$selector().hide(speed);\n } else {\n this.$selector().hide();\n }\n },\n\n /** Toggle whether the view is selected */\n toggleSelect: function(event) {\n if (this.selected) {\n this.deselect(event);\n } else {\n this.select(event);\n }\n },\n\n /** Select this view and re-render the selector control to show it\n * @param {Event} a jQuery event that caused the selection\n * @fires: selected which is passed the view and the DOM event that triggered it (optionally)\n */\n select: function(event) {\n // switch icon, set selected, and trigger event\n if (!this.selected) {\n this.trigger(\"selected\", this, event);\n this.selected = true;\n this._renderSelected();\n }\n return false;\n },\n\n /** De-select this view and re-render the selector control to show it\n * @param {Event} a jQuery event that caused the selection\n * @fires: de-selected which is passed the view and the DOM event that triggered it (optionally)\n */\n deselect: function(event) {\n // switch icon, set selected, and trigger event\n if (this.selected) {\n this.trigger(\"de-selected\", this, event);\n this.selected = false;\n this._renderSelected();\n }\n return false;\n }\n};\n\n//==============================================================================\n/** Return an underscore template fn from an array of strings.\n * @param {String[]} template the template strings to compile into the underscore template fn\n * @param {String} jsonNamespace an optional namespace for the json data passed in (defaults to 'model')\n * @returns {Function} the (wrapped) underscore template fn\n * The function accepts:\n *\n * The template strings can access:\n * the 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Can be used with plain browser console (or something more\n * complex like an AJAX logger).\n *
NOTE: currently only uses the console.debug log function\n * (as opposed to debug, error, warn, etc.)\n * @name LoggableMixin\n *\n * @example\n * // Add to your models/views at the definition using chaining:\n * var MyModel = Backbone.Model.extend( LoggableMixin ).extend({ // ... });\n *\n * // or - more explicitly AFTER the definition:\n * var MyModel = Backbone.Model.extend({\n * logger : console\n * // ...\n * this.log( '$#%& it! - broken already...' );\n * })\n * _.extend( MyModel.prototype, LoggableMixin )\n *\n */\nvar LoggableMixin = /** @lends LoggableMixin# */ {\n // replace null with console (if available) to see all logs for a particular view/model\n /** The logging object whose log function will be used to output\n * messages. Null will supress all logging. 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searchAliases above)\n * @param {String} term plain text or ATTR_SPECIFIER sep. key=val pair\n * @returns {Boolean} was term found in (any) attribute(s)\n */\n matches: function(term) {\n var ATTR_SPECIFIER = \"=\",\n split = term.split(ATTR_SPECIFIER);\n // attribute is specified - search only that\n if (split.length >= 2) {\n var attrKey = split[0];\n attrKey = this.searchAliases[attrKey] || attrKey;\n return this.searchAttribute(attrKey, split[1]);\n }\n // no attribute is specified - search all attributes in searchAttributes\n return !!this.search(term).length;\n },\n\n /** an implicit AND search for all terms; IOW, a model must match all terms given\n * where terms is a whitespace separated value string.\n * e.g. given terms of: 'blah bler database=hg19'\n * an HDA would have to have attributes containing blah AND bler AND a genome_build == hg19\n * To include whitespace in terms: wrap the term in double quotations (name=\"blah bler\").\n */\n matchesAll: function(terms) {\n var 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*/\nvar HiddenUntilActivatedViewMixin = /** @lends hiddenUntilActivatedMixin# */ {\n //TODO: since this is a mixin, consider moving toggle, hidden into HUAVOptions\n\n /** call this in your initialize to set up the mixin\n * @param {jQuery} $activator the 'button' that's clicked to show/hide the view\n * @param {Object} hash with mixin options\n */\n hiddenUntilActivated: function($activator, options) {\n // call this in your view's initialize fn\n options = options || {};\n //TODO: flesh out options - show them all here\n this.HUAVOptions = {\n $elementShown: this.$el,\n showFn: jQuery.prototype.toggle,\n showSpeed: \"fast\"\n };\n _.extend(this.HUAVOptions, options || {});\n /** has this been shown already (and onshowFirstTime called)? */\n this.HUAVOptions.hasBeenShown = this.HUAVOptions.$elementShown.is(\n \":visible\"\n );\n this.hidden = this.isHidden();\n\n if ($activator) {\n var mixin = this;\n $activator.on(\"click\", function(ev) {\n mixin.toggle(mixin.HUAVOptions.showSpeed);\n });\n }\n },\n\n //TODO:?? remove? use .hidden?\n /** returns T/F if the view is hidden */\n isHidden: function() {\n return this.HUAVOptions.$elementShown.is(\":hidden\");\n },\n\n /** toggle the hidden state, show/hide $elementShown, call onshow/hide, trigger events */\n toggle: function() {\n //TODO: more specific name - toggle is too general\n // can be called manually as well with normal toggle arguments\n //TODO: better as a callback (when the show/hide is actually done)\n // show\n if (this.hidden) {\n // fire the optional fns on the first/each showing - good for render()\n if (!this.HUAVOptions.hasBeenShown) {\n if (_.isFunction(this.HUAVOptions.onshowFirstTime)) {\n this.HUAVOptions.hasBeenShown = true;\n this.HUAVOptions.onshowFirstTime.call(this);\n }\n }\n if (_.isFunction(this.HUAVOptions.onshow)) {\n this.HUAVOptions.onshow.call(this);\n this.trigger(\"hiddenUntilActivated:shown\", this);\n }\n this.hidden = false;\n\n // hide\n } else {\n if (_.isFunction(this.HUAVOptions.onhide)) {\n this.HUAVOptions.onhide.call(this);\n this.trigger(\"hiddenUntilActivated:hidden\", this);\n }\n this.hidden = true;\n }\n return this.HUAVOptions.showFn.apply(\n this.HUAVOptions.$elementShown,\n arguments\n );\n }\n};\n\n//==============================================================================\n/** Mixin for views that can be dragged and dropped\n * Allows for the drag behavior to be turned on/off, setting/removing jQuery event\n * handlers each time.\n * dataTransfer data is set to the JSON string of the view's model.toJSON\n * Override '$dragHandle' to define the draggable DOM sub-element.\n */\nvar DraggableViewMixin = {\n /** set up instance vars to track whether this view is currently draggable */\n initialize: function(attributes) {\n /** is the body of this hda view expanded/not? */\n this.draggable = attributes.draggable || false;\n },\n\n /** what part of the view's DOM triggers the dragging */\n $dragHandle: function() {\n //TODO: make abstract/general - move this to listItem\n // override to the element you want to be your view's handle\n return this.$(\".title-bar\");\n },\n\n /** toggle whether this view is draggable */\n toggleDraggable: function() {\n if (this.draggable) {\n this.draggableOff();\n } else {\n this.draggableOn();\n }\n },\n\n /** allow the view to be dragged, set up event handlers */\n draggableOn: function() {\n this.draggable = true;\n this.dragStartHandler = _.bind(this._dragStartHandler, this);\n this.dragEndHandler = _.bind(this._dragEndHandler, this);\n\n var handle = this.$dragHandle()\n .attr(\"draggable\", true)\n .get(0);\n handle.addEventListener(\"dragstart\", this.dragStartHandler, false);\n handle.addEventListener(\"dragend\", this.dragEndHandler, false);\n },\n\n /** turn of view dragging and remove event listeners */\n draggableOff: function() {\n this.draggable = false;\n var handle = this.$dragHandle()\n .attr(\"draggable\", false)\n .get(0);\n handle.removeEventListener(\"dragstart\", this.dragStartHandler, false);\n handle.removeEventListener(\"dragend\", this.dragEndHandler, false);\n },\n\n /** sets the dataTransfer data to the model's toJSON\n * @fires draggable:dragstart (bbone event) which is passed the event and this view\n */\n _dragStartHandler: function(event) {\n event.dataTransfer.effectAllowed = \"move\";\n //ASSUMES: this.model\n //TODO: all except IE: should be 'application/json', IE: must be 'text'\n event.dataTransfer.setData(\"text\", JSON.stringify(this.model.toJSON()));\n this.trigger(\"draggable:dragstart\", event, this);\n return false;\n },\n\n /** handle the dragend\n * @fires draggable:dragend (bbone event) which is passed the event and this view\n */\n _dragEndHandler: function(event) {\n this.trigger(\"draggable:dragend\", event, this);\n return false;\n }\n};\n\n//==============================================================================\n/** Mixin that allows a view to be selected (gen. from a list).\n * Selection controls ($selector) may be hidden/shown/toggled.\n * The bbone event 'selectable' is fired when the controls are shown/hidden (passed T/F).\n * Default rendering is a font-awesome checkbox.\n * Default selector is '.selector' within the view's $el.\n * The bbone events 'selected' and 'de-selected' are fired when the $selector is clicked.\n * Both events are passed the view and the (jQuery) event.\n */\nvar SelectableViewMixin = {\n /** Set up instance state vars for whether the selector is shown and whether the view has been selected */\n initialize: function(attributes) {\n /** is the view currently in selection mode? */\n this.selectable = attributes.selectable || false;\n /** is the view currently selected? */\n this.selected = attributes.selected || false;\n },\n\n /** $el sub-element where the selector is rendered and what can be clicked to select. */\n $selector: function() {\n return this.$(\".selector\");\n },\n\n /** How the selector is rendered - defaults to font-awesome checkbox */\n _renderSelected: function() {\n // override\n this.$selector()\n .find(\"span\")\n .toggleClass(\"fa-check-square-o\", this.selected)\n .toggleClass(\"fa-square-o\", !this.selected);\n },\n\n /** Toggle whether the selector is shown */\n toggleSelector: function() {\n //TODO: use this.selectable\n if (!this.$selector().is(\":visible\")) {\n this.showSelector();\n } else {\n this.hideSelector();\n }\n },\n\n /** Display the selector control.\n * @param {Number} a jQuery fx speed\n * @fires: selectable which is passed true (IOW, the selector is shown) and the view\n */\n showSelector: function(speed) {\n speed = speed !== undefined ? speed : this.fxSpeed;\n // make sure selected state is represented properly\n this.selectable = true;\n this.trigger(\"selectable\", true, this);\n this._renderSelected();\n if (speed) {\n this.$selector().show(speed);\n } else {\n this.$selector().show();\n }\n },\n\n /** remove the selector control\n * @param {Number} a jQuery fx speed\n * @fires: selectable which is passed false (IOW, the selector is not shown) and the view\n */\n hideSelector: function(speed) {\n speed = speed !== undefined ? speed : this.fxSpeed;\n // reverse the process from showSelect\n this.selectable = false;\n this.trigger(\"selectable\", false, this);\n if (speed) {\n this.$selector().hide(speed);\n } else {\n this.$selector().hide();\n }\n },\n\n /** Toggle whether the view is selected */\n toggleSelect: function(event) {\n if (this.selected) {\n this.deselect(event);\n } else {\n this.select(event);\n }\n },\n\n /** Select this view and re-render the selector control to show it\n * @param {Event} a jQuery event that caused the selection\n * @fires: selected which is passed the view and the DOM event that triggered it (optionally)\n */\n select: function(event) {\n // switch icon, set selected, and trigger event\n if (!this.selected) {\n this.trigger(\"selected\", this, event);\n this.selected = true;\n this._renderSelected();\n }\n return false;\n },\n\n /** De-select this view and re-render the selector control to show it\n * @param {Event} a jQuery event that caused the selection\n * @fires: de-selected which is passed the view and the DOM event that triggered it (optionally)\n */\n deselect: function(event) {\n // switch icon, set selected, and trigger event\n if (this.selected) {\n this.trigger(\"de-selected\", this, event);\n this.selected = false;\n this._renderSelected();\n }\n return false;\n }\n};\n\n//==============================================================================\n/** Return an underscore template fn from an array of strings.\n * @param {String[]} template the template strings to compile into the underscore template fn\n * @param {String} jsonNamespace an optional namespace for the json data passed in (defaults to 'model')\n * @returns {Function} the (wrapped) underscore template fn\n * The function accepts:\n *\n * The template strings can access:\n * the json/model hash using model (\"<%- model.myAttr %>) using the jsonNamespace above\n * _l: the localizer function\n * view (if passed): ostensibly, the view using the template (handy for view instance vars)\n * Because they're namespaced, undefined attributes will not throw an error.\n *\n * @example:\n * templateBler : BASE_MVC.wrapTemplate([\n * '\">',\n * '<% print( _l( mynamespace.message ) ); %>:<%= view.status %>'\n * ''\n * ], 'mynamespace' )\n *\n * Meant to be called in a View's definition in order to compile only once.\n *\n */\nfunction wrapTemplate(template, jsonNamespace) {\n jsonNamespace = jsonNamespace || \"model\";\n var templateFn = _.template(template.join(\"\"));\n return function(json, view) {\n var templateVars = { view: view || {}, _l: _l };\n templateVars[jsonNamespace] = json || {};\n return templateFn(templateVars);\n };\n}\n\n//==============================================================================\n/** Return a comparator function for sorted Collections */\nfunction buildComparator(attribute_name, options) {\n options = options || {};\n var ascending = options.ascending ? 1 : -1;\n return function __comparator(a, b) {\n a = a.get(attribute_name);\n b = b.get(attribute_name);\n return (a < b ? -1 : a > b ? 1 : 0) * ascending;\n };\n}\n\n//==============================================================================\nexport default {\n LoggableMixin: LoggableMixin,\n SessionStorageModel: SessionStorageModel,\n mixin: mixin,\n SearchableModelMixin: SearchableModelMixin,\n HiddenUntilActivatedViewMixin: HiddenUntilActivatedViewMixin,\n DraggableViewMixin: DraggableViewMixin,\n SelectableViewMixin: SelectableViewMixin,\n wrapTemplate: wrapTemplate,\n buildComparator: buildComparator\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/base/controlled-fetch-collection.js.map b/static/maps/mvc/base/controlled-fetch-collection.js.map index d4fe6d49193..44c2cafad8b 100644 --- a/static/maps/mvc/base/controlled-fetch-collection.js.map +++ b/static/maps/mvc/base/controlled-fetch-collection.js.map @@ -1 +1 @@ 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_ from \"libs/underscore\";\nimport Backbone from \"libs/backbone\";\nimport BASE_MVC from \"mvc/base-mvc\";\n\n//=============================================================================\n/**\n * A Collection that can be limited/offset/re-ordered/filtered.\n * @type {Backbone.Collection}\n */\nvar ControlledFetchCollection = Backbone.Collection.extend({\n /** call setOrder on initialization to build the comparator based on options */\n initialize: function(models, options) {\n Backbone.Collection.prototype.initialize.call(this, models, options);\n this.setOrder(options.order || this.order, { silent: true });\n },\n\n /** set up to track order changes and re-sort when changed */\n _setUpListeners: function() {\n return this.on({\n \"changed-order\": this.sort\n });\n },\n\n /** override to provide order and offsets based on instance vars, set limit if passed,\n * and set allFetched/fire 'all-fetched' when xhr returns\n */\n fetch: function(options) {\n options = 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collection.comparators[order];\n if (_.isUndefined(comparator)) {\n throw new Error(\"unknown order: \" + order);\n }\n // if( _.isUndefined( comparator ) ){ return; }\n if (comparator === collection.comparator) {\n return;\n }\n\n collection.order = order;\n collection.comparator = comparator;\n\n if (!options.silent) {\n collection.trigger(\"changed-order\", options);\n }\n return collection;\n }\n});\n\n//=============================================================================\n/**\n *\n */\nvar PaginatedCollection = ControlledFetchCollection.extend({\n /** @type {Number} limit used for each page's fetch */\n limitPerPage: 500,\n\n initialize: function(models, options) {\n ControlledFetchCollection.prototype.initialize.call(\n this,\n models,\n options\n );\n this.currentPage = options.currentPage || 0;\n },\n\n getTotalItemCount: function() {\n return this.length;\n },\n\n shouldPaginate: function() {\n return this.getTotalItemCount() >= this.limitPerPage;\n },\n\n 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{Boolean} are all contents fetched? */\n this.allFetched = false;\n /** @type {Integer} what was the offset of the last content returned */\n this.lastFetched = options.lastFetched || 0;\n },\n\n /** build ajax data/parameters from options */\n _buildFetchOptions: function(options) {\n // options (options for backbone.fetch and jquery.ajax generally)\n // backbone option; false here to make fetching an addititive process\n options.remove = options.remove || false;\n return ControlledFetchCollection.prototype._buildFetchOptions.call(\n this,\n options\n );\n },\n\n /** fetch the first 'page' of data */\n fetchFirst: function(options) {\n Galaxy.debug(\"ControlledFetchCollection.fetchFirst:\", options);\n options = options ? _.clone(options) : {};\n this.allFetched = false;\n this.lastFetched = 0;\n return this.fetchMore(\n _.defaults(options, {\n reset: true,\n limit: this.limitOnFirstFetch\n })\n );\n },\n\n /** fetch the next page of data */\n fetchMore: function(options) {\n 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_.isArray(fetchedData)\n ? fetchedData.length\n : 0;\n collection.lastFetched += numFetched;\n Galaxy.debug(\n \"fetchMore, lastFetched:\",\n collection.lastFetched\n );\n // anything less than a full page means we got all there is to get\n if (!limit || numFetched < limit) {\n collection.allFetched = true;\n collection.trigger(\"all-fetched\", this);\n }\n })\n );\n },\n\n /** fetch all the collection */\n fetchAll: function(options) {\n // whitelist options to prevent allowing limit/offset/filters\n // (use vanilla fetch instead)\n options = options || {};\n var self = this;\n options = _.pick(options, \"silent\");\n options.filters = {};\n return self.fetch(options).done(function() {\n self.allFetched = true;\n self.trigger(\"all-fetched\", self);\n });\n }\n});\n\n//==============================================================================\nexport default {\n ControlledFetchCollection: ControlledFetchCollection,\n PaginatedCollection: PaginatedCollection,\n InfinitelyScrollingCollection: InfinitelyScrollingCollection\n};\n"]} \ No newline at end of file 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_ from \"libs/underscore\";\nimport Backbone from \"libs/backbone\";\nimport BASE_MVC from \"mvc/base-mvc\";\n\n//=============================================================================\n/**\n * A Collection that can be limited/offset/re-ordered/filtered.\n * @type {Backbone.Collection}\n */\nvar ControlledFetchCollection = Backbone.Collection.extend({\n /** call setOrder on initialization to build the comparator based on options */\n initialize: function(models, options) {\n Backbone.Collection.prototype.initialize.call(this, models, options);\n this.setOrder(options.order || this.order, { silent: true });\n },\n\n /** set up to track order changes and re-sort when changed */\n _setUpListeners: function() {\n return this.on({\n \"changed-order\": this.sort\n });\n },\n\n /** override to provide order and offsets based on instance vars, set limit if passed,\n * and set allFetched/fire 'all-fetched' when xhr returns\n */\n fetch: function(options) {\n options = this._buildFetchOptions(options);\n Galaxy.debug(\"fetch options:\", options);\n return Backbone.Collection.prototype.fetch.call(this, options);\n },\n\n /** build ajax data/parameters from options */\n _buildFetchOptions: function(options) {\n // note: we normally want options passed in to override the defaults built here\n // so most of these fns will generate defaults\n options = _.clone(options) || {};\n var self = this;\n\n // jquery ajax option; allows multiple q/qv for filters (instead of 'q[]')\n options.traditional = true;\n\n // options.data\n // we keep limit, offset, etc. in options *as well as move it into data* because:\n // - it makes fetch calling convenient to add it to a single options map (instead of as mult. args)\n // - it allows the std. event handlers (for fetch, etc.) to have access\n // to the pagination options too\n // (i.e. this.on( 'sync', function( options ){ if( options.limit ){ ... } }))\n // however, when we send to xhr/jquery we copy them to data also so that they become API query params\n options.data = options.data || self._buildFetchData(options);\n Galaxy.debug(\"data:\", options.data);\n\n // options.data.filters --> options.data.q, options.data.qv\n var filters = this._buildFetchFilters(options);\n Galaxy.debug(\"filters:\", filters);\n if (!_.isEmpty(filters)) {\n _.extend(options.data, this._fetchFiltersToAjaxData(filters));\n }\n Galaxy.debug(\"data:\", options.data);\n return options;\n },\n\n /** Build the dictionary to send to fetch's XHR as data */\n _buildFetchData: function(options) {\n var defaults = {};\n if (this.order) {\n defaults.order = this.order;\n }\n return _.defaults(_.pick(options, this._fetchParams), defaults);\n },\n\n /** These attribute keys are valid params to fetch/API-index */\n _fetchParams: [\n /** model dependent string to control the order of models returned */\n \"order\",\n /** limit the number of models returned from a fetch */\n \"limit\",\n /** skip this number of models when fetching */\n 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collection.comparators[order];\n if (_.isUndefined(comparator)) {\n throw new Error(\"unknown order: \" + order);\n }\n // if( _.isUndefined( comparator ) ){ return; }\n if (comparator === collection.comparator) {\n return;\n }\n\n collection.order = order;\n collection.comparator = comparator;\n\n if (!options.silent) {\n collection.trigger(\"changed-order\", options);\n }\n return collection;\n }\n});\n\n//=============================================================================\n/**\n *\n */\nvar PaginatedCollection = ControlledFetchCollection.extend({\n /** @type {Number} limit used for each page's fetch */\n limitPerPage: 500,\n\n initialize: function(models, options) {\n ControlledFetchCollection.prototype.initialize.call(\n this,\n models,\n options\n );\n this.currentPage = options.currentPage || 0;\n },\n\n getTotalItemCount: function() {\n return this.length;\n },\n\n shouldPaginate: function() {\n return this.getTotalItemCount() >= this.limitPerPage;\n },\n\n 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\");\n return this;\n },\n formattedReference: function() {\n var model = this.model;\n var entryType = model.entryType();\n var fields = model.fields();\n\n var ref = \"\";\n // Code inspired by...\n // https://github.com/vkaravir/bib-publication-list/blob/master/src/bib-publication-list.js\n var authorsAndYear =\n this._asSentence(\n (fields.author ? fields.author : \"\") +\n (fields.year ? \" (\" + fields.year + \")\" : \"\")\n ) + \" \";\n var title = fields.title || \"\";\n var pages = fields.pages ? \"pp. \" + fields.pages : \"\";\n var address = fields.address;\n if (entryType == \"article\") {\n var volume =\n (fields.volume ? fields.volume : \"\") +\n (fields.number ? \" (\" + fields.number + \")\" : \"\") +\n (pages ? \", \" + pages : \"\");\n ref =\n authorsAndYear +\n this._asSentence(title) +\n (fields.journal\n ? \"In \" + fields.journal + \", \"\n : \"\") +\n this._asSentence(volume) +\n this._asSentence(fields.address) +\n \"\";\n } else if (\n entryType == \"inproceedings\" ||\n entryType == \"proceedings\"\n ) {\n ref =\n authorsAndYear +\n this._asSentence(title) +\n (fields.booktitle\n ? \"In \" + fields.booktitle + \", \"\n : \"\") +\n (pages ? pages : \"\") +\n (address ? \", \" + address : \"\") +\n \".\";\n } else if (\n entryType == \"mastersthesis\" ||\n entryType == \"phdthesis\"\n ) {\n ref =\n authorsAndYear +\n this._asSentence(title) +\n (fields.howpublished\n ? fields.howpublished + \". \"\n : \"\") +\n (fields.note ? fields.note + \".\" : \"\");\n } else if (entryType == \"techreport\") {\n ref =\n authorsAndYear +\n this._asSentence(title) +\n this._asSentence(fields.institution) +\n this._asSentence(fields.number) +\n this._asSentence(fields.type);\n } else if (\n entryType == \"book\" ||\n entryType == \"inbook\" ||\n entryType == \"incollection\"\n ) {\n ref = authorsAndYear + \" \" + this._formatBookInfo(fields);\n } else {\n ref =\n authorsAndYear +\n \" \" +\n this._asSentence(title) +\n this._asSentence(fields.howpublished) +\n this._asSentence(fields.note);\n }\n var doiUrl = \"\";\n if (fields.doi) {\n doiUrl = \"http://dx.doi.org/\" + fields.doi;\n ref +=\n '[doi:' +\n fields.doi +\n \"]\";\n }\n var url = fields.url || doiUrl;\n if (url) {\n ref += '[Link]';\n }\n return ref;\n },\n _formatBookInfo: function(fields) {\n var info = \"\";\n if (fields.chapter) {\n info += fields.chapter + \" in \";\n }\n if (fields.title) {\n info += \"\" + fields.title + \"\";\n }\n if (fields.editor) {\n info += \", Edited by \" + fields.editor + \", \";\n }\n if (fields.publisher) {\n info += \", \" + fields.publisher;\n }\n if (fields.pages) {\n info += \", pp. \" + fields.pages + \"\";\n }\n if (fields.series) {\n info += \", \" + fields.series + \"\";\n }\n if (fields.volume) {\n info += \", Vol.\" + fields.volume;\n }\n if (fields.issn) {\n info += \", ISBN: \" + fields.issn;\n }\n return info + \".\";\n },\n _asSentence: function(str) {\n return str && str.trim() ? str + \". \" : \"\";\n }\n });\n\n var CitationListView = Backbone.View.extend({\n el: \"#citations\",\n /**\n * Set up view.\n */\n initialize: function() {\n this.listenTo(this.collection, \"add\", this.renderCitation);\n },\n\n events: {\n \"click .citations-to-bibtex\": \"showBibtex\",\n \"click .citations-to-formatted\": \"showFormatted\"\n },\n\n renderCitation: function(citation) {\n var citationView = new CitationView({ model: citation });\n this.$(\".citations-formatted\").append(citationView.render().el);\n var rawTextarea = this.$(\".citations-bibtex-text\");\n rawTextarea.val(\n rawTextarea.val() + \"\\n\\r\" + citation.attributes.content\n );\n },\n\n render: function() {\n this.$el.html(this.citationsElement());\n this.collection.each(function(item) {\n this.renderCitation(item);\n }, this);\n this.showFormatted();\n },\n\n showBibtex: function() {\n this.$(\".citations-to-formatted\").show();\n this.$(\".citations-to-bibtex\").hide();\n this.$(\".citations-bibtex\").show();\n this.$(\".citations-formatted\").hide();\n this.$(\".citations-bibtex-text\").select();\n },\n\n showFormatted: function() {\n this.$(\".citations-to-formatted\").hide();\n this.$(\".citations-to-bibtex\").show();\n this.$(\".citations-bibtex\").hide();\n this.$(\".citations-formatted\").show();\n },\n\n partialWarningElement: function() {\n if (this.collection.partial) {\n return [\n '',\n \"Warning: This is a experimental feature. Most Galaxy tools will not annotate\",\n \" citations explicitly at this time. When writing up your analysis, please manually\",\n \" review your histories and find all references\",\n \" that should be cited in order to completely describe your work. Also, please remember to\",\n ' cite Galaxy.',\n \"\"\n ].join(\"\");\n } else {\n return \"\";\n }\n },\n\n citationsElement: function() {\n return [\n '',\n '\"\n ].join(\"\");\n }\n });\n\n //==============================================================================\n return {\n CitationView: CitationView,\n CitationListView: CitationListView\n };\n }\n);\n"]} \ No newline at end of file +{"version":3,"sources":["mvc/citation/citation-view.js"],"names":["define","baseMVC","citationModel","_l","CitationView","Backbone","View","extend","tagName","className","render","$el","append","this","formattedReference","model","entryType","ref","authorsAndYear","title","fields","author","pages","address","volume","_asSentence","journal","doiUrl","doi","url","booktitle","info","chapter","publisher","howpublished","note","institution","type","_formatBookInfo","CitationListView","initialize","renderCitation","rawTextarea","citationView","html","collection","each","showFormatted","editor","showBibtex","series","issn","partialWarningElement","str","trim","el","events","click .citations-to-bibtex","click .citations-to-formatted","citation","$","val","attributes","content","citationsElement","item","show","hide","select","partial","join"],"mappings":"kCAAAA,QACK,eAAgB,8BAA+B,sBAChD,SAASC,EAASC,EAAeC,GAFrCH,IACKI,EAADC,SAAiBC,KAAAC,QAETH,QAAAA,MACAI,UAAS,YACTC,OAAAA,WAEI,OADJC,KAAQC,IAAAC,OAAA,MAAWC,KAAAC,qBAAA,QACVH,MAERG,mBANmC,WAOpCA,IAAAA,EAAAA,KAAoBC,MACZA,EAAQA,EAAZC,YACIA,EAAAA,EAAYD,SAGZE,EAAM,GAEVC,EACIA,KAAAA,aAKAC,EAAQC,OAAAA,EAAZC,OAAA,KACYD,EAAOE,KAAQ,KAAAF,EAASA,KAAxB,IAAZ,KACIG,IACAP,EAAAA,EAAaG,OAAW,GACxBG,EAAIE,EACCJ,MAAOI,OAASJ,EAAOI,MAAS,GAGrCP,EACIC,EAAAA,QAQP,GACGF,WAfJA,EAeiB,CAGbC,IAAAA,GASGG,EACHJ,OAAaI,EAAAI,OAAb,KAGAP,EACIC,OAAAA,KACKO,EAAAA,OAAYN,IAChBC,KAIFE,EAAIN,KAAaM,EAAA,IACpBL,EAMGC,EAKHD,KAAMC,YAAAA,IACHE,EAAAM,QAECR,UAAAA,EAEAQ,QAAKD,KAGZ,IACGE,KAASF,YAAbD,GACIJ,KAAOQ,YAAKR,EAAAG,SACZI,aAUAV,EAHH,iBAAAD,GACgBa,eAAbA,EAGHX,EACMD,KAAPQ,YAAAN,IAhGgCC,EAAAU,UAkGnB,UAAAV,EAAAU,UAAA,KACb,KACIV,GAAgB,KAChBW,EAAeC,KAAPT,EAAR,IACH,SAEW,iBAARQ,GACH,aAAAf,EAGAE,EACGE,KAAOa,YAAWd,IAClBY,EAAQG,aACXd,EAAAc,aAAA,KACUZ,KACPS,EAAQI,KAAWf,EAAOE,KAAlB,IAAR,IACH,cAAAN,EAEGe,EACHlB,KAAAY,YAAAN,GACGC,KAAOI,YAAQJ,EAAAgB,aACfL,KAAQN,YAAWL,EAAOI,QAC7BX,KAAAY,YAAAL,EAAAiB,MAEW,QAARN,GACH,UAAAf,GACD,gBAAAA,EAESE,EAAA,IAAAL,KAAcyB,gBAAAlB,GA9H/BF,EA6EgB,IAsDZqB,KAAAA,YAA4BjC,GACxBO,KADoCY,YAAAL,EAAAc,cAExCrB,KAAAY,YAAAL,EAAAe,MAnDI,IAAIR,EAAS,GAsDjBa,EAAYZ,MAL4BX,GA7C5B,cAmDRU,EAAA,qBAAAP,EAA2CqB,KAI3C,yBACArB,EAAAQ,IAXoC,SAcxCa,IAAAA,EAAAA,EAAgBZ,KAAAF,EAIZe,OAHIC,IACJ1B,GAAO,aAAAY,EAAwBjB,+BAE/B8B,GAnDJJ,gBAAiB,SAASlB,GAwD1BV,IAAQqB,EAAA,GAyBA,OAxBJX,EAASwB,UACTb,GAAKc,EAAWC,QAAK,QAElB1B,EAFHD,QAGAY,GAAKgB,OAAL3B,EAAAD,MAAA,SArDIC,EAAO4B,SAwDfC,GAAY,eAAA7B,EAAW4B,OAAA,MAEnB5B,EAAOa,YACPF,GAAO,KAAAX,EAAPa,WAEAb,EAAOE,QApC6BS,GAAA,SAAAX,EAAAE,OAuCxCyB,EAAeG,SACXnB,GAAO,SAAAX,EAAA8B,OAAP,SAEA9B,EAAOI,SACPO,GAAO,SAAAX,EAAPI,QArDIJ,EAAO+B,OAwDfC,GAAAA,WAAuBhC,EAAA+B,MAEfpB,EACI,KASJN,YAAA,SAAA4B,GACH,OAAAA,GAAAA,EAAAC,OAAAD,EAAA,KAAA,MAIDd,EACIlC,SAAAC,KAAAC,QAePgD,GAAA,aAILf,WAAO,WACHpC,KAAAA,SAAcA,KAAAA,WADX,MAAAS,KAAA4B,iBAzNfe,QAgJgBC,6BAA8B,aAC9BC,gCAAiC,iBAGrCjB,eAAgB,SAASkB,GACrB,IAAIhB,EAAe,IAAIvC,GAAeW,MAAO4C,IAC7C9C,KAAK+C,EAAE,wBAAwBhD,OAAO+B,EAAajC,SAAS6C,IAC5D,IAAIb,EAAc7B,KAAK+C,EAAE,0BACzBlB,EAAYmB,IACRnB,EAAYmB,MAAQ,OAASF,EAASG,WAAWC,UAIzDrD,OAAQ,WACJG,KAAKF,IAAIiC,KAAK/B,KAAKmD,oBACnBnD,KAAKgC,WAAWC,KAAK,SAASmB,GAC1BpD,KAAK4B,eAAewB,IACrBpD,MACHA,KAAKkC,iBAGTE,WAAY,WACRpC,KAAK+C,EAAE,2BAA2BM,OAClCrD,KAAK+C,EAAE,wBAAwBO,OAC/BtD,KAAK+C,EAAE,qBAAqBM,OAC5BrD,KAAK+C,EAAE,wBAAwBO,OAC/BtD,KAAK+C,EAAE,0BAA0BQ,UAGrCrB,cAAe,WACXlC,KAAK+C,EAAE,2BAA2BO,OAClCtD,KAAK+C,EAAE,wBAAwBM,OAC/BrD,KAAK+C,EAAE,qBAAqBO,OAC5BtD,KAAK+C,EAAE,wBAAwBM,QAGnCd,sBAAuB,WACnB,OAAIvC,KAAKgC,WAAWwB,SAEZ,iCACA,sFACA,qFACA,iDACA,4FACA,sEACA,UACFC,KAAK,IAEA,IAIfN,iBAAkB,WACd,OACI,yBACA,8BACA7D,EAAG,aACH,8JACA,+JACA,SACA,sDACAU,KAAKuC,wBACL,2EACA,SACA,uEACA,0FACA,SACA,UACFkB,KAAK,OAKf,OACIlE,aAAcA,EACdmC,iBAAkBA","file":"../../../scripts/mvc/citation/citation-view.js","sourcesContent":["define(\n [\"mvc/base-mvc\", \"mvc/citation/citation-model\", \"utils/localization\"],\n function(baseMVC, citationModel, _l) {\n var CitationView = Backbone.View.extend({\n tagName: \"div\",\n className: \"citations\",\n render: function() {\n this.$el.append(\"',\n _l(\"Citations\"),\n ' ',\n ' ',\n \"\",\n '',\n this.partialWarningElement(),\n '',\n \"\",\n '',\n '',\n \"\",\n \"\" + this.formattedReference() + \"
\");\n return this;\n },\n formattedReference: function() {\n var model = this.model;\n var entryType = model.entryType();\n var fields = model.fields();\n\n var ref = \"\";\n // Code inspired by...\n // https://github.com/vkaravir/bib-publication-list/blob/master/src/bib-publication-list.js\n var authorsAndYear =\n this._asSentence(\n (fields.author ? fields.author : \"\") +\n (fields.year ? \" (\" + fields.year + \")\" : \"\")\n ) + \" \";\n var title = fields.title || \"\";\n var pages = fields.pages ? \"pp. \" + fields.pages : \"\";\n var address = fields.address;\n if (entryType == \"article\") {\n var volume =\n (fields.volume ? fields.volume : \"\") +\n (fields.number ? \" (\" + fields.number + \")\" : \"\") +\n (pages ? \", \" + pages : \"\");\n ref =\n authorsAndYear +\n this._asSentence(title) +\n (fields.journal\n ? \"In \" + fields.journal + \", \"\n : \"\") +\n this._asSentence(volume) +\n this._asSentence(fields.address) +\n \"\";\n } else if (\n entryType == \"inproceedings\" ||\n entryType == \"proceedings\"\n ) {\n ref =\n authorsAndYear +\n this._asSentence(title) +\n (fields.booktitle\n ? \"In \" + fields.booktitle + \", \"\n : \"\") +\n (pages ? pages : \"\") +\n (address ? \", \" + address : \"\") +\n \".\";\n } else if (\n entryType == \"mastersthesis\" ||\n entryType == \"phdthesis\"\n ) {\n ref =\n authorsAndYear +\n this._asSentence(title) +\n (fields.howpublished\n ? fields.howpublished + \". \"\n : \"\") +\n (fields.note ? fields.note + \".\" : \"\");\n } else if (entryType == \"techreport\") {\n ref =\n authorsAndYear +\n this._asSentence(title) +\n this._asSentence(fields.institution) +\n this._asSentence(fields.number) +\n this._asSentence(fields.type);\n } else if (\n entryType == \"book\" ||\n entryType == \"inbook\" ||\n entryType == \"incollection\"\n ) {\n ref = authorsAndYear + \" \" + this._formatBookInfo(fields);\n } else {\n ref =\n authorsAndYear +\n \" \" +\n this._asSentence(title) +\n this._asSentence(fields.howpublished) +\n this._asSentence(fields.note);\n }\n var doiUrl = \"\";\n if (fields.doi) {\n doiUrl = \"http://dx.doi.org/\" + fields.doi;\n ref +=\n '[doi:' +\n fields.doi +\n \"]\";\n }\n var url = fields.url || doiUrl;\n if (url) {\n ref += '[Link]';\n }\n return ref;\n },\n _formatBookInfo: function(fields) {\n var info = \"\";\n if (fields.chapter) {\n info += fields.chapter + \" in \";\n }\n if (fields.title) {\n info += \"\" + fields.title + \"\";\n }\n if (fields.editor) {\n info += \", Edited by \" + fields.editor + \", \";\n }\n if (fields.publisher) {\n info += \", \" + fields.publisher;\n }\n if (fields.pages) {\n info += \", pp. \" + fields.pages + \"\";\n }\n if (fields.series) {\n info += \", \" + fields.series + \"\";\n }\n if (fields.volume) {\n info += \", Vol.\" + fields.volume;\n }\n if (fields.issn) {\n info += \", ISBN: \" + fields.issn;\n }\n return info + \".\";\n },\n _asSentence: function(str) {\n return str && str.trim() ? str + \". \" : \"\";\n }\n });\n\n var CitationListView = Backbone.View.extend({\n el: \"#citations\",\n /**\n * Set up view.\n */\n initialize: function() {\n this.listenTo(this.collection, \"add\", this.renderCitation);\n },\n\n events: {\n \"click .citations-to-bibtex\": \"showBibtex\",\n \"click .citations-to-formatted\": \"showFormatted\"\n },\n\n renderCitation: function(citation) {\n var citationView = new CitationView({ model: citation });\n this.$(\".citations-formatted\").append(citationView.render().el);\n var rawTextarea = this.$(\".citations-bibtex-text\");\n rawTextarea.val(\n rawTextarea.val() + \"\\n\\r\" + citation.attributes.content\n );\n },\n\n render: function() {\n this.$el.html(this.citationsElement());\n this.collection.each(function(item) {\n this.renderCitation(item);\n }, this);\n this.showFormatted();\n },\n\n showBibtex: function() {\n this.$(\".citations-to-formatted\").show();\n this.$(\".citations-to-bibtex\").hide();\n this.$(\".citations-bibtex\").show();\n this.$(\".citations-formatted\").hide();\n this.$(\".citations-bibtex-text\").select();\n },\n\n showFormatted: function() {\n this.$(\".citations-to-formatted\").hide();\n this.$(\".citations-to-bibtex\").show();\n this.$(\".citations-bibtex\").hide();\n this.$(\".citations-formatted\").show();\n },\n\n partialWarningElement: function() {\n if (this.collection.partial) {\n return [\n '',\n \"Warning: This is a experimental feature. Most Galaxy tools will not annotate\",\n \" citations explicitly at this time. When writing up your analysis, please manually\",\n \" review your histories and find all references\",\n \" that should be cited in order to completely describe your work. Also, please remember to\",\n ' cite Galaxy.',\n \"\"\n ].join(\"\");\n } else {\n return \"\";\n }\n },\n\n citationsElement: function() {\n return [\n '',\n '\"\n ].join(\"\");\n }\n });\n\n //==============================================================================\n return {\n CitationView: CitationView,\n CitationListView: CitationListView\n };\n }\n);\n"]} \ No newline at end of file diff --git a/static/maps/mvc/collection/base-creator.js.map b/static/maps/mvc/collection/base-creator.js.map index 00aecf08b72..01caf6c53d3 100644 --- a/static/maps/mvc/collection/base-creator.js.map +++ b/static/maps/mvc/collection/base-creator.js.map @@ -1 +1 @@ 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For presentation-related functionality shared across collection creators.\n Particularily overlapping functionality related to name processing and help.\n*/\nvar CollectionCreatorMixin = {\n /** add (or clear if clear is truthy) a validation warning to the DOM element described in what */\n _validationWarning: function(what, clear) {\n var VALIDATION_CLASS = \"validation-warning\";\n if (what === \"name\") {\n what = this.$(\".collection-name\").add(\n this.$(\".collection-name-prompt\")\n );\n this.$(\".collection-name\")\n .focus()\n .select();\n }\n if (clear) {\n what = what || this.$(\".\" + VALIDATION_CLASS);\n what.removeClass(VALIDATION_CLASS);\n } else {\n what.addClass(VALIDATION_CLASS);\n }\n },\n\n _changeHideOriginals: function(ev) {\n this.hideOriginals = this.$(\".hide-originals\").prop(\"checked\");\n },\n\n // ........................................................................ footer\n /** handle a collection name change */\n _changeName: function(ev) {\n this._validationWarning(\"name\", !!this._getName());\n },\n\n /** check for enter key press when in the collection name and submit */\n _nameCheckForEnter: function(ev) {\n if (ev.keyCode === 13 && !this.blocking) {\n this._clickCreate();\n }\n },\n\n /** get the current collection name */\n _getName: function() {\n return _.escape(this.$(\".collection-name\").val());\n },\n\n // ........................................................................ header\n /** expand help */\n _clickMoreHelp: function(ev) {\n ev.stopPropagation();\n this.$(\".main-help\").addClass(\"expanded\");\n this.$(\".more-help\").hide();\n },\n /** collapse help */\n _clickLessHelp: function(ev) {\n ev.stopPropagation();\n this.$(\".main-help\").removeClass(\"expanded\");\n this.$(\".more-help\").show();\n },\n /** toggle help */\n _toggleHelp: function(ev) {\n ev.stopPropagation();\n this.$(\".main-help\").toggleClass(\"expanded\");\n this.$(\".more-help\").toggle();\n },\n\n /** show an alert on the top 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footer, completion controls, and cancel controls */\n _renderFooter: function(speed, callback) {\n var self = this;\n var $footer = this.$(\".footer\")\n .empty()\n .html(this.templates.footer());\n _.each(this.footerSettings, function(property, selector) {\n self.$(selector).prop(\"checked\", self[property]);\n });\n if (typeof this.oncancel === \"function\") {\n this.$(\".cancel-create.btn\").show();\n }\n return $footer;\n },\n\n _creatorTemplates: {\n main: _.template(\n [\n '',\n '',\n ''\n ].join(\"\")\n )\n }\n};\n\n//==============================================================================\nexport default {\n CollectionCreatorMixin: CollectionCreatorMixin\n};\n"]} \ No newline at end of file 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For presentation-related functionality shared across collection creators.\n Particularily overlapping functionality related to name processing and help.\n*/\nvar CollectionCreatorMixin = {\n /** add (or clear if clear is truthy) a validation warning to the DOM element described in what */\n _validationWarning: function(what, clear) {\n var VALIDATION_CLASS = \"validation-warning\";\n if (what === \"name\") {\n what = this.$(\".collection-name\").add(\n this.$(\".collection-name-prompt\")\n );\n this.$(\".collection-name\")\n .focus()\n .select();\n }\n if (clear) {\n what = what || this.$(\".\" + VALIDATION_CLASS);\n what.removeClass(VALIDATION_CLASS);\n } else {\n what.addClass(VALIDATION_CLASS);\n }\n },\n\n _changeHideOriginals: function(ev) {\n this.hideOriginals = this.$(\".hide-originals\").prop(\"checked\");\n },\n\n // ........................................................................ footer\n /** handle a collection name change */\n _changeName: function(ev) {\n 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of the interface containing message (alertClass is bootstrap's alert-*) */\n _showAlert: function(message, alertClass) {\n alertClass = alertClass || \"alert-danger\";\n this.$(\".main-help\").hide();\n this.$(\".header .alert\")\n .attr(\"class\", \"alert alert-dismissable\")\n .addClass(alertClass)\n .show()\n .find(\".alert-message\")\n .html(message);\n },\n /** hide the alerts at the top */\n _hideAlert: function(message) {\n this.$(\".main-help\").show();\n this.$(\".header .alert\").hide();\n },\n\n _cancelCreate: function(ev) {\n if (typeof this.oncancel === \"function\") {\n this.oncancel.call(this);\n }\n },\n\n /** attempt to create the current collection */\n _clickCreate: function(ev) {\n var name = this._getName();\n if (!name) {\n this._validationWarning(\"name\");\n } else if (!this.blocking) {\n this.createList(name);\n }\n },\n\n _setUpCommonSettings: function(attributes) {\n this.hideOriginals = attributes.defaultHideSourceItems || false;\n },\n\n /** render the footer, completion controls, and cancel controls */\n _renderFooter: function(speed, callback) {\n var self = this;\n var $footer = this.$(\".footer\")\n .empty()\n .html(this.templates.footer());\n _.each(this.footerSettings, function(property, selector) {\n self.$(selector).prop(\"checked\", self[property]);\n });\n if (typeof this.oncancel === \"function\") {\n this.$(\".cancel-create.btn\").show();\n }\n return $footer;\n },\n\n _creatorTemplates: {\n main: _.template(\n [\n '',\n '',\n ''\n ].join(\"\")\n )\n }\n};\n\n//==============================================================================\nexport default {\n CollectionCreatorMixin: CollectionCreatorMixin\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/collection/collection-li-edit.js.map b/static/maps/mvc/collection/collection-li-edit.js.map index 453994b1ed0..ff4d07c9895 100644 --- a/static/maps/mvc/collection/collection-li-edit.js.map +++ b/static/maps/mvc/collection/collection-li-edit.js.map @@ -1 +1 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DC_LI from \"mvc/collection/collection-li\";\nimport DATASET_LI_EDIT from \"mvc/dataset/dataset-li-edit\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\nvar DCListItemView = DC_LI.DCListItemView;\n/** @class Edit view for DatasetCollection.\n */\nvar DCListItemEdit = DCListItemView.extend(\n /** @lends DCListItemEdit.prototype */ {\n /** override to add linkTarget */\n initialize: function(attributes) {\n DCListItemView.prototype.initialize.call(this, attributes);\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"DCListItemEdit(\" + modelString + \")\";\n }\n }\n);\n\n//==============================================================================\nvar DCEListItemView = DC_LI.DCEListItemView;\n/** @class Read only view for DatasetCollectionElement.\n */\nvar DCEListItemEdit = DCEListItemView.extend(\n /** @lends DCEListItemEdit.prototype */ {\n //TODO: this might be expendable - compacted with HDAListItemView\n\n /** set up */\n initialize: function(attributes) {\n DCEListItemView.prototype.initialize.call(this, attributes);\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"DCEListItemEdit(\" + modelString + \")\";\n }\n }\n);\n\n//==============================================================================\n// NOTE: this does not inherit from DatasetDCEListItemView as you would expect\n//TODO: but should - if we can find something simpler than using diamond\n/** @class Editable view for a DatasetCollectionElement that is also an DatasetAssociation\n * (a dataset contained in a dataset collection).\n */\nvar DatasetDCEListItemEdit = DATASET_LI_EDIT.DatasetListItemEdit.extend(\n /** @lends DatasetDCEListItemEdit.prototype */ {\n /** set up */\n initialize: function(attributes) {\n DATASET_LI_EDIT.DatasetListItemEdit.prototype.initialize.call(\n this,\n attributes\n );\n },\n\n // NOTE: this does not inherit from DatasetDCEListItemView - so we duplicate this here\n //TODO: fix\n /** In this override, only get details if in the ready state.\n * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n */\n _fetchModelDetails: function() {\n var view = this;\n if (view.model.inReadyState() && !view.model.hasDetails()) {\n return view.model.fetch({ silent: true });\n }\n return jQuery.when();\n },\n\n /** Override to remove delete button */\n _renderDeleteButton: function() {\n return null;\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"DatasetDCEListItemEdit(\" + modelString + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDatasetDCEListItemEdit.prototype.templates = (function() {\n return _.extend(\n {},\n DATASET_LI_EDIT.DatasetListItemEdit.prototype.templates,\n {\n titleBar: DC_LI.DatasetDCEListItemView.prototype.templates.titleBar\n }\n );\n})();\n\n//==============================================================================\n/** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection\n * (a nested DC).\n */\nvar NestedDCDCEListItemEdit = DC_LI.NestedDCDCEListItemView.extend(\n /** @lends NestedDCDCEListItemEdit.prototype */ {\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"NestedDCDCEListItemEdit(\" + modelString + \")\";\n }\n }\n);\n\n//==============================================================================\nexport default {\n DCListItemEdit: DCListItemEdit,\n DCEListItemEdit: DCEListItemEdit,\n DatasetDCEListItemEdit: DatasetDCEListItemEdit,\n NestedDCDCEListItemEdit: NestedDCDCEListItemEdit\n};\n"]} \ No newline at end of file +{"version":3,"sources":["mvc/collection/collection-li-edit.js"],"names":["DCListItemView","_collectionLi2","default","DCListItemEdit","extend","initialize","attributes","prototype","call","this","toString","model","DCEListItemView","modelString","DatasetDCEListItemEdit","_datasetLiEdit2","DatasetListItemEdit","_fetchModelDetails","view","inReadyState","hasDetails","fetch","jQuery","when","_renderDeleteButton","templates","_","titleBar","DatasetDCEListItemView","NestedDCDCEListItemEdit","NestedDCDCEListItemView","DCEListItemEdit"],"mappings":"2QAMIA,aAAiBC,EAAAC,QAAMF,gBAGvBG,EAAiBH,EAAeI,QAG5BC,WAAY,SAASC,GACjBN,EAAeO,UAAUF,WAAWG,KAAKC,KAAMH,IAKnDI,SAAU,WAEN,MAAO,mBADWD,KAAKE,MAAQF,KAAKE,MAAQ,GAAK,cACR,OAVjDC,EAAAX,EAAAC,QAAAU,gBAGQZ,EAAAA,EAAyBK,QAK7BK,WAAU,SAAAJ,GACNM,EAAIC,UAAmBF,WAAaA,KAALF,KAAbH,IAM9BI,SAAA,WAEA,MAAA,oBADsBD,KAAAE,MAAAF,KAAAE,MAAMC,GAAAA,cAC5B,OAWQE,EAAAC,EAAAb,QAAAc,oBAAAZ,QAGIC,WAAIQ,SAAAA,GACJE,EAAAb,QAAOc,oBAAqBH,UAA5BR,WAAAG,KACHC,KAdTH,IAyBIW,mBAAA,WACI,IAAAC,EAAAT,KACAJ,OAAAA,EAAYM,MAAAQ,iBAASb,EAATK,MAAqBS,aAC7BF,EAAAP,MAAAU,OAAgBL,QAAAA,IAgBTM,OAAOC,QAIlBC,oBAAqB,WACjB,OAAO,MANNd,SAAA,WAlBsC,MAAA,2BAmBhCD,KAAPE,MAAAF,KAAAE,MAAA,GAAA,cAnBuC,OA2B3CG,EAAAP,UAAAkB,UACAC,EAAAtB,UAEIW,EAAAb,QAAIW,oBAA2BN,UAAAkB,WAElCE,SAAA1B,EAAAC,QAAA0B,uBAAArB,UAAAkB,UAAAE,WAcR,IAAAE,EARD5B,EAAAC,QAAA4B,wBAAA1B,QAWAM,SAAA,WAQY,MAAO,4BADWD,KAAKE,MAAQF,KAAKE,MAAQ,GAAK,cACC,kBACrDR,eAAAA,EAL2C4B,gBADpDA,EAcIjB,uBAAwBA,EAJ5Be,wBAAAA","file":"../../../scripts/mvc/collection/collection-li-edit.js","sourcesContent":["import DC_LI from \"mvc/collection/collection-li\";\nimport DATASET_LI_EDIT from \"mvc/dataset/dataset-li-edit\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\nvar DCListItemView = DC_LI.DCListItemView;\n/** @class Edit view for DatasetCollection.\n */\nvar DCListItemEdit = DCListItemView.extend(\n /** @lends DCListItemEdit.prototype */ {\n /** override to add linkTarget */\n initialize: function(attributes) {\n DCListItemView.prototype.initialize.call(this, attributes);\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"DCListItemEdit(\" + modelString + \")\";\n }\n }\n);\n\n//==============================================================================\nvar DCEListItemView = DC_LI.DCEListItemView;\n/** @class Read only view for DatasetCollectionElement.\n */\nvar DCEListItemEdit = DCEListItemView.extend(\n /** @lends DCEListItemEdit.prototype */ {\n //TODO: this might be expendable - compacted with HDAListItemView\n\n /** set up */\n initialize: function(attributes) {\n DCEListItemView.prototype.initialize.call(this, attributes);\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"DCEListItemEdit(\" + modelString + \")\";\n }\n }\n);\n\n//==============================================================================\n// NOTE: this does not inherit from DatasetDCEListItemView as you would expect\n//TODO: but should - if we can find something simpler than using diamond\n/** @class Editable view for a DatasetCollectionElement that is also an DatasetAssociation\n * (a dataset contained in a dataset collection).\n */\nvar DatasetDCEListItemEdit = DATASET_LI_EDIT.DatasetListItemEdit.extend(\n /** @lends DatasetDCEListItemEdit.prototype */ {\n /** set up */\n initialize: function(attributes) {\n DATASET_LI_EDIT.DatasetListItemEdit.prototype.initialize.call(\n this,\n attributes\n );\n },\n\n // NOTE: this does not inherit from DatasetDCEListItemView - so we duplicate this here\n //TODO: fix\n /** In this override, only get details if in the ready state.\n * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n */\n _fetchModelDetails: function() {\n var view = this;\n if (view.model.inReadyState() && !view.model.hasDetails()) {\n return view.model.fetch({ silent: true });\n }\n return jQuery.when();\n },\n\n /** Override to remove delete button */\n _renderDeleteButton: function() {\n return null;\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"DatasetDCEListItemEdit(\" + modelString + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDatasetDCEListItemEdit.prototype.templates = (function() {\n return _.extend(\n {},\n DATASET_LI_EDIT.DatasetListItemEdit.prototype.templates,\n {\n titleBar: DC_LI.DatasetDCEListItemView.prototype.templates.titleBar\n }\n );\n})();\n\n//==============================================================================\n/** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection\n * (a nested DC).\n */\nvar NestedDCDCEListItemEdit = DC_LI.NestedDCDCEListItemView.extend(\n /** @lends NestedDCDCEListItemEdit.prototype */ {\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"NestedDCDCEListItemEdit(\" + modelString + \")\";\n }\n }\n);\n\n//==============================================================================\nexport default {\n DCListItemEdit: DCListItemEdit,\n DCEListItemEdit: DCEListItemEdit,\n DatasetDCEListItemEdit: DatasetDCEListItemEdit,\n NestedDCDCEListItemEdit: NestedDCDCEListItemEdit\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/collection/collection-li.js.map b/static/maps/mvc/collection/collection-li.js.map index 3b63b370f00..6fe653eb393 100644 --- a/static/maps/mvc/collection/collection-li.js.map +++ b/static/maps/mvc/collection/collection-li.js.map @@ -1 +1 @@ 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LIST_ITEM from \"mvc/list/list-item\";\nimport DATASET_LI from \"mvc/dataset/dataset-li\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\nvar FoldoutListItemView = LIST_ITEM.FoldoutListItemView,\n ListItemView = LIST_ITEM.ListItemView;\n/** @class Read only view for DatasetCollection.\n */\nvar DCListItemView = FoldoutListItemView.extend(\n /** @lends DCListItemView.prototype */ {\n className:\n FoldoutListItemView.prototype.className + \" dataset-collection\",\n id: function() {\n return [\"dataset_collection\", this.model.get(\"id\")].join(\"-\");\n },\n\n /** override to add linkTarget */\n initialize: function(attributes) {\n this.linkTarget = attributes.linkTarget || \"_blank\";\n this.hasUser = attributes.hasUser;\n FoldoutListItemView.prototype.initialize.call(this, attributes);\n },\n\n /** event listeners */\n _setUpListeners: function() {\n FoldoutListItemView.prototype._setUpListeners.call(this);\n this.listenTo(this.model, \"change\", function(model, options) {\n // if the model has changed deletion status render it entirely\n if (_.has(model.changed, \"deleted\")) {\n this.render();\n\n // if the model has been decorated after the fact with the element count,\n // render the subtitle where the count is displayed\n } else if (_.has(model.changed, \"element_count\")) {\n this.$(\"> .title-bar .subtitle\").replaceWith(\n this._renderSubtitle()\n );\n }\n });\n },\n\n // ......................................................................... rendering\n /** render a subtitle to show the user what sort of collection this is */\n _renderSubtitle: function() {\n return $(this.templates.subtitle(this.model.toJSON(), this));\n },\n\n // ......................................................................... foldout\n /** override to add linktarget to sub-panel */\n _getFoldoutPanelOptions: function() {\n var options = FoldoutListItemView.prototype._getFoldoutPanelOptions.call(\n this\n );\n return _.extend(options, {\n linkTarget: this.linkTarget,\n hasUser: this.hasUser\n });\n },\n\n /** override to not catch sub-panel selectors */\n $selector: function() {\n return this.$(\"> .selector\");\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"DCListItemView(\" + modelString + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDCListItemView.prototype.templates = (function() {\n var warnings = _.extend(\n {},\n FoldoutListItemView.prototype.templates.warnings,\n {\n error: BASE_MVC.wrapTemplate([\n // error during index fetch - show error on dataset\n \"<% if( model.error ){ %>\",\n '\",\n \"<% } %>\"\n ]),\n purged: BASE_MVC.wrapTemplate([\n \"<% if( model.purged ){ %>\",\n '',\n _l(\"Citations\"),\n ' ',\n ' ',\n \"\",\n '',\n this.partialWarningElement(),\n '',\n \"\",\n '',\n '',\n \"\",\n \"',\n _l(\"This collection has been deleted and removed from disk\"),\n \"\",\n \"<% } %>\"\n ]),\n deleted: BASE_MVC.wrapTemplate([\n // deleted not purged\n \"<% if( model.deleted && !model.purged ){ %>\",\n '',\n _l(\"This collection has been deleted\"),\n \"\",\n \"<% } %>\"\n ])\n }\n );\n\n // use element identifier\n var titleBarTemplate = BASE_MVC.wrapTemplate(\n [\n '\"\n ],\n \"collection\"\n );\n\n // use element identifier\n var subtitleTemplate = BASE_MVC.wrapTemplate(\n [\n '',\n '<% var countText = collection.element_count? ( collection.element_count + \" \" ) : \"\"; %>',\n '<% if( collection.collection_type === \"list\" ){ %>',\n _l(\"a list of <%- countText %>datasets\"),\n '<% } else if( collection.collection_type === \"paired\" ){ %>',\n _l(\"a pair of datasets\"),\n '<% } else if( collection.collection_type === \"list:paired\" ){ %>',\n _l(\"a list of <%- countText %>dataset pairs\"),\n '<% } else if( collection.collection_type === \"list:list\" ){ %>',\n _l(\"a list of <%- countText %>dataset lists\"),\n \"<% } %>\",\n \"\"\n ],\n \"collection\"\n );\n\n return _.extend({}, FoldoutListItemView.prototype.templates, {\n warnings: warnings,\n titleBar: titleBarTemplate,\n subtitle: subtitleTemplate\n });\n})();\n\n//==============================================================================\n/** @class Read only view for DatasetCollectionElement.\n */\nvar DCEListItemView = ListItemView.extend(\n /** @lends DCEListItemView.prototype */ {\n /** add the DCE class to the list item */\n className:\n ListItemView.prototype.className + \" dataset-collection-element\",\n\n /** set up */\n initialize: function(attributes) {\n if (attributes.logger) {\n this.logger = this.model.logger = attributes.logger;\n }\n this.log(\"DCEListItemView.initialize:\", attributes);\n ListItemView.prototype.initialize.call(this, attributes);\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"DCEListItemView(\" + modelString + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDCEListItemView.prototype.templates = (function() {\n // use the element identifier here - since that will persist and the user will need it\n var titleBarTemplate = BASE_MVC.wrapTemplate(\n [\n '\"\n ],\n \"element\"\n );\n\n return _.extend({}, ListItemView.prototype.templates, {\n titleBar: titleBarTemplate\n });\n})();\n\n//==============================================================================\n/** @class Read only view for a DatasetCollectionElement that is also an DatasetAssociation\n * (a dataset contained in a dataset collection).\n */\nvar DatasetDCEListItemView = DATASET_LI.DatasetListItemView.extend(\n /** @lends DatasetDCEListItemView.prototype */ {\n className:\n DATASET_LI.DatasetListItemView.prototype.className +\n \" dataset-collection-element\",\n\n /** set up */\n initialize: function(attributes) {\n if (attributes.logger) {\n this.logger = this.model.logger = attributes.logger;\n }\n this.log(\"DatasetDCEListItemView.initialize:\", attributes);\n DATASET_LI.DatasetListItemView.prototype.initialize.call(\n this,\n attributes\n );\n },\n\n /** In this override, only get details if in the ready state.\n * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n */\n _fetchModelDetails: function() {\n var view = this;\n if (view.model.inReadyState() && !view.model.hasDetails()) {\n return view.model.fetch({ silent: true });\n }\n return jQuery.when();\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"DatasetDCEListItemView(\" + modelString + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDatasetDCEListItemView.prototype.templates = (function() {\n // use the element identifier here and not the dataset name\n //TODO:?? can we steal the DCE titlebar?\n var titleBarTemplate = BASE_MVC.wrapTemplate(\n [\n '\"\n ],\n \"element\"\n );\n\n return _.extend({}, DATASET_LI.DatasetListItemView.prototype.templates, {\n titleBar: titleBarTemplate\n });\n})();\n\n//==============================================================================\n/** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection\n * (a nested DC).\n */\nvar NestedDCDCEListItemView = DCListItemView.extend(\n /** @lends NestedDCDCEListItemView.prototype */ {\n className:\n DCListItemView.prototype.className + \" dataset-collection-element\",\n\n /** In this override, add the state as a class for use with state-based CSS */\n _swapNewRender: function($newRender) {\n DCListItemView.prototype._swapNewRender.call(this, $newRender);\n var state = this.model.get(\"state\") || \"ok\";\n this.$el.addClass(\"state-\" + state);\n return this.$el;\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"NestedDCDCEListItemView(\" + modelString + \")\";\n }\n }\n);\n\n//==============================================================================\nexport default {\n DCListItemView: DCListItemView,\n DCEListItemView: DCEListItemView,\n DatasetDCEListItemView: DatasetDCEListItemView,\n NestedDCDCEListItemView: NestedDCDCEListItemView\n};\n"]} \ No newline at end of file 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LIST_ITEM from \"mvc/list/list-item\";\nimport DATASET_LI from \"mvc/dataset/dataset-li\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\nvar FoldoutListItemView = LIST_ITEM.FoldoutListItemView,\n ListItemView = LIST_ITEM.ListItemView;\n/** @class Read only view for DatasetCollection.\n */\nvar DCListItemView = FoldoutListItemView.extend(\n /** @lends DCListItemView.prototype */ {\n className:\n FoldoutListItemView.prototype.className + \" dataset-collection\",\n id: function() {\n return [\"dataset_collection\", this.model.get(\"id\")].join(\"-\");\n },\n\n /** override to add linkTarget */\n initialize: function(attributes) {\n this.linkTarget = attributes.linkTarget || \"_blank\";\n this.hasUser = attributes.hasUser;\n FoldoutListItemView.prototype.initialize.call(this, attributes);\n },\n\n /** event listeners */\n _setUpListeners: function() {\n FoldoutListItemView.prototype._setUpListeners.call(this);\n this.listenTo(this.model, \"change\", function(model, options) {\n // if the model has changed deletion status render it entirely\n if (_.has(model.changed, \"deleted\")) {\n this.render();\n\n // if the model has been decorated after the fact with the element count,\n // render the subtitle where the count is displayed\n } else if (_.has(model.changed, \"element_count\")) {\n this.$(\"> .title-bar .subtitle\").replaceWith(\n this._renderSubtitle()\n );\n }\n });\n },\n\n // ......................................................................... rendering\n /** render a subtitle to show the user what sort of collection this is */\n _renderSubtitle: function() {\n return $(this.templates.subtitle(this.model.toJSON(), this));\n },\n\n // ......................................................................... foldout\n /** override to add linktarget to sub-panel */\n _getFoldoutPanelOptions: function() {\n var options = FoldoutListItemView.prototype._getFoldoutPanelOptions.call(\n this\n );\n return _.extend(options, {\n linkTarget: this.linkTarget,\n hasUser: this.hasUser\n });\n },\n\n /** override to not catch sub-panel selectors */\n $selector: function() {\n return this.$(\"> .selector\");\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"DCListItemView(\" + modelString + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDCListItemView.prototype.templates = (function() {\n var warnings = _.extend(\n {},\n FoldoutListItemView.prototype.templates.warnings,\n {\n error: BASE_MVC.wrapTemplate([\n // error during index fetch - show error on dataset\n \"<% if( model.error ){ %>\",\n '\",\n \"<% } %>\"\n ]),\n purged: BASE_MVC.wrapTemplate([\n \"<% if( model.purged ){ %>\",\n '',\n _l(\"This collection has been deleted and removed from disk\"),\n \"\",\n \"<% } %>\"\n ]),\n deleted: BASE_MVC.wrapTemplate([\n // deleted not purged\n \"<% if( model.deleted && !model.purged ){ %>\",\n '',\n _l(\"This collection has been deleted\"),\n \"\",\n \"<% } %>\"\n ])\n }\n );\n\n // use element identifier\n var titleBarTemplate = BASE_MVC.wrapTemplate(\n [\n '\"\n ],\n \"collection\"\n );\n\n // use element identifier\n var subtitleTemplate = BASE_MVC.wrapTemplate(\n [\n '',\n '<% var countText = collection.element_count? ( collection.element_count + \" \" ) : \"\"; %>',\n '<% if( collection.collection_type === \"list\" ){ %>',\n _l(\"a list of <%- countText %>datasets\"),\n '<% } else if( collection.collection_type === \"paired\" ){ %>',\n _l(\"a pair of datasets\"),\n '<% } else if( collection.collection_type === \"list:paired\" ){ %>',\n _l(\"a list of <%- countText %>dataset pairs\"),\n '<% } else if( collection.collection_type === \"list:list\" ){ %>',\n _l(\"a list of <%- countText %>dataset lists\"),\n \"<% } %>\",\n \"\"\n ],\n \"collection\"\n );\n\n return _.extend({}, FoldoutListItemView.prototype.templates, {\n warnings: warnings,\n titleBar: titleBarTemplate,\n subtitle: subtitleTemplate\n });\n})();\n\n//==============================================================================\n/** @class Read only view for DatasetCollectionElement.\n */\nvar DCEListItemView = ListItemView.extend(\n /** @lends DCEListItemView.prototype */ {\n /** add the DCE class to the list item */\n className:\n ListItemView.prototype.className + \" dataset-collection-element\",\n\n /** set up */\n initialize: function(attributes) {\n if (attributes.logger) {\n this.logger = this.model.logger = attributes.logger;\n }\n this.log(\"DCEListItemView.initialize:\", attributes);\n ListItemView.prototype.initialize.call(this, attributes);\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"DCEListItemView(\" + modelString + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDCEListItemView.prototype.templates = (function() {\n // use the element identifier here - since that will persist and the user will need it\n var titleBarTemplate = BASE_MVC.wrapTemplate(\n [\n '\"\n ],\n \"element\"\n );\n\n return _.extend({}, ListItemView.prototype.templates, {\n titleBar: titleBarTemplate\n });\n})();\n\n//==============================================================================\n/** @class Read only view for a DatasetCollectionElement that is also an DatasetAssociation\n * (a dataset contained in a dataset collection).\n */\nvar DatasetDCEListItemView = DATASET_LI.DatasetListItemView.extend(\n /** @lends DatasetDCEListItemView.prototype */ {\n className:\n DATASET_LI.DatasetListItemView.prototype.className +\n \" dataset-collection-element\",\n\n /** set up */\n initialize: function(attributes) {\n if (attributes.logger) {\n this.logger = this.model.logger = attributes.logger;\n }\n this.log(\"DatasetDCEListItemView.initialize:\", attributes);\n DATASET_LI.DatasetListItemView.prototype.initialize.call(\n this,\n attributes\n );\n },\n\n /** In this override, only get details if in the ready state.\n * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n */\n _fetchModelDetails: function() {\n var view = this;\n if (view.model.inReadyState() && !view.model.hasDetails()) {\n return view.model.fetch({ silent: true });\n }\n return jQuery.when();\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"DatasetDCEListItemView(\" + modelString + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDatasetDCEListItemView.prototype.templates = (function() {\n // use the element identifier here and not the dataset name\n //TODO:?? can we steal the DCE titlebar?\n var titleBarTemplate = BASE_MVC.wrapTemplate(\n [\n '\"\n ],\n \"element\"\n );\n\n return _.extend({}, DATASET_LI.DatasetListItemView.prototype.templates, {\n titleBar: titleBarTemplate\n });\n})();\n\n//==============================================================================\n/** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection\n * (a nested DC).\n */\nvar NestedDCDCEListItemView = DCListItemView.extend(\n /** @lends NestedDCDCEListItemView.prototype */ {\n className:\n DCListItemView.prototype.className + \" dataset-collection-element\",\n\n /** In this override, add the state as a class for use with state-based CSS */\n _swapNewRender: function($newRender) {\n DCListItemView.prototype._swapNewRender.call(this, $newRender);\n var state = this.model.get(\"state\") || \"ok\";\n this.$el.addClass(\"state-\" + state);\n return this.$el;\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"NestedDCDCEListItemView(\" + modelString + \")\";\n }\n }\n);\n\n//==============================================================================\nexport default {\n DCListItemView: DCListItemView,\n DCEListItemView: DCEListItemView,\n DatasetDCEListItemView: DatasetDCEListItemView,\n NestedDCDCEListItemView: NestedDCDCEListItemView\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/collection/collection-model.js.map b/static/maps/mvc/collection/collection-model.js.map index 5e630c88d20..be788c11bc9 100644 --- a/static/maps/mvc/collection/collection-model.js.map +++ b/static/maps/mvc/collection/collection-model.js.map @@ -1 +1 @@ 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DATASET_MODEL from \"mvc/dataset/dataset-model\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\n/*\nNotes:\n\nTerminology:\n DatasetCollection/DC : a container of datasets or nested DatasetCollections\n Element/DatasetCollectionElement/DCE : an item contained in a DatasetCollection\n HistoryDatasetCollectionAssociation/HDCA: a DatasetCollection contained in a history\n\n\nThis all seems too complex unfortunately:\n\n- Terminology collision between DatasetCollections (DCs) and Backbone Collections.\n- In the DatasetCollections API JSON, DC Elements use a 'Has A' stucture to *contain*\n either a dataset or a nested DC. This would make the hierarchy much taller. I've\n decided to merge the contained JSON with the DC element json - making the 'has a'\n relation into an 'is a' relation. This seems simpler to me and allowed a lot of\n DRY in both models and views, but may make tracking or tracing within these models\n more difficult (since DatasetCollectionElements are now *also* DatasetAssociations\n or DatasetCollections (nested)). This also violates the rule of thumb about\n favoring aggregation over inheritance.\n- Currently, there are three DatasetCollection subclasses: List, Pair, and ListPaired.\n These each should a) be usable on their own, b) be usable in the context of\n nesting within a collection model (at least in the case of ListPaired), and\n c) be usable within the context of other container models (like History or\n LibraryFolder, etc.). I've tried to separate/extract classes in order to\n handle those three situations, but it's proven difficult to do in a simple,\n readable manner.\n- Ideally, histories and libraries would inherit from the same server models as\n dataset collections do since they are (in essence) dataset collections themselves -\n making the whole nested structure simpler. This would be a large, error-prone\n refactoring and migration.\n\nMany of the classes and heirarchy are meant as extension points so, while the\nrelations and flow may be difficult to understand initially, they'll allow us to\nhandle the growth or flux dataset collection in the future (w/o actually implementing\nany YAGNI).\n\n*/\n//_________________________________________________________________________________________________ ELEMENTS\n/** @class mixin for Dataset collection elements.\n * When collection elements are passed from the API, the underlying element is\n * in a sub-object 'object' (IOW, a DCE representing an HDA will have HDA json in element.object).\n * This mixin uses the constructor and parse methods to merge that JSON with the DCE attribtues\n * effectively changing a DCE from a container to a subclass (has a --> is a).\n */\nvar DatasetCollectionElementMixin = {\n /** default attributes used by elements in a dataset collection */\n defaults: {\n model_class: \"DatasetCollectionElement\",\n element_identifier: null,\n element_index: null,\n element_type: null\n },\n\n /** merge the attributes of the sub-object 'object' into this model */\n _mergeObject: function(attributes) {\n // if we don't preserve and correct ids here, the element id becomes the object id\n // and collision in backbone's _byId will occur and only\n _.extend(attributes, attributes.object, {\n element_id: attributes.id\n });\n delete attributes.object;\n return attributes;\n },\n\n /** override to merge this.object into this */\n constructor: function(attributes, options) {\n // console.debug( '\\t DatasetCollectionElement.constructor:', attributes, options );\n attributes = this._mergeObject(attributes);\n this.idAttribute = \"element_id\";\n Backbone.Model.apply(this, arguments);\n },\n\n /** when the model is fetched, merge this.object into this */\n parse: function(response, options) {\n var attributes = response;\n attributes = this._mergeObject(attributes);\n return attributes;\n }\n};\n\n/** @class Concrete class of Generic DatasetCollectionElement */\nvar DatasetCollectionElement = Backbone.Model\n .extend(BASE_MVC.LoggableMixin)\n .extend(DatasetCollectionElementMixin)\n .extend({ _logNamespace: \"collections\" });\n\n//==============================================================================\n/** @class Base/Abstract Backbone collection for Generic DCEs. */\nvar DCECollection = Backbone.Collection.extend(BASE_MVC.LoggableMixin).extend(\n /** @lends DCECollection.prototype */ {\n _logNamespace: \"collections\",\n\n model: DatasetCollectionElement,\n\n /** String representation. */\n toString: function() {\n return [\n \"DatasetCollectionElementCollection(\",\n this.length,\n \")\"\n ].join(\"\");\n }\n }\n);\n\n//==============================================================================\n/** @class Backbone model for a dataset collection element that is a dataset (HDA).\n */\nvar DatasetDCE = DATASET_MODEL.DatasetAssociation.extend(\n BASE_MVC.mixin(\n DatasetCollectionElementMixin,\n /** @lends DatasetDCE.prototype */ {\n /** url fn */\n url: function() {\n // won't always be an hda\n if (!this.has(\"history_id\")) {\n console.warn(\n \"no endpoint for non-hdas within a collection yet\"\n );\n // (a little silly since this api endpoint *also* points at hdas)\n return Galaxy.root + \"api/datasets\";\n }\n return (\n Galaxy.root +\n \"api/histories/\" +\n this.get(\"history_id\") +\n \"/contents/\" +\n this.get(\"id\")\n );\n },\n\n defaults: _.extend(\n {},\n DATASET_MODEL.DatasetAssociation.prototype.defaults,\n DatasetCollectionElementMixin.defaults\n ),\n\n _downloadQueryParameters: function() {\n return (\n \"?to_ext=\" +\n this.get(\"file_ext\") +\n \"&hdca_id=\" +\n this.get(\"parent_hdca_id\") +\n \"&element_identifier=\" +\n this.get(\"element_identifier\")\n );\n },\n\n // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n // - re-apply manually for now\n /** call the mixin constructor */\n constructor: function(attributes, options) {\n this.debug(\"\\t DatasetDCE.constructor:\", attributes, options);\n //DATASET_MODEL.DatasetAssociation.prototype.constructor.call( this, attributes, options );\n DatasetCollectionElementMixin.constructor.call(\n this,\n attributes,\n options\n );\n },\n\n /** Does this model already contain detailed data (as opposed to just summary level data)? */\n hasDetails: function() {\n return this.elements && this.elements.length;\n },\n\n /** String representation. */\n toString: function() {\n var objStr = this.get(\"element_identifier\");\n return [\"DatasetDCE(\", objStr, \")\"].join(\"\");\n }\n }\n )\n);\n\n//==============================================================================\n/** @class DCECollection of DatasetDCE's (a list of datasets, a pair of datasets).\n */\nvar DatasetDCECollection = DCECollection.extend(\n /** @lends DatasetDCECollection.prototype */ {\n model: DatasetDCE,\n\n /** String representation. */\n toString: function() {\n return [\"DatasetDCECollection(\", this.length, \")\"].join(\"\");\n }\n }\n);\n\n//_________________________________________________________________________________________________ COLLECTIONS\n/** @class Backbone model for Dataset Collections.\n * The DC API returns an array of JSON objects under the attribute elements.\n * This model:\n * - removes that array/attribute ('elements') from the model,\n * - creates a bbone collection (of the class defined in the 'collectionClass' attribute),\n * - passes that json onto the bbone collection\n * - caches the bbone collection in this.elements\n */\nvar DatasetCollection = Backbone.Model\n .extend(BASE_MVC.LoggableMixin)\n .extend(BASE_MVC.SearchableModelMixin)\n .extend(\n /** @lends DatasetCollection.prototype */ {\n _logNamespace: \"collections\",\n\n /** default attributes for a model */\n defaults: {\n /* 'list', 'paired', or 'list:paired' */\n collection_type: null,\n //??\n deleted: false\n },\n\n /** Which class to use for elements */\n collectionClass: DCECollection,\n\n /** set up: create elements instance var and (on changes to elements) update them */\n initialize: function(model, options) {\n this.debug(\n this + \"(DatasetCollection).initialize:\",\n model,\n options,\n this\n );\n this.elements = this._createElementsModel();\n this.on(\"change:elements\", function() {\n this.log(\"change:elements\");\n //TODO: prob. better to update the collection instead of re-creating it\n this.elements = this._createElementsModel();\n });\n },\n\n /** move elements model attribute to full collection */\n _createElementsModel: function() {\n this.debug(\n this + \"._createElementsModel\",\n this.collectionClass,\n this.get(\"elements\"),\n this.elements\n );\n //TODO: same patterns as DatasetCollectionElement _createObjectModel - refactor to BASE_MVC.hasSubModel?\n var elements = this.get(\"elements\") || [];\n this.unset(\"elements\", { silent: true });\n var self = this;\n _.each(elements, function(element, index) {\n _.extend(element, {\n parent_hdca_id: self.get(\"id\")\n });\n });\n this.elements = new this.collectionClass(elements);\n //this.debug( 'collectionClass:', this.collectionClass + '', this.elements );\n return this.elements;\n },\n\n // ........................................................................ common queries\n /** pass the elements back within the model json when this is serialized */\n toJSON: function() {\n var json = Backbone.Model.prototype.toJSON.call(this);\n if (this.elements) {\n json.elements = this.elements.toJSON();\n }\n return json;\n },\n\n /** Is this collection in a 'ready' state no processing (for the collection) is left\n * to do on the server.\n */\n inReadyState: function() {\n var populated = this.get(\"populated\");\n return this.isDeletedOrPurged() || populated;\n },\n\n //TODO:?? the following are the same interface as DatasetAssociation - can we combine?\n /** Does the DC contain any elements yet? Is a fetch() required? */\n hasDetails: function() {\n return this.elements.length !== 0;\n },\n\n /** Given the filters, what models in this.elements would be returned? */\n getVisibleContents: function(filters) {\n // filters unused for now\n return this.elements;\n },\n\n // ........................................................................ ajax\n /** override to use actual Dates objects for create/update times */\n parse: function(response, options) {\n var parsed = Backbone.Model.prototype.parse.call(\n this,\n response,\n options\n );\n if (parsed.create_time) {\n parsed.create_time = new Date(parsed.create_time);\n }\n if (parsed.update_time) {\n parsed.update_time = new Date(parsed.update_time);\n }\n return parsed;\n },\n\n /** save this dataset, _Mark_ing it as deleted (just a flag) */\n delete: function(options) {\n if (this.get(\"deleted\")) {\n return jQuery.when();\n }\n return this.save({ deleted: true }, options);\n },\n /** save this dataset, _Mark_ing it as undeleted */\n undelete: function(options) {\n if (!this.get(\"deleted\") || this.get(\"purged\")) {\n return jQuery.when();\n }\n return this.save({ deleted: false }, options);\n },\n\n /** Is this collection deleted or purged? */\n isDeletedOrPurged: function() {\n return this.get(\"deleted\") || this.get(\"purged\");\n },\n\n // ........................................................................ searchable\n /** searchable attributes for collections */\n searchAttributes: [\"name\", \"tags\"],\n\n // ........................................................................ misc\n /** String representation */\n toString: function() {\n var idAndName = [\n this.get(\"id\"),\n this.get(\"name\") || this.get(\"element_identifier\")\n ];\n return \"DatasetCollection(\" + idAndName.join(\",\") + \")\";\n }\n }\n );\n\n//==============================================================================\n/** Model for a DatasetCollection containing datasets (non-nested).\n */\nvar ListDatasetCollection = DatasetCollection.extend(\n /** @lends ListDatasetCollection.prototype */ {\n /** override since we know the collection will only contain datasets */\n collectionClass: DatasetDCECollection,\n\n /** String representation. */\n toString: function() {\n return \"List\" + DatasetCollection.prototype.toString.call(this);\n }\n }\n);\n\n//==============================================================================\n/** Model for a DatasetCollection containing fwd/rev datasets (a list of 2).\n */\nvar PairDatasetCollection = ListDatasetCollection.extend(\n /** @lends PairDatasetCollection.prototype */ {\n /** String representation. */\n toString: function() {\n return \"Pair\" + DatasetCollection.prototype.toString.call(this);\n }\n }\n);\n\n//_________________________________________________________________________________________________ NESTED COLLECTIONS\n// this is where things get weird, man. Weird.\n//TODO: it might be possible to compact all the following...I think.\n//==============================================================================\n/** @class Backbone model for a Generic DatasetCollectionElement that is also a DatasetCollection\n * (a nested collection). Currently only list:paired.\n */\nvar NestedDCDCE = DatasetCollection.extend(\n BASE_MVC.mixin(\n DatasetCollectionElementMixin,\n /** @lends NestedDCDCE.prototype */ {\n // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n // - re-apply manually it now\n /** call the mixin constructor */\n constructor: function(attributes, options) {\n this.debug(\"\\t NestedDCDCE.constructor:\", attributes, options);\n DatasetCollectionElementMixin.constructor.call(\n this,\n attributes,\n options\n );\n },\n\n /** String representation. */\n toString: function() {\n var objStr = this.object\n ? \"\" + this.object\n : this.get(\"element_identifier\");\n return [\"NestedDCDCE(\", objStr, \")\"].join(\"\");\n }\n }\n )\n);\n\n//==============================================================================\n/** @class Backbone collection containing Generic NestedDCDCE's (nested dataset collections).\n */\nvar NestedDCDCECollection = DCECollection.extend(\n /** @lends NestedDCDCECollection.prototype */ {\n /** This is a collection of nested collections */\n model: NestedDCDCE,\n\n /** String representation. */\n toString: function() {\n return [\"NestedDCDCECollection(\", this.length, \")\"].join(\"\");\n }\n }\n);\n\n//==============================================================================\n/** @class Backbone model for a paired dataset collection within a list:paired dataset collection.\n */\nvar NestedPairDCDCE = PairDatasetCollection.extend(\n BASE_MVC.mixin(\n DatasetCollectionElementMixin,\n /** @lends NestedPairDCDCE.prototype */ {\n //TODO:?? possibly rename to NestedDatasetCollection?\n\n // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n // - re-apply manually it now\n /** This is both a collection and a collection element - call the constructor */\n constructor: function(attributes, options) {\n this.debug(\n \"\\t NestedPairDCDCE.constructor:\",\n attributes,\n options\n );\n //DatasetCollection.constructor.call( this, attributes, options );\n DatasetCollectionElementMixin.constructor.call(\n this,\n attributes,\n options\n );\n },\n\n /** String representation. */\n toString: function() {\n var objStr = this.object\n ? \"\" + this.object\n : this.get(\"element_identifier\");\n return [\"NestedPairDCDCE(\", objStr, \")\"].join(\"\");\n }\n }\n )\n);\n\n//==============================================================================\n/** @class Backbone collection for a backbone collection containing paired dataset collections.\n */\nvar NestedPairDCDCECollection = NestedDCDCECollection.extend(\n /** @lends PairDCDCECollection.prototype */ {\n /** We know this collection is composed of only nested pair collections */\n model: NestedPairDCDCE,\n\n /** String representation. */\n toString: function() {\n return [\"NestedPairDCDCECollection(\", this.length, \")\"].join(\"\");\n }\n }\n);\n\n//==============================================================================\n/** @class Backbone Model for a DatasetCollection (list) that contains DatasetCollections (pairs).\n */\nvar ListPairedDatasetCollection = DatasetCollection.extend(\n /** @lends ListPairedDatasetCollection.prototype */ {\n /** list:paired is the only collection that itself contains collections */\n collectionClass: NestedPairDCDCECollection,\n\n /** String representation. */\n toString: function() {\n return [\"ListPairedDatasetCollection(\", this.get(\"name\"), \")\"].join(\n \"\"\n );\n }\n }\n);\n\n//==============================================================================\n/** @class Backbone model for a list dataset collection within a list:list dataset collection. */\nvar NestedListDCDCE = ListDatasetCollection.extend(\n BASE_MVC.mixin(\n DatasetCollectionElementMixin,\n /** @lends NestedListDCDCE.prototype */ {\n /** This is both a collection and a collection element - call the constructor */\n constructor: function(attributes, options) {\n this.debug(\n \"\\t NestedListDCDCE.constructor:\",\n attributes,\n options\n );\n DatasetCollectionElementMixin.constructor.call(\n this,\n attributes,\n options\n );\n },\n\n /** String representation. */\n toString: function() {\n var objStr = this.object\n ? \"\" + this.object\n : this.get(\"element_identifier\");\n return [\"NestedListDCDCE(\", objStr, \")\"].join(\"\");\n }\n }\n )\n);\n\n//==============================================================================\n/** @class Backbone collection containing list dataset collections. */\nvar NestedListDCDCECollection = NestedDCDCECollection.extend({\n /** We know this collection is composed of only nested pair collections */\n model: NestedListDCDCE,\n\n /** String representation. */\n toString: function() {\n return [\"NestedListDCDCECollection(\", this.length, \")\"].join(\"\");\n }\n});\n\n//==============================================================================\n/** @class Backbone Model for a DatasetCollection (list) that contains other lists. */\nvar ListOfListsDatasetCollection = DatasetCollection.extend({\n /** list:paired is the only collection that itself contains collections */\n collectionClass: NestedListDCDCECollection,\n\n /** String representation. */\n toString: function() {\n return [\"ListOfListsDatasetCollection(\", this.get(\"name\"), \")\"].join(\n \"\"\n );\n }\n});\n\n//==============================================================================\nexport default {\n ListDatasetCollection: ListDatasetCollection,\n PairDatasetCollection: PairDatasetCollection,\n ListPairedDatasetCollection: ListPairedDatasetCollection,\n ListOfListsDatasetCollection: ListOfListsDatasetCollection\n};\n"]} \ No newline at end of file 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DATASET_MODEL from \"mvc/dataset/dataset-model\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\n/*\nNotes:\n\nTerminology:\n DatasetCollection/DC : a container of datasets or nested DatasetCollections\n Element/DatasetCollectionElement/DCE : an item contained in a DatasetCollection\n HistoryDatasetCollectionAssociation/HDCA: a DatasetCollection contained in a history\n\n\nThis all seems too complex unfortunately:\n\n- Terminology collision between DatasetCollections (DCs) and Backbone Collections.\n- In the DatasetCollections API JSON, DC Elements use a 'Has A' stucture to *contain*\n either a dataset or a nested DC. This would make the hierarchy much taller. I've\n decided to merge the contained JSON with the DC element json - making the 'has a'\n relation into an 'is a' relation. This seems simpler to me and allowed a lot of\n DRY in both models and views, but may make tracking or tracing within these models\n more difficult (since DatasetCollectionElements are now *also* DatasetAssociations\n or DatasetCollections (nested)). This also violates the rule of thumb about\n favoring aggregation over inheritance.\n- Currently, there are three DatasetCollection subclasses: List, Pair, and ListPaired.\n These each should a) be usable on their own, b) be usable in the context of\n nesting within a collection model (at least in the case of ListPaired), and\n c) be usable within the context of other container models (like History or\n LibraryFolder, etc.). I've tried to separate/extract classes in order to\n handle those three situations, but it's proven difficult to do in a simple,\n readable manner.\n- Ideally, histories and libraries would inherit from the same server models as\n dataset collections do since they are (in essence) dataset collections themselves -\n making the whole nested structure simpler. This would be a large, error-prone\n refactoring and migration.\n\nMany of the classes and heirarchy are meant as extension points so, while the\nrelations and flow may be difficult to understand initially, they'll allow us to\nhandle the growth or flux dataset collection in the future (w/o actually implementing\nany YAGNI).\n\n*/\n//_________________________________________________________________________________________________ ELEMENTS\n/** @class mixin for Dataset collection elements.\n * When collection elements are passed from the API, the underlying element is\n * in a sub-object 'object' (IOW, a DCE representing an HDA will have HDA json in element.object).\n * This mixin uses the constructor and parse methods to merge that JSON with the DCE attribtues\n * effectively changing a DCE from a container to a subclass (has a --> is a).\n */\nvar DatasetCollectionElementMixin = {\n /** default attributes used by elements in a dataset collection */\n defaults: {\n model_class: \"DatasetCollectionElement\",\n element_identifier: null,\n element_index: null,\n element_type: null\n },\n\n /** merge the attributes of the sub-object 'object' into this model */\n _mergeObject: function(attributes) {\n // if we don't preserve and correct ids here, the element id becomes the object id\n // and collision in backbone's _byId will occur and only\n _.extend(attributes, attributes.object, {\n element_id: attributes.id\n });\n delete attributes.object;\n return attributes;\n },\n\n /** override to merge this.object into this */\n constructor: function(attributes, options) {\n // console.debug( '\\t DatasetCollectionElement.constructor:', attributes, options );\n attributes = this._mergeObject(attributes);\n this.idAttribute = \"element_id\";\n Backbone.Model.apply(this, arguments);\n },\n\n /** when the model is fetched, merge this.object into this */\n parse: function(response, options) {\n var attributes = response;\n attributes = this._mergeObject(attributes);\n return attributes;\n }\n};\n\n/** @class Concrete class of Generic DatasetCollectionElement */\nvar DatasetCollectionElement = Backbone.Model\n .extend(BASE_MVC.LoggableMixin)\n .extend(DatasetCollectionElementMixin)\n .extend({ _logNamespace: \"collections\" });\n\n//==============================================================================\n/** @class Base/Abstract Backbone collection for Generic DCEs. */\nvar DCECollection = Backbone.Collection.extend(BASE_MVC.LoggableMixin).extend(\n /** @lends DCECollection.prototype */ {\n _logNamespace: \"collections\",\n\n model: DatasetCollectionElement,\n\n /** String representation. */\n toString: function() {\n return [\n \"DatasetCollectionElementCollection(\",\n this.length,\n \")\"\n ].join(\"\");\n }\n }\n);\n\n//==============================================================================\n/** @class Backbone model for a dataset collection element that is a dataset (HDA).\n */\nvar DatasetDCE = DATASET_MODEL.DatasetAssociation.extend(\n BASE_MVC.mixin(\n DatasetCollectionElementMixin,\n /** @lends DatasetDCE.prototype */ {\n /** url fn */\n url: function() {\n // won't always be an hda\n if (!this.has(\"history_id\")) {\n console.warn(\n \"no endpoint for non-hdas within a collection yet\"\n );\n // (a little silly since this api endpoint *also* points at hdas)\n return Galaxy.root + \"api/datasets\";\n }\n return (\n Galaxy.root +\n \"api/histories/\" +\n this.get(\"history_id\") +\n \"/contents/\" +\n this.get(\"id\")\n );\n },\n\n defaults: _.extend(\n {},\n DATASET_MODEL.DatasetAssociation.prototype.defaults,\n DatasetCollectionElementMixin.defaults\n ),\n\n _downloadQueryParameters: function() {\n return (\n \"?to_ext=\" +\n this.get(\"file_ext\") +\n \"&hdca_id=\" +\n this.get(\"parent_hdca_id\") +\n \"&element_identifier=\" +\n this.get(\"element_identifier\")\n );\n },\n\n // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n // - re-apply manually for now\n /** call the mixin constructor */\n constructor: function(attributes, options) {\n this.debug(\"\\t DatasetDCE.constructor:\", attributes, options);\n //DATASET_MODEL.DatasetAssociation.prototype.constructor.call( this, attributes, options );\n DatasetCollectionElementMixin.constructor.call(\n this,\n attributes,\n options\n );\n },\n\n /** Does this model already contain detailed data (as opposed to just summary level data)? */\n hasDetails: function() {\n return this.elements && this.elements.length;\n },\n\n /** String representation. */\n toString: function() {\n var objStr = this.get(\"element_identifier\");\n return [\"DatasetDCE(\", objStr, \")\"].join(\"\");\n }\n }\n )\n);\n\n//==============================================================================\n/** @class DCECollection of DatasetDCE's (a list of datasets, a pair of datasets).\n */\nvar DatasetDCECollection = DCECollection.extend(\n /** @lends DatasetDCECollection.prototype */ {\n model: DatasetDCE,\n\n /** String representation. */\n toString: function() {\n return [\"DatasetDCECollection(\", this.length, \")\"].join(\"\");\n }\n }\n);\n\n//_________________________________________________________________________________________________ COLLECTIONS\n/** @class Backbone model for Dataset Collections.\n * The DC API returns an array of JSON objects under the attribute elements.\n * This model:\n * - removes that array/attribute ('elements') from the model,\n * - creates a bbone collection (of the class defined in the 'collectionClass' attribute),\n * - passes that json onto the bbone collection\n * - caches the bbone collection in this.elements\n */\nvar DatasetCollection = Backbone.Model\n .extend(BASE_MVC.LoggableMixin)\n .extend(BASE_MVC.SearchableModelMixin)\n .extend(\n /** @lends DatasetCollection.prototype */ {\n _logNamespace: \"collections\",\n\n /** default attributes for a model */\n defaults: {\n /* 'list', 'paired', or 'list:paired' */\n collection_type: null,\n //??\n deleted: false\n },\n\n /** Which class to use for elements */\n collectionClass: DCECollection,\n\n /** set up: create elements instance var and (on changes to elements) update them */\n initialize: function(model, options) {\n this.debug(\n this + \"(DatasetCollection).initialize:\",\n model,\n options,\n this\n );\n this.elements = this._createElementsModel();\n this.on(\"change:elements\", function() {\n this.log(\"change:elements\");\n //TODO: prob. better to update the collection instead of re-creating it\n this.elements = this._createElementsModel();\n });\n },\n\n /** move elements model attribute to full collection */\n _createElementsModel: function() {\n this.debug(\n this + \"._createElementsModel\",\n this.collectionClass,\n this.get(\"elements\"),\n this.elements\n );\n //TODO: same patterns as DatasetCollectionElement _createObjectModel - refactor to BASE_MVC.hasSubModel?\n var elements = this.get(\"elements\") || [];\n this.unset(\"elements\", { silent: true });\n var self = this;\n _.each(elements, function(element, index) {\n _.extend(element, {\n parent_hdca_id: self.get(\"id\")\n });\n });\n this.elements = new this.collectionClass(elements);\n //this.debug( 'collectionClass:', this.collectionClass + '', this.elements );\n return this.elements;\n },\n\n // ........................................................................ common queries\n /** pass the elements back within the model json when this is serialized */\n toJSON: function() {\n var json = Backbone.Model.prototype.toJSON.call(this);\n if (this.elements) {\n json.elements = this.elements.toJSON();\n }\n return json;\n },\n\n /** Is this collection in a 'ready' state no processing (for the collection) is left\n * to do on the server.\n */\n inReadyState: function() {\n var populated = this.get(\"populated\");\n return this.isDeletedOrPurged() || populated;\n },\n\n //TODO:?? the following are the same interface as DatasetAssociation - can we combine?\n /** Does the DC contain any elements yet? Is a fetch() required? */\n hasDetails: function() {\n return this.elements.length !== 0;\n },\n\n /** Given the filters, what models in this.elements would be returned? */\n getVisibleContents: function(filters) {\n // filters unused for now\n return this.elements;\n },\n\n // ........................................................................ ajax\n /** override to use actual Dates objects for create/update times */\n parse: function(response, options) {\n var parsed = Backbone.Model.prototype.parse.call(\n this,\n response,\n options\n );\n if (parsed.create_time) {\n parsed.create_time = new Date(parsed.create_time);\n }\n if (parsed.update_time) {\n parsed.update_time = new Date(parsed.update_time);\n }\n return parsed;\n },\n\n /** save this dataset, _Mark_ing it as deleted (just a flag) */\n delete: function(options) {\n if (this.get(\"deleted\")) {\n return jQuery.when();\n }\n return this.save({ deleted: true }, options);\n },\n /** save this dataset, _Mark_ing it as undeleted */\n undelete: function(options) {\n if (!this.get(\"deleted\") || this.get(\"purged\")) {\n return jQuery.when();\n }\n return this.save({ deleted: false }, options);\n },\n\n /** Is this collection deleted or purged? */\n isDeletedOrPurged: function() {\n return this.get(\"deleted\") || this.get(\"purged\");\n },\n\n // ........................................................................ searchable\n /** searchable attributes for collections */\n searchAttributes: [\"name\", \"tags\"],\n\n // ........................................................................ misc\n /** String representation */\n toString: function() {\n var idAndName = [\n this.get(\"id\"),\n this.get(\"name\") || this.get(\"element_identifier\")\n ];\n return \"DatasetCollection(\" + idAndName.join(\",\") + \")\";\n }\n }\n );\n\n//==============================================================================\n/** Model for a DatasetCollection containing datasets (non-nested).\n */\nvar ListDatasetCollection = DatasetCollection.extend(\n /** @lends ListDatasetCollection.prototype */ {\n /** override since we know the collection will only contain datasets */\n collectionClass: DatasetDCECollection,\n\n /** String representation. */\n toString: function() {\n return \"List\" + DatasetCollection.prototype.toString.call(this);\n }\n }\n);\n\n//==============================================================================\n/** Model for a DatasetCollection containing fwd/rev datasets (a list of 2).\n */\nvar PairDatasetCollection = ListDatasetCollection.extend(\n /** @lends PairDatasetCollection.prototype */ {\n /** String representation. */\n toString: function() {\n return \"Pair\" + DatasetCollection.prototype.toString.call(this);\n }\n }\n);\n\n//_________________________________________________________________________________________________ NESTED COLLECTIONS\n// this is where things get weird, man. Weird.\n//TODO: it might be possible to compact all the following...I think.\n//==============================================================================\n/** @class Backbone model for a Generic DatasetCollectionElement that is also a DatasetCollection\n * (a nested collection). Currently only list:paired.\n */\nvar NestedDCDCE = DatasetCollection.extend(\n BASE_MVC.mixin(\n DatasetCollectionElementMixin,\n /** @lends NestedDCDCE.prototype */ {\n // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n // - re-apply manually it now\n /** call the mixin constructor */\n constructor: function(attributes, options) {\n this.debug(\"\\t NestedDCDCE.constructor:\", attributes, options);\n DatasetCollectionElementMixin.constructor.call(\n this,\n attributes,\n options\n );\n },\n\n /** String representation. */\n toString: function() {\n var objStr = this.object\n ? \"\" + this.object\n : this.get(\"element_identifier\");\n return [\"NestedDCDCE(\", objStr, \")\"].join(\"\");\n }\n }\n )\n);\n\n//==============================================================================\n/** @class Backbone collection containing Generic NestedDCDCE's (nested dataset collections).\n */\nvar NestedDCDCECollection = DCECollection.extend(\n /** @lends NestedDCDCECollection.prototype */ {\n /** This is a collection of nested collections */\n model: NestedDCDCE,\n\n /** String representation. */\n toString: function() {\n return [\"NestedDCDCECollection(\", this.length, \")\"].join(\"\");\n }\n }\n);\n\n//==============================================================================\n/** @class Backbone model for a paired dataset collection within a list:paired dataset collection.\n */\nvar NestedPairDCDCE = PairDatasetCollection.extend(\n BASE_MVC.mixin(\n DatasetCollectionElementMixin,\n /** @lends NestedPairDCDCE.prototype */ {\n //TODO:?? possibly rename to NestedDatasetCollection?\n\n // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n // - re-apply manually it now\n /** This is both a collection and a collection element - call the constructor */\n constructor: function(attributes, options) {\n this.debug(\n \"\\t NestedPairDCDCE.constructor:\",\n attributes,\n options\n );\n //DatasetCollection.constructor.call( this, attributes, options );\n DatasetCollectionElementMixin.constructor.call(\n this,\n attributes,\n options\n );\n },\n\n /** String representation. */\n toString: function() {\n var objStr = this.object\n ? \"\" + this.object\n : this.get(\"element_identifier\");\n return [\"NestedPairDCDCE(\", objStr, \")\"].join(\"\");\n }\n }\n )\n);\n\n//==============================================================================\n/** @class Backbone collection for a backbone collection containing paired dataset collections.\n */\nvar NestedPairDCDCECollection = NestedDCDCECollection.extend(\n /** @lends PairDCDCECollection.prototype */ {\n /** We know this collection is composed of only nested pair collections */\n model: NestedPairDCDCE,\n\n /** String representation. */\n toString: function() {\n return [\"NestedPairDCDCECollection(\", this.length, \")\"].join(\"\");\n }\n }\n);\n\n//==============================================================================\n/** @class Backbone Model for a DatasetCollection (list) that contains DatasetCollections (pairs).\n */\nvar ListPairedDatasetCollection = DatasetCollection.extend(\n /** @lends ListPairedDatasetCollection.prototype */ {\n /** list:paired is the only collection that itself contains collections */\n collectionClass: NestedPairDCDCECollection,\n\n /** String representation. */\n toString: function() {\n return [\"ListPairedDatasetCollection(\", this.get(\"name\"), \")\"].join(\n \"\"\n );\n }\n }\n);\n\n//==============================================================================\n/** @class Backbone model for a list dataset collection within a list:list dataset collection. */\nvar NestedListDCDCE = ListDatasetCollection.extend(\n BASE_MVC.mixin(\n DatasetCollectionElementMixin,\n /** @lends NestedListDCDCE.prototype */ {\n /** This is both a collection and a collection element - call the constructor */\n constructor: function(attributes, options) {\n this.debug(\n \"\\t NestedListDCDCE.constructor:\",\n attributes,\n options\n );\n DatasetCollectionElementMixin.constructor.call(\n this,\n attributes,\n options\n );\n },\n\n /** String representation. */\n toString: function() {\n var objStr = this.object\n ? \"\" + this.object\n : this.get(\"element_identifier\");\n return [\"NestedListDCDCE(\", objStr, \")\"].join(\"\");\n }\n }\n )\n);\n\n//==============================================================================\n/** @class Backbone collection containing list dataset collections. */\nvar NestedListDCDCECollection = NestedDCDCECollection.extend({\n /** We know this collection is composed of only nested pair collections */\n model: NestedListDCDCE,\n\n /** String representation. */\n toString: function() {\n return [\"NestedListDCDCECollection(\", this.length, \")\"].join(\"\");\n }\n});\n\n//==============================================================================\n/** @class Backbone Model for a DatasetCollection (list) that contains other lists. */\nvar ListOfListsDatasetCollection = DatasetCollection.extend({\n /** list:paired is the only collection that itself contains collections */\n collectionClass: NestedListDCDCECollection,\n\n /** String representation. */\n toString: function() {\n return [\"ListOfListsDatasetCollection(\", this.get(\"name\"), \")\"].join(\n \"\"\n );\n }\n});\n\n//==============================================================================\nexport default {\n ListDatasetCollection: ListDatasetCollection,\n PairDatasetCollection: PairDatasetCollection,\n ListPairedDatasetCollection: ListPairedDatasetCollection,\n ListOfListsDatasetCollection: ListOfListsDatasetCollection\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/collection/collection-view-edit.js.map b/static/maps/mvc/collection/collection-view-edit.js.map index 544afebe4e8..219ffd2c823 100644 --- a/static/maps/mvc/collection/collection-view-edit.js.map +++ b/static/maps/mvc/collection/collection-view-edit.js.map @@ -1 +1 @@ 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DC_VIEW from \"mvc/collection/collection-view\";\nimport DC_MODEL from \"mvc/collection/collection-model\";\nimport DC_EDIT from \"mvc/collection/collection-li-edit\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport TAGS from \"mvc/tag\";\nimport faIconButton from \"ui/fa-icon-button\";\nimport _l from \"utils/localization\";\nimport \"ui/editable-text\";\n\n/* =============================================================================\nTODO:\n\n============================================================================= */\n/** @class editable View/Controller for a dataset collection.\n */\nvar _super = DC_VIEW.CollectionView;\nvar CollectionViewEdit = _super.extend(\n /** @lends CollectionView.prototype */ {\n //MODEL is either a DatasetCollection (or subclass) or a DatasetCollectionElement (list of pairs)\n\n /** logger used to record this.log messages, commonly set to console */\n //logger : console,\n\n /** sub view class used for datasets */\n DatasetDCEViewClass: DC_EDIT.DatasetDCEListItemEdit,\n /** sub view class used for nested collections */\n NestedDCDCEViewClass: DC_EDIT.NestedDCDCEListItemEdit,\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events\n * @param {Object} attributes optional settings for the panel\n */\n initialize: function(attributes) {\n _super.prototype.initialize.call(this, attributes);\n },\n\n /** In this override, make the collection name editable\n */\n _setUpBehaviors: function($where) {\n $where = $where || this.$el;\n _super.prototype._setUpBehaviors.call(this, $where);\n if (!this.model) {\n return;\n }\n\n // anon users shouldn't have access to any of the following\n if (!Galaxy.user || Galaxy.user.isAnonymous()) {\n return;\n }\n\n this.tagsEditorShown = true;\n\n //TODO: extract\n var panel = this,\n nameSelector = \"> .controls .name\";\n $where\n .find(nameSelector)\n .attr(\"title\", _l(\"Click to rename collection\"))\n .tooltip({ placement: \"bottom\" })\n .make_text_editable({\n on_finish: function(newName) {\n var previousName = panel.model.get(\"name\");\n if (newName && newName !== previousName) {\n panel.$el.find(nameSelector).text(newName);\n panel.model\n .save({ name: newName })\n .fail(function() {\n panel.$el\n .find(nameSelector)\n .text(panel.model.previous(\"name\"));\n });\n } else {\n panel.$el.find(nameSelector).text(previousName);\n }\n }\n });\n this.tagsEditor = new TAGS.TagsEditor({\n model: this.model,\n el: $where.find(\".tags-display\"),\n onshowFirstTime: function() {\n this.render();\n },\n usePrompt: false\n });\n this.tagsEditor.toggle(true);\n },\n\n // ........................................................................ misc\n /** string rep */\n toString: function() {\n return (\n \"CollectionViewEdit(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n// =============================================================================\n/** @class non-editable, read-only View/Controller for a dataset collection. */\nvar ListCollectionViewEdit = CollectionViewEdit.extend(\n /** @lends ListCollectionView.prototype */ {\n //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n /** sub view class used for datasets */\n DatasetDCEViewClass: DC_EDIT.DatasetDCEListItemEdit,\n\n // ........................................................................ misc\n /** string rep */\n toString: function() {\n return (\n \"ListCollectionViewEdit(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n// =============================================================================\n/** @class Editable, read-only View/Controller for a dataset collection. */\nvar PairCollectionViewEdit = ListCollectionViewEdit.extend(\n /** @lends PairCollectionViewEdit.prototype */ {\n // ........................................................................ misc\n /** string rep */\n toString: function() {\n return (\n \"PairCollectionViewEdit(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n// =============================================================================\n/** @class Editable (roughly since these collections are immutable),\n * View/Controller for a dataset collection.\n */\nvar NestedPairCollectionViewEdit = PairCollectionViewEdit.extend(\n /** @lends NestedPairCollectionViewEdit.prototype */ {\n /** Override to remove the editable text from the name/identifier - these collections are considered immutable */\n _setUpBehaviors: function($where) {\n _super.prototype._setUpBehaviors.call(this, $where);\n },\n\n // ........................................................................ misc\n /** string rep */\n toString: function() {\n return (\n \"NestedPairCollectionViewEdit(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n// =============================================================================\n/** @class editable, View/Controller for a list of pairs dataset collection. */\nvar ListOfPairsCollectionViewEdit = CollectionViewEdit.extend(\n /** @lends ListOfPairsCollectionView.prototype */ {\n //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n /** sub view class used for nested collections */\n NestedDCDCEViewClass: DC_EDIT.NestedDCDCEListItemEdit.extend({\n foldoutPanelClass: NestedPairCollectionViewEdit\n }),\n\n // ........................................................................ misc\n /** string rep */\n toString: function() {\n return (\n \"ListOfPairsCollectionViewEdit(\" +\n (this.model ? 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SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events\n * @param {Object} attributes optional settings for the panel\n */\n initialize: function(attributes) {\n _super.prototype.initialize.call(this, attributes);\n },\n\n /** In this override, make the collection name editable\n */\n _setUpBehaviors: function($where) {\n $where = $where || this.$el;\n _super.prototype._setUpBehaviors.call(this, $where);\n if (!this.model) {\n return;\n }\n\n // anon users shouldn't have access to any of the following\n if (!Galaxy.user || Galaxy.user.isAnonymous()) {\n return;\n }\n\n this.tagsEditorShown = true;\n\n //TODO: extract\n var panel = this,\n nameSelector = \"> .controls .name\";\n $where\n .find(nameSelector)\n .attr(\"title\", _l(\"Click to rename collection\"))\n .tooltip({ placement: \"bottom\" })\n .make_text_editable({\n on_finish: function(newName) {\n var previousName = panel.model.get(\"name\");\n if (newName && newName !== previousName) {\n panel.$el.find(nameSelector).text(newName);\n panel.model\n .save({ name: newName })\n .fail(function() {\n panel.$el\n .find(nameSelector)\n .text(panel.model.previous(\"name\"));\n });\n } else {\n panel.$el.find(nameSelector).text(previousName);\n }\n }\n });\n this.tagsEditor = new TAGS.TagsEditor({\n model: this.model,\n el: $where.find(\".tags-display\"),\n onshowFirstTime: function() {\n this.render();\n },\n usePrompt: false\n });\n this.tagsEditor.toggle(true);\n },\n\n // ........................................................................ misc\n /** string rep */\n toString: function() {\n return (\n \"CollectionViewEdit(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n// =============================================================================\n/** @class non-editable, read-only View/Controller for a dataset collection. */\nvar ListCollectionViewEdit = CollectionViewEdit.extend(\n /** @lends ListCollectionView.prototype */ {\n //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n /** sub view class used for datasets */\n DatasetDCEViewClass: DC_EDIT.DatasetDCEListItemEdit,\n\n // ........................................................................ misc\n /** string rep */\n toString: function() {\n return (\n \"ListCollectionViewEdit(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n// =============================================================================\n/** @class Editable, read-only View/Controller for a dataset collection. */\nvar PairCollectionViewEdit = ListCollectionViewEdit.extend(\n /** @lends PairCollectionViewEdit.prototype */ {\n // ........................................................................ misc\n /** string rep */\n toString: function() {\n return (\n \"PairCollectionViewEdit(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n// =============================================================================\n/** @class Editable (roughly since these collections are immutable),\n * View/Controller for a dataset collection.\n */\nvar NestedPairCollectionViewEdit = PairCollectionViewEdit.extend(\n /** @lends NestedPairCollectionViewEdit.prototype */ {\n /** Override to remove the editable text from the name/identifier - these collections are considered immutable */\n _setUpBehaviors: function($where) {\n _super.prototype._setUpBehaviors.call(this, $where);\n },\n\n // ........................................................................ misc\n /** string rep */\n toString: function() {\n return (\n \"NestedPairCollectionViewEdit(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n// =============================================================================\n/** @class editable, View/Controller for a list of pairs dataset collection. */\nvar ListOfPairsCollectionViewEdit = CollectionViewEdit.extend(\n /** @lends ListOfPairsCollectionView.prototype */ {\n //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n /** sub view class used for nested collections */\n NestedDCDCEViewClass: DC_EDIT.NestedDCDCEListItemEdit.extend({\n foldoutPanelClass: NestedPairCollectionViewEdit\n }),\n\n // ........................................................................ misc\n /** string rep */\n toString: function() {\n return (\n \"ListOfPairsCollectionViewEdit(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n// =============================================================================\n/** @class View/Controller for a list of lists dataset collection. */\nvar ListOfListsCollectionViewEdit = CollectionViewEdit.extend(\n /** @lends ListOfListsCollectionView.prototype */ {\n //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n /** sub view class used for nested collections */\n NestedDCDCEViewClass: DC_EDIT.NestedDCDCEListItemEdit.extend({\n foldoutPanelClass: NestedPairCollectionViewEdit\n }),\n\n // ........................................................................ misc\n /** string rep */\n toString: function() {\n return (\n \"ListOfListsCollectionViewEdit(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n//==============================================================================\nexport default {\n CollectionViewEdit: CollectionViewEdit,\n ListCollectionViewEdit: ListCollectionViewEdit,\n PairCollectionViewEdit: PairCollectionViewEdit,\n ListOfPairsCollectionViewEdit: ListOfPairsCollectionViewEdit,\n ListOfListsCollectionViewEdit: ListOfListsCollectionViewEdit\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/collection/collection-view.js.map b/static/maps/mvc/collection/collection-view.js.map index 3a16ae2eaec..0486e22e3f7 100644 --- a/static/maps/mvc/collection/collection-view.js.map +++ 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LIST_VIEW from \"mvc/list/list-view\";\nimport DC_MODEL from \"mvc/collection/collection-model\";\nimport DC_LI from \"mvc/collection/collection-li\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\nvar logNamespace = \"collections\";\n/* =============================================================================\nTODO:\n\n============================================================================= */\n/** @class non-editable, read-only View/Controller for a dataset collection.\n */\nvar _super = LIST_VIEW.ModelListPanel;\nvar CollectionView = _super.extend(\n /** @lends CollectionView.prototype */ {\n //MODEL is either a DatasetCollection (or subclass) or a DatasetCollectionElement (list of pairs)\n _logNamespace: logNamespace,\n\n className: _super.prototype.className + \" dataset-collection-panel\",\n\n /** sub view class used for datasets */\n DatasetDCEViewClass: DC_LI.DatasetDCEListItemView,\n /** sub view class used for nested collections */\n NestedDCDCEViewClass: DC_LI.NestedDCDCEListItemView,\n /** key of attribute in model to assign to this.collection */\n modelCollectionKey: \"elements\",\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events\n * @param {Object} attributes optional settings for the panel\n */\n initialize: function(attributes) {\n _super.prototype.initialize.call(this, attributes);\n this.linkTarget = attributes.linkTarget || \"_blank\";\n\n this.hasUser = attributes.hasUser;\n /** A stack of panels that currently cover or hide this panel */\n this.panelStack = [];\n /** The text of the link to go back to the panel containing this one */\n this.parentName = attributes.parentName;\n /** foldout or drilldown */\n this.foldoutStyle = attributes.foldoutStyle || \"foldout\";\n this.downloadUrl = this.model.attributes.url + \"/download\";\n },\n\n _queueNewRender: function($newRender, speed) {\n speed = speed === undefined ? this.fxSpeed : speed;\n var panel = this;\n panel.log(\"_queueNewRender:\", $newRender, speed);\n\n // TODO: jquery@1.12 doesn't change display when the elem has display: flex\n // this causes display: block for those elems after the use of show/hide animations\n // animations are removed from this view for now until fixed\n panel._swapNewRender($newRender);\n panel.trigger(\"rendered\", panel);\n },\n\n // ------------------------------------------------------------------------ sub-views\n /** In this override, use model.getVisibleContents */\n _filterCollection: function() {\n //TODO: should *not* be model.getVisibleContents - visibility is not model related\n return this.model.getVisibleContents();\n },\n\n /** override to return proper view class based on element_type */\n _getItemViewClass: function(model) {\n //this.debug( this + '._getItemViewClass:', model );\n //TODO: subclasses use DCEViewClass - but are currently unused - decide\n switch (model.get(\"element_type\")) {\n case \"hda\":\n return this.DatasetDCEViewClass;\n case \"dataset_collection\":\n return this.NestedDCDCEViewClass;\n }\n throw new TypeError(\n \"Unknown element type:\",\n model.get(\"element_type\")\n );\n },\n\n /** override to add link target and anon */\n _getItemViewOptions: function(model) {\n var options = _super.prototype._getItemViewOptions.call(\n this,\n model\n );\n return _.extend(options, {\n linkTarget: this.linkTarget,\n hasUser: this.hasUser,\n //TODO: could move to only nested: list:paired\n foldoutStyle: this.foldoutStyle\n });\n },\n\n // ------------------------------------------------------------------------ collection sub-views\n /** In this override, add/remove expanded/collapsed model ids to/from web storage */\n _setUpItemViewListeners: function(view) {\n var panel = this;\n _super.prototype._setUpItemViewListeners.call(panel, view);\n\n // use pub-sub to: handle drilldown expansion and collapse\n panel.listenTo(view, {\n \"expanded:drilldown\": function(v, drilldown) {\n this._expandDrilldownPanel(drilldown);\n },\n \"collapsed:drilldown\": function(v, drilldown) {\n this._collapseDrilldownPanel(drilldown);\n }\n });\n return this;\n },\n\n /** Handle drill 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LIST_VIEW from \"mvc/list/list-view\";\nimport DC_MODEL from \"mvc/collection/collection-model\";\nimport DC_LI from \"mvc/collection/collection-li\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\nvar logNamespace = \"collections\";\n/* =============================================================================\nTODO:\n\n============================================================================= */\n/** @class non-editable, read-only View/Controller for a dataset collection.\n */\nvar _super = LIST_VIEW.ModelListPanel;\nvar CollectionView = _super.extend(\n /** @lends CollectionView.prototype */ {\n //MODEL is either a DatasetCollection (or subclass) or a DatasetCollectionElement (list of pairs)\n _logNamespace: logNamespace,\n\n className: _super.prototype.className + \" dataset-collection-panel\",\n\n /** sub view class used for datasets */\n DatasetDCEViewClass: DC_LI.DatasetDCEListItemView,\n /** sub view class used for nested collections */\n NestedDCDCEViewClass: DC_LI.NestedDCDCEListItemView,\n /** key of attribute in model to assign to this.collection */\n modelCollectionKey: \"elements\",\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events\n * @param {Object} attributes optional settings for the panel\n */\n initialize: function(attributes) {\n _super.prototype.initialize.call(this, attributes);\n this.linkTarget = attributes.linkTarget || \"_blank\";\n\n this.hasUser = attributes.hasUser;\n /** A stack of panels that currently cover or hide this panel */\n this.panelStack = [];\n /** The text of the link to go back to the panel containing this one */\n this.parentName = attributes.parentName;\n /** foldout or drilldown */\n this.foldoutStyle = attributes.foldoutStyle || \"foldout\";\n this.downloadUrl = this.model.attributes.url + \"/download\";\n },\n\n _queueNewRender: function($newRender, speed) {\n speed = speed === undefined ? this.fxSpeed : speed;\n var panel = this;\n panel.log(\"_queueNewRender:\", $newRender, speed);\n\n // TODO: jquery@1.12 doesn't change display when the elem has display: flex\n // this causes display: block for those elems after the use of show/hide animations\n // animations are removed from this view for now until fixed\n panel._swapNewRender($newRender);\n panel.trigger(\"rendered\", panel);\n },\n\n // ------------------------------------------------------------------------ sub-views\n /** In this override, use model.getVisibleContents */\n _filterCollection: function() {\n //TODO: should *not* be model.getVisibleContents - visibility is not model related\n return this.model.getVisibleContents();\n },\n\n /** override to return proper view class based on element_type */\n _getItemViewClass: function(model) {\n //this.debug( this + '._getItemViewClass:', model );\n //TODO: subclasses use DCEViewClass - but are currently unused - decide\n switch (model.get(\"element_type\")) {\n case \"hda\":\n return this.DatasetDCEViewClass;\n case \"dataset_collection\":\n return this.NestedDCDCEViewClass;\n }\n throw new TypeError(\n \"Unknown element type:\",\n model.get(\"element_type\")\n );\n },\n\n /** override to add link target and anon */\n _getItemViewOptions: function(model) {\n var options = _super.prototype._getItemViewOptions.call(\n this,\n model\n );\n return _.extend(options, {\n linkTarget: this.linkTarget,\n hasUser: this.hasUser,\n //TODO: could move to only nested: list:paired\n foldoutStyle: this.foldoutStyle\n });\n },\n\n // ------------------------------------------------------------------------ collection sub-views\n /** In this override, add/remove expanded/collapsed model ids to/from web storage */\n _setUpItemViewListeners: function(view) {\n var panel = this;\n _super.prototype._setUpItemViewListeners.call(panel, view);\n\n // use pub-sub to: handle drilldown expansion and collapse\n panel.listenTo(view, {\n \"expanded:drilldown\": function(v, drilldown) {\n this._expandDrilldownPanel(drilldown);\n },\n \"collapsed:drilldown\": function(v, drilldown) {\n this._collapseDrilldownPanel(drilldown);\n }\n });\n return this;\n },\n\n /** Handle drill down by hiding this panels list and controls and showing the sub-panel */\n _expandDrilldownPanel: function(drilldown) {\n this.panelStack.push(drilldown);\n // hide this panel's controls and list, set the name for back navigation, and attach to the $el\n this.$(\"> .controls\")\n .add(this.$list())\n .hide();\n drilldown.parentName = this.model.get(\"name\");\n this.$el.append(drilldown.render().$el);\n },\n\n /** Handle drilldown close by freeing the panel and re-rendering this panel */\n _collapseDrilldownPanel: function(drilldown) {\n this.panelStack.pop();\n this.render();\n },\n\n // ------------------------------------------------------------------------ panel events\n /** event map */\n events: {\n \"click .navigation .back\": \"close\"\n },\n\n /** close/remove this collection panel */\n close: function(event) {\n this.remove();\n this.trigger(\"close\");\n },\n\n // ........................................................................ misc\n /** string rep */\n toString: function() {\n return (\n \"CollectionView(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n//------------------------------------------------------------------------------ TEMPLATES\nCollectionView.prototype.templates = (function() {\n var controlsTemplate = BASE_MVC.wrapTemplate(\n [\n '',\n '\",\n\n '',\n\n '\",\n \"<%- collection.name || collection.element_identifier %>',\n '',\n '<% if( collection.collection_type === \"list\" ){ %>',\n _l(\"a list of datasets\"),\n '<% } else if( collection.collection_type === \"paired\" ){ %>',\n _l(\"a pair of datasets\"),\n '<% } else if( collection.collection_type === \"list:paired\" ){ %>',\n _l(\"a list of paired datasets\"),\n '<% } else if( collection.collection_type === \"list:list\" ){ %>',\n _l(\"a list of dataset lists\"),\n \"<% } %>\",\n \"\",\n \"',\n '\",\n\n '\"\n ],\n \"collection\"\n );\n\n return _.extend(_.clone(_super.prototype.templates), {\n controls: controlsTemplate\n });\n})();\n\n// =============================================================================\n/** @class non-editable, read-only View/Controller for a dataset collection. */\nvar ListCollectionView = CollectionView.extend(\n /** @lends ListCollectionView.prototype */ {\n //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n /** sub view class used for datasets */\n DatasetDCEViewClass: DC_LI.DatasetDCEListItemView,\n\n // ........................................................................ misc\n /** string rep */\n toString: function() {\n return (\n \"ListCollectionView(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n// =============================================================================\n/** @class non-editable, read-only View/Controller for a dataset collection. */\nvar PairCollectionView = ListCollectionView.extend(\n /** @lends PairCollectionView.prototype */ {\n // ........................................................................ misc\n /** string rep */\n toString: function() {\n return (\n \"PairCollectionView(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n// =============================================================================\n/** @class non-editable, read-only View/Controller for a dataset collection. */\nvar ListOfPairsCollectionView = CollectionView.extend(\n /** @lends ListOfPairsCollectionView.prototype */ {\n //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n /** sub view class used for nested collections */\n NestedDCDCEViewClass: DC_LI.NestedDCDCEListItemView.extend({\n foldoutPanelClass: PairCollectionView\n }),\n\n // ........................................................................ misc\n /** string rep */\n toString: function() {\n return (\n \"ListOfPairsCollectionView(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n// =============================================================================\n/** @class non-editable, read-only View/Controller for a list of lists dataset collection. */\nvar ListOfListsCollectionView = CollectionView.extend({\n /** sub view class used for nested collections */\n NestedDCDCEViewClass: DC_LI.NestedDCDCEListItemView.extend({\n foldoutPanelClass: PairCollectionView\n }),\n\n /** string rep */\n toString: function() {\n return (\n \"ListOfListsCollectionView(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n});\n\n//==============================================================================\nexport default {\n CollectionView: CollectionView,\n ListCollectionView: ListCollectionView,\n PairCollectionView: PairCollectionView,\n ListOfPairsCollectionView: ListOfPairsCollectionView,\n ListOfListsCollectionView: ListOfListsCollectionView\n};\n"]} \ No newline at end of file diff --git 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HDCA from \"mvc/history/hdca-model\";\nimport STATES from \"mvc/dataset/states\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport baseCreator from \"mvc/collection/base-creator\";\nimport UI_MODAL from \"mvc/ui/ui-modal\";\nimport naturalSort from \"utils/natural-sort\";\nimport _l from \"utils/localization\";\nimport \"ui/hoverhighlight\";\n\nvar logNamespace = \"collections\";\n\n/*==============================================================================\nTODO:\n use proper Element model and not just json\n straighten out createFn, collection.createHDCA\n possibly stop using modals for this\n It would be neat to do a drag and drop\n\n==============================================================================*/\n/** A view for both DatasetDCEs and NestedDCDCEs\n * (things that implement collection-model:DatasetCollectionElementMixin)\n */\nvar DatasetCollectionElementView = Backbone.View\n .extend(BASE_MVC.LoggableMixin)\n .extend({\n _logNamespace: logNamespace,\n\n //TODO: use proper class (DatasetDCE or NestedDCDCE (or the union of both))\n tagName: \"li\",\n className: \"collection-element\",\n\n initialize: function(attributes) {\n this.element = attributes.element || {};\n this.selected = attributes.selected || false;\n },\n\n render: function() {\n this.$el\n .attr(\"data-element-id\", this.element.id)\n .attr(\"draggable\", true)\n .html(this.template({ element: this.element }));\n if (this.selected) {\n this.$el.addClass(\"selected\");\n }\n return this;\n },\n\n //TODO: lots of unused space in the element - possibly load details and display them horiz.\n template: _.template(\n [\n '',\n \"<%- element.name %>\",\n \"\",\n '\"\n ].join(\"\")\n ),\n\n /** select this element and pub */\n select: function(toggle) {\n this.$el.toggleClass(\"selected\", toggle);\n this.trigger(\"select\", {\n source: this,\n selected: this.$el.hasClass(\"selected\")\n });\n },\n\n /** animate the removal of this element and pub */\n discard: function() {\n var view = this,\n parentWidth = this.$el.parent().width();\n this.$el.animate(\n { \"margin-right\": parentWidth },\n \"fast\",\n function() {\n view.trigger(\"discard\", {\n source: view\n });\n view.destroy();\n }\n );\n },\n\n /** remove the DOM and any listeners */\n destroy: function() {\n this.off();\n this.$el.remove();\n },\n\n events: {\n click: \"_click\",\n \"click .name\": \"_clickName\",\n \"click .discard\": \"_clickDiscard\",\n\n dragstart: \"_dragstart\",\n dragend: \"_dragend\",\n dragover: \"_sendToParent\",\n drop: \"_sendToParent\"\n },\n\n /** select when the li is clicked */\n _click: function(ev) {\n ev.stopPropagation();\n this.select(ev);\n },\n\n /** rename a pair when the name is clicked */\n _clickName: function(ev) {\n ev.stopPropagation();\n ev.preventDefault();\n var promptString = [\n _l(\"Enter a new name for the element\"),\n \":\\n(\",\n _l(\n \"Note that changing the name here will not rename the dataset\"\n ),\n \")\"\n ].join(\"\"),\n response = prompt(\n _l(\"Enter a new name for the element\") + \":\",\n this.element.name\n );\n if (response) {\n this.element.name = response;\n this.render();\n }\n //TODO: cancelling with ESC leads to closure of the creator...\n },\n\n /** discard when the discard button is clicked */\n _clickDiscard: function(ev) {\n ev.stopPropagation();\n this.discard();\n },\n\n /** dragging pairs for re-ordering */\n _dragstart: function(ev) {\n if (ev.originalEvent) {\n ev = ev.originalEvent;\n }\n ev.dataTransfer.effectAllowed = \"move\";\n ev.dataTransfer.setData(\"text/plain\", JSON.stringify(this.element));\n\n this.$el.addClass(\"dragging\");\n this.$el.parent().trigger(\"collection-element.dragstart\", [this]);\n },\n\n /** dragging for re-ordering */\n _dragend: function(ev) {\n this.$el.removeClass(\"dragging\");\n this.$el.parent().trigger(\"collection-element.dragend\", [this]);\n },\n\n /** manually bubble up an event to the parent/container */\n _sendToParent: function(ev) {\n this.$el.parent().trigger(ev);\n },\n\n /** string rep */\n toString: function() {\n return \"DatasetCollectionElementView()\";\n }\n });\n\n// ============================================================================\n/** An interface for building collections.\n */\nvar ListCollectionCreator = Backbone.View\n .extend(BASE_MVC.LoggableMixin)\n .extend(baseCreator.CollectionCreatorMixin)\n .extend({\n _logNamespace: logNamespace,\n\n /** the class used to display individual elements */\n elementViewClass: DatasetCollectionElementView,\n /** the class this creator will create and save */\n collectionClass: HDCA.HistoryListDatasetCollection,\n className:\n \"list-collection-creator collection-creator flex-row-container\",\n\n /** minimum number of valid elements to start with in order to build a collection of this type */\n minElements: 1,\n\n defaultAttributes: {\n //TODO: remove - use new collectionClass().save()\n /** takes elements and creates the proper collection - returns a promise */\n creationFn: function() {\n throw new TypeError(\"no creation fn for creator\");\n },\n /** fn to call when the collection is created (scoped to this) */\n oncreate: function() {},\n /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */\n oncancel: function() {},\n /** distance from list edge to begin autoscrolling list */\n autoscrollDist: 24,\n /** Color passed to hoverhighlight */\n highlightClr: \"rgba( 64, 255, 255, 1.0 )\"\n },\n\n footerSettings: {\n \".hide-originals\": \"hideOriginals\"\n },\n\n /** set up initial options, instance vars, behaviors */\n initialize: function(attributes) {\n this.metric(\"ListCollectionCreator.initialize\", attributes);\n var creator = this;\n _.each(this.defaultAttributes, function(value, key) {\n value = attributes[key] || value;\n creator[key] = value;\n });\n\n /** unordered, original list - cache to allow reversal */\n creator.initialElements = attributes.elements || [];\n\n this._setUpCommonSettings(attributes);\n this._instanceSetUp();\n this._elementsSetUp();\n this._setUpBehaviors();\n },\n\n /** set up instance vars */\n _instanceSetUp: function() {\n /** Ids of elements that have been selected by the user - to preserve over renders */\n this.selectedIds = {};\n /** DOM elements currently being dragged */\n this.$dragging = null;\n /** Used for blocking UI events during ajax/operations (don't post twice) */\n this.blocking = false;\n },\n\n // ------------------------------------------------------------------------ process raw list\n /** set up main data */\n _elementsSetUp: function() {\n //this.debug( '-- _dataSetUp' );\n /** a list of invalid elements and the reasons they aren't valid */\n this.invalidElements = [];\n //TODO: handle fundamental problem of syncing DOM, views, and list here\n /** data for list in progress */\n this.workingElements = [];\n /** views for workingElements */\n this.elementViews = [];\n\n // copy initial list, sort, add ids if needed\n this.workingElements = this.initialElements.slice(0);\n this._ensureElementIds();\n this._validateElements();\n this._mangleDuplicateNames();\n this._sortElements();\n },\n\n /** add ids to dataset objs in initial list if none */\n _ensureElementIds: function() {\n this.workingElements.forEach(function(element) {\n if (!element.hasOwnProperty(\"id\")) {\n element.id = _.uniqueId();\n }\n });\n return this.workingElements;\n },\n\n /** separate working list into valid and invalid elements for this collection */\n _validateElements: function() {\n var creator = this,\n existingNames = {};\n creator.invalidElements = [];\n\n this.workingElements = this.workingElements.filter(function(\n element\n ) {\n var problem = creator._isElementInvalid(element);\n if (problem) {\n creator.invalidElements.push({\n element: element,\n text: problem\n });\n }\n return !problem;\n });\n return this.workingElements;\n },\n\n /** describe what is wrong with a particular element if anything */\n _isElementInvalid: function(element) {\n if (element.history_content_type !== \"dataset\") {\n return _l(\"is not a dataset\");\n }\n var validState =\n element.state === STATES.OK ||\n _.contains(STATES.NOT_READY_STATES, element.state);\n if (!validState) {\n return _l(\"has errored, is paused, or is not accessible\");\n }\n if (element.deleted || element.purged) {\n return _l(\"has been deleted or purged\");\n }\n return null;\n },\n\n /** mangle duplicate names using a mac-like '(counter)' addition to any duplicates */\n _mangleDuplicateNames: function() {\n var SAFETY = 900,\n counter = 1,\n existingNames = {};\n this.workingElements.forEach(function(element) {\n var currName = element.name;\n while (existingNames.hasOwnProperty(currName)) {\n currName = element.name + \" (\" + counter + \")\";\n counter += 1;\n if (counter >= SAFETY) {\n throw new Error(\n \"Safety hit in while loop - thats impressive\"\n );\n }\n }\n element.name = currName;\n existingNames[element.name] = true;\n });\n },\n\n /** sort a list of elements */\n _sortElements: function(list) {\n // // currently only natural sort by name\n // this.workingElements.sort( function( a, b ){ return naturalSort( a.name, b.name ); });\n // return this.workingElements;\n },\n\n // ------------------------------------------------------------------------ rendering\n // templates : ListCollectionCreator.templates,\n /** render the entire interface */\n render: function(speed, callback) {\n //this.debug( '-- _render' );\n if (this.workingElements.length < this.minElements) {\n return this._renderInvalid(speed, callback);\n }\n\n this.$el.empty().html(this.templates.main());\n this._renderHeader(speed);\n this._renderMiddle(speed);\n this._renderFooter(speed);\n this._addPluginComponents();\n this.$(\".collection-name\").focus();\n this.trigger(\"rendered\", this);\n return this;\n },\n\n /** render a simplified interface aimed at telling the user why they can't move forward */\n _renderInvalid: function(speed, callback) {\n //this.debug( '-- _render' );\n this.$el.empty().html(\n this.templates.invalidInitial({\n problems: this.invalidElements,\n elements: this.workingElements\n })\n );\n if (typeof this.oncancel === \"function\") {\n this.$(\".cancel-create.btn\").show();\n }\n this.trigger(\"rendered\", this);\n return this;\n },\n\n /** render the header section */\n _renderHeader: function(speed, callback) {\n var $header = this.$(\".header\")\n .empty()\n .html(this.templates.header())\n .find(\".help-content\")\n .prepend($(this.templates.helpContent()));\n //TODO: should only show once despite calling _renderHeader again\n if (this.invalidElements.length) {\n this._invalidElementsAlert();\n }\n return $header;\n },\n\n /** render the middle including the elements */\n _renderMiddle: function(speed, callback) {\n var $middle = this.$(\".middle\")\n .empty()\n .html(this.templates.middle());\n this._renderList(speed);\n return $middle;\n },\n\n /** add any jQuery/bootstrap/custom plugins to elements rendered */\n _addPluginComponents: function() {\n this.$(\".help-content i\").hoverhighlight(\n \".collection-creator\",\n this.highlightClr\n );\n },\n\n /** build and show an alert describing any elements that could not be included due to problems */\n _invalidElementsAlert: function() {\n this._showAlert(\n this.templates.invalidElements({\n problems: this.invalidElements\n }),\n \"alert-warning\"\n );\n },\n\n _disableNameAndCreate: function(disable) {\n disable = !_.isUndefined(disable) ? disable : true;\n if (disable) {\n this.$(\".collection-name\").prop(\"disabled\", true);\n this.$(\".create-collection\").toggleClass(\"disabled\", true);\n // } else {\n // this.$( '.collection-name' ).prop( 'disabled', false );\n // this.$( '.create-collection' ).removeClass( 'disable' );\n }\n },\n\n // ------------------------------------------------------------------------ rendering elements\n /** conv. to the main list display DOM */\n $list: function() {\n return this.$(\".collection-elements\");\n },\n\n /** show or hide the clear selected control based on the num of selected elements */\n _renderClearSelected: function() {\n if (_.size(this.selectedIds)) {\n this.$(\n \".collection-elements-controls > .clear-selected\"\n ).show();\n } else {\n this.$(\n \".collection-elements-controls > .clear-selected\"\n ).hide();\n }\n },\n\n /** render the elements in order (or a warning if no elements found) */\n _renderList: function(speed, callback) {\n //this.debug( '-- _renderList' );\n var creator = this,\n $tmp = jQuery(\"\"),\n $list = creator.$list();\n\n _.each(this.elementViews, function(view) {\n view.destroy();\n creator.removeElementView(view);\n });\n\n // if( !this.workingElements.length ){\n // this._renderNoValidElements();\n // return;\n // }\n\n creator.workingElements.forEach(function(element) {\n var elementView = creator._createElementView(element);\n $tmp.append(elementView.$el);\n });\n\n creator._renderClearSelected();\n $list.empty().append($tmp.children());\n _.invoke(creator.elementViews, \"render\");\n\n if ($list.height() > $list.css(\"max-height\")) {\n $list.css(\"border-width\", \"1px 0px 1px 0px\");\n } else {\n $list.css(\"border-width\", \"0px\");\n }\n },\n\n /** create an element view, cache in elementViews, set up listeners, and return */\n _createElementView: function(element) {\n var elementView = new this.elementViewClass({\n //TODO: use non-generic class or not all\n // model : COLLECTION.DatasetDCE( element )\n element: element,\n selected: _.has(this.selectedIds, element.id)\n });\n this.elementViews.push(elementView);\n this._listenToElementView(elementView);\n return elementView;\n },\n\n /** listen to any element events */\n _listenToElementView: function(view) {\n var creator = this;\n creator.listenTo(view, {\n select: function(data) {\n var element = data.source.element;\n if (data.selected) {\n creator.selectedIds[element.id] = true;\n } else {\n delete creator.selectedIds[element.id];\n }\n creator.trigger(\"elements:select\", data);\n },\n discard: function(data) {\n creator.trigger(\"elements:discard\", data);\n }\n });\n },\n\n /** add a new element view based on the json in element */\n addElementView: function(element) {\n //TODO: workingElements is sorted, add element in appropo index\n // add element, sort elements, find element index\n // var view = this._createElementView( element );\n // return view;\n },\n\n /** stop listening to view and remove from caches */\n removeElementView: function(view) {\n delete this.selectedIds[view.element.id];\n this._renderClearSelected();\n\n this.elementViews = _.without(this.elementViews, view);\n this.stopListening(view);\n },\n\n /** render a message in the list that no elements remain to create a collection */\n _renderNoElementsLeft: function() {\n this._disableNameAndCreate(true);\n this.$(\".collection-elements\").append(\n this.templates.noElementsLeft()\n );\n },\n\n // /** render a message in the list that no valid elements were found to create a collection */\n // _renderNoValidElements : function(){\n // this._disableNameAndCreate( true );\n // this.$( '.collection-elements' ).append( this.templates.noValidElements() );\n // },\n\n // ------------------------------------------------------------------------ API\n /** convert element into JSON compatible with the collections API */\n _elementToJSON: function(element) {\n // return element.toJSON();\n return element;\n },\n\n /** create the collection via the API\n * @returns {jQuery.xhr Object} the jquery ajax request\n */\n createList: function(name) {\n if (!this.workingElements.length) {\n var message = _l(\"No valid elements for final list\") + \". \";\n message +=\n '' +\n _l(\"Cancel\") +\n \" \";\n message += _l(\"or\");\n message +=\n ' ' +\n _l(\"start over\") +\n \".\";\n this._showAlert(message);\n return;\n }\n\n var creator = this,\n elements = this.workingElements.map(function(element) {\n return creator._elementToJSON(element);\n });\n\n creator.blocking = true;\n return creator\n .creationFn(elements, name, creator.hideOriginals)\n .always(function() {\n creator.blocking = false;\n })\n .fail(function(xhr, status, message) {\n creator.trigger(\"error\", {\n xhr: xhr,\n status: status,\n message: _l(\n \"An error occurred while creating this collection\"\n )\n });\n })\n .done(function(response, message, xhr) {\n creator.trigger(\n \"collection:created\",\n response,\n message,\n xhr\n );\n creator.metric(\"collection:created\", response);\n if (typeof creator.oncreate === \"function\") {\n creator.oncreate.call(this, response, message, xhr);\n }\n });\n },\n\n // ------------------------------------------------------------------------ events\n /** set up event handlers on self */\n _setUpBehaviors: function() {\n this.on(\"error\", this._errorHandler);\n\n this.once(\"rendered\", function() {\n this.trigger(\"rendered:initial\", this);\n });\n\n this.on(\"elements:select\", function(data) {\n this._renderClearSelected();\n });\n\n this.on(\"elements:discard\", function(data) {\n var element = data.source.element;\n this.removeElementView(data.source);\n\n this.workingElements = _.without(this.workingElements, element);\n if (!this.workingElements.length) {\n this._renderNoElementsLeft();\n }\n });\n\n //this.on( 'all', function(){\n // this.info( arguments );\n //});\n return this;\n },\n\n /** handle errors with feedback and details to the user (if available) */\n _errorHandler: function(data) {\n this.error(data);\n\n var creator = this,\n content = data.message || _l(\"An error occurred\");\n if (data.xhr) {\n var xhr = data.xhr,\n message = data.message;\n if (xhr.readyState === 0 && xhr.status === 0) {\n content +=\n \": \" +\n _l(\"Galaxy could not be reached and may be updating.\") +\n _l(\" Try again in a few minutes.\");\n } else if (xhr.responseJSON) {\n content +=\n \":',\n '\",\n\n '',\n\n '\",\n \"<%- collection.name || collection.element_identifier %>',\n '',\n '<% if( collection.collection_type === \"list\" ){ %>',\n _l(\"a list of datasets\"),\n '<% } else if( collection.collection_type === \"paired\" ){ %>',\n _l(\"a pair of datasets\"),\n '<% } else if( collection.collection_type === \"list:paired\" ){ %>',\n _l(\"a list of paired datasets\"),\n '<% } else if( collection.collection_type === \"list:list\" ){ %>',\n _l(\"a list of dataset lists\"),\n \"<% } %>\",\n \"\",\n \"\" +\n JSON.stringify(xhr.responseJSON) +\n \"
\";\n } else {\n content += \": \" + message;\n }\n }\n creator._showAlert(content, \"alert-danger\");\n },\n\n events: {\n // header\n \"click .more-help\": \"_clickMoreHelp\",\n \"click .less-help\": \"_clickLessHelp\",\n \"click .main-help\": \"_toggleHelp\",\n \"click .header .alert button\": \"_hideAlert\",\n\n \"click .reset\": \"reset\",\n \"click .clear-selected\": \"clearSelectedElements\",\n\n // elements - selection\n \"click .collection-elements\": \"clearSelectedElements\",\n\n // elements - drop target\n // 'dragenter .collection-elements': '_dragenterElements',\n // 'dragleave .collection-elements': '_dragleaveElements',\n \"dragover .collection-elements\": \"_dragoverElements\",\n \"drop .collection-elements\": \"_dropElements\",\n\n // these bubble up from the elements as custom events\n \"collection-element.dragstart .collection-elements\":\n \"_elementDragstart\",\n \"collection-element.dragend .collection-elements\":\n \"_elementDragend\",\n\n // footer\n \"change .collection-name\": \"_changeName\",\n \"keydown .collection-name\": \"_nameCheckForEnter\",\n \"change .hide-originals\": \"_changeHideOriginals\",\n \"click .cancel-create\": \"_cancelCreate\",\n \"click .create-collection\": \"_clickCreate\" //,\n },\n\n // ........................................................................ elements\n /** reset all data to the initial state */\n reset: function() {\n this._instanceSetUp();\n this._elementsSetUp();\n this.render();\n },\n\n /** deselect all elements */\n clearSelectedElements: function(ev) {\n this.$(\".collection-elements .collection-element\").removeClass(\n \"selected\"\n );\n this.$(\".collection-elements-controls > .clear-selected\").hide();\n },\n\n //_dragenterElements : function( ev ){\n // //this.debug( '_dragenterElements:', ev );\n //},\n //TODO: if selected are dragged out of the list area - remove the placeholder - cuz it won't work anyway\n // _dragleaveElements : function( ev ){\n // //this.debug( '_dragleaveElements:', ev );\n // },\n\n /** track the mouse drag over the list adding a placeholder to show where the drop would occur */\n _dragoverElements: function(ev) {\n //this.debug( '_dragoverElements:', ev );\n ev.preventDefault();\n\n var $list = this.$list();\n this._checkForAutoscroll($list, ev.originalEvent.clientY);\n var $nearest = this._getNearestElement(ev.originalEvent.clientY);\n\n //TODO: no need to re-create - move instead\n this.$(\".element-drop-placeholder\").remove();\n var $placeholder = $(\n ''\n );\n if (!$nearest.length) {\n $list.append($placeholder);\n } else {\n $nearest.before($placeholder);\n }\n },\n\n /** If the mouse is near enough to the list's top or bottom, scroll the list */\n _checkForAutoscroll: function($element, y) {\n var AUTOSCROLL_SPEED = 2,\n offset = $element.offset(),\n scrollTop = $element.scrollTop(),\n upperDist = y - offset.top,\n lowerDist = offset.top + $element.outerHeight() - y;\n if (upperDist >= 0 && upperDist < this.autoscrollDist) {\n $element.scrollTop(scrollTop - AUTOSCROLL_SPEED);\n } else if (lowerDist >= 0 && lowerDist < this.autoscrollDist) {\n $element.scrollTop(scrollTop + AUTOSCROLL_SPEED);\n }\n },\n\n /** get the nearest element based on the mouse's Y coordinate.\n * If the y is at the end of the list, return an empty jQuery object.\n */\n _getNearestElement: function(y) {\n var WIGGLE = 4,\n lis = this.$(\n \".collection-elements li.collection-element\"\n ).toArray();\n for (var i = 0; i < lis.length; i++) {\n var $li = $(lis[i]),\n top = $li.offset().top,\n halfHeight = Math.floor($li.outerHeight() / 2) + WIGGLE;\n if (top + halfHeight > y && top - halfHeight < y) {\n return $li;\n }\n }\n return $();\n },\n\n /** drop (dragged/selected elements) onto the list, re-ordering the internal list */\n _dropElements: function(ev) {\n if (ev.originalEvent) {\n ev = ev.originalEvent;\n }\n // both required for firefox\n ev.preventDefault();\n ev.dataTransfer.dropEffect = \"move\";\n\n // insert before the nearest element or after the last.\n var $nearest = this._getNearestElement(ev.clientY);\n if ($nearest.length) {\n this.$dragging.insertBefore($nearest);\n } else {\n // no nearest before - insert after last element\n this.$dragging.insertAfter(\n this.$(\".collection-elements .collection-element\").last()\n );\n }\n // resync the creator's list based on the new DOM order\n this._syncOrderToDom();\n return false;\n },\n\n /** resync the creator's list of elements based on the DOM order */\n _syncOrderToDom: function() {\n var creator = this,\n newElements = [];\n //TODO: doesn't seem wise to use the dom to store these - can't we sync another way?\n this.$(\".collection-elements .collection-element\").each(function() {\n var id = $(this).attr(\"data-element-id\"),\n element = _.findWhere(creator.workingElements, {\n id: id\n });\n if (element) {\n newElements.push(element);\n } else {\n console.error(\"missing element: \", id);\n }\n });\n this.workingElements = newElements;\n this._renderList();\n },\n\n /** drag communication with element sub-views: dragstart */\n _elementDragstart: function(ev, element) {\n // auto select the element causing the event and move all selected\n element.select(true);\n this.$dragging = this.$(\n \".collection-elements .collection-element.selected\"\n );\n },\n\n /** drag communication with element sub-views: dragend - remove the placeholder */\n _elementDragend: function(ev, element) {\n $(\".element-drop-placeholder\").remove();\n this.$dragging = null;\n },\n\n // ------------------------------------------------------------------------ templates\n //TODO: move to require text plugin and load these as text\n //TODO: underscore currently unnecc. bc no vars are used\n //TODO: better way of localizing text-nodes in long strings\n /** underscore template fns attached to class */\n templates: _.extend(\n {},\n baseCreator.CollectionCreatorMixin._creatorTemplates,\n {\n /** the header (not including help text) */\n header: _.template(\n [\n '',\n '',\n _l(\"More help\"),\n \"\",\n '\",\n '',\n '',\n _l(\"Less\"),\n \"\",\n \"\",\n \"',\n '',\n '',\n \"\"\n ].join(\"\")\n ),\n\n /** the middle: element list */\n middle: _.template(\n [\n '',\n '',\n _l(\"Start over\"),\n \"\",\n '',\n _l(\"Clear selected\"),\n \"\",\n \"\",\n '',\n \"\"\n ].join(\"\")\n ),\n\n /** creation and cancel controls */\n footer: _.template(\n [\n '',\n '\",\n\n '',\n '\",\n \"\",\n '',\n '',\n '\",\n \"',\n _l(\"Name\"),\n \":\",\n \"',\n '\",\n\n '\",\n \"\"\n ].join(\"\")\n ),\n\n /** help content */\n helpContent: _.template(\n [\n \"\",\n _l(\n [\n \"Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and \",\n \"workflows in order to have analyses done on each member of the entire group. This interface allows \",\n \"you to create a collection and re-order the final collection.\"\n ].join(\"\")\n ),\n \"
\",\n \"- \",\n \"
\",\n \"\",\n _l(\n [\n 'Once your collection is complete, enter a name and ',\n 'click \"Create list\".'\n ].join(\"\")\n ),\n \"
\"\n ].join(\"\")\n ),\n\n /** shown in list when all elements are discarded */\n invalidElements: _.template(\n [\n _l(\n \"The following selections could not be included due to problems:\"\n ),\n \"- <% _.each( problems, function( problem ){ %>\",\n \"
',\n '\",\n '\"\n ].join(\"\")\n )\n }\n ),\n\n // ------------------------------------------------------------------------ misc\n /** string rep */\n toString: function() {\n return \"ListCollectionCreator\";\n }\n });\n\n//=============================================================================\n/** Create a modal and load its body with the given CreatorClass creator type\n * @returns {Deferred} resolved when creator has built a collection.\n */\nvar collectionCreatorModal = function _collectionCreatorModal(\n elements,\n options,\n CreatorClass\n) {\n var deferred = jQuery.Deferred(),\n modal = Galaxy.modal || new UI_MODAL.View(),\n creator;\n\n options = _.defaults(options || {}, {\n elements: elements,\n oncancel: function() {\n modal.hide();\n deferred.reject(\"cancelled\");\n },\n oncreate: function(creator, response) {\n modal.hide();\n deferred.resolve(response);\n }\n });\n\n creator = new CreatorClass(options);\n modal.show({\n title: options.title || _l(\"Create a collection\"),\n body: creator.$el,\n width: \"80%\",\n height: \"100%\",\n closing_events: true\n });\n creator.render();\n window._collectionCreator = creator;\n\n //TODO: remove modal header\n return deferred;\n};\n\n/** List collection flavor of collectionCreatorModal. */\nvar listCollectionCreatorModal = function _listCollectionCreatorModal(\n elements,\n options\n) {\n options = options || {};\n options.title = _l(\"Create a collection from a list of datasets\");\n return collectionCreatorModal(elements, options, ListCollectionCreator);\n};\n\n//==============================================================================\n/** Use a modal to create a list collection, then add it to the given history contents.\n * @returns {Deferred} resolved when the collection is added to the history.\n */\nfunction createListCollection(contents, defaultHideSourceItems) {\n var elements = contents.toJSON(),\n promise = listCollectionCreatorModal(elements, {\n defaultHideSourceItems: defaultHideSourceItems,\n creationFn: function(elements, name, hideSourceItems) {\n elements = elements.map(function(element) {\n return {\n id: element.id,\n name: element.name,\n //TODO: this allows for list:list even if the filter above does not - reconcile\n src:\n element.history_content_type === \"dataset\"\n ? \"hda\"\n : \"hdca\"\n };\n });\n return contents.createHDCA(\n elements,\n \"list\",\n name,\n hideSourceItems\n );\n }\n });\n return promise;\n}\n\n//==============================================================================\nexport default {\n DatasetCollectionElementView: DatasetCollectionElementView,\n ListCollectionCreator: ListCollectionCreator,\n\n collectionCreatorModal: collectionCreatorModal,\n listCollectionCreatorModal: listCollectionCreatorModal,\n createListCollection: createListCollection\n};\n"]} \ No newline at end of file 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HDCA from \"mvc/history/hdca-model\";\nimport STATES from \"mvc/dataset/states\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport baseCreator from \"mvc/collection/base-creator\";\nimport UI_MODAL from \"mvc/ui/ui-modal\";\nimport naturalSort from \"utils/natural-sort\";\nimport _l from \"utils/localization\";\nimport \"ui/hoverhighlight\";\n\nvar logNamespace = \"collections\";\n\n/*==============================================================================\nTODO:\n use proper Element model and not just json\n straighten out createFn, collection.createHDCA\n possibly stop using modals for this\n It would be neat to do a drag and drop\n\n==============================================================================*/\n/** A view for both DatasetDCEs and NestedDCDCEs\n * (things that implement collection-model:DatasetCollectionElementMixin)\n */\nvar DatasetCollectionElementView = Backbone.View\n .extend(BASE_MVC.LoggableMixin)\n .extend({\n _logNamespace: logNamespace,\n\n //TODO: use proper class (DatasetDCE or NestedDCDCE (or the union of both))\n tagName: \"li\",\n className: \"collection-element\",\n\n initialize: function(attributes) {\n this.element = attributes.element || {};\n this.selected = attributes.selected || false;\n },\n\n render: function() {\n this.$el\n .attr(\"data-element-id\", this.element.id)\n .attr(\"draggable\", true)\n .html(this.template({ element: this.element }));\n if (this.selected) {\n this.$el.addClass(\"selected\");\n }\n return this;\n },\n\n //TODO: lots of unused space in the element - possibly load details and display them horiz.\n template: _.template(\n [\n '',\n \"<%- element.name %>\",\n \"\",\n '\"\n ].join(\"\")\n ),\n\n /** select this element and pub */\n select: function(toggle) {\n this.$el.toggleClass(\"selected\", toggle);\n this.trigger(\"select\", {\n source: this,\n selected: this.$el.hasClass(\"selected\")\n });\n },\n\n /** animate the removal of this element and pub */\n discard: function() {\n var view = this,\n parentWidth = this.$el.parent().width();\n this.$el.animate(\n { \"margin-right\": parentWidth },\n \"fast\",\n function() {\n view.trigger(\"discard\", {\n source: view\n });\n view.destroy();\n }\n );\n },\n\n /** remove the DOM and any listeners */\n destroy: function() {\n this.off();\n this.$el.remove();\n },\n\n events: {\n click: \"_click\",\n \"click .name\": \"_clickName\",\n \"click .discard\": \"_clickDiscard\",\n\n dragstart: \"_dragstart\",\n dragend: \"_dragend\",\n dragover: \"_sendToParent\",\n drop: \"_sendToParent\"\n },\n\n /** select when the li is clicked */\n _click: function(ev) {\n ev.stopPropagation();\n this.select(ev);\n },\n\n /** rename a pair when the name is clicked */\n _clickName: function(ev) {\n ev.stopPropagation();\n ev.preventDefault();\n var promptString = [\n _l(\"Enter a new name for the element\"),\n \":\\n(\",\n _l(\n \"Note that changing the name here will not rename the dataset\"\n ),\n \")\"\n ].join(\"\"),\n response = prompt(\n _l(\"Enter a new name for the element\") + \":\",\n this.element.name\n );\n if (response) {\n this.element.name = response;\n this.render();\n }\n //TODO: cancelling with ESC leads to closure of the creator...\n },\n\n /** discard when the discard button is clicked */\n _clickDiscard: function(ev) {\n ev.stopPropagation();\n this.discard();\n },\n\n /** dragging pairs for re-ordering */\n _dragstart: function(ev) {\n if (ev.originalEvent) {\n ev = ev.originalEvent;\n }\n ev.dataTransfer.effectAllowed = \"move\";\n ev.dataTransfer.setData(\"text/plain\", JSON.stringify(this.element));\n\n this.$el.addClass(\"dragging\");\n this.$el.parent().trigger(\"collection-element.dragstart\", [this]);\n },\n\n /** dragging for re-ordering */\n _dragend: function(ev) {\n this.$el.removeClass(\"dragging\");\n this.$el.parent().trigger(\"collection-element.dragend\", [this]);\n },\n\n /** manually bubble up an event to the parent/container */\n _sendToParent: function(ev) {\n this.$el.parent().trigger(ev);\n },\n\n /** string rep */\n toString: function() {\n return \"DatasetCollectionElementView()\";\n }\n });\n\n// ============================================================================\n/** An interface for building collections.\n */\nvar ListCollectionCreator = Backbone.View\n .extend(BASE_MVC.LoggableMixin)\n .extend(baseCreator.CollectionCreatorMixin)\n .extend({\n _logNamespace: logNamespace,\n\n /** the class used to display individual elements */\n elementViewClass: DatasetCollectionElementView,\n /** the class this creator will create and save */\n collectionClass: HDCA.HistoryListDatasetCollection,\n className:\n \"list-collection-creator collection-creator flex-row-container\",\n\n /** minimum number of valid elements to start with in order to build a collection of this type */\n minElements: 1,\n\n defaultAttributes: {\n //TODO: remove - use new collectionClass().save()\n /** takes elements and creates the proper collection - returns a promise */\n creationFn: function() {\n throw new TypeError(\"no creation fn for creator\");\n },\n /** fn to call when the collection is created (scoped to this) */\n oncreate: function() {},\n /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */\n oncancel: function() {},\n /** distance from list edge to begin autoscrolling list */\n autoscrollDist: 24,\n /** Color passed to hoverhighlight */\n highlightClr: \"rgba( 64, 255, 255, 1.0 )\"\n },\n\n footerSettings: {\n \".hide-originals\": \"hideOriginals\"\n },\n\n /** set up initial options, instance vars, behaviors */\n initialize: function(attributes) {\n this.metric(\"ListCollectionCreator.initialize\", attributes);\n var creator = this;\n _.each(this.defaultAttributes, function(value, key) {\n value = attributes[key] || value;\n creator[key] = value;\n });\n\n /** unordered, original list - cache to allow reversal */\n creator.initialElements = attributes.elements || [];\n\n this._setUpCommonSettings(attributes);\n this._instanceSetUp();\n this._elementsSetUp();\n this._setUpBehaviors();\n },\n\n /** set up instance vars */\n _instanceSetUp: function() {\n /** Ids of elements that have been selected by the user - to preserve over renders */\n this.selectedIds = {};\n /** DOM elements currently being dragged */\n this.$dragging = null;\n /** Used for blocking UI events during ajax/operations (don't post twice) */\n this.blocking = false;\n },\n\n // ------------------------------------------------------------------------ process raw list\n /** set up main data */\n _elementsSetUp: function() {\n //this.debug( '-- _dataSetUp' );\n /** a list of invalid elements and the reasons they aren't valid */\n this.invalidElements = [];\n //TODO: handle fundamental problem of syncing DOM, views, and list here\n /** data for list in progress */\n this.workingElements = [];\n /** views for workingElements */\n this.elementViews = [];\n\n // copy initial list, sort, add ids if needed\n this.workingElements = this.initialElements.slice(0);\n this._ensureElementIds();\n this._validateElements();\n this._mangleDuplicateNames();\n this._sortElements();\n },\n\n /** add ids to dataset objs in initial list if none */\n _ensureElementIds: function() {\n this.workingElements.forEach(function(element) {\n if (!element.hasOwnProperty(\"id\")) {\n element.id = _.uniqueId();\n }\n });\n return this.workingElements;\n },\n\n /** separate working list into valid and invalid elements for this collection */\n _validateElements: function() {\n var creator = this,\n existingNames = {};\n creator.invalidElements = [];\n\n this.workingElements = this.workingElements.filter(function(\n element\n ) {\n var problem = creator._isElementInvalid(element);\n if (problem) {\n creator.invalidElements.push({\n element: element,\n text: problem\n });\n }\n return !problem;\n });\n return this.workingElements;\n },\n\n /** describe what is wrong with a particular element if anything */\n _isElementInvalid: function(element) {\n if (element.history_content_type !== \"dataset\") {\n return _l(\"is not a dataset\");\n }\n var validState =\n element.state === STATES.OK ||\n _.contains(STATES.NOT_READY_STATES, element.state);\n if (!validState) {\n return _l(\"has errored, is paused, or is not accessible\");\n }\n if (element.deleted || element.purged) {\n return _l(\"has been deleted or purged\");\n }\n return null;\n },\n\n /** mangle duplicate names using a mac-like '(counter)' addition to any duplicates */\n _mangleDuplicateNames: function() {\n var SAFETY = 900,\n counter = 1,\n existingNames = {};\n this.workingElements.forEach(function(element) {\n var currName = element.name;\n while (existingNames.hasOwnProperty(currName)) {\n currName = element.name + \" (\" + counter + \")\";\n counter += 1;\n if (counter >= SAFETY) {\n throw new Error(\n \"Safety hit in while loop - thats impressive\"\n );\n }\n }\n element.name = currName;\n existingNames[element.name] = true;\n });\n },\n\n /** sort a list of elements */\n _sortElements: function(list) {\n // // currently only natural sort by name\n // this.workingElements.sort( function( a, b ){ return naturalSort( a.name, b.name ); });\n // return this.workingElements;\n },\n\n // ------------------------------------------------------------------------ rendering\n // templates : ListCollectionCreator.templates,\n /** render the entire interface */\n render: function(speed, callback) {\n //this.debug( '-- _render' );\n if (this.workingElements.length < this.minElements) {\n return this._renderInvalid(speed, callback);\n }\n\n this.$el.empty().html(this.templates.main());\n this._renderHeader(speed);\n this._renderMiddle(speed);\n this._renderFooter(speed);\n this._addPluginComponents();\n this.$(\".collection-name\").focus();\n this.trigger(\"rendered\", this);\n return this;\n },\n\n /** render a simplified interface aimed at telling the user why they can't move forward */\n _renderInvalid: function(speed, callback) {\n //this.debug( '-- _render' );\n this.$el.empty().html(\n this.templates.invalidInitial({\n problems: this.invalidElements,\n elements: this.workingElements\n })\n );\n if (typeof this.oncancel === \"function\") {\n this.$(\".cancel-create.btn\").show();\n }\n this.trigger(\"rendered\", this);\n return this;\n },\n\n /** render the header section */\n _renderHeader: function(speed, callback) {\n var $header = this.$(\".header\")\n .empty()\n .html(this.templates.header())\n .find(\".help-content\")\n .prepend($(this.templates.helpContent()));\n //TODO: should only show once despite calling _renderHeader again\n if (this.invalidElements.length) {\n this._invalidElementsAlert();\n }\n return $header;\n },\n\n /** render the middle including the elements */\n _renderMiddle: function(speed, callback) {\n var $middle = this.$(\".middle\")\n .empty()\n .html(this.templates.middle());\n this._renderList(speed);\n return $middle;\n },\n\n /** add any jQuery/bootstrap/custom plugins to elements rendered */\n _addPluginComponents: function() {\n this.$(\".help-content i\").hoverhighlight(\n \".collection-creator\",\n this.highlightClr\n );\n },\n\n /** build and show an alert describing any elements that could not be included due to problems */\n _invalidElementsAlert: function() {\n this._showAlert(\n this.templates.invalidElements({\n problems: this.invalidElements\n }),\n \"alert-warning\"\n );\n },\n\n _disableNameAndCreate: function(disable) {\n disable = !_.isUndefined(disable) ? disable : true;\n if (disable) {\n this.$(\".collection-name\").prop(\"disabled\", true);\n this.$(\".create-collection\").toggleClass(\"disabled\", true);\n // } else {\n // this.$( '.collection-name' ).prop( 'disabled', false );\n // this.$( '.create-collection' ).removeClass( 'disable' );\n }\n },\n\n // ------------------------------------------------------------------------ rendering elements\n /** conv. to the main list display DOM */\n $list: function() {\n return this.$(\".collection-elements\");\n },\n\n /** show or hide the clear selected control based on the num of selected elements */\n _renderClearSelected: function() {\n if (_.size(this.selectedIds)) {\n this.$(\n \".collection-elements-controls > .clear-selected\"\n ).show();\n } else {\n this.$(\n \".collection-elements-controls > .clear-selected\"\n ).hide();\n }\n },\n\n /** render the elements in order (or a warning if no elements found) */\n _renderList: function(speed, callback) {\n //this.debug( '-- _renderList' );\n var creator = this,\n $tmp = jQuery(\"\"),\n $list = creator.$list();\n\n _.each(this.elementViews, function(view) {\n view.destroy();\n creator.removeElementView(view);\n });\n\n // if( !this.workingElements.length ){\n // this._renderNoValidElements();\n // return;\n // }\n\n creator.workingElements.forEach(function(element) {\n var elementView = creator._createElementView(element);\n $tmp.append(elementView.$el);\n });\n\n creator._renderClearSelected();\n $list.empty().append($tmp.children());\n _.invoke(creator.elementViews, \"render\");\n\n if ($list.height() > $list.css(\"max-height\")) {\n $list.css(\"border-width\", \"1px 0px 1px 0px\");\n } else {\n $list.css(\"border-width\", \"0px\");\n }\n },\n\n /** create an element view, cache in elementViews, set up listeners, and return */\n _createElementView: function(element) {\n var elementView = new this.elementViewClass({\n //TODO: use non-generic class or not all\n // model : COLLECTION.DatasetDCE( element )\n element: element,\n selected: _.has(this.selectedIds, element.id)\n });\n this.elementViews.push(elementView);\n this._listenToElementView(elementView);\n return elementView;\n },\n\n /** listen to any element events */\n _listenToElementView: function(view) {\n var creator = this;\n creator.listenTo(view, {\n select: function(data) {\n var element = data.source.element;\n if (data.selected) {\n creator.selectedIds[element.id] = true;\n } else {\n delete creator.selectedIds[element.id];\n }\n creator.trigger(\"elements:select\", data);\n },\n discard: function(data) {\n creator.trigger(\"elements:discard\", data);\n }\n });\n },\n\n /** add a new element view based on the json in element */\n addElementView: function(element) {\n //TODO: workingElements is sorted, add element in appropo index\n // add element, sort elements, find element index\n // var view = this._createElementView( element );\n // return view;\n },\n\n /** stop listening to view and remove from caches */\n removeElementView: function(view) {\n delete this.selectedIds[view.element.id];\n this._renderClearSelected();\n\n this.elementViews = _.without(this.elementViews, view);\n this.stopListening(view);\n },\n\n /** render a message in the list that no elements remain to create a collection */\n _renderNoElementsLeft: function() {\n this._disableNameAndCreate(true);\n this.$(\".collection-elements\").append(\n this.templates.noElementsLeft()\n );\n },\n\n // /** render a message in the list that no valid elements were found to create a collection */\n // _renderNoValidElements : function(){\n // this._disableNameAndCreate( true );\n // this.$( '.collection-elements' ).append( this.templates.noValidElements() );\n // },\n\n // ------------------------------------------------------------------------ API\n /** convert element into JSON compatible with the collections API */\n _elementToJSON: function(element) {\n // return element.toJSON();\n return element;\n },\n\n /** create the collection via the API\n * @returns {jQuery.xhr Object} the jquery ajax request\n */\n createList: function(name) {\n if (!this.workingElements.length) {\n var message = _l(\"No valid elements for final list\") + \". \";\n message +=\n '' +\n _l(\"Cancel\") +\n \" \";\n message += _l(\"or\");\n message +=\n ' ' +\n _l(\"start over\") +\n \".\";\n this._showAlert(message);\n return;\n }\n\n var creator = this,\n elements = this.workingElements.map(function(element) {\n return creator._elementToJSON(element);\n });\n\n creator.blocking = true;\n return creator\n .creationFn(elements, name, creator.hideOriginals)\n .always(function() {\n creator.blocking = false;\n })\n .fail(function(xhr, status, message) {\n creator.trigger(\"error\", {\n xhr: xhr,\n status: status,\n message: _l(\n \"An error occurred while creating this collection\"\n )\n });\n })\n .done(function(response, message, xhr) {\n creator.trigger(\n \"collection:created\",\n response,\n message,\n xhr\n );\n creator.metric(\"collection:created\", response);\n if (typeof creator.oncreate === \"function\") {\n creator.oncreate.call(this, response, message, xhr);\n }\n });\n },\n\n // ------------------------------------------------------------------------ events\n /** set up event handlers on self */\n _setUpBehaviors: function() {\n this.on(\"error\", this._errorHandler);\n\n this.once(\"rendered\", function() {\n this.trigger(\"rendered:initial\", this);\n });\n\n this.on(\"elements:select\", function(data) {\n this._renderClearSelected();\n });\n\n this.on(\"elements:discard\", function(data) {\n var element = data.source.element;\n this.removeElementView(data.source);\n\n this.workingElements = _.without(this.workingElements, element);\n if (!this.workingElements.length) {\n this._renderNoElementsLeft();\n }\n });\n\n //this.on( 'all', function(){\n // this.info( arguments );\n //});\n return this;\n },\n\n /** handle errors with feedback and details to the user (if available) */\n _errorHandler: function(data) {\n this.error(data);\n\n var creator = this,\n content = data.message || _l(\"An error occurred\");\n if (data.xhr) {\n var xhr = data.xhr,\n message = data.message;\n if (xhr.readyState === 0 && xhr.status === 0) {\n content +=\n \": \" +\n _l(\"Galaxy could not be reached and may be updating.\") +\n _l(\" Try again in a few minutes.\");\n } else if (xhr.responseJSON) {\n content +=\n \":',\n '\",\n \"\",\n \"\" +\n JSON.stringify(xhr.responseJSON) +\n \"
\";\n } else {\n content += \": \" + message;\n }\n }\n creator._showAlert(content, \"alert-danger\");\n },\n\n events: {\n // header\n \"click .more-help\": \"_clickMoreHelp\",\n \"click .less-help\": \"_clickLessHelp\",\n \"click .main-help\": \"_toggleHelp\",\n \"click .header .alert button\": \"_hideAlert\",\n\n \"click .reset\": \"reset\",\n \"click .clear-selected\": \"clearSelectedElements\",\n\n // elements - selection\n \"click .collection-elements\": \"clearSelectedElements\",\n\n // elements - drop target\n // 'dragenter .collection-elements': '_dragenterElements',\n // 'dragleave .collection-elements': '_dragleaveElements',\n \"dragover .collection-elements\": \"_dragoverElements\",\n \"drop .collection-elements\": \"_dropElements\",\n\n // these bubble up from the elements as custom events\n \"collection-element.dragstart .collection-elements\":\n \"_elementDragstart\",\n \"collection-element.dragend .collection-elements\":\n \"_elementDragend\",\n\n // footer\n \"change .collection-name\": \"_changeName\",\n \"keydown .collection-name\": \"_nameCheckForEnter\",\n \"change .hide-originals\": \"_changeHideOriginals\",\n \"click .cancel-create\": \"_cancelCreate\",\n \"click .create-collection\": \"_clickCreate\" //,\n },\n\n // ........................................................................ elements\n /** reset all data to the initial state */\n reset: function() {\n this._instanceSetUp();\n this._elementsSetUp();\n this.render();\n },\n\n /** deselect all elements */\n clearSelectedElements: function(ev) {\n this.$(\".collection-elements .collection-element\").removeClass(\n \"selected\"\n );\n this.$(\".collection-elements-controls > .clear-selected\").hide();\n },\n\n //_dragenterElements : function( ev ){\n // //this.debug( '_dragenterElements:', ev );\n //},\n //TODO: if selected are dragged out of the list area - remove the placeholder - cuz it won't work anyway\n // _dragleaveElements : function( ev ){\n // //this.debug( '_dragleaveElements:', ev );\n // },\n\n /** track the mouse drag over the list adding a placeholder to show where the drop would occur */\n _dragoverElements: function(ev) {\n //this.debug( '_dragoverElements:', ev );\n ev.preventDefault();\n\n var $list = this.$list();\n this._checkForAutoscroll($list, ev.originalEvent.clientY);\n var $nearest = this._getNearestElement(ev.originalEvent.clientY);\n\n //TODO: no need to re-create - move instead\n this.$(\".element-drop-placeholder\").remove();\n var $placeholder = $(\n ''\n );\n if (!$nearest.length) {\n $list.append($placeholder);\n } else {\n $nearest.before($placeholder);\n }\n },\n\n /** If the mouse is near enough to the list's top or bottom, scroll the list */\n _checkForAutoscroll: function($element, y) {\n var AUTOSCROLL_SPEED = 2,\n offset = $element.offset(),\n scrollTop = $element.scrollTop(),\n upperDist = y - offset.top,\n lowerDist = offset.top + $element.outerHeight() - y;\n if (upperDist >= 0 && upperDist < this.autoscrollDist) {\n $element.scrollTop(scrollTop - AUTOSCROLL_SPEED);\n } else if (lowerDist >= 0 && lowerDist < this.autoscrollDist) {\n $element.scrollTop(scrollTop + AUTOSCROLL_SPEED);\n }\n },\n\n /** get the nearest element based on the mouse's Y coordinate.\n * If the y is at the end of the list, return an empty jQuery object.\n */\n _getNearestElement: function(y) {\n var WIGGLE = 4,\n lis = this.$(\n \".collection-elements li.collection-element\"\n ).toArray();\n for (var i = 0; i < lis.length; i++) {\n var $li = $(lis[i]),\n top = $li.offset().top,\n halfHeight = Math.floor($li.outerHeight() / 2) + WIGGLE;\n if (top + halfHeight > y && top - halfHeight < y) {\n return $li;\n }\n }\n return $();\n },\n\n /** drop (dragged/selected elements) onto the list, re-ordering the internal list */\n _dropElements: function(ev) {\n if (ev.originalEvent) {\n ev = ev.originalEvent;\n }\n // both required for firefox\n ev.preventDefault();\n ev.dataTransfer.dropEffect = \"move\";\n\n // insert before the nearest element or after the last.\n var $nearest = this._getNearestElement(ev.clientY);\n if ($nearest.length) {\n this.$dragging.insertBefore($nearest);\n } else {\n // no nearest before - insert after last element\n this.$dragging.insertAfter(\n this.$(\".collection-elements .collection-element\").last()\n );\n }\n // resync the creator's list based on the new DOM order\n this._syncOrderToDom();\n return false;\n },\n\n /** resync the creator's list of elements based on the DOM order */\n _syncOrderToDom: function() {\n var creator = this,\n newElements = [];\n //TODO: doesn't seem wise to use the dom to store these - can't we sync another way?\n this.$(\".collection-elements .collection-element\").each(function() {\n var id = $(this).attr(\"data-element-id\"),\n element = _.findWhere(creator.workingElements, {\n id: id\n });\n if (element) {\n newElements.push(element);\n } else {\n console.error(\"missing element: \", id);\n }\n });\n this.workingElements = newElements;\n this._renderList();\n },\n\n /** drag communication with element sub-views: dragstart */\n _elementDragstart: function(ev, element) {\n // auto select the element causing the event and move all selected\n element.select(true);\n this.$dragging = this.$(\n \".collection-elements .collection-element.selected\"\n );\n },\n\n /** drag communication with element sub-views: dragend - remove the placeholder */\n _elementDragend: function(ev, element) {\n $(\".element-drop-placeholder\").remove();\n this.$dragging = null;\n },\n\n // ------------------------------------------------------------------------ templates\n //TODO: move to require text plugin and load these as text\n //TODO: underscore currently unnecc. bc no vars are used\n //TODO: better way of localizing text-nodes in long strings\n /** underscore template fns attached to class */\n templates: _.extend(\n {},\n baseCreator.CollectionCreatorMixin._creatorTemplates,\n {\n /** the header (not including help text) */\n header: _.template(\n [\n '',\n '',\n _l(\"More help\"),\n \"\",\n '\",\n '',\n '',\n _l(\"Less\"),\n \"\",\n \"\",\n \"',\n '',\n '',\n \"\"\n ].join(\"\")\n ),\n\n /** the middle: element list */\n middle: _.template(\n [\n '',\n '',\n _l(\"Start over\"),\n \"\",\n '',\n _l(\"Clear selected\"),\n \"\",\n \"\",\n '',\n \"\"\n ].join(\"\")\n ),\n\n /** creation and cancel controls */\n footer: _.template(\n [\n '',\n '\",\n\n '',\n '\",\n \"\",\n '',\n '',\n '\",\n \"',\n _l(\"Name\"),\n \":\",\n \"',\n '\",\n\n '\",\n \"\"\n ].join(\"\")\n ),\n\n /** help content */\n helpContent: _.template(\n [\n \"\",\n _l(\n [\n \"Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and \",\n \"workflows in order to have analyses done on each member of the entire group. This interface allows \",\n \"you to create a collection and re-order the final collection.\"\n ].join(\"\")\n ),\n \"
\",\n \"- \",\n \"
\",\n \"\",\n _l(\n [\n 'Once your collection is complete, enter a name and ',\n 'click \"Create list\".'\n ].join(\"\")\n ),\n \"
\"\n ].join(\"\")\n ),\n\n /** shown in list when all elements are discarded */\n invalidElements: _.template(\n [\n _l(\n \"The following selections could not be included due to problems:\"\n ),\n \"- <% _.each( problems, function( problem ){ %>\",\n \"
',\n '\",\n '\"\n ].join(\"\")\n )\n }\n ),\n\n // ------------------------------------------------------------------------ misc\n /** string rep */\n toString: function() {\n return \"ListCollectionCreator\";\n }\n });\n\n//=============================================================================\n/** Create a modal and load its body with the given CreatorClass creator type\n * @returns {Deferred} resolved when creator has built a collection.\n */\nvar collectionCreatorModal = function _collectionCreatorModal(\n elements,\n options,\n CreatorClass\n) {\n var deferred = jQuery.Deferred(),\n modal = Galaxy.modal || new UI_MODAL.View(),\n creator;\n\n options = _.defaults(options || {}, {\n elements: elements,\n oncancel: function() {\n modal.hide();\n deferred.reject(\"cancelled\");\n },\n oncreate: function(creator, response) {\n modal.hide();\n deferred.resolve(response);\n }\n });\n\n creator = new CreatorClass(options);\n modal.show({\n title: options.title || _l(\"Create a collection\"),\n body: creator.$el,\n width: \"80%\",\n height: \"100%\",\n closing_events: true\n });\n creator.render();\n window._collectionCreator = creator;\n\n //TODO: remove modal header\n return deferred;\n};\n\n/** List collection flavor of collectionCreatorModal. */\nvar listCollectionCreatorModal = function _listCollectionCreatorModal(\n elements,\n options\n) {\n options = options || {};\n options.title = _l(\"Create a collection from a list of datasets\");\n return collectionCreatorModal(elements, options, ListCollectionCreator);\n};\n\n//==============================================================================\n/** Use a modal to create a list collection, then add it to the given history contents.\n * @returns {Deferred} resolved when the collection is added to the history.\n */\nfunction createListCollection(contents, defaultHideSourceItems) {\n var elements = contents.toJSON(),\n promise = listCollectionCreatorModal(elements, {\n defaultHideSourceItems: defaultHideSourceItems,\n creationFn: function(elements, name, hideSourceItems) {\n elements = elements.map(function(element) {\n return {\n id: element.id,\n name: element.name,\n //TODO: this allows for list:list even if the filter above does not - reconcile\n src:\n element.history_content_type === \"dataset\"\n ? \"hda\"\n : \"hdca\"\n };\n });\n return contents.createHDCA(\n elements,\n \"list\",\n name,\n hideSourceItems\n );\n }\n });\n return promise;\n}\n\n//==============================================================================\nexport default {\n DatasetCollectionElementView: DatasetCollectionElementView,\n ListCollectionCreator: ListCollectionCreator,\n\n collectionCreatorModal: collectionCreatorModal,\n listCollectionCreatorModal: listCollectionCreatorModal,\n createListCollection: createListCollection\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map b/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map index d7b135ef1d1..80161243841 100644 --- a/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map +++ b/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map @@ -1 +1 @@ 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levenshteinDistance from \"utils/levenshtein\";\nimport naturalSort from \"utils/natural-sort\";\nimport baseCreator from \"mvc/collection/base-creator\";\nimport baseMVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\nimport \"ui/hoverhighlight\";\n\nvar logNamespace = \"collections\";\n/* ============================================================================\nTODO:\n\n\nPROGRAMMATICALLY:\ncurrPanel.once( 'rendered', function(){\n currPanel.showSelectors();\n currPanel.selectAll();\n _.last( currPanel.actionsPopup.options ).func();\n});\n\n============================================================================ */\n/** A view for paired datasets in the collections creator.\n */\nvar PairView = Backbone.View.extend(baseMVC.LoggableMixin).extend({\n _logNamespace: logNamespace,\n\n tagName: \"li\",\n className: \"dataset paired\",\n\n initialize: function(attributes) {\n this.pair = attributes.pair || {};\n },\n\n template: _.template(\n [\n '<%- pair.forward.name %>',\n '',\n '<%- pair.name %>',\n \"\",\n '<%- pair.reverse.name %>'\n ].join(\"\")\n ),\n\n render: function() {\n this.$el\n .attr(\"draggable\", true)\n .data(\"pair\", this.pair)\n .html(this.template({ pair: this.pair }))\n .addClass(\"flex-column-container\");\n return this;\n },\n\n events: {\n dragstart: \"_dragstart\",\n dragend: \"_dragend\",\n dragover: \"_sendToParent\",\n drop: \"_sendToParent\"\n },\n\n /** dragging pairs for re-ordering */\n _dragstart: function(ev) {\n ev.currentTarget.style.opacity = \"0.4\";\n if (ev.originalEvent) {\n ev = ev.originalEvent;\n }\n\n ev.dataTransfer.effectAllowed = \"move\";\n ev.dataTransfer.setData(\"text/plain\", JSON.stringify(this.pair));\n\n this.$el.parent().trigger(\"pair.dragstart\", [this]);\n },\n\n /** dragging pairs for re-ordering */\n _dragend: function(ev) {\n ev.currentTarget.style.opacity = \"1.0\";\n this.$el.parent().trigger(\"pair.dragend\", [this]);\n },\n\n /** manually bubble up an event to the parent/container */\n _sendToParent: function(ev) {\n this.$el.parent().trigger(ev);\n },\n\n /** string rep */\n toString: function() {\n return \"PairView(\" + this.pair.name + \")\";\n }\n});\n\n// ============================================================================\n/** returns an autopair function that uses the provided options.match function */\nfunction autoPairFnBuilder(options) {\n options = options || {};\n options.createPair =\n options.createPair ||\n function _defaultCreatePair(params) {\n params = params || {};\n var a = params.listA.splice(params.indexA, 1)[0],\n b = params.listB.splice(params.indexB, 1)[0],\n aInBIndex = params.listB.indexOf(a),\n bInAIndex = params.listA.indexOf(b);\n if (aInBIndex !== -1) {\n params.listB.splice(aInBIndex, 1);\n }\n if (bInAIndex !== -1) {\n params.listA.splice(bInAIndex, 1);\n }\n return this._pair(a, b, { silent: true });\n };\n // compile these here outside of the loop\n var _regexps = [];\n function getRegExps() {\n if (!_regexps.length) {\n _regexps = [\n new RegExp(this.filters[0]),\n new RegExp(this.filters[1])\n ];\n }\n return _regexps;\n }\n // mangle params as needed\n options.preprocessMatch =\n options.preprocessMatch ||\n function _defaultPreprocessMatch(params) {\n var regexps = getRegExps.call(this);\n return _.extend(params, {\n matchTo: params.matchTo.name.replace(regexps[0], \"\"),\n possible: params.possible.name.replace(regexps[1], \"\")\n });\n };\n\n return function _strategy(params) {\n this.debug(\"autopair _strategy ---------------------------\");\n params = params || {};\n var listA = params.listA,\n listB = params.listB,\n indexA = 0,\n indexB,\n bestMatch = {\n score: 0.0,\n index: null\n },\n paired = [];\n //console.debug( 'params:', JSON.stringify( params, null, ' ' ) );\n this.debug(\"starting list lens:\", listA.length, listB.length);\n this.debug(\n \"bestMatch (starting):\",\n JSON.stringify(bestMatch, null, \" \")\n );\n\n while (indexA < listA.length) {\n var matchTo = listA[indexA];\n bestMatch.score = 0.0;\n\n for (indexB = 0; indexB < listB.length; indexB++) {\n var possible = listB[indexB];\n this.debug(indexA + \":\" + matchTo.name);\n this.debug(indexB + \":\" + possible.name);\n\n // no matching with self\n if (listA[indexA] !== listB[indexB]) {\n bestMatch = options.match.call(\n this,\n options.preprocessMatch.call(this, {\n matchTo: matchTo,\n possible: possible,\n index: indexB,\n bestMatch: bestMatch\n })\n );\n this.debug(\n \"bestMatch:\",\n JSON.stringify(bestMatch, null, \" \")\n );\n if (bestMatch.score === 1.0) {\n this.debug(\"breaking early due to perfect match\");\n break;\n }\n }\n }\n var scoreThreshold = options.scoreThreshold.call(this);\n this.debug(\"scoreThreshold:\", scoreThreshold);\n this.debug(\"bestMatch.score:\", bestMatch.score);\n\n if (bestMatch.score >= scoreThreshold) {\n //console.debug( 'autoPairFnBuilder.strategy', listA[ indexA ].name, listB[ bestMatch.index ].name );\n paired.push(\n options.createPair.call(this, {\n listA: listA,\n indexA: indexA,\n listB: listB,\n indexB: bestMatch.index\n })\n );\n //console.debug( 'list lens now:', listA.length, listB.length );\n } else {\n indexA += 1;\n }\n if (!listA.length || !listB.length) {\n return paired;\n }\n }\n this.debug(\"paired:\", JSON.stringify(paired, null, \" \"));\n this.debug(\"autopair _strategy ---------------------------\");\n return paired;\n };\n}\n\n// ============================================================================\n/** An interface for building collections of paired datasets.\n */\nvar PairedCollectionCreator = Backbone.View\n .extend(baseMVC.LoggableMixin)\n .extend(baseCreator.CollectionCreatorMixin)\n .extend({\n _logNamespace: logNamespace,\n\n className:\n \"list-of-pairs-collection-creator collection-creator flex-row-container\",\n\n /** set up initial options, instance vars, behaviors, and autopair (if set to do so) */\n initialize: function(attributes) {\n this.metric(\"PairedCollectionCreator.initialize\", attributes);\n //this.debug( '-- PairedCollectionCreator:', attributes );\n\n attributes = _.defaults(attributes, {\n datasets: [],\n filters: this.DEFAULT_FILTERS,\n automaticallyPair: true,\n strategy: \"lcs\",\n matchPercentage: 0.9,\n twoPassAutopairing: true\n });\n\n /** unordered, original list */\n this.initialList = attributes.datasets;\n\n /** is this from a history? if so, what's its id? */\n this.historyId = attributes.historyId;\n\n /** which filters should be used initially? (String[2] or name in commonFilters) */\n this.filters =\n this.commonFilters[attributes.filters] ||\n this.commonFilters[this.DEFAULT_FILTERS];\n if (_.isArray(attributes.filters)) {\n this.filters = attributes.filters;\n }\n\n /** try to auto pair the unpaired datasets on load? */\n this.automaticallyPair = attributes.automaticallyPair;\n\n /** what method to use for auto pairing (will be passed aggression level) */\n this.strategy =\n this.strategies[attributes.strategy] ||\n this.strategies[this.DEFAULT_STRATEGY];\n if (_.isFunction(attributes.strategy)) {\n this.strategy = attributes.strategy;\n }\n\n /** distance/mismatch level allowed for autopairing */\n this.matchPercentage = attributes.matchPercentage;\n\n /** try to autopair using simple first, then this.strategy on the remainder */\n this.twoPassAutopairing = attributes.twoPassAutopairing;\n\n /** remove file extensions (\\.*) from created pair names? */\n this.removeExtensions = true;\n //this.removeExtensions = false;\n\n /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */\n this.oncancel = attributes.oncancel;\n /** fn to call when the collection is created (scoped to this) */\n this.oncreate = attributes.oncreate;\n\n /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */\n this.autoscrollDist = attributes.autoscrollDist || 24;\n\n /** is the unpaired panel shown? */\n this.unpairedPanelHidden = false;\n /** is the paired panel shown? */\n this.pairedPanelHidden = false;\n\n /** DOM elements currently being dragged */\n this.$dragging = null;\n\n /** Used for blocking UI events during ajax/operations (don't post twice) */\n this.blocking = false;\n\n this._setUpCommonSettings(attributes);\n this._setUpBehaviors();\n this._dataSetUp();\n },\n\n /** map of common filter pairs by name */\n commonFilters: {\n illumina: [\"_1\", \"_2\"],\n Rs: [\"_R1\", \"_R2\"]\n },\n /** which commonFilter to use by default */\n DEFAULT_FILTERS: \"illumina\",\n\n /** map of name->fn for autopairing */\n strategies: {\n simple: \"autopairSimple\",\n lcs: \"autopairLCS\",\n levenshtein: \"autopairLevenshtein\"\n },\n /** default autopair strategy name */\n DEFAULT_STRATEGY: \"lcs\",\n\n // ------------------------------------------------------------------------ process raw list\n /** set up main data: cache initialList, sort, and autopair */\n _dataSetUp: function() {\n //this.debug( '-- _dataSetUp' );\n\n this.paired = [];\n this.unpaired = [];\n\n this.selectedIds = [];\n\n // sort initial list, add ids if needed, and save new working copy to unpaired\n this._sortInitialList();\n this._ensureIds();\n this.unpaired = this.initialList.slice(0);\n\n if (this.automaticallyPair) {\n this.autoPair();\n this.once(\"rendered:initial\", function() {\n this.trigger(\"autopair\");\n });\n }\n },\n\n /** sort initial list */\n _sortInitialList: function() {\n //this.debug( '-- _sortInitialList' );\n this._sortDatasetList(this.initialList);\n },\n\n /** sort a list of datasets */\n _sortDatasetList: function(list) {\n // currently only natural sort by name\n list.sort(function(a, b) {\n return naturalSort(a.name, b.name);\n });\n return list;\n },\n\n /** add ids to dataset objs in initial list if none */\n _ensureIds: function() {\n this.initialList.forEach(function(dataset) {\n if (!dataset.hasOwnProperty(\"id\")) {\n dataset.id = _.uniqueId();\n }\n });\n return this.initialList;\n },\n\n /** split initial list into two lists, those that pass forward filters & those passing reverse */\n _splitByFilters: function() {\n var regexFilters = this.filters.map(function(stringFilter) {\n return new RegExp(stringFilter);\n }),\n split = [[], []];\n\n function _filter(unpaired, filter) {\n return filter.test(unpaired.name);\n //return dataset.name.indexOf( filter ) >= 0;\n }\n this.unpaired.forEach(function _filterEach(unpaired) {\n // 90% of the time this seems to work, but:\n //TODO: this treats *all* strings as regex which may confuse people - possibly check for // surrounding?\n // would need explanation in help as well\n regexFilters.forEach(function(filter, i) {\n if (_filter(unpaired, filter)) {\n split[i].push(unpaired);\n }\n });\n });\n return split;\n },\n\n /** add a dataset to the unpaired list in it's proper order */\n _addToUnpaired: function(dataset) {\n // currently, unpaired is natural sorted by name, use binary search to find insertion point\n var binSearchSortedIndex = function(low, hi) {\n if (low === hi) {\n return low;\n }\n\n var mid = Math.floor((hi - low) / 2) + low,\n compared = naturalSort(\n dataset.name,\n this.unpaired[mid].name\n );\n\n if (compared < 0) {\n return binSearchSortedIndex(low, mid);\n } else if (compared > 0) {\n return binSearchSortedIndex(mid + 1, hi);\n }\n // walk the equal to find the last\n while (\n this.unpaired[mid] &&\n this.unpaired[mid].name === dataset.name\n ) {\n mid++;\n }\n return mid;\n }.bind(this);\n\n this.unpaired.splice(\n binSearchSortedIndex(0, this.unpaired.length),\n 0,\n dataset\n );\n },\n\n // ------------------------------------------------------------------------ auto pairing\n /** two passes to automatically create pairs:\n * use both simpleAutoPair, then the fn mentioned in strategy\n */\n autoPair: function(strategy) {\n // split first using exact matching\n var split = this._splitByFilters(),\n paired = [];\n if (this.twoPassAutopairing) {\n paired = this.autopairSimple({\n listA: split[0],\n listB: split[1]\n });\n split = this._splitByFilters();\n }\n\n // uncomment to see printlns while running tests\n //this.debug = function(){ console.log.apply( console, arguments ); };\n\n // then try the remainder with something less strict\n strategy = strategy || this.strategy;\n split = this._splitByFilters();\n paired = paired.concat(\n this[strategy].call(this, {\n listA: split[0],\n listB: split[1]\n })\n );\n return paired;\n },\n\n /** autopair by exact match */\n autopairSimple: autoPairFnBuilder({\n scoreThreshold: function() {\n return 0.6;\n },\n match: function _match(params) {\n params = params || {};\n if (params.matchTo === params.possible) {\n return {\n index: params.index,\n score: 1.0\n };\n }\n return params.bestMatch;\n }\n }),\n\n /** autopair by levenshtein edit distance scoring */\n autopairLevenshtein: autoPairFnBuilder({\n scoreThreshold: function() {\n return this.matchPercentage;\n },\n match: function _matches(params) {\n params = params || {};\n var distance = levenshteinDistance(\n params.matchTo,\n params.possible\n ),\n score =\n 1.0 -\n distance /\n Math.max(\n params.matchTo.length,\n params.possible.length\n );\n if (score > params.bestMatch.score) {\n return {\n index: params.index,\n score: score\n };\n }\n return params.bestMatch;\n }\n }),\n\n /** autopair by longest common substrings scoring */\n autopairLCS: autoPairFnBuilder({\n scoreThreshold: function() {\n return this.matchPercentage;\n },\n match: function _matches(params) {\n params = params || {};\n var match = this._naiveStartingAndEndingLCS(\n params.matchTo,\n params.possible\n ).length,\n score =\n match /\n Math.max(params.matchTo.length, params.possible.length);\n if (score > params.bestMatch.score) {\n return {\n index: params.index,\n score: score\n };\n }\n return params.bestMatch;\n }\n }),\n\n /** return the concat'd longest common prefix and suffix from two strings */\n _naiveStartingAndEndingLCS: function(s1, s2) {\n var fwdLCS = \"\",\n revLCS = \"\",\n i = 0,\n j = 0;\n while (i < s1.length && i < s2.length) {\n if (s1[i] !== s2[i]) {\n break;\n }\n fwdLCS += s1[i];\n i += 1;\n }\n if (i === s1.length) {\n return s1;\n }\n if (i === s2.length) {\n return s2;\n }\n\n i = s1.length - 1;\n j = s2.length - 1;\n while (i >= 0 && j >= 0) {\n if (s1[i] !== s2[j]) {\n break;\n }\n revLCS = [s1[i], revLCS].join(\"\");\n i -= 1;\n j -= 1;\n }\n return fwdLCS + revLCS;\n },\n\n // ------------------------------------------------------------------------ pairing / unpairing\n /** create a pair from fwd and rev, removing them from unpaired, and placing the new pair in paired */\n _pair: function(fwd, rev, options) {\n options = options || {};\n this.debug(\"_pair:\", fwd, rev);\n var pair = this._createPair(fwd, rev, options.name);\n this.paired.push(pair);\n this.unpaired = _.without(this.unpaired, fwd, rev);\n if (!options.silent) {\n this.trigger(\"pair:new\", pair);\n }\n return pair;\n },\n\n /** create a pair Object from fwd and rev, adding the name attribute (will guess if not given) */\n _createPair: function(fwd, rev, name) {\n // ensure existance and don't pair something with itself\n if (!(fwd && rev) || fwd === rev) {\n throw new Error(\n \"Bad pairing: \" + [JSON.stringify(fwd), JSON.stringify(rev)]\n );\n }\n name = name || this._guessNameForPair(fwd, rev);\n return { forward: fwd, name: name, reverse: rev };\n },\n\n /** try to find a good pair name for the given fwd and rev datasets */\n _guessNameForPair: function(fwd, rev, removeExtensions) {\n removeExtensions =\n removeExtensions !== undefined\n ? removeExtensions\n : this.removeExtensions;\n var fwdName = fwd.name,\n revName = rev.name,\n lcs = this._naiveStartingAndEndingLCS(\n fwdName.replace(new RegExp(this.filters[0]), \"\"),\n revName.replace(new RegExp(this.filters[1]), \"\")\n );\n if (removeExtensions) {\n var lastDotIndex = lcs.lastIndexOf(\".\");\n if (lastDotIndex > 0) {\n var extension = lcs.slice(lastDotIndex, lcs.length);\n lcs = lcs.replace(extension, \"\");\n fwdName = fwdName.replace(extension, \"\");\n revName = revName.replace(extension, \"\");\n }\n }\n return lcs || fwdName + \" & \" + revName;\n },\n\n /** unpair a pair, removing it from paired, and adding the fwd,rev datasets back into unpaired */\n _unpair: function(pair, options) {\n options = options || {};\n if (!pair) {\n throw new Error(\"Bad pair: \" + JSON.stringify(pair));\n }\n this.paired = _.without(this.paired, pair);\n this._addToUnpaired(pair.forward);\n this._addToUnpaired(pair.reverse);\n\n if (!options.silent) {\n this.trigger(\"pair:unpair\", [pair]);\n }\n return pair;\n },\n\n /** unpair all paired datasets */\n unpairAll: function() {\n var pairs = [];\n while (this.paired.length) {\n pairs.push(this._unpair(this.paired[0], { silent: true }));\n }\n this.trigger(\"pair:unpair\", pairs);\n },\n\n // ------------------------------------------------------------------------ API\n /** convert a pair into JSON compatible with the collections API */\n _pairToJSON: function(pair, src) {\n src = src || \"hda\";\n //TODO: consider making this the pair structure when created instead\n return {\n collection_type: \"paired\",\n src: \"new_collection\",\n name: pair.name,\n element_identifiers: [\n {\n name: \"forward\",\n id: pair.forward.id,\n src: src\n },\n {\n name: \"reverse\",\n id: pair.reverse.id,\n src: src\n }\n ]\n };\n },\n\n /** create the collection via the API\n * @returns {jQuery.xhr Object} the jquery ajax request\n */\n createList: function(name) {\n var creator = this,\n url =\n Galaxy.root +\n \"api/histories/\" +\n this.historyId +\n \"/contents/dataset_collections\";\n\n //TODO: use ListPairedCollection.create()\n var ajaxData = {\n type: \"dataset_collection\",\n collection_type: \"list:paired\",\n hide_source_items: creator.hideOriginals || false,\n name: _.escape(name || creator.$(\".collection-name\").val()),\n element_identifiers: creator.paired.map(function(pair) {\n return creator._pairToJSON(pair);\n })\n };\n //this.debug( JSON.stringify( ajaxData ) );\n creator.blocking = true;\n return jQuery\n .ajax(url, {\n type: \"POST\",\n contentType: \"application/json\",\n dataType: \"json\",\n data: JSON.stringify(ajaxData)\n })\n .always(function() {\n creator.blocking = false;\n })\n .fail(function(xhr, status, message) {\n creator._ajaxErrHandler(xhr, status, message);\n })\n .done(function(response, message, xhr) {\n //this.info( 'ok', response, message, xhr );\n creator.trigger(\n \"collection:created\",\n response,\n message,\n xhr\n );\n creator.metric(\"collection:created\", response);\n if (typeof creator.oncreate === \"function\") {\n creator.oncreate.call(this, response, message, xhr);\n }\n });\n },\n\n /** handle ajax errors with feedback and details to the user (if available) */\n _ajaxErrHandler: function(xhr, status, message) {\n this.error(xhr, status, message);\n var content = _l(\n \"An error occurred while creating this collection\"\n );\n if (xhr) {\n if (xhr.readyState === 0 && xhr.status === 0) {\n content +=\n \": \" +\n _l(\"Galaxy could not be reached and may be updating.\") +\n _l(\" Try again in a few minutes.\");\n } else if (xhr.responseJSON) {\n content +=\n \"',\n '\",\n \"\",\n \"\" +\n JSON.stringify(xhr.responseJSON) +\n \"
\";\n } else {\n content += \": \" + message;\n }\n }\n creator._showAlert(content, \"alert-danger\");\n },\n\n // ------------------------------------------------------------------------ rendering\n /** render the entire interface */\n render: function(speed, callback) {\n //this.debug( '-- _render' );\n //this.$el.empty().html( this.templates.main() );\n this.$el.empty().html(this.templates.main());\n this._renderHeader(speed);\n this._renderMiddle(speed);\n this._renderFooter(speed);\n this._addPluginComponents();\n this.trigger(\"rendered\", this);\n return this;\n },\n\n /** render the header section */\n _renderHeader: function(speed, callback) {\n //this.debug( '-- _renderHeader' );\n var $header = this.$(\".header\")\n .empty()\n .html(this.templates.header())\n .find(\".help-content\")\n .prepend($(this.templates.helpContent()));\n\n this._renderFilters();\n return $header;\n },\n /** fill the filter inputs with the filter values */\n _renderFilters: function() {\n return this.$(\".forward-column .column-header input\")\n .val(this.filters[0])\n .add(\n this.$(\".reverse-column .column-header input\").val(\n this.filters[1]\n )\n );\n },\n\n /** render the middle including unpaired and paired sections (which may be hidden) */\n _renderMiddle: function(speed, callback) {\n var $middle = this.$(\".middle\")\n .empty()\n .html(this.templates.middle());\n\n // (re-) hide the un/paired panels based on instance vars\n if (this.unpairedPanelHidden) {\n this.$(\".unpaired-columns\").hide();\n } else if (this.pairedPanelHidden) {\n this.$(\".paired-columns\").hide();\n }\n\n this._renderUnpaired();\n this._renderPaired();\n return $middle;\n },\n /** render the unpaired section, showing datasets accrd. to filters, update the unpaired counts */\n _renderUnpaired: function(speed, callback) {\n //this.debug( '-- _renderUnpaired' );\n var creator = this,\n $fwd,\n $rev,\n $prd = [],\n split = this._splitByFilters();\n // update unpaired counts\n this.$(\".forward-column .title\").text(\n [split[0].length, _l(\"unpaired forward\")].join(\" \")\n );\n this.$(\".forward-column .unpaired-info\").text(\n this._renderUnpairedDisplayStr(\n this.unpaired.length - split[0].length\n )\n );\n this.$(\".reverse-column .title\").text(\n [split[1].length, _l(\"unpaired reverse\")].join(\" \")\n );\n this.$(\".reverse-column .unpaired-info\").text(\n this._renderUnpairedDisplayStr(\n this.unpaired.length - split[1].length\n )\n );\n\n this.$(\".unpaired-columns .column-datasets\").empty();\n\n // show/hide the auto pair button if any unpaired are left\n this.$(\".autopair-link\").toggle(this.unpaired.length !== 0);\n if (this.unpaired.length === 0) {\n this._renderUnpairedEmpty();\n return;\n }\n\n // create the dataset dom arrays\n $rev = split[1].map(function(dataset, i) {\n // if there'll be a fwd dataset across the way, add a button to pair the row\n if (split[0][i] !== undefined && split[0][i] !== dataset) {\n $prd.push(creator._renderPairButton());\n }\n return creator._renderUnpairedDataset(dataset);\n });\n $fwd = split[0].map(function(dataset) {\n return creator._renderUnpairedDataset(dataset);\n });\n\n if (!$fwd.length && !$rev.length) {\n this._renderUnpairedNotShown();\n return;\n }\n // add to appropo cols\n //TODO: not the best way to render - consider rendering the entire unpaired-columns section in a fragment\n // and swapping out that\n this.$(\".unpaired-columns .forward-column .column-datasets\")\n .append($fwd)\n .add(\n this.$(\n \".unpaired-columns .paired-column .column-datasets\"\n ).append($prd)\n )\n .add(\n this.$(\n \".unpaired-columns .reverse-column .column-datasets\"\n ).append($rev)\n );\n this._adjUnpairedOnScrollbar();\n },\n /** return a string to display the count of filtered out datasets */\n _renderUnpairedDisplayStr: function(numFiltered) {\n return [\"(\", numFiltered, \" \", _l(\"filtered out\"), \")\"].join(\"\");\n },\n /** return an unattached jQuery DOM element to represent an unpaired dataset */\n _renderUnpairedDataset: function(dataset) {\n //TODO: to underscore template\n return (\n $(\"\")\n .attr(\"id\", \"dataset-\" + dataset.id)\n .addClass(\"dataset unpaired\")\n .attr(\"draggable\", true)\n .addClass(dataset.selected ? \"selected\" : \"\")\n .append(\n $(\"\")\n .addClass(\"dataset-name\")\n .text(dataset.name)\n )\n //??\n .data(\"dataset\", dataset)\n );\n },\n /** render the button that may go between unpaired datasets, allowing the user to pair a row */\n _renderPairButton: function() {\n //TODO: *not* a dataset - don't pretend like it is\n return $(\"\")\n .addClass(\"dataset unpaired\")\n .append(\n $(\"\")\n .addClass(\"dataset-name\")\n .text(_l(\"Pair these datasets\"))\n );\n },\n /** a message to display when no unpaired left */\n _renderUnpairedEmpty: function() {\n //this.debug( '-- renderUnpairedEmpty' );\n var $msg = $('').text(\n \"(\" + _l(\"no remaining unpaired datasets\") + \")\"\n );\n this.$(\".unpaired-columns .paired-column .column-datasets\")\n .empty()\n .prepend($msg);\n return $msg;\n },\n /** a message to display when no unpaired can be shown with the current filters */\n _renderUnpairedNotShown: function() {\n //this.debug( '-- renderUnpairedEmpty' );\n var $msg = $('').text(\n \"(\" +\n _l(\"no datasets were found matching the current filters\") +\n \")\"\n );\n this.$(\".unpaired-columns .paired-column .column-datasets\")\n .empty()\n .prepend($msg);\n return $msg;\n },\n /** try to detect if the unpaired section has a scrollbar and adjust left column for better centering of all */\n _adjUnpairedOnScrollbar: function() {\n var $unpairedColumns = this.$(\".unpaired-columns\").last(),\n $firstDataset = this.$(\n \".unpaired-columns .reverse-column .dataset\"\n ).first();\n if (!$firstDataset.length) {\n return;\n }\n var ucRight =\n $unpairedColumns.offset().left +\n $unpairedColumns.outerWidth(),\n dsRight =\n $firstDataset.offset().left + $firstDataset.outerWidth(),\n rightDiff = Math.floor(ucRight) - Math.floor(dsRight);\n //this.debug( 'rightDiff:', ucRight, '-', dsRight, '=', rightDiff );\n this.$(\".unpaired-columns .forward-column\").css(\n \"margin-left\",\n rightDiff > 0 ? rightDiff : 0\n );\n },\n\n /** render the paired section and update counts of paired datasets */\n _renderPaired: function(speed, callback) {\n //this.debug( '-- _renderPaired' );\n this.$(\".paired-column-title .title\").text(\n [this.paired.length, _l(\"paired\")].join(\" \")\n );\n // show/hide the unpair all link\n this.$(\".unpair-all-link\").toggle(this.paired.length !== 0);\n if (this.paired.length === 0) {\n this._renderPairedEmpty();\n return;\n //TODO: would be best to return here (the $columns)\n } else {\n // show/hide 'remove extensions link' when any paired and they seem to have extensions\n this.$(\".remove-extensions-link\").show();\n }\n\n this.$(\".paired-columns .column-datasets\").empty();\n var creator = this;\n this.paired.forEach(function(pair, i) {\n //TODO: cache these?\n var pairView = new PairView({ pair: pair });\n creator\n .$(\".paired-columns .column-datasets\")\n .append(pairView.render().$el)\n .append(\n [\n '\"\n ].join(\"\")\n );\n });\n },\n /** a message to display when none paired */\n _renderPairedEmpty: function() {\n var $msg = $('').text(\n \"(\" + _l(\"no paired datasets yet\") + \")\"\n );\n this.$(\".paired-columns .column-datasets\")\n .empty()\n .prepend($msg);\n return $msg;\n },\n\n footerSettings: {\n \".hide-originals\": \"hideOriginals\",\n \".remove-extensions\": \"removeExtensions\"\n },\n\n /** add any jQuery/bootstrap/custom plugins to elements rendered */\n _addPluginComponents: function() {\n this._chooseFiltersPopover(\".choose-filters-link\");\n this.$(\".help-content i\").hoverhighlight(\n \".collection-creator\",\n \"rgba( 64, 255, 255, 1.0 )\"\n );\n },\n\n /** build a filter selection popover allowing selection of common filter pairs */\n _chooseFiltersPopover: function(selector) {\n function filterChoice(val1, val2) {\n return [\n '\"\n ].join(\"\");\n }\n var $popoverContent = $(\n _.template(\n [\n '',\n '\"\n ].join(\"\")\n )({})\n );\n\n return this.$(selector).popover({\n container: \".collection-creator\",\n placement: \"bottom\",\n html: true,\n //animation : false,\n content: $popoverContent\n });\n },\n\n /** add (or clear if clear is truthy) a validation warning to what */\n _validationWarning: function(what, clear) {\n var VALIDATION_CLASS = \"validation-warning\";\n if (what === \"name\") {\n what = this.$(\".collection-name\").add(\n this.$(\".collection-name-prompt\")\n );\n this.$(\".collection-name\")\n .focus()\n .select();\n }\n if (clear) {\n what = what || this.$(\".\" + VALIDATION_CLASS);\n what.removeClass(VALIDATION_CLASS);\n } else {\n what.addClass(VALIDATION_CLASS);\n }\n },\n\n // ------------------------------------------------------------------------ events\n /** set up event handlers on self */\n _setUpBehaviors: function() {\n this.once(\"rendered\", function() {\n this.trigger(\"rendered:initial\", this);\n });\n\n this.on(\"pair:new\", function() {\n //TODO: ideally only re-render the columns (or even elements) involved\n this._renderUnpaired();\n this._renderPaired();\n\n // scroll to bottom where new pairs are added\n //TODO: this doesn't seem to work - innerHeight sticks at 133...\n // may have to do with improper flex columns\n //var $pairedView = this.$( '.paired-columns' );\n //$pairedView.scrollTop( $pairedView.innerHeight() );\n //this.debug( $pairedView.height() )\n this.$(\".paired-columns\").scrollTop(8000000);\n });\n this.on(\"pair:unpair\", function(pairs) {\n //TODO: ideally only re-render the columns (or even elements) involved\n this._renderUnpaired();\n this._renderPaired();\n this.splitView();\n });\n\n this.on(\"filter-change\", function() {\n this.filters = [\n this.$(\".forward-unpaired-filter input\").val(),\n this.$(\".reverse-unpaired-filter input\").val()\n ];\n this.metric(\"filter-change\", this.filters);\n this._renderFilters();\n this._renderUnpaired();\n });\n\n this.on(\"autopair\", function() {\n this._renderUnpaired();\n this._renderPaired();\n\n var message,\n msgClass = null;\n if (this.paired.length) {\n msgClass = \"alert-success\";\n message = this.paired.length + \" \" + _l(\"pairs created\");\n if (!this.unpaired.length) {\n message +=\n \": \" +\n _l(\"all datasets have been successfully paired\");\n this.hideUnpaired();\n this.$(\".collection-name\").focus();\n }\n } else {\n message = _l(\n [\n \"Could not automatically create any pairs from the given dataset names.\",\n \"You may want to choose or enter different filters and try auto-pairing again.\",\n \"Close this message using the X on the right to view more help.\"\n ].join(\" \")\n );\n }\n this._showAlert(message, msgClass);\n });\n\n //this.on( 'all', function(){\n // this.info( arguments );\n //});\n return this;\n },\n\n events: {\n // header\n \"click .more-help\": \"_clickMoreHelp\",\n \"click .less-help\": \"_clickLessHelp\",\n \"click .main-help\": \"_toggleHelp\",\n \"click .header .alert button\": \"_hideAlert\",\n \"click .forward-column .column-title\": \"_clickShowOnlyUnpaired\",\n \"click .reverse-column .column-title\": \"_clickShowOnlyUnpaired\",\n \"click .unpair-all-link\": \"_clickUnpairAll\",\n //TODO: this seems kinda backasswards - re-sending jq event as a backbone event, can we listen directly?\n \"change .forward-unpaired-filter input\": function(ev) {\n this.trigger(\"filter-change\");\n },\n \"focus .forward-unpaired-filter input\": function(ev) {\n $(ev.currentTarget).select();\n },\n \"click .autopair-link\": \"_clickAutopair\",\n \"click .choose-filters .filter-choice\": \"_clickFilterChoice\",\n \"click .clear-filters-link\": \"_clearFilters\",\n \"change .reverse-unpaired-filter input\": function(ev) {\n this.trigger(\"filter-change\");\n },\n \"focus .reverse-unpaired-filter input\": function(ev) {\n $(ev.currentTarget).select();\n },\n // unpaired\n \"click .forward-column .dataset.unpaired\": \"_clickUnpairedDataset\",\n \"click .reverse-column .dataset.unpaired\": \"_clickUnpairedDataset\",\n \"click .paired-column .dataset.unpaired\": \"_clickPairRow\",\n \"click .unpaired-columns\": \"clearSelectedUnpaired\",\n \"mousedown .unpaired-columns .dataset\": \"_mousedownUnpaired\",\n // divider\n \"click .paired-column-title\": \"_clickShowOnlyPaired\",\n \"mousedown .flexible-partition-drag\": \"_startPartitionDrag\",\n // paired\n \"click .paired-columns .dataset.paired\": \"selectPair\",\n \"click .paired-columns\": \"clearSelectedPaired\",\n \"click .paired-columns .pair-name\": \"_clickPairName\",\n \"click .unpair-btn\": \"_clickUnpair\",\n // paired - drop target\n //'dragenter .paired-columns' : '_dragenterPairedColumns',\n //'dragleave .paired-columns .column-datasets': '_dragleavePairedColumns',\n \"dragover .paired-columns .column-datasets\":\n \"_dragoverPairedColumns\",\n \"drop .paired-columns .column-datasets\": \"_dropPairedColumns\",\n\n \"pair.dragstart .paired-columns .column-datasets\": \"_pairDragstart\",\n \"pair.dragend .paired-columns .column-datasets\": \"_pairDragend\",\n\n // footer\n \"change .remove-extensions\": function(ev) {\n this.toggleExtensions();\n },\n \"change .collection-name\": \"_changeName\",\n \"keydown .collection-name\": \"_nameCheckForEnter\",\n \"change .hide-originals\": \"_changeHideOriginals\",\n \"click .cancel-create\": \"_cancelCreate\",\n \"click .create-collection\": \"_clickCreate\" //,\n },\n\n /** toggle between showing only unpaired and split view */\n _clickShowOnlyUnpaired: function(ev) {\n //this.debug( 'click unpaired', ev.currentTarget );\n if (this.$(\".paired-columns\").is(\":visible\")) {\n this.hidePaired();\n } else {\n this.splitView();\n }\n },\n /** toggle between showing only paired and split view */\n _clickShowOnlyPaired: function(ev) {\n //this.debug( 'click paired' );\n if (this.$(\".unpaired-columns\").is(\":visible\")) {\n this.hideUnpaired();\n } else {\n this.splitView();\n }\n },\n\n /** hide unpaired, show paired */\n hideUnpaired: function(speed, callback) {\n this.unpairedPanelHidden = true;\n this.pairedPanelHidden = false;\n this._renderMiddle(speed, callback);\n },\n /** hide paired, show unpaired */\n hidePaired: function(speed, callback) {\n this.unpairedPanelHidden = false;\n this.pairedPanelHidden = true;\n this._renderMiddle(speed, callback);\n },\n /** show both paired and unpaired (splitting evenly) */\n splitView: function(speed, callback) {\n this.unpairedPanelHidden = this.pairedPanelHidden = false;\n this._renderMiddle(speed, callback);\n return this;\n },\n\n /** unpair all paired and do other super neat stuff which I'm not really sure about yet... */\n _clickUnpairAll: function(ev) {\n this.metric(\"unpairAll\");\n this.unpairAll();\n },\n\n /** attempt to autopair */\n _clickAutopair: function(ev) {\n var paired = this.autoPair();\n this.metric(\"autopair\", paired.length, this.unpaired.length);\n this.trigger(\"autopair\");\n },\n\n /** set the filters based on the data attributes of the button click target */\n _clickFilterChoice: function(ev) {\n var $selected = $(ev.currentTarget);\n this.$(\".forward-unpaired-filter input\").val(\n $selected.data(\"forward\")\n );\n this.$(\".reverse-unpaired-filter input\").val(\n $selected.data(\"reverse\")\n );\n this._hideChooseFilters();\n this.trigger(\"filter-change\");\n },\n\n /** hide the choose filters popover */\n _hideChooseFilters: function() {\n //TODO: update bootstrap and remove the following hack\n // see also: https://github.com/twbs/bootstrap/issues/10260\n this.$(\".choose-filters-link\").popover(\"hide\");\n this.$(\".popover\").css(\"display\", \"none\");\n },\n\n /** clear both filters */\n _clearFilters: function(ev) {\n this.$(\".forward-unpaired-filter input\").val(\"\");\n this.$(\".reverse-unpaired-filter input\").val(\"\");\n this.trigger(\"filter-change\");\n },\n\n // ........................................................................ unpaired\n /** select an unpaired dataset */\n _clickUnpairedDataset: function(ev) {\n ev.stopPropagation();\n return this.toggleSelectUnpaired($(ev.currentTarget));\n },\n\n /** Toggle the selection of an unpaired dataset representation.\n * @param [jQuery] $dataset the unpaired dataset dom rep to select\n * @param [Boolean] options.force if defined, force selection based on T/F; otherwise, toggle\n */\n toggleSelectUnpaired: function($dataset, options) {\n options = options || {};\n var dataset = $dataset.data(\"dataset\"),\n select =\n options.force !== undefined\n ? options.force\n : !$dataset.hasClass(\"selected\");\n //this.debug( id, options.force, $dataset, dataset );\n if (!$dataset.length || dataset === undefined) {\n return $dataset;\n }\n\n if (select) {\n $dataset.addClass(\"selected\");\n if (!options.waitToPair) {\n this.pairAllSelected();\n }\n } else {\n $dataset.removeClass(\"selected\");\n //delete dataset.selected;\n }\n return $dataset;\n },\n\n /** pair all the currently selected unpaired datasets */\n pairAllSelected: function(options) {\n options = options || {};\n var creator = this,\n fwds = [],\n revs = [],\n pairs = [];\n creator\n .$(\".unpaired-columns .forward-column .dataset.selected\")\n .each(function() {\n fwds.push($(this).data(\"dataset\"));\n });\n creator\n .$(\".unpaired-columns .reverse-column .dataset.selected\")\n .each(function() {\n revs.push($(this).data(\"dataset\"));\n });\n fwds.length = revs.length = Math.min(fwds.length, revs.length);\n //this.debug( fwds );\n //this.debug( revs );\n fwds.forEach(function(fwd, i) {\n try {\n pairs.push(creator._pair(fwd, revs[i], { silent: true }));\n } catch (err) {\n //TODO: preserve selected state of those that couldn't be paired\n //TODO: warn that some could not be paired\n creator.error(err);\n }\n });\n if (pairs.length && !options.silent) {\n this.trigger(\"pair:new\", pairs);\n }\n return pairs;\n },\n\n /** clear the selection on all unpaired datasets */\n clearSelectedUnpaired: function() {\n this.$(\".unpaired-columns .dataset.selected\").removeClass(\n \"selected\"\n );\n },\n\n /** when holding down the shift key on a click, 'paint' the moused over datasets as selected */\n _mousedownUnpaired: function(ev) {\n if (ev.shiftKey) {\n var creator = this,\n $startTarget = $(ev.target).addClass(\"selected\"),\n moveListener = function(ev) {\n creator\n .$(ev.target)\n .filter(\".dataset\")\n .addClass(\"selected\");\n };\n $startTarget.parent().on(\"mousemove\", moveListener);\n\n // on any mouseup, stop listening to the move and try to pair any selected\n $(document).one(\"mouseup\", function(ev) {\n $startTarget.parent().off(\"mousemove\", moveListener);\n creator.pairAllSelected();\n });\n }\n },\n\n /** attempt to pair two datasets directly across from one another */\n _clickPairRow: function(ev) {\n //if( !ev.currentTarget ){ return true; }\n var rowIndex = $(ev.currentTarget).index(),\n fwd = $(\".unpaired-columns .forward-column .dataset\")\n .eq(rowIndex)\n .data(\"dataset\"),\n rev = $(\".unpaired-columns .reverse-column .dataset\")\n .eq(rowIndex)\n .data(\"dataset\");\n //this.debug( 'row:', rowIndex, fwd, rev );\n this._pair(fwd, rev);\n },\n\n // ........................................................................ divider/partition\n /** start dragging the visible divider/partition between unpaired and paired panes */\n _startPartitionDrag: function(ev) {\n var creator = this,\n startingY = ev.pageY;\n //this.debug( 'partition drag START:', ev );\n $(\"body\").css(\"cursor\", \"ns-resize\");\n creator.$(\".flexible-partition-drag\").css(\"color\", \"black\");\n\n function endDrag(ev) {\n //creator.debug( 'partition drag STOP:', ev );\n // doing this by an added class didn't really work well - kept flashing still\n creator.$(\".flexible-partition-drag\").css(\"color\", \"\");\n $(\"body\")\n .css(\"cursor\", \"\")\n .unbind(\"mousemove\", trackMouse);\n }\n function trackMouse(ev) {\n var offset = ev.pageY - startingY;\n //creator.debug( 'partition:', startingY, offset );\n if (!creator.adjPartition(offset)) {\n //creator.debug( 'mouseup triggered' );\n $(\"body\").trigger(\"mouseup\");\n }\n creator._adjUnpairedOnScrollbar();\n startingY += offset;\n }\n $(\"body\").mousemove(trackMouse);\n $(\"body\").one(\"mouseup\", endDrag);\n },\n\n /** adjust the parition up/down +/-adj pixels */\n adjPartition: function(adj) {\n var $unpaired = this.$(\".unpaired-columns\"),\n $paired = this.$(\".paired-columns\"),\n unpairedHi = parseInt($unpaired.css(\"height\"), 10),\n pairedHi = parseInt($paired.css(\"height\"), 10);\n //this.debug( adj, 'hi\\'s:', unpairedHi, pairedHi, unpairedHi + adj, pairedHi - adj );\n\n unpairedHi = Math.max(10, unpairedHi + adj);\n pairedHi = pairedHi - adj;\n\n var movingUpwards = adj < 0;\n // when the divider gets close to the top - lock into hiding the unpaired section\n if (movingUpwards) {\n if (this.unpairedPanelHidden) {\n return false;\n } else if (unpairedHi <= 10) {\n this.hideUnpaired();\n return false;\n }\n } else {\n if (this.unpairedPanelHidden) {\n $unpaired.show();\n this.unpairedPanelHidden = false;\n }\n }\n\n // when the divider gets close to the bottom - lock into hiding the paired section\n if (!movingUpwards) {\n if (this.pairedPanelHidden) {\n return false;\n } else if (pairedHi <= 15) {\n this.hidePaired();\n return false;\n }\n } else {\n if (this.pairedPanelHidden) {\n $paired.show();\n this.pairedPanelHidden = false;\n }\n }\n\n $unpaired.css({\n height: unpairedHi + \"px\",\n flex: \"0 0 auto\"\n });\n return true;\n },\n\n // ........................................................................ paired\n /** select a pair when clicked */\n selectPair: function(ev) {\n ev.stopPropagation();\n $(ev.currentTarget).toggleClass(\"selected\");\n },\n\n /** deselect all pairs */\n clearSelectedPaired: function(ev) {\n this.$(\".paired-columns .dataset.selected\").removeClass(\"selected\");\n },\n\n /** rename a pair when the pair name is clicked */\n _clickPairName: function(ev) {\n ev.stopPropagation();\n var $name = $(ev.currentTarget),\n $pair = $name.parent().parent(),\n index = $pair.index(\".dataset.paired\"),\n pair = this.paired[index],\n response = prompt(\"Enter a new name for the pair:\", pair.name);\n if (response) {\n pair.name = response;\n // set a flag (which won't be passed in json creation) for manual naming so we don't overwrite these\n // when adding/removing extensions\n //hackish\n pair.customizedName = true;\n $name.text(pair.name);\n }\n },\n\n /** unpair this pair */\n _clickUnpair: function(ev) {\n //if( !ev.currentTarget ){ return true; }\n var pairIndex = Math.floor(\n $(ev.currentTarget).index(\".unpair-btn\")\n );\n //this.debug( 'pair:', pairIndex );\n this._unpair(this.paired[pairIndex]);\n },\n\n // ........................................................................ paired - drag and drop re-ordering\n //_dragenterPairedColumns : function( ev ){\n // this.debug( '_dragenterPairedColumns:', ev );\n //},\n //_dragleavePairedColumns : function( ev ){\n // //this.debug( '_dragleavePairedColumns:', ev );\n //},\n /** track the mouse drag over the paired list adding a placeholder to show where the drop would occur */\n _dragoverPairedColumns: function(ev) {\n //this.debug( '_dragoverPairedColumns:', ev );\n ev.preventDefault();\n\n var $list = this.$(\".paired-columns .column-datasets\");\n this._checkForAutoscroll($list, ev.originalEvent.clientY);\n //this.debug( ev.originalEvent.clientX, ev.originalEvent.clientY );\n var $nearest = this._getNearestPairedDatasetLi(\n ev.originalEvent.clientY\n );\n\n $(\".element-drop-placeholder\").remove();\n var $placeholder = $(\n ''\n );\n if (!$nearest.length) {\n $list.append($placeholder);\n } else {\n $nearest.before($placeholder);\n }\n },\n\n /** If the mouse is near enough to the list's top or bottom, scroll the list */\n _checkForAutoscroll: function($element, y) {\n var AUTOSCROLL_SPEED = 2;\n var offset = $element.offset(),\n scrollTop = $element.scrollTop(),\n upperDist = y - offset.top,\n lowerDist = offset.top + $element.outerHeight() - y;\n //this.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist );\n if (upperDist >= 0 && upperDist < this.autoscrollDist) {\n $element.scrollTop(scrollTop - AUTOSCROLL_SPEED);\n } else if (lowerDist >= 0 && lowerDist < this.autoscrollDist) {\n $element.scrollTop(scrollTop + AUTOSCROLL_SPEED);\n }\n },\n\n /** get the nearest *previous* paired dataset PairView based on the mouse's Y coordinate.\n * If the y is at the end of the list, return an empty jQuery object.\n */\n _getNearestPairedDatasetLi: function(y) {\n var WIGGLE = 4,\n lis = this.$(\".paired-columns .column-datasets li\").toArray();\n for (var i = 0; i < lis.length; i++) {\n var $li = $(lis[i]),\n top = $li.offset().top,\n halfHeight = Math.floor($li.outerHeight() / 2) + WIGGLE;\n if (top + halfHeight > y && top - halfHeight < y) {\n //this.debug( y, top + halfHeight, top - halfHeight )\n return $li;\n }\n }\n return $();\n },\n /** drop (dragged/selected PairViews) onto the list, re-ordering both the DOM and the internal array of pairs */\n _dropPairedColumns: function(ev) {\n // both required for firefox\n ev.preventDefault();\n ev.dataTransfer.dropEffect = \"move\";\n\n var $nearest = this._getNearestPairedDatasetLi(\n ev.originalEvent.clientY\n );\n if ($nearest.length) {\n this.$dragging.insertBefore($nearest);\n } else {\n // no nearest before - insert after last element (unpair button)\n this.$dragging.insertAfter(\n this.$(\".paired-columns .unpair-btn\").last()\n );\n }\n // resync the creator's list of paired based on the new DOM order\n this._syncPairsToDom();\n return false;\n },\n /** resync the creator's list of paired based on the DOM order of pairs */\n _syncPairsToDom: function() {\n var newPaired = [];\n //TODO: doesn't seem wise to use the dom to store these - can't we sync another way?\n this.$(\".paired-columns .dataset.paired\").each(function() {\n newPaired.push($(this).data(\"pair\"));\n });\n //this.debug( newPaired );\n this.paired = newPaired;\n this._renderPaired();\n },\n /** drag communication with pair sub-views: dragstart */\n _pairDragstart: function(ev, pair) {\n //this.debug( '_pairDragstart', ev, pair )\n // auto select the pair causing the event and move all selected\n pair.$el.addClass(\"selected\");\n var $selected = this.$(\".paired-columns .dataset.selected\");\n this.$dragging = $selected;\n },\n /** drag communication with pair sub-views: dragend - remove the placeholder */\n _pairDragend: function(ev, pair) {\n //this.debug( '_pairDragend', ev, pair )\n $(\".element-drop-placeholder\").remove();\n this.$dragging = null;\n },\n\n // ........................................................................ footer\n toggleExtensions: function(force) {\n var creator = this;\n creator.removeExtensions =\n force !== undefined ? force : !creator.removeExtensions;\n\n _.each(creator.paired, function(pair) {\n // don't overwrite custom names\n if (pair.customizedName) {\n return;\n }\n pair.name = creator._guessNameForPair(\n pair.forward,\n pair.reverse\n );\n });\n\n creator._renderPaired();\n creator._renderFooter();\n },\n\n // ------------------------------------------------------------------------ misc\n /** debug a dataset list */\n _printList: function(list) {\n var creator = this;\n _.each(list, function(e) {\n if (list === creator.paired) {\n creator._printPair(e);\n } else {\n //creator.debug( e );\n }\n });\n },\n\n /** print a pair Object */\n _printPair: function(pair) {\n this.debug(pair.forward.name, pair.reverse.name, \": ->\", pair.name);\n },\n\n /** string rep */\n toString: function() {\n return \"PairedCollectionCreator\";\n },\n\n templates: _.extend(\n {},\n baseCreator.CollectionCreatorMixin._creatorTemplates,\n {\n /** the header (not including help text) */\n header: _.template(\n [\n '',\n _l(\n \"Choose from the following filters to change which unpaired reads are shown in the display\"\n ),\n \":\",\n _.values(this.commonFilters)\n .map(function(filterSet) {\n return filterChoice(filterSet[0], filterSet[1]);\n })\n .join(\"\"),\n \"',\n '',\n _l(\"More help\"),\n \"\",\n '\",\n '',\n '',\n _l(\"Less\"),\n \"\",\n \"\",\n \"',\n '',\n '',\n \"\",\n\n '',\n '\"\n ].join(\"\")\n ),\n\n /** the middle: unpaired, divider, and paired */\n middle: _.template(\n [\n // contains two flex rows (rows that fill available space) and a divider btwn\n '',\n '\",\n '',\n '\",\n \"',\n '',\n _l(\"Unpaired forward\"),\n \"\",\n '',\n \"\",\n '',\n '',\n \"\",\n \"',\n '\",\n '',\n '',\n _l(\"Choose filters\"),\n \"\",\n '',\n _l(\"Clear filters\"),\n \"\",\n \"
\",\n '',\n _l(\"Auto-pair\"),\n \"\",\n \"',\n '\",\n \"',\n '\",\n \"',\n '',\n _l(\"Unpaired reverse\"),\n \"\",\n '',\n \"\",\n '',\n '',\n \"\",\n \"',\n '\",\n '',\n '\",\n '',\n '\",\n '',\n '\",\n \"',\n '',\n '\",\n '',\n '\",\n \"',\n '',\n \"\",\n '',\n _l(\"Unpair all\"),\n \"\",\n \"',\n '\"\n ].join(\"\")\n ),\n\n /** creation and cancel controls */\n footer: _.template(\n [\n '',\n '\",\n\n '',\n '\",\n '\",\n \"\",\n '',\n '',\n '\",\n \"',\n _l(\"Name\"),\n \":\",\n \"',\n '\",\n\n '\",\n \"\"\n ].join(\"\")\n ),\n\n /** help content */\n helpContent: _.template(\n [\n \"\",\n _l(\n [\n \"Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). \",\n \"These collections can be passed to tools and workflows in order to have analyses done on each member of \",\n \"the entire group. This interface allows you to create a collection, choose which datasets are paired, \",\n \"and re-order the final collection.\"\n ].join(\"\")\n ),\n \"
\",\n \"\",\n _l(\n [\n 'Unpaired datasets are shown in the unpaired section ',\n \"(hover over the underlined words to highlight below). \",\n 'Paired datasets are shown in the paired section.',\n \"
- To pair datasets, you can:\",\n \"
\",\n _l(\n [\n \"
- You can filter what is shown in the unpaired sections by:\",\n \"
\",\n _l(\n [\n \"To unpair individual dataset pairs, click the \",\n 'unpair buttons ( ). ',\n 'Click the \"Unpair all\" link to unpair all pairs.'\n ].join(\"\")\n ),\n \"
\",\n \"\",\n _l(\n [\n 'You can include or remove the file extensions (e.g. \".fastq\") from your pair names by toggling the ',\n '\"Remove file extensions from pair names?\" control.'\n ].join(\"\")\n ),\n \"
\",\n \"\",\n _l(\n [\n 'Once your collection is complete, enter a name and ',\n 'click \"Create list\". ',\n \"(Note: you do not have to pair all unpaired datasets to finish.)\"\n ].join(\"\")\n ),\n \"
\"\n ].join(\"\")\n )\n }\n )\n });\n\n//=============================================================================\n/** a modal version of the paired collection creator */\nvar pairedCollectionCreatorModal = function _pairedCollectionCreatorModal(\n datasets,\n options\n) {\n var deferred = jQuery.Deferred(),\n creator;\n\n options = _.defaults(options || {}, {\n datasets: datasets,\n oncancel: function() {\n Galaxy.modal.hide();\n deferred.reject(\"cancelled\");\n },\n oncreate: function(creator, response) {\n Galaxy.modal.hide();\n deferred.resolve(response);\n }\n });\n\n if (!window.Galaxy || !Galaxy.modal) {\n throw new Error(\"Galaxy or Galaxy.modal not found\");\n }\n\n creator = new PairedCollectionCreator(options);\n Galaxy.modal.show({\n title: \"Create a collection of paired datasets\",\n body: creator.$el,\n width: \"80%\",\n height: \"800px\",\n closing_events: true\n });\n creator.render();\n window.creator = creator;\n\n //TODO: remove modal header\n return deferred;\n};\n\n//=============================================================================\nfunction createListOfPairsCollection(collection, defaultHideSourceItems) {\n var elements = collection.toJSON();\n //TODO: validate elements\n return pairedCollectionCreatorModal(elements, {\n historyId: collection.historyId,\n defaultHideSourceItems: defaultHideSourceItems\n });\n}\n\n//=============================================================================\nexport default {\n PairedCollectionCreator: PairedCollectionCreator,\n pairedCollectionCreatorModal: pairedCollectionCreatorModal,\n createListOfPairsCollection: createListOfPairsCollection\n};\n"]} \ No newline at end of file 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levenshteinDistance from \"utils/levenshtein\";\nimport naturalSort from \"utils/natural-sort\";\nimport baseCreator from \"mvc/collection/base-creator\";\nimport baseMVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\nimport \"ui/hoverhighlight\";\n\nvar logNamespace = \"collections\";\n/* ============================================================================\nTODO:\n\n\nPROGRAMMATICALLY:\ncurrPanel.once( 'rendered', function(){\n currPanel.showSelectors();\n currPanel.selectAll();\n _.last( currPanel.actionsPopup.options ).func();\n});\n\n============================================================================ */\n/** A view for paired datasets in the collections creator.\n */\nvar PairView = Backbone.View.extend(baseMVC.LoggableMixin).extend({\n _logNamespace: logNamespace,\n\n tagName: \"li\",\n className: \"dataset paired\",\n\n initialize: function(attributes) {\n this.pair = attributes.pair || {};\n },\n\n template: _.template(\n [\n '<%- pair.forward.name %>',\n '',\n '<%- pair.name %>',\n \"\",\n '<%- pair.reverse.name %>'\n ].join(\"\")\n ),\n\n render: function() {\n this.$el\n .attr(\"draggable\", true)\n .data(\"pair\", this.pair)\n .html(this.template({ pair: this.pair }))\n .addClass(\"flex-column-container\");\n return this;\n },\n\n events: {\n dragstart: \"_dragstart\",\n dragend: \"_dragend\",\n dragover: \"_sendToParent\",\n drop: \"_sendToParent\"\n },\n\n /** dragging pairs for re-ordering */\n _dragstart: function(ev) {\n ev.currentTarget.style.opacity = \"0.4\";\n if (ev.originalEvent) {\n ev = ev.originalEvent;\n }\n\n ev.dataTransfer.effectAllowed = \"move\";\n ev.dataTransfer.setData(\"text/plain\", JSON.stringify(this.pair));\n\n this.$el.parent().trigger(\"pair.dragstart\", [this]);\n },\n\n /** dragging pairs for re-ordering */\n _dragend: function(ev) {\n ev.currentTarget.style.opacity = \"1.0\";\n this.$el.parent().trigger(\"pair.dragend\", [this]);\n },\n\n /** manually bubble up an event to the parent/container */\n _sendToParent: function(ev) {\n this.$el.parent().trigger(ev);\n },\n\n /** string rep */\n toString: function() {\n return \"PairView(\" + this.pair.name + \")\";\n }\n});\n\n// ============================================================================\n/** returns an autopair function that uses the provided options.match function */\nfunction autoPairFnBuilder(options) {\n options = options || {};\n options.createPair =\n options.createPair ||\n function _defaultCreatePair(params) {\n params = params || {};\n var a = params.listA.splice(params.indexA, 1)[0],\n b = params.listB.splice(params.indexB, 1)[0],\n aInBIndex = params.listB.indexOf(a),\n bInAIndex = params.listA.indexOf(b);\n if (aInBIndex !== -1) {\n params.listB.splice(aInBIndex, 1);\n }\n if (bInAIndex !== -1) {\n params.listA.splice(bInAIndex, 1);\n }\n return this._pair(a, b, { silent: true });\n };\n // compile these here outside of the loop\n var _regexps = [];\n function getRegExps() {\n if (!_regexps.length) {\n _regexps = [\n new RegExp(this.filters[0]),\n new RegExp(this.filters[1])\n ];\n }\n return _regexps;\n }\n // mangle params as needed\n options.preprocessMatch =\n options.preprocessMatch ||\n function _defaultPreprocessMatch(params) {\n var regexps = getRegExps.call(this);\n return _.extend(params, {\n matchTo: params.matchTo.name.replace(regexps[0], \"\"),\n possible: params.possible.name.replace(regexps[1], \"\")\n });\n };\n\n return function _strategy(params) {\n this.debug(\"autopair _strategy ---------------------------\");\n params = params || {};\n var listA = params.listA,\n listB = params.listB,\n indexA = 0,\n indexB,\n bestMatch = {\n score: 0.0,\n index: null\n },\n paired = [];\n //console.debug( 'params:', JSON.stringify( params, null, ' ' ) );\n this.debug(\"starting list lens:\", listA.length, listB.length);\n this.debug(\n \"bestMatch (starting):\",\n JSON.stringify(bestMatch, null, \" \")\n );\n\n while (indexA < listA.length) {\n var matchTo = listA[indexA];\n bestMatch.score = 0.0;\n\n for (indexB = 0; indexB < listB.length; indexB++) {\n var possible = listB[indexB];\n this.debug(indexA + \":\" + matchTo.name);\n this.debug(indexB + \":\" + possible.name);\n\n // no matching with self\n if (listA[indexA] !== listB[indexB]) {\n bestMatch = options.match.call(\n this,\n options.preprocessMatch.call(this, {\n matchTo: matchTo,\n possible: possible,\n index: indexB,\n bestMatch: bestMatch\n })\n );\n this.debug(\n \"bestMatch:\",\n JSON.stringify(bestMatch, null, \" \")\n );\n if (bestMatch.score === 1.0) {\n this.debug(\"breaking early due to perfect match\");\n break;\n }\n }\n }\n var scoreThreshold = options.scoreThreshold.call(this);\n this.debug(\"scoreThreshold:\", scoreThreshold);\n this.debug(\"bestMatch.score:\", bestMatch.score);\n\n if (bestMatch.score >= scoreThreshold) {\n //console.debug( 'autoPairFnBuilder.strategy', listA[ indexA ].name, listB[ bestMatch.index ].name );\n paired.push(\n options.createPair.call(this, {\n listA: listA,\n indexA: indexA,\n listB: listB,\n indexB: bestMatch.index\n })\n );\n //console.debug( 'list lens now:', listA.length, listB.length );\n } else {\n indexA += 1;\n }\n if (!listA.length || !listB.length) {\n return paired;\n }\n }\n this.debug(\"paired:\", JSON.stringify(paired, null, \" \"));\n this.debug(\"autopair _strategy ---------------------------\");\n return paired;\n };\n}\n\n// ============================================================================\n/** An interface for building collections of paired datasets.\n */\nvar PairedCollectionCreator = Backbone.View\n .extend(baseMVC.LoggableMixin)\n .extend(baseCreator.CollectionCreatorMixin)\n .extend({\n _logNamespace: logNamespace,\n\n className:\n \"list-of-pairs-collection-creator collection-creator flex-row-container\",\n\n /** set up initial options, instance vars, behaviors, and autopair (if set to do so) */\n initialize: function(attributes) {\n this.metric(\"PairedCollectionCreator.initialize\", attributes);\n //this.debug( '-- PairedCollectionCreator:', attributes );\n\n attributes = _.defaults(attributes, {\n datasets: [],\n filters: this.DEFAULT_FILTERS,\n automaticallyPair: true,\n strategy: \"lcs\",\n matchPercentage: 0.9,\n twoPassAutopairing: true\n });\n\n /** unordered, original list */\n this.initialList = attributes.datasets;\n\n /** is this from a history? if so, what's its id? */\n this.historyId = attributes.historyId;\n\n /** which filters should be used initially? (String[2] or name in commonFilters) */\n this.filters =\n this.commonFilters[attributes.filters] ||\n this.commonFilters[this.DEFAULT_FILTERS];\n if (_.isArray(attributes.filters)) {\n this.filters = attributes.filters;\n }\n\n /** try to auto pair the unpaired datasets on load? */\n this.automaticallyPair = attributes.automaticallyPair;\n\n /** what method to use for auto pairing (will be passed aggression level) */\n this.strategy =\n this.strategies[attributes.strategy] ||\n this.strategies[this.DEFAULT_STRATEGY];\n if (_.isFunction(attributes.strategy)) {\n this.strategy = attributes.strategy;\n }\n\n /** distance/mismatch level allowed for autopairing */\n this.matchPercentage = attributes.matchPercentage;\n\n /** try to autopair using simple first, then this.strategy on the remainder */\n this.twoPassAutopairing = attributes.twoPassAutopairing;\n\n /** remove file extensions (\\.*) from created pair names? */\n this.removeExtensions = true;\n //this.removeExtensions = false;\n\n /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */\n this.oncancel = attributes.oncancel;\n /** fn to call when the collection is created (scoped to this) */\n this.oncreate = attributes.oncreate;\n\n /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */\n this.autoscrollDist = attributes.autoscrollDist || 24;\n\n /** is the unpaired panel shown? */\n this.unpairedPanelHidden = false;\n /** is the paired panel shown? */\n this.pairedPanelHidden = false;\n\n /** DOM elements currently being dragged */\n this.$dragging = null;\n\n /** Used for blocking UI events during ajax/operations (don't post twice) */\n this.blocking = false;\n\n this._setUpCommonSettings(attributes);\n this._setUpBehaviors();\n this._dataSetUp();\n },\n\n /** map of common filter pairs by name */\n commonFilters: {\n illumina: [\"_1\", \"_2\"],\n Rs: [\"_R1\", \"_R2\"]\n },\n /** which commonFilter to use by default */\n DEFAULT_FILTERS: \"illumina\",\n\n /** map of name->fn for autopairing */\n strategies: {\n simple: \"autopairSimple\",\n lcs: \"autopairLCS\",\n levenshtein: \"autopairLevenshtein\"\n },\n /** default autopair strategy name */\n DEFAULT_STRATEGY: \"lcs\",\n\n // ------------------------------------------------------------------------ process raw list\n /** set up main data: cache initialList, sort, and autopair */\n _dataSetUp: function() {\n //this.debug( '-- _dataSetUp' );\n\n this.paired = [];\n this.unpaired = [];\n\n this.selectedIds = [];\n\n // sort initial list, add ids if needed, and save new working copy to unpaired\n this._sortInitialList();\n this._ensureIds();\n this.unpaired = this.initialList.slice(0);\n\n if (this.automaticallyPair) {\n this.autoPair();\n this.once(\"rendered:initial\", function() {\n this.trigger(\"autopair\");\n });\n }\n },\n\n /** sort initial list */\n _sortInitialList: function() {\n //this.debug( '-- _sortInitialList' );\n this._sortDatasetList(this.initialList);\n },\n\n /** sort a list of datasets */\n _sortDatasetList: function(list) {\n // currently only natural sort by name\n list.sort(function(a, b) {\n return naturalSort(a.name, b.name);\n });\n return list;\n },\n\n /** add ids to dataset objs in initial list if none */\n _ensureIds: function() {\n this.initialList.forEach(function(dataset) {\n if (!dataset.hasOwnProperty(\"id\")) {\n dataset.id = _.uniqueId();\n }\n });\n return this.initialList;\n },\n\n /** split initial list into two lists, those that pass forward filters & those passing reverse */\n _splitByFilters: function() {\n var regexFilters = this.filters.map(function(stringFilter) {\n return new RegExp(stringFilter);\n }),\n split = [[], []];\n\n function _filter(unpaired, filter) {\n return filter.test(unpaired.name);\n //return dataset.name.indexOf( filter ) >= 0;\n }\n this.unpaired.forEach(function _filterEach(unpaired) {\n // 90% of the time this seems to work, but:\n //TODO: this treats *all* strings as regex which may confuse people - possibly check for // surrounding?\n // would need explanation in help as well\n regexFilters.forEach(function(filter, i) {\n if (_filter(unpaired, filter)) {\n split[i].push(unpaired);\n }\n });\n });\n return split;\n },\n\n /** add a dataset to the unpaired list in it's proper order */\n _addToUnpaired: function(dataset) {\n // currently, unpaired is natural sorted by name, use binary search to find insertion point\n var binSearchSortedIndex = function(low, hi) {\n if (low === hi) {\n return low;\n }\n\n var mid = Math.floor((hi - low) / 2) + low,\n compared = naturalSort(\n dataset.name,\n this.unpaired[mid].name\n );\n\n if (compared < 0) {\n return binSearchSortedIndex(low, mid);\n } else if (compared > 0) {\n return binSearchSortedIndex(mid + 1, hi);\n }\n // walk the equal to find the last\n while (\n this.unpaired[mid] &&\n this.unpaired[mid].name === dataset.name\n ) {\n mid++;\n }\n return mid;\n }.bind(this);\n\n this.unpaired.splice(\n binSearchSortedIndex(0, this.unpaired.length),\n 0,\n dataset\n );\n },\n\n // ------------------------------------------------------------------------ auto pairing\n /** two passes to automatically create pairs:\n * use both simpleAutoPair, then the fn mentioned in strategy\n */\n autoPair: function(strategy) {\n // split first using exact matching\n var split = this._splitByFilters(),\n paired = [];\n if (this.twoPassAutopairing) {\n paired = this.autopairSimple({\n listA: split[0],\n listB: split[1]\n });\n split = this._splitByFilters();\n }\n\n // uncomment to see printlns while running tests\n //this.debug = function(){ console.log.apply( console, arguments ); };\n\n // then try the remainder with something less strict\n strategy = strategy || this.strategy;\n split = this._splitByFilters();\n paired = paired.concat(\n this[strategy].call(this, {\n listA: split[0],\n listB: split[1]\n })\n );\n return paired;\n },\n\n /** autopair by exact match */\n autopairSimple: autoPairFnBuilder({\n scoreThreshold: function() {\n return 0.6;\n },\n match: function _match(params) {\n params = params || {};\n if (params.matchTo === params.possible) {\n return {\n index: params.index,\n score: 1.0\n };\n }\n return params.bestMatch;\n }\n }),\n\n /** autopair by levenshtein edit distance scoring */\n autopairLevenshtein: autoPairFnBuilder({\n scoreThreshold: function() {\n return this.matchPercentage;\n },\n match: function _matches(params) {\n params = params || {};\n var distance = levenshteinDistance(\n params.matchTo,\n params.possible\n ),\n score =\n 1.0 -\n distance /\n Math.max(\n params.matchTo.length,\n params.possible.length\n );\n if (score > params.bestMatch.score) {\n return {\n index: params.index,\n score: score\n };\n }\n return params.bestMatch;\n }\n }),\n\n /** autopair by longest common substrings scoring */\n autopairLCS: autoPairFnBuilder({\n scoreThreshold: function() {\n return this.matchPercentage;\n },\n match: function _matches(params) {\n params = params || {};\n var match = this._naiveStartingAndEndingLCS(\n params.matchTo,\n params.possible\n ).length,\n score =\n match /\n Math.max(params.matchTo.length, params.possible.length);\n if (score > params.bestMatch.score) {\n return {\n index: params.index,\n score: score\n };\n }\n return params.bestMatch;\n }\n }),\n\n /** return the concat'd longest common prefix and suffix from two strings */\n _naiveStartingAndEndingLCS: function(s1, s2) {\n var fwdLCS = \"\",\n revLCS = \"\",\n i = 0,\n j = 0;\n while (i < s1.length && i < s2.length) {\n if (s1[i] !== s2[i]) {\n break;\n }\n fwdLCS += s1[i];\n i += 1;\n }\n if (i === s1.length) {\n return s1;\n }\n if (i === s2.length) {\n return s2;\n }\n\n i = s1.length - 1;\n j = s2.length - 1;\n while (i >= 0 && j >= 0) {\n if (s1[i] !== s2[j]) {\n break;\n }\n revLCS = [s1[i], revLCS].join(\"\");\n i -= 1;\n j -= 1;\n }\n return fwdLCS + revLCS;\n },\n\n // ------------------------------------------------------------------------ pairing / unpairing\n /** create a pair from fwd and rev, removing them from unpaired, and placing the new pair in paired */\n _pair: function(fwd, rev, options) {\n options = options || {};\n this.debug(\"_pair:\", fwd, rev);\n var pair = this._createPair(fwd, rev, options.name);\n this.paired.push(pair);\n this.unpaired = _.without(this.unpaired, fwd, rev);\n if (!options.silent) {\n this.trigger(\"pair:new\", pair);\n }\n return pair;\n },\n\n /** create a pair Object from fwd and rev, adding the name attribute (will guess if not given) */\n _createPair: function(fwd, rev, name) {\n // ensure existance and don't pair something with itself\n if (!(fwd && rev) || fwd === rev) {\n throw new Error(\n \"Bad pairing: \" + [JSON.stringify(fwd), JSON.stringify(rev)]\n );\n }\n name = name || this._guessNameForPair(fwd, rev);\n return { forward: fwd, name: name, reverse: rev };\n },\n\n /** try to find a good pair name for the given fwd and rev datasets */\n _guessNameForPair: function(fwd, rev, removeExtensions) {\n removeExtensions =\n removeExtensions !== undefined\n ? removeExtensions\n : this.removeExtensions;\n var fwdName = fwd.name,\n revName = rev.name,\n lcs = this._naiveStartingAndEndingLCS(\n fwdName.replace(new RegExp(this.filters[0]), \"\"),\n revName.replace(new RegExp(this.filters[1]), \"\")\n );\n if (removeExtensions) {\n var lastDotIndex = lcs.lastIndexOf(\".\");\n if (lastDotIndex > 0) {\n var extension = lcs.slice(lastDotIndex, lcs.length);\n lcs = lcs.replace(extension, \"\");\n fwdName = fwdName.replace(extension, \"\");\n revName = revName.replace(extension, \"\");\n }\n }\n return lcs || fwdName + \" & \" + revName;\n },\n\n /** unpair a pair, removing it from paired, and adding the fwd,rev datasets back into unpaired */\n _unpair: function(pair, options) {\n options = options || {};\n if (!pair) {\n throw new Error(\"Bad pair: \" + JSON.stringify(pair));\n }\n this.paired = _.without(this.paired, pair);\n this._addToUnpaired(pair.forward);\n this._addToUnpaired(pair.reverse);\n\n if (!options.silent) {\n this.trigger(\"pair:unpair\", [pair]);\n }\n return pair;\n },\n\n /** unpair all paired datasets */\n unpairAll: function() {\n var pairs = [];\n while (this.paired.length) {\n pairs.push(this._unpair(this.paired[0], { silent: true }));\n }\n this.trigger(\"pair:unpair\", pairs);\n },\n\n // ------------------------------------------------------------------------ API\n /** convert a pair into JSON compatible with the collections API */\n _pairToJSON: function(pair, src) {\n src = src || \"hda\";\n //TODO: consider making this the pair structure when created instead\n return {\n collection_type: \"paired\",\n src: \"new_collection\",\n name: pair.name,\n element_identifiers: [\n {\n name: \"forward\",\n id: pair.forward.id,\n src: src\n },\n {\n name: \"reverse\",\n id: pair.reverse.id,\n src: src\n }\n ]\n };\n },\n\n /** create the collection via the API\n * @returns {jQuery.xhr Object} the jquery ajax request\n */\n createList: function(name) {\n var creator = this,\n url =\n Galaxy.root +\n \"api/histories/\" +\n this.historyId +\n \"/contents/dataset_collections\";\n\n //TODO: use ListPairedCollection.create()\n var ajaxData = {\n type: \"dataset_collection\",\n collection_type: \"list:paired\",\n hide_source_items: creator.hideOriginals || false,\n name: _.escape(name || creator.$(\".collection-name\").val()),\n element_identifiers: creator.paired.map(function(pair) {\n return creator._pairToJSON(pair);\n })\n };\n //this.debug( JSON.stringify( ajaxData ) );\n creator.blocking = true;\n return jQuery\n .ajax(url, {\n type: \"POST\",\n contentType: \"application/json\",\n dataType: \"json\",\n data: JSON.stringify(ajaxData)\n })\n .always(function() {\n creator.blocking = false;\n })\n .fail(function(xhr, status, message) {\n creator._ajaxErrHandler(xhr, status, message);\n })\n .done(function(response, message, xhr) {\n //this.info( 'ok', response, message, xhr );\n creator.trigger(\n \"collection:created\",\n response,\n message,\n xhr\n );\n creator.metric(\"collection:created\", response);\n if (typeof creator.oncreate === \"function\") {\n creator.oncreate.call(this, response, message, xhr);\n }\n });\n },\n\n /** handle ajax errors with feedback and details to the user (if available) */\n _ajaxErrHandler: function(xhr, status, message) {\n this.error(xhr, status, message);\n var content = _l(\n \"An error occurred while creating this collection\"\n );\n if (xhr) {\n if (xhr.readyState === 0 && xhr.status === 0) {\n content +=\n \": \" +\n _l(\"Galaxy could not be reached and may be updating.\") +\n _l(\" Try again in a few minutes.\");\n } else if (xhr.responseJSON) {\n content +=\n \"\" +\n JSON.stringify(xhr.responseJSON) +\n \"
\";\n } else {\n content += \": \" + message;\n }\n }\n creator._showAlert(content, \"alert-danger\");\n },\n\n // ------------------------------------------------------------------------ rendering\n /** render the entire interface */\n render: function(speed, callback) {\n //this.debug( '-- _render' );\n //this.$el.empty().html( this.templates.main() );\n this.$el.empty().html(this.templates.main());\n this._renderHeader(speed);\n this._renderMiddle(speed);\n this._renderFooter(speed);\n this._addPluginComponents();\n this.trigger(\"rendered\", this);\n return this;\n },\n\n /** render the header section */\n _renderHeader: function(speed, callback) {\n //this.debug( '-- _renderHeader' );\n var $header = this.$(\".header\")\n .empty()\n .html(this.templates.header())\n .find(\".help-content\")\n .prepend($(this.templates.helpContent()));\n\n this._renderFilters();\n return $header;\n },\n /** fill the filter inputs with the filter values */\n _renderFilters: function() {\n return this.$(\".forward-column .column-header input\")\n .val(this.filters[0])\n .add(\n this.$(\".reverse-column .column-header input\").val(\n this.filters[1]\n )\n );\n },\n\n /** render the middle including unpaired and paired sections (which may be hidden) */\n _renderMiddle: function(speed, callback) {\n var $middle = this.$(\".middle\")\n .empty()\n .html(this.templates.middle());\n\n // (re-) hide the un/paired panels based on instance vars\n if (this.unpairedPanelHidden) {\n this.$(\".unpaired-columns\").hide();\n } else if (this.pairedPanelHidden) {\n this.$(\".paired-columns\").hide();\n }\n\n this._renderUnpaired();\n this._renderPaired();\n return $middle;\n },\n /** render the unpaired section, showing datasets accrd. to filters, update the unpaired counts */\n _renderUnpaired: function(speed, callback) {\n //this.debug( '-- _renderUnpaired' );\n var creator = this,\n $fwd,\n $rev,\n $prd = [],\n split = this._splitByFilters();\n // update unpaired counts\n this.$(\".forward-column .title\").text(\n [split[0].length, _l(\"unpaired forward\")].join(\" \")\n );\n this.$(\".forward-column .unpaired-info\").text(\n this._renderUnpairedDisplayStr(\n this.unpaired.length - split[0].length\n )\n );\n this.$(\".reverse-column .title\").text(\n [split[1].length, _l(\"unpaired reverse\")].join(\" \")\n );\n this.$(\".reverse-column .unpaired-info\").text(\n this._renderUnpairedDisplayStr(\n this.unpaired.length - split[1].length\n )\n );\n\n this.$(\".unpaired-columns .column-datasets\").empty();\n\n // show/hide the auto pair button if any unpaired are left\n this.$(\".autopair-link\").toggle(this.unpaired.length !== 0);\n if (this.unpaired.length === 0) {\n this._renderUnpairedEmpty();\n return;\n }\n\n // create the dataset dom arrays\n $rev = split[1].map(function(dataset, i) {\n // if there'll be a fwd dataset across the way, add a button to pair the row\n if (split[0][i] !== undefined && split[0][i] !== dataset) {\n $prd.push(creator._renderPairButton());\n }\n return creator._renderUnpairedDataset(dataset);\n });\n $fwd = split[0].map(function(dataset) {\n return creator._renderUnpairedDataset(dataset);\n });\n\n if (!$fwd.length && !$rev.length) {\n this._renderUnpairedNotShown();\n return;\n }\n // add to appropo cols\n //TODO: not the best way to render - consider rendering the entire unpaired-columns section in a fragment\n // and swapping out that\n this.$(\".unpaired-columns .forward-column .column-datasets\")\n .append($fwd)\n .add(\n this.$(\n \".unpaired-columns .paired-column .column-datasets\"\n ).append($prd)\n )\n .add(\n this.$(\n \".unpaired-columns .reverse-column .column-datasets\"\n ).append($rev)\n );\n this._adjUnpairedOnScrollbar();\n },\n /** return a string to display the count of filtered out datasets */\n _renderUnpairedDisplayStr: function(numFiltered) {\n return [\"(\", numFiltered, \" \", _l(\"filtered out\"), \")\"].join(\"\");\n },\n /** return an unattached jQuery DOM element to represent an unpaired dataset */\n _renderUnpairedDataset: function(dataset) {\n //TODO: to underscore template\n return (\n $(\"\")\n .attr(\"id\", \"dataset-\" + dataset.id)\n .addClass(\"dataset unpaired\")\n .attr(\"draggable\", true)\n .addClass(dataset.selected ? \"selected\" : \"\")\n .append(\n $(\"\")\n .addClass(\"dataset-name\")\n .text(dataset.name)\n )\n //??\n .data(\"dataset\", dataset)\n );\n },\n /** render the button that may go between unpaired datasets, allowing the user to pair a row */\n _renderPairButton: function() {\n //TODO: *not* a dataset - don't pretend like it is\n return $(\"\")\n .addClass(\"dataset unpaired\")\n .append(\n $(\"\")\n .addClass(\"dataset-name\")\n .text(_l(\"Pair these datasets\"))\n );\n },\n /** a message to display when no unpaired left */\n _renderUnpairedEmpty: function() {\n //this.debug( '-- renderUnpairedEmpty' );\n var $msg = $('').text(\n \"(\" + _l(\"no remaining unpaired datasets\") + \")\"\n );\n this.$(\".unpaired-columns .paired-column .column-datasets\")\n .empty()\n .prepend($msg);\n return $msg;\n },\n /** a message to display when no unpaired can be shown with the current filters */\n _renderUnpairedNotShown: function() {\n //this.debug( '-- renderUnpairedEmpty' );\n var $msg = $('').text(\n \"(\" +\n _l(\"no datasets were found matching the current filters\") +\n \")\"\n );\n this.$(\".unpaired-columns .paired-column .column-datasets\")\n .empty()\n .prepend($msg);\n return $msg;\n },\n /** try to detect if the unpaired section has a scrollbar and adjust left column for better centering of all */\n _adjUnpairedOnScrollbar: function() {\n var $unpairedColumns = this.$(\".unpaired-columns\").last(),\n $firstDataset = this.$(\n \".unpaired-columns .reverse-column .dataset\"\n ).first();\n if (!$firstDataset.length) {\n return;\n }\n var ucRight =\n $unpairedColumns.offset().left +\n $unpairedColumns.outerWidth(),\n dsRight =\n $firstDataset.offset().left + $firstDataset.outerWidth(),\n rightDiff = Math.floor(ucRight) - Math.floor(dsRight);\n //this.debug( 'rightDiff:', ucRight, '-', dsRight, '=', rightDiff );\n this.$(\".unpaired-columns .forward-column\").css(\n \"margin-left\",\n rightDiff > 0 ? rightDiff : 0\n );\n },\n\n /** render the paired section and update counts of paired datasets */\n _renderPaired: function(speed, callback) {\n //this.debug( '-- _renderPaired' );\n this.$(\".paired-column-title .title\").text(\n [this.paired.length, _l(\"paired\")].join(\" \")\n );\n // show/hide the unpair all link\n this.$(\".unpair-all-link\").toggle(this.paired.length !== 0);\n if (this.paired.length === 0) {\n this._renderPairedEmpty();\n return;\n //TODO: would be best to return here (the $columns)\n } else {\n // show/hide 'remove extensions link' when any paired and they seem to have extensions\n this.$(\".remove-extensions-link\").show();\n }\n\n this.$(\".paired-columns .column-datasets\").empty();\n var creator = this;\n this.paired.forEach(function(pair, i) {\n //TODO: cache these?\n var pairView = new PairView({ pair: pair });\n creator\n .$(\".paired-columns .column-datasets\")\n .append(pairView.render().$el)\n .append(\n [\n '\"\n ].join(\"\")\n );\n });\n },\n /** a message to display when none paired */\n _renderPairedEmpty: function() {\n var $msg = $('').text(\n \"(\" + _l(\"no paired datasets yet\") + \")\"\n );\n this.$(\".paired-columns .column-datasets\")\n .empty()\n .prepend($msg);\n return $msg;\n },\n\n footerSettings: {\n \".hide-originals\": \"hideOriginals\",\n \".remove-extensions\": \"removeExtensions\"\n },\n\n /** add any jQuery/bootstrap/custom plugins to elements rendered */\n _addPluginComponents: function() {\n this._chooseFiltersPopover(\".choose-filters-link\");\n this.$(\".help-content i\").hoverhighlight(\n \".collection-creator\",\n \"rgba( 64, 255, 255, 1.0 )\"\n );\n },\n\n /** build a filter selection popover allowing selection of common filter pairs */\n _chooseFiltersPopover: function(selector) {\n function filterChoice(val1, val2) {\n return [\n '\"\n ].join(\"\");\n }\n var $popoverContent = $(\n _.template(\n [\n '',\n '\"\n ].join(\"\")\n )({})\n );\n\n return this.$(selector).popover({\n container: \".collection-creator\",\n placement: \"bottom\",\n html: true,\n //animation : false,\n content: $popoverContent\n });\n },\n\n /** add (or clear if clear is truthy) a validation warning to what */\n _validationWarning: function(what, clear) {\n var VALIDATION_CLASS = \"validation-warning\";\n if (what === \"name\") {\n what = this.$(\".collection-name\").add(\n this.$(\".collection-name-prompt\")\n );\n this.$(\".collection-name\")\n .focus()\n .select();\n }\n if (clear) {\n what = what || this.$(\".\" + VALIDATION_CLASS);\n what.removeClass(VALIDATION_CLASS);\n } else {\n what.addClass(VALIDATION_CLASS);\n }\n },\n\n // ------------------------------------------------------------------------ events\n /** set up event handlers on self */\n _setUpBehaviors: function() {\n this.once(\"rendered\", function() {\n this.trigger(\"rendered:initial\", this);\n });\n\n this.on(\"pair:new\", function() {\n //TODO: ideally only re-render the columns (or even elements) involved\n this._renderUnpaired();\n this._renderPaired();\n\n // scroll to bottom where new pairs are added\n //TODO: this doesn't seem to work - innerHeight sticks at 133...\n // may have to do with improper flex columns\n //var $pairedView = this.$( '.paired-columns' );\n //$pairedView.scrollTop( $pairedView.innerHeight() );\n //this.debug( $pairedView.height() )\n this.$(\".paired-columns\").scrollTop(8000000);\n });\n this.on(\"pair:unpair\", function(pairs) {\n //TODO: ideally only re-render the columns (or even elements) involved\n this._renderUnpaired();\n this._renderPaired();\n this.splitView();\n });\n\n this.on(\"filter-change\", function() {\n this.filters = [\n this.$(\".forward-unpaired-filter input\").val(),\n this.$(\".reverse-unpaired-filter input\").val()\n ];\n this.metric(\"filter-change\", this.filters);\n this._renderFilters();\n this._renderUnpaired();\n });\n\n this.on(\"autopair\", function() {\n this._renderUnpaired();\n this._renderPaired();\n\n var message,\n msgClass = null;\n if (this.paired.length) {\n msgClass = \"alert-success\";\n message = this.paired.length + \" \" + _l(\"pairs created\");\n if (!this.unpaired.length) {\n message +=\n \": \" +\n _l(\"all datasets have been successfully paired\");\n this.hideUnpaired();\n this.$(\".collection-name\").focus();\n }\n } else {\n message = _l(\n [\n \"Could not automatically create any pairs from the given dataset names.\",\n \"You may want to choose or enter different filters and try auto-pairing again.\",\n \"Close this message using the X on the right to view more help.\"\n ].join(\" \")\n );\n }\n this._showAlert(message, msgClass);\n });\n\n //this.on( 'all', function(){\n // this.info( arguments );\n //});\n return this;\n },\n\n events: {\n // header\n \"click .more-help\": \"_clickMoreHelp\",\n \"click .less-help\": \"_clickLessHelp\",\n \"click .main-help\": \"_toggleHelp\",\n \"click .header .alert button\": \"_hideAlert\",\n \"click .forward-column .column-title\": \"_clickShowOnlyUnpaired\",\n \"click .reverse-column .column-title\": \"_clickShowOnlyUnpaired\",\n \"click .unpair-all-link\": \"_clickUnpairAll\",\n //TODO: this seems kinda backasswards - re-sending jq event as a backbone event, can we listen directly?\n \"change .forward-unpaired-filter input\": function(ev) {\n this.trigger(\"filter-change\");\n },\n \"focus .forward-unpaired-filter input\": function(ev) {\n $(ev.currentTarget).select();\n },\n \"click .autopair-link\": \"_clickAutopair\",\n \"click .choose-filters .filter-choice\": \"_clickFilterChoice\",\n \"click .clear-filters-link\": \"_clearFilters\",\n \"change .reverse-unpaired-filter input\": function(ev) {\n this.trigger(\"filter-change\");\n },\n \"focus .reverse-unpaired-filter input\": function(ev) {\n $(ev.currentTarget).select();\n },\n // unpaired\n \"click .forward-column .dataset.unpaired\": \"_clickUnpairedDataset\",\n \"click .reverse-column .dataset.unpaired\": \"_clickUnpairedDataset\",\n \"click .paired-column .dataset.unpaired\": \"_clickPairRow\",\n \"click .unpaired-columns\": \"clearSelectedUnpaired\",\n \"mousedown .unpaired-columns .dataset\": \"_mousedownUnpaired\",\n // divider\n \"click .paired-column-title\": \"_clickShowOnlyPaired\",\n \"mousedown .flexible-partition-drag\": \"_startPartitionDrag\",\n // paired\n \"click .paired-columns .dataset.paired\": \"selectPair\",\n \"click .paired-columns\": \"clearSelectedPaired\",\n \"click .paired-columns .pair-name\": \"_clickPairName\",\n \"click .unpair-btn\": \"_clickUnpair\",\n // paired - drop target\n //'dragenter .paired-columns' : '_dragenterPairedColumns',\n //'dragleave .paired-columns .column-datasets': '_dragleavePairedColumns',\n \"dragover .paired-columns .column-datasets\":\n \"_dragoverPairedColumns\",\n \"drop .paired-columns .column-datasets\": \"_dropPairedColumns\",\n\n \"pair.dragstart .paired-columns .column-datasets\": \"_pairDragstart\",\n \"pair.dragend .paired-columns .column-datasets\": \"_pairDragend\",\n\n // footer\n \"change .remove-extensions\": function(ev) {\n this.toggleExtensions();\n },\n \"change .collection-name\": \"_changeName\",\n \"keydown .collection-name\": \"_nameCheckForEnter\",\n \"change .hide-originals\": \"_changeHideOriginals\",\n \"click .cancel-create\": \"_cancelCreate\",\n \"click .create-collection\": \"_clickCreate\" //,\n },\n\n /** toggle between showing only unpaired and split view */\n _clickShowOnlyUnpaired: function(ev) {\n //this.debug( 'click unpaired', ev.currentTarget );\n if (this.$(\".paired-columns\").is(\":visible\")) {\n this.hidePaired();\n } else {\n this.splitView();\n }\n },\n /** toggle between showing only paired and split view */\n _clickShowOnlyPaired: function(ev) {\n //this.debug( 'click paired' );\n if (this.$(\".unpaired-columns\").is(\":visible\")) {\n this.hideUnpaired();\n } else {\n this.splitView();\n }\n },\n\n /** hide unpaired, show paired */\n hideUnpaired: function(speed, callback) {\n this.unpairedPanelHidden = true;\n this.pairedPanelHidden = false;\n this._renderMiddle(speed, callback);\n },\n /** hide paired, show unpaired */\n hidePaired: function(speed, callback) {\n this.unpairedPanelHidden = false;\n this.pairedPanelHidden = true;\n this._renderMiddle(speed, callback);\n },\n /** show both paired and unpaired (splitting evenly) */\n splitView: function(speed, callback) {\n this.unpairedPanelHidden = this.pairedPanelHidden = false;\n this._renderMiddle(speed, callback);\n return this;\n },\n\n /** unpair all paired and do other super neat stuff which I'm not really sure about yet... */\n _clickUnpairAll: function(ev) {\n this.metric(\"unpairAll\");\n this.unpairAll();\n },\n\n /** attempt to autopair */\n _clickAutopair: function(ev) {\n var paired = this.autoPair();\n this.metric(\"autopair\", paired.length, this.unpaired.length);\n this.trigger(\"autopair\");\n },\n\n /** set the filters based on the data attributes of the button click target */\n _clickFilterChoice: function(ev) {\n var $selected = $(ev.currentTarget);\n this.$(\".forward-unpaired-filter input\").val(\n $selected.data(\"forward\")\n );\n this.$(\".reverse-unpaired-filter input\").val(\n $selected.data(\"reverse\")\n );\n this._hideChooseFilters();\n this.trigger(\"filter-change\");\n },\n\n /** hide the choose filters popover */\n _hideChooseFilters: function() {\n //TODO: update bootstrap and remove the following hack\n // see also: https://github.com/twbs/bootstrap/issues/10260\n this.$(\".choose-filters-link\").popover(\"hide\");\n this.$(\".popover\").css(\"display\", \"none\");\n },\n\n /** clear both filters */\n _clearFilters: function(ev) {\n this.$(\".forward-unpaired-filter input\").val(\"\");\n this.$(\".reverse-unpaired-filter input\").val(\"\");\n this.trigger(\"filter-change\");\n },\n\n // ........................................................................ unpaired\n /** select an unpaired dataset */\n _clickUnpairedDataset: function(ev) {\n ev.stopPropagation();\n return this.toggleSelectUnpaired($(ev.currentTarget));\n },\n\n /** Toggle the selection of an unpaired dataset representation.\n * @param [jQuery] $dataset the unpaired dataset dom rep to select\n * @param [Boolean] options.force if defined, force selection based on T/F; otherwise, toggle\n */\n toggleSelectUnpaired: function($dataset, options) {\n options = options || {};\n var dataset = $dataset.data(\"dataset\"),\n select =\n options.force !== undefined\n ? options.force\n : !$dataset.hasClass(\"selected\");\n //this.debug( id, options.force, $dataset, dataset );\n if (!$dataset.length || dataset === undefined) {\n return $dataset;\n }\n\n if (select) {\n $dataset.addClass(\"selected\");\n if (!options.waitToPair) {\n this.pairAllSelected();\n }\n } else {\n $dataset.removeClass(\"selected\");\n //delete dataset.selected;\n }\n return $dataset;\n },\n\n /** pair all the currently selected unpaired datasets */\n pairAllSelected: function(options) {\n options = options || {};\n var creator = this,\n fwds = [],\n revs = [],\n pairs = [];\n creator\n .$(\".unpaired-columns .forward-column .dataset.selected\")\n .each(function() {\n fwds.push($(this).data(\"dataset\"));\n });\n creator\n .$(\".unpaired-columns .reverse-column .dataset.selected\")\n .each(function() {\n revs.push($(this).data(\"dataset\"));\n });\n fwds.length = revs.length = Math.min(fwds.length, revs.length);\n //this.debug( fwds );\n //this.debug( revs );\n fwds.forEach(function(fwd, i) {\n try {\n pairs.push(creator._pair(fwd, revs[i], { silent: true }));\n } catch (err) {\n //TODO: preserve selected state of those that couldn't be paired\n //TODO: warn that some could not be paired\n creator.error(err);\n }\n });\n if (pairs.length && !options.silent) {\n this.trigger(\"pair:new\", pairs);\n }\n return pairs;\n },\n\n /** clear the selection on all unpaired datasets */\n clearSelectedUnpaired: function() {\n this.$(\".unpaired-columns .dataset.selected\").removeClass(\n \"selected\"\n );\n },\n\n /** when holding down the shift key on a click, 'paint' the moused over datasets as selected */\n _mousedownUnpaired: function(ev) {\n if (ev.shiftKey) {\n var creator = this,\n $startTarget = $(ev.target).addClass(\"selected\"),\n moveListener = function(ev) {\n creator\n .$(ev.target)\n .filter(\".dataset\")\n .addClass(\"selected\");\n };\n $startTarget.parent().on(\"mousemove\", moveListener);\n\n // on any mouseup, stop listening to the move and try to pair any selected\n $(document).one(\"mouseup\", function(ev) {\n $startTarget.parent().off(\"mousemove\", moveListener);\n creator.pairAllSelected();\n });\n }\n },\n\n /** attempt to pair two datasets directly across from one another */\n _clickPairRow: function(ev) {\n //if( !ev.currentTarget ){ return true; }\n var rowIndex = $(ev.currentTarget).index(),\n fwd = $(\".unpaired-columns .forward-column .dataset\")\n .eq(rowIndex)\n .data(\"dataset\"),\n rev = $(\".unpaired-columns .reverse-column .dataset\")\n .eq(rowIndex)\n .data(\"dataset\");\n //this.debug( 'row:', rowIndex, fwd, rev );\n this._pair(fwd, rev);\n },\n\n // ........................................................................ divider/partition\n /** start dragging the visible divider/partition between unpaired and paired panes */\n _startPartitionDrag: function(ev) {\n var creator = this,\n startingY = ev.pageY;\n //this.debug( 'partition drag START:', ev );\n $(\"body\").css(\"cursor\", \"ns-resize\");\n creator.$(\".flexible-partition-drag\").css(\"color\", \"black\");\n\n function endDrag(ev) {\n //creator.debug( 'partition drag STOP:', ev );\n // doing this by an added class didn't really work well - kept flashing still\n creator.$(\".flexible-partition-drag\").css(\"color\", \"\");\n $(\"body\")\n .css(\"cursor\", \"\")\n .unbind(\"mousemove\", trackMouse);\n }\n function trackMouse(ev) {\n var offset = ev.pageY - startingY;\n //creator.debug( 'partition:', startingY, offset );\n if (!creator.adjPartition(offset)) {\n //creator.debug( 'mouseup triggered' );\n $(\"body\").trigger(\"mouseup\");\n }\n creator._adjUnpairedOnScrollbar();\n startingY += offset;\n }\n $(\"body\").mousemove(trackMouse);\n $(\"body\").one(\"mouseup\", endDrag);\n },\n\n /** adjust the parition up/down +/-adj pixels */\n adjPartition: function(adj) {\n var $unpaired = this.$(\".unpaired-columns\"),\n $paired = this.$(\".paired-columns\"),\n unpairedHi = parseInt($unpaired.css(\"height\"), 10),\n pairedHi = parseInt($paired.css(\"height\"), 10);\n //this.debug( adj, 'hi\\'s:', unpairedHi, pairedHi, unpairedHi + adj, pairedHi - adj );\n\n unpairedHi = Math.max(10, unpairedHi + adj);\n pairedHi = pairedHi - adj;\n\n var movingUpwards = adj < 0;\n // when the divider gets close to the top - lock into hiding the unpaired section\n if (movingUpwards) {\n if (this.unpairedPanelHidden) {\n return false;\n } else if (unpairedHi <= 10) {\n this.hideUnpaired();\n return false;\n }\n } else {\n if (this.unpairedPanelHidden) {\n $unpaired.show();\n this.unpairedPanelHidden = false;\n }\n }\n\n // when the divider gets close to the bottom - lock into hiding the paired section\n if (!movingUpwards) {\n if (this.pairedPanelHidden) {\n return false;\n } else if (pairedHi <= 15) {\n this.hidePaired();\n return false;\n }\n } else {\n if (this.pairedPanelHidden) {\n $paired.show();\n this.pairedPanelHidden = false;\n }\n }\n\n $unpaired.css({\n height: unpairedHi + \"px\",\n flex: \"0 0 auto\"\n });\n return true;\n },\n\n // ........................................................................ paired\n /** select a pair when clicked */\n selectPair: function(ev) {\n ev.stopPropagation();\n $(ev.currentTarget).toggleClass(\"selected\");\n },\n\n /** deselect all pairs */\n clearSelectedPaired: function(ev) {\n this.$(\".paired-columns .dataset.selected\").removeClass(\"selected\");\n },\n\n /** rename a pair when the pair name is clicked */\n _clickPairName: function(ev) {\n ev.stopPropagation();\n var $name = $(ev.currentTarget),\n $pair = $name.parent().parent(),\n index = $pair.index(\".dataset.paired\"),\n pair = this.paired[index],\n response = prompt(\"Enter a new name for the pair:\", pair.name);\n if (response) {\n pair.name = response;\n // set a flag (which won't be passed in json creation) for manual naming so we don't overwrite these\n // when adding/removing extensions\n //hackish\n pair.customizedName = true;\n $name.text(pair.name);\n }\n },\n\n /** unpair this pair */\n _clickUnpair: function(ev) {\n //if( !ev.currentTarget ){ return true; }\n var pairIndex = Math.floor(\n $(ev.currentTarget).index(\".unpair-btn\")\n );\n //this.debug( 'pair:', pairIndex );\n this._unpair(this.paired[pairIndex]);\n },\n\n // ........................................................................ paired - drag and drop re-ordering\n //_dragenterPairedColumns : function( ev ){\n // this.debug( '_dragenterPairedColumns:', ev );\n //},\n //_dragleavePairedColumns : function( ev ){\n // //this.debug( '_dragleavePairedColumns:', ev );\n //},\n /** track the mouse drag over the paired list adding a placeholder to show where the drop would occur */\n _dragoverPairedColumns: function(ev) {\n //this.debug( '_dragoverPairedColumns:', ev );\n ev.preventDefault();\n\n var $list = this.$(\".paired-columns .column-datasets\");\n this._checkForAutoscroll($list, ev.originalEvent.clientY);\n //this.debug( ev.originalEvent.clientX, ev.originalEvent.clientY );\n var $nearest = this._getNearestPairedDatasetLi(\n ev.originalEvent.clientY\n );\n\n $(\".element-drop-placeholder\").remove();\n var $placeholder = $(\n ''\n );\n if (!$nearest.length) {\n $list.append($placeholder);\n } else {\n $nearest.before($placeholder);\n }\n },\n\n /** If the mouse is near enough to the list's top or bottom, scroll the list */\n _checkForAutoscroll: function($element, y) {\n var AUTOSCROLL_SPEED = 2;\n var offset = $element.offset(),\n scrollTop = $element.scrollTop(),\n upperDist = y - offset.top,\n lowerDist = offset.top + $element.outerHeight() - y;\n //this.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist );\n if (upperDist >= 0 && upperDist < this.autoscrollDist) {\n $element.scrollTop(scrollTop - AUTOSCROLL_SPEED);\n } else if (lowerDist >= 0 && lowerDist < this.autoscrollDist) {\n $element.scrollTop(scrollTop + AUTOSCROLL_SPEED);\n }\n },\n\n /** get the nearest *previous* paired dataset PairView based on the mouse's Y coordinate.\n * If the y is at the end of the list, return an empty jQuery object.\n */\n _getNearestPairedDatasetLi: function(y) {\n var WIGGLE = 4,\n lis = this.$(\".paired-columns .column-datasets li\").toArray();\n for (var i = 0; i < lis.length; i++) {\n var $li = $(lis[i]),\n top = $li.offset().top,\n halfHeight = Math.floor($li.outerHeight() / 2) + WIGGLE;\n if (top + halfHeight > y && top - halfHeight < y) {\n //this.debug( y, top + halfHeight, top - halfHeight )\n return $li;\n }\n }\n return $();\n },\n /** drop (dragged/selected PairViews) onto the list, re-ordering both the DOM and the internal array of pairs */\n _dropPairedColumns: function(ev) {\n // both required for firefox\n ev.preventDefault();\n ev.dataTransfer.dropEffect = \"move\";\n\n var $nearest = this._getNearestPairedDatasetLi(\n ev.originalEvent.clientY\n );\n if ($nearest.length) {\n this.$dragging.insertBefore($nearest);\n } else {\n // no nearest before - insert after last element (unpair button)\n this.$dragging.insertAfter(\n this.$(\".paired-columns .unpair-btn\").last()\n );\n }\n // resync the creator's list of paired based on the new DOM order\n this._syncPairsToDom();\n return false;\n },\n /** resync the creator's list of paired based on the DOM order of pairs */\n _syncPairsToDom: function() {\n var newPaired = [];\n //TODO: doesn't seem wise to use the dom to store these - can't we sync another way?\n this.$(\".paired-columns .dataset.paired\").each(function() {\n newPaired.push($(this).data(\"pair\"));\n });\n //this.debug( newPaired );\n this.paired = newPaired;\n this._renderPaired();\n },\n /** drag communication with pair sub-views: dragstart */\n _pairDragstart: function(ev, pair) {\n //this.debug( '_pairDragstart', ev, pair )\n // auto select the pair causing the event and move all selected\n pair.$el.addClass(\"selected\");\n var $selected = this.$(\".paired-columns .dataset.selected\");\n this.$dragging = $selected;\n },\n /** drag communication with pair sub-views: dragend - remove the placeholder */\n _pairDragend: function(ev, pair) {\n //this.debug( '_pairDragend', ev, pair )\n $(\".element-drop-placeholder\").remove();\n this.$dragging = null;\n },\n\n // ........................................................................ footer\n toggleExtensions: function(force) {\n var creator = this;\n creator.removeExtensions =\n force !== undefined ? force : !creator.removeExtensions;\n\n _.each(creator.paired, function(pair) {\n // don't overwrite custom names\n if (pair.customizedName) {\n return;\n }\n pair.name = creator._guessNameForPair(\n pair.forward,\n pair.reverse\n );\n });\n\n creator._renderPaired();\n creator._renderFooter();\n },\n\n // ------------------------------------------------------------------------ misc\n /** debug a dataset list */\n _printList: function(list) {\n var creator = this;\n _.each(list, function(e) {\n if (list === creator.paired) {\n creator._printPair(e);\n } else {\n //creator.debug( e );\n }\n });\n },\n\n /** print a pair Object */\n _printPair: function(pair) {\n this.debug(pair.forward.name, pair.reverse.name, \": ->\", pair.name);\n },\n\n /** string rep */\n toString: function() {\n return \"PairedCollectionCreator\";\n },\n\n templates: _.extend(\n {},\n baseCreator.CollectionCreatorMixin._creatorTemplates,\n {\n /** the header (not including help text) */\n header: _.template(\n [\n '',\n _l(\n \"Choose from the following filters to change which unpaired reads are shown in the display\"\n ),\n \":\",\n _.values(this.commonFilters)\n .map(function(filterSet) {\n return filterChoice(filterSet[0], filterSet[1]);\n })\n .join(\"\"),\n \"',\n '',\n _l(\"More help\"),\n \"\",\n '\",\n '',\n '',\n _l(\"Less\"),\n \"\",\n \"\",\n \"',\n '',\n '',\n \"\",\n\n '',\n '\"\n ].join(\"\")\n ),\n\n /** the middle: unpaired, divider, and paired */\n middle: _.template(\n [\n // contains two flex rows (rows that fill available space) and a divider btwn\n '',\n '\",\n '',\n '\",\n \"',\n '',\n _l(\"Unpaired forward\"),\n \"\",\n '',\n \"\",\n '',\n '',\n \"\",\n \"',\n '\",\n '',\n '',\n _l(\"Choose filters\"),\n \"\",\n '',\n _l(\"Clear filters\"),\n \"\",\n \"
\",\n '',\n _l(\"Auto-pair\"),\n \"\",\n \"',\n '\",\n \"',\n '\",\n \"',\n '',\n _l(\"Unpaired reverse\"),\n \"\",\n '',\n \"\",\n '',\n '',\n \"\",\n \"',\n '\",\n '',\n '\",\n '',\n '\",\n '',\n '\",\n \"',\n '',\n '\",\n '',\n '\",\n \"',\n '',\n \"\",\n '',\n _l(\"Unpair all\"),\n \"\",\n \"',\n '\"\n ].join(\"\")\n ),\n\n /** creation and cancel controls */\n footer: _.template(\n [\n '',\n '\",\n\n '',\n '\",\n '\",\n \"\",\n '',\n '',\n '\",\n \"',\n _l(\"Name\"),\n \":\",\n \"',\n '\",\n\n '\",\n \"\"\n ].join(\"\")\n ),\n\n /** help content */\n helpContent: _.template(\n [\n \"\",\n _l(\n [\n \"Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). \",\n \"These collections can be passed to tools and workflows in order to have analyses done on each member of \",\n \"the entire group. This interface allows you to create a collection, choose which datasets are paired, \",\n \"and re-order the final collection.\"\n ].join(\"\")\n ),\n \"
\",\n \"\",\n _l(\n [\n 'Unpaired datasets are shown in the unpaired section ',\n \"(hover over the underlined words to highlight below). \",\n 'Paired datasets are shown in the paired section.',\n \"
- To pair datasets, you can:\",\n \"
\",\n _l(\n [\n \"
- You can filter what is shown in the unpaired sections by:\",\n \"
\",\n _l(\n [\n \"To unpair individual dataset pairs, click the \",\n 'unpair buttons ( ). ',\n 'Click the \"Unpair all\" link to unpair all pairs.'\n ].join(\"\")\n ),\n \"
\",\n \"\",\n _l(\n [\n 'You can include or remove the file extensions (e.g. \".fastq\") from your pair names by toggling the ',\n '\"Remove file extensions from pair names?\" control.'\n ].join(\"\")\n ),\n \"
\",\n \"\",\n _l(\n [\n 'Once your collection is complete, enter a name and ',\n 'click \"Create list\". ',\n \"(Note: you do not have to pair all unpaired datasets to finish.)\"\n ].join(\"\")\n ),\n \"
\"\n ].join(\"\")\n )\n }\n )\n });\n\n//=============================================================================\n/** a modal version of the paired collection creator */\nvar pairedCollectionCreatorModal = function _pairedCollectionCreatorModal(\n datasets,\n options\n) {\n var deferred = jQuery.Deferred(),\n creator;\n\n options = _.defaults(options || {}, {\n datasets: datasets,\n oncancel: function() {\n Galaxy.modal.hide();\n deferred.reject(\"cancelled\");\n },\n oncreate: function(creator, response) {\n Galaxy.modal.hide();\n deferred.resolve(response);\n }\n });\n\n if (!window.Galaxy || !Galaxy.modal) {\n throw new Error(\"Galaxy or Galaxy.modal not found\");\n }\n\n creator = new PairedCollectionCreator(options);\n Galaxy.modal.show({\n title: \"Create a collection of paired datasets\",\n body: creator.$el,\n width: \"80%\",\n height: \"800px\",\n closing_events: true\n });\n creator.render();\n window.creator = creator;\n\n //TODO: remove modal header\n return deferred;\n};\n\n//=============================================================================\nfunction createListOfPairsCollection(collection, defaultHideSourceItems) {\n var elements = collection.toJSON();\n //TODO: validate elements\n return pairedCollectionCreatorModal(elements, {\n historyId: collection.historyId,\n defaultHideSourceItems: defaultHideSourceItems\n });\n}\n\n//=============================================================================\nexport default {\n PairedCollectionCreator: PairedCollectionCreator,\n pairedCollectionCreatorModal: pairedCollectionCreatorModal,\n createListOfPairsCollection: createListOfPairsCollection\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/collection/pair-collection-creator.js.map b/static/maps/mvc/collection/pair-collection-creator.js.map index aac21e26eaf..ca9be0f8dca 100644 --- a/static/maps/mvc/collection/pair-collection-creator.js.map +++ b/static/maps/mvc/collection/pair-collection-creator.js.map @@ -1 +1 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LIST_CREATOR from \"mvc/collection/list-collection-creator\";\nimport HDCA from \"mvc/history/hdca-model\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\nvar logNamespace = \"collections\";\n/*==============================================================================\nTODO:\n the paired creator doesn't really mesh with the list creator as parent\n it may be better to make an abstract super class for both\n composites may inherit from this (or vis-versa)\n PairedDatasetCollectionElementView doesn't make a lot of sense\n\n==============================================================================*/\n/** */\nvar PairedDatasetCollectionElementView = Backbone.View\n .extend(BASE_MVC.LoggableMixin)\n .extend({\n _logNamespace: logNamespace,\n\n //TODO: use proper class (DatasetDCE or NestedDCDCE (or the union of both))\n tagName: \"li\",\n className: \"collection-element\",\n\n initialize: function(attributes) {\n this.element = attributes.element || {};\n this.identifier = attributes.identifier;\n },\n\n render: function() {\n this.$el.attr(\"data-element-id\", this.element.id).html(\n this.template({\n identifier: this.identifier,\n element: this.element\n })\n );\n return this;\n },\n\n //TODO: lots of unused space in the element - possibly load details and display them horiz.\n template: _.template(\n [\n '<%- identifier %>',\n '<%- element.name %>'\n ].join(\"\")\n ),\n\n /** remove the DOM and any listeners */\n destroy: function() {\n this.off();\n this.$el.remove();\n },\n\n /** string rep */\n toString: function() {\n return \"DatasetCollectionElementView()\";\n }\n });\n\n// ============================================================================\nvar _super = LIST_CREATOR.ListCollectionCreator;\n\n/** An interface for building collections.\n */\nvar PairCollectionCreator = _super.extend({\n /** the class used to display individual elements */\n elementViewClass: PairedDatasetCollectionElementView,\n /** the class 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The pair collections can be passed to tools and \",\n \"workflows in order to have analyses done on both datasets. This interface allows \",\n \"you to create a pair, name it, and swap which is forward and which reverse.\"\n ].join(\"\")\n ),\n \"
\",\n \"- \",\n \"
\",\n \"\",\n _l(\n [\n 'Once your collection is complete, enter a name and ',\n 'click \"Create list\".'\n ].join(\"\")\n ),\n \"
\"\n ].join(\"\")\n ),\n\n /** a simplified page communicating what went wrong and why the user needs to reselect something else */\n invalidInitial: _.template(\n [\n '',\n '\",\n '\"\n ].join(\"\")\n )\n }),\n\n // ------------------------------------------------------------------------ misc\n /** string rep */\n toString: function() {\n return \"PairCollectionCreator\";\n }\n});\n\n//==============================================================================\n/** List collection flavor of collectionCreatorModal. */\nvar pairCollectionCreatorModal = function _pairCollectionCreatorModal(\n elements,\n options\n) {\n options = options || {};\n options.title = _l(\"Create a collection from a pair of datasets\");\n return LIST_CREATOR.collectionCreatorModal(\n elements,\n options,\n PairCollectionCreator\n );\n};\n\n//==============================================================================\n/** Use a modal to create a pair collection, then add it to the given history contents.\n * @returns {Deferred} resolved when the collection is added to the history.\n */\nfunction createPairCollection(contents, defaultHideSourceItems) {\n var elements = contents.toJSON(),\n promise = pairCollectionCreatorModal(elements, {\n defaultHideSourceItems: defaultHideSourceItems,\n creationFn: function(elements, name, hideSourceItems) {\n elements = [\n { name: \"forward\", src: \"hda\", id: elements[0].id },\n { name: \"reverse\", src: \"hda\", id: elements[1].id }\n ];\n return contents.createHDCA(\n elements,\n \"paired\",\n name,\n hideSourceItems\n );\n }\n });\n return promise;\n}\n\n//==============================================================================\nexport default {\n PairCollectionCreator: PairCollectionCreator,\n pairCollectionCreatorModal: pairCollectionCreatorModal,\n createPairCollection: createPairCollection\n};\n"]} \ No newline at end of file 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\",\n \"- \",\n \"
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* @returns {Deferred} resolved when the collection is added to the history.\n */\nfunction createPairCollection(contents, defaultHideSourceItems) {\n var elements = contents.toJSON(),\n promise = pairCollectionCreatorModal(elements, {\n defaultHideSourceItems: defaultHideSourceItems,\n creationFn: function(elements, name, hideSourceItems) {\n elements = [\n { name: \"forward\", src: \"hda\", id: elements[0].id },\n { name: \"reverse\", src: \"hda\", id: elements[1].id }\n ];\n return contents.createHDCA(\n elements,\n \"paired\",\n name,\n hideSourceItems\n );\n }\n });\n return promise;\n}\n\n//==============================================================================\nexport default {\n PairCollectionCreator: PairCollectionCreator,\n pairCollectionCreatorModal: pairCollectionCreatorModal,\n createPairCollection: createPairCollection\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/dataset/data.js.map b/static/maps/mvc/dataset/data.js.map index 4593efd5577..e707891af87 100644 --- a/static/maps/mvc/dataset/data.js.map +++ b/static/maps/mvc/dataset/data.js.map @@ -1 +1 @@ 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Additional dependencies: jQuery, underscore.\nimport Modal from \"mvc/ui/ui-modal\";\nimport Frames from \"mvc/ui/ui-frames\";\nimport mod_icon_btn from \"mvc/ui/icon-button\";\n/**\n * Dataset metedata.\n */\nvar DatasetMetadata = Backbone.Model.extend({});\n\n/**\n * A dataset. In Galaxy, datasets are associated with a history, so\n * this object is also known as a HistoryDatasetAssociation.\n */\nvar Dataset = Backbone.Model.extend({\n defaults: {\n id: \"\",\n type: \"\",\n name: \"\",\n hda_ldda: \"hda\",\n metadata: null\n },\n\n initialize: function() {\n // Metadata can be passed in as a model or a set of attributes; if it's\n // already a model, there's no need to set metadata.\n if (!this.get(\"metadata\")) {\n this._set_metadata();\n }\n\n // Update metadata on change.\n this.on(\"change\", this._set_metadata, this);\n },\n\n _set_metadata: function() {\n var metadata = new DatasetMetadata();\n\n // Move metadata from dataset attributes to metadata object.\n _.each(\n _.keys(this.attributes),\n function(k) {\n if (k.indexOf(\"metadata_\") === 0) {\n // Found metadata.\n var new_key = k.split(\"metadata_\")[1];\n metadata.set(new_key, this.attributes[k]);\n delete this.attributes[k];\n }\n },\n this\n );\n\n // Because this is an internal change, silence it.\n this.set(\"metadata\", metadata, { silent: true });\n },\n\n /**\n * Returns dataset metadata for a given attribute.\n */\n get_metadata: function(attribute) {\n return this.attributes.metadata.get(attribute);\n },\n\n urlRoot: Galaxy.root + \"api/datasets\"\n});\n\n/**\n * A tabular dataset. This object extends dataset to provide incremental chunked data.\n */\nvar TabularDataset = Dataset.extend({\n defaults: _.extend({}, Dataset.prototype.defaults, {\n chunk_url: null,\n first_data_chunk: null,\n offset: 0,\n at_eof: false\n }),\n\n initialize: function(options) {\n Dataset.prototype.initialize.call(this);\n\n // If first data chunk is available, next chunk is 1.\n if (this.attributes.first_data_chunk) {\n this.attributes.offset = this.attributes.first_data_chunk.offset;\n }\n this.attributes.chunk_url =\n Galaxy.root + \"dataset/display?dataset_id=\" + this.id;\n this.attributes.url_viz = Galaxy.root + \"visualization\";\n },\n\n /**\n * Returns a jQuery Deferred object that resolves to the next data chunk or null if at EOF.\n */\n get_next_chunk: function() {\n // If already at end of file, do nothing.\n if (this.attributes.at_eof) {\n return null;\n }\n\n // Get next chunk.\n var self = this,\n next_chunk = $.Deferred();\n $.getJSON(this.attributes.chunk_url, {\n offset: self.attributes.offset\n }).success(function(chunk) {\n var rval;\n if (chunk.ck_data !== \"\") {\n // Found chunk.\n rval = chunk;\n self.attributes.offset = chunk.offset;\n } else {\n // At EOF.\n self.attributes.at_eof = true;\n rval = null;\n }\n next_chunk.resolve(rval);\n });\n\n return next_chunk;\n }\n});\n\nvar DatasetCollection = Backbone.Collection.extend({\n model: Dataset\n});\n\n/**\n * Provides a base for table-based, dynamic view of a tabular dataset.\n * Do not instantiate directly; use either TopLevelTabularDatasetChunkedView\n * or EmbeddedTabularDatasetChunkedView.\n */\nvar TabularDatasetChunkedView = Backbone.View.extend({\n /**\n * Initialize view and, importantly, set a scroll element.\n */\n initialize: function(options) {\n // Row count for rendering.\n this.row_count = 0;\n this.loading_chunk = false;\n\n // load trackster button\n new TabularButtonTracksterView({\n model: options.model,\n $el: this.$el\n });\n },\n\n expand_to_container: function() {\n if (this.$el.height() < this.scroll_elt.height()) {\n this.attempt_to_fetch();\n }\n },\n\n attempt_to_fetch: function(func) {\n var self = this;\n if (!this.loading_chunk && this.scrolled_to_bottom()) {\n this.loading_chunk = true;\n this.loading_indicator.show();\n $.when(self.model.get_next_chunk()).then(function(result) {\n if (result) {\n self._renderChunk(result);\n self.loading_chunk = false;\n }\n self.loading_indicator.hide();\n self.expand_to_container();\n });\n }\n },\n\n render: function() {\n // Add loading indicator.\n this.loading_indicator = $(\"\").attr(\"id\", \"loading_indicator\");\n this.$el.append(this.loading_indicator);\n\n // Add data table and header.\n var data_table = $(\"',\n '\",\n \"\",\n \"\").attr({\n id: \"content_table\",\n cellpadding: 0\n });\n this.$el.append(data_table);\n var column_names = this.model.get_metadata(\"column_names\"),\n header_container = $(\"\").appendTo(data_table),\n header_row = $(\"
\").appendTo(header_container);\n if (column_names) {\n header_row.append(\n \" \" + column_names.join(\" \") + \" \"\n );\n } else {\n for (var j = 1; j <= this.model.get_metadata(\"columns\"); j++) {\n header_row.append(\"\" + j + \" \");\n }\n }\n\n // Render first chunk.\n var self = this,\n first_chunk = this.model.get(\"first_data_chunk\");\n if (first_chunk) {\n // First chunk is bootstrapped, so render now.\n this._renderChunk(first_chunk);\n } else {\n // No bootstrapping, so get first chunk and then render.\n $.when(self.model.get_next_chunk()).then(function(result) {\n self._renderChunk(result);\n });\n }\n\n // -- Show new chunks during scrolling. --\n\n // Set up chunk loading when scrolling using the scrolling element.\n this.scroll_elt.scroll(function() {\n self.attempt_to_fetch();\n });\n },\n\n /**\n * Returns true if user has scrolled to the bottom of the view.\n */\n scrolled_to_bottom: function() {\n return false;\n },\n\n // -- Helper functions. --\n\n _renderCell: function(cell_contents, index, colspan) {\n var $cell = $(\"\").text(cell_contents);\n var column_types = this.model.get_metadata(\"column_types\");\n if (colspan !== undefined) {\n $cell.attr(\"colspan\", colspan).addClass(\"stringalign\");\n } else if (column_types) {\n if (index < column_types.length) {\n if (\n column_types[index] === \"str\" ||\n column_types[index] === \"list\"\n ) {\n /* Left align all str columns, right align the rest */\n $cell.addClass(\"stringalign\");\n }\n }\n }\n return $cell;\n },\n\n _renderRow: function(line) {\n // Check length of cells to ensure this is a complete row.\n var cells = line.split(\"\\t\"),\n row = $(\" \"),\n num_columns = this.model.get_metadata(\"columns\");\n\n if (this.row_count % 2 !== 0) {\n row.addClass(\"dark_row\");\n }\n\n if (cells.length === num_columns) {\n _.each(\n cells,\n function(cell_contents, index) {\n row.append(this._renderCell(cell_contents, index));\n },\n this\n );\n } else if (cells.length > num_columns) {\n // SAM file or like format with optional metadata included.\n _.each(\n cells.slice(0, num_columns - 1),\n function(cell_contents, index) {\n row.append(this._renderCell(cell_contents, index));\n },\n this\n );\n row.append(\n this._renderCell(\n cells.slice(num_columns - 1).join(\"\\t\"),\n num_columns - 1\n )\n );\n } else if (cells.length === 1) {\n // Comment line, just return the one cell.\n row.append(this._renderCell(line, 0, num_columns));\n } else {\n // cells.length is greater than one, but less than num_columns. Render cells and pad tds.\n // Possibly a SAM file or like format with optional metadata missing.\n // Could also be a tabular file with a line with missing columns.\n _.each(\n cells,\n function(cell_contents, index) {\n row.append(this._renderCell(cell_contents, index));\n },\n this\n );\n _.each(_.range(num_columns - cells.length), function() {\n row.append($(\" \"));\n });\n }\n\n this.row_count++;\n return row;\n },\n\n _renderChunk: function(chunk) {\n var data_table = this.$el.find(\"table\");\n _.each(\n chunk.ck_data.split(\"\\n\"),\n function(line, index) {\n if (line !== \"\") {\n data_table.append(this._renderRow(line));\n }\n },\n this\n );\n }\n});\n\n/**\n * Tabular view that is placed at the top level of page. Scrolling occurs\n * view top-level elements outside of view.\n */\nvar TopLevelTabularDatasetChunkedView = TabularDatasetChunkedView.extend({\n initialize: function(options) {\n TabularDatasetChunkedView.prototype.initialize.call(this, options);\n\n // Scrolling happens in top-level elements.\n var scroll_elt = _.find(this.$el.parents(), function(p) {\n return $(p).css(\"overflow\") === \"auto\";\n });\n\n // If no scrolling element found, use window.\n if (!scroll_elt) {\n scroll_elt = window;\n }\n\n // Wrap scrolling element for easy access.\n this.scroll_elt = $(scroll_elt);\n },\n\n /**\n * Returns true if user has scrolled to the bottom of the view.\n */\n scrolled_to_bottom: function() {\n return (\n this.$el.height() -\n this.scroll_elt.scrollTop() -\n this.scroll_elt.height() <=\n 0\n );\n }\n});\n\n/**\n * Tabular view tnat is embedded in a page. Scrolling occurs in view's el.\n */\nvar EmbeddedTabularDatasetChunkedView = TabularDatasetChunkedView.extend({\n initialize: function(options) {\n TabularDatasetChunkedView.prototype.initialize.call(this, options);\n\n // Because view is embedded, set up div to do scrolling.\n this.scroll_elt = this.$el.css({\n position: \"relative\",\n overflow: \"scroll\",\n height: options.height || \"500px\"\n });\n },\n\n /**\n * Returns true if user has scrolled to the bottom of the view.\n */\n scrolled_to_bottom: function() {\n return (\n this.$el.scrollTop() + this.$el.innerHeight() >=\n this.el.scrollHeight\n );\n }\n});\n\n/** Button for trackster visualization */\nvar TabularButtonTracksterView = Backbone.View.extend({\n // gene region columns\n col: {\n chrom: null,\n start: null,\n end: null\n },\n\n // url for trackster\n url_viz: null,\n\n // dataset id\n dataset_id: null,\n\n // database key\n genome_build: null,\n\n // data type\n file_ext: null,\n\n // backbone initialize\n initialize: function(options) {\n // check if environment is available\n var Galaxy = parent.Galaxy;\n\n // link galaxy modal or create one\n if (Galaxy && Galaxy.modal) {\n this.modal = Galaxy.modal;\n }\n\n // link galaxy frames\n if (Galaxy && Galaxy.frame) {\n this.frame = Galaxy.frame;\n }\n\n // check\n if (!this.modal || !this.frame) {\n return;\n }\n\n // model/metadata\n var model = options.model;\n var metadata = model.get(\"metadata\");\n\n // check for datatype\n if (!model.get(\"file_ext\")) {\n return;\n }\n\n // get data type\n this.file_ext = model.get(\"file_ext\");\n\n // check for bed-file format\n if (this.file_ext == \"bed\") {\n // verify that metadata exists\n if (\n metadata.get(\"chromCol\") &&\n metadata.get(\"startCol\") &&\n metadata.get(\"endCol\")\n ) {\n // read in columns\n this.col.chrom = metadata.get(\"chromCol\") - 1;\n this.col.start = metadata.get(\"startCol\") - 1;\n this.col.end = metadata.get(\"endCol\") - 1;\n } else {\n console.log(\n \"TabularButtonTrackster : Bed-file metadata incomplete.\"\n );\n return;\n }\n }\n\n // check for vcf-file format\n if (this.file_ext == \"vcf\") {\n // search array\n function search(str, array) {\n for (var j = 0; j < array.length; j++)\n if (array[j].match(str)) return j;\n return -1;\n }\n\n // load\n this.col.chrom = search(\"Chrom\", metadata.get(\"column_names\"));\n this.col.start = search(\"Pos\", metadata.get(\"column_names\"));\n this.col.end = null;\n\n // verify that metadata exists\n if (this.col.chrom == -1 || this.col.start == -1) {\n console.log(\n \"TabularButtonTrackster : VCF-file metadata incomplete.\"\n );\n return;\n }\n }\n\n // check\n if (this.col.chrom === undefined) {\n return;\n }\n\n // get dataset id\n if (model.id) {\n this.dataset_id = model.id;\n } else {\n console.log(\n \"TabularButtonTrackster : Dataset identification is missing.\"\n );\n return;\n }\n\n // get url\n if (model.get(\"url_viz\")) {\n this.url_viz = model.get(\"url_viz\");\n } else {\n console.log(\n \"TabularButtonTrackster : Url for visualization controller is missing.\"\n );\n return;\n }\n\n // get genome_build / database key\n if (model.get(\"genome_build\")) {\n this.genome_build = model.get(\"genome_build\");\n }\n\n // create the icon\n var btn_viz = new mod_icon_btn.IconButtonView({\n model: new mod_icon_btn.IconButton({\n title: \"Visualize\",\n icon_class: \"chart_curve\",\n id: \"btn_viz\"\n })\n });\n\n // set element\n this.setElement(options.$el);\n\n // add to element\n this.$el.append(btn_viz.render().$el);\n\n // hide the button\n this.hide();\n },\n\n /** Add event handlers */\n events: {\n \"mouseover tr\": \"show\",\n mouseleave: \"hide\"\n },\n\n // show button\n show: function(e) {\n var self = this;\n\n // is numeric\n function is_numeric(n) {\n return !isNaN(parseFloat(n)) && isFinite(n);\n }\n\n // check\n if (this.col.chrom === null) return;\n\n // get selected data line\n var row = $(e.target).parent();\n\n // verify that location has been found\n var chrom = row\n .children()\n .eq(this.col.chrom)\n .html();\n var start = row\n .children()\n .eq(this.col.start)\n .html();\n\n // end is optional\n var end = this.col.end\n ? row\n .children()\n .eq(this.col.end)\n .html()\n : start;\n\n // double check location\n if (!chrom.match(\"^#\") && chrom !== \"\" && is_numeric(start)) {\n // get target gene region\n var btn_viz_pars = {\n dataset_id: this.dataset_id,\n gene_region: chrom + \":\" + start + \"-\" + end\n };\n\n // get button position\n var offset = row.offset();\n var left = offset.left - 10;\n var top = offset.top - $(window).scrollTop() + 3;\n\n // update css\n $(\"#btn_viz\").css({\n position: \"fixed\",\n top: top + \"px\",\n left: left + \"px\"\n });\n $(\"#btn_viz\").off(\"click\");\n $(\"#btn_viz\").click(function() {\n self.frame.add({\n title: \"Trackster\",\n url: self.url_viz + \"/trackster?\" + $.param(btn_viz_pars)\n });\n });\n\n // show the button\n $(\"#btn_viz\").show();\n } else {\n // hide the button\n $(\"#btn_viz\").hide();\n }\n },\n\n /** hide button */\n hide: function() {\n this.$(\"#btn_viz\").hide();\n }\n});\n\n// -- Utility functions. --\n\n/**\n * Create a model, attach it to a view, render view, and attach it to a parent element.\n */\nvar createModelAndView = function(model, view, model_config, parent_elt) {\n // Create model, view.\n var a_view = new view({\n model: new model(model_config)\n });\n\n // Render view and add to parent element.\n a_view.render();\n if (parent_elt) {\n parent_elt.append(a_view.$el);\n }\n\n return a_view;\n};\n\n/**\n * Create a tabular dataset chunked view (and requisite tabular dataset model)\n * and appends to parent_elt.\n */\nvar createTabularDatasetChunkedView = function(options) {\n // If no model, create and set model from dataset config.\n if (!options.model) {\n options.model = new TabularDataset(options.dataset_config);\n }\n\n var parent_elt = options.parent_elt;\n var embedded = options.embedded;\n\n // Clean up options so that only needed options are passed to view.\n delete options.embedded;\n delete options.parent_elt;\n delete options.dataset_config;\n\n // Create and set up view.\n var view = embedded\n ? new EmbeddedTabularDatasetChunkedView(options)\n : new TopLevelTabularDatasetChunkedView(options);\n view.render();\n\n if (parent_elt) {\n parent_elt.append(view.$el);\n // If we're sticking this in another element, once it's appended check\n // to make sure we've filled enough space.\n // Without this, the scroll elements don't work.\n view.expand_to_container();\n }\n\n return view;\n};\n\nexport default {\n Dataset: Dataset,\n TabularDataset: TabularDataset,\n DatasetCollection: DatasetCollection,\n TabularDatasetChunkedView: TabularDatasetChunkedView,\n createTabularDatasetChunkedView: createTabularDatasetChunkedView\n};\n"]} \ No newline at end of file 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In Galaxy, datasets are associated with a history, so\n * this object is also known as a HistoryDatasetAssociation.\n */\nvar Dataset = Backbone.Model.extend({\n defaults: {\n id: \"\",\n type: \"\",\n name: \"\",\n hda_ldda: \"hda\",\n metadata: null\n },\n\n initialize: function() {\n // Metadata can be passed in as a model or a set of attributes; if it's\n // already a model, there's no need to set metadata.\n if (!this.get(\"metadata\")) {\n this._set_metadata();\n }\n\n // Update metadata on change.\n this.on(\"change\", this._set_metadata, this);\n },\n\n _set_metadata: function() {\n var metadata = new DatasetMetadata();\n\n // Move metadata from dataset attributes to metadata object.\n _.each(\n _.keys(this.attributes),\n function(k) {\n if (k.indexOf(\"metadata_\") === 0) {\n // Found metadata.\n var new_key = k.split(\"metadata_\")[1];\n metadata.set(new_key, this.attributes[k]);\n delete this.attributes[k];\n }\n },\n this\n );\n\n // Because this is an internal change, silence it.\n this.set(\"metadata\", metadata, { silent: true });\n },\n\n /**\n * Returns dataset metadata for a given attribute.\n */\n get_metadata: function(attribute) {\n return this.attributes.metadata.get(attribute);\n },\n\n urlRoot: Galaxy.root + \"api/datasets\"\n});\n\n/**\n * A tabular dataset. This object extends dataset to provide incremental chunked data.\n */\nvar TabularDataset = Dataset.extend({\n defaults: _.extend({}, Dataset.prototype.defaults, {\n chunk_url: null,\n first_data_chunk: null,\n offset: 0,\n at_eof: false\n }),\n\n initialize: function(options) {\n Dataset.prototype.initialize.call(this);\n\n // If first data chunk is available, next chunk is 1.\n if (this.attributes.first_data_chunk) {\n this.attributes.offset = this.attributes.first_data_chunk.offset;\n }\n this.attributes.chunk_url =\n Galaxy.root + \"dataset/display?dataset_id=\" + this.id;\n this.attributes.url_viz = Galaxy.root + \"visualization\";\n },\n\n /**\n * Returns a jQuery Deferred object that resolves to the next data chunk or null if at EOF.\n */\n get_next_chunk: function() {\n // If already at end of file, do nothing.\n if (this.attributes.at_eof) {\n return null;\n }\n\n // Get next chunk.\n var self = this,\n next_chunk = $.Deferred();\n $.getJSON(this.attributes.chunk_url, {\n offset: self.attributes.offset\n }).success(function(chunk) {\n var rval;\n if (chunk.ck_data !== \"\") {\n // Found chunk.\n rval = chunk;\n self.attributes.offset = chunk.offset;\n } else {\n // At EOF.\n self.attributes.at_eof = true;\n rval = null;\n }\n next_chunk.resolve(rval);\n });\n\n return next_chunk;\n }\n});\n\nvar DatasetCollection = Backbone.Collection.extend({\n model: Dataset\n});\n\n/**\n * Provides a base for table-based, dynamic view of a tabular dataset.\n * Do not instantiate directly; use either TopLevelTabularDatasetChunkedView\n * or EmbeddedTabularDatasetChunkedView.\n */\nvar TabularDatasetChunkedView = Backbone.View.extend({\n /**\n * Initialize view and, importantly, set a scroll element.\n */\n initialize: function(options) {\n // Row count for rendering.\n this.row_count = 0;\n this.loading_chunk = false;\n\n // load trackster button\n new TabularButtonTracksterView({\n model: options.model,\n $el: this.$el\n });\n },\n\n expand_to_container: function() {\n if (this.$el.height() < this.scroll_elt.height()) {\n this.attempt_to_fetch();\n }\n },\n\n attempt_to_fetch: function(func) {\n var self = this;\n if (!this.loading_chunk && this.scrolled_to_bottom()) {\n this.loading_chunk = true;\n this.loading_indicator.show();\n $.when(self.model.get_next_chunk()).then(function(result) {\n if (result) {\n self._renderChunk(result);\n self.loading_chunk = false;\n }\n self.loading_indicator.hide();\n self.expand_to_container();\n });\n }\n },\n\n render: function() {\n // Add loading indicator.\n this.loading_indicator = $(\"\").attr(\"id\", \"loading_indicator\");\n this.$el.append(this.loading_indicator);\n\n // Add data table and header.\n var data_table = $(\" \").attr({\n id: \"content_table\",\n cellpadding: 0\n });\n this.$el.append(data_table);\n var column_names = this.model.get_metadata(\"column_names\"),\n header_container = $(\"\").appendTo(data_table),\n header_row = $(\"
\").appendTo(header_container);\n if (column_names) {\n header_row.append(\n \" \" + column_names.join(\" \") + \" \"\n );\n } else {\n for (var j = 1; j <= this.model.get_metadata(\"columns\"); j++) {\n header_row.append(\"\" + j + \" \");\n }\n }\n\n // Render first chunk.\n var self = this,\n first_chunk = this.model.get(\"first_data_chunk\");\n if (first_chunk) {\n // First chunk is bootstrapped, so render now.\n this._renderChunk(first_chunk);\n } else {\n // No bootstrapping, so get first chunk and then render.\n $.when(self.model.get_next_chunk()).then(function(result) {\n self._renderChunk(result);\n });\n }\n\n // -- Show new chunks during scrolling. --\n\n // Set up chunk loading when scrolling using the scrolling element.\n this.scroll_elt.scroll(function() {\n self.attempt_to_fetch();\n });\n },\n\n /**\n * Returns true if user has scrolled to the bottom of the view.\n */\n scrolled_to_bottom: function() {\n return false;\n },\n\n // -- Helper functions. --\n\n _renderCell: function(cell_contents, index, colspan) {\n var $cell = $(\"\").text(cell_contents);\n var column_types = this.model.get_metadata(\"column_types\");\n if (colspan !== undefined) {\n $cell.attr(\"colspan\", colspan).addClass(\"stringalign\");\n } else if (column_types) {\n if (index < column_types.length) {\n if (\n column_types[index] === \"str\" ||\n column_types[index] === \"list\"\n ) {\n /* Left align all str columns, right align the rest */\n $cell.addClass(\"stringalign\");\n }\n }\n }\n return $cell;\n },\n\n _renderRow: function(line) {\n // Check length of cells to ensure this is a complete row.\n var cells = line.split(\"\\t\"),\n row = $(\" \"),\n num_columns = this.model.get_metadata(\"columns\");\n\n if (this.row_count % 2 !== 0) {\n row.addClass(\"dark_row\");\n }\n\n if (cells.length === num_columns) {\n _.each(\n cells,\n function(cell_contents, index) {\n row.append(this._renderCell(cell_contents, index));\n },\n this\n );\n } else if (cells.length > num_columns) {\n // SAM file or like format with optional metadata included.\n _.each(\n cells.slice(0, num_columns - 1),\n function(cell_contents, index) {\n row.append(this._renderCell(cell_contents, index));\n },\n this\n );\n row.append(\n this._renderCell(\n cells.slice(num_columns - 1).join(\"\\t\"),\n num_columns - 1\n )\n );\n } else if (cells.length === 1) {\n // Comment line, just return the one cell.\n row.append(this._renderCell(line, 0, num_columns));\n } else {\n // cells.length is greater than one, but less than num_columns. Render cells and pad tds.\n // Possibly a SAM file or like format with optional metadata missing.\n // Could also be a tabular file with a line with missing columns.\n _.each(\n cells,\n function(cell_contents, index) {\n row.append(this._renderCell(cell_contents, index));\n },\n this\n );\n _.each(_.range(num_columns - cells.length), function() {\n row.append($(\" \"));\n });\n }\n\n this.row_count++;\n return row;\n },\n\n _renderChunk: function(chunk) {\n var data_table = this.$el.find(\"table\");\n _.each(\n chunk.ck_data.split(\"\\n\"),\n function(line, index) {\n if (line !== \"\") {\n data_table.append(this._renderRow(line));\n }\n },\n this\n );\n }\n});\n\n/**\n * Tabular view that is placed at the top level of page. 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initialize: function(options) {\n // check if environment is available\n var Galaxy = parent.Galaxy;\n\n // link galaxy modal or create one\n if (Galaxy && Galaxy.modal) {\n this.modal = Galaxy.modal;\n }\n\n // link galaxy frames\n if (Galaxy && Galaxy.frame) {\n this.frame = Galaxy.frame;\n }\n\n // check\n if (!this.modal || !this.frame) {\n return;\n }\n\n // model/metadata\n var model = options.model;\n var metadata = model.get(\"metadata\");\n\n // check for datatype\n if (!model.get(\"file_ext\")) {\n return;\n }\n\n // get data type\n this.file_ext = model.get(\"file_ext\");\n\n // check for bed-file format\n if (this.file_ext == \"bed\") {\n // verify that metadata exists\n if (\n metadata.get(\"chromCol\") &&\n metadata.get(\"startCol\") &&\n metadata.get(\"endCol\")\n ) {\n // read in columns\n this.col.chrom = metadata.get(\"chromCol\") - 1;\n this.col.start = metadata.get(\"startCol\") - 1;\n this.col.end = metadata.get(\"endCol\") - 1;\n } else {\n console.log(\n \"TabularButtonTrackster : Bed-file metadata incomplete.\"\n );\n return;\n }\n }\n\n // check for vcf-file format\n if (this.file_ext == \"vcf\") {\n // search array\n function search(str, array) {\n for (var j = 0; j < array.length; j++)\n if (array[j].match(str)) return j;\n return -1;\n }\n\n // load\n this.col.chrom = search(\"Chrom\", metadata.get(\"column_names\"));\n this.col.start = search(\"Pos\", metadata.get(\"column_names\"));\n this.col.end = null;\n\n // verify that metadata exists\n if (this.col.chrom == -1 || this.col.start == -1) {\n console.log(\n \"TabularButtonTrackster : VCF-file metadata incomplete.\"\n );\n return;\n }\n }\n\n // check\n if (this.col.chrom === undefined) {\n return;\n }\n\n // get dataset id\n if (model.id) {\n this.dataset_id = model.id;\n } else {\n console.log(\n \"TabularButtonTrackster : Dataset identification is missing.\"\n );\n return;\n }\n\n // get url\n if (model.get(\"url_viz\")) {\n this.url_viz = model.get(\"url_viz\");\n } else 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been found\n var chrom = row\n .children()\n .eq(this.col.chrom)\n .html();\n var start = row\n .children()\n .eq(this.col.start)\n .html();\n\n // end is optional\n var end = this.col.end\n ? row\n .children()\n .eq(this.col.end)\n .html()\n : start;\n\n // double check location\n if (!chrom.match(\"^#\") && chrom !== \"\" && is_numeric(start)) {\n // get target gene region\n var btn_viz_pars = {\n dataset_id: this.dataset_id,\n gene_region: chrom + \":\" + start + \"-\" + end\n };\n\n // get button position\n var offset = row.offset();\n var left = offset.left - 10;\n var top = offset.top - $(window).scrollTop() + 3;\n\n // update css\n $(\"#btn_viz\").css({\n position: \"fixed\",\n top: top + \"px\",\n left: left + \"px\"\n });\n $(\"#btn_viz\").off(\"click\");\n $(\"#btn_viz\").click(function() {\n self.frame.add({\n title: \"Trackster\",\n url: self.url_viz + \"/trackster?\" + $.param(btn_viz_pars)\n });\n });\n\n // show the button\n $(\"#btn_viz\").show();\n } else {\n // hide the button\n $(\"#btn_viz\").hide();\n }\n },\n\n /** hide button */\n hide: function() {\n this.$(\"#btn_viz\").hide();\n }\n});\n\n// -- Utility functions. --\n\n/**\n * Create a model, attach it to a view, render view, and attach it to a parent element.\n */\nvar createModelAndView = function(model, view, model_config, parent_elt) {\n // Create model, view.\n var a_view = new view({\n model: new model(model_config)\n });\n\n // Render view and add to parent element.\n a_view.render();\n if (parent_elt) {\n parent_elt.append(a_view.$el);\n }\n\n return a_view;\n};\n\n/**\n * Create a tabular dataset chunked view (and requisite tabular dataset model)\n * and appends to parent_elt.\n */\nvar createTabularDatasetChunkedView = function(options) {\n // If no model, create and set model from dataset config.\n if (!options.model) {\n options.model = new TabularDataset(options.dataset_config);\n }\n\n var parent_elt = options.parent_elt;\n var embedded = options.embedded;\n\n // Clean up options so that only needed options are passed to view.\n delete options.embedded;\n delete options.parent_elt;\n delete options.dataset_config;\n\n // Create and set up view.\n var view = embedded\n ? new EmbeddedTabularDatasetChunkedView(options)\n : new TopLevelTabularDatasetChunkedView(options);\n view.render();\n\n if (parent_elt) {\n parent_elt.append(view.$el);\n // If we're sticking this in another element, once it's appended check\n // to make sure we've filled enough space.\n // Without this, the scroll elements don't work.\n view.expand_to_container();\n }\n\n return view;\n};\n\nexport default {\n Dataset: Dataset,\n TabularDataset: TabularDataset,\n DatasetCollection: DatasetCollection,\n TabularDatasetChunkedView: TabularDatasetChunkedView,\n createTabularDatasetChunkedView: createTabularDatasetChunkedView\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/dataset/dataset-choice.js.map b/static/maps/mvc/dataset/dataset-choice.js.map index 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DATASET from \"mvc/dataset/dataset-model\";\nimport DATASET_LIST from \"mvc/dataset/dataset-list\";\nimport MODAL from \"mvc/ui/ui-modal\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\nvar logNamespace = \"dataset\";\n/* ============================================================================\nTODO:\n does this really work with mixed contents?\n Single dataset choice: allow none?\n tooltips rendered *behind* modal\n collection selector\n better handling when no results returned from filterDatasetJSON\n pass optional subtitle from choice display to modal\n onfirstclick\n drop target\n return modal with promise?\n\n auto showing the modal may not be best\n\n============================================================================ */\n/** Filters an array of dataset plain JSON objs.\n */\nfunction _filterDatasetJSON(datasetJSON, where, datasetsOnly) {\n //TODO: replace with _.matches (underscore 1.6.0)\n function matches(obj, toMatch) {\n for 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*\n * @example:\n * var datasetJSON = // from ajax or bootstrap\n * // returns a jQuery promise (that 'fail's only if no datasets are found matching 'where' below)\n * var choice = new DatasetChoiceModal( datasetJSON, {\n * datasetsOnly : false,\n * where : { state: 'ok', file_ext: 'bed', ... },\n * multiselect : true,\n * selected : [ 'df7a1f0c02a5b08e', 'abcdef0123456789' ]\n *\n * }).done( function( json ){\n * if( json ){\n * console.debug( json );\n * // returned choice will always be an array (single or multi)\n * // [{ , , ... }]\n * // ... do stuff\n * } else {\n * // json will === null if the user cancelled selection\n * console.debug( 'cancelled' );\n * }\n * });\n */\nvar DatasetChoiceModal = function(datasetJSON, options) {\n // option defaults\n options = _.defaults(options || {}, {\n // show datasets or datasets and collections\n datasetsOnly: true,\n // map of attributes to filter datasetJSON by\n where: { state: \"ok\" },\n // select more than one dataset?\n multiselect: false,\n // any dataset ids that will display as already selected\n selected: []\n });\n // default title should depend on multiselect\n options.title =\n options.title ||\n (options.multiselect\n ? _l(\"Choose datasets:\")\n : _l(\"Choose a dataset:\"));\n\n var modal,\n list,\n buttons,\n promise = jQuery.Deferred(),\n filterFn = options.filter || _filterDatasetJSON;\n\n // filter the given datasets and if none left return a rejected promise for use with fail()\n datasetJSON = filterFn(datasetJSON, options.where, options.datasetsOnly);\n if (!datasetJSON.length) {\n return promise.reject(\"No matches found\");\n }\n\n // resolve the returned promise with the json of the selected datasets\n function resolveWithSelected() {\n promise.resolve(\n list.getSelectedModels().map(function(model) {\n return model.toJSON();\n })\n );\n }\n // if multiselect - add a button for the user to complete the changes\n if (options.multiselect) {\n buttons = {};\n buttons[_l(\"Ok\")] = resolveWithSelected;\n }\n\n // create a full-height modal that's cancellable, remove unneeded elements and styles\n modal = new MODAL.View({\n height: \"auto\",\n buttons: buttons,\n closing_events: true,\n closing_callback: function() {\n promise.resolve(null);\n },\n body: [''].join(\"\")\n });\n modal.$(\".modal-header\").remove();\n modal.$(\".modal-footer\").css(\"margin-top\", \"0px\");\n\n // attach a dataset list (of the filtered datasets) to that modal that's selectable\n list = new DATASET_LIST.DatasetList({\n title: options.title,\n subtitle:\n options.subtitle ||\n _l(\n [\n //TODO: as option\n \"Click the checkboxes on the right to select datasets. \",\n \"Click the datasets names to see their details. \"\n ].join(\"\")\n ),\n el: modal.$body.find(\".list-panel\"),\n selecting: true,\n selected: options.selected,\n collection: new DATASET.DatasetAssociationCollection(datasetJSON)\n });\n\n // when the list is rendered, show the modal (also add a specifying class for css)\n list.once(\"rendered:initial\", function() {\n modal.show();\n modal.$el.addClass(\"dataset-choice-modal\");\n });\n if (!options.multiselect) {\n // if single select, remove the all/none list actions from the panel\n list.on(\"rendered\", function() {\n list.$(\".list-actions\").hide();\n });\n // if single select, immediately resolve on a single selection\n list.on(\"view:selected\", function(view) {\n promise.resolve([view.model.toJSON()]);\n });\n }\n list.render(0);\n\n // return the promise, and on any resolution close the modal\n return promise.always(function() {\n modal.hide();\n });\n};\n\n// ============================================================================\n/** Activator for single dataset selection modal and display of the selected dataset.\n * The activator/display will show as a single div and, when a dataset is selected,\n * show the name and details of the selected dataset.\n *\n * When clicked the div will generate a DatasetChoiceModal of the available choices.\n *\n * Options:\n * datasetJSON: array of plain json objects representing allowed choices\n * datasetsOnly: T: only show datasets in the allowed choices, F: datasets + collections\n * where: map of attributes to filter datasetJSON by (e.g. { file_ext: 'bed' })\n * label: the label/prompt displayed\n * selected: array of dataset ids that will show as already selected in the control\n *\n * @example:\n * var choice1 = new DATASET_CHOICE.DatasetChoice({\n * datasetJSON : datasetJSON,\n * label : 'Input dataset',\n * selected : [ 'df7a1f0c02a5b08e' ]\n * });\n * $( 'body' ).append( choice1.render().$el )\n *\n * Listen to the DatasetChoice to react to changes in the user's choice/selection:\n * @example:\n * choice1.on( 'selected', function( chooser, selectionJSONArray ){\n * // ... do stuff with new selections\n * });\n */\nvar DatasetChoice = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({\n _logNamespace: logNamespace,\n\n className: \"dataset-choice\",\n\n /** set up defaults, options, and listeners */\n initialize: function(attributes) {\n this.debug(this + \"(DatasetChoice).initialize:\", attributes);\n\n this.label = attributes.label !== undefined ? _l(attributes.label) : \"\";\n this.where = attributes.where;\n this.datasetsOnly =\n attributes.datasetsOnly !== undefined\n ? attributes.datasetsOnly\n : true;\n\n this.datasetJSON = attributes.datasetJSON || [];\n this.selected = attributes.selected || [];\n\n this._setUpListeners();\n },\n\n /** add any (bbone) listeners */\n _setUpListeners: function() {\n //this.on( 'all', function(){\n // this.log( this + '', arguments );\n //});\n },\n\n /** render the view */\n render: function() {\n var json = this.toJSON();\n this.$el.html(this._template(json));\n this.$(\".selected\").replaceWith(this._renderSelected(json));\n return this;\n },\n\n /** return plain html for the overall control */\n _template: function(json) {\n return _.template(\n [\n \"\"\n ].join(\"\")\n )(json);\n },\n\n /** return jQ DOM for the selected dataset (only one) */\n _renderSelected: function(json) {\n if (json.selected.length) {\n //TODO: break out?\n return $(\n _.template(\n [\n ' ',\n '<%- selected.hid %>: <%- selected.name %>',\n '',\n \"<%- selected.misc_blurb %>\",\n \"\",\n _l(\"format\") + \": \",\n \"<%- selected.file_ext %>\",\n \"<%- selected.misc_info %>\",\n \"\",\n \"\"\n ].join(\"\"),\n { variable: \"selected\" }\n )(json.selected[0])\n );\n }\n return $(\n [\n '(',\n _l(\"click to select a dataset\"),\n \")\"\n ].join(\"\")\n );\n },\n\n //TODO:?? why not just pass in view?\n /** return a plain JSON object with both the view and dataset attributes */\n toJSON: function() {\n var chooser = this;\n return {\n label: chooser.label,\n datasets: chooser.datasetJSON,\n selected: _.compact(\n _.map(chooser.selected, function(id) {\n return _.findWhere(chooser.datasetJSON, {\n id: id\n });\n })\n )\n };\n },\n\n /** event map: when to open the modal */\n events: {\n // the whole thing 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_createModal: function() {\n return new DatasetChoiceModal(\n this.datasetJSON,\n this._getModalOptions()\n );\n },\n\n /** return a plain JSON containing the options to pass to the modal */\n _getModalOptions: function() {\n return {\n title: this.label,\n multiselect: false,\n selected: this.selected,\n where: this.where,\n datasetsOnly: this.datasetsOnly\n };\n },\n\n // ------------------------------------------------------------------------ misc\n /** string rep */\n toString: function() {\n return \"DatasetChoice(\" + this.selected + \")\";\n }\n});\n\n// ============================================================================\n/** Activator for multiple dataset selection modal and display of the selected datasets.\n * The activator/display will show as a table of all choices.\n *\n * See DatasetChoice (above) for example usage.\n *\n * Additional options:\n * showHeaders: T: show headers for selected dataset attributes in the display table\n * cells: map of attribute keys -> Human readable/localized column headers\n * (e.g. { file_ext: _l( 'Format' ) }) - defaults are listed below\n */\nvar MultiDatasetChoice = DatasetChoice.extend({\n className: DatasetChoice.prototype.className + \" multi\",\n\n /** default (dataset attribute key -> table header text) map of what cells to display in the table */\n cells: {\n hid: _l(\"History #\"),\n name: _l(\"Name\"),\n misc_blurb: _l(\"Summary\"),\n file_ext: _l(\"Format\"),\n genome_build: _l(\"Genome\"),\n tags: _l(\"Tags\"),\n annotation: _l(\"Annotation\")\n },\n\n /** in this override, add the showHeaders and cells options */\n initialize: function(attributes) {\n this.showHeaders =\n attributes.showHeaders !== undefined\n ? attributes.showHeaders\n : true;\n this.cells = attributes.cells || this.cells;\n DatasetChoice.prototype.initialize.call(this, attributes);\n },\n\n /** in this override, display the selected datasets as a table with optional headers */\n _renderSelected: function(json) {\n if (json.selected.length) {\n return $(\n _.template(\n [\n '',\n \"<% if( json.showHeaders ){ %>\",\n \"
\"\n ].join(\"\"),\n { variable: \"json\" }\n )(json)\n );\n }\n return $(\n [\n '(',\n _l(\"click to select a dataset\"),\n \")\"\n ].join(\"\")\n );\n },\n\n /** in this override, send the showHeaders and cells options as well */\n toJSON: function() {\n return _.extend(DatasetChoice.prototype.toJSON.call(this), {\n showHeaders: this.showHeaders,\n cells: this.cells\n });\n },\n\n /** in this override, set multiselect to true */\n _getModalOptions: function() {\n return _.extend(DatasetChoice.prototype._getModalOptions.call(this), {\n multiselect: true\n });\n },\n\n // ------------------------------------------------------------------------ misc\n /** string rep */\n toString: function() {\n return \"DatasetChoice(\" + this.selected + \")\";\n }\n});\n\n// ============================================================================\nexport default {\n DatasetChoiceModal: DatasetChoiceModal,\n DatasetChoice: DatasetChoice,\n MultiDatasetChoice: MultiDatasetChoice\n};\n"]} \ No newline at end of file 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DATASET from \"mvc/dataset/dataset-model\";\nimport DATASET_LIST from \"mvc/dataset/dataset-list\";\nimport MODAL from \"mvc/ui/ui-modal\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\nvar logNamespace = \"dataset\";\n/* ============================================================================\nTODO:\n does this really work with mixed contents?\n Single dataset choice: allow none?\n tooltips rendered *behind* modal\n collection selector\n better handling when no results returned from filterDatasetJSON\n pass optional subtitle from choice display to modal\n onfirstclick\n drop target\n return modal with promise?\n\n auto showing the modal may not be best\n\n============================================================================ */\n/** Filters an array of dataset plain JSON objs.\n */\nfunction _filterDatasetJSON(datasetJSON, where, datasetsOnly) {\n //TODO: replace with _.matches (underscore 1.6.0)\n function matches(obj, toMatch) {\n for (var key in toMatch) {\n if (toMatch.hasOwnProperty(key)) {\n if (obj[key] !== toMatch[key]) {\n return false;\n }\n }\n }\n return true;\n }\n\n return datasetJSON.filter(function(json) {\n console.debug(json);\n return (\n !json.deleted &&\n json.visible &&\n (!datasetsOnly || json.collection_type === undefined) &&\n matches(json, where)\n );\n });\n}\n\n// ============================================================================\n/** Given an array of plain JSON objs rep. datasets, show a modal allowing a choice\n * of one or more of those datasets.\n *\n * Pass:\n * an array of plain JSON objects representing allowed dataset choices\n * a map of options (see below)\n *\n * Options:\n * datasetsOnly: T: display only datasets, F: datasets + dataset collections\n * where: a map of attributes available choices *must have* (defaults to { state: 'ok' })\n * multiselect: T: user can select more than one, F: only one\n * selected: array of dataset ids to make them selected by default\n *\n * @example:\n * var datasetJSON = // from ajax or bootstrap\n * // returns a jQuery promise (that 'fail's only if no datasets are found matching 'where' below)\n * var choice = new DatasetChoiceModal( datasetJSON, {\n * datasetsOnly : false,\n * where : { state: 'ok', file_ext: 'bed', ... },\n * multiselect : true,\n * selected : [ 'df7a1f0c02a5b08e', 'abcdef0123456789' ]\n *\n * }).done( function( json ){\n * if( json ){\n * console.debug( json );\n * // returned choice will always be an array (single or multi)\n * // [{\",\n \"<% _.map( json.cells, function( val, key ){ %>\",\n \" \",\n \"<% } %>\",\n \"\",\n \"<% _.map( json.selected, function( selected ){ %>\",\n \"<%- val %> \",\n \"<% }); %>\",\n \"\",\n \"<% _.map( json.cells, function( val, key ){ %>\",\n ' \",\n \"<% }); %>\",\n \"\",\n \"\"><%- selected[ key ] %> ',\n \"<% }) %>\",\n \", , ... }]\n * // ... do stuff\n * } else {\n * // json will === null if the user cancelled selection\n * console.debug( 'cancelled' );\n * }\n * });\n */\nvar DatasetChoiceModal = function(datasetJSON, options) {\n // option defaults\n options = _.defaults(options || {}, {\n // show datasets or datasets and collections\n datasetsOnly: true,\n // map of attributes to filter datasetJSON by\n where: { state: \"ok\" },\n // select more than one dataset?\n multiselect: false,\n // any dataset ids that will display as already selected\n selected: []\n });\n // default title should depend on multiselect\n options.title =\n options.title ||\n (options.multiselect\n ? _l(\"Choose datasets:\")\n : _l(\"Choose a dataset:\"));\n\n var modal,\n list,\n buttons,\n promise = jQuery.Deferred(),\n filterFn = options.filter || _filterDatasetJSON;\n\n // filter the given datasets and if none left return a rejected promise for use with fail()\n datasetJSON = filterFn(datasetJSON, options.where, options.datasetsOnly);\n if (!datasetJSON.length) {\n return promise.reject(\"No matches found\");\n }\n\n // resolve the returned promise with the json of the selected datasets\n function resolveWithSelected() {\n promise.resolve(\n list.getSelectedModels().map(function(model) {\n return model.toJSON();\n })\n );\n }\n // if multiselect - add a button for the user to complete the changes\n if (options.multiselect) {\n buttons = {};\n buttons[_l(\"Ok\")] = resolveWithSelected;\n }\n\n // create a full-height modal that's cancellable, remove unneeded elements and styles\n modal = new MODAL.View({\n height: \"auto\",\n buttons: buttons,\n closing_events: true,\n closing_callback: function() {\n promise.resolve(null);\n },\n body: [''].join(\"\")\n });\n modal.$(\".modal-header\").remove();\n modal.$(\".modal-footer\").css(\"margin-top\", \"0px\");\n\n // attach a dataset list (of the filtered datasets) to that modal that's selectable\n list = new DATASET_LIST.DatasetList({\n title: options.title,\n subtitle:\n options.subtitle ||\n _l(\n [\n //TODO: as option\n \"Click the checkboxes on the right to select datasets. \",\n \"Click the datasets names to see their details. \"\n ].join(\"\")\n ),\n el: modal.$body.find(\".list-panel\"),\n selecting: true,\n selected: options.selected,\n collection: new DATASET.DatasetAssociationCollection(datasetJSON)\n });\n\n // when the list is rendered, show the modal (also add a specifying class for css)\n list.once(\"rendered:initial\", function() {\n modal.show();\n modal.$el.addClass(\"dataset-choice-modal\");\n });\n if (!options.multiselect) {\n // if single select, remove the all/none list actions from the panel\n list.on(\"rendered\", function() {\n list.$(\".list-actions\").hide();\n });\n // if single select, immediately resolve on a single selection\n list.on(\"view:selected\", function(view) {\n promise.resolve([view.model.toJSON()]);\n });\n }\n list.render(0);\n\n // return the promise, and on any resolution close the modal\n return promise.always(function() {\n modal.hide();\n });\n};\n\n// ============================================================================\n/** Activator for single dataset selection modal and display of the selected dataset.\n * The activator/display will show as a single div and, when a dataset is selected,\n * show the name and details of the selected dataset.\n *\n * When clicked the div will generate a DatasetChoiceModal of the available choices.\n *\n * Options:\n * datasetJSON: array of plain json objects representing allowed choices\n * datasetsOnly: T: only show datasets in the allowed choices, F: datasets + collections\n * where: map of attributes to filter datasetJSON by (e.g. { file_ext: 'bed' })\n * label: the label/prompt displayed\n * selected: array of dataset ids that will show as already selected in the control\n *\n * @example:\n * var choice1 = new DATASET_CHOICE.DatasetChoice({\n * datasetJSON : datasetJSON,\n * label : 'Input dataset',\n * selected : [ 'df7a1f0c02a5b08e' ]\n * });\n * $( 'body' ).append( choice1.render().$el )\n *\n * Listen to the DatasetChoice to react to changes in the user's choice/selection:\n * @example:\n * choice1.on( 'selected', function( chooser, selectionJSONArray ){\n * // ... do stuff with new selections\n * });\n */\nvar DatasetChoice = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({\n _logNamespace: logNamespace,\n\n className: \"dataset-choice\",\n\n /** set up defaults, options, and listeners */\n initialize: function(attributes) {\n this.debug(this + \"(DatasetChoice).initialize:\", attributes);\n\n this.label = attributes.label !== undefined ? _l(attributes.label) : \"\";\n this.where = attributes.where;\n this.datasetsOnly =\n attributes.datasetsOnly !== undefined\n ? attributes.datasetsOnly\n : true;\n\n this.datasetJSON = attributes.datasetJSON || [];\n this.selected = attributes.selected || [];\n\n this._setUpListeners();\n },\n\n /** add any (bbone) listeners */\n _setUpListeners: function() {\n //this.on( 'all', function(){\n // this.log( this + '', arguments );\n //});\n },\n\n /** render the view */\n render: function() {\n var json = this.toJSON();\n this.$el.html(this._template(json));\n this.$(\".selected\").replaceWith(this._renderSelected(json));\n return this;\n },\n\n /** return plain html for the overall control */\n _template: function(json) {\n return _.template(\n [\n \"\"\n ].join(\"\")\n )(json);\n },\n\n /** return jQ DOM for the selected dataset (only one) */\n _renderSelected: function(json) {\n if (json.selected.length) {\n //TODO: break out?\n return $(\n _.template(\n [\n ' ',\n '<%- selected.hid %>: <%- selected.name %>',\n '',\n \"<%- selected.misc_blurb %>\",\n \"\",\n _l(\"format\") + \": \",\n \"<%- selected.file_ext %>\",\n \"<%- selected.misc_info %>\",\n \"\",\n \"\"\n ].join(\"\"),\n { variable: \"selected\" }\n )(json.selected[0])\n );\n }\n return $(\n [\n '(',\n _l(\"click to select a dataset\"),\n \")\"\n ].join(\"\")\n );\n },\n\n //TODO:?? why not just pass in view?\n /** return a plain JSON object with both the view and dataset attributes */\n toJSON: function() {\n var chooser = this;\n return {\n label: chooser.label,\n datasets: chooser.datasetJSON,\n selected: _.compact(\n _.map(chooser.selected, function(id) {\n return _.findWhere(chooser.datasetJSON, {\n id: id\n });\n })\n )\n };\n },\n\n /** event map: when to open the modal */\n events: {\n // the whole thing functions as a button\n click: \"chooseWithModal\"\n },\n\n //TODO:?? modal to prop of this?\n //TODO:?? should be able to handle 'none selectable' on initialize\n /** open the modal and handle the promise representing the user's choice\n * @fires 'selected' when the user selects dataset(s) - passed full json of the selected datasets\n * @fires 'cancelled' when the user clicks away/closes the modal (no selection made) - passed this\n * @fires 'error' if the modal has no selectable datasets based on this.where - passed this and other args\n */\n chooseWithModal: function() {\n var chooser = this;\n\n return this._createModal()\n .done(function(json) {\n if (json) {\n chooser.selected = _.pluck(json, \"id\");\n chooser.trigger(\"selected\", chooser, json);\n chooser.render();\n } else {\n chooser.trigger(\"cancelled\", chooser);\n }\n })\n .fail(function() {\n chooser.trigger(\"error\", chooser, arguments);\n });\n },\n\n /** create and return the modal to use for choosing */\n _createModal: function() {\n return new DatasetChoiceModal(\n this.datasetJSON,\n this._getModalOptions()\n );\n },\n\n /** return a plain JSON containing the options to pass to the modal */\n _getModalOptions: function() {\n return {\n title: this.label,\n multiselect: false,\n selected: this.selected,\n where: this.where,\n datasetsOnly: this.datasetsOnly\n };\n },\n\n // ------------------------------------------------------------------------ misc\n /** string rep */\n toString: function() {\n return \"DatasetChoice(\" + this.selected + \")\";\n }\n});\n\n// ============================================================================\n/** Activator for multiple dataset selection modal and display of the selected datasets.\n * The activator/display will show as a table of all choices.\n *\n * See DatasetChoice (above) for example usage.\n *\n * Additional options:\n * showHeaders: T: show headers for selected dataset attributes in the display table\n * cells: map of attribute keys -> Human readable/localized column headers\n * (e.g. { file_ext: _l( 'Format' ) }) - defaults are listed below\n */\nvar MultiDatasetChoice = DatasetChoice.extend({\n className: DatasetChoice.prototype.className + \" multi\",\n\n /** default (dataset attribute key -> table header text) map of what cells to display in the table */\n cells: {\n hid: _l(\"History #\"),\n name: _l(\"Name\"),\n misc_blurb: _l(\"Summary\"),\n file_ext: _l(\"Format\"),\n genome_build: _l(\"Genome\"),\n tags: _l(\"Tags\"),\n annotation: _l(\"Annotation\")\n },\n\n /** in this override, add the showHeaders and cells options */\n initialize: function(attributes) {\n this.showHeaders =\n attributes.showHeaders !== undefined\n ? attributes.showHeaders\n : true;\n this.cells = attributes.cells || this.cells;\n DatasetChoice.prototype.initialize.call(this, attributes);\n },\n\n /** in this override, display the selected datasets as a table with optional headers */\n _renderSelected: function(json) {\n if (json.selected.length) {\n return $(\n _.template(\n [\n '',\n \"<% if( json.showHeaders ){ %>\",\n \"
\"\n ].join(\"\"),\n { variable: \"json\" }\n )(json)\n );\n }\n return $(\n [\n '(',\n _l(\"click to select a dataset\"),\n \")\"\n ].join(\"\")\n );\n },\n\n /** in this override, send the showHeaders and cells options as well */\n toJSON: function() {\n return _.extend(DatasetChoice.prototype.toJSON.call(this), {\n showHeaders: this.showHeaders,\n cells: this.cells\n });\n },\n\n /** in this override, set multiselect to true */\n _getModalOptions: function() {\n return _.extend(DatasetChoice.prototype._getModalOptions.call(this), {\n multiselect: true\n });\n },\n\n // ------------------------------------------------------------------------ misc\n /** string rep */\n toString: function() {\n return \"DatasetChoice(\" + this.selected + \")\";\n }\n});\n\n// ============================================================================\nexport default {\n DatasetChoiceModal: DatasetChoiceModal,\n DatasetChoice: DatasetChoice,\n MultiDatasetChoice: MultiDatasetChoice\n};\n"]} \ No 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Dataset edit attributes view */\nimport Utils from \"utils/utils\";\nimport Tabs from \"mvc/ui/ui-tabs\";\nimport Ui from \"mvc/ui/ui-misc\";\nimport Form from \"mvc/form/form-view\";\nvar View = Backbone.View.extend({\n initialize: function() {\n this.setElement(\"\");\n this.model = new Backbone.Model({\n dataset_id: Galaxy.params.dataset_id\n });\n this.message = new Ui.Message({ persistent: true });\n this.tabs = this._createTabs();\n this.$el\n .append($(\"\").append(\"Edit dataset attributes\"))\n .append(this.message.$el)\n .append(\"\")\n .append(this.tabs.$el)\n .hide();\n this.render();\n },\n\n /** fetch data for the selected dataset and build forms */\n render: function() {\n var self = this;\n $.ajax({\n url:\n Galaxy.root +\n \"dataset/get_edit?dataset_id=\" +\n self.model.get(\"dataset_id\"),\n success: function(response) {\n !self.initial_message && self.message.update(response);\n self.initial_message = true;\n _.each(self.forms, function(form, key) {\n form.model.set(\"inputs\", response[key + \"_inputs\"]);\n form.model.set(\n \"hide_operations\",\n response[key + \"_disable\"]\n );\n form.render();\n });\n self.$el.show();\n },\n error: function(response) {\n var err_msg =\n response.responseJSON && response.responseJSON.err_msg;\n self.message.update({\n status: \"danger\",\n message:\n err_msg || \"Error occured while loading the dataset.\"\n });\n }\n });\n },\n\n /** submit data to backend to update attributes */\n _submit: function(operation, form) {\n var self = this;\n var data = form.data.create();\n data.dataset_id = this.model.get(\"dataset_id\");\n data.operation = operation;\n $.ajax({\n type: \"PUT\",\n url: Galaxy.root + \"dataset/set_edit\",\n data: data,\n success: function(response) {\n self.message.update(response);\n self.render();\n self._reloadHistory();\n },\n error: function(response) {\n var err_msg =\n response.responseJSON && response.responseJSON.err_msg;\n self.message.update({\n status: \"danger\",\n message:\n err_msg ||\n \"Error occured while editing the dataset attributes.\"\n });\n }\n });\n },\n\n /** create tabs for different dataset attribute categories*/\n _createTabs: function() {\n this.forms = {\n attribute: this._getAttribute(),\n conversion: this._getConversion(),\n datatype: this._getDatatype(),\n permission: this._getPermission()\n };\n var tabs = new Tabs.View();\n tabs.add({\n id: \"attribute\",\n title: \"Attributes\",\n icon: \"fa fa-bars\",\n tooltip: \"Edit dataset attributes\",\n $el: this.forms.attribute.$el\n });\n tabs.add({\n id: \"convert\",\n title: \"Convert\",\n icon: \"fa-gear\",\n tooltip: \"Convert to new format\",\n $el: this.forms.conversion.$el\n });\n tabs.add({\n id: \"datatype\",\n title: \"Datatypes\",\n icon: \"fa-database\",\n tooltip: \"Change data type\",\n $el: this.forms.datatype.$el\n });\n tabs.add({\n id: \"permissions\",\n title: \"Permissions\",\n icon: \"fa-user\",\n tooltip: \"Permissions\",\n $el: this.forms.permission.$el\n });\n return tabs;\n },\n\n /** edit main attributes form */\n _getAttribute: function() {\n var self = this;\n var form = new Form({\n title: \"Edit attributes\",\n operations: {\n submit_attributes: new Ui.ButtonIcon({\n tooltip: \"Save attributes of the dataset.\",\n icon: \"fa-floppy-o\",\n title: \"Save\",\n onclick: function() {\n self._submit(\"attributes\", form);\n }\n }),\n submit_autodetect: new Ui.ButtonIcon({\n tooltip:\n \"This will inspect the dataset and attempt to correct the values of fields if they are not accurate.\",\n icon: \"fa-undo\",\n title: \"Auto-detect\",\n onclick: function() {\n self._submit(\"autodetect\", form);\n }\n })\n }\n });\n return form;\n },\n\n /** datatype conversion form */\n _getConversion: function() {\n var self = this;\n var form = new Form({\n title: \"Convert to new format\",\n operations: {\n submit_conversion: new Ui.ButtonIcon({\n tooltip: \"Convert the datatype to a new format.\",\n title: \"Convert datatype\",\n icon: \"fa-exchange\",\n onclick: function() {\n self._submit(\"conversion\", form);\n }\n })\n }\n });\n return form;\n },\n\n /** change datatype form */\n _getDatatype: function() {\n var self = this;\n var form = new Form({\n title: \"Change datatype\",\n operations: {\n submit_datatype: new Ui.ButtonIcon({\n tooltip: \"Change the datatype to a new type.\",\n title: \"Change datatype\",\n icon: \"fa-exchange\",\n onclick: function() {\n self._submit(\"datatype\", form);\n }\n })\n }\n });\n return form;\n },\n\n /** dataset permissions form */\n _getPermission: function() {\n var self = this;\n var form = new Form({\n title: \"Manage dataset permissions\",\n operations: {\n submit_permission: new Ui.ButtonIcon({\n tooltip: \"Save permissions.\",\n title: \"Save permissions\",\n icon: \"fa-floppy-o \",\n onclick: function() {\n self._submit(\"permission\", form);\n }\n })\n }\n });\n return form;\n },\n\n /** reload Galaxy's history after updating dataset's attributes */\n _reloadHistory: 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Dataset edit attributes view */\nimport Utils from \"utils/utils\";\nimport Tabs from \"mvc/ui/ui-tabs\";\nimport Ui from \"mvc/ui/ui-misc\";\nimport Form from \"mvc/form/form-view\";\nvar View = Backbone.View.extend({\n initialize: function() {\n this.setElement(\"\");\n this.model = new Backbone.Model({\n dataset_id: Galaxy.params.dataset_id\n });\n this.message = new Ui.Message({ persistent: true });\n this.tabs = this._createTabs();\n this.$el\n .append($(\"\").append(\"Edit dataset attributes\"))\n .append(this.message.$el)\n .append(\"\")\n .append(this.tabs.$el)\n .hide();\n this.render();\n },\n\n /** fetch data for the selected dataset and build forms */\n render: function() {\n var self = this;\n $.ajax({\n url:\n Galaxy.root +\n \"dataset/get_edit?dataset_id=\" +\n self.model.get(\"dataset_id\"),\n success: function(response) {\n !self.initial_message && self.message.update(response);\n self.initial_message = true;\n _.each(self.forms, function(form, key) {\n form.model.set(\"inputs\", response[key + \"_inputs\"]);\n form.model.set(\n \"hide_operations\",\n response[key + \"_disable\"]\n );\n form.render();\n });\n self.$el.show();\n },\n error: function(response) {\n var err_msg =\n response.responseJSON && response.responseJSON.err_msg;\n self.message.update({\n status: \"danger\",\n message:\n err_msg || \"Error occured while loading the dataset.\"\n });\n }\n });\n },\n\n /** submit data to backend to update attributes */\n _submit: function(operation, form) {\n var self = this;\n var data = form.data.create();\n data.dataset_id = this.model.get(\"dataset_id\");\n data.operation = operation;\n $.ajax({\n type: \"PUT\",\n url: Galaxy.root + \"dataset/set_edit\",\n data: data,\n success: function(response) {\n self.message.update(response);\n self.render();\n self._reloadHistory();\n },\n error: function(response) {\n var err_msg =\n response.responseJSON && response.responseJSON.err_msg;\n self.message.update({\n status: \"danger\",\n message:\n err_msg ||\n \"Error occured while editing the dataset attributes.\"\n });\n }\n });\n },\n\n /** create tabs for different dataset attribute categories*/\n _createTabs: function() {\n this.forms = {\n attribute: this._getAttribute(),\n conversion: this._getConversion(),\n datatype: this._getDatatype(),\n permission: this._getPermission()\n };\n var tabs = new Tabs.View();\n tabs.add({\n id: \"attribute\",\n title: \"Attributes\",\n icon: \"fa fa-bars\",\n tooltip: \"Edit dataset attributes\",\n $el: this.forms.attribute.$el\n });\n tabs.add({\n id: \"convert\",\n title: \"Convert\",\n icon: \"fa-gear\",\n tooltip: \"Convert to new format\",\n $el: this.forms.conversion.$el\n });\n tabs.add({\n id: \"datatype\",\n title: \"Datatypes\",\n icon: \"fa-database\",\n tooltip: \"Change data type\",\n $el: this.forms.datatype.$el\n });\n tabs.add({\n id: \"permissions\",\n title: \"Permissions\",\n icon: \"fa-user\",\n tooltip: \"Permissions\",\n $el: this.forms.permission.$el\n });\n return tabs;\n },\n\n /** edit main attributes form */\n _getAttribute: function() {\n var self = this;\n var form = new Form({\n title: \"Edit attributes\",\n operations: {\n submit_attributes: new Ui.ButtonIcon({\n tooltip: \"Save attributes of the dataset.\",\n icon: \"fa-floppy-o\",\n title: \"Save\",\n onclick: function() {\n self._submit(\"attributes\", form);\n }\n }),\n submit_autodetect: new Ui.ButtonIcon({\n tooltip:\n \"This will inspect the dataset and attempt to correct the values of fields if they are not accurate.\",\n icon: \"fa-undo\",\n title: \"Auto-detect\",\n onclick: function() {\n self._submit(\"autodetect\", form);\n }\n })\n }\n });\n return form;\n },\n\n /** datatype conversion form */\n _getConversion: function() {\n var self = this;\n var form = new Form({\n title: \"Convert to new format\",\n operations: {\n submit_conversion: new Ui.ButtonIcon({\n tooltip: \"Convert the datatype to a new format.\",\n title: \"Convert datatype\",\n icon: 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Utils from \"utils/utils\";\nimport Ui from \"mvc/ui/ui-misc\";\nimport Form from \"mvc/form/form-view\";\n/** Dataset edit attributes view */\nvar View = Backbone.View.extend({\n initialize: function() {\n this.setElement(\"\");\n this.model = new Backbone.Model({\n dataset_id: Galaxy.params.dataset_id\n });\n this.render();\n },\n\n // Fetch data for the selected dataset and\n render: function() {\n var data_url =\n Galaxy.root + \"api/datasets/\" + this.model.get(\"dataset_id\"),\n self = this;\n\n Utils.get({\n url: data_url,\n success: function(dataset) {\n var job_url =\n Galaxy.root +\n \"api/jobs/\" +\n dataset.creating_job +\n \"?full=True\";\n Utils.get({\n url: job_url,\n success: function(job) {\n var job_url =\n Galaxy.root +\n \"api/jobs/\" +\n dataset.creating_job +\n \"?full=True\";\n self.render_error_page(self, dataset, job);\n },\n error: function(response) {\n var error_response = {\n status: \"error\",\n message: \"Error occured while loading the job.\",\n persistent: true,\n cls: \"errormessage\"\n };\n self.display_message(\n error_response,\n self.$(\".response-message\")\n );\n }\n });\n },\n error: function(response) {\n var error_response = {\n status: \"error\",\n message: \"Error occured while loading the dataset.\",\n persistent: true,\n cls: \"errormessage\"\n };\n self.display_message(\n error_response,\n self.$(\".response-message\")\n );\n }\n });\n },\n\n /** Render the view */\n render_error_page: function(self, dataset, job) {\n self.$el.empty().append(self._templateHeader());\n self.$el.append(\"\",\n \"<% _.map( json.cells, function( val, key ){ %>\",\n \" \",\n \"<% } %>\",\n \"\",\n \"<% _.map( json.selected, function( selected ){ %>\",\n \"<%- val %> \",\n \"<% }); %>\",\n \"\",\n \"<% _.map( json.cells, function( val, key ){ %>\",\n ' \",\n \"<% }); %>\",\n \"\",\n \"\"><%- selected[ key ] %> ',\n \"<% }) %>\",\n \"Dataset Error
\");\n self.$el.append(\n \"An error occured while running the tool \" +\n job.tool_id +\n \".
\"\n );\n self.$el.append(\n \"Tool execution generated the following messages:
\"\n );\n self.$el.append('' + job.stderr + \"
\");\n self.$el.append(\"Report This Error\");\n self.$el.append(\n \"
Usually the local Galaxy administrators regularly review errors that occur on the server. However, if you would like to provide additional information (such as what you were trying to do when the error occurred) and a contact e-mail address, we will be better able to investigate your problem and get back to you.
\"\n );\n self.$el.append(self._getBugFormTemplate(dataset, job));\n },\n\n /** Display actions messages */\n display_message: function(response, $el, doNotClear, safe) {\n if (!safe) {\n if (doNotClear) {\n $el.append(new Ui.Message(response).$el);\n } else {\n $el.empty().html(new Ui.Message(response).$el);\n }\n } else {\n if (doNotClear) {\n $el.append(new Ui.UnescapedMessage(response).$el);\n } else {\n $el.empty().html(new Ui.UnescapedMessage(response).$el);\n }\n }\n },\n\n /** Main template */\n _templateHeader: function() {\n return (\n '' +\n '' +\n \"\"\n );\n },\n\n /** Convert tab template */\n _getBugFormTemplate: function(dataset, job) {\n var self = this;\n var inputs = [\n {\n help: \"Your email address\",\n options: [],\n type: \"text\",\n name: \"email\",\n label: \"Your email\",\n value: Galaxy.user.get(\"email\")\n },\n {\n help:\n \"Any additional comments you can provide regarding what you were doing at the time of the bug.\",\n options: [],\n type: \"text\",\n area: true,\n name: \"message\",\n label: \"Message\"\n }\n ];\n\n // TODO\n if (false && response.any_public) {\n inputs.push({\n name: \"public_consent\",\n label: \"Public Disclosure Consent\",\n help:\n \"This Galaxy is configured to report to one or more error reporting backends that public to the world. 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\");\n self.$el.append(\n \"An error occured while running the tool \" +\n job.tool_id +\n \".
\"\n );\n self.$el.append(\n \"Tool execution generated the following messages:
\"\n );\n self.$el.append('' + job.stderr + \"
\");\n self.$el.append(\"Report This Error\");\n self.$el.append(\n \"
Usually the local Galaxy administrators regularly review errors that occur on the server. However, if you would like to provide additional information (such as what you were trying to do when the error occurred) and a contact e-mail address, we will be better able to investigate your problem and get back to you.
\"\n );\n self.$el.append(self._getBugFormTemplate(dataset, job));\n },\n\n /** Display actions messages */\n display_message: function(response, $el, doNotClear, safe) {\n if (!safe) {\n if (doNotClear) {\n $el.append(new Ui.Message(response).$el);\n } else {\n $el.empty().html(new Ui.Message(response).$el);\n }\n } else {\n if (doNotClear) {\n $el.append(new Ui.UnescapedMessage(response).$el);\n } else {\n $el.empty().html(new Ui.UnescapedMessage(response).$el);\n }\n }\n },\n\n /** Main template */\n _templateHeader: function() {\n return (\n '' +\n '' +\n \"\"\n );\n },\n\n /** Convert tab template */\n _getBugFormTemplate: function(dataset, job) {\n var self = this;\n var inputs = [\n {\n help: \"Your email address\",\n options: [],\n type: \"text\",\n name: \"email\",\n label: \"Your email\",\n value: Galaxy.user.get(\"email\")\n },\n {\n help:\n \"Any additional comments you can provide regarding what you were doing at the time of the bug.\",\n options: [],\n type: \"text\",\n area: true,\n name: \"message\",\n label: \"Message\"\n }\n ];\n\n // TODO\n if (false && response.any_public) {\n inputs.push({\n name: \"public_consent\",\n label: \"Public Disclosure Consent\",\n help:\n \"This Galaxy is configured to report to one or more error reporting backends that public to the world. By selecting 'yes', you acknowledge that this bug report will be made public.\",\n value: String(Boolean(false)),\n options: [],\n type: \"boolean\"\n });\n }\n\n var form = new Form({\n title: \"Error Report\",\n inputs: inputs,\n buttons: {\n save: new Ui.Button({\n icon: \"fa-bug\",\n title: \"Report\",\n cls: \"ui-button btn btn-primary\",\n floating: \"clear\",\n onclick: function() {\n var form_data = form.data.create();\n var url = Galaxy.root + \"api/jobs/\" + job.id + \"/error\";\n form_data.dataset_id = dataset.id;\n self.submit(form_data, url);\n }\n })\n }\n });\n return form.$el;\n },\n\n /** Make ajax request */\n submit: function(form_data, url) {\n var self = this;\n // Some required metadata\n $.ajax({\n type: \"POST\",\n url: url,\n data: form_data,\n success: function(response) {\n // Clear out the div\n self.$el.empty().append(self._templateHeader());\n // And display the messages.\n response.messages.forEach(function(message) {\n self.display_message(\n {\n status: message[1],\n message: message[0],\n persistent: true\n },\n self.$(\".response-message\"),\n true,\n true\n );\n });\n },\n error: function(response) {\n var error_response = {\n status: \"error\",\n message:\n \"Error occured while saving. 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STATES from \"mvc/dataset/states\";\nimport DATASET_LI from \"mvc/dataset/dataset-li\";\nimport TAGS from \"mvc/tag\";\nimport ANNOTATIONS from \"mvc/annotation\";\nimport faIconButton from \"ui/fa-icon-button\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\nvar _super = DATASET_LI.DatasetListItemView;\n/** @class Editing view for DatasetAssociation.\n */\nvar DatasetListItemEdit = _super.extend(\n /** @lends DatasetListItemEdit.prototype */ {\n /** set up: options */\n initialize: function(attributes) {\n _super.prototype.initialize.call(this, attributes);\n this.hasUser = attributes.hasUser;\n\n /** allow user purge of dataset files? */\n this.purgeAllowed = attributes.purgeAllowed || false;\n\n //TODO: move to HiddenUntilActivatedViewMixin\n /** should the tags editor be shown or hidden initially? */\n this.tagsEditorShown = attributes.tagsEditorShown || false;\n /** should the tags editor be shown or hidden initially? */\n this.annotationEditorShown =\n attributes.annotationEditorShown || false;\n },\n\n // ......................................................................... titlebar actions\n /** In this override, add the other two primary actions: edit and delete */\n _renderPrimaryActions: function() {\n var actions = _super.prototype._renderPrimaryActions.call(this);\n if (this.model.get(\"state\") === STATES.NOT_VIEWABLE) {\n return actions;\n }\n // render the display, edit attr and delete icon-buttons\n return _super.prototype._renderPrimaryActions\n .call(this)\n .concat([this._renderEditButton(), this._renderDeleteButton()]);\n },\n\n //TODO: move titleButtons into state renderers, remove state checks in the buttons\n\n /** Render icon-button to edit the attributes (format, permissions, etc.) this dataset. */\n _renderEditButton: function() {\n var self = this;\n // don't show edit while uploading, in-accessible\n // DO show if in error (ala previous history panel)\n if (\n this.model.get(\"state\") === STATES.DISCARDED ||\n !this.model.get(\"accessible\")\n ) {\n return null;\n }\n var purged = this.model.get(\"purged\"),\n deleted = this.model.get(\"deleted\"),\n editBtnData = {\n title: _l(\"Edit attributes\"),\n href:\n Galaxy.root +\n \"datasets/edit?dataset_id=\" +\n this.model.attributes.id,\n faIcon: \"fa-pencil\",\n classes: \"edit-btn\",\n onclick: function(ev) {\n if (Galaxy.router) {\n ev.preventDefault();\n Galaxy.router.push(\"datasets/edit\", {\n dataset_id: self.model.attributes.id\n });\n }\n }\n };\n // disable if purged or deleted and explain why in the tooltip\n if (deleted || purged) {\n editBtnData.disabled = true;\n if (purged) {\n editBtnData.title = _l(\n \"Cannot edit attributes of datasets removed from disk\"\n );\n } else if (deleted) {\n editBtnData.title = _l(\n \"Undelete dataset to edit attributes\"\n );\n }\n\n // disable if still uploading or new\n } else if (\n _.contains([STATES.UPLOAD, STATES.NEW], this.model.get(\"state\"))\n ) {\n editBtnData.disabled = true;\n editBtnData.title = _l(\"This dataset is not yet editable\");\n }\n return faIconButton(editBtnData);\n },\n\n /** Render icon-button to delete this hda. */\n _renderDeleteButton: function() {\n // don't show delete if...\n if (!this.model.get(\"accessible\")) {\n return null;\n }\n\n var self = this,\n deletedAlready = this.model.isDeletedOrPurged();\n return faIconButton({\n title: !deletedAlready\n ? _l(\"Delete\")\n : _l(\"Dataset is already deleted\"),\n disabled: deletedAlready,\n faIcon: \"fa-times\",\n classes: \"delete-btn\",\n onclick: function() {\n // ...bler... tooltips being left behind in DOM (hover out never called on deletion)\n self.$el.find(\".icon-btn.delete-btn\").trigger(\"mouseout\");\n self.model[\"delete\"]();\n }\n });\n },\n\n // ......................................................................... details\n /** In this override, add tags and annotations controls, make the ? dbkey a link to editing page */\n _renderDetails: function() {\n //TODO: generalize to be allow different details for each state\n var $details = _super.prototype._renderDetails.call(this),\n state = this.model.get(\"state\");\n\n if (\n !this.model.isDeletedOrPurged() &&\n _.contains([STATES.OK, STATES.FAILED_METADATA], state)\n ) {\n this._renderTags($details);\n this._renderAnnotation($details);\n this._makeDbkeyEditLink($details);\n }\n\n this._setUpBehaviors($details);\n return $details;\n },\n\n /**************************************************************************\n * Render help button to show tool help text without rerunning the tool.\n * Issue #2100\n */\n _renderToolHelpButton: function() {\n var datasetID = this.model.attributes.dataset_id;\n var jobID = this.model.attributes.creating_job;\n var self = this;\n\n var parseToolBuild = function(data) {\n var helpString =\n '';\n if (data.name && data.help) {\n helpString +=\n \"Tool help for \" + data.name + \"\";\n self.$el.find(\".details\").append($.parseHTML(helpString));\n };\n var parseToolID = function(data) {\n $.ajax({\n url: Galaxy.root + \"api/tools/\" + data.tool_id + \"/build\"\n })\n .done(function(data) {\n parseToolBuild(data);\n })\n .fail(function() {\n parseToolBuild({});\n });\n };\n if (Galaxy.user.id === null) {\n return null;\n }\n return faIconButton({\n title: _l(\"Tool Help\"),\n classes: \"icon-btn\",\n href: \"#\",\n faIcon: \"fa-question\",\n onclick: function() {\n var divString = \"thdiv-\" + datasetID;\n if (self.$el.find(\".toolhelp\").length > 0) {\n self.$el.find(\".toolhelp\").toggle();\n } else {\n $.ajax({\n url: Galaxy.root + \"api/jobs/\" + jobID\n })\n .done(function(data) {\n parseToolID(data);\n })\n .fail(function() {\n console.log(\n 'Failed at recovering job information from the Galaxy API for job id \"' +\n jobID +\n '\".'\n );\n });\n }\n }\n });\n },\n //*************************************************************************\n\n /** Add less commonly used actions in the details section based on state */\n _renderSecondaryActions: function() {\n var actions = _super.prototype._renderSecondaryActions.call(this);\n switch (this.model.get(\"state\")) {\n case STATES.UPLOAD:\n case STATES.NOT_VIEWABLE:\n return actions;\n case STATES.ERROR:\n // error button comes first\n actions.unshift(this._renderErrButton());\n return actions.concat([\n this._renderRerunButton(),\n this._renderToolHelpButton()\n ]);\n case STATES.OK:\n case STATES.FAILED_METADATA:\n return actions.concat([\n this._renderRerunButton(),\n this._renderVisualizationsButton(),\n this._renderToolHelpButton()\n ]);\n }\n return actions.concat([\n this._renderRerunButton(),\n this._renderToolHelpButton()\n ]);\n },\n\n /** Render icon-button to report an error on this dataset to the galaxy admin. */\n _renderErrButton: function() {\n var self = this;\n return faIconButton({\n title: _l(\"View or report this error\"),\n href:\n Galaxy.root +\n \"datasets/error?dataset_id=\" +\n this.model.attributes.id,\n classes: \"report-error-btn\",\n faIcon: \"fa-bug\",\n onclick: function(ev) {\n if (Galaxy.router) {\n ev.preventDefault();\n Galaxy.router.push(\"datasets/error\", {\n dataset_id: self.model.attributes.id\n });\n }\n }\n });\n },\n\n /** Render icon-button to re-run the job that created this dataset. */\n _renderRerunButton: function() {\n var creating_job = this.model.get(\"creating_job\");\n if (this.model.get(\"rerunnable\")) {\n return faIconButton({\n title: _l(\"Run this job again\"),\n href: this.model.urls.rerun,\n classes: \"rerun-btn\",\n target: this.linkTarget,\n faIcon: \"fa-refresh\",\n onclick: function(ev) {\n if (Galaxy.router) {\n ev.preventDefault();\n Galaxy.router.push(\"/\", {\n job_id: creating_job\n });\n }\n }\n });\n }\n },\n\n /** Render an icon-button or popupmenu of links based on the applicable visualizations */\n _renderVisualizationsButton: function() {\n //TODO: someday - lazyload visualizations\n var visualizations = this.model.get(\"visualizations\");\n if (\n this.model.isDeletedOrPurged() ||\n !this.hasUser ||\n !this.model.hasData() ||\n _.isEmpty(visualizations)\n ) {\n return null;\n }\n if (!_.isObject(visualizations[0])) {\n this.warn(\"Visualizations have been switched off\");\n return null;\n }\n\n var $visualizations = $(\n this.templates.visualizations(visualizations, this)\n );\n //HACK: need to re-write those directed at galaxy_main with linkTarget\n $visualizations\n .find('[target=\"galaxy_main\"]')\n .attr(\"target\", this.linkTarget);\n // use addBack here to include the root $visualizations elem (for the case of 1 visualization)\n this._addScratchBookFn(\n $visualizations\n .find(\".visualization-link\")\n .addBack(\".visualization-link\")\n );\n return $visualizations;\n },\n\n /** add scratchbook functionality to visualization links */\n _addScratchBookFn: function($links) {\n var li = this;\n $links.click(function(ev) {\n if (Galaxy.frame && Galaxy.frame.active) {\n Galaxy.frame.add({\n title: \"Visualization\",\n url: $(this).attr(\"href\")\n });\n ev.preventDefault();\n ev.stopPropagation();\n }\n });\n },\n\n //TODO: if possible move these to readonly view - but display the owner's tags/annotation (no edit)\n /** Render the tags list/control */\n _renderTags: function($where) {\n if (!this.hasUser) {\n return;\n }\n var view = this;\n this.tagsEditor = new TAGS.TagsEditor({\n model: this.model,\n el: $where.find(\".tags-display\"),\n onshowFirstTime: function() {\n this.render();\n },\n // persist state on the hda view (and not the editor) since these are currently re-created each time\n onshow: function() {\n view.tagsEditorShown = true;\n },\n onhide: function() {\n view.tagsEditorShown = false;\n },\n $activator: faIconButton({\n title: _l(\"Edit dataset tags\"),\n classes: \"tag-btn\",\n faIcon: \"fa-tags\"\n }).appendTo($where.find(\".actions .right\"))\n });\n if (this.tagsEditorShown) {\n this.tagsEditor.toggle(true);\n }\n },\n\n /** Render the annotation display/control */\n _renderAnnotation: function($where) {\n if (!this.hasUser) {\n return;\n }\n var view = this;\n this.annotationEditor = new ANNOTATIONS.AnnotationEditor({\n model: this.model,\n el: $where.find(\".annotation-display\"),\n onshowFirstTime: function() {\n this.render();\n },\n // persist state on the hda view (and not the editor) since these are currently re-created each time\n onshow: function() {\n view.annotationEditorShown = true;\n },\n onhide: function() {\n view.annotationEditorShown = false;\n },\n $activator: faIconButton({\n title: _l(\"Edit dataset annotation\"),\n classes: \"annotate-btn\",\n faIcon: \"fa-comment\"\n }).appendTo($where.find(\".actions .right\"))\n });\n if (this.annotationEditorShown) {\n this.annotationEditor.toggle(true);\n }\n },\n\n /** If the format/dbkey/genome_build isn't set, make the display a link to the edit page */\n _makeDbkeyEditLink: function($details) {\n // make the dbkey a link to editing\n if (\n this.model.get(\"metadata_dbkey\") === \"?\" &&\n !this.model.isDeletedOrPurged()\n ) {\n var editableDbkey = $('?')\n .attr(\"href\", this.model.urls.edit)\n .attr(\"target\", \"_top\");\n $details.find(\".dbkey .value\").replaceWith(editableDbkey);\n }\n },\n\n // ......................................................................... events\n /** event map */\n events: _.extend(_.clone(_super.prototype.events), {\n \"click .undelete-link\": \"_clickUndeleteLink\",\n \"click .purge-link\": \"_clickPurgeLink\",\n\n \"click .edit-btn\": function(ev) {\n this.trigger(\"edit\", this, ev);\n },\n \"click .delete-btn\": function(ev) {\n this.trigger(\"delete\", this, ev);\n },\n \"click .rerun-btn\": function(ev) {\n this.trigger(\"rerun\", this, ev);\n },\n \"click .report-err-btn\": function(ev) {\n this.trigger(\"report-err\", this, ev);\n },\n \"click 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Are you sure?\"\n )\n )\n ) {\n this.model.purge();\n }\n return false;\n },\n\n // ......................................................................... misc\n /** string rep */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"HDAEditView(\" + modelString + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDatasetListItemEdit.prototype.templates = (function() {\n var warnings = _.extend({}, _super.prototype.templates.warnings, {\n failed_metadata: BASE_MVC.wrapTemplate(\n [\n // in this override, provide a link to the edit page\n '<% if( dataset.state === \"failed_metadata\" ){ %>',\n '\",\n \"<% } %>\"\n ],\n \"dataset\"\n ),\n\n deleted: BASE_MVC.wrapTemplate(\n [\n // in this override, provide links to undelete or purge the dataset\n \"<% if( dataset.deleted && !dataset.purged ){ %>\",\n // deleted not purged\n '
\";\n helpString += data.help;\n } else {\n helpString +=\n \"Tool help is unavailable for this dataset.
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STATES from \"mvc/dataset/states\";\nimport DATASET_LI from \"mvc/dataset/dataset-li\";\nimport TAGS from \"mvc/tag\";\nimport ANNOTATIONS from \"mvc/annotation\";\nimport faIconButton from \"ui/fa-icon-button\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\nvar _super = DATASET_LI.DatasetListItemView;\n/** @class Editing view for DatasetAssociation.\n */\nvar DatasetListItemEdit = _super.extend(\n /** @lends DatasetListItemEdit.prototype */ {\n /** set up: options */\n initialize: function(attributes) {\n _super.prototype.initialize.call(this, attributes);\n this.hasUser = attributes.hasUser;\n\n /** allow user purge of dataset files? */\n this.purgeAllowed = attributes.purgeAllowed || false;\n\n //TODO: move to HiddenUntilActivatedViewMixin\n /** should the tags editor be shown or hidden initially? */\n this.tagsEditorShown = attributes.tagsEditorShown || false;\n /** should the tags editor be shown or hidden initially? */\n this.annotationEditorShown =\n attributes.annotationEditorShown || false;\n },\n\n // ......................................................................... titlebar actions\n /** In this override, add the other two primary actions: edit and delete */\n _renderPrimaryActions: function() {\n var actions = _super.prototype._renderPrimaryActions.call(this);\n if (this.model.get(\"state\") === STATES.NOT_VIEWABLE) {\n return actions;\n }\n // render the display, edit attr and delete icon-buttons\n return _super.prototype._renderPrimaryActions\n .call(this)\n .concat([this._renderEditButton(), this._renderDeleteButton()]);\n },\n\n //TODO: move titleButtons into state renderers, remove state checks in the buttons\n\n /** Render icon-button to edit the attributes (format, permissions, etc.) this dataset. */\n _renderEditButton: function() {\n var self = this;\n // don't show edit while uploading, in-accessible\n // DO show if in error (ala previous history panel)\n if (\n this.model.get(\"state\") === STATES.DISCARDED ||\n !this.model.get(\"accessible\")\n ) {\n return null;\n }\n var purged = this.model.get(\"purged\"),\n deleted = this.model.get(\"deleted\"),\n editBtnData = {\n title: _l(\"Edit attributes\"),\n href:\n Galaxy.root +\n \"datasets/edit?dataset_id=\" +\n this.model.attributes.id,\n faIcon: \"fa-pencil\",\n classes: \"edit-btn\",\n onclick: function(ev) {\n if (Galaxy.router) {\n ev.preventDefault();\n Galaxy.router.push(\"datasets/edit\", {\n dataset_id: self.model.attributes.id\n });\n }\n }\n };\n // disable if purged or deleted and explain why in the tooltip\n if (deleted || purged) {\n editBtnData.disabled = true;\n if (purged) {\n editBtnData.title = _l(\n \"Cannot edit attributes of datasets removed from disk\"\n );\n } else if (deleted) {\n editBtnData.title = _l(\n \"Undelete dataset to edit attributes\"\n );\n }\n\n // disable if still uploading or new\n } else if (\n _.contains([STATES.UPLOAD, STATES.NEW], this.model.get(\"state\"))\n ) {\n editBtnData.disabled = true;\n editBtnData.title = _l(\"This dataset is not yet editable\");\n }\n return faIconButton(editBtnData);\n },\n\n /** Render icon-button to delete this hda. */\n _renderDeleteButton: function() {\n // don't show delete if...\n if (!this.model.get(\"accessible\")) {\n return null;\n }\n\n var self = this,\n deletedAlready = this.model.isDeletedOrPurged();\n return faIconButton({\n title: !deletedAlready\n ? _l(\"Delete\")\n : _l(\"Dataset is already deleted\"),\n disabled: deletedAlready,\n faIcon: \"fa-times\",\n classes: \"delete-btn\",\n onclick: function() {\n // ...bler... tooltips being left behind in DOM (hover out never called on deletion)\n self.$el.find(\".icon-btn.delete-btn\").trigger(\"mouseout\");\n self.model[\"delete\"]();\n }\n });\n },\n\n // ......................................................................... details\n /** In this override, add tags and annotations controls, make the ? dbkey a link to editing page */\n _renderDetails: function() {\n //TODO: generalize to be allow different details for each state\n var $details = _super.prototype._renderDetails.call(this),\n state = this.model.get(\"state\");\n\n if (\n !this.model.isDeletedOrPurged() &&\n _.contains([STATES.OK, STATES.FAILED_METADATA], state)\n ) {\n this._renderTags($details);\n this._renderAnnotation($details);\n this._makeDbkeyEditLink($details);\n }\n\n this._setUpBehaviors($details);\n return $details;\n },\n\n /**************************************************************************\n * Render help button to show tool help text without rerunning the tool.\n * Issue #2100\n */\n _renderToolHelpButton: function() {\n var datasetID = this.model.attributes.dataset_id;\n var jobID = this.model.attributes.creating_job;\n var self = this;\n\n var parseToolBuild = function(data) {\n var helpString =\n '';\n if (data.name && data.help) {\n helpString +=\n \"Tool help for \" + data.name + \"\";\n self.$el.find(\".details\").append($.parseHTML(helpString));\n };\n var parseToolID = function(data) {\n $.ajax({\n url: Galaxy.root + \"api/tools/\" + data.tool_id + \"/build\"\n })\n .done(function(data) {\n parseToolBuild(data);\n })\n .fail(function() {\n parseToolBuild({});\n });\n };\n if (Galaxy.user.id === null) {\n return null;\n }\n return faIconButton({\n title: _l(\"Tool Help\"),\n classes: \"icon-btn\",\n href: \"#\",\n faIcon: \"fa-question\",\n onclick: function() {\n var divString = \"thdiv-\" + datasetID;\n if (self.$el.find(\".toolhelp\").length > 0) {\n self.$el.find(\".toolhelp\").toggle();\n } else {\n $.ajax({\n url: Galaxy.root + \"api/jobs/\" + jobID\n })\n .done(function(data) {\n parseToolID(data);\n })\n .fail(function() {\n console.log(\n 'Failed at recovering job information from the Galaxy API for job id \"' +\n jobID +\n '\".'\n );\n });\n }\n }\n });\n },\n //*************************************************************************\n\n /** Add less commonly used actions in the details section based on state */\n _renderSecondaryActions: function() {\n var actions = _super.prototype._renderSecondaryActions.call(this);\n switch (this.model.get(\"state\")) {\n case STATES.UPLOAD:\n case STATES.NOT_VIEWABLE:\n return actions;\n case STATES.ERROR:\n // error button comes first\n actions.unshift(this._renderErrButton());\n return actions.concat([\n this._renderRerunButton(),\n this._renderToolHelpButton()\n ]);\n case STATES.OK:\n case STATES.FAILED_METADATA:\n return actions.concat([\n this._renderRerunButton(),\n this._renderVisualizationsButton(),\n this._renderToolHelpButton()\n ]);\n }\n return actions.concat([\n this._renderRerunButton(),\n this._renderToolHelpButton()\n ]);\n },\n\n /** Render icon-button to report an error on this dataset to the galaxy admin. */\n _renderErrButton: function() {\n var self = this;\n return faIconButton({\n title: _l(\"View or report this error\"),\n href:\n Galaxy.root +\n \"datasets/error?dataset_id=\" +\n this.model.attributes.id,\n classes: \"report-error-btn\",\n faIcon: \"fa-bug\",\n onclick: function(ev) {\n if (Galaxy.router) {\n ev.preventDefault();\n Galaxy.router.push(\"datasets/error\", {\n dataset_id: self.model.attributes.id\n });\n }\n }\n });\n },\n\n /** Render icon-button to re-run the job that created this dataset. */\n _renderRerunButton: function() {\n var creating_job = this.model.get(\"creating_job\");\n if (this.model.get(\"rerunnable\")) {\n return faIconButton({\n title: _l(\"Run this job again\"),\n href: this.model.urls.rerun,\n classes: \"rerun-btn\",\n target: this.linkTarget,\n faIcon: \"fa-refresh\",\n onclick: function(ev) {\n if (Galaxy.router) {\n ev.preventDefault();\n Galaxy.router.push(\"/\", {\n job_id: creating_job\n });\n }\n }\n });\n }\n },\n\n /** Render an icon-button or popupmenu of links based on the applicable visualizations */\n _renderVisualizationsButton: function() {\n //TODO: someday - lazyload visualizations\n var visualizations = this.model.get(\"visualizations\");\n if (\n this.model.isDeletedOrPurged() ||\n !this.hasUser ||\n !this.model.hasData() ||\n _.isEmpty(visualizations)\n ) {\n return null;\n }\n if (!_.isObject(visualizations[0])) {\n this.warn(\"Visualizations have been switched off\");\n return null;\n }\n\n var $visualizations = $(\n this.templates.visualizations(visualizations, this)\n );\n //HACK: need to re-write those directed at galaxy_main with linkTarget\n $visualizations\n .find('[target=\"galaxy_main\"]')\n .attr(\"target\", this.linkTarget);\n // use addBack here to include the root $visualizations elem (for the case of 1 visualization)\n this._addScratchBookFn(\n $visualizations\n .find(\".visualization-link\")\n .addBack(\".visualization-link\")\n );\n return $visualizations;\n },\n\n /** add scratchbook functionality to visualization links */\n _addScratchBookFn: function($links) {\n var li = this;\n $links.click(function(ev) {\n if (Galaxy.frame && Galaxy.frame.active) {\n Galaxy.frame.add({\n title: \"Visualization\",\n url: $(this).attr(\"href\")\n });\n ev.preventDefault();\n ev.stopPropagation();\n }\n });\n },\n\n //TODO: if possible move these to readonly view - but display the owner's tags/annotation (no edit)\n /** Render the tags list/control */\n _renderTags: function($where) {\n if (!this.hasUser) {\n return;\n }\n var view = this;\n this.tagsEditor = new TAGS.TagsEditor({\n model: this.model,\n el: $where.find(\".tags-display\"),\n onshowFirstTime: function() {\n this.render();\n },\n // persist state on the hda view (and not the editor) since these are currently re-created each time\n onshow: function() {\n view.tagsEditorShown = true;\n },\n onhide: function() {\n view.tagsEditorShown = false;\n },\n $activator: faIconButton({\n title: _l(\"Edit dataset tags\"),\n classes: \"tag-btn\",\n faIcon: \"fa-tags\"\n }).appendTo($where.find(\".actions .right\"))\n });\n if (this.tagsEditorShown) {\n this.tagsEditor.toggle(true);\n }\n },\n\n /** Render the annotation display/control */\n _renderAnnotation: function($where) {\n if (!this.hasUser) {\n return;\n }\n var view = this;\n this.annotationEditor = new ANNOTATIONS.AnnotationEditor({\n model: this.model,\n el: $where.find(\".annotation-display\"),\n onshowFirstTime: function() {\n this.render();\n },\n // persist state on the hda view (and not the editor) since these are currently re-created each time\n onshow: function() {\n view.annotationEditorShown = true;\n },\n onhide: function() {\n view.annotationEditorShown = false;\n },\n $activator: faIconButton({\n title: _l(\"Edit dataset annotation\"),\n classes: \"annotate-btn\",\n faIcon: \"fa-comment\"\n }).appendTo($where.find(\".actions .right\"))\n });\n if (this.annotationEditorShown) {\n this.annotationEditor.toggle(true);\n }\n },\n\n /** If the format/dbkey/genome_build isn't set, make the display a link to the edit page */\n _makeDbkeyEditLink: function($details) {\n // make the dbkey a link to editing\n if (\n this.model.get(\"metadata_dbkey\") === \"?\" &&\n !this.model.isDeletedOrPurged()\n ) {\n var editableDbkey = $('?')\n .attr(\"href\", this.model.urls.edit)\n .attr(\"target\", \"_top\");\n $details.find(\".dbkey .value\").replaceWith(editableDbkey);\n }\n },\n\n // ......................................................................... events\n /** event map */\n events: _.extend(_.clone(_super.prototype.events), {\n \"click .undelete-link\": \"_clickUndeleteLink\",\n \"click .purge-link\": \"_clickPurgeLink\",\n\n \"click .edit-btn\": function(ev) {\n this.trigger(\"edit\", this, ev);\n },\n \"click .delete-btn\": function(ev) {\n this.trigger(\"delete\", this, ev);\n },\n \"click .rerun-btn\": function(ev) {\n this.trigger(\"rerun\", this, ev);\n },\n \"click .report-err-btn\": function(ev) {\n this.trigger(\"report-err\", this, ev);\n },\n \"click .visualization-btn\": function(ev) {\n this.trigger(\"visualize\", this, ev);\n },\n \"click .dbkey a\": function(ev) {\n this.trigger(\"edit\", this, ev);\n }\n }),\n\n /** listener for item undelete (in the messages section) */\n _clickUndeleteLink: function(ev) {\n this.model.undelete();\n return false;\n },\n\n /** listener for item purge (in the messages section) */\n _clickPurgeLink: function(ev) {\n if (\n confirm(\n _l(\n \"This will permanently remove the data in your dataset. Are you sure?\"\n )\n )\n ) {\n this.model.purge();\n }\n return false;\n },\n\n // ......................................................................... misc\n /** string rep */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"HDAEditView(\" + modelString + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDatasetListItemEdit.prototype.templates = (function() {\n var warnings = _.extend({}, _super.prototype.templates.warnings, {\n failed_metadata: BASE_MVC.wrapTemplate(\n [\n // in this override, provide a link to the edit page\n '<% if( dataset.state === \"failed_metadata\" ){ %>',\n '\",\n \"<% } %>\"\n ],\n \"dataset\"\n ),\n\n deleted: BASE_MVC.wrapTemplate(\n [\n // in this override, provide links to undelete or purge the dataset\n \"<% if( dataset.deleted && !dataset.purged ){ %>\",\n // deleted not purged\n '
\";\n helpString += data.help;\n } else {\n helpString +=\n \"Tool help is unavailable for this dataset.
\";\n }\n helpString += \"',\n _l(\"This dataset has been deleted\"),\n '\",\n \"<% } %>\"\n ],\n \"dataset\"\n )\n });\n\n var visualizationsTemplate = BASE_MVC.wrapTemplate(\n [\n \"<% if( visualizations.length === 1 ){ %>\",\n '\"',\n ' target=\"<%- visualizations[0].target %>\" title=\"',\n _l(\"Visualize in\"),\n ' <%- visualizations[0].html %>\">',\n '',\n \"\",\n\n \"<% } else { %>\",\n '
',\n _l(\"Undelete it\"),\n \"\",\n \"<% if( view.purgeAllowed ){ %>\",\n '
',\n _l(\"Permanently remove it from disk\"),\n \"\",\n \"<% } %>\",\n \"',\n '',\n '',\n \"\",\n '\",\n \"\",\n \"<% } %>\"\n ],\n \"visualizations\"\n );\n\n return _.extend({}, _super.prototype.templates, {\n warnings: warnings,\n visualizations: visualizationsTemplate\n });\n})();\n\n//==============================================================================\nexport default {\n DatasetListItemEdit: DatasetListItemEdit\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/dataset/dataset-li.js.map b/static/maps/mvc/dataset/dataset-li.js.map index 6103987a219..f0f4977329e 100644 --- a/static/maps/mvc/dataset/dataset-li.js.map +++ b/static/maps/mvc/dataset/dataset-li.js.map @@ -1 +1 @@ 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LIST_ITEM from \"mvc/list/list-item\";\nimport STATES from \"mvc/dataset/states\";\nimport faIconButton from \"ui/fa-icon-button\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\nvar logNamespace = \"dataset\";\n/*==============================================================================\nTODO:\n straighten out state rendering and templates used\n inaccessible/STATES.NOT_VIEWABLE is a special case\n simplify button rendering\n\n==============================================================================*/\nvar _super = LIST_ITEM.ListItemView;\n/** @class Read only list view for either LDDAs, HDAs, or HDADCEs.\n * Roughly, any DatasetInstance (and not a raw Dataset).\n */\nvar DatasetListItemView = _super.extend(\n /** @lends DatasetListItemView.prototype */ {\n _logNamespace: logNamespace,\n\n className: _super.prototype.className + \" dataset\",\n //TODO:?? doesn't exactly match an hda's type_id\n id: function() {\n return [\"dataset\", this.model.get(\"id\")].join(\"-\");\n },\n\n /** Set up: instance vars, options, and event handlers */\n initialize: function(attributes) {\n if (attributes.logger) {\n this.logger = this.model.logger = attributes.logger;\n }\n this.log(this + \".initialize:\", attributes);\n _super.prototype.initialize.call(this, attributes);\n\n /** where should pages from links be displayed? (default to new tab/window) */\n this.linkTarget = attributes.linkTarget || \"_blank\";\n },\n\n /** event listeners */\n _setUpListeners: function() {\n _super.prototype._setUpListeners.call(this);\n var self = this;\n\n // re-rendering on any model changes\n return self.listenTo(self.model, {\n change: function(model) {\n // if the model moved into the ready state and is expanded without details, fetch those details now\n if (\n self.model.changedAttributes().state &&\n self.model.inReadyState() &&\n self.expanded &&\n !self.model.hasDetails()\n ) {\n // normally, will render automatically (due to fetch -> change),\n // but! setting_metadata sometimes doesn't cause any other changes besides state\n // so, not rendering causes it to seem frozen in setting_metadata state\n self.model.fetch({ silent: true }).done(function() {\n self.render();\n });\n } else {\n if (\n _.has(model.changed, \"tags\") &&\n _.keys(model.changed).length === 1\n ) {\n // If only the tags have changed, rerender specifically\n // the titlebar region. Otherwise default to the full\n // render.\n self.$(\".nametags\").html(self._renderNametags());\n } else {\n self.render();\n }\n }\n }\n });\n },\n\n // ......................................................................... expandable\n /** In this override, only get details if in the ready state, get rerunnable if in other states.\n * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n */\n _fetchModelDetails: function() {\n var view = this;\n if (view.model.inReadyState() && !view.model.hasDetails()) {\n return view.model.fetch({ silent: true });\n }\n return jQuery.when();\n },\n\n // ......................................................................... removal\n /** Remove this view's html from the DOM and remove all event listeners.\n * @param {Number or String} speed jq effect speed\n * @param {Function} callback an optional function called when removal is done (scoped to this view)\n */\n remove: function(speed, callback) {\n var view = this;\n speed = speed || this.fxSpeed;\n this.$el.fadeOut(speed, function() {\n Backbone.View.prototype.remove.call(view);\n if (callback) {\n callback.call(view);\n }\n });\n },\n\n // ......................................................................... rendering\n /* TODO:\n dataset states are the issue primarily making dataset rendering complex\n each state should have it's own way of displaying/set of details\n often with different actions that can be applied\n throw in deleted/purged/visible and things get complicated easily\n I've considered (a couple of times) - creating a view for each state\n - but recreating the view during an update...seems wrong\n */\n /** In this override, add the dataset state as a class for use with state-based CSS */\n _swapNewRender: function($newRender) {\n _super.prototype._swapNewRender.call(this, $newRender);\n if (this.model.has(\"state\")) {\n this.$el.addClass(\"state-\" + this.model.get(\"state\"));\n }\n return this.$el;\n },\n\n // ................................................................................ titlebar\n /** In this override, add the dataset display button. */\n _renderPrimaryActions: function() {\n // render just the display for read-only\n return [this._renderDisplayButton()];\n },\n\n /** Render icon-button to display dataset data */\n _renderDisplayButton: function() {\n // don't show display if not viewable or not accessible\n var state = this.model.get(\"state\");\n if (\n state === STATES.NOT_VIEWABLE ||\n state === STATES.DISCARDED ||\n !this.model.get(\"accessible\")\n ) {\n return null;\n }\n\n var displayBtnData = {\n target: this.linkTarget,\n classes: \"display-btn\"\n };\n\n // show a disabled display if the data's been purged\n if (this.model.get(\"purged\")) {\n displayBtnData.disabled = true;\n displayBtnData.title = _l(\n \"Cannot display datasets removed from disk\"\n );\n\n // disable if still uploading\n } else if (state === STATES.UPLOAD) {\n displayBtnData.disabled = true;\n displayBtnData.title = _l(\n \"This dataset must finish uploading before it can be viewed\"\n );\n\n // disable if still new\n } else if (state === STATES.NEW) {\n displayBtnData.disabled = true;\n displayBtnData.title = _l(\"This dataset is not yet viewable\");\n } else {\n displayBtnData.title = _l(\"View data\");\n\n // default link for dataset\n displayBtnData.href = this.model.urls.display;\n\n // add frame manager option onclick event\n var self = this;\n displayBtnData.onclick = function(ev) {\n if (Galaxy.frame && Galaxy.frame.active) {\n // Add dataset to frames.\n Galaxy.frame.addDataset(self.model.get(\"id\"));\n ev.preventDefault();\n }\n };\n }\n displayBtnData.faIcon = \"fa-eye\";\n return faIconButton(displayBtnData);\n },\n\n // ......................................................................... rendering details\n /** Render the enclosing div of the hda body and, if expanded, the html in the body\n * @returns {jQuery} rendered DOM\n */\n _renderDetails: function() {\n //TODO: generalize to be allow different details for each state\n\n // no access - render nothing but a message\n if (this.model.get(\"state\") === STATES.NOT_VIEWABLE) {\n return $(this.templates.noAccess(this.model.toJSON(), this));\n }\n\n var $details = _super.prototype._renderDetails.call(this);\n $details\n .find(\".actions .left\")\n .empty()\n .append(this._renderSecondaryActions());\n $details\n .find(\".summary\")\n .html(this._renderSummary())\n .prepend(this._renderDetailMessages());\n $details\n .find(\".display-applications\")\n .html(this._renderDisplayApplications());\n\n this._setUpBehaviors($details);\n return $details;\n },\n\n /** Defer to the appropo summary rendering fn based on state */\n _renderSummary: function() {\n var json = this.model.toJSON(),\n summaryRenderFn = this.templates.summaries[json.state];\n summaryRenderFn =\n summaryRenderFn || this.templates.summaries.unknown;\n return summaryRenderFn(json, this);\n },\n\n /** Render messages to be displayed only when the details are shown */\n _renderDetailMessages: function() {\n var view = this,\n $warnings = $(''),\n json = view.model.toJSON();\n //TODO:! unordered (map)\n _.each(view.templates.detailMessages, function(templateFn) {\n $warnings.append($(templateFn(json, view)));\n });\n return $warnings;\n },\n\n /** Render the external display application links */\n _renderDisplayApplications: function() {\n if (this.model.isDeletedOrPurged()) {\n return \"\";\n }\n // render both old and new display apps using the same template\n return [\n this.templates.displayApplications(\n this.model.get(\"display_apps\"),\n this\n ),\n this.templates.displayApplications(\n this.model.get(\"display_types\"),\n this\n )\n ].join(\"\");\n },\n\n // ......................................................................... secondary/details actions\n /** A series of links/buttons for less commonly used actions: re-run, info, etc. */\n _renderSecondaryActions: function() {\n this.debug(\"_renderSecondaryActions\");\n switch (this.model.get(\"state\")) {\n case STATES.NOT_VIEWABLE:\n return [];\n case STATES.OK:\n case STATES.FAILED_METADATA:\n case STATES.ERROR:\n return [\n this._renderDownloadButton(),\n this._renderShowParamsButton()\n ];\n }\n return [this._renderShowParamsButton()];\n },\n\n /** Render icon-button to show the input and output (stdout/err) for the job that created this.\n * @returns {jQuery} rendered DOM\n */\n _renderShowParamsButton: function() {\n // gen. safe to show in all cases\n return faIconButton({\n title: _l(\"View details\"),\n classes: \"params-btn\",\n href: this.model.urls.show_params,\n target: this.linkTarget,\n faIcon: \"fa-info-circle\",\n onclick: function(ev) {\n if (Galaxy.frame && Galaxy.frame.active) {\n Galaxy.frame.add({\n title: \"Dataset details\",\n url: this.href\n });\n ev.preventDefault();\n ev.stopPropagation();\n }\n }\n });\n },\n\n /** Render icon-button/popupmenu to download the data (and/or the associated meta files (bai, etc.)) for this.\n * @returns {jQuery} rendered DOM\n */\n _renderDownloadButton: function() {\n // don't show anything if the data's been purged\n if (this.model.get(\"purged\") || !this.model.hasData()) {\n return null;\n }\n\n // return either: a popupmenu with links to download assoc. meta files (if there are meta files)\n // or a single download icon-button (if there are no meta files)\n if (!_.isEmpty(this.model.get(\"meta_files\"))) {\n return this._renderMetaFileDownloadButton();\n }\n\n return $(\n [\n '',\n '',\n \"\"\n ].join(\"\")\n );\n },\n\n /** Render the download button which opens a dropdown with links to download assoc. meta files (indeces, etc.) */\n _renderMetaFileDownloadButton: function() {\n var urls = this.model.urls;\n return $(\n [\n '\"\n ].join(\"\\n\")\n );\n },\n\n _renderNametags: function() {\n var tpl = _.template(\n [\n \"<% _.each(_.sortBy(_.uniq(tags), function(x) { return x }), function(tag){ %>\",\n '<% if (tag.indexOf(\"name:\") == 0){ %>',\n '<%- tag.slice(5) %>',\n \"<% } %>\",\n \"<% }); %>\"\n ].join(\"\")\n );\n return tpl({ tags: this.model.get(\"tags\") });\n },\n\n // ......................................................................... misc\n events: _.extend(_.clone(_super.prototype.events), {\n \"click .display-btn\": function(ev) {\n this.trigger(\"display\", this, ev);\n },\n \"click .params-btn\": function(ev) {\n this.trigger(\"params\", this, ev);\n },\n \"click .download-btn\": function(ev) {\n this.trigger(\"download\", this, ev);\n }\n }),\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"DatasetListItemView(\" + modelString + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDatasetListItemView.prototype.templates = (function() {\n //TODO: move to require text! plugin\n\n var warnings = _.extend({}, _super.prototype.templates.warnings, {\n failed_metadata: BASE_MVC.wrapTemplate([\n // failed metadata is rendered as a warning on an otherwise ok dataset view\n '<% if( model.state === \"failed_metadata\" ){ %>',\n '\",\n \"<% } %>\"\n ]),\n error: BASE_MVC.wrapTemplate([\n // error during index fetch - show error on dataset\n \"<% if( model.error ){ %>\",\n '\",\n \"<% } %>\"\n ]),\n purged: BASE_MVC.wrapTemplate([\n \"<% if( model.purged ){ %>\",\n '',\n _l(\"This dataset has been deleted and removed from disk\"),\n \"\",\n \"<% } %>\"\n ]),\n deleted: BASE_MVC.wrapTemplate([\n // deleted not purged\n \"<% if( model.deleted && !model.purged ){ %>\",\n '',\n _l(\"This dataset has been deleted\"),\n \"\",\n \"<% } %>\"\n ])\n\n //NOTE: hidden warning is only needed for HDAs\n });\n\n var detailsTemplate = BASE_MVC.wrapTemplate(\n [\n '',\n '',\n\n '\"\n ],\n \"dataset\"\n );\n\n var noAccessTemplate = BASE_MVC.wrapTemplate(\n [\n '',\n '',\n '',\n \"\",\n\n // do not display tags, annotation, display apps, or peek when deleted\n \"<% if( !dataset.deleted && !dataset.purged ){ %>\",\n '',\n '',\n\n '',\n\n \"<% if( dataset.peek ){ %>\",\n '<%= dataset.peek %>
',\n \"<% } %>\",\n \"<% } %>\",\n \"',\n '\"\n ],\n \"dataset\"\n );\n\n //TODO: still toooooooooooooo complex - rework\n var summaryTemplates = {};\n summaryTemplates[STATES.OK] = summaryTemplates[\n STATES.FAILED_METADATA\n ] = BASE_MVC.wrapTemplate(\n [\n \"<% if( dataset.misc_blurb ){ %>\",\n '',\n _l(\"You do not have permission to view this dataset\"),\n \"\",\n \"',\n '<%- dataset.misc_blurb %>',\n \"\",\n \"<% } %>\",\n\n \"<% if( dataset.file_ext ){ %>\",\n '',\n '\",\n '<%- dataset.file_ext %>',\n \"\",\n \"<% } %>\",\n\n \"<% if( dataset.metadata_dbkey ){ %>\",\n '',\n '\",\n '',\n \"<%- dataset.metadata_dbkey %>\",\n \"\",\n \"\",\n \"<% } %>\",\n\n \"<% if( dataset.misc_info ){ %>\",\n '',\n '<%- dataset.misc_info %>',\n \"\",\n \"<% } %>\"\n ],\n \"dataset\"\n );\n summaryTemplates[STATES.NEW] = BASE_MVC.wrapTemplate(\n [\n \"\",\n _l(\n \"This is a new dataset and not all of its data are available yet\"\n ),\n \"\"\n ],\n \"dataset\"\n );\n summaryTemplates[STATES.NOT_VIEWABLE] = BASE_MVC.wrapTemplate(\n [\n \"\",\n _l(\"You do not have permission to view this dataset\"),\n \"\"\n ],\n \"dataset\"\n );\n summaryTemplates[STATES.DISCARDED] = BASE_MVC.wrapTemplate(\n [\n \"\",\n _l(\"The job creating this dataset was cancelled before completion\"),\n \"\"\n ],\n \"dataset\"\n );\n summaryTemplates[STATES.QUEUED] = BASE_MVC.wrapTemplate(\n [\"\", _l(\"This job is waiting to run\"), \"\"],\n \"dataset\"\n );\n summaryTemplates[STATES.RUNNING] = BASE_MVC.wrapTemplate(\n [\"\", _l(\"This job is currently running\"), \"\"],\n \"dataset\"\n );\n summaryTemplates[STATES.UPLOAD] = BASE_MVC.wrapTemplate(\n [\"\", _l(\"This dataset is currently uploading\"), \"\"],\n \"dataset\"\n );\n summaryTemplates[STATES.SETTING_METADATA] = BASE_MVC.wrapTemplate(\n [\"\", _l(\"Metadata is being auto-detected\"), \"\"],\n \"dataset\"\n );\n summaryTemplates[STATES.PAUSED] = BASE_MVC.wrapTemplate(\n [\n \"\",\n _l(\n 'This job is paused. Use the \"Resume Paused Jobs\" in the history menu to resume'\n ),\n \"\"\n ],\n \"dataset\"\n );\n summaryTemplates[STATES.ERROR] = BASE_MVC.wrapTemplate(\n [\n \"<% if( !dataset.purged ){ %>\",\n \"<%- dataset.misc_blurb %>\",\n \"<% } %>\",\n '',\n _l(\"An error occurred with this dataset\"),\n \":\",\n '<%- dataset.misc_info %>'\n ],\n \"dataset\"\n );\n summaryTemplates[STATES.EMPTY] = BASE_MVC.wrapTemplate(\n [\"\", _l(\"No data\"), \": <%- dataset.misc_blurb %>\"],\n \"dataset\"\n );\n summaryTemplates.unknown = BASE_MVC.wrapTemplate(\n ['Error: unknown dataset state: \"<%- dataset.state %>\"'],\n \"dataset\"\n );\n\n // messages to be displayed only within the details section ('below the fold')\n var detailMessageTemplates = {\n resubmitted: BASE_MVC.wrapTemplate([\n // deleted not purged\n \"<% if( model.resubmitted ){ %>\",\n '',\n _l(\"The job creating this dataset has been resubmitted\"),\n \"\",\n \"<% } %>\"\n ])\n };\n\n // this is applied to both old and new style display apps\n var displayApplicationsTemplate = BASE_MVC.wrapTemplate(\n [\n \"<% _.each( apps, function( app ){ %>\",\n '',\n '<%- app.label %> ',\n '',\n \"<% _.each( app.links, function( link ){ %>\",\n '\" href=\"<%- link.href %>\">',\n \"<% print( _l( link.text ) ); %>\",\n \" \",\n \"<% }); %>\",\n \"\",\n \"\",\n \"<% }); %>\"\n ],\n \"apps\"\n );\n\n return _.extend({}, _super.prototype.templates, {\n warnings: warnings,\n details: detailsTemplate,\n noAccess: noAccessTemplate,\n summaries: summaryTemplates,\n detailMessages: detailMessageTemplates,\n displayApplications: displayApplicationsTemplate\n });\n})();\n\n// ============================================================================\nexport default {\n DatasetListItemView: DatasetListItemView\n};\n"]} \ No newline at end of file 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LIST_ITEM from \"mvc/list/list-item\";\nimport STATES from \"mvc/dataset/states\";\nimport faIconButton from \"ui/fa-icon-button\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\nvar logNamespace = \"dataset\";\n/*==============================================================================\nTODO:\n straighten out state rendering and templates used\n inaccessible/STATES.NOT_VIEWABLE is a special case\n simplify button rendering\n\n==============================================================================*/\nvar _super = LIST_ITEM.ListItemView;\n/** @class Read only list view for either LDDAs, HDAs, or HDADCEs.\n * Roughly, any DatasetInstance (and not a raw Dataset).\n */\nvar DatasetListItemView = _super.extend(\n /** @lends DatasetListItemView.prototype */ {\n _logNamespace: logNamespace,\n\n className: _super.prototype.className + \" dataset\",\n //TODO:?? doesn't exactly match an hda's type_id\n id: function() {\n return [\"dataset\", this.model.get(\"id\")].join(\"-\");\n },\n\n /** Set up: instance vars, options, and event handlers */\n initialize: function(attributes) {\n if (attributes.logger) {\n this.logger = this.model.logger = attributes.logger;\n }\n this.log(this + \".initialize:\", attributes);\n _super.prototype.initialize.call(this, attributes);\n\n /** where should pages from links be displayed? (default to new tab/window) */\n this.linkTarget = attributes.linkTarget || \"_blank\";\n },\n\n /** event listeners */\n _setUpListeners: function() {\n _super.prototype._setUpListeners.call(this);\n var self = this;\n\n // re-rendering on any model changes\n return self.listenTo(self.model, {\n change: function(model) {\n // if the model moved into the ready state and is expanded without details, fetch those details now\n if (\n self.model.changedAttributes().state &&\n self.model.inReadyState() &&\n self.expanded &&\n !self.model.hasDetails()\n ) {\n // normally, will render automatically (due to fetch -> change),\n // but! setting_metadata sometimes doesn't cause any other changes besides state\n // so, not rendering causes it to seem frozen in setting_metadata state\n self.model.fetch({ silent: true }).done(function() {\n self.render();\n });\n } else {\n if (\n _.has(model.changed, \"tags\") &&\n _.keys(model.changed).length === 1\n ) {\n // If only the tags have changed, rerender specifically\n // the titlebar region. Otherwise default to the full\n // render.\n self.$(\".nametags\").html(self._renderNametags());\n } else {\n self.render();\n }\n }\n }\n });\n },\n\n // ......................................................................... expandable\n /** In this override, only get details if in the ready state, get rerunnable if in other states.\n * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n */\n _fetchModelDetails: function() {\n var view = this;\n if (view.model.inReadyState() && !view.model.hasDetails()) {\n return view.model.fetch({ silent: true });\n }\n return jQuery.when();\n },\n\n // ......................................................................... removal\n /** Remove this view's html from the DOM and remove all event listeners.\n * @param {Number or String} speed jq effect speed\n * @param {Function} callback an optional function called when removal is done (scoped to this view)\n */\n remove: function(speed, callback) {\n var view = this;\n speed = speed || this.fxSpeed;\n this.$el.fadeOut(speed, function() {\n Backbone.View.prototype.remove.call(view);\n if (callback) {\n callback.call(view);\n }\n });\n },\n\n // ......................................................................... rendering\n /* TODO:\n dataset states are the issue primarily making dataset rendering complex\n each state should have it's own way of displaying/set of details\n often with different actions that can be applied\n throw in deleted/purged/visible and things get complicated easily\n I've considered (a couple of times) - creating a view for each state\n - but recreating the view during an update...seems wrong\n */\n /** In this override, add the dataset state as a class for use with state-based CSS */\n _swapNewRender: function($newRender) {\n _super.prototype._swapNewRender.call(this, $newRender);\n if (this.model.has(\"state\")) {\n this.$el.addClass(\"state-\" + this.model.get(\"state\"));\n }\n return this.$el;\n },\n\n // ................................................................................ titlebar\n /** In this override, add the dataset display button. */\n _renderPrimaryActions: function() {\n // render just the display for read-only\n return [this._renderDisplayButton()];\n },\n\n /** Render icon-button to display dataset data */\n _renderDisplayButton: function() {\n // don't show display if not viewable or not accessible\n var state = this.model.get(\"state\");\n if (\n state === STATES.NOT_VIEWABLE ||\n state === STATES.DISCARDED ||\n !this.model.get(\"accessible\")\n ) {\n return null;\n }\n\n var displayBtnData = {\n target: this.linkTarget,\n classes: \"display-btn\"\n };\n\n // show a disabled display if the data's been purged\n if (this.model.get(\"purged\")) {\n displayBtnData.disabled = true;\n displayBtnData.title = _l(\n \"Cannot display datasets removed from disk\"\n );\n\n // disable if still uploading\n } else if (state === STATES.UPLOAD) {\n displayBtnData.disabled = true;\n displayBtnData.title = _l(\n \"This dataset must finish uploading before it can be viewed\"\n );\n\n // disable if still new\n } else if (state === STATES.NEW) {\n displayBtnData.disabled = true;\n displayBtnData.title = _l(\"This dataset is not yet viewable\");\n } else {\n displayBtnData.title = _l(\"View data\");\n\n // default link for dataset\n displayBtnData.href = this.model.urls.display;\n\n // add frame manager option onclick event\n var self = this;\n displayBtnData.onclick = function(ev) {\n if (Galaxy.frame && Galaxy.frame.active) {\n // Add dataset to frames.\n Galaxy.frame.addDataset(self.model.get(\"id\"));\n ev.preventDefault();\n }\n };\n }\n displayBtnData.faIcon = \"fa-eye\";\n return faIconButton(displayBtnData);\n },\n\n // ......................................................................... rendering details\n /** Render the enclosing div of the hda body and, if expanded, the html in the body\n * @returns {jQuery} rendered DOM\n */\n _renderDetails: function() {\n //TODO: generalize to be allow different details for each state\n\n // no access - render nothing but a message\n if (this.model.get(\"state\") === STATES.NOT_VIEWABLE) {\n return $(this.templates.noAccess(this.model.toJSON(), this));\n }\n\n var $details = _super.prototype._renderDetails.call(this);\n $details\n .find(\".actions .left\")\n .empty()\n .append(this._renderSecondaryActions());\n $details\n .find(\".summary\")\n .html(this._renderSummary())\n .prepend(this._renderDetailMessages());\n $details\n .find(\".display-applications\")\n .html(this._renderDisplayApplications());\n\n this._setUpBehaviors($details);\n return $details;\n },\n\n /** Defer to the appropo summary rendering fn based on state */\n _renderSummary: function() {\n var json = this.model.toJSON(),\n summaryRenderFn = this.templates.summaries[json.state];\n summaryRenderFn =\n summaryRenderFn || this.templates.summaries.unknown;\n return summaryRenderFn(json, this);\n },\n\n /** Render messages to be displayed only when the details are shown */\n _renderDetailMessages: function() {\n var view = this,\n $warnings = $(''),\n json = view.model.toJSON();\n //TODO:! unordered (map)\n _.each(view.templates.detailMessages, function(templateFn) {\n $warnings.append($(templateFn(json, view)));\n });\n return $warnings;\n },\n\n /** Render the external display application links */\n _renderDisplayApplications: function() {\n if (this.model.isDeletedOrPurged()) {\n return \"\";\n }\n // render both old and new display apps using the same template\n return [\n this.templates.displayApplications(\n this.model.get(\"display_apps\"),\n this\n ),\n this.templates.displayApplications(\n this.model.get(\"display_types\"),\n this\n )\n ].join(\"\");\n },\n\n // ......................................................................... secondary/details actions\n /** A series of links/buttons for less commonly used actions: re-run, info, etc. */\n _renderSecondaryActions: function() {\n this.debug(\"_renderSecondaryActions\");\n switch (this.model.get(\"state\")) {\n case STATES.NOT_VIEWABLE:\n return [];\n case STATES.OK:\n case STATES.FAILED_METADATA:\n case STATES.ERROR:\n return [\n this._renderDownloadButton(),\n this._renderShowParamsButton()\n ];\n }\n return [this._renderShowParamsButton()];\n },\n\n /** Render icon-button to show the input and output (stdout/err) for the job that created this.\n * @returns {jQuery} rendered DOM\n */\n _renderShowParamsButton: function() {\n // gen. safe to show in all cases\n return faIconButton({\n title: _l(\"View details\"),\n classes: \"params-btn\",\n href: this.model.urls.show_params,\n target: this.linkTarget,\n faIcon: \"fa-info-circle\",\n onclick: function(ev) {\n if (Galaxy.frame && Galaxy.frame.active) {\n Galaxy.frame.add({\n title: \"Dataset details\",\n url: this.href\n });\n ev.preventDefault();\n ev.stopPropagation();\n }\n }\n });\n },\n\n /** Render icon-button/popupmenu to download the data (and/or the associated meta files (bai, etc.)) for this.\n * @returns {jQuery} rendered DOM\n */\n _renderDownloadButton: function() {\n // don't show anything if the data's been purged\n if (this.model.get(\"purged\") || !this.model.hasData()) {\n return null;\n }\n\n // return either: a popupmenu with links to download assoc. meta files (if there are meta files)\n // or a single download icon-button (if there are no meta files)\n if (!_.isEmpty(this.model.get(\"meta_files\"))) {\n return this._renderMetaFileDownloadButton();\n }\n\n return $(\n [\n '',\n '',\n \"\"\n ].join(\"\")\n );\n },\n\n /** Render the download button which opens a dropdown with links to download assoc. meta files (indeces, etc.) */\n _renderMetaFileDownloadButton: function() {\n var urls = this.model.urls;\n return $(\n [\n '\"\n ].join(\"\\n\")\n );\n },\n\n _renderNametags: function() {\n var tpl = _.template(\n [\n \"<% _.each(_.sortBy(_.uniq(tags), function(x) { return x }), function(tag){ %>\",\n '<% if (tag.indexOf(\"name:\") == 0){ %>',\n '<%- tag.slice(5) %>',\n \"<% } %>\",\n \"<% }); %>\"\n ].join(\"\")\n );\n return tpl({ tags: this.model.get(\"tags\") });\n },\n\n // ......................................................................... misc\n events: _.extend(_.clone(_super.prototype.events), {\n \"click .display-btn\": function(ev) {\n this.trigger(\"display\", this, ev);\n },\n \"click .params-btn\": function(ev) {\n this.trigger(\"params\", this, ev);\n },\n \"click .download-btn\": function(ev) {\n this.trigger(\"download\", this, ev);\n }\n }),\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"DatasetListItemView(\" + modelString + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDatasetListItemView.prototype.templates = (function() {\n //TODO: move to require text! plugin\n\n var warnings = _.extend({}, _super.prototype.templates.warnings, {\n failed_metadata: BASE_MVC.wrapTemplate([\n // failed metadata is rendered as a warning on an otherwise ok dataset view\n '<% if( model.state === \"failed_metadata\" ){ %>',\n '\",\n \"<% } %>\"\n ]),\n error: BASE_MVC.wrapTemplate([\n // error during index fetch - show error on dataset\n \"<% if( model.error ){ %>\",\n '\",\n \"<% } %>\"\n ]),\n purged: BASE_MVC.wrapTemplate([\n \"<% if( model.purged ){ %>\",\n '',\n _l(\"This dataset has been deleted and removed from disk\"),\n \"\",\n \"<% } %>\"\n ]),\n deleted: BASE_MVC.wrapTemplate([\n // deleted not purged\n \"<% if( model.deleted && !model.purged ){ %>\",\n '',\n _l(\"This dataset has been deleted\"),\n \"\",\n \"<% } %>\"\n ])\n\n //NOTE: hidden warning is only needed for HDAs\n });\n\n var detailsTemplate = BASE_MVC.wrapTemplate(\n [\n '',\n '',\n\n '\"\n ],\n \"dataset\"\n );\n\n var noAccessTemplate = BASE_MVC.wrapTemplate(\n [\n '',\n '',\n '',\n \"\",\n\n // do not display tags, annotation, display apps, or peek when deleted\n \"<% if( !dataset.deleted && !dataset.purged ){ %>\",\n '',\n '',\n\n '',\n\n \"<% if( dataset.peek ){ %>\",\n '<%= dataset.peek %>
',\n \"<% } %>\",\n \"<% } %>\",\n \"',\n '\"\n ],\n \"dataset\"\n );\n\n //TODO: still toooooooooooooo complex - rework\n var summaryTemplates = {};\n summaryTemplates[STATES.OK] = summaryTemplates[\n STATES.FAILED_METADATA\n ] = BASE_MVC.wrapTemplate(\n [\n \"<% if( dataset.misc_blurb ){ %>\",\n '',\n _l(\"You do not have permission to view this dataset\"),\n \"\",\n \"',\n '<%- dataset.misc_blurb %>',\n \"\",\n \"<% } %>\",\n\n \"<% if( dataset.file_ext ){ %>\",\n '',\n '\",\n '<%- dataset.file_ext %>',\n \"\",\n \"<% } %>\",\n\n \"<% if( dataset.metadata_dbkey ){ %>\",\n '',\n '\",\n '',\n \"<%- dataset.metadata_dbkey %>\",\n \"\",\n \"\",\n \"<% } %>\",\n\n \"<% if( dataset.misc_info ){ %>\",\n '',\n '<%- dataset.misc_info %>',\n \"\",\n \"<% } %>\"\n ],\n \"dataset\"\n );\n summaryTemplates[STATES.NEW] = BASE_MVC.wrapTemplate(\n [\n \"\",\n _l(\n \"This is a new dataset and not all of its data are available yet\"\n ),\n \"\"\n ],\n \"dataset\"\n );\n summaryTemplates[STATES.NOT_VIEWABLE] = BASE_MVC.wrapTemplate(\n [\n \"\",\n _l(\"You do not have permission to view this dataset\"),\n \"\"\n ],\n \"dataset\"\n );\n summaryTemplates[STATES.DISCARDED] = BASE_MVC.wrapTemplate(\n [\n \"\",\n _l(\"The job creating this dataset was cancelled before completion\"),\n \"\"\n ],\n \"dataset\"\n );\n summaryTemplates[STATES.QUEUED] = BASE_MVC.wrapTemplate(\n [\"\", _l(\"This job is waiting to run\"), \"\"],\n \"dataset\"\n );\n summaryTemplates[STATES.RUNNING] = BASE_MVC.wrapTemplate(\n [\"\", _l(\"This job is currently running\"), \"\"],\n \"dataset\"\n );\n summaryTemplates[STATES.UPLOAD] = BASE_MVC.wrapTemplate(\n [\"\", _l(\"This dataset is currently uploading\"), \"\"],\n \"dataset\"\n );\n summaryTemplates[STATES.SETTING_METADATA] = BASE_MVC.wrapTemplate(\n [\"\", _l(\"Metadata is being auto-detected\"), \"\"],\n \"dataset\"\n );\n summaryTemplates[STATES.PAUSED] = BASE_MVC.wrapTemplate(\n [\n \"\",\n _l(\n 'This job is paused. Use the \"Resume Paused Jobs\" in the history menu to resume'\n ),\n \"\"\n ],\n \"dataset\"\n );\n summaryTemplates[STATES.ERROR] = BASE_MVC.wrapTemplate(\n [\n \"<% if( !dataset.purged ){ %>\",\n \"<%- dataset.misc_blurb %>\",\n \"<% } %>\",\n '',\n _l(\"An error occurred with this dataset\"),\n \":\",\n '<%- dataset.misc_info %>'\n ],\n \"dataset\"\n );\n summaryTemplates[STATES.EMPTY] = BASE_MVC.wrapTemplate(\n [\"\", _l(\"No data\"), \": <%- dataset.misc_blurb %>\"],\n \"dataset\"\n );\n summaryTemplates.unknown = BASE_MVC.wrapTemplate(\n ['Error: unknown dataset state: \"<%- dataset.state %>\"'],\n \"dataset\"\n );\n\n // messages to be displayed only within the details section ('below the fold')\n var detailMessageTemplates = {\n resubmitted: BASE_MVC.wrapTemplate([\n // deleted not purged\n \"<% if( model.resubmitted ){ %>\",\n '',\n _l(\"The job creating this dataset has been resubmitted\"),\n \"\",\n \"<% } %>\"\n ])\n };\n\n // this is applied to both old and new style display apps\n var displayApplicationsTemplate = BASE_MVC.wrapTemplate(\n [\n \"<% _.each( apps, function( app ){ %>\",\n '',\n '<%- app.label %> ',\n '',\n \"<% _.each( app.links, function( link ){ %>\",\n '\" href=\"<%- link.href %>\">',\n \"<% print( _l( link.text ) ); %>\",\n \" \",\n \"<% }); %>\",\n \"\",\n \"\",\n \"<% }); %>\"\n ],\n \"apps\"\n );\n\n return _.extend({}, _super.prototype.templates, {\n warnings: warnings,\n details: detailsTemplate,\n noAccess: noAccessTemplate,\n summaries: summaryTemplates,\n detailMessages: detailMessageTemplates,\n displayApplications: displayApplicationsTemplate\n });\n})();\n\n// ============================================================================\nexport default {\n DatasetListItemView: DatasetListItemView\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/dataset/dataset-list.js.map b/static/maps/mvc/dataset/dataset-list.js.map index 9f813cd7a9e..dbb4234769f 100644 --- a/static/maps/mvc/dataset/dataset-list.js.map +++ b/static/maps/mvc/dataset/dataset-list.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/dataset/dataset-list.js"],"names":["_listView","require","_datasetLi","_baseMvc","_localization","logNamespace","_super","_listView2","default","ListPanel","DatasetList","extend","_logNamespace","viewClass","_datasetLi2","DatasetListItemView","className","prototype","noneFoundMsg","_localization2","initialize","attributes","this","toString","collection"],"mappings":"4IAAA,IAAAA,UAAAC,QAAA,mEACAC,WAAAD,QAAA,yEACAE,SAAAF,QAAA,2DACAG,cAAAH,QAAA,2EAEII,aAAe,UAJnBC,OAAAC,WAAAC,QAAAC,UAYIC,YAAcJ,OAAOK,QAEjBC,cAAeP,aAZvBQ,UAAAC,YAAAN,QAAAO,oBAgBQC,UAAWV,OAAOW,UAAUD,UAAY,gBAGxCE,cAAc,EAAAC,eAAAX,SAAG,8BAMjBY,WAAY,SAASC,GAlBzBf,OAASW,UAAAG,WAAUX,KAAvBa,KAAAD,IAIIE,SAAA,WACIX,MAAeP,eADiBiB,KAAAE,WAAA,wBAQhCN,YAAAA","file":"../../../scripts/mvc/dataset/dataset-list.js","sourcesContent":["import LIST_VIEW from \"mvc/list/list-view\";\nimport DATASET_LI from \"mvc/dataset/dataset-li\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\nvar logNamespace = \"dataset\";\n/* =============================================================================\nTODO:\n\n============================================================================= */\nvar _super = LIST_VIEW.ListPanel;\n/** @class non-editable, read-only View/Controller for a list of datasets.\n */\nvar DatasetList = _super.extend(\n /** @lends DatasetList.prototype */ {\n _logNamespace: logNamespace,\n\n /** class to use for constructing the sub-views */\n viewClass: DATASET_LI.DatasetListItemView,\n className: _super.prototype.className + \" dataset-list\",\n\n /** string to no hdas match the search terms */\n noneFoundMsg: _l(\"No matching datasets found\"),\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events\n * @param {Object} attributes optional settings for the panel\n */\n initialize: function(attributes) {\n _super.prototype.initialize.call(this, attributes);\n },\n\n /** Return a string rep of the history */\n toString: function() {\n return \"DatasetList(\" + this.collection + \")\";\n }\n }\n);\n\n//==============================================================================\nexport default {\n DatasetList: DatasetList\n};\n"]} \ No newline at end of file +{"version":3,"sources":["mvc/dataset/dataset-list.js"],"names":["_super","_listView2","default","ListPanel","DatasetList","extend","_logNamespace","viewClass","_datasetLi2","DatasetListItemView","className","prototype","noneFoundMsg","_localization2","initialize","attributes","call","this","toString"],"mappings":"0QAUIA,EAASC,EAAAC,QAAUC,UAGnBC,EAAcJ,EAAOK,QAEjBC,cAVW,UAaXC,UAAWC,EAAAN,QAAWO,oBACtBC,UAAWV,EAAOW,UAAUD,UAAY,gBAbhDE,cAAA,EAAAC,EAAAX,SAAA,8BAsBQY,WAAY,SAASC,GAfzBX,EAAAA,UAAqBC,WAAPW,KAAAC,KAAAF,IAIVG,SAAA,WACAX,MAAW,eAAAU,KAAWR,WAAAA,kBAOtBL,YAAAA","file":"../../../scripts/mvc/dataset/dataset-list.js","sourcesContent":["import LIST_VIEW from \"mvc/list/list-view\";\nimport DATASET_LI from \"mvc/dataset/dataset-li\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\nvar logNamespace = \"dataset\";\n/* =============================================================================\nTODO:\n\n============================================================================= */\nvar _super = LIST_VIEW.ListPanel;\n/** @class non-editable, read-only View/Controller for a list of datasets.\n */\nvar DatasetList = _super.extend(\n /** @lends DatasetList.prototype */ {\n _logNamespace: logNamespace,\n\n /** class to use for constructing the sub-views */\n viewClass: DATASET_LI.DatasetListItemView,\n className: _super.prototype.className + \" dataset-list\",\n\n /** string to no hdas match the search terms */\n noneFoundMsg: _l(\"No matching datasets found\"),\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events\n * @param {Object} attributes optional settings for the panel\n */\n initialize: function(attributes) {\n _super.prototype.initialize.call(this, attributes);\n },\n\n /** Return a string rep of the history */\n toString: function() {\n return \"DatasetList(\" + this.collection + \")\";\n }\n }\n);\n\n//==============================================================================\nexport default {\n DatasetList: DatasetList\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/dataset/dataset-model.js.map b/static/maps/mvc/dataset/dataset-model.js.map index decbea0998e..01be6b16638 100644 --- a/static/maps/mvc/dataset/dataset-model.js.map +++ b/static/maps/mvc/dataset/dataset-model.js.map @@ -1 +1 @@ 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STATES from \"mvc/dataset/states\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\nvar logNamespace = \"dataset\";\n//==============================================================================\nvar searchableMixin = BASE_MVC.SearchableModelMixin;\n/** @class base model for any DatasetAssociation (HDAs, LDDAs, DatasetCollectionDAs).\n * No knowledge of what type (HDA/LDDA/DCDA) should be needed here.\n * The DA's are made searchable (by attribute) by mixing in SearchableModelMixin.\n */\nvar DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(\n BASE_MVC.mixin(\n searchableMixin,\n /** @lends DatasetAssociation.prototype */ {\n _logNamespace: logNamespace,\n\n /** default attributes for a model */\n defaults: {\n state: STATES.NEW,\n deleted: false,\n purged: false,\n name: \"(unnamed dataset)\",\n accessible: true,\n // sniffed datatype (sam, tabular, bed, etc.)\n data_type: \"\",\n file_ext: \"\",\n file_size: 0,\n\n // array of associated file types (eg. [ 'bam_index', ... ])\n meta_files: [],\n\n misc_blurb: \"\",\n misc_info: \"\",\n\n tags: []\n // do NOT default on annotation, as this default is valid and will be passed on 'save'\n // which is incorrect behavior when the model is only partially fetched (annos are not passed in summary data)\n //annotation : ''\n },\n\n /** instance vars and listeners */\n initialize: function(attributes, options) {\n this.debug(this + \"(Dataset).initialize\", attributes, options);\n\n //!! this state is not in trans.app.model.Dataset.states - set it here -\n if (!this.get(\"accessible\")) {\n this.set(\"state\", STATES.NOT_VIEWABLE);\n }\n\n /** Datasets rely/use some web controllers - have the model generate those URLs on startup */\n this.urls = this._generateUrls();\n\n this._setUpListeners();\n },\n\n /** returns misc. web urls for rendering things like re-run, display, etc. */\n _generateUrls: function() {\n var id = this.get(\"id\");\n if (!id) {\n return {};\n }\n var urls = {\n purge: \"datasets/\" + id + \"/purge_async\",\n display: \"datasets/\" + id + \"/display/?preview=True\",\n edit: \"datasets/edit?dataset_id=\" + id,\n download:\n \"datasets/\" +\n id +\n \"/display\" +\n this._downloadQueryParameters(),\n report_error: \"dataset/errors?id=\" + id,\n rerun: \"tool_runner/rerun?id=\" + id,\n show_params: \"datasets/\" + id + \"/show_params\",\n visualization: \"visualization\",\n meta_download:\n \"dataset/get_metadata_file?hda_id=\" +\n id +\n \"&metadata_name=\"\n };\n _.each(urls, function(value, key) {\n urls[key] = Galaxy.root + value;\n });\n this.urls = urls;\n return urls;\n },\n\n _downloadQueryParameters: function() {\n return \"?to_ext=\" + this.get(\"file_ext\");\n },\n\n /** set up any event listeners\n * event: state:ready fired when this DA moves into/is already in a ready state\n */\n _setUpListeners: function() {\n // if the state has changed and the new state is a ready state, fire an event\n this.on(\"change:state\", function(currModel, newState) {\n this.log(this + \" has changed state:\", currModel, newState);\n if (this.inReadyState()) {\n this.trigger(\n \"state:ready\",\n currModel,\n newState,\n this.previous(\"state\")\n );\n }\n });\n // the download url (currently) relies on having a correct file extension\n this.on(\"change:id change:file_ext\", function(currModel) {\n this._generateUrls();\n });\n },\n\n // ........................................................................ common queries\n /** override to add urls */\n toJSON: function() {\n var json = Backbone.Model.prototype.toJSON.call(this);\n //console.warn( 'returning json?' );\n //return json;\n return _.extend(json, {\n urls: this.urls\n });\n },\n\n /** Is this dataset deleted or purged? */\n isDeletedOrPurged: function() {\n return this.get(\"deleted\") || this.get(\"purged\");\n },\n\n /** Is this dataset in a 'ready' state; where 'Ready' states are states where no\n * processing (for the ds) is left to do on the server.\n */\n inReadyState: function() {\n var ready = _.contains(STATES.READY_STATES, this.get(\"state\"));\n return this.isDeletedOrPurged() || ready;\n },\n\n /** Does this model already contain detailed data (as opposed to just summary level data)? */\n hasDetails: function() {\n // if it's inaccessible assume it has everything it needs\n if (!this.get(\"accessible\")) {\n return true;\n }\n return this.has(\"annotation\");\n },\n\n /** Convenience function to match dataset.has_data. */\n hasData: function() {\n return this.get(\"file_size\") > 0;\n },\n\n // ........................................................................ ajax\n fetch: function(options) {\n var dataset = this;\n return Backbone.Model.prototype.fetch\n .call(this, options)\n .always(function() {\n dataset._generateUrls();\n });\n },\n\n /** override to use actual Dates objects for create/update times */\n parse: function(response, options) {\n var parsed = Backbone.Model.prototype.parse.call(\n this,\n response,\n options\n );\n if (parsed.create_time) {\n parsed.create_time = new Date(parsed.create_time);\n }\n if (parsed.update_time) {\n parsed.update_time = new Date(parsed.update_time);\n }\n return parsed;\n },\n\n /** override to wait by default */\n save: function(attrs, options) {\n options = options || {};\n options.wait = _.isUndefined(options.wait)\n ? true\n : options.wait;\n return Backbone.Model.prototype.save.call(this, attrs, options);\n },\n\n //NOTE: subclasses of DA's will need to implement url and urlRoot in order to have these work properly\n /** save this dataset, _Mark_ing it as deleted (just a flag) */\n delete: function(options) {\n if (this.get(\"deleted\")) {\n return jQuery.when();\n }\n return this.save({ deleted: true }, options);\n },\n /** save this dataset, _Mark_ing it as undeleted */\n undelete: function(options) {\n if (!this.get(\"deleted\") || this.get(\"purged\")) {\n return jQuery.when();\n }\n return this.save({ deleted: false }, options);\n },\n\n /** remove the file behind this dataset from the filesystem (if permitted) */\n purge: function _purge(options) {\n //TODO: use, override model.destroy, HDA.delete({ purge: true })\n if (this.get(\"purged\")) {\n return jQuery.when();\n }\n options = options || {};\n options.url = this.urls.purge;\n\n //TODO: ideally this would be a DELETE call to the api\n // using purge async for now\n var hda = this,\n xhr = jQuery.ajax(options);\n xhr.done(function(message, status, responseObj) {\n hda.set({ deleted: true, purged: true });\n });\n xhr.fail(function(xhr, status, message) {\n // Exception messages are hidden within error page including: '...not allowed in this Galaxy instance.'\n // unbury and re-add to xhr\n var error = _l(\"Unable to purge dataset\");\n var messageBuriedInUnfortunatelyFormattedError =\n \"Removal of datasets by users \" +\n \"is not allowed in this Galaxy instance\";\n if (xhr.responseJSON && xhr.responseJSON.error) {\n error = xhr.responseJSON.error;\n } else if (\n xhr.responseText.indexOf(\n messageBuriedInUnfortunatelyFormattedError\n ) !== -1\n ) {\n error = messageBuriedInUnfortunatelyFormattedError;\n }\n xhr.responseText = error;\n hda.trigger(\"error\", hda, xhr, options, _l(error), {\n error: error\n });\n });\n return xhr;\n },\n\n // ........................................................................ searching\n /** what attributes of an HDA will be used in a text search */\n searchAttributes: [\n \"name\",\n \"file_ext\",\n \"genome_build\",\n \"misc_blurb\",\n \"misc_info\",\n \"annotation\",\n \"tags\"\n ],\n\n /** our attr keys don't often match the labels we display to the user - so, when using\n * attribute specifiers ('name=\"bler\"') in a term, allow passing in aliases for the\n * following attr keys.\n */\n searchAliases: {\n title: \"name\",\n format: \"file_ext\",\n database: \"genome_build\",\n blurb: \"misc_blurb\",\n description: \"misc_blurb\",\n info: \"misc_info\",\n tag: \"tags\"\n },\n\n // ........................................................................ misc\n /** String representation */\n toString: function() {\n var nameAndId = this.get(\"id\") || \"\";\n if (this.get(\"name\")) {\n nameAndId = '\"' + this.get(\"name\") + '\",' + nameAndId;\n }\n return \"Dataset(\" + nameAndId + \")\";\n }\n }\n )\n);\n\n//==============================================================================\n/** @class Backbone collection for dataset associations.\n */\nvar DatasetAssociationCollection = Backbone.Collection\n .extend(BASE_MVC.LoggableMixin)\n .extend(\n /** @lends HistoryContents.prototype */ {\n _logNamespace: logNamespace,\n\n model: DatasetAssociation,\n\n /** root api url */\n urlRoot: Galaxy.root + \"api/datasets\",\n\n /** url fn */\n url: function() {\n return this.urlRoot;\n },\n\n // ........................................................................ common queries\n /** Get the ids of every item in this collection\n * @returns array of encoded ids\n */\n ids: function() {\n return this.map(function(item) {\n return item.get(\"id\");\n });\n },\n\n /** Get contents that are not ready\n * @returns array of content models\n */\n notReady: function() {\n return this.filter(function(content) {\n return !content.inReadyState();\n });\n },\n\n /** return true if any datasets don't have details */\n haveDetails: function() {\n return this.all(function(dataset) {\n return dataset.hasDetails();\n });\n },\n\n // ........................................................................ ajax\n /** using a queue, perform ajaxFn on each of the models in this collection */\n ajaxQueue: function(ajaxFn, options) {\n var deferred = jQuery.Deferred(),\n startingLength = this.length,\n responses = [];\n\n if (!startingLength) {\n deferred.resolve([]);\n return deferred;\n }\n\n // use reverse order (stylistic choice)\n var ajaxFns = this.chain()\n .reverse()\n .map(function(dataset, i) {\n return function() {\n var xhr = ajaxFn.call(dataset, options);\n // if successful, notify using the deferred to allow tracking progress\n xhr.done(function(response) {\n deferred.notify({\n curr: i,\n total: startingLength,\n response: response,\n model: dataset\n });\n });\n // (regardless of previous error or success) if not last ajax call, shift and call the next\n // if last fn, resolve deferred\n xhr.always(function(response) {\n responses.push(response);\n if (ajaxFns.length) {\n ajaxFns.shift()();\n } else {\n deferred.resolve(responses);\n }\n });\n };\n })\n .value();\n // start the queue\n ajaxFns.shift()();\n\n return deferred;\n },\n\n // ........................................................................ sorting/filtering\n /** return a new collection of datasets whose attributes contain the substring matchesWhat */\n matches: function(matchesWhat) {\n return this.filter(function(dataset) {\n return dataset.matches(matchesWhat);\n });\n },\n\n /** String representation. */\n toString: function() {\n return 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STATES from \"mvc/dataset/states\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\nvar logNamespace = \"dataset\";\n//==============================================================================\nvar searchableMixin = BASE_MVC.SearchableModelMixin;\n/** @class base model for any DatasetAssociation (HDAs, LDDAs, DatasetCollectionDAs).\n * No knowledge of what type (HDA/LDDA/DCDA) should be needed here.\n * The DA's are made searchable (by attribute) by mixing in SearchableModelMixin.\n */\nvar DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(\n BASE_MVC.mixin(\n searchableMixin,\n /** @lends DatasetAssociation.prototype */ {\n _logNamespace: logNamespace,\n\n /** default attributes for a model */\n defaults: {\n state: STATES.NEW,\n deleted: false,\n purged: false,\n name: \"(unnamed dataset)\",\n accessible: true,\n // sniffed datatype (sam, tabular, bed, etc.)\n data_type: \"\",\n file_ext: \"\",\n file_size: 0,\n\n // array of associated file types (eg. [ 'bam_index', ... ])\n meta_files: [],\n\n misc_blurb: \"\",\n misc_info: \"\",\n\n tags: []\n // do NOT default on annotation, as this default is valid and will be passed on 'save'\n // which is incorrect behavior when the model is only partially fetched (annos are not passed in summary data)\n //annotation : ''\n },\n\n /** instance vars and listeners */\n initialize: function(attributes, options) {\n this.debug(this + \"(Dataset).initialize\", attributes, options);\n\n //!! this state is not in trans.app.model.Dataset.states - set it here -\n if (!this.get(\"accessible\")) {\n this.set(\"state\", STATES.NOT_VIEWABLE);\n }\n\n /** Datasets rely/use some web controllers - have the model generate those URLs on startup */\n this.urls = this._generateUrls();\n\n this._setUpListeners();\n },\n\n /** returns misc. web urls for rendering things like re-run, display, etc. */\n _generateUrls: function() {\n var id = this.get(\"id\");\n if (!id) {\n return {};\n }\n var urls = {\n purge: \"datasets/\" + id + \"/purge_async\",\n display: \"datasets/\" + id + \"/display/?preview=True\",\n edit: \"datasets/edit?dataset_id=\" + id,\n download:\n \"datasets/\" +\n id +\n \"/display\" +\n this._downloadQueryParameters(),\n report_error: \"dataset/errors?id=\" + id,\n rerun: \"tool_runner/rerun?id=\" + id,\n show_params: \"datasets/\" + id + \"/show_params\",\n visualization: \"visualization\",\n meta_download:\n \"dataset/get_metadata_file?hda_id=\" +\n id +\n \"&metadata_name=\"\n };\n _.each(urls, function(value, key) {\n urls[key] = Galaxy.root + value;\n });\n this.urls = urls;\n return urls;\n },\n\n _downloadQueryParameters: function() {\n return \"?to_ext=\" + this.get(\"file_ext\");\n },\n\n /** set up any event listeners\n * event: state:ready fired when this DA moves into/is already in a ready state\n */\n _setUpListeners: function() {\n // if the state has changed and the new state is a ready state, fire an event\n this.on(\"change:state\", function(currModel, newState) {\n this.log(this + \" has changed state:\", currModel, newState);\n if (this.inReadyState()) {\n this.trigger(\n \"state:ready\",\n currModel,\n newState,\n this.previous(\"state\")\n );\n }\n });\n // the download url (currently) relies on having a correct file extension\n this.on(\"change:id change:file_ext\", function(currModel) {\n this._generateUrls();\n });\n },\n\n // ........................................................................ common queries\n /** override to add urls */\n toJSON: function() {\n var json = Backbone.Model.prototype.toJSON.call(this);\n //console.warn( 'returning json?' );\n //return json;\n return _.extend(json, {\n urls: this.urls\n });\n },\n\n /** Is this dataset deleted or purged? */\n isDeletedOrPurged: function() {\n return this.get(\"deleted\") || this.get(\"purged\");\n },\n\n /** Is this dataset in a 'ready' state; where 'Ready' states are states where no\n * processing (for the ds) is left to do on the server.\n */\n inReadyState: function() {\n var ready = _.contains(STATES.READY_STATES, this.get(\"state\"));\n return this.isDeletedOrPurged() || ready;\n },\n\n /** Does this model already contain detailed data (as opposed to just summary level data)? */\n hasDetails: function() {\n // if it's inaccessible assume it has everything it needs\n if (!this.get(\"accessible\")) {\n return true;\n }\n return this.has(\"annotation\");\n },\n\n /** Convenience function to match dataset.has_data. */\n hasData: function() {\n return this.get(\"file_size\") > 0;\n },\n\n // ........................................................................ ajax\n fetch: function(options) {\n var dataset = this;\n return Backbone.Model.prototype.fetch\n .call(this, options)\n .always(function() {\n dataset._generateUrls();\n });\n },\n\n /** override to use actual Dates objects for create/update times */\n parse: function(response, options) {\n var parsed = Backbone.Model.prototype.parse.call(\n this,\n response,\n options\n );\n if (parsed.create_time) {\n parsed.create_time = new Date(parsed.create_time);\n }\n if (parsed.update_time) {\n parsed.update_time = new Date(parsed.update_time);\n }\n return parsed;\n },\n\n /** override to wait by default */\n save: function(attrs, options) {\n options = options || {};\n options.wait = _.isUndefined(options.wait)\n ? true\n : options.wait;\n return Backbone.Model.prototype.save.call(this, attrs, options);\n },\n\n //NOTE: subclasses of DA's will need to implement url and urlRoot in order to have these work properly\n /** save this dataset, _Mark_ing it as deleted (just a flag) */\n delete: function(options) {\n if (this.get(\"deleted\")) {\n return jQuery.when();\n }\n return this.save({ deleted: true }, options);\n },\n /** save this dataset, _Mark_ing it as undeleted */\n undelete: function(options) {\n if (!this.get(\"deleted\") || this.get(\"purged\")) {\n return jQuery.when();\n }\n return this.save({ deleted: false }, options);\n },\n\n /** remove the file behind this dataset from the filesystem (if permitted) */\n purge: function _purge(options) {\n //TODO: use, override model.destroy, HDA.delete({ purge: true })\n if (this.get(\"purged\")) {\n return jQuery.when();\n }\n options = options || {};\n options.url = this.urls.purge;\n\n //TODO: ideally this would be a DELETE call to the api\n // using purge async for now\n var hda = this,\n xhr = jQuery.ajax(options);\n xhr.done(function(message, status, responseObj) {\n hda.set({ deleted: true, purged: true });\n });\n xhr.fail(function(xhr, status, message) {\n // Exception messages are hidden within error page including: '...not allowed in this Galaxy instance.'\n // unbury and re-add to xhr\n var error = _l(\"Unable to purge dataset\");\n var messageBuriedInUnfortunatelyFormattedError =\n \"Removal of datasets by users \" +\n \"is not allowed in this Galaxy instance\";\n if (xhr.responseJSON && xhr.responseJSON.error) {\n error = xhr.responseJSON.error;\n } else if (\n xhr.responseText.indexOf(\n messageBuriedInUnfortunatelyFormattedError\n ) !== -1\n ) {\n error = messageBuriedInUnfortunatelyFormattedError;\n }\n xhr.responseText = error;\n hda.trigger(\"error\", hda, xhr, options, _l(error), {\n error: error\n });\n });\n return xhr;\n },\n\n // ........................................................................ searching\n /** what attributes of an HDA will be used in a text search */\n searchAttributes: [\n \"name\",\n \"file_ext\",\n \"genome_build\",\n \"misc_blurb\",\n \"misc_info\",\n \"annotation\",\n \"tags\"\n ],\n\n /** our attr keys don't often match the labels we display to the user - so, when using\n * attribute specifiers ('name=\"bler\"') in a term, allow passing in aliases for the\n * following attr keys.\n */\n searchAliases: {\n title: \"name\",\n format: \"file_ext\",\n database: \"genome_build\",\n blurb: \"misc_blurb\",\n description: \"misc_blurb\",\n info: \"misc_info\",\n tag: \"tags\"\n },\n\n // ........................................................................ misc\n /** String representation */\n toString: function() {\n var nameAndId = this.get(\"id\") || \"\";\n if (this.get(\"name\")) {\n nameAndId = '\"' + this.get(\"name\") + '\",' + nameAndId;\n }\n return \"Dataset(\" + nameAndId + \")\";\n }\n }\n )\n);\n\n//==============================================================================\n/** @class Backbone collection for dataset associations.\n */\nvar DatasetAssociationCollection = Backbone.Collection\n .extend(BASE_MVC.LoggableMixin)\n .extend(\n /** @lends HistoryContents.prototype */ {\n _logNamespace: logNamespace,\n\n model: DatasetAssociation,\n\n /** root api url */\n urlRoot: Galaxy.root + \"api/datasets\",\n\n /** url fn */\n url: function() {\n return this.urlRoot;\n },\n\n // ........................................................................ common queries\n /** Get the ids of every item in this collection\n * @returns array of encoded ids\n */\n ids: function() {\n return this.map(function(item) {\n return item.get(\"id\");\n });\n },\n\n /** Get contents that are not ready\n * @returns array of content models\n */\n notReady: function() {\n return this.filter(function(content) {\n return !content.inReadyState();\n });\n },\n\n /** return true if any datasets don't have details */\n haveDetails: function() {\n return this.all(function(dataset) {\n return dataset.hasDetails();\n });\n },\n\n // ........................................................................ ajax\n /** using a queue, perform ajaxFn on each of the models in this collection */\n ajaxQueue: function(ajaxFn, options) {\n var deferred = jQuery.Deferred(),\n startingLength = this.length,\n responses = [];\n\n if (!startingLength) {\n deferred.resolve([]);\n return deferred;\n }\n\n // use reverse order (stylistic choice)\n var ajaxFns = this.chain()\n .reverse()\n .map(function(dataset, i) {\n return function() {\n var xhr = ajaxFn.call(dataset, options);\n // if successful, notify using the deferred to allow tracking progress\n xhr.done(function(response) {\n deferred.notify({\n curr: i,\n total: startingLength,\n response: response,\n model: dataset\n });\n });\n // (regardless of previous error or success) if not last ajax call, shift and call the next\n // if last fn, resolve deferred\n xhr.always(function(response) {\n responses.push(response);\n if (ajaxFns.length) {\n ajaxFns.shift()();\n } else {\n deferred.resolve(responses);\n }\n });\n };\n })\n .value();\n // start the queue\n ajaxFns.shift()();\n\n return deferred;\n },\n\n // ........................................................................ sorting/filtering\n /** return a new collection of datasets whose attributes contain the substring matchesWhat */\n matches: function(matchesWhat) {\n return this.filter(function(dataset) {\n return dataset.matches(matchesWhat);\n });\n },\n\n /** String representation. */\n toString: function() {\n return 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QUEUED: \"queued\",\n /** the job that will produce the dataset is running */\n RUNNING: \"running\",\n /** metadata for the dataset is being discovered/set */\n SETTING_METADATA: \"setting_metadata\",\n\n // ready states\n /** was created without a tool */\n NEW: \"new\",\n /** has no data */\n EMPTY: \"empty\",\n /** has successfully completed running */\n OK: \"ok\",\n\n /** the job that will produce the dataset paused */\n PAUSED: \"paused\",\n /** metadata discovery/setting failed or errored (but otherwise ok) */\n FAILED_METADATA: \"failed_metadata\",\n //TODO: not in trans.app.model.Dataset.states - is in database\n /** not accessible to the current user (i.e. due to permissions) */\n NOT_VIEWABLE: \"noPermission\",\n /** deleted while uploading */\n DISCARDED: \"discarded\",\n /** the tool producing this dataset failed */\n ERROR: \"error\"\n};\n\nSTATES.READY_STATES = [\n STATES.OK,\n STATES.EMPTY,\n STATES.PAUSED,\n STATES.FAILED_METADATA,\n STATES.NOT_VIEWABLE,\n 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+{"version":3,"sources":["mvc/dataset/states.js"],"names":["STATES","UPLOAD","QUEUED","RUNNING","SETTING_METADATA","OK","PAUSED","FAILED_METADATA","NOT_VIEWABLE","DISCARDED","ERROR","READY_STATES","EMPTY","NOT_READY_STATES","NEW"],"mappings":"6FAIA,IAAIA,GAHJC,OAAA,SAQIC,OAAQ,SAJRC,QAAA,UAEAF,iBAAQ,mBAIRE,IAAAA,MAEAC,MAAAA,QAEAC,GAAA,KAGAC,OAAA,SAEAC,gBAAA,kBAGAC,aAAA,eAEAC,UAAA,YAEAC,MAAA,SAGAV,EAAAW,cACAF,EAAAA,GACAT,EAAAY,MACAF,EAAAA,OA7BSV,EAAbO,gBAqCIP,EAAOQ,aALXR,EAAOW,UAOHX,EAAOU,OAWXV,EAAAa,kBAPIb,EAAOC,OACPD,EAAOE,OACPF,EAAOG,QACPH,EAAOI,iBACPJ,EAAOc,eAIId","file":"../../../scripts/mvc/dataset/states.js","sourcesContent":["//==============================================================================\n/** Map of possible HDA/collection/job states to their string equivalents.\n * A port of galaxy.model.Dataset.states.\n */\nvar STATES = {\n // NOT ready states\n /** is uploading and not ready */\n UPLOAD: \"upload\",\n /** the job that will produce the dataset queued in the runner */\n QUEUED: \"queued\",\n /** the job that will produce the dataset is running */\n RUNNING: \"running\",\n /** metadata for the dataset is being discovered/set */\n SETTING_METADATA: \"setting_metadata\",\n\n // ready states\n /** was created without a tool */\n NEW: \"new\",\n /** has no data */\n EMPTY: \"empty\",\n /** has successfully completed running */\n OK: \"ok\",\n\n /** the job that will produce the dataset paused */\n PAUSED: \"paused\",\n /** metadata discovery/setting failed or errored (but otherwise ok) */\n FAILED_METADATA: \"failed_metadata\",\n //TODO: not in trans.app.model.Dataset.states - is in database\n /** not accessible to the current user (i.e. due to permissions) */\n NOT_VIEWABLE: \"noPermission\",\n /** deleted while uploading */\n DISCARDED: \"discarded\",\n /** the tool producing this dataset failed */\n ERROR: \"error\"\n};\n\nSTATES.READY_STATES = [\n STATES.OK,\n STATES.EMPTY,\n STATES.PAUSED,\n STATES.FAILED_METADATA,\n STATES.NOT_VIEWABLE,\n 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flat_id + \"_\" + index++,\n node[block_prefix + block_indices[i]]\n );\n }\n break;\n case \"conditional\":\n var value = self.app.field_list[input.id].value();\n add(\n flat_id + \"|\" + input.test_param.name,\n input.id,\n value\n );\n var selectedCase = matchCase(input, value);\n if (selectedCase != -1) {\n convert(\n flat_id,\n head[input.id + \"-section-\" + selectedCase]\n );\n }\n break;\n case \"section\":\n convert((!input.flat && flat_id) || \"\", node);\n break;\n default:\n var field = self.app.field_list[input.id];\n if (field && field.value) {\n var value = field.value();\n if (\n input.ignore === undefined ||\n input.ignore != value\n ) {\n if (\n field.collapsed &&\n input.collapsible_value\n ) {\n value = input.collapsible_value;\n }\n add(flat_id, input.id, value);\n if (input.payload) {\n for (var p_id in input.payload) {\n add(\n p_id,\n input.id,\n input.payload[p_id]\n );\n }\n }\n }\n }\n }\n }\n }\n }\n convert(\"\", dict);\n return result_dict;\n },\n\n /** 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= i;\n if (id !== \"\") {\n var separator = \"|\";\n if (head instanceof Array) {\n separator = \"_\";\n }\n new_id = id + separator + new_id;\n }\n search(new_id, head[i]);\n }\n }\n }\n search(\"\", response);\n return result;\n },\n\n /** Map dom tree to dictionary tree with input elements.\n */\n _iterate: function(parent, dict) {\n var self = this;\n var children = $(parent).children();\n children.each(function() {\n var child = this;\n var id = $(child).attr(\"id\");\n if ($(child).hasClass(\"section-row\")) {\n var input = self.app.input_list[id];\n dict[id] = (input && { input: input }) || {};\n self._iterate(child, dict[id]);\n } else {\n self._iterate(child, dict);\n }\n });\n }\n});\n\n/** Match conditional values to selected cases\n * @param{dict} input - Definition of conditional input parameter\n * @param{dict} value - Current value\n */\nvar matchCase = function(input, value) {\n if (input.test_param.type == \"boolean\") {\n if (value == \"true\") {\n value = 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This class maps the form dom to an api compatible javascript dictionary. */\nimport Utils from \"utils/utils\";\nvar Manager = Backbone.Model.extend({\n initialize: function(app) {\n this.app = app;\n },\n\n /** Creates a checksum. */\n checksum: function() {\n var sum = \"\";\n var self = this;\n this.app.section.$el.find(\".section-row\").each(function() {\n var id = $(this).attr(\"id\");\n var field = self.app.field_list[id];\n if (field) {\n sum +=\n id +\n \":\" +\n JSON.stringify(field.value && field.value()) +\n \":\" +\n field.collapsed +\n \";\";\n }\n });\n return sum;\n },\n\n /** Convert dom into a dictionary of flat id/value pairs used e.g. on job submission. */\n create: function() {\n var self = this;\n\n // get raw dictionary from dom\n var dict = {};\n this._iterate(this.app.section.$el, dict);\n\n // add to result dictionary, label elements\n var result_dict = {};\n this.flat_dict = {};\n function add(flat_id, input_id, input_value) {\n self.flat_dict[flat_id] = input_id;\n result_dict[flat_id] = input_value;\n self.app.element_list[input_id] &&\n self.app.element_list[input_id].$el.attr(\"tour_id\", flat_id);\n }\n // converter between raw dictionary and job dictionary\n function convert(identifier, head) {\n for (var index in head) {\n var node = head[index];\n if (node.input) {\n var input = node.input;\n var flat_id = identifier;\n if (identifier != \"\") {\n flat_id += \"|\";\n }\n flat_id += input.name;\n switch (input.type) {\n case \"repeat\":\n var section_label = \"section-\";\n var block_indices = [];\n var block_prefix = null;\n for (var block_label in node) {\n var pos = block_label.indexOf(section_label);\n if (pos != -1) {\n pos += section_label.length;\n block_indices.push(\n parseInt(block_label.substr(pos))\n );\n if (!block_prefix) {\n block_prefix = block_label.substr(\n 0,\n pos\n );\n }\n }\n }\n block_indices.sort(function(a, b) {\n return a - b;\n });\n var index = 0;\n for (var i in block_indices) {\n convert(\n flat_id + \"_\" + index++,\n node[block_prefix + block_indices[i]]\n );\n }\n break;\n case \"conditional\":\n var value = self.app.field_list[input.id].value();\n add(\n flat_id + \"|\" + input.test_param.name,\n input.id,\n value\n );\n var selectedCase = matchCase(input, value);\n if (selectedCase != -1) {\n convert(\n flat_id,\n head[input.id + \"-section-\" + selectedCase]\n );\n }\n break;\n case \"section\":\n convert((!input.flat && flat_id) || \"\", node);\n break;\n default:\n var field = self.app.field_list[input.id];\n if (field && field.value) {\n var value = field.value();\n if (\n input.ignore === undefined ||\n input.ignore != value\n ) {\n if (\n field.collapsed &&\n input.collapsible_value\n ) {\n value = input.collapsible_value;\n }\n add(flat_id, input.id, value);\n if (input.payload) {\n for (var p_id in input.payload) {\n add(\n p_id,\n input.id,\n input.payload[p_id]\n );\n }\n }\n }\n }\n }\n }\n }\n }\n convert(\"\", dict);\n return result_dict;\n },\n\n /** 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= i;\n if (id !== \"\") {\n var separator = \"|\";\n if (head instanceof Array) {\n separator = \"_\";\n }\n new_id = id + separator + new_id;\n }\n search(new_id, head[i]);\n }\n }\n }\n search(\"\", response);\n return result;\n },\n\n /** Map dom tree to dictionary tree with input elements.\n */\n _iterate: function(parent, dict) {\n var self = this;\n var children = $(parent).children();\n children.each(function() {\n var child = this;\n var id = $(child).attr(\"id\");\n if ($(child).hasClass(\"section-row\")) {\n var input = self.app.input_list[id];\n dict[id] = (input && { input: input }) || {};\n self._iterate(child, dict[id]);\n } else {\n self._iterate(child, dict);\n }\n });\n }\n});\n\n/** Match conditional values to selected cases\n * @param{dict} input - Definition of conditional input parameter\n * @param{dict} value - Current value\n */\nvar matchCase = function(input, value) {\n if (input.test_param.type == \"boolean\") {\n if (value == \"true\") {\n value = input.test_param.truevalue || \"true\";\n } else {\n value = input.test_param.falsevalue || \"false\";\n }\n }\n for (var i in input.cases) {\n if (input.cases[i].value == value) {\n return i;\n }\n }\n return -1;\n};\n\n/** Visits tool inputs\n * @param{dict} inputs - Nested dictionary of input elements\n * @param{dict} callback - Called with the mapped dictionary object and corresponding model node\n */\nvar visitInputs = function(inputs, callback, prefix, context) {\n context = $.extend(true, {}, context);\n _.each(inputs, function(input) {\n if (input && input.type && input.name) {\n context[input.name] = input;\n }\n });\n for (var key in inputs) {\n var node = inputs[key];\n node.name = node.name || key;\n var name = prefix ? prefix + \"|\" + node.name : node.name;\n switch (node.type) {\n case \"repeat\":\n _.each(node.cache, function(cache, j) {\n visitInputs(cache, callback, name + \"_\" + j, context);\n });\n break;\n case \"conditional\":\n if (node.test_param) {\n 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this.$(\".ui-form-collapsible-text\");\n this.$collapsible_icon = this.$(\".ui-form-collapsible-icon\");\n this.$title = this.$(\".ui-form-title\");\n this.$title_text = this.$(\".ui-form-title-text\");\n this.$error_text = this.$(\".ui-form-error-text\");\n this.$error = this.$(\".ui-form-error\");\n this.$backdrop = this.$(\".ui-form-backdrop\");\n\n // add field element\n this.$field.prepend(this.field.$el);\n\n // decide wether to expand or collapse fields\n var collapsible_value = this.model.get(\"collapsible_value\");\n this.field.collapsed =\n collapsible_value !== undefined &&\n JSON.stringify(this.model.get(\"value\")) ==\n JSON.stringify(collapsible_value);\n this.listenTo(this.model, \"change\", this.render, this);\n this.render();\n\n // add click handler\n var self = this;\n this.$collapsible.on(\"click\", function() {\n self.field.collapsed = !self.field.collapsed;\n app.trigger && app.trigger(\"change\");\n self.render();\n });\n\n // hide error on value change\n if 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this.$(\".ui-form-collapsible-text\");\n this.$collapsible_icon = this.$(\".ui-form-collapsible-icon\");\n this.$title = this.$(\".ui-form-title\");\n this.$title_text = this.$(\".ui-form-title-text\");\n this.$error_text = this.$(\".ui-form-error-text\");\n this.$error = this.$(\".ui-form-error\");\n this.$backdrop = this.$(\".ui-form-backdrop\");\n\n // add field element\n this.$field.prepend(this.field.$el);\n\n // decide wether to expand or collapse fields\n var collapsible_value = this.model.get(\"collapsible_value\");\n this.field.collapsed =\n collapsible_value !== undefined &&\n JSON.stringify(this.model.get(\"value\")) ==\n JSON.stringify(collapsible_value);\n this.listenTo(this.model, \"change\", this.render, this);\n this.render();\n\n // add click handler\n var self = this;\n this.$collapsible.on(\"click\", function() {\n self.field.collapsed = !self.field.collapsed;\n app.trigger && app.trigger(\"change\");\n self.render();\n });\n\n // hide error on value change\n if (this.field.model && !this.model.get(\"always_refresh\")) {\n this.listenTo(this.field.model, \"change:value\", function() {\n self.reset();\n });\n }\n },\n\n /** Set backdrop for input element */\n backdrop: function() {\n this.model.set(\"backdrop\", true);\n },\n\n /** Set error text */\n error: function(text) {\n this.model.set(\"error_text\", text);\n },\n\n /** Reset this view */\n reset: function() {\n !this.model.get(\"fixed\") && this.model.set(\"error_text\", null);\n },\n\n render: function() {\n // render help\n $(\".tooltip\").hide();\n var help_text = this.model.get(\"help\", \"\");\n var help_argument = this.model.get(\"argument\");\n if (\n help_argument &&\n help_text.indexOf(\"(\" + help_argument + \")\") == -1\n ) {\n help_text += \" (\" + help_argument + \")\";\n }\n this.$info.html(help_text);\n // render visibility\n this.$el[this.model.get(\"hidden\") ? \"hide\" : \"show\"]();\n // render preview view for collapsed fields\n this.$preview\n [\n (this.field.collapsed &&\n this.model.get(\"collapsible_preview\")) ||\n this.model.get(\"disabled\")\n ? \"show\"\n : \"hide\"\n ]()\n .html(_.escape(this.model.get(\"text_value\")));\n // render error messages\n var error_text = this.model.get(\"error_text\");\n this.$error[error_text ? \"show\" : \"hide\"]();\n this.$el[error_text ? \"addClass\" : \"removeClass\"](\"ui-error\");\n this.$error_text.html(error_text);\n // render backdrop\n this.$backdrop[this.model.get(\"backdrop\") ? \"show\" : \"hide\"]();\n // render input field\n this.field.collapsed || this.model.get(\"disabled\")\n ? this.$field.hide()\n : this.$field.show();\n // render input field color and style\n this.field.model &&\n this.field.model.set({\n color: this.model.get(\"color\"),\n style: this.model.get(\"style\")\n });\n // render collapsible options\n if (\n !this.model.get(\"disabled\") &&\n this.model.get(\"collapsible_value\") !== undefined\n ) {\n var collapsible_state = this.field.collapsed ? \"enable\" : \"disable\";\n this.$title_text.hide();\n this.$collapsible.show();\n this.$collapsible_text.text(this.model.get(\"label\"));\n this.$collapsible_icon\n .removeClass()\n .addClass(\"icon\")\n .addClass(this.model.get(\"cls_\" + collapsible_state))\n .attr(\n \"data-original-title\",\n this.model.get(\"text_\" + collapsible_state)\n )\n .tooltip({ placement: \"bottom\" });\n } else {\n this.$title_text.show().text(this.model.get(\"label\"));\n this.$collapsible.hide();\n }\n },\n\n _template: function() {\n return $(\"\")\n .addClass(\"ui-form-element\")\n .append(\n $(\"\")\n .addClass(\"ui-form-error ui-error\")\n .append($(\"\").addClass(\"fa fa-arrow-down\"))\n .append($(\"\").addClass(\"ui-form-error-text\"))\n )\n .append(\n $(\"\")\n .addClass(\"ui-form-title\")\n .append(\n $(\"\")\n .addClass(\"ui-form-collapsible\")\n .append(\n $(\"\").addClass(\"ui-form-collapsible-icon\")\n )\n .append(\n $(\"\").addClass(\n \"ui-form-collapsible-text\"\n )\n )\n )\n 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This class creates input elements. New input parameter types should be added to the types dictionary.\n*/\nimport Utils from \"utils/utils\";\nimport Ui from \"mvc/ui/ui-misc\";\nimport SelectContent from \"mvc/ui/ui-select-content\";\nimport SelectLibrary from \"mvc/ui/ui-select-library\";\nimport SelectFtp from \"mvc/ui/ui-select-ftp\";\nimport SelectGenomeSpace from \"mvc/ui/ui-select-genomespace\";\nimport ColorPicker from \"mvc/ui/ui-color-picker\";\n// create form view\nexport default Backbone.Model.extend({\n /** Available parameter types */\n types: {\n text: \"_fieldText\",\n password: \"_fieldText\",\n select: \"_fieldSelect\",\n data_column: \"_fieldSelect\",\n genomebuild: \"_fieldSelect\",\n data: \"_fieldData\",\n data_collection: \"_fieldData\",\n integer: \"_fieldSlider\",\n float: \"_fieldSlider\",\n boolean: \"_fieldBoolean\",\n drill_down: \"_fieldDrilldown\",\n color: \"_fieldColor\",\n hidden: \"_fieldHidden\",\n hidden_data: \"_fieldHidden\",\n baseurl: \"_fieldHidden\",\n library_data: \"_fieldLibrary\",\n ftpfile: \"_fieldFtp\",\n upload: \"_fieldUpload\",\n genomespacefile: \"_fieldGenomeSpace\"\n },\n\n /** Returns an input field for a given field type */\n create: function(input_def) {\n var fieldClass = this.types[input_def.type];\n var field =\n typeof this[fieldClass] === \"function\"\n ? this[fieldClass].call(this, input_def)\n : null;\n if (!field) {\n field = input_def.options\n ? this._fieldSelect(input_def)\n : this._fieldText(input_def);\n Galaxy.emit.debug(\n \"form-parameters::_addRow()\",\n \"Auto matched field type (\" + input_def.type + \").\"\n );\n }\n input_def.value === undefined && (input_def.value = null);\n field.value(input_def.value);\n return field;\n },\n\n /** Data input field */\n _fieldData: function(input_def) {\n return new SelectContent.View({\n id: \"field-\" + input_def.id,\n extensions: input_def.extensions,\n optional: input_def.optional,\n multiple: input_def.multiple,\n type: input_def.type,\n flavor: input_def.flavor,\n data: input_def.options,\n onchange: input_def.onchange\n });\n },\n\n /** Select/Checkbox/Radio options field */\n _fieldSelect: function(input_def) {\n // show text field e.g. in workflow editor\n if (input_def.is_workflow) {\n return this._fieldText(input_def);\n }\n\n // customize properties\n if (input_def.type == \"data_column\") {\n input_def.error_text = \"Missing columns in referenced dataset.\";\n }\n\n // identify available options\n var data = input_def.data;\n if (!data) {\n data = [];\n _.each(input_def.options, function(option) {\n data.push({ label: option[0], value: option[1] });\n });\n }\n\n // identify display type\n var SelectClass = Ui.Select;\n switch (input_def.display) {\n case \"checkboxes\":\n SelectClass = Ui.Checkbox;\n break;\n case \"radio\":\n SelectClass = Ui.Radio;\n break;\n case \"radiobutton\":\n SelectClass = Ui.RadioButton;\n break;\n }\n\n // create select field\n return new SelectClass.View({\n id: \"field-\" + input_def.id,\n data: data,\n error_text: input_def.error_text || \"No options available\",\n readonly: input_def.readonly,\n multiple: input_def.multiple,\n optional: input_def.optional,\n onchange: input_def.onchange,\n individual: input_def.individual,\n searchable: input_def.flavor !== \"workflow\"\n });\n },\n\n /** Drill down options field */\n _fieldDrilldown: function(input_def) {\n // show text field e.g. in workflow editor\n if (input_def.is_workflow) {\n return this._fieldText(input_def);\n }\n\n // create drill down field\n return new Ui.Drilldown.View({\n id: \"field-\" + input_def.id,\n data: input_def.options,\n display: input_def.display,\n optional: input_def.optional,\n onchange: input_def.onchange\n });\n },\n\n /** Text input field */\n _fieldText: function(input_def) {\n // field replaces e.g. a select field\n if (input_def.options && input_def.data) {\n input_def.area = input_def.multiple;\n if (Utils.isEmpty(input_def.value)) {\n input_def.value = null;\n } else {\n if ($.isArray(input_def.value)) {\n var str_value = \"\";\n for (var i in input_def.value) {\n str_value += String(input_def.value[i]);\n if (!input_def.multiple) {\n break;\n }\n str_value += \"\\n\";\n }\n input_def.value = str_value;\n }\n }\n }\n // create input element\n return new Ui.Input({\n id: \"field-\" + input_def.id,\n type: input_def.type,\n area: input_def.area,\n readonly: input_def.readonly,\n placeholder: input_def.placeholder,\n datalist: input_def.datalist,\n onchange: input_def.onchange\n });\n },\n\n /** Slider field */\n _fieldSlider: function(input_def) {\n return new Ui.Slider.View({\n id: \"field-\" + input_def.id,\n precise: input_def.type == \"float\",\n is_workflow: input_def.is_workflow,\n min: input_def.min,\n max: input_def.max,\n onchange: input_def.onchange\n });\n },\n\n /** Hidden field */\n _fieldHidden: function(input_def) {\n return new Ui.Hidden({\n id: \"field-\" + input_def.id,\n info: input_def.info\n });\n },\n\n /** Boolean field */\n _fieldBoolean: function(input_def) {\n return new Ui.RadioButton.View({\n id: \"field-\" + input_def.id,\n data: [\n { label: \"Yes\", value: \"true\" },\n { label: \"No\", value: \"false\" }\n ],\n onchange: input_def.onchange\n });\n },\n\n /** Color picker field */\n _fieldColor: function(input_def) {\n return new ColorPicker({\n id: \"field-\" + input_def.id,\n onchange: input_def.onchange\n });\n },\n\n /** Library dataset field */\n _fieldLibrary: function(input_def) {\n return new SelectLibrary.View({\n id: \"field-\" + input_def.id,\n optional: input_def.optional,\n multiple: input_def.multiple,\n onchange: input_def.onchange\n });\n },\n\n /** FTP file field */\n _fieldFtp: function(input_def) {\n return new SelectFtp.View({\n id: \"field-\" + input_def.id,\n optional: input_def.optional,\n multiple: input_def.multiple,\n onchange: input_def.onchange\n });\n },\n\n /** GenomeSpace file select field\n */\n _fieldGenomeSpace: function(input_def) {\n var self = this;\n return new 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This class creates input elements. New input parameter types should be added to the types dictionary.\n*/\nimport Utils from \"utils/utils\";\nimport Ui from \"mvc/ui/ui-misc\";\nimport SelectContent from \"mvc/ui/ui-select-content\";\nimport SelectLibrary from \"mvc/ui/ui-select-library\";\nimport SelectFtp from \"mvc/ui/ui-select-ftp\";\nimport SelectGenomeSpace from \"mvc/ui/ui-select-genomespace\";\nimport ColorPicker from \"mvc/ui/ui-color-picker\";\n// create form view\nexport default Backbone.Model.extend({\n /** Available parameter types */\n types: {\n text: \"_fieldText\",\n password: \"_fieldText\",\n select: \"_fieldSelect\",\n data_column: \"_fieldSelect\",\n genomebuild: \"_fieldSelect\",\n data: \"_fieldData\",\n data_collection: \"_fieldData\",\n integer: \"_fieldSlider\",\n float: \"_fieldSlider\",\n boolean: \"_fieldBoolean\",\n drill_down: \"_fieldDrilldown\",\n color: \"_fieldColor\",\n hidden: \"_fieldHidden\",\n hidden_data: \"_fieldHidden\",\n baseurl: \"_fieldHidden\",\n library_data: \"_fieldLibrary\",\n ftpfile: \"_fieldFtp\",\n upload: \"_fieldUpload\",\n genomespacefile: \"_fieldGenomeSpace\"\n },\n\n /** Returns an input field for a given field type */\n create: function(input_def) {\n var fieldClass = this.types[input_def.type];\n var field =\n typeof this[fieldClass] === \"function\"\n ? this[fieldClass].call(this, input_def)\n : null;\n if (!field) {\n field = input_def.options\n ? this._fieldSelect(input_def)\n : this._fieldText(input_def);\n Galaxy.emit.debug(\n \"form-parameters::_addRow()\",\n \"Auto matched field type (\" + input_def.type + \").\"\n );\n }\n input_def.value === undefined && (input_def.value = null);\n field.value(input_def.value);\n return field;\n },\n\n /** Data input field */\n _fieldData: function(input_def) {\n return new SelectContent.View({\n id: \"field-\" + input_def.id,\n extensions: input_def.extensions,\n optional: input_def.optional,\n multiple: input_def.multiple,\n type: input_def.type,\n flavor: input_def.flavor,\n data: input_def.options,\n onchange: input_def.onchange\n });\n },\n\n /** Select/Checkbox/Radio options field */\n _fieldSelect: function(input_def) {\n // show text field e.g. in workflow editor\n if (input_def.is_workflow) {\n return this._fieldText(input_def);\n }\n\n // customize properties\n if (input_def.type == \"data_column\") {\n input_def.error_text = \"Missing columns in referenced dataset.\";\n }\n\n // identify available options\n var data = input_def.data;\n if (!data) {\n data = [];\n _.each(input_def.options, function(option) {\n data.push({ label: option[0], value: option[1] });\n });\n }\n\n // identify display type\n var SelectClass = Ui.Select;\n switch (input_def.display) {\n case \"checkboxes\":\n SelectClass = Ui.Checkbox;\n break;\n case \"radio\":\n SelectClass = Ui.Radio;\n break;\n case \"radiobutton\":\n SelectClass = Ui.RadioButton;\n break;\n }\n\n // create select field\n return new SelectClass.View({\n id: \"field-\" + input_def.id,\n data: data,\n error_text: input_def.error_text || \"No options available\",\n readonly: input_def.readonly,\n multiple: input_def.multiple,\n optional: input_def.optional,\n onchange: input_def.onchange,\n individual: input_def.individual,\n searchable: input_def.flavor !== \"workflow\"\n });\n },\n\n /** Drill down options field */\n _fieldDrilldown: function(input_def) {\n // show text field e.g. in workflow editor\n if (input_def.is_workflow) {\n return this._fieldText(input_def);\n }\n\n // create drill down field\n return new Ui.Drilldown.View({\n id: \"field-\" + input_def.id,\n data: input_def.options,\n display: input_def.display,\n optional: input_def.optional,\n onchange: input_def.onchange\n });\n },\n\n /** Text input field */\n _fieldText: function(input_def) {\n // field replaces e.g. a select field\n if (input_def.options && input_def.data) {\n input_def.area = input_def.multiple;\n if (Utils.isEmpty(input_def.value)) {\n input_def.value = null;\n } else {\n if ($.isArray(input_def.value)) {\n var str_value = \"\";\n for (var i in input_def.value) {\n str_value += String(input_def.value[i]);\n if (!input_def.multiple) {\n break;\n }\n str_value += \"\\n\";\n }\n input_def.value = str_value;\n }\n }\n }\n // create input element\n return new Ui.Input({\n id: \"field-\" + input_def.id,\n type: input_def.type,\n area: input_def.area,\n readonly: input_def.readonly,\n placeholder: input_def.placeholder,\n datalist: input_def.datalist,\n onchange: input_def.onchange\n });\n },\n\n /** Slider field */\n _fieldSlider: function(input_def) {\n return new Ui.Slider.View({\n id: \"field-\" + input_def.id,\n precise: input_def.type == \"float\",\n is_workflow: input_def.is_workflow,\n min: input_def.min,\n max: input_def.max,\n onchange: input_def.onchange\n });\n },\n\n /** Hidden field */\n _fieldHidden: function(input_def) {\n return new Ui.Hidden({\n id: \"field-\" + input_def.id,\n info: input_def.info\n });\n },\n\n /** Boolean field */\n _fieldBoolean: function(input_def) {\n return new Ui.RadioButton.View({\n id: \"field-\" + input_def.id,\n data: [\n { label: \"Yes\", value: \"true\" },\n { label: \"No\", value: \"false\" }\n ],\n onchange: input_def.onchange\n });\n },\n\n /** Color picker field */\n _fieldColor: function(input_def) {\n return new ColorPicker({\n id: \"field-\" + input_def.id,\n onchange: input_def.onchange\n });\n },\n\n /** Library dataset field */\n _fieldLibrary: function(input_def) {\n return new SelectLibrary.View({\n id: \"field-\" + input_def.id,\n optional: input_def.optional,\n multiple: input_def.multiple,\n onchange: input_def.onchange\n });\n },\n\n /** FTP file field */\n _fieldFtp: function(input_def) {\n return new SelectFtp.View({\n id: \"field-\" + input_def.id,\n optional: input_def.optional,\n multiple: input_def.multiple,\n onchange: input_def.onchange\n });\n },\n\n /** GenomeSpace file select field\n */\n _fieldGenomeSpace: function(input_def) {\n var self = this;\n return new 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This class creates a ui component which enables the dynamic creation of portlets */\nimport Utils from \"utils/utils\";\nimport Portlet from \"mvc/ui/ui-portlet\";\nimport Ui from \"mvc/ui/ui-misc\";\nvar View = Backbone.View.extend({\n initialize: function(options) {\n this.list = {};\n this.options = Utils.merge(options, {\n title: \"Repeat\",\n empty_text: \"Not available.\",\n max: null,\n min: null\n });\n this.button_new = new Ui.ButtonIcon({\n icon: \"fa-plus\",\n title: \"Insert \" + this.options.title,\n tooltip: \"Add new \" + this.options.title + \" block\",\n cls: \"ui-button-icon ui-clear-float form-repeat-add\",\n onclick: function() {\n options.onnew && options.onnew();\n }\n });\n this.setElement(\n $(\"\")\n .append((this.$list = $(\"\")))\n .append($(\"\").append(this.button_new.$el))\n );\n },\n\n /** Number of repeat blocks */\n size: function() {\n return _.size(this.list);\n },\n\n /** Add new repeat block */\n add: function(options) {\n if (!options.id || this.list[options.id]) {\n Galaxy.emit.debug(\n \"form-repeat::add()\",\n \"Duplicate or invalid repeat block id.\"\n );\n return;\n }\n var button_delete = new Ui.ButtonIcon({\n icon: \"fa-trash-o\",\n tooltip: \"Delete this repeat block\",\n cls: \"ui-button-icon-plain form-repeat-delete\",\n onclick: function() {\n options.ondel && options.ondel();\n }\n });\n var portlet = new Portlet.View({\n id: options.id,\n title: \"placeholder\",\n cls: options.cls || \"ui-portlet-repeat\",\n operations: { button_delete: button_delete }\n });\n portlet.append(options.$el);\n portlet.$el.addClass(\"section-row\").hide();\n this.list[options.id] = portlet;\n this.$list.append(portlet.$el.fadeIn(\"fast\"));\n this.options.max > 0 &&\n this.size() >= this.options.max &&\n this.button_new.disable();\n this._refresh();\n },\n\n /** Delete repeat block */\n del: function(id) {\n if (!this.list[id]) {\n Galaxy.emit.debug(\"form-repeat::del()\", \"Invalid repeat block id.\");\n return;\n }\n 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This class creates a ui component which enables the dynamic creation of portlets */\nimport Utils from \"utils/utils\";\nimport Portlet from \"mvc/ui/ui-portlet\";\nimport Ui from \"mvc/ui/ui-misc\";\nvar View = Backbone.View.extend({\n initialize: function(options) {\n this.list = {};\n this.options = Utils.merge(options, {\n title: \"Repeat\",\n empty_text: \"Not available.\",\n max: null,\n min: null\n });\n this.button_new = new Ui.ButtonIcon({\n icon: \"fa-plus\",\n title: \"Insert \" + this.options.title,\n tooltip: \"Add new \" + this.options.title + \" block\",\n cls: \"ui-button-icon ui-clear-float form-repeat-add\",\n onclick: function() {\n options.onnew && options.onnew();\n }\n });\n this.setElement(\n $(\"\")\n .append((this.$list = $(\"\")))\n .append($(\"\").append(this.button_new.$el))\n );\n },\n\n /** Number of repeat blocks */\n size: function() {\n return _.size(this.list);\n },\n\n /** Add new repeat block */\n add: function(options) {\n if (!options.id || this.list[options.id]) {\n Galaxy.emit.debug(\n \"form-repeat::add()\",\n \"Duplicate or invalid repeat block id.\"\n );\n return;\n }\n var button_delete = new Ui.ButtonIcon({\n icon: \"fa-trash-o\",\n tooltip: \"Delete this repeat block\",\n cls: \"ui-button-icon-plain form-repeat-delete\",\n onclick: function() {\n options.ondel && options.ondel();\n }\n });\n var portlet = new Portlet.View({\n id: options.id,\n title: \"placeholder\",\n cls: options.cls || \"ui-portlet-repeat\",\n operations: { button_delete: button_delete }\n });\n portlet.append(options.$el);\n portlet.$el.addClass(\"section-row\").hide();\n this.list[options.id] = portlet;\n this.$list.append(portlet.$el.fadeIn(\"fast\"));\n this.options.max > 0 &&\n this.size() >= this.options.max &&\n this.button_new.disable();\n this._refresh();\n },\n\n /** Delete repeat block */\n del: function(id) {\n if (!this.list[id]) {\n Galaxy.emit.debug(\"form-repeat::del()\", \"Invalid repeat block id.\");\n return;\n }\n this.$list.find(\"#\" + id).remove();\n delete this.list[id];\n this.button_new.enable();\n this._refresh();\n },\n\n /** Remove all */\n delAll: function() {\n for (var id in this.list) {\n this.del(id);\n }\n },\n\n /** Hides add/del options */\n hideOptions: function() {\n this.button_new.$el.hide();\n _.each(this.list, function(portlet) {\n portlet.hideOperation(\"button_delete\");\n });\n _.isEmpty(this.list) &&\n this.$el.append(\n $(\"\")\n .addClass(\"ui-form-info\")\n .html(this.options.empty_text)\n );\n },\n\n /** Refresh view */\n _refresh: function() {\n var index = 0;\n for (var id in this.list) {\n var portlet = this.list[id];\n portlet.title(++index + \": \" + this.options.title);\n portlet[\n this.size() > this.options.min\n ? \"showOperation\"\n : \"hideOperation\"\n ](\"button_delete\");\n }\n }\n});\n\nexport default {\n View: View\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/form/form-section.js.map b/static/maps/mvc/form/form-section.js.map 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This class creates a form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections.\n*/\nimport Utils from \"utils/utils\";\nimport Ui from \"mvc/ui/ui-misc\";\nimport Portlet from \"mvc/ui/ui-portlet\";\nimport Repeat from \"mvc/form/form-repeat\";\nimport InputElement from \"mvc/form/form-input\";\nimport Parameters from \"mvc/form/form-parameters\";\nvar View = Backbone.View.extend({\n initialize: function(app, options) {\n this.app = app;\n this.inputs = options.inputs;\n this.parameters = new Parameters();\n this.setElement($(\"\"));\n this.render();\n },\n\n /** Render section view */\n render: function() {\n var self = this;\n this.$el.empty();\n _.each(this.inputs, function(input) {\n self.add(input);\n });\n },\n\n /** Add a new input element */\n add: function(input) {\n var input_def = jQuery.extend(true, {}, input);\n input_def.id = input.id = Utils.uid();\n this.app.input_list[input_def.id] = input_def;\n switch (input_def.type) {\n case \"conditional\":\n 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section_row.fadeIn(\"fast\");\n } else {\n section_row.hide();\n }\n }\n self.app.trigger(\"change\");\n });\n\n // add conditional sub sections\n for (var i in input_def.cases) {\n var sub_section = new View(this.app, {\n inputs: input_def.cases[i].inputs\n });\n this._append(\n sub_section.$el.addClass(\"ui-form-section\"),\n input_def.id + \"-section-\" + i\n );\n }\n\n // trigger refresh on conditional input field after all input elements have been created\n field.trigger(\"change\");\n },\n\n /** Add a repeat block */\n _addRepeat: function(input_def) {\n var self = this;\n var block_index = 0;\n\n // create repeat block element\n var repeat = new Repeat.View({\n title: input_def.title || \"Repeat\",\n min: input_def.min,\n max: input_def.max,\n onnew: function() {\n create(input_def.inputs);\n self.app.trigger(\"change\");\n }\n });\n\n // helper function to create new repeat blocks\n function create(inputs) {\n var sub_section_id = input_def.id + \"-section-\" + block_index++;\n var sub_section = new View(self.app, { inputs: inputs });\n repeat.add({\n id: sub_section_id,\n $el: sub_section.$el,\n ondel: function() {\n repeat.del(sub_section_id);\n self.app.trigger(\"change\");\n }\n });\n }\n\n //\n // add parsed/minimum number of repeat blocks\n //\n var n_cache = _.size(input_def.cache);\n for (\n var i = 0;\n i <\n Math.max(\n Math.max(n_cache, input_def.min || 0),\n input_def.default || 0\n );\n i++\n ) {\n create(i < n_cache ? input_def.cache[i] : input_def.inputs);\n }\n\n // hide options\n this.app.model.get(\"sustain_repeats\") && repeat.hideOptions();\n\n // create input field wrapper\n var input_element = new InputElement(this.app, {\n label: input_def.title || input_def.name,\n help: input_def.help,\n field: repeat\n });\n this._append(input_element.$el, input_def.id);\n },\n\n /** Add a customized section */\n _addSection: function(input_def) {\n var portlet = new Portlet.View({\n title: input_def.title || input_def.name,\n cls: 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This class creates a form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections.\n*/\nimport Utils from \"utils/utils\";\nimport Ui from \"mvc/ui/ui-misc\";\nimport Portlet from \"mvc/ui/ui-portlet\";\nimport Repeat from \"mvc/form/form-repeat\";\nimport InputElement from \"mvc/form/form-input\";\nimport Parameters from \"mvc/form/form-parameters\";\nvar View = Backbone.View.extend({\n initialize: function(app, options) {\n this.app = app;\n this.inputs = options.inputs;\n this.parameters = new Parameters();\n this.setElement($(\"\"));\n this.render();\n },\n\n /** Render section view */\n render: function() {\n var self = this;\n this.$el.empty();\n _.each(this.inputs, function(input) {\n self.add(input);\n });\n },\n\n /** Add a new input element */\n add: function(input) {\n var input_def = jQuery.extend(true, {}, input);\n input_def.id = input.id = Utils.uid();\n this.app.input_list[input_def.id] = input_def;\n switch (input_def.type) {\n case \"conditional\":\n 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It is referenced as 'app' in lower level modules.\n*/\nimport Utils from \"utils/utils\";\nimport Portlet from \"mvc/ui/ui-portlet\";\nimport Ui from \"mvc/ui/ui-misc\";\nimport FormSection from \"mvc/form/form-section\";\nimport FormData from \"mvc/form/form-data\";\nexport default Backbone.View.extend({\n initialize: function(options) {\n this.model = new Backbone.Model({\n initial_errors: false,\n cls: \"ui-portlet-limited\",\n icon: null,\n always_refresh: true,\n status: \"warning\",\n hide_operations: false,\n onchange: function() {}\n }).set(options);\n this.setElement(\"\");\n this.render();\n },\n\n /** Update available options */\n update: function(new_model) {\n var self = this;\n this.data.matchModel(new_model, function(node, input_id) {\n var input = self.input_list[input_id];\n if (input && input.options) {\n if (!_.isEqual(input.options, node.options)) {\n input.options = node.options;\n var field = self.field_list[input_id];\n if (field.update) {\n var new_options = [];\n if (\n [\"data\", \"data_collection\", \"drill_down\"].indexOf(\n input.type\n ) != -1\n ) {\n new_options = input.options;\n } else {\n for (var i in node.options) {\n var opt = node.options[i];\n if (opt.length > 2) {\n new_options.push({\n label: opt[0],\n value: opt[1]\n });\n }\n }\n }\n field.update(new_options);\n field.trigger(\"change\");\n Galaxy.emit.debug(\n \"form-view::update()\",\n \"Updating options for \" + input_id\n );\n }\n }\n }\n });\n },\n\n /** Set form into wait mode */\n wait: function(active) {\n for (var i in this.input_list) {\n var field = this.field_list[i];\n var input = this.input_list[i];\n if (input.is_dynamic && field.wait && field.unwait) {\n field[active ? \"wait\" : \"unwait\"]();\n }\n }\n },\n\n /** Highlight and scroll to input element (currently only used for error notifications) */\n highlight: function(input_id, message, silent) {\n var input_element = this.element_list[input_id];\n if (input_element) {\n input_element.error(message || \"Please verify this parameter.\");\n this.portlet.expand();\n this.trigger(\"expand\", input_id);\n if (!silent) {\n var $panel = this.$el\n .parents()\n .filter(function() {\n return (\n [\"auto\", \"scroll\"].indexOf(\n $(this).css(\"overflow\")\n ) != -1\n );\n })\n .first();\n $panel.animate(\n {\n scrollTop:\n $panel.scrollTop() +\n input_element.$el.offset().top -\n 120\n },\n 500\n );\n }\n }\n },\n\n /** Highlights errors */\n errors: function(options) {\n this.trigger(\"reset\");\n if (options && options.errors) {\n var error_messages = this.data.matchResponse(options.errors);\n for (var input_id in this.element_list) {\n var input = this.element_list[input_id];\n if (error_messages[input_id]) {\n this.highlight(input_id, error_messages[input_id], true);\n }\n }\n }\n },\n\n /** Render tool form */\n render: function() {\n var self = this;\n this.off(\"change\");\n this.off(\"reset\");\n // contains the dom field elements as created by the parameter factory i.e. 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Galaxy.emit.debug(\"form-view::initialize()\", \"Completed\");\n }\n});\n"]} \ No newline at end of file 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This is the main class of the form plugin. It is referenced as 'app' in lower level modules.\n*/\nimport Utils from \"utils/utils\";\nimport Portlet from \"mvc/ui/ui-portlet\";\nimport Ui from \"mvc/ui/ui-misc\";\nimport FormSection from \"mvc/form/form-section\";\nimport FormData from \"mvc/form/form-data\";\nexport default Backbone.View.extend({\n initialize: function(options) {\n this.model = new Backbone.Model({\n initial_errors: false,\n cls: \"ui-portlet-limited\",\n icon: null,\n always_refresh: true,\n status: \"warning\",\n hide_operations: false,\n onchange: function() {}\n }).set(options);\n this.setElement(\"\");\n this.render();\n },\n\n /** Update available options */\n update: function(new_model) {\n var self = this;\n this.data.matchModel(new_model, function(node, input_id) {\n var input = self.input_list[input_id];\n if (input && input.options) {\n if (!_.isEqual(input.options, node.options)) {\n input.options = node.options;\n var field = self.field_list[input_id];\n if (field.update) {\n var new_options = [];\n if (\n [\"data\", \"data_collection\", \"drill_down\"].indexOf(\n input.type\n ) != -1\n ) {\n new_options = input.options;\n } else {\n for (var i in node.options) {\n var opt = node.options[i];\n if (opt.length > 2) {\n new_options.push({\n label: opt[0],\n value: opt[1]\n });\n }\n }\n }\n field.update(new_options);\n field.trigger(\"change\");\n Galaxy.emit.debug(\n \"form-view::update()\",\n \"Updating options for \" + input_id\n );\n }\n }\n }\n });\n },\n\n /** Set form into wait mode */\n wait: function(active) {\n for (var i in this.input_list) {\n var field = this.field_list[i];\n var input = this.input_list[i];\n if (input.is_dynamic && field.wait && field.unwait) {\n field[active ? \"wait\" : \"unwait\"]();\n }\n }\n },\n\n /** Highlight and scroll to input element (currently only used for error notifications) */\n highlight: function(input_id, message, silent) {\n var input_element = this.element_list[input_id];\n if (input_element) {\n input_element.error(message || \"Please verify this parameter.\");\n this.portlet.expand();\n this.trigger(\"expand\", input_id);\n if (!silent) {\n var $panel = this.$el\n .parents()\n .filter(function() {\n return (\n [\"auto\", \"scroll\"].indexOf(\n $(this).css(\"overflow\")\n ) != -1\n );\n })\n .first();\n $panel.animate(\n {\n scrollTop:\n $panel.scrollTop() +\n input_element.$el.offset().top -\n 120\n },\n 500\n );\n }\n }\n },\n\n /** Highlights errors */\n errors: function(options) {\n this.trigger(\"reset\");\n if (options && options.errors) {\n var error_messages = this.data.matchResponse(options.errors);\n for (var input_id in this.element_list) {\n var input = this.element_list[input_id];\n if (error_messages[input_id]) {\n this.highlight(input_id, error_messages[input_id], true);\n }\n }\n }\n },\n\n /** Render tool form */\n render: function() {\n var self = this;\n this.off(\"change\");\n this.off(\"reset\");\n // contains the dom field elements as created by the parameter factory i.e. form-parameters\n this.field_list = {};\n // contains input definitions/dictionaries as provided by the parameters to_dict() function through the api\n this.input_list = {};\n // contains the dom elements of each input element i.e. form-input which wraps the actual input field\n this.element_list = {};\n // converts the form into a json data structure\n this.data = new FormData.Manager(this);\n this._renderForm();\n this.data.create();\n this.model.get(\"initial_errors\") && this.errors(this.model.attributes);\n // add listener which triggers on checksum change, and reset the form input wrappers\n var current_check = this.data.checksum();\n this.on(\"change\", function(input_id) {\n var input = self.input_list[input_id];\n if (\n !input ||\n input.refresh_on_change ||\n self.model.get(\"always_refresh\")\n ) {\n var new_check = self.data.checksum();\n if (new_check != current_check) {\n current_check = new_check;\n self.model.get(\"onchange\")();\n }\n }\n });\n this.on(\"reset\", function() {\n _.each(self.element_list, function(input_element) {\n input_element.reset();\n });\n });\n return this;\n },\n\n /** Renders/appends dom elements of the form */\n _renderForm: function() {\n $(\".tooltip\").remove();\n var options = this.model.attributes;\n this.message = new Ui.UnescapedMessage();\n this.section = new FormSection.View(this, {\n inputs: options.inputs\n });\n this.portlet = new Portlet.View({\n icon: options.icon,\n title: options.title,\n cls: options.cls,\n operations: !options.hide_operations && options.operations,\n buttons: options.buttons,\n collapsible: options.collapsible,\n collapsed: options.collapsed,\n onchange_title: options.onchange_title\n });\n this.portlet.append(this.message.$el);\n this.portlet.append(this.section.$el);\n this.$el.empty();\n options.inputs && this.$el.append(this.portlet.$el);\n options.message &&\n this.message.update({\n persistent: true,\n status: options.status,\n message: options.message\n });\n Galaxy.emit.debug(\"form-view::initialize()\", \"Completed\");\n }\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/form/form-wrapper.js.map b/static/maps/mvc/form/form-wrapper.js.map index 06b1be0b4ca..465fe3d9870 100644 --- a/static/maps/mvc/form/form-wrapper.js.map +++ b/static/maps/mvc/form/form-wrapper.js.map @@ -1 +1 @@ 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Generic form view */\nimport Form from \"mvc/form/form-view\";\nimport Ui from \"mvc/ui/ui-misc\";\nvar View = Backbone.View.extend({\n initialize: function(options) {\n this.model = new Backbone.Model(options);\n this.url = this.model.get(\"url\");\n this.redirect = this.model.get(\"redirect\");\n this.setElement(\"\");\n this.render();\n },\n\n render: function() {\n var self = this;\n $.ajax({\n url: Galaxy.root + this.url,\n type: \"GET\"\n })\n .done(function(response) {\n var options = $.extend({}, self.model.attributes, response);\n var form = new Form({\n title: options.title,\n message: options.message,\n status: options.status || \"warning\",\n icon: options.icon,\n inputs: options.inputs,\n buttons: {\n submit: new Ui.Button({\n tooltip: options.submit_tooltip,\n title: options.submit_title || \"Save\",\n icon: options.submit_icon || \"fa-save\",\n cls: \"btn btn-primary ui-clear-float\",\n onclick: function() {\n self._submit(form);\n }\n })\n }\n });\n 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dependencies\n\n// grid model\nexport default Backbone.Model.extend({\n defaults: {\n url_base: \"\",\n async: false,\n async_ops: [],\n categorical_filters: [],\n filters: {},\n sort_key: null,\n show_item_checkboxes: false,\n advanced_search: false,\n cur_page: 1,\n num_pages: 1,\n operation: undefined,\n item_ids: undefined\n },\n\n /**\n * Return true if operation can be done asynchronously.\n */\n can_async_op: function(op) {\n return _.indexOf(this.attributes.async_ops, op) !== -1;\n },\n\n /**\n * Add filtering criterion.\n */\n add_filter: function(key, value, append) {\n // Update URL arg with new condition.\n if (append) {\n // Update or append value.\n var cur_val = this.attributes.filters[key],\n new_val;\n if (cur_val === null || cur_val === undefined) {\n new_val = value;\n } else if (typeof cur_val == \"string\") {\n if (cur_val == \"All\" || cur_val == value) {\n new_val = value;\n } else {\n // Replace string with array.\n var values = [];\n values[0] = cur_val;\n 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this.model.get(\"plural\") +\n \" shared with you by others
\" +\n \"' +\n '
\"\n );\n _.each(options.shared_by_others, function(it, index) {\n var display_url =\n Galaxy.root +\n self.item +\n \"/display_by_username_and_slug?username=\" +\n it.username +\n \"&slug=\" +\n it.slug;\n $table.append(\n \"' +\n \" \" +\n \"Title \" +\n \"Owner \" +\n \"\" +\n \" \"\n );\n });\n $tmpl.append($table);\n } else {\n $tmpl.append(\n \"No \" +\n this.model.get(\"plural\").toLowerCase() +\n \" have been shared with you.\"\n );\n }\n return $tmpl;\n }\n});\n\nexport default {\n View: View\n};\n"]} \ No newline at end of file +{"version":3,"sources":["mvc/grid/grid-shared.js"],"names":["View","Backbone","extend","initialize","options","self","this","setElement","$","model","Model","item","get","title","ajax","url","Galaxy","root","params","success","response","set","render","attributes","grid","$el","append","_templateShared","$tmpl","shared_by_others","length","it","index","display_url","username","slug","$table","_","escape","toLowerCase"],"mappings":"+KAEIA,EAAOC,SAASD,KAAKE,QACrBC,WAAY,SAASC,GACjB,IAAIC,EAAOC,KACXA,KAAKC,WAAWC,EAAE,WAClBF,KAAKG,MAAQ,IAAIR,SAASS,MAAMN,GAChCE,KAAKK,KAAOL,KAAKG,MAAMG,IAAI,QAC3BN,KAAKO,MAAQP,KAAKG,MAAMG,IAAI,UAC5BJ,EAAEM,MACEC,IACIC,OAAOC,KACPX,KAAKK,KACL,IACAL,KAAKG,MAAMG,IAAI,aAZpBX,IACPE,EAAAA,MAAYa,OAAAE,QACRC,QAAId,SAAJe,GACAA,EAAA,aAAA,EACAf,EAAKI,MAAQY,IAAIpB,GACjBI,EAAAiB,aAWQF,OAAAA,WACAf,IAAAA,EAAAA,IAAAA,EAAAA,QAAWgB,KAAID,MAAfG,YACAlB,KAAAA,IAAAA,QAAKiB,OAALE,EAAAC,KACHnB,KAAAmB,IAAAC,OAAApB,KAAAqB,oBAUTA,gBAAiB,WANjBL,IAAAA,EAAQhB,KACJsB,EAAIJ,EACJ,YAzBwBlB,KAAAG,MAAAG,IAAA,UAmChB,yCAJRR,EAAIwB,KACAnB,MAAAc,WAMJ,GAAAnB,EAAIA,kBAAqBmB,EAAzBM,iBAAAC,OAAA,EAAA,CACA,IAAI1B,EAAQyB,EACR,+IAiCAD,EAAAA,KAAAA,EAAMF,iBAEOjB,SAAUsB,EAAAC,GAG1B,IAAAC,EACML,OAAPX,KACHZ,EAAAM,KAlFL,0CAuDoBoB,EA8BLG,SACLlC,SA7BU+B,EAAGI,KACPC,EAAOV,OACH,oBAGIO,EACA,KACAI,EAAEC,OAAOP,EAAGlB,OACZ,gBAGAwB,EAAEC,OAAOP,EAAGG,UACZ,gBAIZN,EAAMF,OAAOU,QAEbR,EAAMF,OACF,MACIpB,KAAKG,MAAMG,IAAI,UAAU2B,cACzB,+BAGZ,OAAOX,gBAKX5B,KAAMA","file":"../../../scripts/mvc/grid/grid-shared.js","sourcesContent":["/** This class renders the grid list with shared section. */\nimport GridView from \"mvc/grid/grid-view\";\nvar View = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.setElement($(\"\"));\n this.model = new Backbone.Model(options);\n this.item = this.model.get(\"item\");\n this.title = this.model.get(\"plural\");\n $.ajax({\n url:\n Galaxy.root +\n this.item +\n \"/\" +\n this.model.get(\"action_id\") +\n \"?\" +\n $.param(Galaxy.params),\n success: function(response) {\n response[\"dict_format\"] = true;\n self.model.set(response);\n self.render();\n }\n });\n },\n\n render: function() {\n var grid = new GridView(this.model.attributes);\n this.$el.empty().append(grid.$el);\n this.$el.append(this._templateShared());\n },\n\n _templateShared: function() {\n var self = this;\n var $tmpl = $(\n \"\" +\n '' +\n _.escape(it.title) +\n \"\" +\n \" \" +\n \"\" +\n _.escape(it.username) +\n \" \" +\n \"\" +\n \"\"\n );\n var options = this.model.attributes;\n if (options.shared_by_others && options.shared_by_others.length > 0) {\n var $table = $(\n '\" +\n this.model.get(\"plural\") +\n \" shared with you by others
\" +\n \"' +\n '
\"\n );\n _.each(options.shared_by_others, function(it, index) {\n var display_url =\n Galaxy.root +\n self.item +\n \"/display_by_username_and_slug?username=\" +\n it.username +\n \"&slug=\" +\n it.slug;\n $table.append(\n \"' +\n \" \" +\n \"Title \" +\n \"Owner \" +\n \"\" +\n \" \"\n );\n });\n $tmpl.append($table);\n } else {\n $tmpl.append(\n \"No \" +\n this.model.get(\"plural\").toLowerCase() +\n \" have been shared with you.\"\n );\n }\n return $tmpl;\n }\n});\n\nexport default {\n View: View\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/grid/grid-template.js.map b/static/maps/mvc/grid/grid-template.js.map index 1583e0e637b..3f3661048b1 100644 --- a/static/maps/mvc/grid/grid-template.js.map +++ b/static/maps/mvc/grid/grid-template.js.map @@ -1 +1 @@ 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dependencies\nimport Utils from \"utils/utils\";\n// grid view templates\nexport default {\n // template\n grid: function(options) {\n var tmpl = \"\";\n if (options.embedded) {\n tmpl = this.grid_header(options) + this.grid_table(options);\n } else {\n tmpl =\n '' +\n \"\" +\n '' +\n _.escape(it.title) +\n \"\" +\n \" \" +\n \"\" +\n _.escape(it.username) +\n \" \" +\n \"\" +\n \"
\" +\n this.grid_table(options);\n }\n\n // add info text\n if (options.info_text) {\n tmpl +=\n '\" +\n ' \" +\n \"' +\n this.grid_header(options) +\n \" \" +\n \"\" +\n \" \" +\n \" \" +\n ' \" +\n \"' +\n \" \" +\n \" \" +\n \" ' +\n options.info_text +\n \"\";\n }\n\n // return\n return tmpl;\n },\n\n // template\n grid_table: function(options) {\n return (\n '\"\n );\n },\n\n // template\n grid_header: function(options) {\n var tmpl = '';\n if (!options.embedded) {\n tmpl += \"\";\n\n // return template\n return tmpl;\n },\n\n // template\n header: function(options) {\n // start\n var tmpl = \"\" + options.title + \"
\";\n }\n if (options.global_actions) {\n tmpl += '- ';\n var show_popup = options.global_actions.length >= 3;\n if (show_popup) {\n tmpl +=\n '
';\n }\n for (var i in options.global_actions) {\n var action = options.global_actions[i];\n tmpl +=\n \"\";\n }\n tmpl += \"\";\n\n // add checkbox\n if (options.show_item_checkboxes) {\n tmpl += \" \";\n\n // return template\n return tmpl;\n },\n\n // template\n body: function(options) {\n // initialize\n var tmpl = \"\";\n var num_rows_rendered = 0;\n var items_length = options.items.length;\n\n // empty grid?\n if (items_length == 0) {\n // No results.\n tmpl += '\";\n if (options.items.length > 0) {\n tmpl +=\n '' +\n '';\n }\n tmpl += \" \";\n }\n\n // create header elements\n for (var i in options.columns) {\n var column = options.columns[i];\n if (column.visible) {\n tmpl += '';\n if (column.href) {\n tmpl +=\n '' +\n column.label +\n \"\";\n } else {\n tmpl += column.label;\n }\n tmpl +=\n '' +\n column.extra +\n \"\" +\n \" \";\n }\n }\n\n // finalize\n tmpl += \"No Items \";\n\n // Item selection column\n if (options.show_item_checkboxes) {\n tmpl +=\n ' \";\n num_rows_rendered++;\n }\n return tmpl;\n },\n\n // template\n footer: function(options) {\n // create template string\n var tmpl = \"\";\n\n // paging\n if (options.use_paging && options.num_pages > 1) {\n // get configuration\n var num_page_links = options.num_page_links;\n var cur_page_num = options.cur_page_num;\n var num_pages = options.num_pages;\n\n // First pass on min page.\n var page_link_range = num_page_links / 2;\n var min_page = cur_page_num - page_link_range;\n var min_offset = 0;\n if (min_page <= 0) {\n // Min page is too low.\n min_page = 1;\n min_offset = page_link_range - (cur_page_num - min_page);\n }\n\n // Set max page.\n var max_range = page_link_range + min_offset;\n var max_page = cur_page_num + max_range;\n var max_offset;\n if (max_page <= num_pages) {\n // Max page is fine.\n max_offset = 0;\n } else {\n // Max page is too high.\n max_page = num_pages;\n // +1 to account for the +1 in the loop below.\n max_offset = max_range - (max_page + 1 - cur_page_num);\n }\n\n // Second and final pass on min page to add any unused\n // offset from max to min.\n if (max_offset != 0) {\n min_page -= max_offset;\n if (min_page < 1) {\n min_page = 1;\n }\n }\n\n // template header\n tmpl += '' +\n '' +\n \" \";\n }\n\n // Data columns\n for (var j in options.columns) {\n var column = options.columns[j];\n if (column.visible) {\n // Nowrap\n var nowrap = \"\";\n if (column.nowrap) {\n nowrap = 'style=\"white-space:nowrap;\"';\n }\n\n // get column settings\n var column_settings = item.column_config[column.label];\n\n // load attributes\n var link = column_settings.link;\n var value = column_settings.value;\n var target = column_settings.target;\n\n // unescape value\n if (jQuery.type(value) === \"string\") {\n value = value.replace(/\\/\\//g, \"/\");\n }\n\n // Attach popup menu?\n var id = \"\";\n var cls = \"\";\n if (column.attach_popup) {\n id = \"grid-\" + i + \"-popup\";\n cls = \"menubutton\";\n if (link != \"\") {\n cls += \" split\";\n }\n cls += \" popup\";\n }\n\n // Check for row wrapping\n tmpl += \"\";\n\n // Link\n if (link) {\n if (options.operations.length != 0) {\n tmpl +=\n ' \";\n }\n }\n tmpl += \"';\n }\n tmpl +=\n '' +\n value +\n \"\";\n if (options.operations.length != 0) {\n tmpl += \"\";\n }\n } else {\n tmpl +=\n '\";\n }\n tmpl += \"';\n if (options.show_item_checkboxes) {\n tmpl += \" \";\n }\n\n // Grid operations for multiple items.\n if (options.show_item_checkboxes) {\n // start template\n tmpl +=\n \"\";\n }\n tmpl +=\n ' ' +\n '' +\n \"Page:\";\n\n if (min_page > 1) {\n tmpl +=\n '1 ...';\n }\n\n // create page urls\n for (\n var page_index = min_page;\n page_index < max_page + 1;\n page_index++\n ) {\n if (page_index == options.cur_page_num) {\n tmpl +=\n '' +\n page_index +\n \"\";\n } else {\n tmpl +=\n '' +\n page_index +\n \"\";\n }\n }\n\n // show last page\n if (max_page < num_pages) {\n tmpl +=\n \"...\" +\n '' +\n num_pages +\n \"\";\n }\n tmpl += \"\";\n\n // Show all link\n tmpl +=\n ' | Show All' +\n \" \" +\n \"\" +\n '' +\n \" \";\n }\n\n // count global operations\n var found_global = false;\n for (i in options.operations) {\n if (options.operations[i].global_operation) {\n found_global = true;\n break;\n }\n }\n\n // add global operations\n if (found_global) {\n tmpl += \"\" +\n ' ' +\n 'For selected items: ';\n\n // configure buttons for operations\n for (var i in options.operations) {\n var operation = options.operations[i];\n if (operation.allow_multiple) {\n tmpl +=\n ' ';\n }\n }\n\n // finalize template\n tmpl += \" \" + \"\" + ' \";\n }\n\n // add legend\n if (options.legend) {\n tmpl +=\n \"';\n for (i in options.operations) {\n var operation = options.operations[i];\n if (operation.global_operation) {\n tmpl +=\n '' +\n operation.label +\n \"\";\n }\n }\n tmpl += \" \" + \"\" +\n ' \";\n }\n\n // return\n return tmpl;\n },\n\n // template\n message: function(options) {\n var status = options.status == \"success\" ? \"done\" : options.status;\n return (\n \"' +\n options.legend +\n \" \" +\n \"\" +\n '
' +\n _.escape(options.message) +\n \"\" +\n '' +\n \"\"\n );\n },\n\n // template\n grid_filters: function(options) {\n // get filters\n var default_filter_dict = options.default_filter_dict;\n var filters = options.filters;\n\n // show advanced search if flag set or if there are filters for advanced search fields\n var advanced_search_display = \"none\";\n if (options.advanced_search) {\n advanced_search_display = \"block\";\n }\n\n // identify columns with advanced filtering\n var show_advanced_search_link = false;\n for (var i in options.columns) {\n var column = options.columns[i];\n if (column.filterable == \"advanced\") {\n var column_key = column.key;\n var f_key = filters[column_key];\n var d_key = default_filter_dict[column_key];\n if (f_key && d_key && f_key != d_key) {\n advanced_search_display = \"block\";\n }\n show_advanced_search_link = true;\n }\n }\n\n // hide standard search if advanced is shown\n var standard_search_display = \"block\";\n if (advanced_search_display == \"block\") {\n standard_search_display = \"none\";\n }\n\n //\n // standard search\n //\n var tmpl =\n '' +\n \"\";\n\n //\n // advanced search\n //\n tmpl +=\n '\" +\n \"
\" + \"\" +\n ' \" + \"' +\n \" \" + \"\";\n\n // add standard filters\n for (var i in options.columns) {\n var column = options.columns[i];\n if (column.filterable == \"standard\") {\n tmpl += this.grid_column_filter(options, column);\n }\n }\n\n // finalize standard search\n tmpl += \"
\" + \"\" + \" \" + \"\";\n\n // show advanced search link in standard display\n if (show_advanced_search_link) {\n tmpl +=\n 'Advanced Search';\n }\n\n // finalize standard search display\n tmpl += \" \" + \"' +\n \"\";\n\n // return template\n return tmpl;\n },\n\n // template\n grid_column_filter: function(options, column) {\n // collect parameters\n var default_filter_dict = options.default_filter_dict;\n var filters = options.filters;\n var column_label = column.label;\n var column_key = column.key;\n if (column.filterable == \"advanced\") {\n column_label = column_label.toLowerCase();\n }\n\n // start\n var tmpl = \"\" +\n \"
\" + \"\" +\n ' \";\n\n // add advanced filters\n for (var i in options.columns) {\n var column = options.columns[i];\n if (column.filterable == \"advanced\") {\n tmpl += this.grid_column_filter(options, column);\n }\n }\n\n // finalize advanced search template\n tmpl += \"' +\n 'Close Advanced Search' +\n \" \" +\n \"\";\n\n if (column.filterable == \"advanced\") {\n tmpl +=\n ' \";\n\n // return template\n return tmpl;\n },\n\n // template for filter items\n filter_element: function(filter_key, filter_value) {\n filter_value = Utils.sanitize(filter_value);\n return (\n '' +\n filter_value +\n '' +\n '' +\n \"\" +\n \"\"\n );\n }\n};\n"]} \ No newline at end of file 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dependencies\nimport Utils from \"utils/utils\";\n// grid view templates\nexport default {\n // template\n grid: function(options) {\n var tmpl = \"\";\n if (options.embedded) {\n tmpl = this.grid_header(options) + this.grid_table(options);\n } else {\n tmpl =\n '' +\n \"' +\n column_label +\n \": \";\n }\n tmpl += '';\n if (column.is_text) {\n tmpl +=\n '\";\n } else {\n // filter criteria\n tmpl += '';\n\n // add category filters\n var seperator = false;\n for (var cf_label in options.categorical_filters[column_key]) {\n // get category filter\n var cf = options.categorical_filters[column_key][cf_label];\n\n // each filter will have only a single argument, so get that single argument\n var cf_key = \"\";\n var cf_arg = \"\";\n for (var key in cf) {\n cf_key = key;\n cf_arg = cf[key];\n }\n\n // add seperator\n if (seperator) {\n tmpl += \" | \";\n }\n seperator = true;\n\n // add category\n var filter = filters[column_key];\n if (filter && cf[column_key] && filter == cf_arg) {\n tmpl +=\n '' +\n cf_label +\n \"\";\n } else {\n tmpl +=\n '' +\n '' +\n cf_label +\n \"\" +\n \"\";\n }\n }\n tmpl += \"\";\n }\n tmpl += \" \" + \"\" +\n \"
\" +\n this.grid_table(options);\n }\n\n // add info text\n if (options.info_text) {\n tmpl +=\n '\" +\n ' \" +\n \"' +\n this.grid_header(options) +\n \" \" +\n \"\" +\n \" \" +\n \" \" +\n ' \" +\n \"' +\n \" \" +\n \" \" +\n \" ' +\n options.info_text +\n \"\";\n }\n\n // return\n return tmpl;\n },\n\n // template\n grid_table: function(options) {\n return (\n '\"\n );\n },\n\n // template\n grid_header: function(options) {\n var tmpl = '';\n if (!options.embedded) {\n tmpl += \"\";\n\n // return template\n return tmpl;\n },\n\n // template\n header: function(options) {\n // start\n var tmpl = \"\" + options.title + \"
\";\n }\n if (options.global_actions) {\n tmpl += '- ';\n var show_popup = options.global_actions.length >= 3;\n if (show_popup) {\n tmpl +=\n '
';\n }\n for (var i in options.global_actions) {\n var action = options.global_actions[i];\n tmpl +=\n \"\";\n }\n tmpl += \"\";\n\n // add checkbox\n if (options.show_item_checkboxes) {\n tmpl += \" \";\n\n // return template\n return tmpl;\n },\n\n // template\n body: function(options) {\n // initialize\n var tmpl = \"\";\n var num_rows_rendered = 0;\n var items_length = options.items.length;\n\n // empty grid?\n if (items_length == 0) {\n // No results.\n tmpl += '\";\n if (options.items.length > 0) {\n tmpl +=\n '' +\n '';\n }\n tmpl += \" \";\n }\n\n // create header elements\n for (var i in options.columns) {\n var column = options.columns[i];\n if (column.visible) {\n tmpl += '';\n if (column.href) {\n tmpl +=\n '' +\n column.label +\n \"\";\n } else {\n tmpl += column.label;\n }\n tmpl +=\n '' +\n column.extra +\n \"\" +\n \" \";\n }\n }\n\n // finalize\n tmpl += \"No Items \";\n\n // Item selection column\n if (options.show_item_checkboxes) {\n tmpl +=\n ' \";\n num_rows_rendered++;\n }\n return tmpl;\n },\n\n // template\n footer: function(options) {\n // create template string\n var tmpl = \"\";\n\n // paging\n if (options.use_paging && options.num_pages > 1) {\n // get configuration\n var num_page_links = options.num_page_links;\n var cur_page_num = options.cur_page_num;\n var num_pages = options.num_pages;\n\n // First pass on min page.\n var page_link_range = num_page_links / 2;\n var min_page = cur_page_num - page_link_range;\n var min_offset = 0;\n if (min_page <= 0) {\n // Min page is too low.\n min_page = 1;\n min_offset = page_link_range - (cur_page_num - min_page);\n }\n\n // Set max page.\n var max_range = page_link_range + min_offset;\n var max_page = cur_page_num + max_range;\n var max_offset;\n if (max_page <= num_pages) {\n // Max page is fine.\n max_offset = 0;\n } else {\n // Max page is too high.\n max_page = num_pages;\n // +1 to account for the +1 in the loop below.\n max_offset = max_range - (max_page + 1 - cur_page_num);\n }\n\n // Second and final pass on min page to add any unused\n // offset from max to min.\n if (max_offset != 0) {\n min_page -= max_offset;\n if (min_page < 1) {\n min_page = 1;\n }\n }\n\n // template header\n tmpl += '' +\n '' +\n \" \";\n }\n\n // Data columns\n for (var j in options.columns) {\n var column = options.columns[j];\n if (column.visible) {\n // Nowrap\n var nowrap = \"\";\n if (column.nowrap) {\n nowrap = 'style=\"white-space:nowrap;\"';\n }\n\n // get column settings\n var column_settings = item.column_config[column.label];\n\n // load attributes\n var link = column_settings.link;\n var value = column_settings.value;\n var target = column_settings.target;\n\n // unescape value\n if (jQuery.type(value) === \"string\") {\n value = value.replace(/\\/\\//g, \"/\");\n }\n\n // Attach popup menu?\n var id = \"\";\n var cls = \"\";\n if (column.attach_popup) {\n id = \"grid-\" + i + \"-popup\";\n cls = \"menubutton\";\n if (link != \"\") {\n cls += \" split\";\n }\n cls += \" popup\";\n }\n\n // Check for row wrapping\n tmpl += \"\";\n\n // Link\n if (link) {\n if (options.operations.length != 0) {\n tmpl +=\n ' \";\n }\n }\n tmpl += \"';\n }\n tmpl +=\n '' +\n value +\n \"\";\n if (options.operations.length != 0) {\n tmpl += \"\";\n }\n } else {\n tmpl +=\n '\";\n }\n tmpl += \"';\n if (options.show_item_checkboxes) {\n tmpl += \" \";\n }\n\n // Grid operations for multiple items.\n if (options.show_item_checkboxes) {\n // start template\n tmpl +=\n \"\";\n }\n tmpl +=\n ' ' +\n '' +\n \"Page:\";\n\n if (min_page > 1) {\n tmpl +=\n '1 ...';\n }\n\n // create page urls\n for (\n var page_index = min_page;\n page_index < max_page + 1;\n page_index++\n ) {\n if (page_index == options.cur_page_num) {\n tmpl +=\n '' +\n page_index +\n \"\";\n } else {\n tmpl +=\n '' +\n page_index +\n \"\";\n }\n }\n\n // show last page\n if (max_page < num_pages) {\n tmpl +=\n \"...\" +\n '' +\n num_pages +\n \"\";\n }\n tmpl += \"\";\n\n // Show all link\n tmpl +=\n ' | Show All' +\n \" \" +\n \"\" +\n '' +\n \" \";\n }\n\n // count global operations\n var found_global = false;\n for (i in options.operations) {\n if (options.operations[i].global_operation) {\n found_global = true;\n break;\n }\n }\n\n // add global operations\n if (found_global) {\n tmpl += \"\" +\n ' ' +\n 'For selected items: ';\n\n // configure buttons for operations\n for (var i in options.operations) {\n var operation = options.operations[i];\n if (operation.allow_multiple) {\n tmpl +=\n ' ';\n }\n }\n\n // finalize template\n tmpl += \" \" + \"\" + ' \";\n }\n\n // add legend\n if (options.legend) {\n tmpl +=\n \"';\n for (i in options.operations) {\n var operation = options.operations[i];\n if (operation.global_operation) {\n tmpl +=\n '' +\n operation.label +\n \"\";\n }\n }\n tmpl += \" \" + \"\" +\n ' \";\n }\n\n // return\n return tmpl;\n },\n\n // template\n message: function(options) {\n var status = options.status == \"success\" ? \"done\" : options.status;\n return (\n \"' +\n options.legend +\n \" \" +\n \"\" +\n '
' +\n _.escape(options.message) +\n \"\" +\n '' +\n \"\"\n );\n },\n\n // template\n grid_filters: function(options) {\n // get filters\n var default_filter_dict = options.default_filter_dict;\n var filters = options.filters;\n\n // show advanced search if flag set or if there are filters for advanced search fields\n var advanced_search_display = \"none\";\n if (options.advanced_search) {\n advanced_search_display = \"block\";\n }\n\n // identify columns with advanced filtering\n var show_advanced_search_link = false;\n for (var i in options.columns) {\n var column = options.columns[i];\n if (column.filterable == \"advanced\") {\n var column_key = column.key;\n var f_key = filters[column_key];\n var d_key = default_filter_dict[column_key];\n if (f_key && d_key && f_key != d_key) {\n advanced_search_display = \"block\";\n }\n show_advanced_search_link = true;\n }\n }\n\n // hide standard search if advanced is shown\n var standard_search_display = \"block\";\n if (advanced_search_display == \"block\") {\n standard_search_display = \"none\";\n }\n\n //\n // standard search\n //\n var tmpl =\n '' +\n \"\";\n\n //\n // advanced search\n //\n tmpl +=\n '\" +\n \"
\" + \"\" +\n ' \" + \"' +\n \" \" + \"\";\n\n // add standard filters\n for (var i in options.columns) {\n var column = options.columns[i];\n if (column.filterable == \"standard\") {\n tmpl += this.grid_column_filter(options, column);\n }\n }\n\n // finalize standard search\n tmpl += \"
\" + \"\" + \" \" + \"\";\n\n // show advanced search link in standard display\n if (show_advanced_search_link) {\n tmpl +=\n 'Advanced Search';\n }\n\n // finalize standard search display\n tmpl += \" \" + \"' +\n \"\";\n\n // return template\n return tmpl;\n },\n\n // template\n grid_column_filter: function(options, column) {\n // collect parameters\n var default_filter_dict = options.default_filter_dict;\n var filters = options.filters;\n var column_label = column.label;\n var column_key = column.key;\n if (column.filterable == \"advanced\") {\n column_label = column_label.toLowerCase();\n }\n\n // start\n var tmpl = \"\" +\n \"
\" + \"\" +\n ' \";\n\n // add advanced filters\n for (var i in options.columns) {\n var column = options.columns[i];\n if (column.filterable == \"advanced\") {\n tmpl += this.grid_column_filter(options, column);\n }\n }\n\n // finalize advanced search template\n tmpl += \"' +\n 'Close Advanced Search' +\n \" \" +\n \"\";\n\n if (column.filterable == \"advanced\") {\n tmpl +=\n ' \";\n\n // return template\n return tmpl;\n },\n\n // template for filter items\n filter_element: function(filter_key, filter_value) {\n filter_value = Utils.sanitize(filter_value);\n return (\n '' +\n filter_value +\n '' +\n '' +\n \"\" +\n \"\"\n );\n }\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/grid/grid-view.js.map b/static/maps/mvc/grid/grid-view.js.map index 5374970ac3a..0adc19ef4cd 100644 --- a/static/maps/mvc/grid/grid-view.js.map +++ b/static/maps/mvc/grid/grid-view.js.map @@ -1 +1 @@ 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This is necessary so that, when nested arrays are used in ajax/post/get methods, square brackets ('[]') are\n// not appended to the identifier of a nested array.\njQuery.ajaxSettings.traditional = true;\n\n// dependencies\nimport Utils from \"utils/utils\";\nimport GridModel from \"mvc/grid/grid-model\";\nimport Templates from \"mvc/grid/grid-template\";\nimport PopupMenu from \"mvc/ui/popup-menu\";\n// grid view\nexport default Backbone.View.extend({\n // model\n grid: null,\n\n // Initialize\n initialize: function(grid_config) {\n this.grid = new GridModel();\n this.dict_format = grid_config.dict_format;\n this.title = grid_config.title;\n var self = this;\n window.add_tag_to_grid_filter = function(tag_name, tag_value) {\n // Put tag name and value together.\n var tag =\n tag_name +\n (tag_value !== undefined && tag_value !== \"\"\n ? \":\" + tag_value\n : \"\");\n var advanced_search = $(\"#advanced-search\").is(\":visible\");\n if (!advanced_search) {\n $(\"#standard-search\").slideToggle(\"fast\");\n $(\"#advanced-search\").slideToggle(\"fast\");\n }\n self.add_filter_condition(\"tags\", tag);\n };\n\n // set element\n if (this.dict_format) {\n this.setElement(\"\");\n if (grid_config.url_base && !grid_config.items) {\n var url_data = grid_config.url_data || {};\n _.each(grid_config.filters, function(v, k) {\n url_data[\"f-\" + k] = v;\n });\n $.ajax({\n url: grid_config.url_base + \"?\" + $.param(url_data),\n success: function(response) {\n response.embedded = grid_config.embedded;\n response.filters = grid_config.filters || {};\n self.init_grid(response);\n }\n });\n } else {\n this.init_grid(grid_config);\n }\n } else {\n this.setElement(\"#grid-container\");\n this.init_grid(grid_config);\n }\n\n // fix padding\n if (grid_config.use_panels) {\n $(\"#center\").css({\n padding: \"10px\",\n overflow: \"auto\"\n });\n }\n },\n\n // refresh frames\n handle_refresh: function(refresh_frames) {\n if (refresh_frames) {\n if ($.inArray(\"history\", refresh_frames) > -1) {\n if (top.Galaxy && top.Galaxy.currHistoryPanel) {\n top.Galaxy.currHistoryPanel.loadCurrentHistory();\n }\n }\n }\n },\n\n // Initialize\n init_grid: function(grid_config) {\n this.grid.set(grid_config);\n\n // get options\n var options = this.grid.attributes;\n\n if (this.allow_title_display && options.title) {\n Utils.setWindowTitle(options.title);\n }\n // handle refresh requests\n this.handle_refresh(options.refresh_frames);\n\n // strip protocol and domain\n var url = this.grid.get(\"url_base\");\n url = url.replace(/^.*\\/\\/[^\\/]+/, \"\");\n this.grid.set(\"url_base\", url);\n\n // append main template\n this.$el.html(Templates.grid(options));\n\n // update div contents\n this.$el.find(\"#grid-table-header\").html(Templates.header(options));\n this.$el.find(\"#grid-table-body\").html(Templates.body(options));\n this.$el.find(\"#grid-table-footer\").html(Templates.footer(options));\n\n // update message\n if (options.message) {\n this.$el.find(\"#grid-message\").html(Templates.message(options));\n var self = this;\n if (options.use_hide_message) {\n setTimeout(function() {\n self.$el.find(\"#grid-message\").html(\"\");\n }, 5000);\n }\n }\n\n // configure elements\n this.init_grid_elements();\n this.init_grid_controls();\n\n // attach global event handler\n // TODO: redundant (the onload/standard page handlers do this) - but needed because these are constructed after page ready\n init_refresh_on_change();\n },\n\n // Initialize grid controls\n init_grid_controls: function() {\n // link\n var self = this;\n\n // Initialize grid operation button.\n this.$el.find(\".operation-button\").each(function() {\n $(this).off();\n $(this).click(function() {\n self.submit_operation(this);\n return false;\n });\n });\n\n // Initialize text filters to select text on click and use normal font when user is typing.\n this.$el.find(\"input[type=text]\").each(function() {\n $(this).off();\n $(this)\n .click(function() {\n $(this).select();\n })\n .keyup(function() {\n $(this).css(\"font-style\", \"normal\");\n });\n });\n\n // Initialize sort links.\n this.$el.find(\".sort-link\").each(function() {\n $(this).off();\n $(this).click(function() {\n self.set_sort_condition($(this).attr(\"sort_key\"));\n return false;\n });\n });\n\n // Initialize text filters.\n this.$el.find(\".text-filter-form\").each(function() {\n $(this).off();\n $(this).submit(function() {\n var column_key = $(this).attr(\"column_key\");\n var text_input_obj = $(\"#input-\" + column_key + \"-filter\");\n var text_input = text_input_obj.val();\n text_input_obj.val(\"\");\n self.add_filter_condition(column_key, text_input);\n return false;\n });\n });\n\n // Initialize categorical filters.\n this.$el.find(\".text-filter-val > a\").each(function() {\n $(this).off();\n $(this).click(function() {\n // Remove visible element.\n $(this)\n .parent()\n .remove();\n\n // Remove filter condition.\n self.remove_filter_condition(\n $(this).attr(\"filter_key\"),\n $(this).attr(\"filter_val\")\n );\n\n // Return\n return false;\n });\n });\n\n // Initialize categorical filters.\n this.$el.find(\".categorical-filter > a\").each(function() {\n $(this).off();\n $(this).click(function() {\n self.set_categorical_filter(\n $(this).attr(\"filter_key\"),\n $(this).attr(\"filter_val\")\n );\n return false;\n });\n });\n\n // Initialize standard, advanced search toggles.\n this.$el.find(\".advanced-search-toggle\").each(function() {\n $(this).off();\n $(this).click(function() {\n self.$el.find(\"#standard-search\").slideToggle(\"fast\");\n self.$el.find(\"#advanced-search\").slideToggle(\"fast\");\n return false;\n });\n });\n\n // Add event to check all box\n this.$el.find(\"#check_all\").off();\n this.$el.find(\"#check_all\").on(\"click\", function() {\n self.check_all_items();\n });\n },\n\n // Initialize grid elements.\n init_grid_elements: function() {\n // Initialize grid selection checkboxes.\n this.$el.find(\".grid\").each(function() {\n var checkboxes = $(this).find(\"input.grid-row-select-checkbox\");\n var check_count = $(this).find(\"span.grid-selected-count\");\n var update_checked = function() {\n check_count.text($(checkboxes).filter(\":checked\").length);\n };\n\n $(checkboxes).each(function() {\n $(this).change(update_checked);\n });\n update_checked();\n });\n\n // Initialize ratings.\n if (this.$el.find(\".community_rating_star\").length !== 0)\n this.$el.find(\".community_rating_star\").rating({});\n\n // get options\n var options = this.grid.attributes;\n var self = this;\n\n //\n // add page click events\n //\n this.$el.find(\".page-link > a\").each(function() {\n $(this).click(function() {\n self.set_page($(this).attr(\"page_num\"));\n return false;\n });\n });\n\n //\n // add inbound/outbound events\n //\n this.$el.find(\".use-target\").each(function() {\n $(this).click(function(e) {\n self.execute({\n href: $(this).attr(\"href\"),\n target: $(this).attr(\"target\")\n });\n return false;\n });\n });\n\n // empty grid?\n var items_length = options.items.length;\n if (items_length == 0) {\n return;\n }\n\n // add operation popup menus\n _.each(options.items, function(item, index) {\n var button = self.$(\"#grid-\" + index + \"-popup\").off();\n var popup = new PopupMenu(button);\n _.each(options[\"operations\"], function(operation) {\n self._add_operation(popup, operation, item);\n });\n });\n },\n\n /** Add an operation to the items menu */\n _add_operation: function(popup, operation, item) {\n var self = this;\n var settings = item.operation_config[operation.label];\n if (settings.allowed && operation.allow_popup) {\n popup.addItem({\n html: operation.label,\n href: settings.url_args,\n target: settings.target,\n confirmation_text: operation.confirm,\n func: function(e) {\n e.preventDefault();\n var label = $(e.target).html();\n if (operation.onclick) {\n operation.onclick(item.encode_id);\n } else {\n self.execute(this.findItemByHtml(label));\n }\n }\n });\n }\n },\n\n // Add a condition to the grid filter; this adds the condition and refreshes the grid.\n add_filter_condition: function(name, value) {\n // Do nothing is value is empty.\n if (value === \"\") {\n return false;\n }\n\n // Add condition to grid.\n this.grid.add_filter(name, value, true);\n\n // Add button that displays filter and provides a button to delete it.\n var t = $(Templates.filter_element(name, value));\n var self = this;\n t.click(function() {\n // Remove visible element.\n $(this).remove();\n\n // Remove filter condition.\n self.remove_filter_condition(name, value);\n });\n\n // append to container\n var container = this.$el.find(\"#\" + name + \"-filtering-criteria\");\n container.append(t);\n\n // execute\n this.go_page_one();\n this.execute();\n },\n\n // Remove a condition to the grid filter; this adds the condition and refreshes the grid.\n remove_filter_condition: function(name, value) {\n // Remove filter condition.\n this.grid.remove_filter(name, value);\n\n // Execute\n this.go_page_one();\n this.execute();\n },\n\n // Set sort condition for grid.\n set_sort_condition: function(col_key) {\n // Set new sort condition. New sort is col_key if sorting new column; if reversing sort on\n // currently sorted column, sort is reversed.\n var cur_sort = this.grid.get(\"sort_key\");\n var new_sort = col_key;\n if (cur_sort.indexOf(col_key) !== -1) {\n // Reverse sort.\n if (cur_sort.substring(0, 1) !== \"-\") {\n new_sort = \"-\" + col_key;\n }\n }\n\n // Remove sort arrows elements.\n this.$el.find(\".sort-arrow\").remove();\n\n // Add sort arrow element to new sort column.\n var sort_arrow = new_sort.substring(0, 1) == \"-\" ? \"↑\" : \"↓\";\n var t = $(\"\" + sort_arrow + \"\").addClass(\"sort-arrow\");\n\n // Add to header\n this.$el.find(\"#\" + col_key + \"-header\").append(t);\n\n // Update grid.\n this.grid.set(\"sort_key\", new_sort);\n this.go_page_one();\n this.execute();\n },\n\n // Set new value for categorical filter.\n set_categorical_filter: function(name, new_value) {\n // Update filter hyperlinks to reflect new filter value.\n var category_filter = this.grid.get(\"categorical_filters\")[name],\n cur_value = this.grid.get(\"filters\")[name];\n var self = this;\n this.$el.find(\".\" + name + \"-filter\").each(function() {\n var text = $.trim($(this).text());\n var filter = category_filter[text];\n var filter_value = filter[name];\n if (filter_value == new_value) {\n // Remove filter link since grid will be using this filter. It is assumed that\n // this element has a single child, a hyperlink/anchor with text.\n $(this).empty();\n $(this).addClass(\"current-filter\");\n $(this).append(text);\n } else if (filter_value == cur_value) {\n // Add hyperlink for this filter since grid will no longer be using this filter. It is assumed that\n // this element has a single child, a hyperlink/anchor.\n $(this).empty();\n var t = $('' + text + \"\");\n t.click(function() {\n self.set_categorical_filter(name, filter_value);\n });\n $(this).removeClass(\"current-filter\");\n $(this).append(t);\n }\n });\n\n // Update grid.\n this.grid.add_filter(name, new_value);\n this.go_page_one();\n this.execute();\n },\n\n // Set page to view.\n set_page: function(new_page) {\n // Update page hyperlink to reflect new page.\n var self = this;\n this.$el.find(\".page-link\").each(function() {\n var id = $(this).attr(\"id\"),\n page_num = parseInt(id.split(\"-\")[2], 10), // Id has form 'page-link-' +\n column_label +\n \": \";\n }\n tmpl += '';\n if (column.is_text) {\n tmpl +=\n '\";\n } else {\n // filter criteria\n tmpl += '';\n\n // add category filters\n var seperator = false;\n for (var cf_label in options.categorical_filters[column_key]) {\n // get category filter\n var cf = options.categorical_filters[column_key][cf_label];\n\n // each filter will have only a single argument, so get that single argument\n var cf_key = \"\";\n var cf_arg = \"\";\n for (var key in cf) {\n cf_key = key;\n cf_arg = cf[key];\n }\n\n // add seperator\n if (seperator) {\n tmpl += \" | \";\n }\n seperator = true;\n\n // add category\n var filter = filters[column_key];\n if (filter && cf[column_key] && filter == cf_arg) {\n tmpl +=\n '' +\n cf_label +\n \"\";\n } else {\n tmpl +=\n '' +\n '' +\n cf_label +\n \"\" +\n \"\";\n }\n }\n tmpl += \"\";\n }\n tmpl += \" \" + \"\n cur_page = self.grid.get(\"cur_page\"),\n text;\n if (page_num === new_page) {\n // Remove link to page since grid will be on this page. It is assumed that\n // this element has a single child, a hyperlink/anchor with text.\n text = $(this)\n .children()\n .text();\n $(this).empty();\n $(this).addClass(\"inactive-link\");\n $(this).text(text);\n } else if (page_num === cur_page) {\n // Add hyperlink to this page since grid will no longer be on this page. It is assumed that\n // this element has a single child, a hyperlink/anchor.\n text = $(this).text();\n $(this).empty();\n $(this).removeClass(\"inactive-link\");\n var t = $('' + text + \"\");\n t.click(function() {\n self.set_page(page_num);\n });\n $(this).append(t);\n }\n });\n\n if (new_page === \"all\") {\n this.grid.set(\"cur_page\", new_page);\n } else {\n this.grid.set(\"cur_page\", parseInt(new_page, 10));\n }\n this.execute();\n },\n\n // confirmation/submission of operation request\n submit_operation: function(operation_button, confirmation_text) {\n // identify operation\n var operation_name = $(operation_button).val();\n\n // verify in any item is selected\n var number_of_checked_ids = this.$el.find('input[name=\"id\"]:checked')\n .length;\n if (!number_of_checked_ids > 0) {\n return false;\n }\n\n // Check to see if there's grid confirmation text for this operation\n var operation = _.findWhere(this.grid.attributes.operations, {\n label: operation_name\n });\n if (operation && !confirmation_text) {\n confirmation_text = operation.confirm || \"\";\n }\n\n // collect ids\n var item_ids = [];\n this.$el.find(\"input[name=id]:checked\").each(function() {\n item_ids.push($(this).val());\n });\n\n // execute operation\n var options = {\n operation: operation_name,\n id: item_ids,\n confirmation_text: confirmation_text\n };\n if (operation.target == \"top\") {\n options = _.extend(options, {\n href: operation.href,\n target: operation.target\n });\n }\n this.execute(options);\n return true;\n },\n\n check_all_items: function() {\n var check = this.$(\".grid-row-select-checkbox\");\n var state = this.$(\"#check_all\").prop(\"checked\");\n _.each(check, function(c) {\n $(c).prop(\"checked\", state);\n });\n this.init_grid_elements();\n },\n\n // Go back to page one; this is useful when a filter is applied.\n go_page_one: function() {\n // Need to go back to page 1 if not showing all.\n var cur_page = this.grid.get(\"cur_page\");\n if (cur_page !== null && cur_page !== undefined && cur_page !== \"all\") {\n this.grid.set(\"cur_page\", 1);\n }\n },\n\n //\n // execute operations and hyperlink requests\n //\n execute: function(options) {\n // get url\n var id = null;\n var href = null;\n var operation = null;\n var confirmation_text = null;\n var target = null;\n\n // check for options\n if (options) {\n // get options\n href = options.href;\n operation = options.operation;\n id = options.id;\n confirmation_text = options.confirmation_text;\n target = options.target;\n\n // check if input contains the operation tag\n if (href !== undefined && href.indexOf(\"operation=\") != -1) {\n // Get operation, id in hyperlink's href.\n var href_parts = href.split(\"?\");\n if (href_parts.length > 1) {\n var href_parms_str = href_parts[1];\n var href_parms = href_parms_str.split(\"&\");\n for (var index = 0; index < href_parms.length; index++) {\n if (href_parms[index].indexOf(\"operation\") != -1) {\n // Found operation parm; get operation value.\n operation = href_parms[index].split(\"=\")[1];\n operation = operation.replace(/\\+/g, \" \");\n } else if (href_parms[index].indexOf(\"id\") != -1) {\n // Found id parm; get id value.\n id = href_parms[index].split(\"=\")[1];\n }\n }\n }\n }\n }\n\n // check for operation details\n if (operation && id) {\n // show confirmation box\n if (\n confirmation_text &&\n confirmation_text != \"\" &&\n confirmation_text != \"None\" &&\n confirmation_text != \"null\"\n )\n if (!confirm(confirmation_text)) return false;\n\n // use small characters for operation?!\n operation = operation.toLowerCase();\n\n // Update grid.\n this.grid.set({\n operation: operation,\n item_ids: id\n });\n\n // Do operation. If operation cannot be performed asynchronously, redirect to location.\n if (target == \"top\") {\n window.top.location =\n href + \"?\" + $.param(this.grid.get_url_data());\n } else if (this.grid.can_async_op(operation) || this.dict_format) {\n this.update_grid();\n } else {\n this.go_to(target, href);\n }\n\n // done\n return false;\n }\n\n // refresh grid\n if (href) {\n this.go_to(target, href);\n return false;\n }\n\n // refresh grid\n if (this.grid.get(\"async\") || this.dict_format) {\n this.update_grid();\n } else {\n this.go_to(target, href);\n }\n\n // done\n return false;\n },\n\n // go to url\n go_to: function(target, href) {\n // get aysnc status\n var async = this.grid.get(\"async\");\n this.grid.set(\"async\", false);\n\n // get slide status\n var advanced_search = this.$el.find(\"#advanced-search\").is(\":visible\");\n this.grid.set(\"advanced_search\", advanced_search);\n\n // get default url\n if (!href) {\n href =\n this.grid.get(\"url_base\") +\n \"?\" +\n $.param(this.grid.get_url_data());\n }\n\n // clear grid of transient request attributes.\n this.grid.set({\n operation: undefined,\n item_ids: undefined,\n async: async\n });\n switch (target) {\n case \"inbound\":\n // this currently assumes that there is only a single grid shown at a time\n var $div = $(\".grid-header\").closest(\".inbound\");\n if ($div.length !== 0) {\n $div.load(href);\n return;\n }\n break;\n case \"top\":\n window.top.location = href;\n break;\n default:\n window.location = href;\n }\n },\n\n // Update grid.\n update_grid: function() {\n // If there's an operation, do POST; otherwise, do GET.\n var method = this.grid.get(\"operation\") ? \"POST\" : \"GET\";\n\n // Show overlay to indicate loading and prevent user actions.\n this.$el.find(\".loading-elt-overlay\").show();\n var self = this;\n $.ajax({\n type: method,\n url: self.grid.get(\"url_base\"),\n data: self.grid.get_url_data(),\n error: function(response) {\n alert(\"Grid refresh failed\");\n },\n success: function(response_text) {\n // backup\n var embedded = self.grid.get(\"embedded\");\n var insert = self.grid.get(\"insert\");\n var advanced_search = self.$el\n .find(\"#advanced-search\")\n .is(\":visible\");\n\n // request new configuration\n var json = self.dict_format\n ? response_text\n : $.parseJSON(response_text);\n\n // update\n json.embedded = embedded;\n json.insert = insert;\n json.advanced_search = advanced_search;\n\n // Initialize new grid config\n self.init_grid(json);\n\n // Hide loading overlay.\n self.$el.find(\".loading-elt-overlay\").hide();\n },\n complete: function() {\n // Clear grid of transient request attributes.\n self.grid.set({\n operation: undefined,\n item_ids: undefined\n });\n }\n });\n }\n});\n"]} \ No newline at end of file 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This is necessary so that, when nested arrays are used in ajax/post/get methods, square brackets ('[]') are\n// not appended to the identifier of a nested array.\njQuery.ajaxSettings.traditional = true;\n\n// dependencies\nimport Utils from \"utils/utils\";\nimport GridModel from \"mvc/grid/grid-model\";\nimport Templates from \"mvc/grid/grid-template\";\nimport PopupMenu from \"mvc/ui/popup-menu\";\n// grid view\nexport default Backbone.View.extend({\n // model\n grid: null,\n\n // Initialize\n initialize: function(grid_config) {\n this.grid = new GridModel();\n this.dict_format = grid_config.dict_format;\n this.title = grid_config.title;\n var self = this;\n window.add_tag_to_grid_filter = function(tag_name, tag_value) {\n // Put tag name and value together.\n var tag =\n tag_name +\n (tag_value !== undefined && tag_value !== \"\"\n ? \":\" + tag_value\n : \"\");\n var advanced_search = $(\"#advanced-search\").is(\":visible\");\n if (!advanced_search) {\n $(\"#standard-search\").slideToggle(\"fast\");\n $(\"#advanced-search\").slideToggle(\"fast\");\n }\n self.add_filter_condition(\"tags\", tag);\n };\n\n // set element\n if (this.dict_format) {\n this.setElement(\"\");\n if (grid_config.url_base && !grid_config.items) {\n var url_data = grid_config.url_data || {};\n _.each(grid_config.filters, function(v, k) {\n url_data[\"f-\" + k] = v;\n });\n $.ajax({\n url: grid_config.url_base + \"?\" + $.param(url_data),\n success: function(response) {\n response.embedded = grid_config.embedded;\n response.filters = grid_config.filters || {};\n self.init_grid(response);\n }\n });\n } else {\n this.init_grid(grid_config);\n }\n } else {\n this.setElement(\"#grid-container\");\n this.init_grid(grid_config);\n }\n\n // fix padding\n if (grid_config.use_panels) {\n $(\"#center\").css({\n padding: \"10px\",\n overflow: \"auto\"\n });\n }\n },\n\n // refresh frames\n handle_refresh: function(refresh_frames) {\n if (refresh_frames) {\n if ($.inArray(\"history\", refresh_frames) > -1) {\n if (top.Galaxy && top.Galaxy.currHistoryPanel) {\n top.Galaxy.currHistoryPanel.loadCurrentHistory();\n }\n }\n }\n },\n\n // Initialize\n init_grid: function(grid_config) {\n this.grid.set(grid_config);\n\n // get options\n var options = this.grid.attributes;\n\n if (this.allow_title_display && options.title) {\n Utils.setWindowTitle(options.title);\n }\n // handle refresh requests\n this.handle_refresh(options.refresh_frames);\n\n // strip protocol and domain\n var url = this.grid.get(\"url_base\");\n url = url.replace(/^.*\\/\\/[^\\/]+/, \"\");\n this.grid.set(\"url_base\", url);\n\n // append main template\n this.$el.html(Templates.grid(options));\n\n // update div contents\n this.$el.find(\"#grid-table-header\").html(Templates.header(options));\n this.$el.find(\"#grid-table-body\").html(Templates.body(options));\n this.$el.find(\"#grid-table-footer\").html(Templates.footer(options));\n\n // update message\n if (options.message) {\n this.$el.find(\"#grid-message\").html(Templates.message(options));\n var self = this;\n if (options.use_hide_message) {\n setTimeout(function() {\n self.$el.find(\"#grid-message\").html(\"\");\n }, 5000);\n }\n }\n\n // configure elements\n this.init_grid_elements();\n this.init_grid_controls();\n\n // attach global event handler\n // TODO: redundant (the onload/standard page handlers do this) - but needed because these are constructed after page ready\n init_refresh_on_change();\n },\n\n // Initialize grid controls\n init_grid_controls: function() {\n // link\n var self = this;\n\n // Initialize grid operation button.\n this.$el.find(\".operation-button\").each(function() {\n $(this).off();\n $(this).click(function() {\n self.submit_operation(this);\n return false;\n });\n });\n\n // Initialize text filters to select text on click and use normal font when user is typing.\n this.$el.find(\"input[type=text]\").each(function() {\n $(this).off();\n $(this)\n .click(function() {\n $(this).select();\n })\n .keyup(function() {\n $(this).css(\"font-style\", \"normal\");\n });\n });\n\n // Initialize sort links.\n this.$el.find(\".sort-link\").each(function() {\n $(this).off();\n $(this).click(function() {\n self.set_sort_condition($(this).attr(\"sort_key\"));\n return false;\n });\n });\n\n // Initialize text filters.\n this.$el.find(\".text-filter-form\").each(function() {\n $(this).off();\n $(this).submit(function() {\n var column_key = $(this).attr(\"column_key\");\n var text_input_obj = $(\"#input-\" + column_key + \"-filter\");\n var text_input = text_input_obj.val();\n text_input_obj.val(\"\");\n self.add_filter_condition(column_key, text_input);\n return false;\n });\n });\n\n // Initialize categorical filters.\n this.$el.find(\".text-filter-val > a\").each(function() {\n $(this).off();\n $(this).click(function() {\n // Remove visible element.\n $(this)\n .parent()\n .remove();\n\n // Remove filter condition.\n self.remove_filter_condition(\n $(this).attr(\"filter_key\"),\n $(this).attr(\"filter_val\")\n );\n\n // Return\n return false;\n });\n });\n\n // Initialize categorical filters.\n this.$el.find(\".categorical-filter > a\").each(function() {\n $(this).off();\n $(this).click(function() {\n self.set_categorical_filter(\n $(this).attr(\"filter_key\"),\n $(this).attr(\"filter_val\")\n );\n return false;\n });\n });\n\n // Initialize standard, advanced search toggles.\n this.$el.find(\".advanced-search-toggle\").each(function() {\n $(this).off();\n $(this).click(function() {\n self.$el.find(\"#standard-search\").slideToggle(\"fast\");\n self.$el.find(\"#advanced-search\").slideToggle(\"fast\");\n return false;\n });\n });\n\n // Add event to check all box\n this.$el.find(\"#check_all\").off();\n this.$el.find(\"#check_all\").on(\"click\", function() {\n self.check_all_items();\n });\n },\n\n // Initialize grid elements.\n init_grid_elements: function() {\n // Initialize grid selection checkboxes.\n this.$el.find(\".grid\").each(function() {\n var checkboxes = $(this).find(\"input.grid-row-select-checkbox\");\n var check_count = $(this).find(\"span.grid-selected-count\");\n var update_checked = function() {\n check_count.text($(checkboxes).filter(\":checked\").length);\n };\n\n $(checkboxes).each(function() {\n $(this).change(update_checked);\n });\n update_checked();\n });\n\n // Initialize ratings.\n if (this.$el.find(\".community_rating_star\").length !== 0)\n this.$el.find(\".community_rating_star\").rating({});\n\n // get options\n var options = this.grid.attributes;\n var self = this;\n\n //\n // add page click events\n //\n this.$el.find(\".page-link > a\").each(function() {\n $(this).click(function() {\n self.set_page($(this).attr(\"page_num\"));\n return false;\n });\n });\n\n //\n // add inbound/outbound events\n //\n this.$el.find(\".use-target\").each(function() {\n $(this).click(function(e) {\n self.execute({\n href: $(this).attr(\"href\"),\n target: $(this).attr(\"target\")\n });\n return false;\n });\n });\n\n // empty grid?\n var items_length = options.items.length;\n if (items_length == 0) {\n return;\n }\n\n // add operation popup menus\n _.each(options.items, function(item, index) {\n var button = self.$(\"#grid-\" + index + \"-popup\").off();\n var popup = new PopupMenu(button);\n _.each(options[\"operations\"], function(operation) {\n self._add_operation(popup, operation, item);\n });\n });\n },\n\n /** Add an operation to the items menu */\n _add_operation: function(popup, operation, item) {\n var self = this;\n var settings = item.operation_config[operation.label];\n if (settings.allowed && operation.allow_popup) {\n popup.addItem({\n html: operation.label,\n href: settings.url_args,\n target: settings.target,\n confirmation_text: operation.confirm,\n func: function(e) {\n e.preventDefault();\n var label = $(e.target).html();\n if (operation.onclick) {\n operation.onclick(item.encode_id);\n } else {\n self.execute(this.findItemByHtml(label));\n }\n }\n });\n }\n },\n\n // Add a condition to the grid filter; this adds the condition and refreshes the grid.\n add_filter_condition: function(name, value) {\n // Do nothing is value is empty.\n if (value === \"\") {\n return false;\n }\n\n // Add condition to grid.\n this.grid.add_filter(name, value, true);\n\n // Add button that displays filter and provides a button to delete it.\n var t = $(Templates.filter_element(name, value));\n var self = this;\n t.click(function() {\n // Remove visible element.\n $(this).remove();\n\n // Remove filter condition.\n self.remove_filter_condition(name, value);\n });\n\n // append to container\n var container = this.$el.find(\"#\" + name + \"-filtering-criteria\");\n container.append(t);\n\n // execute\n this.go_page_one();\n this.execute();\n },\n\n // Remove a condition to the grid filter; this adds the condition and refreshes the grid.\n remove_filter_condition: function(name, value) {\n // Remove filter condition.\n this.grid.remove_filter(name, value);\n\n // Execute\n this.go_page_one();\n this.execute();\n },\n\n // Set sort condition for grid.\n set_sort_condition: function(col_key) {\n // Set new sort condition. New sort is col_key if sorting new column; if reversing sort on\n // currently sorted column, sort is reversed.\n var cur_sort = this.grid.get(\"sort_key\");\n var new_sort = col_key;\n if (cur_sort.indexOf(col_key) !== -1) {\n // Reverse sort.\n if (cur_sort.substring(0, 1) !== \"-\") {\n new_sort = \"-\" + col_key;\n }\n }\n\n // Remove sort arrows elements.\n this.$el.find(\".sort-arrow\").remove();\n\n // Add sort arrow element to new sort column.\n var sort_arrow = new_sort.substring(0, 1) == \"-\" ? \"↑\" : \"↓\";\n var t = $(\"\" + sort_arrow + \"\").addClass(\"sort-arrow\");\n\n // Add to header\n this.$el.find(\"#\" + col_key + \"-header\").append(t);\n\n // Update grid.\n this.grid.set(\"sort_key\", new_sort);\n this.go_page_one();\n this.execute();\n },\n\n // Set new value for categorical filter.\n set_categorical_filter: function(name, new_value) {\n // Update filter hyperlinks to reflect new filter value.\n var category_filter = this.grid.get(\"categorical_filters\")[name],\n cur_value = this.grid.get(\"filters\")[name];\n var self = this;\n this.$el.find(\".\" + name + \"-filter\").each(function() {\n var text = $.trim($(this).text());\n var filter = category_filter[text];\n var filter_value = filter[name];\n if (filter_value == new_value) {\n // Remove filter link since grid will be using this filter. It is assumed that\n // this element has a single child, a hyperlink/anchor with text.\n $(this).empty();\n $(this).addClass(\"current-filter\");\n $(this).append(text);\n } else if (filter_value == cur_value) {\n // Add hyperlink for this filter since grid will no longer be using this filter. It is assumed that\n // this element has a single child, a hyperlink/anchor.\n $(this).empty();\n var t = $('' + text + \"\");\n t.click(function() {\n self.set_categorical_filter(name, filter_value);\n });\n $(this).removeClass(\"current-filter\");\n $(this).append(t);\n }\n });\n\n // Update grid.\n this.grid.add_filter(name, new_value);\n this.go_page_one();\n this.execute();\n },\n\n // Set page to view.\n set_page: function(new_page) {\n // Update page hyperlink to reflect new page.\n var self = this;\n this.$el.find(\".page-link\").each(function() {\n var id = $(this).attr(\"id\"),\n page_num = parseInt(id.split(\"-\")[2], 10), // Id has form 'page-link- \n cur_page = self.grid.get(\"cur_page\"),\n text;\n if (page_num === new_page) {\n // Remove link to page since grid will be on this page. It is assumed that\n // this element has a single child, a hyperlink/anchor with text.\n text = $(this)\n .children()\n .text();\n $(this).empty();\n $(this).addClass(\"inactive-link\");\n $(this).text(text);\n } else if (page_num === cur_page) {\n // Add hyperlink to this page since grid will no longer be on this page. It is assumed that\n // this element has a single child, a hyperlink/anchor.\n text = $(this).text();\n $(this).empty();\n $(this).removeClass(\"inactive-link\");\n var t = $('' + text + \"\");\n t.click(function() {\n self.set_page(page_num);\n });\n $(this).append(t);\n }\n });\n\n if (new_page === \"all\") {\n this.grid.set(\"cur_page\", new_page);\n } else {\n this.grid.set(\"cur_page\", parseInt(new_page, 10));\n }\n this.execute();\n },\n\n // confirmation/submission of operation request\n submit_operation: function(operation_button, confirmation_text) {\n // identify operation\n var operation_name = $(operation_button).val();\n\n // verify in any item is selected\n var number_of_checked_ids = this.$el.find('input[name=\"id\"]:checked')\n .length;\n if (!number_of_checked_ids > 0) {\n return false;\n }\n\n // Check to see if there's grid confirmation text for this operation\n var operation = _.findWhere(this.grid.attributes.operations, {\n label: operation_name\n });\n if (operation && !confirmation_text) {\n confirmation_text = operation.confirm || \"\";\n }\n\n // collect ids\n var item_ids = [];\n this.$el.find(\"input[name=id]:checked\").each(function() {\n item_ids.push($(this).val());\n });\n\n // execute operation\n var options = {\n operation: operation_name,\n id: item_ids,\n confirmation_text: confirmation_text\n };\n if (operation.target == \"top\") {\n options = _.extend(options, {\n href: operation.href,\n target: operation.target\n });\n }\n this.execute(options);\n return true;\n },\n\n check_all_items: function() {\n var check = this.$(\".grid-row-select-checkbox\");\n var state = this.$(\"#check_all\").prop(\"checked\");\n _.each(check, function(c) {\n $(c).prop(\"checked\", state);\n });\n this.init_grid_elements();\n },\n\n // Go back to page one; this is useful when a filter is applied.\n go_page_one: function() {\n // Need to go back to page 1 if not showing all.\n var cur_page = this.grid.get(\"cur_page\");\n if (cur_page !== null && cur_page !== undefined && cur_page !== \"all\") {\n this.grid.set(\"cur_page\", 1);\n }\n },\n\n //\n // execute operations and hyperlink requests\n //\n execute: function(options) {\n // get url\n var id = null;\n var href = null;\n var operation = null;\n var confirmation_text = null;\n var target = null;\n\n // check for options\n if (options) {\n // get options\n href = options.href;\n operation = options.operation;\n id = options.id;\n confirmation_text = options.confirmation_text;\n target = options.target;\n\n // check if input contains the operation tag\n if (href !== undefined && href.indexOf(\"operation=\") != -1) {\n // Get operation, id in hyperlink's href.\n var href_parts = href.split(\"?\");\n if (href_parts.length > 1) {\n var href_parms_str = href_parts[1];\n var href_parms = href_parms_str.split(\"&\");\n for (var index = 0; index < href_parms.length; index++) {\n if (href_parms[index].indexOf(\"operation\") != -1) {\n // Found operation parm; get operation value.\n operation = href_parms[index].split(\"=\")[1];\n operation = operation.replace(/\\+/g, \" \");\n } else if (href_parms[index].indexOf(\"id\") != -1) {\n // Found id parm; get id value.\n id = href_parms[index].split(\"=\")[1];\n }\n }\n }\n }\n }\n\n // check for operation details\n if (operation && id) {\n // show confirmation box\n if (\n confirmation_text &&\n confirmation_text != \"\" &&\n confirmation_text != \"None\" &&\n confirmation_text != \"null\"\n )\n if (!confirm(confirmation_text)) return false;\n\n // use small characters for operation?!\n operation = operation.toLowerCase();\n\n // Update grid.\n this.grid.set({\n operation: operation,\n item_ids: id\n });\n\n // Do operation. If operation cannot be performed asynchronously, redirect to location.\n if (target == \"top\") {\n window.top.location =\n href + \"?\" + $.param(this.grid.get_url_data());\n } else if (this.grid.can_async_op(operation) || this.dict_format) {\n this.update_grid();\n } else {\n this.go_to(target, href);\n }\n\n // done\n return false;\n }\n\n // refresh grid\n if (href) {\n this.go_to(target, href);\n return false;\n }\n\n // refresh grid\n if (this.grid.get(\"async\") || this.dict_format) {\n this.update_grid();\n } else {\n this.go_to(target, href);\n }\n\n // done\n return false;\n },\n\n // go to url\n go_to: function(target, href) {\n // get aysnc status\n var async = this.grid.get(\"async\");\n this.grid.set(\"async\", false);\n\n // get slide status\n var advanced_search = this.$el.find(\"#advanced-search\").is(\":visible\");\n this.grid.set(\"advanced_search\", advanced_search);\n\n // get default url\n if (!href) {\n href =\n this.grid.get(\"url_base\") +\n \"?\" +\n $.param(this.grid.get_url_data());\n }\n\n // clear grid of transient request attributes.\n this.grid.set({\n operation: undefined,\n item_ids: undefined,\n async: async\n });\n switch (target) {\n case \"inbound\":\n // this currently assumes that there is only a single grid shown at a time\n var $div = $(\".grid-header\").closest(\".inbound\");\n if ($div.length !== 0) {\n $div.load(href);\n return;\n }\n break;\n case \"top\":\n window.top.location = href;\n break;\n default:\n window.location = href;\n }\n },\n\n // Update grid.\n update_grid: function() {\n // If there's an operation, do POST; otherwise, do GET.\n var method = this.grid.get(\"operation\") ? \"POST\" : \"GET\";\n\n // Show overlay to indicate loading and prevent user actions.\n this.$el.find(\".loading-elt-overlay\").show();\n var self = this;\n $.ajax({\n type: method,\n url: self.grid.get(\"url_base\"),\n data: self.grid.get_url_data(),\n error: function(response) {\n alert(\"Grid refresh failed\");\n },\n success: function(response_text) {\n // backup\n var embedded = self.grid.get(\"embedded\");\n var insert = self.grid.get(\"insert\");\n var advanced_search = self.$el\n .find(\"#advanced-search\")\n .is(\":visible\");\n\n // request new configuration\n var json = self.dict_format\n ? response_text\n : $.parseJSON(response_text);\n\n // update\n json.embedded = embedded;\n json.insert = insert;\n json.advanced_search = advanced_search;\n\n // Initialize new grid config\n self.init_grid(json);\n\n // Hide loading overlay.\n self.$el.find(\".loading-elt-overlay\").hide();\n },\n complete: function() {\n // Clear grid of transient request attributes.\n self.grid.set({\n operation: undefined,\n item_ids: undefined\n });\n }\n });\n }\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/history/copy-dialog.js.map b/static/maps/mvc/history/copy-dialog.js.map index 07b4e87de9b..8e2513b54eb 100644 --- a/static/maps/mvc/history/copy-dialog.js.map +++ b/static/maps/mvc/history/copy-dialog.js.map @@ -1 +1 @@ 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MODAL from \"mvc/ui/ui-modal\";\nimport ERROR_MODAL from \"mvc/ui/error-modal\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\n/**\n * A dialog/modal that allows copying a user history or 'importing' from user\n * another. Generally called via historyCopyDialog below.\n * @type {Object}\n */\nvar CopyDialog = {\n // language related strings/fns\n defaultName: _.template(\"Copy of '<%- name %>'\"),\n title: _.template(_l(\"Copying history\") + ' \"<%- name %>\"'),\n submitLabel: _l(\"Copy\"),\n errorMessage: _l(\"History could not be copied.\"),\n progressive: _l(\"Copying history\"),\n activeLabel: _l(\"Copy only the active, non-deleted datasets\"),\n allLabel: _l(\"Copy all datasets including deleted ones\"),\n anonWarning:\n _l(\n \"As an anonymous user, unless you login or register, you will lose your current history \"\n ) + _l(\"after copying this history. \"),\n\n // template for modal body\n _template: _.template(\n [\n //TODO: remove inline styles\n // show a warning message for losing current to anon users\n \"<% if( isAnon ){ %>\",\n '\",\n \"<% } %>\",\n \"\"\n ].join(\"\")\n ),\n\n // empty modal body and let the user know the copy is happening\n _showAjaxIndicator: function _showAjaxIndicator() {\n var indicator =\n ' ' +\n this.progressive +\n \"...
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Generally called via historyCopyDialog below.\n * @type {Object}\n */\nvar CopyDialog = {\n // language related strings/fns\n defaultName: _.template(\"Copy of '<%- name %>'\"),\n title: _.template(_l(\"Copying history\") + ' \"<%- name %>\"'),\n submitLabel: _l(\"Copy\"),\n errorMessage: _l(\"History could not be copied.\"),\n progressive: _l(\"Copying history\"),\n activeLabel: _l(\"Copy only the active, non-deleted datasets\"),\n allLabel: _l(\"Copy all datasets including deleted ones\"),\n anonWarning:\n _l(\n \"As an anonymous user, unless you login or register, you will lose your current history \"\n ) + _l(\"after copying this history. \"),\n\n // template for modal body\n _template: _.template(\n [\n //TODO: remove inline styles\n // show a warning message for losing current to anon users\n \"<% if( isAnon ){ %>\",\n '\",\n \"<% } %>\",\n \"\"\n ].join(\"\")\n ),\n\n // empty modal body and let the user know the copy is happening\n _showAjaxIndicator: function _showAjaxIndicator() {\n var indicator =\n ' ' +\n this.progressive +\n \"...
\";\n this.modal\n .$(\".modal-body\")\n .empty()\n .append(indicator)\n .css({ \"margin-top\": \"8px\" });\n },\n\n // (sorta) public interface - display the modal, render the form, and potentially copy the history\n // returns a jQuery.Deferred done->history copied, fail->user cancelled\n dialog: function _dialog(modal, history, options) {\n options = options || {};\n\n var dialog = this,\n deferred = jQuery.Deferred(),\n // TODO: getting a little byzantine here\n defaultCopyNameFn = options.nameFn || this.defaultName,\n defaultCopyName = defaultCopyNameFn({\n name: history.get(\"name\")\n }),\n // TODO: these two might be simpler as one 3 state option (all,active,no-choice)\n defaultCopyWhat = options.allDatasets\n ? \"copy-all\"\n : \"copy-non-deleted\",\n allowAll = !_.isUndefined(options.allowAll)\n ? options.allowAll\n : true,\n autoClose = !_.isUndefined(options.autoClose)\n ? options.autoClose\n : true;\n\n this.modal = modal;\n\n // validate the name and copy if good\n function checkNameAndCopy() {\n var name = modal.$(\"#copy-modal-title\").val();\n if (!name) {\n modal.$(\".invalid-title\").show();\n return;\n }\n // get further settings, shut down and indicate the ajax call, then hide and resolve/reject\n var copyAllDatasets =\n modal.$('input[name=\"copy-what\"]:checked').val() === \"copy-all\";\n modal.$(\"button\").prop(\"disabled\", true);\n dialog._showAjaxIndicator();\n history\n .copy(true, name, copyAllDatasets)\n .done(function(response) {\n deferred.resolve(response);\n })\n .fail(function(xhr, status, message) {\n var options = {\n name: name,\n copyAllDatasets: copyAllDatasets\n };\n ERROR_MODAL.ajaxErrorModal(\n history,\n xhr,\n options,\n dialog.errorMessage\n );\n deferred.rejectWith(deferred, arguments);\n })\n .done(function() {\n if (autoClose) {\n modal.hide();\n }\n });\n }\n\n var originalClosingCallback = options.closing_callback;\n modal.show(\n _.extend(options, {\n title: this.title({ name: history.get(\"name\") }),\n body: $(\n dialog._template({\n name: defaultCopyName,\n isAnon: Galaxy.user.isAnonymous(),\n allowAll: allowAll,\n copyWhat: defaultCopyWhat,\n activeLabel: this.activeLabel,\n allLabel: this.allLabel,\n anonWarning: this.anonWarning\n })\n ),\n buttons: _.object([\n [\n _l(\"Cancel\"),\n function() {\n modal.hide();\n }\n ],\n [this.submitLabel, checkNameAndCopy]\n ]),\n height: \"auto\",\n closing_events: true,\n closing_callback: function _historyCopyClose(cancelled) {\n if (cancelled) {\n deferred.reject({ cancelled: true });\n }\n if (originalClosingCallback) {\n originalClosingCallback(cancelled);\n }\n }\n })\n );\n\n // set the default dataset copy, autofocus the title, and set up for a simple return\n modal\n .$(\"#copy-modal-title\")\n .focus()\n .select();\n modal.$(\"#copy-modal-title\").on(\"keydown\", function(ev) {\n if (ev.keyCode === 13) {\n ev.preventDefault();\n checkNameAndCopy();\n }\n });\n\n return deferred;\n }\n};\n\n//==============================================================================\n// maintain the (slight) distinction between copy and import\n/**\n * Subclass CopyDialog to use the import language.\n */\nvar ImportDialog = _.extend({}, CopyDialog, {\n defaultName: _.template(\"imported: <%- name %>\"),\n title: _.template(_l(\"Importing history\") + ' \"<%- name %>\"'),\n submitLabel: _l(\"Import\"),\n errorMessage: _l(\"History could not be imported.\"),\n progressive: _l(\"Importing history\"),\n activeLabel: _l(\"Import only the active, non-deleted datasets\"),\n allLabel: _l(\"Import all datasets including deleted ones\"),\n anonWarning:\n _l(\n \"As an anonymous user, unless you login or register, you will lose your current history \"\n ) + _l(\"after importing this history. \")\n});\n\n//==============================================================================\n/**\n * Main interface for both history import and history copy dialogs.\n * @param {Backbone.Model} history the history to copy\n * @param {Object} options a hash\n * @return {jQuery.Deferred} promise that fails on close and succeeds on copy\n *\n * options:\n * (this object is also passed to the modal used to display the dialog and accepts modal options)\n * {Function} nameFn if defined, use this to build the default name shown to the user\n * (the fn is passed: {name:})\n * {bool} useImport if true, use the 'import' language (instead of Copy)\n * {bool} allowAll if true, allow the user to choose between copying all datasets and\n * only non-deleted datasets\n * {String} allDatasets default initial checked radio button: 'copy-all' or 'copy-non-deleted',\n */\nvar historyCopyDialog = function(history, options) {\n options = options || {};\n // create our own modal if Galaxy doesn't have one (mako tab without use_panels)\n var modal = window.parent.Galaxy.modal || new MODAL.View({});\n return options.useImport\n ? ImportDialog.dialog(modal, history, options)\n : CopyDialog.dialog(modal, history, options);\n};\n\n//==============================================================================\nexport default historyCopyDialog;\n"]} \ No newline at end of file diff --git a/static/maps/mvc/history/hda-li-edit.js.map b/static/maps/mvc/history/hda-li-edit.js.map index 0de832a10c0..f5f80271c43 100644 --- a/static/maps/mvc/history/hda-li-edit.js.map +++ b/static/maps/mvc/history/hda-li-edit.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/history/hda-li-edit.js"],"names":["_datasetLiEdit","require","_hdaLi","_baseMvc","_localization","_super","_datasetLiEdit2","default","DatasetListItemEdit","HDAListItemEdit","extend","className","prototype","_fetchModelDetails","view","this","model","inReadyState","hasDetails","fetch","silent","has","jQuery","when","data","join","events","_","clone","templates","warnings","_localization2","modelString","hidden","_hdaLi2","HDAListItemView","wrapTemplate","titleBar"],"mappings":"4IAAA,IAAAA,eAAAC,QAAA,sFACAC,OAAAD,QAAA,6DACAE,SAAAF,QAAA,2DACAG,cAAAH,QAAA,2EAHAI,OAAAC,gBAAAC,QAAAC,oBASIC,gBAAkBJ,OAAOK,QAErBC,UAAWN,OAAOO,UAAUD,UAAY,mBAKxCE,mBAAoB,WAChB,IAAIC,EAAOC,KAdvB,OAAAD,EAAAE,MAAAC,iBAAAH,EAAAE,MAAAE,aAgBuBJ,EAAKE,MAAMG,OAAQC,QAAQ,IAI1BN,EAAKE,MAAMK,IAAI,cAV/BC,OAAAC,OARRT,EAAAE,MAAAG,OACaC,QAAA,EACbI,MAEsBnB,MAAOK,aAAP,gBAAAe,KAAA,SAQVC,OAAIZ,EAAAA,OAAJa,EAAAC,MAAAvB,OAAAO,UAAAc,SACIZ,qBAAWG,SAAmBH,GAqB9B,OApBAC,KAAOD,MAAKE,UAoBL,KAdHI,SAAAA,WAEI,MAAA,oBADEL,KAAAC,MAAAD,KAAAC,MAAA,GAAA,cACF,OA0BxBP,gBAAgBG,UAAUiB,UAAa,WAlB/B,IAAAC,EAAAH,EAAAjB,UAAAL,OAAAO,UAAAiB,UAAAC,UACAJ,OAAUhB,UAAAA,QAASkB,cAEX,gCAEH,gDA9B+B,EAAAG,eAAAxB,SAAA,gCAmD5B,8DAlBR,EAAAwB,eAAAxB,SAAA,aACU,OACFyB,SACG,WArCnB,aA4CAvB,OAAAA,EAAAA,UAAgBG,OAAUiB,UAAaA,WAE/BI,SAAQC,QAAA3B,QAAA4B,gBAASC,UAETP,UAAAQ,SACAP,SAAAA,IALuB,oBAoB/BO,gBAAU5B","file":"../../../scripts/mvc/history/hda-li-edit.js","sourcesContent":["import DATASET_LI_EDIT from \"mvc/dataset/dataset-li-edit\";\nimport HDA_LI from \"mvc/history/hda-li\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\nvar _super = DATASET_LI_EDIT.DatasetListItemEdit;\n/** @class Editing view for HistoryDatasetAssociation.\n */\nvar HDAListItemEdit = _super.extend(\n /** @lends HDAListItemEdit.prototype */ {\n className: _super.prototype.className + \" history-content\",\n\n /** In this override, only get details if in the ready state, get rerunnable if in other states.\n * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n */\n _fetchModelDetails: function() {\n var view = this;\n if (view.model.inReadyState() && !view.model.hasDetails()) {\n return view.model.fetch({ silent: true });\n\n // special case the need for the rerunnable and creating_job attributes\n // needed for rendering re-run button on queued, running datasets\n } else if (!view.model.has(\"rerunnable\")) {\n return view.model.fetch({\n silent: true,\n data: {\n // only fetch rerunnable and creating_job to keep overhead down\n keys: [\"rerunnable\", \"creating_job\"].join(\",\")\n }\n });\n }\n return jQuery.when();\n },\n\n /** event map */\n events: _.extend(_.clone(_super.prototype.events), {\n \"click .unhide-link\": function(ev) {\n this.model.unhide();\n return false;\n }\n }),\n\n /** string rep */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"HDAListItemEdit(\" + modelString + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nHDAListItemEdit.prototype.templates = (function() {\n var warnings = _.extend({}, _super.prototype.templates.warnings, {\n hidden: BASE_MVC.wrapTemplate(\n [\n \"<% if( !dataset.visible ){ %>\",\n // add a link to unhide a dataset\n ' ',\n _l(\"This dataset has been hidden\"),\n '\",\n \"<% } %>\"\n ],\n \"dataset\"\n )\n });\n\n return _.extend({}, _super.prototype.templates, {\n //NOTE: *steal* the HDAListItemView titleBar\n titleBar: HDA_LI.HDAListItemView.prototype.templates.titleBar,\n warnings: warnings\n });\n})();\n\n//==============================================================================\nexport default {\n HDAListItemEdit: HDAListItemEdit\n};\n"]} \ No newline at end of file +{"version":3,"sources":["mvc/history/hda-li-edit.js"],"names":["_super","_datasetLiEdit2","default","DatasetListItemEdit","HDAListItemEdit","extend","className","prototype","_fetchModelDetails","view","this","model","inReadyState","hasDetails","fetch","silent","has","data","keys","join","events","_","clone","click .unhide-link","ev","unhide","templates","warnings","hidden","_baseMvc2","wrapTemplate","toString","modelString","_localization2","titleBar","_hdaLi2","HDAListItemView"],"mappings":"+QAMIA,EAASC,EAAAC,QAAgBC,oBAGzBC,EAAkBJ,EAAOK,QAErBC,UAAWN,EAAOO,UAAUD,UAAY,mBAKxCE,mBAAoB,WAChB,IAAIC,EAAOC,KACX,OAAID,EAAKE,MAAMC,iBAAmBH,EAAKE,MAAME,aAClCJ,EAAKE,MAAMG,OAAQC,QAAQ,IAZlDN,EAAAE,MAAAK,IAAA,cASQR,OAAAA,OAQeC,EAAKE,MAAMG,OAf9BV,QAAkBJ,EAClBiB,MAkBoBC,MAAO,aAAc,gBAAgBC,KAAK,SAQ1DC,OAAQC,EAAEhB,OAAOgB,EAAEC,MAAMtB,EAAOO,UAAUa,SAflCG,qBAAA,SAAAC,GAHJ,OAIId,KAAAC,MAAAc,UACO,KAKCP,SAAAA,WAJgB,MAAxB,oBAEUR,KAAAC,MAAAD,KAAAC,MAAA,GAAA,cAFV,OAaJP,EAAAG,UAAAmB,UAAsB,WAClB,IAAAC,EAAAN,EAAKV,UAAMc,EAAXlB,UAAAmB,UAAAC,UACAC,OAAAC,EAAA3B,QAAO4B,cA7BqB,gCAiCpC,gDACAC,EAAAA,EAAAA,SAAU,gCACFC,8DACJ,EAAAC,EAAA/B,SAAO,aACV,OAtCT,SAwDgB,WAbhB,aAMgB,OAAAmB,EAAAhB,UAAAL,EAAAO,UAAAmB,WAJqDQ,SAAjEC,EAAAjC,QAAAkC,gBAAA7B,UAAAmB,UAAAQ,SAoBIP,SAAUA,IArCgB,cAuCjCvB,gBAvBDA","file":"../../../scripts/mvc/history/hda-li-edit.js","sourcesContent":["import DATASET_LI_EDIT from \"mvc/dataset/dataset-li-edit\";\nimport HDA_LI from \"mvc/history/hda-li\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\nvar _super = DATASET_LI_EDIT.DatasetListItemEdit;\n/** @class Editing view for HistoryDatasetAssociation.\n */\nvar HDAListItemEdit = _super.extend(\n /** @lends HDAListItemEdit.prototype */ {\n className: _super.prototype.className + \" history-content\",\n\n /** In this override, only get details if in the ready state, get rerunnable if in other states.\n * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n */\n _fetchModelDetails: function() {\n var view = this;\n if (view.model.inReadyState() && !view.model.hasDetails()) {\n return view.model.fetch({ silent: true });\n\n // special case the need for the rerunnable and creating_job attributes\n // needed for rendering re-run button on queued, running datasets\n } else if (!view.model.has(\"rerunnable\")) {\n return view.model.fetch({\n silent: true,\n data: {\n // only fetch rerunnable and creating_job to keep overhead down\n keys: [\"rerunnable\", \"creating_job\"].join(\",\")\n }\n });\n }\n return jQuery.when();\n },\n\n /** event map */\n events: _.extend(_.clone(_super.prototype.events), {\n \"click .unhide-link\": function(ev) {\n this.model.unhide();\n return false;\n }\n }),\n\n /** string rep */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"HDAListItemEdit(\" + modelString + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nHDAListItemEdit.prototype.templates = (function() {\n var warnings = _.extend({}, _super.prototype.templates.warnings, {\n hidden: BASE_MVC.wrapTemplate(\n [\n \"<% if( !dataset.visible ){ %>\",\n // add a link to unhide a dataset\n '
',\n _l(\"Unhide it\"),\n \"\",\n \"',\n _l(\"This dataset has been hidden\"),\n '\",\n \"<% } %>\"\n ],\n \"dataset\"\n )\n });\n\n return _.extend({}, _super.prototype.templates, {\n //NOTE: *steal* the HDAListItemView titleBar\n titleBar: HDA_LI.HDAListItemView.prototype.templates.titleBar,\n warnings: warnings\n });\n})();\n\n//==============================================================================\nexport default {\n HDAListItemEdit: HDAListItemEdit\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/history/hda-li.js.map b/static/maps/mvc/history/hda-li.js.map index 7275283c93a..63163ce732d 100644 --- a/static/maps/mvc/history/hda-li.js.map +++ b/static/maps/mvc/history/hda-li.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/history/hda-li.js"],"names":["_datasetLi","require","_baseMvc","_localization","_super","_datasetLi2","default","DatasetListItemView","HDAListItemView","extend","className","prototype","initialize","attributes","options","call","this","model","templates","_baseMvc2","modelString","titleBarTemplate","warnings","_","hidden","wrapTemplate","titleBar"],"mappings":"4IAAA,IAAAA,WAAAC,QAAA,yEACAC,SAAAD,QAAA,2DACAE,cAAAF,QAAA,2EAGIG,OAASC,YAAAC,QAAWC,oBAMpBC,gBAAkBJ,OAAOK,QAErBC,UAAWN,OAAOO,UAAUD,UAAY,mBAExCE,WAAY,SAASC,EAAYC,GAC7BV,OAAOO,UAAUC,WAAWG,KAAKC,KAAMH,EAAYC,IAX3DV,SAAS,WAkBD,MAAO,oBAjBnBY,KAAAC,MAAAD,KAAAC,MAAA,GAAA,cAiBsD,OAOtDT,gBAAgBG,UAAUO,UAAa,WAf/BN,IAAAA,EAAYO,UAAAb,QAASO,cAmBjB,6CAfJ,mCACA,sBAEQO,+CACJ,gDACH,SAbT,QA+BY,0BAdZ,wFACA,wCACAZ,4DACQa,UAEI,YACA,UAGA,UAcJ,WAMQC,EAAAC,EAAAd,UAAAL,OAAAO,UAAAO,UAAAI,UACAE,OAAAL,UAAAb,QAAAmB,cAUHhB,gCACLiB,gDACAJ,EAAAA,eAAAA,SAAUA,gCAFd,SAtCJ,WA4CA,aANI,OAAOC,EAAEd,UAAWL,OAAOO,UAAUO,WACjCQ,SAAUL,EACVC,SAAUA,IAxCqB,oBA8CnCd,gBAAiBA","file":"../../../scripts/mvc/history/hda-li.js","sourcesContent":["import DATASET_LI from \"mvc/dataset/dataset-li\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\nvar _super = DATASET_LI.DatasetListItemView;\n/** @class Read only view for HistoryDatasetAssociation.\n * Since there are no controls on the HDAView to hide the dataset,\n * the primary thing this class does (currently) is override templates\n * to render the HID.\n */\nvar HDAListItemView = _super.extend(\n /** @lends HDAListItemView.prototype */ {\n className: _super.prototype.className + \" history-content\",\n\n initialize: function(attributes, options) {\n _super.prototype.initialize.call(this, attributes, options);\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"HDAListItemView(\" + modelString + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nHDAListItemView.prototype.templates = (function() {\n var titleBarTemplate = BASE_MVC.wrapTemplate(\n [\n // adding the hid display to the title\n '\"\n ],\n \"dataset\"\n );\n\n var warnings = _.extend({}, _super.prototype.templates.warnings, {\n hidden: BASE_MVC.wrapTemplate(\n [\n // add a warning when hidden\n \"<% if( !dataset.visible ){ %>\",\n '
',\n _l(\"Unhide it\"),\n \"\",\n \"',\n _l(\"This dataset has been hidden\"),\n \"\",\n \"<% } %>\"\n ],\n \"dataset\"\n )\n });\n\n return _.extend({}, _super.prototype.templates, {\n titleBar: titleBarTemplate,\n warnings: warnings\n });\n})();\n\n//==============================================================================\nexport default {\n HDAListItemView: HDAListItemView\n};\n"]} \ No newline at end of file +{"version":3,"sources":["mvc/history/hda-li.js"],"names":["_super","_datasetLi2","default","DatasetListItemView","HDAListItemView","extend","className","prototype","initialize","attributes","options","call","this","toString","model","templates","titleBarTemplate","warnings","_","hidden","_baseMvc2","wrapTemplate","titleBar","_localization2"],"mappings":"4OAKIA,EAASC,EAAAC,QAAWC,oBAMpBC,EAAkBJ,EAAOK,QAErBC,UAAWN,EAAOO,UAAUD,UAAY,mBAExCE,WAAY,SAASC,EAAYC,GAC7BV,EAAOO,UAAUC,WAAWG,KAAKC,KAAMH,EAAYC,IAV/DG,SAAA,WAiBY,MAAO,oBADWD,KAAKE,MAAQF,KAAKE,MAAQ,GAAK,cACP,OAR9CN,EAAAA,UAAYO,UAAA,WACRf,IAAAA,EAAOO,EAAAA,QAAUC,cAGrB,6CACA,mCACAK,sBAEI,+CACH,gDAbT,SA8BY,QAbZ,0BACA,wFACAT,wCACQY,4DAEI,UACA,YAGA,UACA,UAgBR,WAIYC,EAAAC,EAAAb,UAAAL,EAAAO,UACAQ,UAAAE,UALqDE,OAAjEC,EAAAlB,QAAAmB,cAeIC,gCACAL,gDAFJ,EAAAM,EAAArB,SAAA,gCAtCJ,SAgCgB,WAEJ,aAIR,OAAOgB,EAAEb,UAAWL,EAAOO,UAAUQ,WACjCO,SAAUN,EACVC,SAAUA,IAvDE,cA6DhBb,gBAAiBA","file":"../../../scripts/mvc/history/hda-li.js","sourcesContent":["import DATASET_LI from \"mvc/dataset/dataset-li\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\nvar _super = DATASET_LI.DatasetListItemView;\n/** @class Read only view for HistoryDatasetAssociation.\n * Since there are no controls on the HDAView to hide the dataset,\n * the primary thing this class does (currently) is override templates\n * to render the HID.\n */\nvar HDAListItemView = _super.extend(\n /** @lends HDAListItemView.prototype */ {\n className: _super.prototype.className + \" history-content\",\n\n initialize: function(attributes, options) {\n _super.prototype.initialize.call(this, attributes, options);\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"HDAListItemView(\" + modelString + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nHDAListItemView.prototype.templates = (function() {\n var titleBarTemplate = BASE_MVC.wrapTemplate(\n [\n // adding the hid display to the title\n '\"\n ],\n \"dataset\"\n );\n\n var warnings = _.extend({}, _super.prototype.templates.warnings, {\n hidden: BASE_MVC.wrapTemplate(\n [\n // add a warning when hidden\n \"<% if( !dataset.visible ){ %>\",\n '',\n _l(\"This dataset has been hidden\"),\n \"\",\n \"<% } %>\"\n ],\n \"dataset\"\n )\n });\n\n return _.extend({}, _super.prototype.templates, {\n titleBar: titleBarTemplate,\n warnings: warnings\n });\n})();\n\n//==============================================================================\nexport default {\n HDAListItemView: HDAListItemView\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/history/hda-model.js.map b/static/maps/mvc/history/hda-model.js.map index 6a7bbb8f13d..2e7bf3a07d6 100644 --- a/static/maps/mvc/history/hda-model.js.map +++ b/static/maps/mvc/history/hda-model.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/history/hda-model.js"],"names":["_datasetModel","require","_historyContentModel","_baseMvc","_localization","_super","_datasetModel2","default","DatasetAssociation","hcontentMixin","_historyContentModel2","HistoryContentMixin","HistoryDatasetAssociation","extend","_baseMvc2","mixin","defaults","_","prototype","history_content_type","model_class"],"mappings":"4IAAA,IAAAA,cAAAC,QAAA,kFACAC,qBAAAD,QAAA,wGACAE,SAAAF,QAAA,2DACAG,cAAAH,QAAA,2EAHAI,OAAAC,eAAAC,QAAAC,mBAOIC,cAAgBC,sBAAAH,QAAgBI,oBANpCC,0BAAAP,OAAAQ,OAUIC,UAAAP,QAASQ,MACLN,eAGIO,SAAUC,EAAEJ,UAERR,OAAOa,UAAUF,SAdjCP,cAAAO,UAiBoBG,qBAAsB,UACtBC,YAAa,kDARzBR,0BAAAA","file":"../../../scripts/mvc/history/hda-model.js","sourcesContent":["import DATASET from \"mvc/dataset/dataset-model\";\nimport HISTORY_CONTENT from \"mvc/history/history-content-model\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\nvar _super = DATASET.DatasetAssociation,\n hcontentMixin = HISTORY_CONTENT.HistoryContentMixin;\n/** @class (HDA) model for a Galaxy dataset contained in and related to a history.\n */\nvar HistoryDatasetAssociation = _super.extend(\n BASE_MVC.mixin(\n hcontentMixin,\n /** @lends HistoryDatasetAssociation.prototype */ {\n /** default attributes for a model */\n defaults: _.extend(\n {},\n _super.prototype.defaults,\n hcontentMixin.defaults,\n {\n history_content_type: \"dataset\",\n model_class: \"HistoryDatasetAssociation\"\n }\n )\n }\n )\n);\n\n//==============================================================================\nexport default {\n HistoryDatasetAssociation: HistoryDatasetAssociation\n};\n"]} \ No newline at end of file +{"version":3,"sources":["mvc/history/hda-model.js"],"names":["_super","_datasetModel2","default","DatasetAssociation","hcontentMixin","_historyContentModel2","HistoryContentMixin","HistoryDatasetAssociation","extend","_baseMvc2","mixin","defaults","_","prototype","history_content_type","model_class"],"mappings":"qRAMIA,QAASC,EAAAC,QAAQC,oBACjBC,EAAgBC,EAAAH,QAAgBI,oBAGhCC,EAA4BP,EAAOQ,OACnCC,EAAAP,QAASQ,MACLN,GAGIO,SAAUC,EAAEJ,UAERR,EAAOa,UAAUF,SACjBP,EAAcO,UAEVG,qBAAsB,UAf1CC,YAAA,4CAeoBD,0BAAAA","file":"../../../scripts/mvc/history/hda-model.js","sourcesContent":["import DATASET from \"mvc/dataset/dataset-model\";\nimport HISTORY_CONTENT from \"mvc/history/history-content-model\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\nvar _super = DATASET.DatasetAssociation,\n hcontentMixin = HISTORY_CONTENT.HistoryContentMixin;\n/** @class (HDA) model for a Galaxy dataset contained in and related to a history.\n */\nvar HistoryDatasetAssociation = _super.extend(\n BASE_MVC.mixin(\n hcontentMixin,\n /** @lends HistoryDatasetAssociation.prototype */ {\n /** default attributes for a model */\n defaults: _.extend(\n {},\n _super.prototype.defaults,\n hcontentMixin.defaults,\n {\n history_content_type: \"dataset\",\n model_class: \"HistoryDatasetAssociation\"\n }\n )\n }\n )\n);\n\n//==============================================================================\nexport default {\n HistoryDatasetAssociation: HistoryDatasetAssociation\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/history/hdca-li-edit.js.map b/static/maps/mvc/history/hdca-li-edit.js.map index 95c217db878..74e906d62bd 100644 --- a/static/maps/mvc/history/hdca-li-edit.js.map +++ b/static/maps/mvc/history/hdca-li-edit.js.map @@ -1 +1 @@ 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HDCA_LI from \"mvc/history/hdca-li\";\nimport DC_VIEW_EDIT from \"mvc/collection/collection-view-edit\";\nimport faIconButton from \"ui/fa-icon-button\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\nvar _super = HDCA_LI.HDCAListItemView;\n/** @class Editing view for HistoryDatasetCollectionAssociation.\n */\nvar HDCAListItemEdit = _super.extend(\n /** @lends HDCAListItemEdit.prototype */ {\n /** logger used to record this.log messages, commonly set to console */\n //logger : console,\n\n /** Override to return editable versions of the collection panels */\n _getFoldoutPanelClass: function() {\n switch (this.model.get(\"collection_type\")) {\n case \"list\":\n return DC_VIEW_EDIT.ListCollectionViewEdit;\n case \"paired\":\n return DC_VIEW_EDIT.PairCollectionViewEdit;\n case \"list:paired\":\n return DC_VIEW_EDIT.ListOfPairsCollectionViewEdit;\n case \"list:list\":\n return DC_VIEW_EDIT.ListOfListsCollectionViewEdit;\n }\n throw new TypeError(\n \"Uknown collection_type: \" + this.model.get(\"collection_type\")\n );\n },\n\n // ......................................................................... delete\n /** In this override, add the delete button. */\n _renderPrimaryActions: function() {\n this.log(this + \"._renderPrimaryActions\");\n // render the display, edit attr and delete icon-buttons\n return _super.prototype._renderPrimaryActions\n .call(this)\n .concat([this._renderDeleteButton()]);\n },\n\n /** Render icon-button to delete this collection. */\n _renderDeleteButton: function() {\n var self = this,\n deleted = this.model.get(\"deleted\");\n return faIconButton({\n title: deleted\n ? _l(\"Dataset collection is already deleted\")\n : _l(\"Delete\"),\n classes: \"delete-btn\",\n faIcon: \"fa-times\",\n disabled: deleted,\n onclick: function() {\n // ...bler... tooltips being left behind in DOM (hover out never called on deletion)\n self.$el.find(\".icon-btn.delete-btn\").trigger(\"mouseout\");\n self.model[\"delete\"]();\n }\n });\n },\n\n // ......................................................................... misc\n /** string rep */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"HDCAListItemEdit(\" + modelString + \")\";\n }\n }\n);\n\n//==============================================================================\nexport default {\n HDCAListItemEdit: HDCAListItemEdit\n};\n"]} \ No newline at end of file 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HDCA_LI from \"mvc/history/hdca-li\";\nimport DC_VIEW_EDIT from \"mvc/collection/collection-view-edit\";\nimport faIconButton from \"ui/fa-icon-button\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\nvar _super = HDCA_LI.HDCAListItemView;\n/** @class Editing view for HistoryDatasetCollectionAssociation.\n */\nvar HDCAListItemEdit = _super.extend(\n /** @lends HDCAListItemEdit.prototype */ {\n /** logger used to record this.log messages, commonly set to console */\n //logger : console,\n\n /** Override to return editable versions of the collection panels */\n _getFoldoutPanelClass: function() {\n switch (this.model.get(\"collection_type\")) {\n case \"list\":\n return DC_VIEW_EDIT.ListCollectionViewEdit;\n case \"paired\":\n return DC_VIEW_EDIT.PairCollectionViewEdit;\n case \"list:paired\":\n return DC_VIEW_EDIT.ListOfPairsCollectionViewEdit;\n case \"list:list\":\n return DC_VIEW_EDIT.ListOfListsCollectionViewEdit;\n }\n throw new TypeError(\n \"Uknown collection_type: \" + this.model.get(\"collection_type\")\n );\n },\n\n // ......................................................................... delete\n /** In this override, add the delete button. */\n _renderPrimaryActions: function() {\n this.log(this + \"._renderPrimaryActions\");\n // render the display, edit attr and delete icon-buttons\n return _super.prototype._renderPrimaryActions\n .call(this)\n .concat([this._renderDeleteButton()]);\n },\n\n /** Render icon-button to delete this collection. */\n _renderDeleteButton: function() {\n var self = this,\n deleted = this.model.get(\"deleted\");\n return faIconButton({\n title: deleted\n ? _l(\"Dataset collection is already deleted\")\n : _l(\"Delete\"),\n classes: \"delete-btn\",\n faIcon: \"fa-times\",\n disabled: deleted,\n onclick: function() {\n // ...bler... tooltips being left behind in DOM (hover out never called on deletion)\n self.$el.find(\".icon-btn.delete-btn\").trigger(\"mouseout\");\n self.model[\"delete\"]();\n }\n });\n },\n\n // ......................................................................... misc\n /** string rep */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"HDCAListItemEdit(\" + modelString + \")\";\n }\n }\n);\n\n//==============================================================================\nexport default {\n HDCAListItemEdit: HDCAListItemEdit\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/history/hdca-li.js.map b/static/maps/mvc/history/hdca-li.js.map index fb80862a2c5..632807d0a33 100644 --- a/static/maps/mvc/history/hdca-li.js.map +++ b/static/maps/mvc/history/hdca-li.js.map @@ -1 +1 @@ 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STATES from \"mvc/dataset/states\";\nimport DC_LI from \"mvc/collection/collection-li\";\nimport DC_VIEW from \"mvc/collection/collection-view\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\nvar _super = DC_LI.DCListItemView;\n/** @class Read only view for HistoryDatasetCollectionAssociation (a dataset collection inside a history).\n */\nvar HDCAListItemView = _super.extend(\n /** @lends HDCAListItemView.prototype */ {\n className: _super.prototype.className + \" history-content\",\n\n /** event listeners */\n _setUpListeners: function() {\n _super.prototype._setUpListeners.call(this);\n this.listenTo(this.model, {\n \"change:tags change:populated change:visible\": function(\n model,\n options\n ) {\n this.render();\n }\n });\n },\n\n /** Override to provide the proper collections panels as the foldout */\n _getFoldoutPanelClass: function() {\n switch (this.model.get(\"collection_type\")) {\n case \"list\":\n return DC_VIEW.ListCollectionView;\n case \"paired\":\n return DC_VIEW.PairCollectionView;\n case \"list:paired\":\n return DC_VIEW.ListOfPairsCollectionView;\n case \"list:list\":\n return DC_VIEW.ListOfListsCollectionView;\n }\n throw new TypeError(\n \"Uknown collection_type: \" + this.model.get(\"collection_type\")\n );\n },\n\n /** In this override, add the state as a class for use with state-based CSS */\n _swapNewRender: function($newRender) {\n _super.prototype._swapNewRender.call(this, $newRender);\n //TODO: model currently has no state\n var state = !this.model.get(\"populated\")\n ? STATES.RUNNING\n : STATES.OK;\n //if( this.model.has( 'state' ) ){\n this.$el.addClass(\"state-\" + state);\n //}\n return this.$el;\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"HDCAListItemView(\" + modelString + \")\";\n }\n }\n);\n\n/** underscore templates */\nHDCAListItemView.prototype.templates = (function() {\n var warnings = _.extend({}, _super.prototype.templates.warnings, {\n hidden: BASE_MVC.wrapTemplate(\n [\n // add a warning when hidden\n \"<% if( !collection.visible ){ %>\",\n '',\n _l(\"This collection has been hidden\"),\n \"\",\n \"<% } %>\"\n ],\n \"collection\"\n )\n });\n\n // could steal this from hda-base (or use mixed content)\n var titleBarTemplate = BASE_MVC.wrapTemplate(\n [\n // adding the hid display to the title\n '\"\n ],\n \"collection\"\n );\n\n return _.extend({}, _super.prototype.templates, {\n warnings: warnings,\n titleBar: titleBarTemplate\n });\n})();\n\n//==============================================================================\nexport default {\n HDCAListItemView: HDCAListItemView\n};\n"]} \ No newline at end of file +{"version":3,"sources":["mvc/history/hdca-li.js"],"names":["_super","_collectionLi2","default","DCListItemView","HDCAListItemView","extend","className","prototype","_setUpListeners","call","this","listenTo","model","change:tags change:populated change:visible","options","render","_getFoldoutPanelClass","_collectionView2","ListCollectionView","ListOfPairsCollectionView","ListOfListsCollectionView","TypeError","get","_swapNewRender","$newRender","state","_states2","OK","RUNNING","$el","addClass","toString","templates","warnings","_","wrapTemplate","_localization2","hidden","titleBarTemplate","_baseMvc2","titleBar"],"mappings":"0TAOIA,EAASC,EAAAC,QAAMC,eAGfC,EAAmBJ,EAAOK,QAEtBC,UAAWN,EAAOO,UAAUD,UAAY,mBAGxCE,gBAAiB,WACbR,EAAOO,UAAUC,gBAAgBC,KAAKC,MACtCA,KAAKC,SAASD,KAAKE,OACfC,8CAA+C,SAC3CD,EACAE,GAEAJ,KAAKK,aAXrBC,sBAAA,WACIV,OAAWN,KAAAA,MAAOO,IAAP,oBAkBH,IAAK,OAhBb,OAAAU,EAAAf,QAAAgB,mBACAV,IAAAA,SACWD,OAAAA,EAAAA,QAAUC,mBACjB,IAAKG,cACD,OAAAM,EAAAf,QAAAiB,0BAII,IAAA,YACH,OAAAF,EAAAf,QAAAkB,0BAZ4B,MAAA,IAAAC,UA6B7B,2BAA6BX,KAAKE,MAAMU,IAAI,qBATxCC,eAAA,SAAOC,GACXxB,EAAAO,UAAAgB,eAAAd,KAAAC,KAAAc,GAEA,IAAAC,EAAKf,KAAAE,MAALU,IAAA,aAEAI,EAAAxB,QAAKyB,GADDD,EAAAxB,QAAA0B,QAxByB,OAkBjClB,KAAAmB,IAAAC,SAAA,SAAAL,GAlBiCf,KAAAmB,KAoCjCE,SAAA,WAIA,MAAA,qBAHkBnB,KAALA,MAAeF,KAAAE,MACtB,GAAA,cAEN,OAMJR,EAAAG,UAAAyB,UAAA,WACA,IAAAC,EAAAC,EAAA7B,UAAAL,EAAAO,UAAAyB,UAAAC,UACAF,OAAAA,EAAAA,QAAUI,cAGT,mCApDT,gDAgEgB,EAAAC,EAAAlC,SAAG,mCARnB,SACAE,WAEQiC,gBAaJC,EAAAC,EAAArC,QAAAiC,cAIQ,6CAGA,mCACA,sBAgBR,kDACIF,mDACAO,SAFJ,+BAvCJ,0BA4BY,2FAiBZ,wCAfY,4DAiBRpC,UAfQ,YACA,UACA,UAEJ,cAGJ,OAAO8B,EAAE7B,UAAWL,EAAOO,UAAUyB,WACjCC,SAAUA,EACVO,SAAUF,IAnDV,cAyDJlC,iBAAkBA","file":"../../../scripts/mvc/history/hdca-li.js","sourcesContent":["import STATES from \"mvc/dataset/states\";\nimport DC_LI from \"mvc/collection/collection-li\";\nimport DC_VIEW from \"mvc/collection/collection-view\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\nvar _super = DC_LI.DCListItemView;\n/** @class Read only view for HistoryDatasetCollectionAssociation (a dataset collection inside a history).\n */\nvar HDCAListItemView = _super.extend(\n /** @lends HDCAListItemView.prototype */ {\n className: _super.prototype.className + \" history-content\",\n\n /** event listeners */\n _setUpListeners: function() {\n _super.prototype._setUpListeners.call(this);\n this.listenTo(this.model, {\n \"change:tags change:populated change:visible\": function(\n model,\n options\n ) {\n this.render();\n }\n });\n },\n\n /** Override to provide the proper collections panels as the foldout */\n _getFoldoutPanelClass: function() {\n switch (this.model.get(\"collection_type\")) {\n case \"list\":\n return DC_VIEW.ListCollectionView;\n case \"paired\":\n return DC_VIEW.PairCollectionView;\n case \"list:paired\":\n return DC_VIEW.ListOfPairsCollectionView;\n case \"list:list\":\n return DC_VIEW.ListOfListsCollectionView;\n }\n throw new TypeError(\n \"Uknown collection_type: \" + this.model.get(\"collection_type\")\n );\n },\n\n /** In this override, add the state as a class for use with state-based CSS */\n _swapNewRender: function($newRender) {\n _super.prototype._swapNewRender.call(this, $newRender);\n //TODO: model currently has no state\n var state = !this.model.get(\"populated\")\n ? STATES.RUNNING\n : STATES.OK;\n //if( this.model.has( 'state' ) ){\n this.$el.addClass(\"state-\" + state);\n //}\n return this.$el;\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"HDCAListItemView(\" + modelString + \")\";\n }\n }\n);\n\n/** underscore templates */\nHDCAListItemView.prototype.templates = (function() {\n var warnings = _.extend({}, _super.prototype.templates.warnings, {\n hidden: BASE_MVC.wrapTemplate(\n [\n // add a warning when hidden\n \"<% if( !collection.visible ){ %>\",\n '',\n _l(\"This collection has been hidden\"),\n \"\",\n \"<% } %>\"\n ],\n \"collection\"\n )\n });\n\n // could steal this from hda-base (or use mixed content)\n var titleBarTemplate = BASE_MVC.wrapTemplate(\n [\n // adding the hid display to the title\n '\"\n ],\n \"collection\"\n );\n\n return _.extend({}, _super.prototype.templates, {\n warnings: warnings,\n titleBar: titleBarTemplate\n });\n})();\n\n//==============================================================================\nexport default {\n HDCAListItemView: HDCAListItemView\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/history/hdca-model.js.map b/static/maps/mvc/history/hdca-model.js.map index c7dbbf8f5f2..c4244d9cac3 100644 --- a/static/maps/mvc/history/hdca-model.js.map +++ b/static/maps/mvc/history/hdca-model.js.map @@ -1 +1 @@ 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options || {};\n options.url = this.urlRoot + this.get(\"history_id\") + \"/contents\";\n attributes = attributes || {};\n attributes.type = \"dataset_collection\";\n }\n return _super.call(this, attributes, options);\n };\n}\n\n//==============================================================================\n/** @class Backbone model for List Dataset Collection within a History.\n */\nvar HistoryListDatasetCollection = ListDC.extend(hcontentMixin).extend(\n /** @lends HistoryListDatasetCollection.prototype */ {\n defaults: _.extend(_.clone(ListDC.prototype.defaults), {\n history_content_type: \"dataset_collection\",\n collection_type: \"list\",\n model_class: \"HistoryDatasetCollectionAssociation\"\n }),\n\n /** Override to post to contents route w/o id. */\n save: buildHDCASave(ListDC.prototype.save),\n\n /** String representation. */\n toString: function() {\n return \"History\" + ListDC.prototype.toString.call(this);\n }\n }\n);\n\n//==============================================================================\n/** @class Backbone model for Pair Dataset Collection within a History.\n * @constructs\n */\nvar HistoryPairDatasetCollection = PairDC.extend(hcontentMixin).extend(\n /** @lends HistoryPairDatasetCollection.prototype */ {\n defaults: _.extend(_.clone(PairDC.prototype.defaults), {\n history_content_type: \"dataset_collection\",\n collection_type: \"paired\",\n model_class: \"HistoryDatasetCollectionAssociation\"\n }),\n\n /** Override to post to contents route w/o id. */\n save: buildHDCASave(PairDC.prototype.save),\n\n /** String representation. */\n toString: function() {\n return \"History\" + PairDC.prototype.toString.call(this);\n }\n }\n);\n\n//==============================================================================\n/** @class Backbone model for List of Pairs Dataset Collection within a History. */\nvar HistoryListPairedDatasetCollection = ListPairedDC.extend(\n 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DC_MODEL from \"mvc/collection/collection-model\";\nimport HISTORY_CONTENT from \"mvc/history/history-content-model\";\nimport _l from \"utils/localization\";\n\n/*==============================================================================\n\nModels for DatasetCollections contained within a history.\n\nTODO:\n these might be compactable to one class if some duplication with\n collection-model is used.\n\n==============================================================================*/\nvar hcontentMixin = HISTORY_CONTENT.HistoryContentMixin,\n ListDC = DC_MODEL.ListDatasetCollection,\n PairDC = DC_MODEL.PairDatasetCollection,\n ListPairedDC = DC_MODEL.ListPairedDatasetCollection,\n ListOfListsDC = DC_MODEL.ListOfListsDatasetCollection;\n\n//==============================================================================\n/** Override to post to contents route w/o id. */\nfunction buildHDCASave(_super) {\n return function _save(attributes, options) {\n if (this.isNew()) {\n options = options || {};\n options.url = this.urlRoot + this.get(\"history_id\") + \"/contents\";\n attributes = attributes || {};\n attributes.type = \"dataset_collection\";\n }\n return _super.call(this, attributes, options);\n };\n}\n\n//==============================================================================\n/** @class Backbone model for List Dataset Collection within a History.\n */\nvar HistoryListDatasetCollection = ListDC.extend(hcontentMixin).extend(\n /** @lends HistoryListDatasetCollection.prototype */ {\n defaults: _.extend(_.clone(ListDC.prototype.defaults), {\n history_content_type: \"dataset_collection\",\n collection_type: \"list\",\n model_class: \"HistoryDatasetCollectionAssociation\"\n }),\n\n /** Override to post to contents route w/o id. */\n save: buildHDCASave(ListDC.prototype.save),\n\n /** String representation. */\n toString: function() {\n return \"History\" + ListDC.prototype.toString.call(this);\n }\n }\n);\n\n//==============================================================================\n/** @class Backbone model for Pair Dataset Collection within a History.\n * @constructs\n */\nvar HistoryPairDatasetCollection = PairDC.extend(hcontentMixin).extend(\n /** @lends HistoryPairDatasetCollection.prototype */ {\n defaults: _.extend(_.clone(PairDC.prototype.defaults), {\n history_content_type: \"dataset_collection\",\n collection_type: \"paired\",\n model_class: \"HistoryDatasetCollectionAssociation\"\n }),\n\n /** Override to post to contents route w/o id. */\n save: buildHDCASave(PairDC.prototype.save),\n\n /** String representation. */\n toString: function() {\n return \"History\" + PairDC.prototype.toString.call(this);\n }\n }\n);\n\n//==============================================================================\n/** @class Backbone model for List of Pairs Dataset Collection within a History. */\nvar HistoryListPairedDatasetCollection = ListPairedDC.extend(\n hcontentMixin\n).extend({\n defaults: _.extend(_.clone(ListPairedDC.prototype.defaults), {\n history_content_type: \"dataset_collection\",\n collection_type: \"list:paired\",\n model_class: \"HistoryDatasetCollectionAssociation\"\n }),\n\n /** Override to post to contents route w/o id. */\n save: buildHDCASave(ListPairedDC.prototype.save),\n\n /** String representation. */\n toString: function() {\n return \"History\" + ListPairedDC.prototype.toString.call(this);\n }\n});\n\n//==============================================================================\n/** @class Backbone model for List of Lists Dataset Collection within a History. */\nvar HistoryListOfListsDatasetCollection = ListOfListsDC.extend(\n hcontentMixin\n).extend({\n defaults: _.extend(_.clone(ListOfListsDC.prototype.defaults), {\n history_content_type: \"dataset_collection\",\n collection_type: \"list:list\",\n model_class: \"HistoryDatasetCollectionAssociation\"\n }),\n\n /** Override to post to contents route w/o id. */\n save: buildHDCASave(ListOfListsDC.prototype.save),\n\n /** String representation. */\n toString: function() {\n return [\n \"HistoryListOfListsDatasetCollection(\",\n this.get(\"name\"),\n \")\"\n ].join(\"\");\n }\n});\n\n//==============================================================================\nexport default {\n HistoryListDatasetCollection: HistoryListDatasetCollection,\n HistoryPairDatasetCollection: HistoryPairDatasetCollection,\n HistoryListPairedDatasetCollection: HistoryListPairedDatasetCollection,\n HistoryListOfListsDatasetCollection: HistoryListOfListsDatasetCollection\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/history/history-content-model.js.map b/static/maps/mvc/history/history-content-model.js.map index 506b58b1da0..516160003d0 100644 --- a/static/maps/mvc/history/history-content-model.js.map +++ b/static/maps/mvc/history/history-content-model.js.map @@ -1 +1 @@ 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default {\n HistoryContentMixin: HistoryContentMixin\n};\n"]} \ No newline at end of file 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STATES from \"mvc/dataset/states\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\n/** @class Mixin for HistoryContents content (HDAs, HDCAs).\n */\nvar HistoryContentMixin = {\n /** default attributes for a model */\n defaults: {\n /** parent (containing) history */\n history_id: null,\n /** some content_type (HistoryContents can contain mixed model classes) */\n history_content_type: null,\n /** indicating when/what order the content was generated in the context of the history */\n hid: null,\n /** whether the user wants the content shown (visible) */\n visible: true\n },\n\n // ........................................................................ mixed content element\n // In order to be part of a MIXED bbone collection, we can't rely on the id\n // (which may collide btwn models of different classes)\n // Instead, use type_id which prefixes the 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default {\n HistoryContentMixin: HistoryContentMixin\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/history/history-contents.js.map b/static/maps/mvc/history/history-contents.js.map index ce017463a4c..b61b63e4463 100644 --- a/static/maps/mvc/history/history-contents.js.map +++ b/static/maps/mvc/history/history-contents.js.map @@ -1 +1 @@ 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CONTROLLED_FETCH_COLLECTION from \"mvc/base/controlled-fetch-collection\";\nimport HDA_MODEL from \"mvc/history/hda-model\";\nimport HDCA_MODEL from \"mvc/history/hdca-model\";\nimport HISTORY_PREFS from \"mvc/history/history-preferences\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport AJAX_QUEUE from \"utils/ajax-queue\";\n\n//==============================================================================\nvar _super = CONTROLLED_FETCH_COLLECTION.PaginatedCollection;\n/** @class Backbone collection for history content.\n * NOTE: history content seems like a dataset collection, but differs in that it is mixed:\n * each element can be either an HDA (dataset) or a DatasetCollection and co-exist on\n * the same level.\n * Dataset collections on the other hand are not mixed and (so far) can only contain either\n * HDAs or child dataset collections on one level.\n * This is why this does not inherit from any of the DatasetCollections (currently).\n */\nvar HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({\n _logNamespace: \"history\",\n\n // ........................................................................ composite collection\n /** since history content is a mix, override model fn into a factory, creating based on history_content_type */\n model: function(attrs, options) {\n if (attrs.history_content_type === \"dataset\") {\n return new HDA_MODEL.HistoryDatasetAssociation(attrs, options);\n } else if (attrs.history_content_type === \"dataset_collection\") {\n switch (attrs.collection_type) {\n case \"list\":\n return new HDCA_MODEL.HistoryListDatasetCollection(\n attrs,\n options\n );\n case \"paired\":\n return new HDCA_MODEL.HistoryPairDatasetCollection(\n attrs,\n options\n );\n case \"list:paired\":\n return new HDCA_MODEL.HistoryListPairedDatasetCollection(\n attrs,\n options\n );\n case \"list:list\":\n return new HDCA_MODEL.HistoryListOfListsDatasetCollection(\n attrs,\n options\n );\n }\n // This is a hack inside a hack:\n // Raise a plain object with validationError to fake a model.validationError\n // (since we don't have a model to use validate with)\n // (the outer hack being the mixed content/model function in this collection)\n var msg = \"Unknown collection_type: \" + attrs.collection_type;\n console.warn(msg, attrs);\n return { validationError: msg };\n }\n return {\n validationError:\n \"Unknown history_content_type: \" + attrs.history_content_type\n };\n },\n\n // ........................................................................ set up\n limitPerPage: 500,\n\n /** @type {Integer} how many contents per call to fetch when using progressivelyFetchDetails */\n limitPerProgressiveFetch: 500,\n\n /** @type {String} order used here and when fetching from server */\n order: \"hid\",\n\n /** root api url */\n urlRoot: Galaxy.root + \"api/histories\",\n\n /** complete api url */\n url: function() {\n return this.urlRoot + \"/\" + this.historyId + \"/contents\";\n },\n\n /** Set up */\n initialize: function(models, options) {\n options = options || {};\n _super.prototype.initialize.call(this, models, options);\n\n this.history = options.history || null;\n this.setHistoryId(options.historyId || null);\n /** @type {Boolean} does this collection contain and fetch deleted elements */\n this.includeDeleted = options.includeDeleted || this.includeDeleted;\n /** @type {Boolean} does this collection contain and fetch non-visible elements */\n this.includeHidden = options.includeHidden || this.includeHidden;\n\n // backbonejs uses collection.model.prototype.idAttribute to determine if a model is *already* in a collection\n // and either merged or replaced. In this case, our 'model' is a function so we need to add idAttribute\n // manually here - if we don't, contents will not merge but be replaced/swapped.\n this.model.prototype.idAttribute = \"type_id\";\n },\n\n setHistoryId: function(newId) {\n this.historyId = newId;\n this._setUpWebStorage();\n },\n\n /** Set up client side storage. 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ControlledFetch stuff\n /** override to include the API versioning flag */\n _buildFetchData: function(options) {\n return _.extend(_super.prototype._buildFetchData.call(this, options), {\n v: \"dev\"\n });\n },\n\n /** Extend to include details and version */\n _fetchParams: _super.prototype._fetchParams.concat([\n // TODO: remove (the need for) both\n /** version */\n \"v\",\n /** dataset ids to get full details of */\n \"details\"\n ]),\n\n /** override to add deleted/hidden filters */\n _buildFetchFilters: function(options) {\n var superFilters =\n _super.prototype._buildFetchFilters.call(this, options) || {};\n var filters = {};\n if (!this.includeDeleted) {\n filters.deleted = false;\n filters.purged = false;\n }\n if (!this.includeHidden) {\n filters.visible = true;\n }\n return _.defaults(superFilters, filters);\n },\n\n // ............ paginated collection\n getTotalItemCount: function() {\n return this.history.contentsShown();\n },\n\n // ............ history contents 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self.trigger(\"fetching-deleted-done\", self);\n });\n },\n\n /** fetch all the visible==false contents of this collection */\n fetchHidden: function(options) {\n options = options || {};\n var self = this;\n options.filters = _.extend(options.filters, {\n visible: false\n });\n options.remove = false;\n\n self.trigger(\"fetching-hidden\", self);\n return self.fetch(options).always(function() {\n self.trigger(\"fetching-hidden-done\", self);\n });\n },\n\n /** fetch detailed model data for all contents in this collection */\n fetchAllDetails: function(options) {\n options = options || {};\n var detailsFlag = { details: \"all\" };\n options.data = _.extend(options.data || {}, detailsFlag);\n return this.fetch(options);\n },\n\n /** specialty fetch method for retrieving the element_counts of all hdcas in the history */\n fetchCollectionCounts: function(options) {\n options = options || {};\n options.keys = [\"type_id\", \"element_count\"].join(\",\");\n options.filters = 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offset === 0,\n remove: false\n });\n\n _.defer(function() {\n self.fetch\n .call(self, _options)\n .fail(deferred.reject)\n .done(function(response) {\n deferred.notify(response, limit, offset);\n if (response.length !== limit) {\n self.allFetched = true;\n deferred.resolve(response, limit, offset);\n } else {\n _recursivelyFetch(offset + limit);\n }\n });\n });\n }\n _recursivelyFetch();\n return deferred;\n },\n\n /** does some bit of JSON represent something that can be copied into this contents collection */\n isCopyable: function(contentsJSON) {\n var copyableModelClasses = [\n \"HistoryDatasetAssociation\",\n \"HistoryDatasetCollectionAssociation\"\n ];\n return (\n _.isObject(contentsJSON) &&\n contentsJSON.id &&\n _.contains(copyableModelClasses, contentsJSON.model_class)\n );\n },\n\n /** copy an existing, accessible hda into this collection */\n copy: function(json) {\n // TODO: somehow showhorn all this into 'save'\n var id, type, contentType;\n if (_.isString(json)) {\n id = json;\n contentType = \"hda\";\n type = \"dataset\";\n } else {\n id = json.id;\n contentType =\n {\n HistoryDatasetAssociation: \"hda\",\n LibraryDatasetDatasetAssociation: \"ldda\",\n HistoryDatasetCollectionAssociation: \"hdca\"\n }[json.model_class] || \"hda\";\n type = contentType === \"hdca\" ? \"dataset_collection\" : \"dataset\";\n }\n var collection = this,\n xhr = jQuery\n .ajax(this.url(), {\n method: \"POST\",\n contentType: \"application/json\",\n data: JSON.stringify({\n content: id,\n source: contentType,\n type: type\n })\n })\n .done(function(response) {\n collection.add([response], { parse: true });\n })\n .fail(function(error, status, message) {\n collection.trigger(\n \"error\",\n collection,\n xhr,\n {},\n \"Error copying contents\",\n { type: type, id: id, source: contentType }\n );\n });\n return xhr;\n },\n\n /** create a new HDCA in this collection */\n createHDCA: function(\n elementIdentifiers,\n collectionType,\n name,\n hideSourceItems,\n options\n ) {\n // normally collection.create returns the new model, but we need the promise from the ajax, so we fake create\n //precondition: elementIdentifiers is an array of plain js objects\n // in the proper form to create the collectionType\n var hdca = this.model({\n history_content_type: \"dataset_collection\",\n collection_type: collectionType,\n history_id: this.historyId,\n name: name,\n hide_source_items: hideSourceItems || false,\n // should probably be able to just send in a bunch of json here and restruct per class\n // note: element_identifiers is now (incorrectly) an attribute\n element_identifiers: elementIdentifiers\n // do not create the model on the client until the ajax returns\n });\n return hdca.save(options);\n },\n\n // ........................................................................ searching\n /** return true if all contents have the searchable attributes */\n haveSearchDetails: function() {\n return (\n this.allFetched &&\n this.all(function(content) {\n // null (which is a valid returned annotation value)\n // will return false when using content.has( 'annotation' )\n //TODO: a bit hacky - formalize\n return _.has(content.attributes, \"annotation\");\n })\n );\n },\n\n /** return a new collection of contents whose attributes contain the substring matchesWhat */\n matches: function(matchesWhat) {\n return this.filter(function(content) {\n return content.matches(matchesWhat);\n });\n },\n\n // ........................................................................ misc\n /** In this override, copy the historyId to the clone */\n clone: function() {\n var clone = Backbone.Collection.prototype.clone.call(this);\n clone.historyId = this.historyId;\n return clone;\n },\n\n /** String representation. */\n toString: function() {\n return [\n \"HistoryContents(\",\n [this.historyId, this.length].join(),\n \")\"\n ].join(\"\");\n }\n});\n\n//==============================================================================\nexport default {\n 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CONTROLLED_FETCH_COLLECTION from \"mvc/base/controlled-fetch-collection\";\nimport HDA_MODEL from \"mvc/history/hda-model\";\nimport HDCA_MODEL from \"mvc/history/hdca-model\";\nimport HISTORY_PREFS from \"mvc/history/history-preferences\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport AJAX_QUEUE from \"utils/ajax-queue\";\n\n//==============================================================================\nvar _super = CONTROLLED_FETCH_COLLECTION.PaginatedCollection;\n/** @class Backbone collection for history content.\n * NOTE: history content seems like a dataset collection, but differs in that it is mixed:\n * each element can be either an HDA (dataset) or a DatasetCollection and co-exist on\n * the same level.\n * Dataset collections on the other hand are not mixed and (so far) can only contain either\n * HDAs or child dataset collections on one level.\n * This is why this does not inherit from any of the DatasetCollections (currently).\n */\nvar HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({\n _logNamespace: \"history\",\n\n // ........................................................................ composite collection\n /** since history content is a mix, override model fn into a factory, creating based on history_content_type */\n model: function(attrs, options) {\n if (attrs.history_content_type === \"dataset\") {\n return new HDA_MODEL.HistoryDatasetAssociation(attrs, options);\n } else if (attrs.history_content_type === \"dataset_collection\") {\n switch (attrs.collection_type) {\n case \"list\":\n return new HDCA_MODEL.HistoryListDatasetCollection(\n attrs,\n options\n );\n case \"paired\":\n return new HDCA_MODEL.HistoryPairDatasetCollection(\n attrs,\n options\n );\n case \"list:paired\":\n return new HDCA_MODEL.HistoryListPairedDatasetCollection(\n attrs,\n options\n );\n case \"list:list\":\n return new HDCA_MODEL.HistoryListOfListsDatasetCollection(\n attrs,\n options\n );\n }\n // This is a hack inside a hack:\n // Raise a plain object with validationError to fake a model.validationError\n // (since we don't have a model to use validate with)\n // (the outer hack being the mixed content/model function in this collection)\n var msg = \"Unknown collection_type: \" + attrs.collection_type;\n console.warn(msg, attrs);\n return { validationError: msg };\n }\n return {\n validationError:\n \"Unknown history_content_type: \" + attrs.history_content_type\n };\n },\n\n // ........................................................................ set up\n limitPerPage: 500,\n\n /** @type {Integer} how many contents per call to fetch when using progressivelyFetchDetails */\n limitPerProgressiveFetch: 500,\n\n /** @type {String} order used here and when fetching from server */\n order: \"hid\",\n\n /** root api url */\n urlRoot: Galaxy.root + \"api/histories\",\n\n /** complete api url */\n url: function() {\n return this.urlRoot + \"/\" + this.historyId + \"/contents\";\n },\n\n /** Set up */\n initialize: function(models, options) {\n options = options || {};\n _super.prototype.initialize.call(this, models, options);\n\n this.history = options.history || null;\n this.setHistoryId(options.historyId || null);\n /** @type {Boolean} does this collection contain and fetch deleted elements */\n this.includeDeleted = options.includeDeleted || this.includeDeleted;\n /** @type {Boolean} does this collection contain and fetch non-visible elements */\n this.includeHidden = options.includeHidden || this.includeHidden;\n\n // backbonejs uses collection.model.prototype.idAttribute to determine if a model is *already* in a collection\n // and either merged or replaced. In this case, our 'model' is a function so we need to add idAttribute\n // manually here - if we don't, contents will not merge but be replaced/swapped.\n this.model.prototype.idAttribute = \"type_id\";\n },\n\n setHistoryId: function(newId) {\n this.historyId = newId;\n this._setUpWebStorage();\n },\n\n /** Set up client side storage. Currently PersistanStorage keyed under 'history: ' */\n _setUpWebStorage: function(initialSettings) {\n // TODO: use initialSettings\n if (!this.historyId) {\n return;\n }\n this.storage = new HISTORY_PREFS.HistoryPrefs({\n id: HISTORY_PREFS.HistoryPrefs.historyStorageKey(this.historyId)\n });\n this.trigger(\"new-storage\", this.storage, this);\n\n this.on({\n \"include-deleted\": function(newVal) {\n this.storage.includeDeleted(newVal);\n },\n \"include-hidden\": function(newVal) {\n this.storage.includeHidden(newVal);\n }\n });\n\n this.includeDeleted = this.storage.includeDeleted() || false;\n this.includeHidden = this.storage.includeHidden() || false;\n return this;\n },\n\n // ........................................................................ common queries\n /** @type {Object} map of collection available sorting orders containing comparator fns */\n comparators: _.extend(_.clone(_super.prototype.comparators), {\n name: BASE_MVC.buildComparator(\"name\", { ascending: true }),\n \"name-dsc\": BASE_MVC.buildComparator(\"name\", {\n ascending: false\n }),\n hid: BASE_MVC.buildComparator(\"hid\", { ascending: false }),\n \"hid-asc\": BASE_MVC.buildComparator(\"hid\", { ascending: true })\n }),\n\n /** Get every model in this collection not in a 'ready' state (running). */\n running: function() {\n return this.filter(function(c) {\n return !c.inReadyState();\n });\n },\n\n /** return contents that are not ready and not deleted/hidden */\n runningAndActive: function() {\n return this.filter(function(c) {\n return (\n !c.inReadyState() &&\n c.get(\"visible\") &&\n // TODO: deletedOrPurged?\n !c.get(\"deleted\")\n );\n });\n },\n\n /** Get the model with the given hid\n * @param {Int} hid the hid to search for\n * @returns {HistoryDatasetAssociation} the model with the given hid or undefined if not found\n */\n getByHid: function(hid) {\n // note: there *can* be more than one content with a given hid, this finds the first based on order\n return this.findWhere({ hid: hid });\n },\n\n /** return true if all contents have details */\n haveDetails: function() {\n return this.all(function(c) {\n return c.hasDetails();\n });\n },\n\n // ........................................................................ hidden / deleted\n /** return a new contents collection of only hidden items */\n hidden: function() {\n return this.filter(function(c) {\n return c.hidden();\n });\n },\n\n /** return a new contents collection of only hidden items */\n deleted: function() {\n return this.filter(function(c) {\n return c.get(\"deleted\");\n });\n },\n\n /** return a new contents collection of only hidden items */\n visibleAndUndeleted: function() {\n return this.filter(function(c) {\n return (\n c.get(\"visible\") &&\n // TODO: deletedOrPurged?\n !c.get(\"deleted\")\n );\n });\n },\n\n /** create a setter in order to publish the change */\n setIncludeDeleted: function(setting, options) {\n if (_.isBoolean(setting) && setting !== this.includeDeleted) {\n this.includeDeleted = setting;\n if (_.result(options, \"silent\")) {\n return;\n }\n this.trigger(\"include-deleted\", setting, this);\n }\n },\n\n /** create a setter in order to publish the change */\n setIncludeHidden: function(setting, options) {\n if (_.isBoolean(setting) && setting !== this.includeHidden) {\n this.includeHidden = setting;\n options = options || {};\n if (_.result(options, \"silent\")) {\n return;\n }\n this.trigger(\"include-hidden\", setting, this);\n }\n },\n\n // ........................................................................ ajax\n // ............ controlled fetch collection\n /** override to get expanded ids from sessionStorage and pass to API as details */\n fetch: function(options) {\n options = options || {};\n if (this.historyId && !options.details) {\n var prefs = HISTORY_PREFS.HistoryPrefs.get(this.historyId).toJSON();\n if (!_.isEmpty(prefs.expandedIds)) {\n options.details = _.values(prefs.expandedIds).join(\",\");\n }\n }\n return _super.prototype.fetch.call(this, options);\n },\n\n // ............. ControlledFetch stuff\n /** override to include the API versioning flag */\n _buildFetchData: function(options) {\n return _.extend(_super.prototype._buildFetchData.call(this, options), {\n v: \"dev\"\n });\n },\n\n /** Extend to include details and version */\n _fetchParams: _super.prototype._fetchParams.concat([\n // TODO: remove (the need for) both\n /** version */\n \"v\",\n /** dataset ids to get full details of */\n \"details\"\n ]),\n\n /** override to add deleted/hidden filters */\n _buildFetchFilters: function(options) {\n var superFilters =\n _super.prototype._buildFetchFilters.call(this, options) || {};\n var filters = {};\n if (!this.includeDeleted) {\n filters.deleted = false;\n filters.purged = false;\n }\n if (!this.includeHidden) {\n filters.visible = true;\n }\n return _.defaults(superFilters, filters);\n },\n\n // ............ paginated collection\n getTotalItemCount: function() {\n return this.history.contentsShown();\n },\n\n // ............ history contents specific ajax\n /** override to filter requested contents to those updated after the Date 'since' */\n fetchUpdated: function(since, options) {\n if (since) {\n options = options || { filters: {} };\n options.remove = false;\n options.filters = {\n \"update_time-ge\": since.toISOString(),\n // workflows will produce hidden datasets (non-output datasets) that still\n // need to be updated in the collection or they'll update forever\n // we can remove the default visible filter by using an 'empty' value\n visible: \"\"\n };\n }\n return this.fetch(options);\n },\n\n /** fetch all the deleted==true contents of this collection */\n fetchDeleted: function(options) {\n options = options || {};\n var self = this;\n options.filters = _.extend(options.filters, {\n // all deleted, purged or not\n deleted: true,\n purged: undefined\n });\n options.remove = false;\n\n self.trigger(\"fetching-deleted\", self);\n return self.fetch(options).always(function() {\n self.trigger(\"fetching-deleted-done\", self);\n });\n },\n\n /** fetch all the visible==false contents of this collection */\n fetchHidden: function(options) {\n options = options || {};\n var self = this;\n options.filters = _.extend(options.filters, {\n visible: false\n });\n options.remove = false;\n\n self.trigger(\"fetching-hidden\", self);\n return self.fetch(options).always(function() {\n self.trigger(\"fetching-hidden-done\", self);\n });\n },\n\n /** fetch detailed model data for all contents in this collection */\n fetchAllDetails: function(options) {\n options = options || {};\n var detailsFlag = { details: \"all\" };\n options.data = _.extend(options.data || {}, detailsFlag);\n return this.fetch(options);\n },\n\n /** specialty fetch method for retrieving the element_counts of all hdcas in the history */\n fetchCollectionCounts: function(options) {\n options = options || {};\n options.keys = [\"type_id\", \"element_count\"].join(\",\");\n options.filters = _.extend(options.filters || {}, {\n history_content_type: \"dataset_collection\"\n });\n options.remove = false;\n return this.fetch(options);\n },\n\n // ............. quasi-batch ops\n // TODO: to batch\n /** helper that fetches using filterParams then calls save on each fetched using updateWhat as the save params */\n _filterAndUpdate: function(filterParams, updateWhat) {\n var self = this;\n var idAttribute = self.model.prototype.idAttribute;\n var updateArgs = [updateWhat];\n\n return self\n .fetch({ filters: filterParams, remove: false })\n .then(function(fetched) {\n // convert filtered json array to model array\n fetched = fetched.reduce(function(modelArray, currJson, i) {\n var model = self.get(currJson[idAttribute]);\n return model ? modelArray.concat(model) : modelArray;\n }, []);\n return self.ajaxQueue(\"save\", updateArgs, fetched);\n });\n },\n\n /** using a queue, perform ajaxFn on each of the models in this collection */\n ajaxQueue: function(ajaxFn, args, collection) {\n collection = collection || this.models;\n return new AJAX_QUEUE.AjaxQueue(\n collection\n .slice()\n .reverse()\n .map(function(content, i) {\n var fn = _.isString(ajaxFn) ? content[ajaxFn] : ajaxFn;\n return function() {\n return fn.apply(content, args);\n };\n })\n ).deferred;\n },\n\n /** fetch contents' details in batches of limitPerCall - note: only get searchable details here */\n progressivelyFetchDetails: function(options) {\n options = options || {};\n var deferred = jQuery.Deferred();\n var self = this;\n var limit = options.limitPerCall || self.limitPerProgressiveFetch;\n // TODO: only fetch tags and annotations if specifically requested\n var searchAttributes =\n HDA_MODEL.HistoryDatasetAssociation.prototype.searchAttributes;\n var detailKeys = searchAttributes.join(\",\");\n\n function _recursivelyFetch(offset) {\n offset = offset || 0;\n var _options = _.extend(_.clone(options), {\n view: \"summary\",\n keys: detailKeys,\n limit: limit,\n offset: offset,\n reset: offset === 0,\n remove: false\n });\n\n _.defer(function() {\n self.fetch\n .call(self, _options)\n .fail(deferred.reject)\n .done(function(response) {\n deferred.notify(response, limit, offset);\n if (response.length !== limit) {\n self.allFetched = true;\n deferred.resolve(response, limit, offset);\n } else {\n _recursivelyFetch(offset + limit);\n }\n });\n });\n }\n _recursivelyFetch();\n return deferred;\n },\n\n /** does some bit of JSON represent something that can be copied into this contents collection */\n isCopyable: function(contentsJSON) {\n var copyableModelClasses = [\n \"HistoryDatasetAssociation\",\n \"HistoryDatasetCollectionAssociation\"\n ];\n return (\n _.isObject(contentsJSON) &&\n contentsJSON.id &&\n _.contains(copyableModelClasses, contentsJSON.model_class)\n );\n },\n\n /** copy an existing, accessible hda into this collection */\n copy: function(json) {\n // TODO: somehow showhorn all this into 'save'\n var id, type, contentType;\n if (_.isString(json)) {\n id = json;\n contentType = \"hda\";\n type = \"dataset\";\n } else {\n id = json.id;\n contentType =\n {\n HistoryDatasetAssociation: \"hda\",\n LibraryDatasetDatasetAssociation: \"ldda\",\n HistoryDatasetCollectionAssociation: \"hdca\"\n }[json.model_class] || \"hda\";\n type = contentType === \"hdca\" ? \"dataset_collection\" : \"dataset\";\n }\n var collection = this,\n xhr = jQuery\n .ajax(this.url(), {\n method: \"POST\",\n contentType: \"application/json\",\n data: JSON.stringify({\n content: id,\n source: contentType,\n type: type\n })\n })\n .done(function(response) {\n collection.add([response], { parse: true });\n })\n .fail(function(error, status, message) {\n collection.trigger(\n \"error\",\n collection,\n xhr,\n {},\n \"Error copying contents\",\n { type: type, id: id, source: contentType }\n );\n });\n return xhr;\n },\n\n /** create a new HDCA in this collection */\n createHDCA: function(\n elementIdentifiers,\n collectionType,\n name,\n hideSourceItems,\n options\n ) {\n // normally collection.create returns the new model, but we need the promise from the ajax, so we fake create\n //precondition: elementIdentifiers is an array of plain js objects\n // in the proper form to create the collectionType\n var hdca = this.model({\n history_content_type: \"dataset_collection\",\n collection_type: collectionType,\n history_id: this.historyId,\n name: name,\n hide_source_items: hideSourceItems || false,\n // should probably be able to just send in a bunch of json here and restruct per class\n // note: element_identifiers is now (incorrectly) an attribute\n element_identifiers: elementIdentifiers\n // do not create the model on the client until the ajax returns\n });\n return hdca.save(options);\n },\n\n // ........................................................................ searching\n /** return true if all contents have the searchable attributes */\n haveSearchDetails: function() {\n return (\n this.allFetched &&\n this.all(function(content) {\n // null (which is a valid returned annotation value)\n // will return false when using content.has( 'annotation' )\n //TODO: a bit hacky - formalize\n return _.has(content.attributes, \"annotation\");\n })\n );\n },\n\n /** return a new collection of contents whose attributes contain the substring matchesWhat */\n matches: function(matchesWhat) {\n return this.filter(function(content) {\n return content.matches(matchesWhat);\n });\n },\n\n // ........................................................................ misc\n /** In this override, copy the historyId to the clone */\n clone: function() {\n var clone = Backbone.Collection.prototype.clone.call(this);\n clone.historyId = this.historyId;\n return clone;\n },\n\n /** String representation. */\n toString: function() {\n return [\n \"HistoryContents(\",\n [this.historyId, this.length].join(),\n \")\"\n ].join(\"\");\n }\n});\n\n//==============================================================================\nexport default {\n HistoryContents: HistoryContents\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/history/history-list.js.map b/static/maps/mvc/history/history-list.js.map index 73e22d1537b..2d9dfb42d93 100644 --- a/static/maps/mvc/history/history-list.js.map +++ b/static/maps/mvc/history/history-list.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/history/history-list.js"],"names":["_utils","require","_gridView","_historyModel","_copyDialog","View","Backbone","extend","title","initialize","options","self","this","setElement","$","model","Model","_utils2","default","get","url","Galaxy","root","action_id","param","params","success","response","_","each","operation","label","onclick","id","_showCopyDialog","set","render","attributes","grid","$el","history","_historyModel2","History","fetch","done","_copyDialog2","window","parent","currHistoryPanel","location","reload"],"mappings":"4IACA,IAAAA,OAAAC,QAAA,sDACAC,UAAAD,QAAA,mEACAE,cAAAF,QAAA,kFACAG,YAAAH,QAAA,4EACII,KAAOC,SAASD,KAAKE,QAJzBC,MAAA,YAMIC,WAAY,SAASC,GACjB,IAAIC,EAAOC,KACXA,KAAKC,WAAWC,EAAE,WAP1BF,KAAAG,MAAA,IAAAT,SAAAU,MASQC,QAAAC,QAAMC,KACFC,IACIC,OAAOC,KAVvB,WAYgBZ,EAAQa,UACR,IACAT,EAAEU,MAAMH,OAAOI,QAb/BC,QAAA,SAAAC,GAegBA,EAAA,aAA0B,EAC1BC,EAAEC,KAAKF,EAAA,WAAwB,SAASG,GACb,QAAnBA,EAAUC,QACVD,EAAUE,QAAU,SAASC,GACzBtB,EAAKuB,gBAAgBD,OAhBjCtB,EAAAI,MAAAoB,IAAAR,GACJhB,EAAOyB,aAUPV,OAAAA,WACIC,IAAAA,EAAAA,IAAAA,WAAAA,QAASf,KAAAG,MAAiBsB,YAC1BT,KAAAA,IAAAA,QAAOD,OAASW,EAAAC,MAGJ5B,gBAAAA,SAAAA,GACH,IAAA6B,EAAA,IAFDC,eAAAvB,QAAAwB,SAAAT,GAAAA,IAGHO,EACJG,QACDhC,KAAAA,WACAA,MACH,mEAkBAiC,KAAK,YAdN,EAAAC,aAAA3B,SAAWsB,MAAAI,KAAA,WAEfE,OAAAC,QA9BwBD,OAAAC,OAAA1B,QA+CRyB,OAAOC,OAAO1B,OAAO2B,kBAbvBF,OAAIC,OAAA1B,OAAA2B,iBAAuBf,qBAK7Ba,OAAAG,SAAAC,QAAA,2BAaH7C,KAAAA","file":"../../../scripts/mvc/history/history-list.js","sourcesContent":["/** This class renders the grid list. */\nimport Utils from \"utils/utils\";\nimport GridView from \"mvc/grid/grid-view\";\nimport HistoryModel from \"mvc/history/history-model\";\nimport historyCopyDialog from \"mvc/history/copy-dialog\";\nvar View = Backbone.View.extend({\n title: \"Histories\",\n initialize: function(options) {\n var self = this;\n this.setElement($(\"\"));\n this.model = new Backbone.Model();\n Utils.get({\n url:\n Galaxy.root +\n \"history/\" +\n options.action_id +\n \"?\" +\n $.param(Galaxy.params),\n success: function(response) {\n response[\"dict_format\"] = true;\n _.each(response[\"operations\"], function(operation) {\n if (operation.label == \"Copy\") {\n operation.onclick = function(id) {\n self._showCopyDialog(id);\n };\n }\n });\n self.model.set(response);\n self.render();\n }\n });\n },\n\n render: function() {\n var grid = new GridView(this.model.attributes);\n this.$el.empty().append(grid.$el);\n },\n\n _showCopyDialog: function(id) {\n var history = new HistoryModel.History({ id: id });\n history\n .fetch()\n .fail(function() {\n alert(\n \"History could not be fetched. 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HISTORY_CONTENTS from \"mvc/history/history-contents\";\nimport HISTORY_PREFS from \"mvc/history/history-preferences\";\nimport CONTROLLED_FETCH_COLLECTION from \"mvc/base/controlled-fetch-collection\";\nimport UTILS from \"utils/utils\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\n/** @class Model for a Galaxy history resource - both a record of user\n * tool use and a collection of the datasets those tools produced.\n * @name History\n * @augments Backbone.Model\n */\nvar History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(\n BASE_MVC.mixin(\n BASE_MVC.SearchableModelMixin,\n /** @lends History.prototype */ {\n _logNamespace: \"history\",\n\n /** ms between fetches when checking running jobs/datasets for updates */\n UPDATE_DELAY: 4000,\n\n // values from api (may need more)\n defaults: {\n model_class: \"History\",\n id: null,\n name: \"Unnamed 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},\n\n // ........................................................................ derived attributes\n /** */\n contentsShown: function() {\n var contentsActive = this.get(\"contents_active\");\n var shown = contentsActive.active || 0;\n shown += this.contents.includeDeleted\n ? contentsActive.deleted\n : 0;\n shown += this.contents.includeHidden\n ? contentsActive.hidden\n : 0;\n return shown;\n },\n\n /** convert size in bytes to a more human readable version */\n nice_size: function() {\n var size = this.get(\"size\");\n return size\n ? UTILS.bytesToString(size, true, 2)\n : _l(\"(empty)\");\n },\n\n /** override to add nice_size */\n toJSON: function() {\n return _.extend(Backbone.Model.prototype.toJSON.call(this), {\n nice_size: this.nice_size()\n });\n },\n\n /** override to allow getting nice_size */\n get: function(key) {\n if (key === \"nice_size\") {\n return this.nice_size();\n }\n return Backbone.Model.prototype.get.apply(this, arguments);\n },\n\n // ........................................................................ common queries\n /** T/F is this history owned by the current user (Galaxy.user)\n * Note: that this will return false for an anon user even if the history is theirs.\n */\n ownedByCurrUser: function() {\n // no currUser\n if (!Galaxy || !Galaxy.user) {\n return false;\n }\n // user is anon or history isn't owned\n if (\n Galaxy.user.isAnonymous() ||\n Galaxy.user.id !== this.get(\"user_id\")\n ) {\n return false;\n }\n return true;\n },\n\n /** Return the number of running jobs assoc with this history (note: unknown === 0) */\n numOfUnfinishedJobs: function() {\n var unfinishedJobIds = this.get(\"non_ready_jobs\");\n return unfinishedJobIds ? unfinishedJobIds.length : 0;\n },\n\n /** Return the number of running hda/hdcas in this history (note: unknown === 0) */\n numOfUnfinishedShownContents: function() {\n return this.contents.runningAndActive().length || 0;\n },\n\n // ........................................................................ updates\n _fetchContentRelatedAttributes: function() {\n var contentRelatedAttrs = [\n \"size\",\n \"non_ready_jobs\",\n \"contents_active\",\n \"hid_counter\"\n ];\n return this.fetch({\n data: $.param({\n keys: contentRelatedAttrs.join(\",\")\n })\n });\n },\n\n /** check for any changes since the last time we updated (or fetch all if ) */\n refresh: function(options) {\n // console.log( this + '.refresh' );\n options = options || {};\n var self = this;\n\n // note if there was no previous update time, all summary contents will be fetched\n var lastUpdateTime = self.lastUpdateTime;\n // if we don't flip this, then a fully-fetched list will not be re-checked via fetch\n this.contents.allFetched = false;\n var fetchFn =\n self.contents.currentPage !== 0\n ? function() {\n return self.contents.fetchPage(\n self.contents.currentPage\n );\n }\n : function() {\n return self.contents.fetchUpdated(lastUpdateTime);\n };\n // note: if there was no previous update time, all summary contents will be fetched\n return fetchFn().done(function(response, status, xhr) {\n var serverResponseDatetime;\n try {\n serverResponseDatetime = new Date(\n xhr.getResponseHeader(\"Date\")\n );\n } catch (err) {}\n self.lastUpdateTime = serverResponseDatetime || new Date();\n self.checkForUpdates(options);\n });\n },\n\n /** continuously fetch updated contents every UPDATE_DELAY ms if this history's datasets or jobs are unfinished */\n checkForUpdates: function(options) {\n // console.log( this + '.checkForUpdates' );\n options = options || {};\n var delay = this.UPDATE_DELAY;\n var self = this;\n if (!self.id) {\n return;\n }\n\n function _delayThenUpdate() {\n // prevent buildup of updater timeouts by clearing previous if any, then set new and cache id\n self.clearUpdateTimeout();\n self.updateTimeoutId = setTimeout(function() {\n self.refresh(options);\n }, delay);\n }\n\n // if there are still datasets in the non-ready state, recurse into this function with the new time\n var nonReadyContentCount = this.numOfUnfinishedShownContents();\n // console.log( 'nonReadyContentCount:', nonReadyContentCount );\n if (nonReadyContentCount > 0) {\n _delayThenUpdate();\n } else {\n // no datasets are running, but currently runnning jobs may still produce new datasets\n // see if the history has any running jobs and continue to update if so\n // (also update the size for the user in either case)\n self\n ._fetchContentRelatedAttributes()\n .done(function(historyData) {\n // console.log( 'non_ready_jobs:', historyData.non_ready_jobs );\n if (self.numOfUnfinishedJobs() > 0) {\n _delayThenUpdate();\n } else {\n // otherwise, let listeners know that all updates have stopped\n self.trigger(\"ready\");\n }\n });\n }\n },\n\n /** clear the timeout and the cached timeout id */\n clearUpdateTimeout: function() {\n if (this.updateTimeoutId) {\n clearTimeout(this.updateTimeoutId);\n this.updateTimeoutId = null;\n }\n },\n\n // ........................................................................ ajax\n /** override to use actual Dates objects for create/update times */\n parse: function(response, options) {\n var parsed = Backbone.Model.prototype.parse.call(\n this,\n response,\n options\n );\n if (parsed.create_time) {\n parsed.create_time = new Date(parsed.create_time);\n }\n if (parsed.update_time) {\n parsed.update_time = new Date(parsed.update_time);\n }\n return parsed;\n },\n\n /** fetch this histories data (using options) then it's contents (using contentsOptions) */\n fetchWithContents: function(options, contentsOptions) {\n options = options || {};\n var self = this;\n\n // console.log( this + '.fetchWithContents' );\n // TODO: push down to a base class\n options.view = \"dev-detailed\";\n\n // fetch history then use history data to fetch (paginated) contents\n return this.fetch(options).then(function getContents(history) {\n self.contents.history = self;\n self.contents.setHistoryId(history.id);\n return self.fetchContents(contentsOptions);\n });\n },\n\n /** fetch this histories contents, adjusting options based on the stored history preferences */\n fetchContents: function(options) {\n options = options || {};\n var self = this;\n\n // we're updating, reset the update time\n self.lastUpdateTime = new Date();\n return self.contents.fetchCurrentPage(options);\n },\n\n /** save this history, _Mark_ing it as deleted (just a flag) */\n _delete: function(options) {\n if (this.get(\"deleted\")) {\n return jQuery.when();\n }\n return this.save({ deleted: true }, options);\n },\n /** purge this history, _Mark_ing it as purged and removing all dataset data from the server */\n purge: function(options) {\n if (this.get(\"purged\")) {\n return jQuery.when();\n }\n return this.save({ deleted: true, purged: true }, options);\n },\n /** save this history, _Mark_ing it as undeleted */\n undelete: function(options) {\n if (!this.get(\"deleted\")) {\n return jQuery.when();\n }\n return this.save({ deleted: false }, options);\n },\n\n /** Make a copy of this history on the server\n * @param {Boolean} current if true, set the copy as the new current history (default: true)\n * @param {String} name name of new history (default: none - server sets to: Copy of )\n * @fires copied passed this history and the response JSON from the copy\n * @returns {xhr}\n */\n copy: function(current, name, allDatasets) {\n current = current !== undefined ? current : true;\n if (!this.id) {\n throw new Error(\n \"You must set the history ID before copying it.\"\n );\n }\n\n var postData = { history_id: this.id };\n if (current) {\n postData.current = true;\n }\n if (name) {\n postData.name = name;\n }\n if (!allDatasets) {\n postData.all_datasets = false;\n }\n postData.view = \"dev-detailed\";\n\n var history = this;\n var copy = jQuery.post(this.urlRoot, postData);\n // if current - queue to setAsCurrent before firing 'copied'\n if (current) {\n return copy.then(function(response) {\n var newHistory = new History(response);\n return newHistory.setAsCurrent().done(function() {\n history.trigger(\"copied\", history, response);\n });\n });\n }\n return copy.done(function(response) {\n history.trigger(\"copied\", history, response);\n });\n },\n\n setAsCurrent: function() {\n var history = this,\n xhr = jQuery.getJSON(\n Galaxy.root + \"history/set_as_current?id=\" + this.id\n );\n\n xhr.done(function() {\n history.trigger(\"set-as-current\", history);\n });\n return xhr;\n },\n\n // ........................................................................ misc\n toString: function() {\n return (\n \"History(\" + this.get(\"id\") + \",\" + this.get(\"name\") + \")\"\n );\n }\n }\n )\n);\n\n//==============================================================================\nvar _collectionSuper =\n CONTROLLED_FETCH_COLLECTION.InfinitelyScrollingCollection;\n/** @class A collection of histories (per user)\n * that maintains the current history as the first in the collection.\n * New or copied histories become the current history.\n */\nvar HistoryCollection = _collectionSuper.extend(BASE_MVC.LoggableMixin).extend({\n _logNamespace: \"history\",\n\n model: History,\n /** @type {String} initial order used by collection */\n order: \"update_time\",\n /** @type {Number} limit used for the first fetch (or a reset) */\n limitOnFirstFetch: 10,\n /** @type {Number} limit used for each subsequent fetch */\n limitPerFetch: 10,\n\n initialize: function(models, options) {\n options = options || {};\n this.log(\"HistoryCollection.initialize\", models, options);\n _collectionSuper.prototype.initialize.call(this, models, options);\n\n /** @type {boolean} should deleted histories be included */\n this.includeDeleted = options.includeDeleted || false;\n\n /** @type {String} encoded id of the history that's current */\n this.currentHistoryId = options.currentHistoryId;\n\n this.setUpListeners();\n // note: models are sent to reset *after* this fn ends; up to this point\n // the collection *is empty*\n },\n\n urlRoot: Galaxy.root + \"api/histories\",\n url: function() {\n return this.urlRoot;\n },\n\n /** set up reflexive event handlers */\n setUpListeners: function setUpListeners() {\n return this.on({\n // when a history is deleted, remove it from the collection (if optionally set to do so)\n \"change:deleted\": function(history) {\n // TODO: this becomes complicated when more filters are used\n this.debug(\n \"change:deleted\",\n this.includeDeleted,\n history.get(\"deleted\")\n );\n if (!this.includeDeleted && history.get(\"deleted\")) {\n this.remove(history);\n }\n },\n // listen for a history copy, setting it to current\n copied: function(original, newData) {\n this.setCurrent(new History(newData, []));\n },\n // when a history is made current, track the id in the collection\n \"set-as-current\": function(history) {\n var oldCurrentId = this.currentHistoryId;\n this.trigger(\"no-longer-current\", oldCurrentId);\n this.currentHistoryId = history.id;\n }\n });\n },\n\n /** override to change view */\n _buildFetchData: function(options) {\n return _.extend(\n _collectionSuper.prototype._buildFetchData.call(this, options),\n {\n view: \"dev-detailed\"\n }\n );\n },\n\n /** override to filter out deleted and purged */\n _buildFetchFilters: function(options) {\n var superFilters =\n _collectionSuper.prototype._buildFetchFilters.call(this, options) ||\n {};\n var filters = {};\n if (!this.includeDeleted) {\n filters.deleted = false;\n filters.purged = false;\n } else {\n // force API to return both deleted and non\n //TODO: when the API is updated, remove this\n filters.deleted = null;\n }\n return _.defaults(superFilters, filters);\n },\n\n /** override to fetch current as well (as it may be outside the first 10, etc.) */\n fetchFirst: function(options) {\n var self = this;\n // TODO: batch?\n var xhr = $.when();\n if (this.currentHistoryId) {\n xhr = _collectionSuper.prototype.fetchFirst.call(self, {\n silent: true,\n limit: 1,\n filters: {\n // without these a deleted current history will return [] here and block the other xhr\n purged: \"\",\n deleted: \"\",\n \"encoded_id-in\": this.currentHistoryId\n }\n });\n }\n return xhr.then(function() {\n options = options || {};\n options.offset = 0;\n return self.fetchMore(options);\n });\n },\n\n /** @type {Object} map of collection available sorting orders containing comparator fns */\n comparators: _.extend(_.clone(_collectionSuper.prototype.comparators), {\n name: BASE_MVC.buildComparator(\"name\", {\n ascending: true\n }),\n \"name-dsc\": BASE_MVC.buildComparator(\"name\", {\n ascending: false\n }),\n size: BASE_MVC.buildComparator(\"size\", {\n ascending: false\n }),\n \"size-asc\": BASE_MVC.buildComparator(\"size\", {\n ascending: true\n })\n }),\n\n /** override to always have the current history first */\n sort: function(options) {\n options = options || {};\n var silent = options.silent;\n var currentHistory = this.remove(this.get(this.currentHistoryId));\n _collectionSuper.prototype.sort.call(\n this,\n _.defaults({ silent: true }, options)\n );\n this.unshift(currentHistory, { silent: true });\n if (!silent) {\n this.trigger(\"sort\", this, options);\n }\n return this;\n },\n\n /** create a new history and by default set it to be the current history */\n create: function create(data, hdas, historyOptions, xhrOptions) {\n //TODO: .create is actually a collection function that's overridden here\n var collection = this,\n xhr = jQuery.getJSON(Galaxy.root + \"history/create_new_current\");\n return xhr.done(function(newData) {\n collection.setCurrent(\n new History(newData, [], historyOptions || {})\n );\n });\n },\n\n /** set the current history to the given history, placing it first in the collection.\n * Pass standard bbone options for use in unshift.\n * @triggers new-current passed history and this collection\n */\n setCurrent: function(history, options) {\n options = options || {};\n // new histories go in the front\n this.unshift(history, options);\n this.currentHistoryId = history.get(\"id\");\n if (!options.silent) {\n this.trigger(\"new-current\", history, this);\n }\n return this;\n },\n\n toString: function toString() {\n return (\n \"HistoryCollection(\" +\n this.length +\n \",current:\" +\n this.currentHistoryId +\n \")\"\n );\n }\n});\n\n//==============================================================================\nexport default {\n History: History,\n HistoryCollection: HistoryCollection\n};\n"]} \ No newline at end of file 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HISTORY_CONTENTS from \"mvc/history/history-contents\";\nimport HISTORY_PREFS from \"mvc/history/history-preferences\";\nimport CONTROLLED_FETCH_COLLECTION from \"mvc/base/controlled-fetch-collection\";\nimport UTILS from \"utils/utils\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n//==============================================================================\n/** @class Model for a Galaxy history resource - both a record of user\n * tool use and a collection of the datasets those tools produced.\n * @name History\n * @augments Backbone.Model\n */\nvar History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(\n BASE_MVC.mixin(\n BASE_MVC.SearchableModelMixin,\n /** @lends History.prototype */ {\n _logNamespace: \"history\",\n\n /** ms between fetches when checking running jobs/datasets for updates */\n UPDATE_DELAY: 4000,\n\n // values from api (may need more)\n defaults: {\n model_class: \"History\",\n id: null,\n name: \"Unnamed History\",\n state: \"new\",\n\n deleted: false,\n contents_active: {},\n contents_states: {}\n },\n\n urlRoot: Galaxy.root + \"api/histories\",\n\n contentsClass: HISTORY_CONTENTS.HistoryContents,\n\n /** What model fields to search with */\n searchAttributes: [\"name\", \"annotation\", \"tags\"],\n\n /** Adding title and singular tag */\n searchAliases: {\n title: \"name\",\n tag: \"tags\"\n },\n\n // ........................................................................ set up/tear down\n /** Set up the model\n * @param {Object} historyJSON model data for this History\n * @param {Object} options any extra settings including logger\n */\n initialize: function(historyJSON, options) {\n options = options || {};\n this.logger = options.logger || null;\n this.log(this + \".initialize:\", historyJSON, options);\n\n /** HistoryContents collection of the HDAs contained in this history. */\n this.contents = new this.contentsClass([], {\n history: this,\n historyId: this.get(\"id\"),\n order: options.order\n });\n\n this._setUpListeners();\n this._setUpCollectionListeners();\n\n /** cached timeout id for the dataset updater */\n this.updateTimeoutId = null;\n },\n\n /** set up any event listeners for this history including those to the contained HDAs\n * events: error:contents if an error occurred with the contents collection\n */\n _setUpListeners: function() {\n // if the model's id changes ('current' or null -> an actual id), update the contents history_id\n return this.on({\n error: function(model, xhr, options, msg, details) {\n this.clearUpdateTimeout();\n },\n \"change:id\": function(model, newId) {\n if (this.contents) {\n this.contents.historyId = newId;\n }\n }\n });\n },\n\n /** event handlers for the contents submodels */\n _setUpCollectionListeners: function() {\n if (!this.contents) {\n return this;\n }\n // bubble up errors\n return this.listenTo(this.contents, {\n error: function() {\n this.trigger.apply(this, jQuery.makeArray(arguments));\n }\n });\n },\n\n // ........................................................................ derived attributes\n /** */\n contentsShown: function() {\n var contentsActive = this.get(\"contents_active\");\n var shown = contentsActive.active || 0;\n shown += this.contents.includeDeleted\n ? contentsActive.deleted\n : 0;\n shown += this.contents.includeHidden\n ? contentsActive.hidden\n : 0;\n return shown;\n },\n\n /** convert size in bytes to a more human readable version */\n nice_size: function() {\n var size = this.get(\"size\");\n return size\n ? UTILS.bytesToString(size, true, 2)\n : _l(\"(empty)\");\n },\n\n /** override to add nice_size */\n toJSON: function() {\n return _.extend(Backbone.Model.prototype.toJSON.call(this), {\n nice_size: this.nice_size()\n });\n },\n\n /** override to allow getting nice_size */\n get: function(key) {\n if (key === \"nice_size\") {\n return this.nice_size();\n }\n return Backbone.Model.prototype.get.apply(this, arguments);\n },\n\n // ........................................................................ common queries\n /** T/F is this history owned by the current user (Galaxy.user)\n * Note: that this will return false for an anon user even if the history is theirs.\n */\n ownedByCurrUser: function() {\n // no currUser\n if (!Galaxy || !Galaxy.user) {\n return false;\n }\n // user is anon or history isn't owned\n if (\n Galaxy.user.isAnonymous() ||\n Galaxy.user.id !== this.get(\"user_id\")\n ) {\n return false;\n }\n return true;\n },\n\n /** Return the number of running jobs assoc with this history (note: unknown === 0) */\n numOfUnfinishedJobs: function() {\n var unfinishedJobIds = this.get(\"non_ready_jobs\");\n return unfinishedJobIds ? unfinishedJobIds.length : 0;\n },\n\n /** Return the number of running hda/hdcas in this history (note: unknown === 0) */\n numOfUnfinishedShownContents: function() {\n return this.contents.runningAndActive().length || 0;\n },\n\n // ........................................................................ updates\n _fetchContentRelatedAttributes: function() {\n var contentRelatedAttrs = [\n \"size\",\n \"non_ready_jobs\",\n \"contents_active\",\n \"hid_counter\"\n ];\n return this.fetch({\n data: $.param({\n keys: contentRelatedAttrs.join(\",\")\n })\n });\n },\n\n /** check for any changes since the last time we updated (or fetch all if ) */\n refresh: function(options) {\n // console.log( this + '.refresh' );\n options = options || {};\n var self = this;\n\n // note if there was no previous update time, all summary contents will be fetched\n var lastUpdateTime = self.lastUpdateTime;\n // if we don't flip this, then a fully-fetched list will not be re-checked via fetch\n this.contents.allFetched = false;\n var fetchFn =\n self.contents.currentPage !== 0\n ? function() {\n return self.contents.fetchPage(\n self.contents.currentPage\n );\n }\n : function() {\n return self.contents.fetchUpdated(lastUpdateTime);\n };\n // note: if there was no previous update time, all summary contents will be fetched\n return fetchFn().done(function(response, status, xhr) {\n var serverResponseDatetime;\n try {\n serverResponseDatetime = new Date(\n xhr.getResponseHeader(\"Date\")\n );\n } catch (err) {}\n self.lastUpdateTime = serverResponseDatetime || new Date();\n self.checkForUpdates(options);\n });\n },\n\n /** continuously fetch updated contents every UPDATE_DELAY ms if this history's datasets or jobs are unfinished */\n checkForUpdates: function(options) {\n // console.log( this + '.checkForUpdates' );\n options = options || {};\n var delay = this.UPDATE_DELAY;\n var self = this;\n if (!self.id) {\n return;\n }\n\n function _delayThenUpdate() {\n // prevent buildup of updater timeouts by clearing previous if any, then set new and cache id\n self.clearUpdateTimeout();\n self.updateTimeoutId = setTimeout(function() {\n self.refresh(options);\n }, delay);\n }\n\n // if there are still datasets in the non-ready state, recurse into this function with the new time\n var nonReadyContentCount = this.numOfUnfinishedShownContents();\n // console.log( 'nonReadyContentCount:', nonReadyContentCount );\n if (nonReadyContentCount > 0) {\n _delayThenUpdate();\n } else {\n // no datasets are running, but currently runnning jobs may still produce new datasets\n // see if the history has any running jobs and continue to update if so\n // (also update the size for the user in either case)\n self\n ._fetchContentRelatedAttributes()\n .done(function(historyData) {\n // console.log( 'non_ready_jobs:', historyData.non_ready_jobs );\n if (self.numOfUnfinishedJobs() > 0) {\n _delayThenUpdate();\n } else {\n // otherwise, let listeners know that all updates have stopped\n self.trigger(\"ready\");\n }\n });\n }\n },\n\n /** clear the timeout and the cached timeout id */\n clearUpdateTimeout: function() {\n if (this.updateTimeoutId) {\n clearTimeout(this.updateTimeoutId);\n this.updateTimeoutId = null;\n }\n },\n\n // ........................................................................ ajax\n /** override to use actual Dates objects for create/update times */\n parse: function(response, options) {\n var parsed = Backbone.Model.prototype.parse.call(\n this,\n response,\n options\n );\n if (parsed.create_time) {\n parsed.create_time = new Date(parsed.create_time);\n }\n if (parsed.update_time) {\n parsed.update_time = new Date(parsed.update_time);\n }\n return parsed;\n },\n\n /** fetch this histories data (using options) then it's contents (using contentsOptions) */\n fetchWithContents: function(options, contentsOptions) {\n options = options || {};\n var self = this;\n\n // console.log( this + '.fetchWithContents' );\n // TODO: push down to a base class\n options.view = \"dev-detailed\";\n\n // fetch history then use history data to fetch (paginated) contents\n return this.fetch(options).then(function getContents(history) {\n self.contents.history = self;\n self.contents.setHistoryId(history.id);\n return self.fetchContents(contentsOptions);\n });\n },\n\n /** fetch this histories contents, adjusting options based on the stored history preferences */\n fetchContents: function(options) {\n options = options || {};\n var self = this;\n\n // we're updating, reset the update time\n self.lastUpdateTime = new Date();\n return self.contents.fetchCurrentPage(options);\n },\n\n /** save this history, _Mark_ing it as deleted (just a flag) */\n _delete: function(options) {\n if (this.get(\"deleted\")) {\n return jQuery.when();\n }\n return this.save({ deleted: true }, options);\n },\n /** purge this history, _Mark_ing it as purged and removing all dataset data from the server */\n purge: function(options) {\n if (this.get(\"purged\")) {\n return jQuery.when();\n }\n return this.save({ deleted: true, purged: true }, options);\n },\n /** save this history, _Mark_ing it as undeleted */\n undelete: function(options) {\n if (!this.get(\"deleted\")) {\n return jQuery.when();\n }\n return this.save({ deleted: false }, options);\n },\n\n /** Make a copy of this history on the server\n * @param {Boolean} current if true, set the copy as the new current history (default: true)\n * @param {String} name name of new history (default: none - server sets to: Copy of )\n * @fires copied passed this history and the response JSON from the copy\n * @returns {xhr}\n */\n copy: function(current, name, allDatasets) {\n current = current !== undefined ? current : true;\n if (!this.id) {\n throw new Error(\n \"You must set the history ID before copying it.\"\n );\n }\n\n var postData = { history_id: this.id };\n if (current) {\n postData.current = true;\n }\n if (name) {\n postData.name = name;\n }\n if (!allDatasets) {\n postData.all_datasets = false;\n }\n postData.view = \"dev-detailed\";\n\n var history = this;\n var copy = jQuery.post(this.urlRoot, postData);\n // if current - queue to setAsCurrent before firing 'copied'\n if (current) {\n return copy.then(function(response) {\n var newHistory = new History(response);\n return newHistory.setAsCurrent().done(function() {\n history.trigger(\"copied\", history, response);\n });\n });\n }\n return copy.done(function(response) {\n history.trigger(\"copied\", history, response);\n });\n },\n\n setAsCurrent: function() {\n var history = this,\n xhr = jQuery.getJSON(\n Galaxy.root + \"history/set_as_current?id=\" + this.id\n );\n\n xhr.done(function() {\n history.trigger(\"set-as-current\", history);\n });\n return xhr;\n },\n\n // ........................................................................ misc\n toString: function() {\n return (\n \"History(\" + this.get(\"id\") + \",\" + this.get(\"name\") + \")\"\n );\n }\n }\n )\n);\n\n//==============================================================================\nvar _collectionSuper =\n CONTROLLED_FETCH_COLLECTION.InfinitelyScrollingCollection;\n/** @class A collection of histories (per user)\n * that maintains the current history as the first in the collection.\n * New or copied histories become the current history.\n */\nvar HistoryCollection = _collectionSuper.extend(BASE_MVC.LoggableMixin).extend({\n _logNamespace: \"history\",\n\n model: History,\n /** @type {String} initial order used by collection */\n order: \"update_time\",\n /** @type {Number} limit used for the first fetch (or a reset) */\n limitOnFirstFetch: 10,\n /** @type {Number} limit used for each subsequent fetch */\n limitPerFetch: 10,\n\n initialize: function(models, options) {\n options = options || {};\n this.log(\"HistoryCollection.initialize\", models, options);\n _collectionSuper.prototype.initialize.call(this, models, options);\n\n /** @type {boolean} should deleted histories be included */\n this.includeDeleted = options.includeDeleted || false;\n\n /** @type {String} encoded id of the history that's current */\n this.currentHistoryId = options.currentHistoryId;\n\n this.setUpListeners();\n // note: models are sent to reset *after* this fn ends; up to this point\n // the collection *is empty*\n },\n\n urlRoot: Galaxy.root + \"api/histories\",\n url: function() {\n return this.urlRoot;\n },\n\n /** set up reflexive event handlers */\n setUpListeners: function setUpListeners() {\n return this.on({\n // when a history is deleted, remove it from the collection (if optionally set to do so)\n \"change:deleted\": function(history) {\n // TODO: this becomes complicated when more filters are used\n this.debug(\n \"change:deleted\",\n this.includeDeleted,\n history.get(\"deleted\")\n );\n if (!this.includeDeleted && history.get(\"deleted\")) {\n this.remove(history);\n }\n },\n // listen for a history copy, setting it to current\n copied: function(original, newData) {\n this.setCurrent(new History(newData, []));\n },\n // when a history is made current, track the id in the collection\n \"set-as-current\": function(history) {\n var oldCurrentId = this.currentHistoryId;\n this.trigger(\"no-longer-current\", oldCurrentId);\n this.currentHistoryId = history.id;\n }\n });\n },\n\n /** override to change view */\n _buildFetchData: function(options) {\n return _.extend(\n _collectionSuper.prototype._buildFetchData.call(this, options),\n {\n view: \"dev-detailed\"\n }\n );\n },\n\n /** override to filter out deleted and purged */\n _buildFetchFilters: function(options) {\n var superFilters =\n _collectionSuper.prototype._buildFetchFilters.call(this, options) ||\n {};\n var filters = {};\n if (!this.includeDeleted) {\n filters.deleted = false;\n filters.purged = false;\n } else {\n // force API to return both deleted and non\n //TODO: when the API is updated, remove this\n filters.deleted = null;\n }\n return _.defaults(superFilters, filters);\n },\n\n /** override to fetch current as well (as it may be outside the first 10, etc.) */\n fetchFirst: function(options) {\n var self = this;\n // TODO: batch?\n var xhr = $.when();\n if (this.currentHistoryId) {\n xhr = _collectionSuper.prototype.fetchFirst.call(self, {\n silent: true,\n limit: 1,\n filters: {\n // without these a deleted current history will return [] here and block the other xhr\n purged: \"\",\n deleted: \"\",\n \"encoded_id-in\": this.currentHistoryId\n }\n });\n }\n return xhr.then(function() {\n options = options || {};\n options.offset = 0;\n return self.fetchMore(options);\n });\n },\n\n /** @type {Object} map of collection available sorting orders containing comparator fns */\n comparators: _.extend(_.clone(_collectionSuper.prototype.comparators), {\n name: BASE_MVC.buildComparator(\"name\", {\n ascending: true\n }),\n \"name-dsc\": BASE_MVC.buildComparator(\"name\", {\n ascending: false\n }),\n size: BASE_MVC.buildComparator(\"size\", {\n ascending: false\n }),\n \"size-asc\": BASE_MVC.buildComparator(\"size\", {\n ascending: true\n })\n }),\n\n /** override to always have the current history first */\n sort: function(options) {\n options = options || {};\n var silent = options.silent;\n var currentHistory = this.remove(this.get(this.currentHistoryId));\n _collectionSuper.prototype.sort.call(\n this,\n _.defaults({ silent: true }, options)\n );\n this.unshift(currentHistory, { silent: true });\n if (!silent) {\n this.trigger(\"sort\", this, options);\n }\n return this;\n },\n\n /** create a new history and by default set it to be the current history */\n create: function create(data, hdas, historyOptions, xhrOptions) {\n //TODO: .create is actually a collection function that's overridden here\n var collection = this,\n xhr = jQuery.getJSON(Galaxy.root + \"history/create_new_current\");\n return xhr.done(function(newData) {\n collection.setCurrent(\n new History(newData, [], historyOptions || {})\n );\n });\n },\n\n /** set the current history to the given history, placing it first in the collection.\n * Pass standard bbone options for use in unshift.\n * @triggers new-current passed history and this collection\n */\n setCurrent: function(history, options) {\n options = options || {};\n // new histories go in the front\n this.unshift(history, options);\n this.currentHistoryId = history.get(\"id\");\n if (!options.silent) {\n this.trigger(\"new-current\", history, this);\n }\n return this;\n },\n\n toString: function toString() {\n return (\n \"HistoryCollection(\" +\n this.length +\n \",current:\" +\n this.currentHistoryId +\n \")\"\n );\n }\n});\n\n//==============================================================================\nexport default {\n History: History,\n HistoryCollection: HistoryCollection\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/history/history-preferences.js.map b/static/maps/mvc/history/history-preferences.js.map index 12d3f745229..42708270c94 100644 --- a/static/maps/mvc/history/history-preferences.js.map +++ b/static/maps/mvc/history/history-preferences.js.map @@ -1 +1 @@ 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BASE_MVC from \"mvc/base-mvc\";\n\nvar logNamespace = \"history\";\n\n// ============================================================================\n/** session storage for individual history preferences */\nvar HistoryPrefs = BASE_MVC.SessionStorageModel.extend(\n /** @lends HistoryPrefs.prototype */ {\n //TODO:?? move to user prefs?\n defaults: {\n //TODO:?? expandedIds to array?\n expandedIds: {},\n show_deleted: false,\n show_hidden: false\n },\n\n /** add an hda id to the hash of expanded hdas */\n addExpanded: function(model) {\n //TODO: use type_id and not model\n var current = this.get(\"expandedIds\");\n current[model.id] = model.get(\"id\");\n this.save(\"expandedIds\", current);\n },\n\n /** remove an hda id from the hash of expanded hdas */\n removeExpanded: function(model) {\n var current = this.get(\"expandedIds\");\n delete current[model.id];\n this.save(\"expandedIds\", current);\n },\n\n isExpanded: function(contentId) {\n return _.result(this.get(\"expandedIds\"), contentId, false);\n },\n\n allExpanded: function() {\n return _.values(this.get(\"expandedIds\"));\n },\n\n clearExpanded: function() {\n this.set(\"expandedIds\", {});\n },\n\n includeDeleted: function(val) {\n // moving the invocation here so other components don't need to know the key\n // TODO: change this key later\n if (!_.isUndefined(val)) {\n this.set(\"show_deleted\", val);\n }\n return this.get(\"show_deleted\");\n },\n\n includeHidden: function(val) {\n // TODO: change this key later\n if (!_.isUndefined(val)) {\n this.set(\"show_hidden\", val);\n }\n return this.get(\"show_hidden\");\n },\n\n toString: function() {\n return \"HistoryPrefs(\" + this.id + \")\";\n }\n },\n {\n // ........................................................................ class vars\n // class lvl for access w/o instantiation\n storageKeyPrefix: \"history:\",\n\n /** key string to store each histories settings under */\n historyStorageKey: function historyStorageKey(historyId) {\n if (!historyId) {\n throw new Error(\n \"HistoryPrefs.historyStorageKey needs valid id: \" +\n historyId\n );\n }\n // single point of change\n return HistoryPrefs.storageKeyPrefix + historyId;\n },\n\n /** return the existing storage for the history with the given id (or create one if it doesn't exist) */\n get: function get(historyId) {\n return new HistoryPrefs({\n id: HistoryPrefs.historyStorageKey(historyId)\n });\n },\n\n /** clear all history related items in sessionStorage */\n clearAll: function clearAll(historyId) {\n for (var key in sessionStorage) {\n if (key.indexOf(HistoryPrefs.storageKeyPrefix) === 0) {\n sessionStorage.removeItem(key);\n }\n }\n }\n }\n);\n\n//==============================================================================\nexport default {\n HistoryPrefs: HistoryPrefs\n};\n"]} \ No newline at end of file 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BASE_MVC from \"mvc/base-mvc\";\n\nvar logNamespace = \"history\";\n\n// ============================================================================\n/** session storage for individual history preferences */\nvar HistoryPrefs = BASE_MVC.SessionStorageModel.extend(\n /** @lends HistoryPrefs.prototype */ {\n //TODO:?? move to user prefs?\n defaults: {\n //TODO:?? expandedIds to array?\n expandedIds: {},\n show_deleted: false,\n show_hidden: false\n },\n\n /** add an hda id to the hash of expanded hdas */\n addExpanded: function(model) {\n //TODO: use type_id and not model\n var current = this.get(\"expandedIds\");\n current[model.id] = model.get(\"id\");\n this.save(\"expandedIds\", current);\n },\n\n /** remove an hda id from the hash of expanded hdas */\n removeExpanded: function(model) {\n var current = this.get(\"expandedIds\");\n delete current[model.id];\n this.save(\"expandedIds\", current);\n },\n\n isExpanded: function(contentId) {\n return _.result(this.get(\"expandedIds\"), contentId, false);\n },\n\n allExpanded: function() {\n return _.values(this.get(\"expandedIds\"));\n },\n\n clearExpanded: function() {\n this.set(\"expandedIds\", {});\n },\n\n includeDeleted: function(val) {\n // moving the invocation here so other components don't need to know the key\n // TODO: change this key later\n if (!_.isUndefined(val)) {\n this.set(\"show_deleted\", val);\n }\n return this.get(\"show_deleted\");\n },\n\n includeHidden: function(val) {\n // TODO: change this key later\n if (!_.isUndefined(val)) {\n this.set(\"show_hidden\", val);\n }\n return this.get(\"show_hidden\");\n },\n\n toString: function() {\n return \"HistoryPrefs(\" + this.id + \")\";\n }\n },\n {\n // ........................................................................ class vars\n // class lvl for access w/o instantiation\n storageKeyPrefix: \"history:\",\n\n /** key string to store each histories settings under */\n historyStorageKey: function historyStorageKey(historyId) {\n if (!historyId) {\n throw new Error(\n \"HistoryPrefs.historyStorageKey needs valid id: \" +\n historyId\n );\n }\n // single point of change\n return HistoryPrefs.storageKeyPrefix + historyId;\n },\n\n /** return the existing storage for the history with the given id (or create one if it doesn't exist) */\n get: function get(historyId) {\n return new HistoryPrefs({\n id: HistoryPrefs.historyStorageKey(historyId)\n });\n },\n\n /** clear all history related items in sessionStorage */\n clearAll: function clearAll(historyId) {\n for (var key in sessionStorage) {\n if (key.indexOf(HistoryPrefs.storageKeyPrefix) === 0) {\n sessionStorage.removeItem(key);\n }\n }\n }\n }\n);\n\n//==============================================================================\nexport default {\n HistoryPrefs: HistoryPrefs\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/history/history-structure-view.js.map b/static/maps/mvc/history/history-structure-view.js.map index 973758f60a5..f2a70ac8ee3 100644 --- a/static/maps/mvc/history/history-structure-view.js.map +++ b/static/maps/mvc/history/history-structure-view.js.map @@ -1 +1 @@ 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JobDAG from \"mvc/history/job-dag\";\nimport JOB from \"mvc/job/job-model\";\nimport JOB_LI from \"mvc/job/job-li\";\nimport DATASET_LI from \"mvc/dataset/dataset-li\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\nimport \"libs/d3\";\n\nvar logNamespace = \"history\";\n// ============================================================================\n/*\nTODO:\n disruptive:\n handle collections\n retain contents to job relationships (out/input name)\n\n display when *only* copied datasets\n need to change when/how joblessVertices are created\n\n components should be full height containers that scroll individually\n\n use history contents views for job outputCollection, not vanilla datasets\n need hid\n\n show datasets when job not expanded\n make them external to the job display\n connect jobs by dataset\n which datasets from job X are which inputs in job Y?\n\n make job data human readable (needs tool data)\n show only tool.inputs with labels (w/ job.params as values)\n input datasets are special\n they don't appear in job.params\n have to connect to datasets in the dag\n connect job.inputs to any tool.inputs by tool.input.name (in params)\n\nAPI: seems like this could be handled there - duplicating the input data in the proper param space\n\n collections\n\n use cases:\n operations by thread:\n copy to new history\n rerun\n to workflow\n operations by branch (all descendants):\n copy to new history\n rerun\n to workflow\n signal to noise:\n collapse/expand branch\n hide jobs\n visually isolate branch (hide other jobs) of thread\n zoom (somehow)\n\n layout changes:\n move branch to new column in component\n complicated\n pyramid\n circular\n sources on inner radius\n expansion in vertical:\n obscures relations due to height\n could move details to side panel\n difficult to compare two+ jobs/datasets when at different points in the topo\n\n (other) controls:\n (optionally) filter all deleted\n (optionally) filter all hidden\n //(optionally) filter __SET_METADATA__\n //(optionally) filter error'd jobs\n help and explanation\n filtering/searching of jobs\n\n challenges:\n difficult to scale dom (for zoomout)\n possible to use css transforms?\n transform svg and dom elements\n it is possible to use css transforms on svg nodes\n use transform-origin to select origin to top left\n on larger histories the svg section may become extremely large due to distance from output to input\n\n how-to:\n descendant ids: _.keys( component.depth/breadthFirstSearchTree( start ).vertices )\n\n in-panel view of anc desc\n\n\n*/\n// ============================================================================\n/**\n *\n */\nwindow.JobDAG = JobDAG;\nvar HistoryStructureComponent = Backbone.View\n .extend(BASE_MVC.LoggableMixin)\n .extend({\n _logNamespace: logNamespace,\n\n className: \"history-structure-component\",\n\n _INITIAL_ZOOM_LEVEL: 1.0,\n _MIN_ZOOM_LEVEL: 0.25,\n _LINK_ID_SEP: \"-to-\",\n _VERTEX_NAME_DATA_KEY: \"vertex-name\",\n\n JobItemClass: JOB_LI.JobListItemView,\n ContentItemClass: DATASET_LI.DatasetListItemView,\n\n initialize: function(attributes) {\n this.log(\n this + \"(HistoryStructureComponent).initialize:\",\n attributes\n );\n this.component = attributes.component;\n\n this._liMap = {};\n this._createVertexItems();\n\n this.zoomLevel = attributes.zoomLevel || this._INITIAL_ZOOM_LEVEL;\n\n this.layout = this._createLayout(attributes.layoutOptions);\n },\n\n _createVertexItems: function() {\n var view = this;\n view.component.eachVertex(function(vertex) {\n //TODO: hack\n var type = vertex.data.job ? \"job\" : \"copy\",\n li;\n if (type === \"job\") {\n li = view._createJobListItem(vertex);\n } else if (type === \"copy\") {\n li = view._createContentListItem(vertex);\n }\n view._liMap[vertex.name] = li;\n });\n view.debug(\"_liMap:\", view._liMap);\n },\n\n _createJobListItem: function(vertex) {\n this.debug(\"_createJobListItem:\", vertex);\n var view = this,\n jobData = vertex.data,\n job = new JOB.Job(jobData.job);\n\n // get the models of the outputs for this job from the history\n var outputModels = _.map(job.get(\"outputs\"), function(output) {\n //note: output is { src: 'hda/dataset_collection', id: }\n // job output doesn't *quite* match up to normal typeId\n return view.model.contents.get(output.type_id);\n });\n // set the collection (HistoryContents) for the job to that json (setting historyId for proper ajax urls)\n job.outputCollection.reset(outputModels);\n job.outputCollection.historyId = view.model.id;\n //this.debug( job.outputCollection );\n\n // create the bbone view for the job (to be positioned later accrd. to the layout) and cache\n var li = new view.JobItemClass({\n model: job,\n tool: jobData.tool,\n jobData: jobData\n });\n view.listenTo(\n li,\n \"expanding expanded collapsing collapsed\",\n view.renderGraph\n );\n view.listenTo(\n li.foldout,\n \"view:expanding view:expanded view:collapsing view:collapsed\",\n view.renderGraph\n );\n return li;\n },\n\n _createContentListItem: function(vertex) {\n this.debug(\"_createContentListItem:\", vertex);\n var view = this;\n var content = vertex.data;\n content = view.model.contents.get(content.type_id);\n var li = new view.ContentItemClass({ model: content });\n view.listenTo(\n li,\n \"expanding expanded collapsing collapsed\",\n view.renderGraph\n );\n return li;\n },\n\n layoutDefaults: {\n linkSpacing: 16,\n linkWidth: 0,\n linkHeight: 0,\n jobWidth: 300,\n jobHeight: 300,\n jobSpacing: 12,\n linkAdjX: 4,\n linkAdjY: 0\n },\n\n _createLayout: function(options) {\n options = _.defaults(_.clone(options || {}), this.layoutDefaults);\n var view = this,\n vertices = _.values(view.component.vertices),\n layout = _.extend(options, {\n nodeMap: {},\n links: [],\n svg: { width: 0, height: 0 }\n });\n\n vertices.forEach(function(v, j) {\n var node = { name: v.name, x: 0, y: 0 };\n layout.nodeMap[v.name] = node;\n });\n\n view.component.edges(function(e) {\n var link = {\n source: e.source,\n target: e.target\n };\n layout.links.push(link);\n });\n //this.debug( JSON.stringify( layout, null, ' ' ) );\n return layout;\n },\n\n render: function(options) {\n this.debug(this + \".render:\", options);\n var view = this;\n view.$el.html(\n [\n \" \",\n '',\n ' ',\n \"\"\n ].join(\"\")\n );\n\n var $graph = view.$graph();\n view.component.eachVertex(function(vertex) {\n view._liMap[vertex.name]\n .render(0)\n .$el.appendTo($graph)\n // store the name in the DOM and cache by that name\n .data(view._VERTEX_NAME_DATA_KEY, vertex.name);\n });\n view.renderGraph();\n return this;\n },\n\n $graph: function() {\n return this.$(\".graph\");\n },\n\n renderGraph: function(options) {\n this.debug(this + \".renderGraph:\", options);\n var view = this;\n\n function _render() {\n view._updateLayout();\n // set up the display containers\n view\n .$graph()\n // use css3 transform to scale component graph\n .css(\n \"transform\",\n [\n \"scale(\",\n view.zoomLevel,\n \",\",\n view.zoomLevel,\n \")\"\n ].join(\"\")\n )\n .width(view.layout.svg.width)\n .height(view.layout.svg.height);\n view.renderSVG();\n\n // position the job views accrd. to the layout\n view.component.eachVertex(function(v) {\n //TODO:?? liMap needed - can't we attach to vertex?\n var li = view._liMap[v.name],\n position = view.layout.nodeMap[v.name];\n //this.debug( position );\n li.$el.css({ top: position.y, left: position.x });\n });\n }\n //TODO: hack - li's invisible in updateLayout without this delay\n if (!this.$el.is(\":visible\")) {\n _.delay(_render, 0);\n } else {\n _render();\n }\n return this;\n },\n\n _updateLayout: function() {\n this.debug(this + \"._updateLayout:\");\n var view = this,\n layout = view.layout;\n\n layout.linkHeight = layout.linkSpacing * _.size(layout.nodeMap);\n layout.svg.height = layout.linkHeight + layout.jobHeight;\n\n // reset for later max comparison\n layout.svg.width = 0;\n\n //TODO:?? can't we just alter the component v and e's directly?\n // layout the job views putting jobSpacing btwn each\n var x = 0,\n y = layout.linkHeight;\n _.each(layout.nodeMap, function(node, jobId) {\n //this.debug( node, jobId );\n node.x = x;\n node.y = y;\n x += layout.jobWidth + layout.jobSpacing;\n });\n layout.svg.width = layout.linkWidth = Math.max(layout.svg.width, x);\n\n // layout the links - connecting each job by it's main coords (currently)\n //TODO: somehow adjust the svg height based on the largest distance the longest connection needs\n layout.links.forEach(function(link) {\n var source = layout.nodeMap[link.source],\n target = layout.nodeMap[link.target];\n link.x1 = source.x + layout.linkAdjX;\n link.y1 = source.y + layout.linkAdjY;\n link.x2 = target.x + layout.linkAdjX;\n link.y2 = target.y + layout.linkAdjY;\n });\n\n this.debug(JSON.stringify(layout, null, \" \"));\n return this.layout;\n },\n\n renderSVG: function() {\n this.debug(this + \".renderSVG:\");\n var view = this,\n layout = view.layout;\n\n var svg = d3.select(this.$graph().get(0)).select(\"svg\");\n if (svg.empty()) {\n svg = d3.select(this.$graph().get(0)).append(\"svg\");\n }\n\n svg\n .attr(\"width\", layout.svg.width)\n .attr(\"height\", layout.svg.height);\n\n function highlightConnect(d) {\n d3.select(this).classed(\"highlighted\", true);\n view._liMap[d.source].$el.addClass(\"highlighted\");\n view._liMap[d.target].$el.addClass(\"highlighted\");\n }\n\n function unhighlightConnect(d) {\n d3.select(this).classed(\"highlighted\", false);\n view._liMap[d.source].$el.removeClass(\"highlighted\");\n view._liMap[d.target].$el.removeClass(\"highlighted\");\n }\n\n var connections = svg.selectAll(\".connection\").data(layout.links);\n\n connections\n .enter()\n .append(\"path\")\n .attr(\"class\", \"connection\")\n .attr(\"id\", function(d) {\n return [d.source, d.target].join(view._LINK_ID_SEP);\n })\n .on(\"mouseover\", highlightConnect)\n .on(\"mouseout\", unhighlightConnect);\n\n connections.attr(\"d\", function(d) {\n return view._connectionPath(d);\n });\n\n return svg.node();\n },\n\n _connectionPath: function(d) {\n var CURVE_X = 0,\n controlY =\n (d.x2 - d.x1) /\n this.layout.svg.width *\n this.layout.linkHeight;\n return [\n \"M\",\n d.x1,\n \",\",\n d.y1,\n \" \",\n \"C\",\n d.x1 + CURVE_X,\n \",\",\n d.y1 - controlY,\n \" \",\n d.x2 - CURVE_X,\n \",\",\n d.y2 - controlY,\n \" \",\n d.x2,\n \",\",\n d.y2\n ].join(\"\");\n },\n\n events: {\n \"mouseover .graph > .list-item\": function(ev) {\n this.highlightConnected(ev.currentTarget, true);\n },\n \"mouseout .graph > .list-item\": function(ev) {\n this.highlightConnected(ev.currentTarget, false);\n }\n },\n\n highlightConnected: function(jobElement, highlight) {\n this.debug(\"highlightConnected\", jobElement, highlight);\n highlight = highlight !== undefined ? highlight : true;\n\n var view = this,\n component = view.component,\n jobClassFn = highlight\n ? jQuery.prototype.addClass\n : jQuery.prototype.removeClass,\n connectionClass = highlight\n ? \"connection highlighted\"\n : \"connection\";\n\n //console.debug( 'mouseover', this );\n var $hoverTarget = jobClassFn.call($(jobElement), \"highlighted\"),\n id = $hoverTarget.data(view._VERTEX_NAME_DATA_KEY);\n\n // immed. ancestors\n component.edges({ target: id }).forEach(function(edge) {\n var ancestorId = edge.source,\n ancestorLi = view._liMap[ancestorId];\n //view.debug( '\\t ancestor:', ancestorId, ancestorLi );\n jobClassFn.call(ancestorLi.$el, \"highlighted\");\n view\n .$(\"#\" + ancestorId + view._LINK_ID_SEP + id)\n .attr(\"class\", connectionClass);\n });\n // descendants\n component.vertices[id].eachEdge(function(edge) {\n var descendantId = edge.target,\n descendantLi = view._liMap[descendantId];\n //view.debug( '\\t descendant:', descendantId, descendantLi );\n jobClassFn.call(descendantLi.$el, \"highlighted\");\n view\n .$(\"#\" + id + view._LINK_ID_SEP + descendantId)\n .attr(\"class\", connectionClass);\n });\n },\n\n zoom: function(level) {\n this.zoomLevel = Math.min(\n 1.0,\n Math.max(this._MIN_ZOOM_LEVEL, level)\n );\n return this.renderGraph();\n },\n\n toString: function() {\n return \"HistoryStructureComponent(\" + this.model.id + \")\";\n }\n });\n\n// ============================================================================\n/**\n *\n */\nvar VerticalHistoryStructureComponent = HistoryStructureComponent.extend({\n //logger : console,\n\n className: HistoryStructureComponent.prototype.className + \" vertical\",\n\n layoutDefaults: _.extend(\n _.clone(HistoryStructureComponent.prototype.layoutDefaults),\n {\n linkAdjX: 0,\n linkAdjY: 4\n }\n ),\n\n //TODO: how can we use the dom height of the job li's - they're not visible when this is called?\n _updateLayout: function() {\n this.debug(this + \"._updateLayout:\");\n var view = this,\n layout = view.layout;\n //this.info( this.cid, '_updateLayout' )\n\n layout.linkWidth = layout.linkSpacing * _.size(layout.nodeMap);\n layout.svg.width = layout.linkWidth + layout.jobWidth;\n\n // reset height - we'll get the max Y below to assign to it\n layout.svg.height = 0;\n\n //TODO:?? can't we just alter the component v and e's directly?\n var x = layout.linkWidth,\n y = 0;\n _.each(layout.nodeMap, function(node, nodeId) {\n node.x = x;\n node.y = y;\n var li = view._liMap[nodeId];\n y += li.$el.height() + layout.jobSpacing;\n });\n layout.linkHeight = layout.svg.height = Math.max(layout.svg.height, y);\n\n // layout the links - connecting each job by it's main coords (currently)\n layout.links.forEach(function(link) {\n var source = layout.nodeMap[link.source],\n target = layout.nodeMap[link.target];\n link.x1 = source.x + layout.linkAdjX;\n link.y1 = source.y + layout.linkAdjY;\n link.x2 = target.x + layout.linkAdjX;\n link.y2 = target.y + layout.linkAdjY;\n //view.debug( 'link:', link.x1, link.y1, link.x2, link.y2, link );\n });\n\n this.debug(JSON.stringify(layout, null, \" \"));\n return layout;\n },\n\n _connectionPath: function(d) {\n var CURVE_Y = 0,\n controlX =\n (d.y2 - d.y1) / this.layout.svg.height * this.layout.linkWidth;\n return [\n \"M\",\n d.x1,\n \",\",\n d.y1,\n \" \",\n \"C\",\n d.x1 - controlX,\n \",\",\n d.y1 + CURVE_Y,\n \" \",\n d.x2 - controlX,\n \",\",\n d.y2 - CURVE_Y,\n \" \",\n d.x2,\n \",\",\n d.y2\n ].join(\"\");\n },\n\n toString: function() {\n return \"VerticalHistoryStructureComponent(\" + this.model.id + \")\";\n }\n});\n\n// ============================================================================\n/**\n *\n */\nvar HistoryStructureView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({\n _logNamespace: logNamespace,\n\n className: \"history-structure\",\n\n _layoutToComponentClass: {\n horizontal: HistoryStructureComponent,\n vertical: VerticalHistoryStructureComponent\n },\n //_DEFAULT_LAYOUT : 'horizontal',\n _DEFAULT_LAYOUT: \"vertical\",\n\n initialize: function(attributes) {\n this.layout = _.contains(\n attributes.layout,\n _.keys(this._layoutToComponentClass)\n )\n ? attributes.layout\n : this._DEFAULT_LAYOUT;\n this.log(\n this + \"(HistoryStructureView).initialize:\",\n attributes,\n this.model\n );\n //TODO:?? to model - maybe glom jobs onto model in order to persist\n // cache jobs since we need to re-create the DAG if settings change\n this._processTools(attributes.tools);\n this._processJobs(attributes.jobs);\n this._createDAG();\n },\n\n _processTools: function(tools) {\n this.tools = tools || {};\n return this.tools;\n },\n\n _processJobs: function(jobs) {\n this.jobs = jobs || [];\n return this.jobs;\n },\n\n _createDAG: function() {\n this.dag = new JobDAG({\n historyContents: this.model.contents.toJSON(),\n tools: this.tools,\n jobs: this.jobs,\n excludeSetMetadata: true,\n excludeErroredJobs: true\n });\n this.debug(this + \".dag:\", this.dag);\n this._createComponents();\n },\n\n _createComponents: function() {\n this.log(this + \"._createComponents\");\n var structure = this;\n\n structure.componentViews = structure.dag\n .weakComponentGraphArray()\n .map(function(componentGraph) {\n return structure._createComponent(componentGraph);\n });\n return structure.componentViews;\n },\n\n _createComponent: function(component) {\n this.log(this + \"._createComponent:\", component);\n var ComponentClass = this._layoutToComponentClass[this.layout];\n return new ComponentClass({\n model: this.model,\n component: component\n });\n },\n\n render: function(options) {\n this.log(this + \".render:\", options);\n var structure = this;\n\n structure.$el\n .addClass(\"clear\")\n .html(\n [\n '',\n ''\n ].join(\"\")\n );\n\n structure.componentViews.forEach(function(component) {\n component.render().$el.appendTo(structure.$components());\n });\n return structure;\n },\n\n $components: function() {\n return this.$(\".components\");\n },\n\n changeLayout: function(layout) {\n if (!(layout in this._layoutToComponentClass)) {\n throw new Error(this + \": unknown layout: \" + layout);\n }\n this.layout = layout;\n this._createComponents();\n return this.render();\n },\n\n toString: function() {\n return \"HistoryStructureView(\" + this.model.id + \")\";\n }\n});\n\n// ============================================================================\nexport default HistoryStructureView;\n"]} \ No newline at end of file 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JobDAG from \"mvc/history/job-dag\";\nimport JOB from \"mvc/job/job-model\";\nimport JOB_LI from \"mvc/job/job-li\";\nimport DATASET_LI from \"mvc/dataset/dataset-li\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\nimport \"libs/d3\";\n\nvar logNamespace = \"history\";\n// ============================================================================\n/*\nTODO:\n disruptive:\n handle collections\n retain contents to job relationships (out/input name)\n\n display when *only* copied datasets\n need to change when/how joblessVertices are created\n\n components should be full height containers that scroll individually\n\n use history contents views for job outputCollection, not vanilla datasets\n need hid\n\n show datasets when job not expanded\n make them external to the job display\n connect jobs by dataset\n which datasets from job X are which inputs in job Y?\n\n make job data human readable (needs tool data)\n show only tool.inputs with labels (w/ job.params as values)\n input datasets are special\n they don't appear in job.params\n have to connect to datasets in the dag\n connect job.inputs to any tool.inputs by tool.input.name (in params)\n\nAPI: seems like this could be handled there - duplicating the input data in the proper param space\n\n collections\n\n use cases:\n operations by thread:\n copy to new history\n rerun\n to workflow\n operations by branch (all descendants):\n copy to new history\n rerun\n to workflow\n signal to noise:\n collapse/expand branch\n hide jobs\n visually isolate branch (hide other jobs) of thread\n zoom (somehow)\n\n layout changes:\n move branch to new column in component\n complicated\n pyramid\n circular\n sources on inner radius\n expansion in vertical:\n obscures relations due to height\n could move details to side panel\n difficult to compare two+ jobs/datasets when at different points in the topo\n\n (other) controls:\n (optionally) filter all deleted\n (optionally) filter all hidden\n //(optionally) filter __SET_METADATA__\n //(optionally) filter error'd jobs\n help and explanation\n filtering/searching of jobs\n\n challenges:\n difficult to scale dom (for zoomout)\n possible to use css transforms?\n transform svg and dom elements\n it is possible to use css transforms on svg nodes\n use transform-origin to select origin to top left\n on larger histories the svg section may become extremely large due to distance from output to input\n\n how-to:\n descendant ids: _.keys( component.depth/breadthFirstSearchTree( start ).vertices )\n\n in-panel view of anc desc\n\n\n*/\n// ============================================================================\n/**\n *\n */\nwindow.JobDAG = JobDAG;\nvar HistoryStructureComponent = Backbone.View\n .extend(BASE_MVC.LoggableMixin)\n .extend({\n _logNamespace: logNamespace,\n\n className: \"history-structure-component\",\n\n _INITIAL_ZOOM_LEVEL: 1.0,\n _MIN_ZOOM_LEVEL: 0.25,\n _LINK_ID_SEP: \"-to-\",\n _VERTEX_NAME_DATA_KEY: \"vertex-name\",\n\n JobItemClass: JOB_LI.JobListItemView,\n ContentItemClass: DATASET_LI.DatasetListItemView,\n\n initialize: function(attributes) {\n this.log(\n this + \"(HistoryStructureComponent).initialize:\",\n attributes\n );\n this.component = attributes.component;\n\n this._liMap = {};\n this._createVertexItems();\n\n this.zoomLevel = attributes.zoomLevel || this._INITIAL_ZOOM_LEVEL;\n\n this.layout = this._createLayout(attributes.layoutOptions);\n },\n\n _createVertexItems: function() {\n var view = this;\n view.component.eachVertex(function(vertex) {\n //TODO: hack\n var type = vertex.data.job ? \"job\" : \"copy\",\n li;\n if (type === \"job\") {\n li = view._createJobListItem(vertex);\n } else if (type === \"copy\") {\n li = view._createContentListItem(vertex);\n }\n view._liMap[vertex.name] = li;\n });\n view.debug(\"_liMap:\", view._liMap);\n },\n\n _createJobListItem: function(vertex) {\n this.debug(\"_createJobListItem:\", vertex);\n var view = this,\n jobData = vertex.data,\n job = new JOB.Job(jobData.job);\n\n // get the models of the outputs for this job from the history\n var outputModels = _.map(job.get(\"outputs\"), function(output) {\n //note: output is { src: 'hda/dataset_collection', id: }\n // job output doesn't *quite* match up to normal typeId\n return view.model.contents.get(output.type_id);\n });\n // set the collection (HistoryContents) for the job to that json (setting historyId for proper ajax urls)\n job.outputCollection.reset(outputModels);\n job.outputCollection.historyId = view.model.id;\n //this.debug( job.outputCollection );\n\n // create the bbone view for the job (to be positioned later accrd. to the layout) and cache\n var li = new view.JobItemClass({\n model: job,\n tool: jobData.tool,\n jobData: jobData\n });\n view.listenTo(\n li,\n \"expanding expanded collapsing collapsed\",\n view.renderGraph\n );\n view.listenTo(\n li.foldout,\n \"view:expanding view:expanded view:collapsing view:collapsed\",\n view.renderGraph\n );\n return li;\n },\n\n _createContentListItem: function(vertex) {\n this.debug(\"_createContentListItem:\", vertex);\n var view = this;\n var content = vertex.data;\n content = view.model.contents.get(content.type_id);\n var li = new view.ContentItemClass({ model: content });\n view.listenTo(\n li,\n \"expanding expanded collapsing collapsed\",\n view.renderGraph\n );\n return li;\n },\n\n layoutDefaults: {\n linkSpacing: 16,\n linkWidth: 0,\n linkHeight: 0,\n jobWidth: 300,\n jobHeight: 300,\n jobSpacing: 12,\n linkAdjX: 4,\n linkAdjY: 0\n },\n\n _createLayout: function(options) {\n options = _.defaults(_.clone(options || {}), this.layoutDefaults);\n var view = this,\n vertices = _.values(view.component.vertices),\n layout = _.extend(options, {\n nodeMap: {},\n links: [],\n svg: { width: 0, height: 0 }\n });\n\n vertices.forEach(function(v, j) {\n var node = { name: v.name, x: 0, y: 0 };\n layout.nodeMap[v.name] = node;\n });\n\n view.component.edges(function(e) {\n var link = {\n source: e.source,\n target: e.target\n };\n layout.links.push(link);\n });\n //this.debug( JSON.stringify( layout, null, ' ' ) );\n return layout;\n },\n\n render: function(options) {\n this.debug(this + \".render:\", options);\n var view = this;\n view.$el.html(\n [\n \" \",\n '',\n ' ',\n \"\"\n ].join(\"\")\n );\n\n var $graph = view.$graph();\n view.component.eachVertex(function(vertex) {\n view._liMap[vertex.name]\n .render(0)\n .$el.appendTo($graph)\n // store the name in the DOM and cache by that name\n .data(view._VERTEX_NAME_DATA_KEY, vertex.name);\n });\n view.renderGraph();\n return this;\n },\n\n $graph: function() {\n return this.$(\".graph\");\n },\n\n renderGraph: function(options) {\n this.debug(this + \".renderGraph:\", options);\n var view = this;\n\n function _render() {\n view._updateLayout();\n // set up the display containers\n view\n .$graph()\n // use css3 transform to scale component graph\n .css(\n \"transform\",\n [\n \"scale(\",\n view.zoomLevel,\n \",\",\n view.zoomLevel,\n \")\"\n ].join(\"\")\n )\n .width(view.layout.svg.width)\n .height(view.layout.svg.height);\n view.renderSVG();\n\n // position the job views accrd. to the layout\n view.component.eachVertex(function(v) {\n //TODO:?? liMap needed - can't we attach to vertex?\n var li = view._liMap[v.name],\n position = view.layout.nodeMap[v.name];\n //this.debug( position );\n li.$el.css({ top: position.y, left: position.x });\n });\n }\n //TODO: hack - li's invisible in updateLayout without this delay\n if (!this.$el.is(\":visible\")) {\n _.delay(_render, 0);\n } else {\n _render();\n }\n return this;\n },\n\n _updateLayout: function() {\n this.debug(this + \"._updateLayout:\");\n var view = this,\n layout = view.layout;\n\n layout.linkHeight = layout.linkSpacing * _.size(layout.nodeMap);\n layout.svg.height = layout.linkHeight + layout.jobHeight;\n\n // reset for later max comparison\n layout.svg.width = 0;\n\n //TODO:?? can't we just alter the component v and e's directly?\n // layout the job views putting jobSpacing btwn each\n var x = 0,\n y = layout.linkHeight;\n _.each(layout.nodeMap, function(node, jobId) {\n //this.debug( node, jobId );\n node.x = x;\n node.y = y;\n x += layout.jobWidth + layout.jobSpacing;\n });\n layout.svg.width = layout.linkWidth = Math.max(layout.svg.width, x);\n\n // layout the links - connecting each job by it's main coords (currently)\n //TODO: somehow adjust the svg height based on the largest distance the longest connection needs\n layout.links.forEach(function(link) {\n var source = layout.nodeMap[link.source],\n target = layout.nodeMap[link.target];\n link.x1 = source.x + layout.linkAdjX;\n link.y1 = source.y + layout.linkAdjY;\n link.x2 = target.x + layout.linkAdjX;\n link.y2 = target.y + layout.linkAdjY;\n });\n\n this.debug(JSON.stringify(layout, null, \" \"));\n return this.layout;\n },\n\n renderSVG: function() {\n this.debug(this + \".renderSVG:\");\n var view = this,\n layout = view.layout;\n\n var svg = d3.select(this.$graph().get(0)).select(\"svg\");\n if (svg.empty()) {\n svg = d3.select(this.$graph().get(0)).append(\"svg\");\n }\n\n svg\n .attr(\"width\", layout.svg.width)\n .attr(\"height\", layout.svg.height);\n\n function highlightConnect(d) {\n d3.select(this).classed(\"highlighted\", true);\n view._liMap[d.source].$el.addClass(\"highlighted\");\n view._liMap[d.target].$el.addClass(\"highlighted\");\n }\n\n function unhighlightConnect(d) {\n d3.select(this).classed(\"highlighted\", false);\n view._liMap[d.source].$el.removeClass(\"highlighted\");\n view._liMap[d.target].$el.removeClass(\"highlighted\");\n }\n\n var connections = svg.selectAll(\".connection\").data(layout.links);\n\n connections\n .enter()\n .append(\"path\")\n .attr(\"class\", \"connection\")\n .attr(\"id\", function(d) {\n return [d.source, d.target].join(view._LINK_ID_SEP);\n })\n .on(\"mouseover\", highlightConnect)\n .on(\"mouseout\", unhighlightConnect);\n\n connections.attr(\"d\", function(d) {\n return view._connectionPath(d);\n });\n\n return svg.node();\n },\n\n _connectionPath: function(d) {\n var CURVE_X = 0,\n controlY =\n (d.x2 - d.x1) /\n this.layout.svg.width *\n this.layout.linkHeight;\n return [\n \"M\",\n d.x1,\n \",\",\n d.y1,\n \" \",\n \"C\",\n d.x1 + CURVE_X,\n \",\",\n d.y1 - controlY,\n \" \",\n d.x2 - CURVE_X,\n \",\",\n d.y2 - controlY,\n \" \",\n d.x2,\n \",\",\n d.y2\n ].join(\"\");\n },\n\n events: {\n \"mouseover .graph > .list-item\": function(ev) {\n this.highlightConnected(ev.currentTarget, true);\n },\n \"mouseout .graph > .list-item\": function(ev) {\n this.highlightConnected(ev.currentTarget, false);\n }\n },\n\n highlightConnected: function(jobElement, highlight) {\n this.debug(\"highlightConnected\", jobElement, highlight);\n highlight = highlight !== undefined ? highlight : true;\n\n var view = this,\n component = view.component,\n jobClassFn = highlight\n ? jQuery.prototype.addClass\n : jQuery.prototype.removeClass,\n connectionClass = highlight\n ? \"connection highlighted\"\n : \"connection\";\n\n //console.debug( 'mouseover', this );\n var $hoverTarget = jobClassFn.call($(jobElement), \"highlighted\"),\n id = $hoverTarget.data(view._VERTEX_NAME_DATA_KEY);\n\n // immed. ancestors\n component.edges({ target: id }).forEach(function(edge) {\n var ancestorId = edge.source,\n ancestorLi = view._liMap[ancestorId];\n //view.debug( '\\t ancestor:', ancestorId, ancestorLi );\n jobClassFn.call(ancestorLi.$el, \"highlighted\");\n view\n .$(\"#\" + ancestorId + view._LINK_ID_SEP + id)\n .attr(\"class\", connectionClass);\n });\n // descendants\n component.vertices[id].eachEdge(function(edge) {\n var descendantId = edge.target,\n descendantLi = view._liMap[descendantId];\n //view.debug( '\\t descendant:', descendantId, descendantLi );\n jobClassFn.call(descendantLi.$el, \"highlighted\");\n view\n .$(\"#\" + id + view._LINK_ID_SEP + descendantId)\n .attr(\"class\", connectionClass);\n });\n },\n\n zoom: function(level) {\n this.zoomLevel = Math.min(\n 1.0,\n Math.max(this._MIN_ZOOM_LEVEL, level)\n );\n return this.renderGraph();\n },\n\n toString: function() {\n return \"HistoryStructureComponent(\" + this.model.id + \")\";\n }\n });\n\n// ============================================================================\n/**\n *\n */\nvar VerticalHistoryStructureComponent = HistoryStructureComponent.extend({\n //logger : console,\n\n className: HistoryStructureComponent.prototype.className + \" vertical\",\n\n layoutDefaults: _.extend(\n _.clone(HistoryStructureComponent.prototype.layoutDefaults),\n {\n linkAdjX: 0,\n linkAdjY: 4\n }\n ),\n\n //TODO: how can we use the dom height of the job li's - they're not visible when this is called?\n _updateLayout: function() {\n this.debug(this + \"._updateLayout:\");\n var view = this,\n layout = view.layout;\n //this.info( this.cid, '_updateLayout' )\n\n layout.linkWidth = layout.linkSpacing * _.size(layout.nodeMap);\n layout.svg.width = layout.linkWidth + layout.jobWidth;\n\n // reset height - we'll get the max Y below to assign to it\n layout.svg.height = 0;\n\n //TODO:?? can't we just alter the component v and e's directly?\n var x = layout.linkWidth,\n y = 0;\n _.each(layout.nodeMap, function(node, nodeId) {\n node.x = x;\n node.y = y;\n var li = view._liMap[nodeId];\n y += li.$el.height() + layout.jobSpacing;\n });\n layout.linkHeight = layout.svg.height = Math.max(layout.svg.height, y);\n\n // layout the links - connecting each job by it's main coords (currently)\n layout.links.forEach(function(link) {\n var source = layout.nodeMap[link.source],\n target = layout.nodeMap[link.target];\n link.x1 = source.x + layout.linkAdjX;\n link.y1 = source.y + layout.linkAdjY;\n link.x2 = target.x + layout.linkAdjX;\n link.y2 = target.y + layout.linkAdjY;\n //view.debug( 'link:', link.x1, link.y1, link.x2, link.y2, link );\n });\n\n this.debug(JSON.stringify(layout, null, \" \"));\n return layout;\n },\n\n _connectionPath: function(d) {\n var CURVE_Y = 0,\n controlX =\n (d.y2 - d.y1) / this.layout.svg.height * this.layout.linkWidth;\n return [\n \"M\",\n d.x1,\n \",\",\n d.y1,\n \" \",\n \"C\",\n d.x1 - controlX,\n \",\",\n d.y1 + CURVE_Y,\n \" \",\n d.x2 - controlX,\n \",\",\n d.y2 - CURVE_Y,\n \" \",\n d.x2,\n \",\",\n d.y2\n ].join(\"\");\n },\n\n toString: function() {\n return \"VerticalHistoryStructureComponent(\" + this.model.id + \")\";\n }\n});\n\n// ============================================================================\n/**\n *\n */\nvar HistoryStructureView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({\n _logNamespace: logNamespace,\n\n className: \"history-structure\",\n\n _layoutToComponentClass: {\n horizontal: HistoryStructureComponent,\n vertical: VerticalHistoryStructureComponent\n },\n //_DEFAULT_LAYOUT : 'horizontal',\n _DEFAULT_LAYOUT: \"vertical\",\n\n initialize: function(attributes) {\n this.layout = _.contains(\n attributes.layout,\n _.keys(this._layoutToComponentClass)\n )\n ? attributes.layout\n : this._DEFAULT_LAYOUT;\n this.log(\n this + \"(HistoryStructureView).initialize:\",\n attributes,\n this.model\n );\n //TODO:?? to model - maybe glom jobs onto model in order to persist\n // cache jobs since we need to re-create the DAG if settings change\n this._processTools(attributes.tools);\n this._processJobs(attributes.jobs);\n this._createDAG();\n },\n\n _processTools: function(tools) {\n this.tools = tools || {};\n return this.tools;\n },\n\n _processJobs: function(jobs) {\n this.jobs = jobs || [];\n return this.jobs;\n },\n\n _createDAG: function() {\n this.dag = new JobDAG({\n historyContents: this.model.contents.toJSON(),\n tools: this.tools,\n jobs: this.jobs,\n excludeSetMetadata: true,\n excludeErroredJobs: true\n });\n this.debug(this + \".dag:\", this.dag);\n this._createComponents();\n },\n\n _createComponents: function() {\n this.log(this + \"._createComponents\");\n var structure = this;\n\n structure.componentViews = structure.dag\n .weakComponentGraphArray()\n .map(function(componentGraph) {\n return structure._createComponent(componentGraph);\n });\n return structure.componentViews;\n },\n\n _createComponent: function(component) {\n this.log(this + \"._createComponent:\", component);\n var ComponentClass = this._layoutToComponentClass[this.layout];\n return new ComponentClass({\n model: this.model,\n component: component\n });\n },\n\n render: function(options) {\n this.log(this + \".render:\", options);\n var structure = this;\n\n structure.$el\n .addClass(\"clear\")\n .html(\n [\n '',\n ''\n ].join(\"\")\n );\n\n structure.componentViews.forEach(function(component) {\n component.render().$el.appendTo(structure.$components());\n });\n return structure;\n },\n\n $components: function() {\n return this.$(\".components\");\n },\n\n changeLayout: function(layout) {\n if (!(layout in this._layoutToComponentClass)) {\n throw new Error(this + \": unknown layout: \" + layout);\n }\n this.layout = layout;\n this._createComponents();\n return this.render();\n },\n\n toString: function() {\n return \"HistoryStructureView(\" + this.model.id + \")\";\n }\n});\n\n// ============================================================================\nexport default HistoryStructureView;\n"]} \ No newline at end of file diff --git a/static/maps/mvc/history/history-view-annotated.js.map b/static/maps/mvc/history/history-view-annotated.js.map index 1f59e530601..b456de96251 100644 --- a/static/maps/mvc/history/history-view-annotated.js.map +++ b/static/maps/mvc/history/history-view-annotated.js.map @@ -1 +1 @@ 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HISTORY_VIEW from \"mvc/history/history-view\";\nimport HDA_LI from \"mvc/history/hda-li\";\nimport HDCA_LI from \"mvc/history/hdca-li\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n/* =============================================================================\nTODO:\n\n============================================================================= */\nvar _super = HISTORY_VIEW.HistoryView;\n// used in history/display.mako and history/embed.mako\n/** @class View/Controller for a tabular view of the history model.\n *\n * As ReadOnlyHistoryView, but with:\n * history annotation always shown\n * datasets displayed in a table:\n * datasets in left cells, dataset annotations in the right\n */\nvar AnnotatedHistoryView = _super.extend(\n /** @lends AnnotatedHistoryView.prototype */ {\n className: _super.prototype.className + \" annotated-history-panel\",\n\n // ------------------------------------------------------------------------ panel rendering\n /** In this override, add the history annotation */\n _buildNewRender: function() {\n //TODO: shouldn't this display regardless (on all non-current panels)?\n var $newRender = _super.prototype._buildNewRender.call(this);\n this.renderHistoryAnnotation($newRender);\n return $newRender;\n },\n\n /** render the history's annotation as its own field */\n renderHistoryAnnotation: function($newRender) {\n var annotation = this.model.get(\"annotation\");\n if (!annotation) {\n return;\n }\n $newRender.find(\"> .controls .subtitle\").text(annotation);\n },\n\n /** override to add headers to indicate the dataset, annotation columns */\n renderItems: function($whereTo) {\n $whereTo = $whereTo || this.$el;\n _super.prototype.renderItems.call(this, $whereTo);\n\n var $controls = $whereTo.find(\"> .controls\");\n $controls.find(\".contents-container.headers\").remove();\n\n var $headers = $('')\n .append([\n $('').text(\n _l(\"Dataset\")\n ),\n $('').text(\n _l(\"Annotation\")\n )\n ])\n .appendTo($controls);\n\n return self.views;\n },\n\n // ------------------------------------------------------------------------ sub-views\n /** override to wrap each subview */\n _renderItemView$el: function(view) {\n return $(' ').append([\n view.render(0).$el,\n $('').text(\n view.model.get(\"annotation\") || \"\"\n )\n ]);\n },\n\n // ------------------------------------------------------------------------ panel events\n events: _.extend(_.clone(_super.prototype.events), {\n // clicking on any part of the row will expand the items\n \"click .contents-container\": function(ev) {\n ev.stopPropagation();\n $(ev.currentTarget)\n .find(\".list-item .title-bar\")\n .click();\n },\n // prevent propagation on icon btns so they won't bubble up to tr and toggleBodyVisibility\n \"click .icon-btn\": function(ev) {\n ev.stopPropagation();\n // stopProp will prevent bootstrap from getting the click needed to open a dropdown\n // in the case of metafile download buttons - workaround here\n var 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HISTORY_VIEW from \"mvc/history/history-view\";\nimport HDA_LI from \"mvc/history/hda-li\";\nimport HDCA_LI from \"mvc/history/hdca-li\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n/* =============================================================================\nTODO:\n\n============================================================================= */\nvar _super = HISTORY_VIEW.HistoryView;\n// used in history/display.mako and history/embed.mako\n/** @class View/Controller for a tabular view of the history model.\n *\n * As ReadOnlyHistoryView, but with:\n * history annotation always shown\n * datasets displayed in a table:\n * datasets in left cells, dataset annotations in the right\n */\nvar AnnotatedHistoryView = _super.extend(\n /** @lends AnnotatedHistoryView.prototype */ {\n className: _super.prototype.className + \" annotated-history-panel\",\n\n // ------------------------------------------------------------------------ panel rendering\n 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a/static/maps/mvc/history/history-view-edit-current.js.map +++ b/static/maps/mvc/history/history-view-edit-current.js.map @@ -1 +1 @@ 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HISTORY_MODEL from \"mvc/history/history-model\";\nimport HISTORY_VIEW_EDIT from \"mvc/history/history-view-edit\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n// ============================================================================\n/** session storage for history panel preferences (and to maintain state)\n */\nvar HistoryViewPrefs = BASE_MVC.SessionStorageModel.extend(\n /** @lends HistoryViewPrefs.prototype */ {\n defaults: {\n /** should the tags editor be shown or hidden initially? */\n tagsEditorShown: false,\n /** should the annotation editor be shown or hidden initially? */\n annotationEditorShown: false,\n ///** what is the currently focused content (dataset or collection) in the current history?\n // * (the history panel will highlight and scroll to the focused content view)\n // */\n //focusedContentId : null\n /** Current scroll position */\n scrollPosition: 0\n },\n toString: function() {\n return \"HistoryViewPrefs(\" + JSON.stringify(this.toJSON()) + \")\";\n }\n }\n);\n\n/** key string to store panel prefs (made accessible on class so you can access sessionStorage directly) */\nHistoryViewPrefs.storageKey = function storageKey() {\n return \"history-panel\";\n};\n\n/* =============================================================================\nTODO:\n\n============================================================================= */\nvar _super = HISTORY_VIEW_EDIT.HistoryViewEdit;\n// used in root/index.mako\n/** @class View/Controller for the user's current history model as used in the history\n * panel (current right hand panel) of the analysis page.\n *\n * The only history panel that:\n * will poll for updates.\n * displays datasets in reverse hid order.\n */\nvar CurrentHistoryView = _super.extend(\n /** @lends CurrentHistoryView.prototype */ {\n className: _super.prototype.className + \" current-history-panel\",\n\n /** override to use drilldown (and not foldout) for how collections are displayed */\n HDCAViewClass: _super.prototype.HDCAViewClass.extend({\n foldoutStyle: \"drilldown\"\n }),\n\n emptyMsg: [\n _l(\"This history is empty\"),\n \". \",\n _l(\"You can \"),\n '',\n _l(\"load your own data\"),\n \"\",\n _l(\" or \"),\n '',\n _l(\"get data from an external source\"),\n \"\"\n ].join(\"\"),\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events */\n initialize: function(attributes) {\n attributes = attributes || {};\n\n // ---- persistent preferences\n /** maintain state / preferences over page loads */\n this.preferences = new HistoryViewPrefs(\n _.extend(\n {\n id: HistoryViewPrefs.storageKey()\n },\n _.pick(\n attributes,\n _.keys(HistoryViewPrefs.prototype.defaults)\n )\n )\n );\n\n _super.prototype.initialize.call(this, attributes);\n\n /** sub-views that will overlay this panel (collections) */\n this.panelStack = [];\n\n /** id of currently focused content */\n this.currentContentId = attributes.currentContentId || null;\n //NOTE: purposely not sent to localstorage since panel recreation roughly lines up with a reset of this value\n },\n\n /** Override to cache the current scroll position with a listener */\n _setUpListeners: function() {\n _super.prototype._setUpListeners.call(this);\n\n var panel = this;\n // reset scroll position when there's a new history\n this.on(\"new-model\", function() {\n panel.preferences.set(\"scrollPosition\", 0);\n });\n },\n\n // ------------------------------------------------------------------------ loading history/item models\n // TODO: next three more appropriate moved to the app level\n /** (re-)loads the user's current history & contents w/ details */\n loadCurrentHistory: function() {\n return this.loadHistory(null, {\n url: Galaxy.root + \"history/current_history_json\"\n });\n },\n\n /** loads a history & contents w/ details and makes them the current history */\n switchToHistory: function(historyId, attributes) {\n if (Galaxy.user.isAnonymous()) {\n this.trigger(\n \"error\",\n _l(\"You must be logged in to switch histories\"),\n _l(\"Anonymous user\")\n );\n return $.when();\n }\n return this.loadHistory(historyId, {\n url: Galaxy.root + \"history/set_as_current?id=\" + historyId\n });\n },\n\n /** creates a new history on the server and sets it as the user's current history */\n createNewHistory: function(attributes) {\n if (Galaxy.user.isAnonymous()) {\n this.trigger(\n \"error\",\n _l(\"You must be logged in to create histories\"),\n _l(\"Anonymous user\")\n );\n return $.when();\n }\n return this.loadHistory(null, {\n url: Galaxy.root + \"history/create_new_current\"\n });\n },\n\n /** release/free/shutdown old models and set up panel for new models */\n setModel: function(model, attributes, render) {\n _super.prototype.setModel.call(this, model, attributes, render);\n if (this.model && this.model.id) {\n this.log(\"checking for updates\");\n this.model.checkForUpdates();\n }\n return this;\n },\n\n // ------------------------------------------------------------------------ history/content event listening\n /** listening for history events */\n _setUpModelListeners: function() {\n _super.prototype._setUpModelListeners.call(this);\n // re-broadcast any model change events so that listeners don't have to re-bind to each history\n return this.listenTo(this.model, {\n \"change:nice_size change:size\": function() {\n this.trigger(\n \"history-size-change\",\n this,\n this.model,\n arguments\n );\n },\n \"change:id\": function() {\n this.once(\"loading-done\", function() {\n this.model.checkForUpdates();\n });\n }\n });\n },\n\n /** listening for collection events */\n _setUpCollectionListeners: function() {\n _super.prototype._setUpCollectionListeners.call(this);\n // if a hidden item is created (gen. by a workflow), moves thru the updater to the ready state,\n // then: remove it from the collection if the panel is set to NOT show hidden datasets\n this.listenTo(this.collection, \"state:ready\", function(\n model,\n newState,\n oldState\n ) {\n if (\n !model.get(\"visible\") &&\n !this.collection.storage.includeHidden()\n ) {\n this.removeItemView(model);\n }\n });\n },\n\n // ------------------------------------------------------------------------ panel rendering\n /** override to add a handler to capture the scroll position when the parent scrolls */\n _setUpBehaviors: function($where) {\n $where = $where || this.$el;\n // console.log( '_setUpBehaviors', this.$scrollContainer( $where ).get(0), this.$list( $where ) );\n // we need to call this in _setUpBehaviors which is called after render since the $el\n // may not be attached to $el.parent and $scrollContainer() may not work\n var panel = this;\n _super.prototype._setUpBehaviors.call(panel, $where);\n\n // cache the handler to remove and re-add so we don't pile up the handlers\n if (!this._debouncedScrollCaptureHandler) {\n this._debouncedScrollCaptureHandler = _.debounce(\n function scrollCapture() {\n // cache the scroll position (only if visible)\n if (panel.$el.is(\":visible\")) {\n panel.preferences.set(\n \"scrollPosition\",\n $(this).scrollTop()\n );\n }\n },\n 40\n );\n }\n\n panel\n .$scrollContainer($where)\n .off(\"scroll\", this._debouncedScrollCaptureHandler)\n .on(\"scroll\", this._debouncedScrollCaptureHandler);\n return panel;\n },\n\n /** In this override, handle null models and move the search input to the top */\n _buildNewRender: function() {\n if (!this.model) {\n return $();\n }\n var $newRender = _super.prototype._buildNewRender.call(this);\n $newRender\n .find(\".search\")\n .prependTo($newRender.find(\"> .controls\"));\n this._renderQuotaMessage($newRender);\n return $newRender;\n },\n\n /** render the message displayed when a user is over quota and can't run jobs */\n _renderQuotaMessage: function($whereTo) {\n $whereTo = $whereTo || this.$el;\n return $(this.templates.quotaMsg({}, this)).prependTo(\n $whereTo.find(\".messages\")\n );\n },\n\n /** In this override, get and set current panel preferences when editor is used */\n _renderTags: function($where) {\n var panel = this;\n // render tags and show/hide based on preferences\n _super.prototype._renderTags.call(panel, $where);\n if (panel.preferences.get(\"tagsEditorShown\")) {\n panel.tagsEditor.toggle(true);\n }\n // store preference when shown or hidden\n panel.listenTo(\n panel.tagsEditor,\n \"hiddenUntilActivated:shown hiddenUntilActivated:hidden\",\n function(tagsEditor) {\n panel.preferences.set(\"tagsEditorShown\", tagsEditor.hidden);\n }\n );\n },\n\n /** In this override, get and set current panel preferences when editor is used */\n _renderAnnotation: function($where) {\n var panel = this;\n // render annotation and show/hide based on preferences\n _super.prototype._renderAnnotation.call(panel, $where);\n if (panel.preferences.get(\"annotationEditorShown\")) {\n panel.annotationEditor.toggle(true);\n }\n // store preference when shown or hidden\n panel.listenTo(\n panel.annotationEditor,\n \"hiddenUntilActivated:shown hiddenUntilActivated:hidden\",\n function(annotationEditor) {\n panel.preferences.set(\n \"annotationEditorShown\",\n annotationEditor.hidden\n );\n }\n );\n },\n\n /** Override to scroll to cached position (in prefs) after swapping */\n _swapNewRender: function($newRender) {\n _super.prototype._swapNewRender.call(this, $newRender);\n var panel = this;\n _.delay(function() {\n var pos = panel.preferences.get(\"scrollPosition\");\n if (pos) {\n panel.scrollTo(pos, 0);\n }\n }, 10);\n //TODO: is this enough of a delay on larger histories?\n\n return this;\n },\n\n // ------------------------------------------------------------------------ sub-views\n /** Override to add the current-content highlight class to currentContentId's view */\n _attachItems: function($whereTo) {\n _super.prototype._attachItems.call(this, $whereTo);\n var panel = this;\n if (panel.currentContentId) {\n panel._setCurrentContentById(panel.currentContentId);\n }\n return this;\n },\n\n /** Override to remove any drill down panels */\n addItemView: function(model, collection, options) {\n var view = _super.prototype.addItemView.call(\n this,\n model,\n collection,\n options\n );\n if (!view) {\n return view;\n }\n if (this.panelStack.length) {\n return this._collapseDrilldownPanel();\n }\n return view;\n },\n\n // ------------------------------------------------------------------------ collection sub-views\n /** In this override, add/remove expanded/collapsed model ids to/from web storage */\n _setUpItemViewListeners: function(view) {\n var panel = this;\n _super.prototype._setUpItemViewListeners.call(panel, view);\n // use pub-sub to: handle drilldown expansion and collapse\n return panel.listenTo(view, {\n \"expanded:drilldown\": function(v, drilldown) {\n this._expandDrilldownPanel(drilldown);\n },\n \"collapsed:drilldown\": function(v, drilldown) {\n this._collapseDrilldownPanel(drilldown);\n }\n });\n },\n\n /** display 'current content': add a visible highlight and store the id of a content item */\n setCurrentContent: function(view) {\n this.$(\".history-content.current-content\").removeClass(\n \"current-content\"\n );\n if (view) {\n view.$el.addClass(\"current-content\");\n this.currentContentId = view.model.id;\n } else {\n this.currentContentId = null;\n }\n },\n\n /** find the view with the id and then call setCurrentContent on it */\n _setCurrentContentById: function(id) {\n var view = this.viewFromModelId(id) || null;\n this.setCurrentContent(view);\n },\n\n /** Handle drill down by hiding this panels list and controls and showing the sub-panel */\n _expandDrilldownPanel: function(drilldown) {\n this.panelStack.push(drilldown);\n // hide this panel's controls and list, set the name for back navigation, and attach to the $el\n this.$controls()\n .add(this.$list())\n .hide();\n drilldown.parentName = this.model.get(\"name\");\n drilldown\n .delegateEvents()\n .render()\n .$el.appendTo(this.$el);\n },\n\n /** Handle drilldown close by freeing the panel and re-rendering this panel */\n _collapseDrilldownPanel: function(drilldown) {\n this.panelStack.pop();\n //TODO: MEM: free the panel\n this.$controls()\n .add(this.$list())\n .show();\n },\n\n // ........................................................................ panel events\n /** event map */\n events: _.extend(_.clone(_super.prototype.events), {\n // the two links in the empty message\n \"click .uploader-link\": function(ev) {\n Galaxy.upload.show(ev);\n },\n \"click .get-data-link\": function(ev) {\n var $toolMenu = $(\".toolMenuContainer\");\n $toolMenu.parent().scrollTop(0);\n $toolMenu.find('span:contains(\"Get Data\")').click();\n }\n }),\n\n // ........................................................................ external objects/MVC\n listenToGalaxy: function(galaxy) {\n this.listenTo(galaxy, {\n // when the galaxy_main iframe is loaded with a new page,\n // compare the url to the following list and if there's a match\n // pull the id from url and indicate in the history view that\n // the dataset with that id is the 'current'ly active dataset\n \"center-frame:load\": function(data) {\n var pathToMatch = data.fullpath;\n var hdaId = null;\n var useToURLRegexMap = {\n display: /datasets\\/([a-f0-9]+)\\/display/,\n edit: /datasets\\/([a-f0-9]+)\\/edit/,\n report_error: /dataset\\/errors\\?id=([a-f0-9]+)/,\n rerun: /tool_runner\\/rerun\\?id=([a-f0-9]+)/,\n show_params: /datasets\\/([a-f0-9]+)\\/show_params/\n // no great way to do this here? (leave it in the dataset event handlers above?)\n // 'visualization' : 'visualization',\n };\n _.find(useToURLRegexMap, function(regex, use) {\n // grab the more specific match result (1), save, and use it as the find flag\n hdaId = _.result(pathToMatch.match(regex), 1);\n return hdaId;\n });\n // need to type mangle to go from web route to history contents\n this._setCurrentContentById(\n hdaId ? \"dataset-\" + hdaId : null\n );\n },\n // when the center panel is given a new view, clear the current indicator\n \"center-panel:load\": function(view) {\n this._setCurrentContentById();\n }\n });\n },\n\n //TODO: remove quota meter from panel and remove this\n /** add listeners to an external quota meter (mvc/user/user-quotameter.js) */\n connectToQuotaMeter: function(quotaMeter) {\n if (!quotaMeter) {\n return this;\n }\n // show/hide the 'over quota message' in the history when the meter tells it to\n this.listenTo(quotaMeter, \"quota:over\", this.showQuotaMessage);\n this.listenTo(quotaMeter, \"quota:under\", this.hideQuotaMessage);\n\n // having to add this to handle re-render of hview while overquota (the above do not fire)\n this.on(\"rendered rendered:initial\", function() {\n if (quotaMeter && quotaMeter.isOverQuota()) {\n this.showQuotaMessage();\n }\n });\n return this;\n },\n\n /** Override to preserve the quota message */\n clearMessages: function(ev) {\n var $target = !_.isUndefined(ev)\n ? $(ev.currentTarget)\n : this.$messages().children('[class$=\"message\"]');\n $target = $target.not(\".quota-message\");\n $target.fadeOut(this.fxSpeed, function() {\n $(this).remove();\n });\n return this;\n },\n\n /** Show the over quota message (which happens to be in the history panel).\n */\n showQuotaMessage: function() {\n var $msg = this.$(\".quota-message\");\n if ($msg.is(\":hidden\")) {\n $msg.slideDown(this.fxSpeed);\n }\n },\n\n /** Hide the over quota message (which happens to be in the history panel).\n */\n hideQuotaMessage: function() {\n var $msg = this.$(\".quota-message\");\n if (!$msg.is(\":hidden\")) {\n $msg.slideUp(this.fxSpeed);\n }\n },\n\n // ........................................................................ options menu\n //TODO: remove to batch\n /** unhide any hidden datasets */\n unhideHidden: function() {\n var self = this;\n if (confirm(_l(\"Really unhide all hidden datasets?\"))) {\n // get all hidden, regardless of deleted/purged\n return self.model.contents\n ._filterAndUpdate(\n { visible: false, deleted: \"\", purged: \"\" },\n { visible: true }\n )\n .done(function() {\n // TODO: would be better to render these as they're unhidden instead of all at once\n if (!self.model.contents.includeHidden) {\n self.renderItems();\n }\n });\n }\n return jQuery.when();\n },\n\n /** delete any hidden datasets */\n deleteHidden: function() {\n var self = this;\n if (confirm(_l(\"Really delete all hidden datasets?\"))) {\n return self.model.contents._filterAndUpdate(\n // get all hidden, regardless of deleted/purged\n { visible: false, deleted: \"\", purged: \"\" },\n // both delete *and* unhide them\n { deleted: true, visible: true }\n );\n }\n return jQuery.when();\n },\n\n /** Return a string rep of the history */\n toString: function() {\n return (\n \"CurrentHistoryView(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n//------------------------------------------------------------------------------ TEMPLATES\nCurrentHistoryView.prototype.templates = (function() {\n var quotaMsgTemplate = BASE_MVC.wrapTemplate(\n [\n '\"\n ],\n \"history\"\n );\n return _.extend(_.clone(_super.prototype.templates), {\n quotaMsg: quotaMsgTemplate\n });\n})();\n\n//==============================================================================\nexport default {\n CurrentHistoryView: CurrentHistoryView\n};\n"]} \ No newline at end of file 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HISTORY_MODEL from \"mvc/history/history-model\";\nimport HISTORY_VIEW_EDIT from \"mvc/history/history-view-edit\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n// ============================================================================\n/** session storage for history panel preferences (and to maintain state)\n */\nvar HistoryViewPrefs = BASE_MVC.SessionStorageModel.extend(\n /** @lends HistoryViewPrefs.prototype */ {\n defaults: {\n /** should the tags editor be shown or hidden initially? */\n tagsEditorShown: false,\n /** should the annotation editor be shown or hidden initially? */\n annotationEditorShown: false,\n ///** what is the currently focused content (dataset or collection) in the current history?\n // * (the history panel will highlight and scroll to the focused content view)\n // */\n //focusedContentId : null\n /** Current scroll position */\n scrollPosition: 0\n },\n toString: function() {\n return \"HistoryViewPrefs(\" + JSON.stringify(this.toJSON()) + \")\";\n }\n }\n);\n\n/** key string to store panel prefs (made accessible on class so you can access sessionStorage directly) */\nHistoryViewPrefs.storageKey = function storageKey() {\n return \"history-panel\";\n};\n\n/* =============================================================================\nTODO:\n\n============================================================================= */\nvar _super = HISTORY_VIEW_EDIT.HistoryViewEdit;\n// used in root/index.mako\n/** @class View/Controller for the user's current history model as used in the history\n * panel (current right hand panel) of the analysis page.\n *\n * The only history panel that:\n * will poll for updates.\n * displays datasets in reverse hid order.\n */\nvar CurrentHistoryView = _super.extend(\n /** @lends CurrentHistoryView.prototype */ {\n className: _super.prototype.className + \" current-history-panel\",\n\n /** override to use drilldown (and not foldout) for how collections are displayed */\n HDCAViewClass: _super.prototype.HDCAViewClass.extend({\n foldoutStyle: \"drilldown\"\n }),\n\n emptyMsg: [\n _l(\"This history is empty\"),\n \". \",\n _l(\"You can \"),\n '',\n _l(\"load your own data\"),\n \"\",\n _l(\" or \"),\n '',\n _l(\"get data from an external source\"),\n \"\"\n ].join(\"\"),\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events */\n initialize: function(attributes) {\n attributes = attributes || {};\n\n // ---- persistent preferences\n /** maintain state / preferences over page loads */\n this.preferences = new HistoryViewPrefs(\n _.extend(\n {\n id: HistoryViewPrefs.storageKey()\n },\n _.pick(\n attributes,\n _.keys(HistoryViewPrefs.prototype.defaults)\n )\n )\n );\n\n _super.prototype.initialize.call(this, attributes);\n\n /** sub-views that will overlay this panel (collections) */\n this.panelStack = [];\n\n /** id of currently focused content */\n this.currentContentId = attributes.currentContentId || null;\n //NOTE: purposely not sent to localstorage since panel recreation roughly lines up with a reset of this value\n },\n\n /** Override to cache the current scroll position with a listener */\n _setUpListeners: function() {\n _super.prototype._setUpListeners.call(this);\n\n var panel = this;\n // reset scroll position when there's a new history\n this.on(\"new-model\", function() {\n panel.preferences.set(\"scrollPosition\", 0);\n });\n },\n\n // ------------------------------------------------------------------------ loading history/item models\n // TODO: next three more appropriate moved to the app level\n /** (re-)loads the user's current history & contents w/ details */\n loadCurrentHistory: function() {\n return this.loadHistory(null, {\n url: Galaxy.root + \"history/current_history_json\"\n });\n },\n\n /** loads a history & contents w/ details and makes them the current history */\n switchToHistory: function(historyId, attributes) {\n if (Galaxy.user.isAnonymous()) {\n this.trigger(\n \"error\",\n _l(\"You must be logged in to switch histories\"),\n _l(\"Anonymous user\")\n );\n return $.when();\n }\n return this.loadHistory(historyId, {\n url: Galaxy.root + \"history/set_as_current?id=\" + historyId\n });\n },\n\n /** creates a new history on the server and sets it as the user's current history */\n createNewHistory: function(attributes) {\n if (Galaxy.user.isAnonymous()) {\n this.trigger(\n \"error\",\n _l(\"You must be logged in to create histories\"),\n _l(\"Anonymous user\")\n );\n return $.when();\n }\n return this.loadHistory(null, {\n url: Galaxy.root + \"history/create_new_current\"\n });\n },\n\n /** release/free/shutdown old models and set up panel for new models */\n setModel: function(model, attributes, render) {\n _super.prototype.setModel.call(this, model, attributes, render);\n if (this.model && this.model.id) {\n this.log(\"checking for updates\");\n this.model.checkForUpdates();\n }\n return this;\n },\n\n // ------------------------------------------------------------------------ history/content event listening\n /** listening for history events */\n _setUpModelListeners: function() {\n _super.prototype._setUpModelListeners.call(this);\n // re-broadcast any model change events so that listeners don't have to re-bind to each history\n return this.listenTo(this.model, {\n \"change:nice_size change:size\": function() {\n this.trigger(\n \"history-size-change\",\n this,\n this.model,\n arguments\n );\n },\n \"change:id\": function() {\n this.once(\"loading-done\", function() {\n this.model.checkForUpdates();\n });\n }\n });\n },\n\n /** listening for collection events */\n _setUpCollectionListeners: function() {\n _super.prototype._setUpCollectionListeners.call(this);\n // if a hidden item is created (gen. by a workflow), moves thru the updater to the ready state,\n // then: remove it from the collection if the panel is set to NOT show hidden datasets\n this.listenTo(this.collection, \"state:ready\", function(\n model,\n newState,\n oldState\n ) {\n if (\n !model.get(\"visible\") &&\n !this.collection.storage.includeHidden()\n ) {\n this.removeItemView(model);\n }\n });\n },\n\n // ------------------------------------------------------------------------ panel rendering\n /** override to add a handler to capture the scroll position when the parent scrolls */\n _setUpBehaviors: function($where) {\n $where = $where || this.$el;\n // console.log( '_setUpBehaviors', this.$scrollContainer( $where ).get(0), this.$list( $where ) );\n // we need to call this in _setUpBehaviors which is called after render since the $el\n // may not be attached to $el.parent and $scrollContainer() may not work\n var panel = this;\n _super.prototype._setUpBehaviors.call(panel, $where);\n\n // cache the handler to remove and re-add so we don't pile up the handlers\n if (!this._debouncedScrollCaptureHandler) {\n this._debouncedScrollCaptureHandler = _.debounce(\n function scrollCapture() {\n // cache the scroll position (only if visible)\n if (panel.$el.is(\":visible\")) {\n panel.preferences.set(\n \"scrollPosition\",\n $(this).scrollTop()\n );\n }\n },\n 40\n );\n }\n\n panel\n .$scrollContainer($where)\n .off(\"scroll\", this._debouncedScrollCaptureHandler)\n .on(\"scroll\", this._debouncedScrollCaptureHandler);\n return panel;\n },\n\n /** In this override, handle null models and move the search input to the top */\n _buildNewRender: function() {\n if (!this.model) {\n return $();\n }\n var $newRender = _super.prototype._buildNewRender.call(this);\n $newRender\n .find(\".search\")\n .prependTo($newRender.find(\"> .controls\"));\n this._renderQuotaMessage($newRender);\n return $newRender;\n },\n\n /** render the message displayed when a user is over quota and can't run jobs */\n _renderQuotaMessage: function($whereTo) {\n $whereTo = $whereTo || this.$el;\n return $(this.templates.quotaMsg({}, this)).prependTo(\n $whereTo.find(\".messages\")\n );\n },\n\n /** In this override, get and set current panel preferences when editor is used */\n _renderTags: function($where) {\n var panel = this;\n // render tags and show/hide based on preferences\n _super.prototype._renderTags.call(panel, $where);\n if (panel.preferences.get(\"tagsEditorShown\")) {\n panel.tagsEditor.toggle(true);\n }\n // store preference when shown or hidden\n panel.listenTo(\n panel.tagsEditor,\n \"hiddenUntilActivated:shown hiddenUntilActivated:hidden\",\n function(tagsEditor) {\n panel.preferences.set(\"tagsEditorShown\", tagsEditor.hidden);\n }\n );\n },\n\n /** In this override, get and set current panel preferences when editor is used */\n _renderAnnotation: function($where) {\n var panel = this;\n // render annotation and show/hide based on preferences\n _super.prototype._renderAnnotation.call(panel, $where);\n if (panel.preferences.get(\"annotationEditorShown\")) {\n panel.annotationEditor.toggle(true);\n }\n // store preference when shown or hidden\n panel.listenTo(\n panel.annotationEditor,\n \"hiddenUntilActivated:shown hiddenUntilActivated:hidden\",\n function(annotationEditor) {\n panel.preferences.set(\n \"annotationEditorShown\",\n annotationEditor.hidden\n );\n }\n );\n },\n\n /** Override to scroll to cached position (in prefs) after swapping */\n _swapNewRender: function($newRender) {\n _super.prototype._swapNewRender.call(this, $newRender);\n var panel = this;\n _.delay(function() {\n var pos = panel.preferences.get(\"scrollPosition\");\n if (pos) {\n panel.scrollTo(pos, 0);\n }\n }, 10);\n //TODO: is this enough of a delay on larger histories?\n\n return this;\n },\n\n // ------------------------------------------------------------------------ sub-views\n /** Override to add the current-content highlight class to currentContentId's view */\n _attachItems: function($whereTo) {\n _super.prototype._attachItems.call(this, $whereTo);\n var panel = this;\n if (panel.currentContentId) {\n panel._setCurrentContentById(panel.currentContentId);\n }\n return this;\n },\n\n /** Override to remove any drill down panels */\n addItemView: function(model, collection, options) {\n var view = _super.prototype.addItemView.call(\n this,\n model,\n collection,\n options\n );\n if (!view) {\n return view;\n }\n if (this.panelStack.length) {\n return this._collapseDrilldownPanel();\n }\n return view;\n },\n\n // ------------------------------------------------------------------------ collection sub-views\n /** In this override, add/remove expanded/collapsed model ids to/from web storage */\n _setUpItemViewListeners: function(view) {\n var panel = this;\n _super.prototype._setUpItemViewListeners.call(panel, view);\n // use pub-sub to: handle drilldown expansion and collapse\n return panel.listenTo(view, {\n \"expanded:drilldown\": function(v, drilldown) {\n this._expandDrilldownPanel(drilldown);\n },\n \"collapsed:drilldown\": function(v, drilldown) {\n this._collapseDrilldownPanel(drilldown);\n }\n });\n },\n\n /** display 'current content': add a visible highlight and store the id of a content item */\n setCurrentContent: function(view) {\n this.$(\".history-content.current-content\").removeClass(\n \"current-content\"\n );\n if (view) {\n view.$el.addClass(\"current-content\");\n this.currentContentId = view.model.id;\n } else {\n this.currentContentId = null;\n }\n },\n\n /** find the view with the id and then call setCurrentContent on it */\n _setCurrentContentById: function(id) {\n var view = this.viewFromModelId(id) || null;\n this.setCurrentContent(view);\n },\n\n /** Handle drill down by hiding this panels list and controls and showing the sub-panel */\n _expandDrilldownPanel: function(drilldown) {\n this.panelStack.push(drilldown);\n // hide this panel's controls and list, set the name for back navigation, and attach to the $el\n this.$controls()\n .add(this.$list())\n .hide();\n drilldown.parentName = this.model.get(\"name\");\n drilldown\n .delegateEvents()\n .render()\n .$el.appendTo(this.$el);\n },\n\n /** Handle drilldown close by freeing the panel and re-rendering this panel */\n _collapseDrilldownPanel: function(drilldown) {\n this.panelStack.pop();\n //TODO: MEM: free the panel\n this.$controls()\n .add(this.$list())\n .show();\n },\n\n // ........................................................................ panel events\n /** event map */\n events: _.extend(_.clone(_super.prototype.events), {\n // the two links in the empty message\n \"click .uploader-link\": function(ev) {\n Galaxy.upload.show(ev);\n },\n \"click .get-data-link\": function(ev) {\n var $toolMenu = $(\".toolMenuContainer\");\n $toolMenu.parent().scrollTop(0);\n $toolMenu.find('span:contains(\"Get Data\")').click();\n }\n }),\n\n // ........................................................................ external objects/MVC\n listenToGalaxy: function(galaxy) {\n this.listenTo(galaxy, {\n // when the galaxy_main iframe is loaded with a new page,\n // compare the url to the following list and if there's a match\n // pull the id from url and indicate in the history view that\n // the dataset with that id is the 'current'ly active dataset\n \"center-frame:load\": function(data) {\n var pathToMatch = data.fullpath;\n var hdaId = null;\n var useToURLRegexMap = {\n display: /datasets\\/([a-f0-9]+)\\/display/,\n edit: /datasets\\/([a-f0-9]+)\\/edit/,\n report_error: /dataset\\/errors\\?id=([a-f0-9]+)/,\n rerun: /tool_runner\\/rerun\\?id=([a-f0-9]+)/,\n show_params: /datasets\\/([a-f0-9]+)\\/show_params/\n // no great way to do this here? (leave it in the dataset event handlers above?)\n // 'visualization' : 'visualization',\n };\n _.find(useToURLRegexMap, function(regex, use) {\n // grab the more specific match result (1), save, and use it as the find flag\n hdaId = _.result(pathToMatch.match(regex), 1);\n return hdaId;\n });\n // need to type mangle to go from web route to history contents\n this._setCurrentContentById(\n hdaId ? \"dataset-\" + hdaId : null\n );\n },\n // when the center panel is given a new view, clear the current indicator\n \"center-panel:load\": function(view) {\n this._setCurrentContentById();\n }\n });\n },\n\n //TODO: remove quota meter from panel and remove this\n /** add listeners to an external quota meter (mvc/user/user-quotameter.js) */\n connectToQuotaMeter: function(quotaMeter) {\n if (!quotaMeter) {\n return this;\n }\n // show/hide the 'over quota message' in the history when the meter tells it to\n this.listenTo(quotaMeter, \"quota:over\", this.showQuotaMessage);\n this.listenTo(quotaMeter, \"quota:under\", this.hideQuotaMessage);\n\n // having to add this to handle re-render of hview while overquota (the above do not fire)\n this.on(\"rendered rendered:initial\", function() {\n if (quotaMeter && quotaMeter.isOverQuota()) {\n this.showQuotaMessage();\n }\n });\n return this;\n },\n\n /** Override to preserve the quota message */\n clearMessages: function(ev) {\n var $target = !_.isUndefined(ev)\n ? $(ev.currentTarget)\n : this.$messages().children('[class$=\"message\"]');\n $target = $target.not(\".quota-message\");\n $target.fadeOut(this.fxSpeed, function() {\n $(this).remove();\n });\n return this;\n },\n\n /** Show the over quota message (which happens to be in the history panel).\n */\n showQuotaMessage: function() {\n var $msg = this.$(\".quota-message\");\n if ($msg.is(\":hidden\")) {\n $msg.slideDown(this.fxSpeed);\n }\n },\n\n /** Hide the over quota message (which happens to be in the history panel).\n */\n hideQuotaMessage: function() 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deleted/purged\n { visible: false, deleted: \"\", purged: \"\" },\n // both delete *and* unhide them\n { deleted: true, visible: true }\n );\n }\n return jQuery.when();\n },\n\n /** Return a string rep of the history */\n toString: function() {\n return (\n \"CurrentHistoryView(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n//------------------------------------------------------------------------------ TEMPLATES\nCurrentHistoryView.prototype.templates = (function() {\n var quotaMsgTemplate = BASE_MVC.wrapTemplate(\n [\n '\"\n ],\n \"history\"\n );\n return _.extend(_.clone(_super.prototype.templates), {\n quotaMsg: quotaMsgTemplate\n });\n})();\n\n//==============================================================================\nexport default {\n CurrentHistoryView: CurrentHistoryView\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/history/history-view-edit.js.map b/static/maps/mvc/history/history-view-edit.js.map index 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HISTORY_VIEW from \"mvc/history/history-view\";\nimport HISTORY_CONTENTS from \"mvc/history/history-contents\";\nimport STATES from \"mvc/dataset/states\";\nimport HDA_MODEL from \"mvc/history/hda-model\";\nimport HDA_LI_EDIT from \"mvc/history/hda-li-edit\";\nimport HDCA_LI_EDIT from \"mvc/history/hdca-li-edit\";\nimport TAGS from \"mvc/tag\";\nimport ANNOTATIONS from \"mvc/annotation\";\nimport LIST_COLLECTION_CREATOR from \"mvc/collection/list-collection-creator\";\nimport PAIR_COLLECTION_CREATOR from \"mvc/collection/pair-collection-creator\";\nimport LIST_OF_PAIRS_COLLECTION_CREATOR from \"mvc/collection/list-of-pairs-collection-creator\";\nimport faIconButton from \"ui/fa-icon-button\";\nimport PopupMenu from \"mvc/ui/popup-menu\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\nimport \"ui/editable-text\";\n\n/* =============================================================================\nTODO:\n\n============================================================================= */\nvar _super = HISTORY_VIEW.HistoryView;\n// base class for history-view-edit-current and used as-is in history/view.mako\n/** @class Editable View/Controller for the history model.\n *\n * Allows:\n * (everything HistoryView allows)\n * changing the name\n * displaying and editing tags and annotations\n * multi-selection and operations on mulitple content items\n */\nvar HistoryViewEdit = _super.extend(\n /** @lends HistoryViewEdit.prototype */ {\n /** class to use for constructing the HistoryDatasetAssociation views */\n HDAViewClass: HDA_LI_EDIT.HDAListItemEdit,\n /** class to use for constructing the HistoryDatasetCollectionAssociation views */\n HDCAViewClass: HDCA_LI_EDIT.HDCAListItemEdit,\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events\n * @param {Object} attributes\n */\n initialize: function(attributes) {\n attributes = attributes || {};\n _super.prototype.initialize.call(this, attributes);\n\n // ---- set up instance vars\n /** editor for tags - sub-view */\n this.tagsEditor = null;\n\n /** enable drag and drop - sub-view */\n this.dragItems = true;\n\n /** editor for annotations - sub-view */\n this.annotationEditor = null;\n\n /** allow user purge of dataset files? */\n this.purgeAllowed = attributes.purgeAllowed || false;\n\n // states/modes the panel can be in\n /** is the panel currently showing the dataset selection controls? */\n this.annotationEditorShown =\n attributes.annotationEditorShown || false;\n this.tagsEditorShown = attributes.tagsEditorShown || false;\n },\n\n /** Override to handle history as drag-drop target */\n _setUpListeners: function() {\n _super.prototype._setUpListeners.call(this);\n return this.on({\n \"droptarget:drop\": function(ev, data) {\n // process whatever was dropped and re-hide the drop target\n this.dataDropped(data);\n this.dropTargetOff();\n },\n \"view:attached view:removed\": function() {\n this._renderCounts();\n },\n \"search:loading-progress\": this._renderSearchProgress,\n \"search:searching\": this._renderSearchFindings\n });\n },\n\n // ------------------------------------------------------------------------ listeners\n /** listening for history and HDA events */\n _setUpModelListeners: function() {\n _super.prototype._setUpModelListeners.call(this);\n this.listenTo(\n this.model,\n \"change:size\",\n this.updateHistoryDiskSize\n );\n return this;\n },\n\n /** listening for collection events */\n _setUpCollectionListeners: function() {\n _super.prototype._setUpCollectionListeners.call(this);\n this.listenTo(this.collection, {\n \"change:deleted\": this._handleItemDeletedChange,\n \"change:visible\": this._handleItemVisibleChange,\n \"change:purged\": function(model) {\n // hafta get the new nice-size w/o the purged model\n this.model.fetch();\n },\n // loading indicators for deleted/hidden\n \"fetching-deleted\": function(collection) {\n this.$(\"> .controls .deleted-count\").html(\n \"\" + _l(\"loading...\") + \"\"\n );\n },\n \"fetching-hidden\": function(collection) {\n this.$(\"> .controls .hidden-count\").html(\n \"\" + _l(\"loading...\") + \"\"\n );\n },\n \"fetching-deleted-done fetching-hidden-done\": this._renderCounts\n });\n return this;\n },\n\n // ------------------------------------------------------------------------ panel rendering\n /** In this override, add tag and annotation editors and a btn to toggle the selectors */\n _buildNewRender: function() {\n // create a new render using a skeleton template, render title buttons, render body, and set up events, etc.\n var $newRender = _super.prototype._buildNewRender.call(this);\n if (!this.model) {\n return $newRender;\n }\n\n if (\n Galaxy &&\n Galaxy.user &&\n Galaxy.user.id &&\n Galaxy.user.id === this.model.get(\"user_id\")\n ) {\n this._renderTags($newRender);\n this._renderAnnotation($newRender);\n }\n return $newRender;\n },\n\n /** Update the history size display (curr. upper right of panel). */\n updateHistoryDiskSize: function() {\n this.$(\".history-size\").text(this.model.get(\"nice_size\"));\n },\n\n /** override to render counts when the items are rendered */\n renderItems: function($whereTo) {\n var views = _super.prototype.renderItems.call(this, $whereTo);\n if (!this.searchFor) {\n this._renderCounts($whereTo);\n } else {\n this._renderSearchFindings($whereTo);\n }\n return views;\n },\n\n /** override to show counts, what's deleted/hidden, and links to toggle those */\n _renderCounts: function($whereTo) {\n $whereTo = $whereTo instanceof jQuery ? $whereTo : this.$el;\n var html = this.templates.counts(this.model.toJSON(), this);\n return $whereTo.find(\"> .controls .subtitle\").html(html);\n },\n\n /** render the tags sub-view controller */\n _renderTags: function($where) {\n var panel = this;\n this.tagsEditor = new TAGS.TagsEditor({\n model: this.model,\n el: $where.find(\".controls .tags-display\"),\n onshowFirstTime: function() {\n this.render();\n },\n // show hide sub-view tag editors when this is shown/hidden\n onshow: function() {\n panel.toggleHDATagEditors(true, panel.fxSpeed);\n },\n onhide: function() {\n panel.toggleHDATagEditors(false, panel.fxSpeed);\n },\n $activator: faIconButton({\n title: _l(\"Edit history tags\"),\n classes: \"history-tag-btn\",\n faIcon: \"fa-tags\"\n }).appendTo($where.find(\".controls .actions\"))\n });\n },\n /** render the annotation sub-view controller */\n _renderAnnotation: function($where) {\n var panel = this;\n this.annotationEditor = new ANNOTATIONS.AnnotationEditor({\n model: this.model,\n el: $where.find(\".controls .annotation-display\"),\n onshowFirstTime: function() {\n this.render();\n },\n // show hide sub-view view annotation editors when this is shown/hidden\n onshow: function() {\n panel.toggleHDAAnnotationEditors(true, panel.fxSpeed);\n },\n onhide: function() {\n panel.toggleHDAAnnotationEditors(false, panel.fxSpeed);\n },\n $activator: faIconButton({\n title: _l(\"Edit history annotation\"),\n classes: \"history-annotate-btn\",\n faIcon: \"fa-comment\"\n }).appendTo($where.find(\".controls .actions\"))\n });\n },\n\n /** Set up HistoryViewEdit js/widget behaviours\n * In this override, make the name editable\n */\n _setUpBehaviors: function($where) {\n $where = $where || this.$el;\n _super.prototype._setUpBehaviors.call(this, $where);\n if (!this.model) {\n return;\n }\n\n // anon users shouldn't have access to any of the following\n if (\n !Galaxy.user ||\n Galaxy.user.isAnonymous() ||\n Galaxy.user.id !== this.model.get(\"user_id\")\n ) {\n return;\n }\n\n var panel = this,\n nameSelector = \"> .controls .name\";\n $where\n .find(nameSelector)\n .attr(\"title\", _l(\"Click to rename history\"))\n .tooltip({ placement: \"bottom\" })\n .make_text_editable({\n on_finish: function(newName) {\n var previousName = panel.model.get(\"name\");\n if (newName && newName !== previousName) {\n panel.$el.find(nameSelector).text(newName);\n panel.model\n .save({ name: newName })\n .fail(function() {\n panel.$el\n .find(nameSelector)\n .text(panel.model.previous(\"name\"));\n });\n } else {\n panel.$el.find(nameSelector).text(previousName);\n }\n }\n });\n },\n\n /** return a new popup menu for choosing a multi selection action\n * ajax calls made for multiple datasets are queued\n */\n multiselectActions: function() {\n var panel = this,\n actions = [\n {\n html: _l(\"Hide datasets\"),\n func: function() {\n var action =\n HDA_MODEL.HistoryDatasetAssociation.prototype\n .hide;\n panel.getSelectedModels().ajaxQueue(action);\n }\n },\n {\n html: _l(\"Unhide datasets\"),\n func: function() {\n var action =\n HDA_MODEL.HistoryDatasetAssociation.prototype\n .unhide;\n panel.getSelectedModels().ajaxQueue(action);\n }\n },\n {\n html: _l(\"Delete datasets\"),\n func: function() {\n var action =\n HDA_MODEL.HistoryDatasetAssociation.prototype[\n \"delete\"\n ];\n panel.getSelectedModels().ajaxQueue(action);\n }\n },\n {\n html: _l(\"Undelete datasets\"),\n func: function() {\n var action =\n HDA_MODEL.HistoryDatasetAssociation.prototype\n .undelete;\n panel.getSelectedModels().ajaxQueue(action);\n }\n }\n ];\n if (panel.purgeAllowed) {\n actions.push({\n html: _l(\"Permanently delete datasets\"),\n func: function() {\n if (\n confirm(\n _l(\n \"This will permanently remove the data in your datasets. Are you sure?\"\n )\n )\n ) {\n var action =\n HDA_MODEL.HistoryDatasetAssociation.prototype\n .purge;\n panel.getSelectedModels().ajaxQueue(action);\n }\n }\n });\n }\n actions = actions.concat(panel._collectionActions());\n return actions;\n },\n\n /** */\n _collectionActions: function() {\n var panel = this;\n return [\n {\n html: _l(\"Build Dataset List\"),\n func: function() {\n panel.buildCollection(\"list\");\n }\n },\n // TODO: Only show quick pair if two things selected.\n {\n html: _l(\"Build Dataset Pair\"),\n func: function() {\n panel.buildCollection(\"paired\");\n }\n },\n {\n html: _l(\"Build List of Dataset Pairs\"),\n func: function() {\n panel.buildCollection(\"list:paired\");\n }\n }\n ];\n },\n\n buildCollection: function(collectionType, selection, hideSourceItems) {\n var panel = this;\n var selection = selection || panel.getSelectedModels();\n var hideSourceItems = hideSourceItems || false;\n var createFunc;\n if (collectionType == \"list\") {\n createFunc = LIST_COLLECTION_CREATOR.createListCollection;\n } else if (collectionType == \"paired\") {\n createFunc = PAIR_COLLECTION_CREATOR.createPairCollection;\n } else if (collectionType == \"list:paired\") {\n createFunc =\n LIST_OF_PAIRS_COLLECTION_CREATOR.createListOfPairsCollection;\n } else {\n console.warn(\n \"Unknown collectionType encountered \" + collectionType\n );\n }\n createFunc(selection, hideSourceItems).done(function() {\n panel.model.refresh();\n });\n },\n\n // ------------------------------------------------------------------------ sub-views\n /** In this override, add purgeAllowed and whether tags/annotation editors should be shown */\n _getItemViewOptions: function(model) {\n var options = _super.prototype._getItemViewOptions.call(\n this,\n model\n );\n _.extend(options, {\n purgeAllowed: this.purgeAllowed,\n tagsEditorShown: this.tagsEditor && !this.tagsEditor.hidden,\n annotationEditorShown:\n this.annotationEditor && !this.annotationEditor.hidden\n });\n return options;\n },\n\n /** If this item is deleted and we're not showing deleted items, remove the view\n * @param {Model} the item model to check\n */\n _handleItemDeletedChange: function(itemModel) {\n if (itemModel.get(\"deleted\")) {\n this._handleItemDeletion(itemModel);\n } else {\n this._handleItemUndeletion(itemModel);\n }\n this._renderCounts();\n },\n\n _handleItemDeletion: function(itemModel) {\n var contentsShown = this.model.get(\"contents_active\");\n contentsShown.deleted += 1;\n contentsShown.active -= 1;\n if (!this.model.contents.includeDeleted) {\n this.removeItemView(itemModel);\n }\n this.model.set(\"contents_active\", contentsShown);\n },\n\n _handleItemUndeletion: function(itemModel) {\n var contentsShown = this.model.get(\"contents_active\");\n contentsShown.deleted -= 1;\n if (!this.model.contents.includeDeleted) {\n contentsShown.active -= 1;\n }\n this.model.set(\"contents_active\", contentsShown);\n },\n\n /** If this item is hidden and we're not showing hidden items, remove the view\n * @param {Model} the item model to check\n */\n _handleItemVisibleChange: function(itemModel) {\n if (itemModel.hidden()) {\n this._handleItemHidden(itemModel);\n } else {\n this._handleItemUnhidden(itemModel);\n }\n this._renderCounts();\n },\n\n _handleItemHidden: function(itemModel) {\n var contentsShown = this.model.get(\"contents_active\");\n contentsShown.hidden += 1;\n contentsShown.active -= 1;\n if (!this.model.contents.includeHidden) {\n this.removeItemView(itemModel);\n }\n this.model.set(\"contents_active\", contentsShown);\n },\n\n _handleItemUnhidden: function(itemModel) {\n var contentsShown = this.model.get(\"contents_active\");\n contentsShown.hidden -= 1;\n if (!this.model.contents.includeHidden) {\n contentsShown.active -= 1;\n }\n this.model.set(\"contents_active\", contentsShown);\n },\n\n /** toggle the visibility of each content's tagsEditor applying all the args sent to this function */\n toggleHDATagEditors: function(showOrHide, speed) {\n _.each(this.views, function(view) {\n if (view.tagsEditor) {\n view.tagsEditor.toggle(showOrHide, speed);\n }\n });\n },\n\n /** toggle the visibility of each content's annotationEditor applying all the args sent to this function */\n toggleHDAAnnotationEditors: function(showOrHide, speed) {\n _.each(this.views, function(view) {\n if (view.annotationEditor) {\n view.annotationEditor.toggle(showOrHide, speed);\n }\n });\n },\n\n // ------------------------------------------------------------------------ panel events\n /** event map */\n events: _.extend(_.clone(_super.prototype.events), {\n \"click .show-selectors-btn\": \"toggleSelectors\",\n \"click .toggle-deleted-link\": function(ev) {\n this.toggleShowDeleted();\n },\n \"click .toggle-hidden-link\": function(ev) {\n this.toggleShowHidden();\n }\n }),\n\n // ------------------------------------------------------------------------ search\n _renderSearchProgress: function(limit, offset) {\n var stop = limit + offset;\n return this.$(\"> .controls .subtitle\").html(\n [\n \"\",\n _l(\"Searching \"),\n stop,\n \"/\",\n this.model.contentsShown(),\n \"\"\n ].join(\"\")\n );\n },\n\n /** override to display number found in subtitle */\n _renderSearchFindings: function($whereTo) {\n $whereTo = $whereTo instanceof jQuery ? $whereTo : this.$el;\n var html = this.templates.found(this.model.toJSON(), this);\n $whereTo.find(\"> .controls .subtitle\").html(html);\n return this;\n },\n\n // ------------------------------------------------------------------------ as drop target\n /** turn all the drag and drop handlers on and add some help text above the drop area */\n dropTargetOn: function() {\n if (this.dropTarget) {\n return this;\n }\n this.dropTarget = true;\n\n //TODO: to init\n var dropHandlers = {\n dragenter: _.bind(this.dragenter, this),\n dragover: _.bind(this.dragover, this),\n dragleave: _.bind(this.dragleave, this),\n drop: _.bind(this.drop, this)\n };\n\n var $dropTarget = this._renderDropTarget();\n this.$list().before([this._renderDropTargetHelp(), $dropTarget]);\n for (var evName in dropHandlers) {\n if (dropHandlers.hasOwnProperty(evName)) {\n //console.debug( evName, dropHandlers[ evName ] );\n $dropTarget.on(evName, dropHandlers[evName]);\n }\n }\n return this;\n },\n\n /** render a box to serve as a 'drop here' area on the history */\n _renderDropTarget: function() {\n this.$(\".history-drop-target\").remove();\n return $(\"\").addClass(\"history-drop-target\");\n },\n\n /** tell the user how it works */\n _renderDropTargetHelp: function() {\n this.$(\".history-drop-target-help\").remove();\n return $(\"\")\n .addClass(\"history-drop-target-help\")\n .text(\n _l(\"Drag datasets here to copy them to the current history\")\n );\n },\n\n /** shut down drag and drop event handlers and remove drop target */\n dropTargetOff: function() {\n if (!this.dropTarget) {\n return this;\n }\n //this.log( 'dropTargetOff' );\n this.dropTarget = false;\n var dropTarget = this.$(\".history-drop-target\").get(0);\n for (var evName in this._dropHandlers) {\n if (this._dropHandlers.hasOwnProperty(evName)) {\n dropTarget.off(evName, this._dropHandlers[evName]);\n }\n }\n this.$(\".history-drop-target\").remove();\n this.$(\".history-drop-target-help\").remove();\n return this;\n },\n /** toggle the target on/off */\n dropTargetToggle: function() {\n if (this.dropTarget) {\n this.dropTargetOff();\n } else {\n this.dropTargetOn();\n }\n return this;\n },\n\n dragenter: function(ev) {\n //console.debug( 'dragenter:', this, ev );\n ev.preventDefault();\n ev.stopPropagation();\n this.$(\".history-drop-target\").css(\"border\", \"2px solid black\");\n },\n dragover: function(ev) {\n ev.preventDefault();\n ev.stopPropagation();\n },\n dragleave: function(ev) {\n //console.debug( 'dragleave:', this, ev );\n ev.preventDefault();\n ev.stopPropagation();\n this.$(\".history-drop-target\").css(\"border\", \"1px dashed black\");\n },\n /** when (text) is dropped try to parse as json and trigger an event */\n drop: function(ev) {\n ev.preventDefault();\n //ev.stopPropagation();\n\n var self = this;\n var dataTransfer = ev.originalEvent.dataTransfer;\n var data = dataTransfer.getData(\"text\");\n\n dataTransfer.dropEffect = \"move\";\n try {\n data = JSON.parse(data);\n } catch (err) {\n self.warn(\"error parsing JSON from drop:\", data);\n }\n\n self.trigger(\"droptarget:drop\", ev, data, self);\n return false;\n },\n\n /** handler that copies data into the contents */\n dataDropped: function(data) {\n var self = this;\n // HDA: dropping will copy it to the history\n if (\n _.isObject(data) &&\n data.model_class === \"HistoryDatasetAssociation\" &&\n data.id\n ) {\n if (self.contents.currentPage !== 0) {\n return self.contents.fetchPage(0).then(function() {\n return self.model.contents.copy(data.id);\n });\n }\n return self.model.contents.copy(data.id);\n }\n return jQuery.when();\n },\n\n // ........................................................................ misc\n /** Return a string rep of the history */\n toString: function() {\n return (\n \"HistoryViewEdit(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n//------------------------------------------------------------------------------ TEMPLATES\nHistoryViewEdit.prototype.templates = (function() {\n var countsTemplate = BASE_MVC.wrapTemplate(\n [\n \"<% var shown = Math.max( view.views.length, history.contents_active.active ) %>\",\n \"<% if( shown ){ %>\",\n '',\n \"<%- shown %> \",\n _l(\"shown\"),\n \"\",\n \"<% } %>\",\n\n \"<% if( history.contents_active.deleted ){ %>\",\n '',\n \"<% if( view.model.contents.includeDeleted ){ %>\",\n '',\n _l(\"hide deleted\"),\n \"\",\n \"<% } else { %>\",\n \"<%- history.contents_active.deleted %> \",\n '',\n _l(\"deleted\"),\n \"\",\n \"<% } %>\",\n \"\",\n \"<% } %>\",\n\n \"<% if( history.contents_active.hidden ){ %>\",\n '',\n \"<% if( view.model.contents.includeHidden ){ %>\",\n '',\n _l(\"hide hidden\"),\n \"\",\n \"<% } else { %>\",\n \"<%- history.contents_active.hidden %> \",\n '',\n _l(\"hidden\"),\n \"\",\n \"<% } %>\",\n \"\",\n \"<% } %>\"\n ],\n \"history\"\n );\n\n var foundTemplate = BASE_MVC.wrapTemplate(\n [\n _l(\"Found\"),\n \" <%- view.views.length %>, \",\n\n \"<% if( history.contents_active.deleted ){ %>\",\n \"<% if( view.model.contents.includeDeleted ){ %>\",\n '',\n _l(\"hide deleted\"),\n \", \",\n \"<% } else { %>\",\n '',\n _l(\"show deleted\"),\n \", \",\n \"<% } %>\",\n \"<% } %>\",\n\n \"<% if( history.contents_active.hidden ){ %>\",\n \"<% if( view.model.contents.includeHidden ){ %>\",\n '',\n _l(\"hide hidden\"),\n \"\",\n \"<% } else { %>\",\n '',\n _l(\"show hidden\"),\n \"\",\n \"<% } %>\",\n \"<% } %>\"\n ],\n \"history\"\n );\n\n return _.extend(_.clone(_super.prototype.templates), {\n counts: countsTemplate,\n found: foundTemplate\n });\n})();\n\n//==============================================================================\nexport default {\n HistoryViewEdit: HistoryViewEdit\n};\n"]} \ No newline at end of file +{"version":3,"sources":["mvc/history/history-view-edit.js"],"names":["_super","_historyView2","default","HistoryView","HistoryViewEdit","extend","HDAViewClass","_hdaLiEdit2","HDAListItemEdit","HDCAViewClass","_hdcaLiEdit2","HDCAListItemEdit","initialize","attributes","prototype","call","this","tagsEditor","dragItems","annotationEditor","purgeAllowed","annotationEditorShown","tagsEditorShown","_setUpListeners","ev","data","dataDropped","dropTargetOff","view:attached 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HISTORY_VIEW from \"mvc/history/history-view\";\nimport HISTORY_CONTENTS from \"mvc/history/history-contents\";\nimport STATES from \"mvc/dataset/states\";\nimport HDA_MODEL from \"mvc/history/hda-model\";\nimport HDA_LI_EDIT from \"mvc/history/hda-li-edit\";\nimport HDCA_LI_EDIT from \"mvc/history/hdca-li-edit\";\nimport TAGS from \"mvc/tag\";\nimport ANNOTATIONS from \"mvc/annotation\";\nimport LIST_COLLECTION_CREATOR from \"mvc/collection/list-collection-creator\";\nimport PAIR_COLLECTION_CREATOR from \"mvc/collection/pair-collection-creator\";\nimport LIST_OF_PAIRS_COLLECTION_CREATOR from \"mvc/collection/list-of-pairs-collection-creator\";\nimport faIconButton from \"ui/fa-icon-button\";\nimport PopupMenu from \"mvc/ui/popup-menu\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\nimport \"ui/editable-text\";\n\n/* =============================================================================\nTODO:\n\n============================================================================= */\nvar _super = HISTORY_VIEW.HistoryView;\n// base class for history-view-edit-current and used as-is in history/view.mako\n/** @class Editable View/Controller for the history model.\n *\n * Allows:\n * (everything HistoryView allows)\n * changing the name\n * displaying and editing tags and annotations\n * multi-selection and operations on mulitple content items\n */\nvar HistoryViewEdit = _super.extend(\n /** @lends HistoryViewEdit.prototype */ {\n /** class to use for constructing the HistoryDatasetAssociation views */\n HDAViewClass: HDA_LI_EDIT.HDAListItemEdit,\n /** class to use for constructing the HistoryDatasetCollectionAssociation views */\n HDCAViewClass: HDCA_LI_EDIT.HDCAListItemEdit,\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events\n * @param {Object} attributes\n */\n initialize: function(attributes) {\n attributes = attributes || {};\n _super.prototype.initialize.call(this, attributes);\n\n // ---- set up instance vars\n /** editor for tags - sub-view */\n this.tagsEditor = null;\n\n /** enable drag and drop - sub-view */\n this.dragItems = true;\n\n /** editor for annotations - sub-view */\n this.annotationEditor = null;\n\n /** allow user purge of dataset files? */\n this.purgeAllowed = attributes.purgeAllowed || false;\n\n // states/modes the panel can be in\n /** is the panel currently showing the dataset selection controls? */\n this.annotationEditorShown =\n attributes.annotationEditorShown || false;\n this.tagsEditorShown = attributes.tagsEditorShown || false;\n },\n\n /** Override to handle history as drag-drop target */\n _setUpListeners: function() {\n _super.prototype._setUpListeners.call(this);\n return this.on({\n \"droptarget:drop\": function(ev, data) {\n // process whatever was dropped and re-hide the drop target\n this.dataDropped(data);\n this.dropTargetOff();\n },\n \"view:attached view:removed\": function() {\n this._renderCounts();\n },\n \"search:loading-progress\": this._renderSearchProgress,\n \"search:searching\": this._renderSearchFindings\n });\n },\n\n // ------------------------------------------------------------------------ listeners\n /** listening for history and HDA events */\n _setUpModelListeners: function() {\n _super.prototype._setUpModelListeners.call(this);\n this.listenTo(\n this.model,\n \"change:size\",\n this.updateHistoryDiskSize\n );\n return this;\n },\n\n /** listening for collection events */\n _setUpCollectionListeners: function() {\n _super.prototype._setUpCollectionListeners.call(this);\n this.listenTo(this.collection, {\n \"change:deleted\": this._handleItemDeletedChange,\n \"change:visible\": this._handleItemVisibleChange,\n \"change:purged\": function(model) {\n // hafta get the new nice-size w/o the purged model\n this.model.fetch();\n },\n // loading indicators for deleted/hidden\n \"fetching-deleted\": function(collection) {\n this.$(\"> .controls .deleted-count\").html(\n \"\" + _l(\"loading...\") + \"\"\n );\n },\n \"fetching-hidden\": function(collection) {\n this.$(\"> .controls .hidden-count\").html(\n \"\" + _l(\"loading...\") + \"\"\n );\n },\n \"fetching-deleted-done fetching-hidden-done\": this._renderCounts\n });\n return this;\n },\n\n // ------------------------------------------------------------------------ panel rendering\n /** In this override, add tag and annotation editors and a btn to toggle the selectors */\n _buildNewRender: function() {\n // create a new render using a skeleton template, render title buttons, render body, and set up events, etc.\n var $newRender = _super.prototype._buildNewRender.call(this);\n if (!this.model) {\n return $newRender;\n }\n\n if (\n Galaxy &&\n Galaxy.user &&\n Galaxy.user.id &&\n Galaxy.user.id === this.model.get(\"user_id\")\n ) {\n this._renderTags($newRender);\n this._renderAnnotation($newRender);\n }\n return $newRender;\n },\n\n /** Update the history size display (curr. upper right of panel). */\n updateHistoryDiskSize: function() {\n this.$(\".history-size\").text(this.model.get(\"nice_size\"));\n },\n\n /** override to render counts when the items are rendered */\n renderItems: function($whereTo) {\n var views = _super.prototype.renderItems.call(this, $whereTo);\n if (!this.searchFor) {\n this._renderCounts($whereTo);\n } else {\n this._renderSearchFindings($whereTo);\n }\n return views;\n },\n\n /** override to show counts, what's deleted/hidden, and links to toggle those */\n _renderCounts: function($whereTo) {\n $whereTo = $whereTo instanceof jQuery ? $whereTo : this.$el;\n var html = this.templates.counts(this.model.toJSON(), this);\n return $whereTo.find(\"> .controls .subtitle\").html(html);\n },\n\n /** render the tags sub-view controller */\n _renderTags: function($where) {\n var panel = this;\n this.tagsEditor = new TAGS.TagsEditor({\n model: this.model,\n el: $where.find(\".controls .tags-display\"),\n onshowFirstTime: function() {\n this.render();\n },\n // show hide sub-view tag editors when this is shown/hidden\n onshow: function() {\n panel.toggleHDATagEditors(true, panel.fxSpeed);\n },\n onhide: function() {\n panel.toggleHDATagEditors(false, panel.fxSpeed);\n },\n $activator: faIconButton({\n title: _l(\"Edit history tags\"),\n classes: \"history-tag-btn\",\n faIcon: \"fa-tags\"\n }).appendTo($where.find(\".controls .actions\"))\n });\n },\n /** render the annotation sub-view controller */\n _renderAnnotation: function($where) {\n var panel = this;\n this.annotationEditor = new ANNOTATIONS.AnnotationEditor({\n model: this.model,\n el: $where.find(\".controls .annotation-display\"),\n onshowFirstTime: function() {\n this.render();\n },\n // show hide sub-view view annotation editors when this is shown/hidden\n onshow: function() {\n panel.toggleHDAAnnotationEditors(true, panel.fxSpeed);\n },\n onhide: function() {\n panel.toggleHDAAnnotationEditors(false, panel.fxSpeed);\n },\n $activator: faIconButton({\n title: _l(\"Edit history annotation\"),\n classes: \"history-annotate-btn\",\n faIcon: \"fa-comment\"\n }).appendTo($where.find(\".controls .actions\"))\n });\n },\n\n /** Set up HistoryViewEdit js/widget behaviours\n * In this override, make the name editable\n */\n _setUpBehaviors: function($where) {\n $where = $where || this.$el;\n _super.prototype._setUpBehaviors.call(this, $where);\n if (!this.model) {\n return;\n }\n\n // anon users shouldn't have access to any of the following\n if (\n !Galaxy.user ||\n Galaxy.user.isAnonymous() ||\n Galaxy.user.id !== this.model.get(\"user_id\")\n ) {\n return;\n }\n\n var panel = this,\n nameSelector = \"> .controls .name\";\n $where\n .find(nameSelector)\n .attr(\"title\", _l(\"Click to rename history\"))\n .tooltip({ placement: \"bottom\" })\n .make_text_editable({\n on_finish: function(newName) {\n var previousName = panel.model.get(\"name\");\n if (newName && newName !== previousName) {\n panel.$el.find(nameSelector).text(newName);\n panel.model\n .save({ name: newName })\n .fail(function() {\n panel.$el\n .find(nameSelector)\n .text(panel.model.previous(\"name\"));\n });\n } else {\n panel.$el.find(nameSelector).text(previousName);\n }\n }\n });\n },\n\n /** return a new popup menu for choosing a multi selection action\n * ajax calls made for multiple datasets are queued\n */\n multiselectActions: function() {\n var panel = this,\n actions = [\n {\n html: _l(\"Hide datasets\"),\n func: function() {\n var action =\n HDA_MODEL.HistoryDatasetAssociation.prototype\n .hide;\n panel.getSelectedModels().ajaxQueue(action);\n }\n },\n {\n html: _l(\"Unhide datasets\"),\n func: function() {\n var action =\n HDA_MODEL.HistoryDatasetAssociation.prototype\n .unhide;\n panel.getSelectedModels().ajaxQueue(action);\n }\n },\n {\n html: _l(\"Delete datasets\"),\n func: function() {\n var action =\n HDA_MODEL.HistoryDatasetAssociation.prototype[\n \"delete\"\n ];\n panel.getSelectedModels().ajaxQueue(action);\n }\n },\n {\n html: _l(\"Undelete datasets\"),\n func: function() {\n var action =\n HDA_MODEL.HistoryDatasetAssociation.prototype\n .undelete;\n panel.getSelectedModels().ajaxQueue(action);\n }\n }\n ];\n if (panel.purgeAllowed) {\n actions.push({\n html: _l(\"Permanently delete datasets\"),\n func: function() {\n if (\n confirm(\n _l(\n \"This will permanently remove the data in your datasets. Are you sure?\"\n )\n )\n ) {\n var action =\n HDA_MODEL.HistoryDatasetAssociation.prototype\n .purge;\n panel.getSelectedModels().ajaxQueue(action);\n }\n }\n });\n }\n actions = actions.concat(panel._collectionActions());\n return actions;\n },\n\n /** */\n _collectionActions: function() {\n var panel = this;\n return [\n {\n html: _l(\"Build Dataset List\"),\n func: function() {\n panel.buildCollection(\"list\");\n }\n },\n // TODO: Only show quick pair if two things selected.\n {\n html: _l(\"Build Dataset Pair\"),\n func: function() {\n panel.buildCollection(\"paired\");\n }\n },\n {\n html: _l(\"Build List of Dataset Pairs\"),\n func: function() {\n panel.buildCollection(\"list:paired\");\n }\n }\n ];\n },\n\n buildCollection: function(collectionType, selection, hideSourceItems) {\n var panel = this;\n var selection = selection || panel.getSelectedModels();\n var hideSourceItems = hideSourceItems || false;\n var createFunc;\n if (collectionType == \"list\") {\n createFunc = LIST_COLLECTION_CREATOR.createListCollection;\n } else if (collectionType == \"paired\") {\n createFunc = PAIR_COLLECTION_CREATOR.createPairCollection;\n } else if (collectionType == \"list:paired\") {\n createFunc =\n LIST_OF_PAIRS_COLLECTION_CREATOR.createListOfPairsCollection;\n } else {\n console.warn(\n \"Unknown collectionType encountered \" + collectionType\n );\n }\n createFunc(selection, hideSourceItems).done(function() {\n panel.model.refresh();\n });\n },\n\n // ------------------------------------------------------------------------ sub-views\n /** In this override, add purgeAllowed and whether tags/annotation editors should be shown */\n _getItemViewOptions: function(model) {\n var options = _super.prototype._getItemViewOptions.call(\n this,\n model\n );\n _.extend(options, {\n purgeAllowed: this.purgeAllowed,\n tagsEditorShown: this.tagsEditor && !this.tagsEditor.hidden,\n annotationEditorShown:\n this.annotationEditor && !this.annotationEditor.hidden\n });\n return options;\n },\n\n /** If this item is deleted and we're not showing deleted items, remove the view\n * @param {Model} the item model to check\n */\n _handleItemDeletedChange: function(itemModel) {\n if (itemModel.get(\"deleted\")) {\n this._handleItemDeletion(itemModel);\n } else {\n this._handleItemUndeletion(itemModel);\n }\n this._renderCounts();\n },\n\n _handleItemDeletion: function(itemModel) {\n var contentsShown = this.model.get(\"contents_active\");\n contentsShown.deleted += 1;\n contentsShown.active -= 1;\n if (!this.model.contents.includeDeleted) {\n this.removeItemView(itemModel);\n }\n this.model.set(\"contents_active\", contentsShown);\n },\n\n _handleItemUndeletion: function(itemModel) {\n var contentsShown = this.model.get(\"contents_active\");\n contentsShown.deleted -= 1;\n if (!this.model.contents.includeDeleted) {\n contentsShown.active -= 1;\n }\n this.model.set(\"contents_active\", contentsShown);\n },\n\n /** If this item is hidden and we're not showing hidden items, remove the view\n * @param {Model} the item model to check\n */\n _handleItemVisibleChange: function(itemModel) {\n if (itemModel.hidden()) {\n this._handleItemHidden(itemModel);\n } else {\n this._handleItemUnhidden(itemModel);\n }\n this._renderCounts();\n },\n\n _handleItemHidden: function(itemModel) {\n var contentsShown = this.model.get(\"contents_active\");\n contentsShown.hidden += 1;\n contentsShown.active -= 1;\n if (!this.model.contents.includeHidden) {\n this.removeItemView(itemModel);\n }\n this.model.set(\"contents_active\", contentsShown);\n },\n\n _handleItemUnhidden: function(itemModel) {\n var contentsShown = this.model.get(\"contents_active\");\n contentsShown.hidden -= 1;\n if (!this.model.contents.includeHidden) {\n contentsShown.active -= 1;\n }\n this.model.set(\"contents_active\", contentsShown);\n },\n\n /** toggle the visibility of each content's tagsEditor applying all the args sent to this function */\n toggleHDATagEditors: function(showOrHide, speed) {\n _.each(this.views, function(view) {\n if (view.tagsEditor) {\n view.tagsEditor.toggle(showOrHide, speed);\n }\n });\n },\n\n /** toggle the visibility of each content's annotationEditor applying all the args sent to this function */\n toggleHDAAnnotationEditors: function(showOrHide, speed) {\n _.each(this.views, function(view) {\n if (view.annotationEditor) {\n view.annotationEditor.toggle(showOrHide, speed);\n }\n });\n },\n\n // ------------------------------------------------------------------------ panel events\n /** event map */\n events: _.extend(_.clone(_super.prototype.events), {\n \"click .show-selectors-btn\": \"toggleSelectors\",\n \"click .toggle-deleted-link\": function(ev) {\n this.toggleShowDeleted();\n },\n \"click .toggle-hidden-link\": function(ev) {\n this.toggleShowHidden();\n }\n }),\n\n // ------------------------------------------------------------------------ search\n _renderSearchProgress: function(limit, offset) {\n var stop = limit + offset;\n return this.$(\"> .controls .subtitle\").html(\n [\n \"\",\n _l(\"Searching \"),\n stop,\n \"/\",\n this.model.contentsShown(),\n \"\"\n ].join(\"\")\n );\n },\n\n /** override to display number found in subtitle */\n _renderSearchFindings: function($whereTo) {\n $whereTo = $whereTo instanceof jQuery ? $whereTo : this.$el;\n var html = this.templates.found(this.model.toJSON(), this);\n $whereTo.find(\"> .controls .subtitle\").html(html);\n return this;\n },\n\n // ------------------------------------------------------------------------ as drop target\n /** turn all the drag and drop handlers on and add some help text above the drop area */\n dropTargetOn: function() {\n if (this.dropTarget) {\n return this;\n }\n this.dropTarget = true;\n\n //TODO: to init\n var dropHandlers = {\n dragenter: _.bind(this.dragenter, this),\n dragover: _.bind(this.dragover, this),\n dragleave: _.bind(this.dragleave, this),\n drop: _.bind(this.drop, this)\n };\n\n var $dropTarget = this._renderDropTarget();\n this.$list().before([this._renderDropTargetHelp(), $dropTarget]);\n for (var evName in dropHandlers) {\n if (dropHandlers.hasOwnProperty(evName)) {\n //console.debug( evName, dropHandlers[ evName ] );\n $dropTarget.on(evName, dropHandlers[evName]);\n }\n }\n return this;\n },\n\n /** render a box to serve as a 'drop here' area on the history */\n _renderDropTarget: function() {\n this.$(\".history-drop-target\").remove();\n return $(\"\").addClass(\"history-drop-target\");\n },\n\n /** tell the user how it works */\n _renderDropTargetHelp: function() {\n this.$(\".history-drop-target-help\").remove();\n return $(\"\")\n .addClass(\"history-drop-target-help\")\n .text(\n _l(\"Drag datasets here to copy them to the current history\")\n );\n },\n\n /** shut down drag and drop event handlers and remove drop target */\n dropTargetOff: function() {\n if (!this.dropTarget) {\n return this;\n }\n //this.log( 'dropTargetOff' );\n this.dropTarget = false;\n var dropTarget = this.$(\".history-drop-target\").get(0);\n for (var evName in this._dropHandlers) {\n if (this._dropHandlers.hasOwnProperty(evName)) {\n dropTarget.off(evName, this._dropHandlers[evName]);\n }\n }\n this.$(\".history-drop-target\").remove();\n this.$(\".history-drop-target-help\").remove();\n return this;\n },\n /** toggle the target on/off */\n dropTargetToggle: function() {\n if (this.dropTarget) {\n this.dropTargetOff();\n } else {\n this.dropTargetOn();\n }\n return this;\n },\n\n dragenter: function(ev) {\n //console.debug( 'dragenter:', this, ev );\n ev.preventDefault();\n ev.stopPropagation();\n this.$(\".history-drop-target\").css(\"border\", \"2px solid black\");\n },\n dragover: function(ev) {\n ev.preventDefault();\n ev.stopPropagation();\n },\n dragleave: function(ev) {\n //console.debug( 'dragleave:', this, ev );\n ev.preventDefault();\n ev.stopPropagation();\n this.$(\".history-drop-target\").css(\"border\", \"1px dashed black\");\n },\n /** when (text) is dropped try to parse as json and trigger an event */\n drop: function(ev) {\n ev.preventDefault();\n //ev.stopPropagation();\n\n var self = this;\n var dataTransfer = ev.originalEvent.dataTransfer;\n var data = dataTransfer.getData(\"text\");\n\n dataTransfer.dropEffect = \"move\";\n try {\n data = JSON.parse(data);\n } catch (err) {\n self.warn(\"error parsing JSON from drop:\", data);\n }\n\n self.trigger(\"droptarget:drop\", ev, data, self);\n return false;\n },\n\n /** handler that copies data into the contents */\n dataDropped: function(data) {\n var self = this;\n // HDA: dropping will copy it to the history\n if (\n _.isObject(data) &&\n data.model_class === \"HistoryDatasetAssociation\" &&\n data.id\n ) {\n if (self.contents.currentPage !== 0) {\n return self.contents.fetchPage(0).then(function() {\n return self.model.contents.copy(data.id);\n });\n }\n return self.model.contents.copy(data.id);\n }\n return jQuery.when();\n },\n\n // ........................................................................ misc\n /** Return a string rep of the history */\n toString: function() {\n return (\n \"HistoryViewEdit(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n }\n);\n\n//------------------------------------------------------------------------------ TEMPLATES\nHistoryViewEdit.prototype.templates = (function() {\n var countsTemplate = BASE_MVC.wrapTemplate(\n [\n \"<% var shown = Math.max( view.views.length, history.contents_active.active ) %>\",\n \"<% if( shown ){ %>\",\n '',\n \"<%- shown %> \",\n _l(\"shown\"),\n \"\",\n \"<% } %>\",\n\n \"<% if( history.contents_active.deleted ){ %>\",\n '',\n \"<% if( view.model.contents.includeDeleted ){ %>\",\n '',\n _l(\"hide deleted\"),\n \"\",\n \"<% } else { %>\",\n \"<%- history.contents_active.deleted %> \",\n '',\n _l(\"deleted\"),\n \"\",\n \"<% } %>\",\n \"\",\n \"<% } %>\",\n\n \"<% if( history.contents_active.hidden ){ %>\",\n '',\n \"<% if( view.model.contents.includeHidden ){ %>\",\n '',\n _l(\"hide hidden\"),\n \"\",\n \"<% } else { %>\",\n \"<%- history.contents_active.hidden %> \",\n '',\n _l(\"hidden\"),\n \"\",\n \"<% } %>\",\n \"\",\n \"<% } %>\"\n ],\n \"history\"\n );\n\n var foundTemplate = BASE_MVC.wrapTemplate(\n [\n _l(\"Found\"),\n \" <%- view.views.length %>, \",\n\n \"<% if( history.contents_active.deleted ){ %>\",\n \"<% if( view.model.contents.includeDeleted ){ %>\",\n '',\n _l(\"hide deleted\"),\n \", \",\n \"<% } else { %>\",\n '',\n _l(\"show deleted\"),\n \", \",\n \"<% } %>\",\n \"<% } %>\",\n\n \"<% if( history.contents_active.hidden ){ %>\",\n \"<% if( view.model.contents.includeHidden ){ %>\",\n '',\n _l(\"hide hidden\"),\n \"\",\n \"<% } else { %>\",\n '',\n _l(\"show hidden\"),\n \"\",\n \"<% } %>\",\n \"<% } %>\"\n ],\n \"history\"\n );\n\n return _.extend(_.clone(_super.prototype.templates), {\n counts: countsTemplate,\n found: foundTemplate\n });\n})();\n\n//==============================================================================\nexport default {\n HistoryViewEdit: HistoryViewEdit\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/history/history-view.js.map b/static/maps/mvc/history/history-view.js.map index 246274fa057..05a67fd9960 100644 --- a/static/maps/mvc/history/history-view.js.map +++ b/static/maps/mvc/history/history-view.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/history/history-view.js"],"names":["_listView","require","_historyModel","_historyContents","_historyPreferences","_hdaLi","_hdcaLi","_userModel","_errorModal","_faIconButton","_baseMvc","_localization","_super","_listView2","default","ModelListPanel","HistoryView","extend","_logNamespace","HDAViewClass","_hdaLi2","HDAListItemView","HDCAViewClass","_hdcaLi2","HDCAListItemView","collectionClass","_historyContents2","HistoryContents","modelCollectionKey","tagName","className","prototype","emptyMsg","_localization2","noneFoundMsg","searchPlaceholder","FETCH_COLLECTION_COUNTS_DELAY","initialize","attributes","call","this","linkTarget","detailedFetchTimeoutId","_createDefaultCollection","history","model","freeModel","clearUpdateTimeout","on","error","xhr","options","msg","details","errorHandler","loading-done","self","_","delay","contents","fetchCollectionCounts","views:ready view:attached 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LIST_VIEW from \"mvc/list/list-view\";\nimport HISTORY_MODEL from \"mvc/history/history-model\";\nimport HISTORY_CONTENTS from \"mvc/history/history-contents\";\nimport HISTORY_PREFS from \"mvc/history/history-preferences\";\nimport HDA_LI from \"mvc/history/hda-li\";\nimport HDCA_LI from \"mvc/history/hdca-li\";\nimport USER from \"mvc/user/user-model\";\nimport ERROR_MODAL from \"mvc/ui/error-modal\";\nimport faIconButton from \"ui/fa-icon-button\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\nimport \"ui/search-input\";\n\n/* =============================================================================\nTODO:\n\n============================================================================= */\n/** @class non-editable, read-only View/Controller for a history model.\n * Allows:\n * changing the loaded history\n * displaying data, info, and download\n * tracking history attrs: size, tags, annotations, name, etc.\n * Does not allow:\n * changing the name\n */\nvar _super = LIST_VIEW.ModelListPanel;\nvar HistoryView = _super.extend(\n /** @lends HistoryView.prototype */ {\n _logNamespace: \"history\",\n\n /** class to use for constructing the HDA views */\n HDAViewClass: HDA_LI.HDAListItemView,\n /** class to use for constructing the HDCA views */\n HDCAViewClass: HDCA_LI.HDCAListItemView,\n /** class to used for constructing collection of sub-view models */\n collectionClass: HISTORY_CONTENTS.HistoryContents,\n /** key of attribute in model to assign to this.collection */\n modelCollectionKey: \"contents\",\n\n tagName: \"div\",\n className: _super.prototype.className + \" history-panel\",\n\n /** string to display when the collection is empty */\n emptyMsg: _l(\"This history is empty\"),\n /** displayed when no items match the search terms */\n noneFoundMsg: _l(\"No matching datasets found\"),\n /** string used for search placeholder */\n searchPlaceholder: _l(\"search datasets\"),\n\n /** @type {Number} ms to wait after history load to fetch/decorate hdcas with element_count */\n FETCH_COLLECTION_COUNTS_DELAY: 2000,\n\n // ......................................................................... SET UP\n /** Set up the view, bind listeners.\n * @param {Object} attributes optional settings for the panel\n */\n initialize: function(attributes) {\n _super.prototype.initialize.call(this, attributes);\n // ---- instance vars\n // control contents/behavior based on where (and in what context) the panel is being used\n /** where should pages from links be displayed? (default to new tab/window) */\n this.linkTarget = attributes.linkTarget || \"_blank\";\n\n /** timeout id for detailed fetch of collection counts, etc... */\n this.detailedFetchTimeoutId = null;\n },\n\n /** create and return a collection for when none is initially passed */\n _createDefaultCollection: function() {\n // override\n return new this.collectionClass([], {\n history: this.model\n });\n },\n\n /** In this override, clear the update timer on the model */\n freeModel: function() {\n _super.prototype.freeModel.call(this);\n if (this.model) {\n this.model.clearUpdateTimeout();\n }\n this._clearDetailedFetchTimeout();\n return this;\n },\n\n /** clear the timeout and the cached timeout id */\n _clearDetailedFetchTimeout: function() {\n if (this.detailedFetchTimeoutId) {\n clearTimeout(this.detailedFetchTimeoutId);\n this.detailedFetchTimeoutId = null;\n }\n },\n\n /** create any event listeners for the panel\n * @fires: rendered:initial on the first render\n * @fires: empty-history when switching to a history with no contents or creating a new history\n */\n _setUpListeners: function() {\n _super.prototype._setUpListeners.call(this);\n this.on({\n error: function(model, xhr, options, msg, details) {\n this.errorHandler(model, xhr, options, msg, details);\n },\n \"loading-done\": function() {\n var self = this;\n // after the initial load, decorate with more time consuming fields (like HDCA element_counts)\n self.detailedFetchTimeoutId = _.delay(function() {\n self.detailedFetchTimeoutId = null;\n self.model.contents.fetchCollectionCounts();\n }, self.FETCH_COLLECTION_COUNTS_DELAY);\n },\n \"views:ready view:attached view:removed\": function(view) {\n this._renderSelectButton();\n },\n \"view:attached\": function(view) {\n this.scrollTo(0);\n }\n });\n // this.on( 'all', function(){ console.debug( arguments ); });\n },\n\n // ------------------------------------------------------------------------ loading history/hda models\n /** load the history with the given id then it's contents, sending ajax options to both */\n loadHistory: function(historyId, options, contentsOptions) {\n contentsOptions = _.extend(contentsOptions || { silent: true });\n this.info(\"loadHistory:\", historyId, options, contentsOptions);\n var self = this;\n self.setModel(new HISTORY_MODEL.History({ id: historyId }));\n\n contentsOptions.silent = true;\n self.trigger(\"loading\");\n return self.model\n .fetchWithContents(options, contentsOptions)\n .always(function() {\n self.render();\n self.trigger(\"loading-done\");\n });\n },\n\n /** convenience alias to the model. 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this.hideSelectors();\n $where.find(\".controls .actions .show-selectors-btn\").remove();\n return null;\n }\n // don't bother rendering if there's one already\n var $existing = $where.find(\n \".controls .actions .show-selectors-btn\"\n );\n if ($existing.length) {\n return $existing;\n }\n\n return faIconButton({\n title: _l(\"Operations on multiple datasets\"),\n classes: \"show-selectors-btn\",\n faIcon: \"fa-check-square-o\"\n }).prependTo($where.find(\".controls .actions\"));\n },\n\n /** override to avoid showing intial empty message using contents_active */\n _renderEmptyMessage: function($whereTo) {\n var self = this;\n var $emptyMsg = self.$emptyMessage($whereTo);\n\n var empty = self.model.get(\"contents_active\").active <= 0;\n if (empty) {\n return $emptyMsg\n .empty()\n .append(self.emptyMsg)\n .show();\n } else if (\n self.searchFor &&\n self.model.contents.haveSearchDetails() &&\n !self.views.length\n ) {\n return $emptyMsg\n .empty()\n .append(self.noneFoundMsg)\n .show();\n }\n $emptyMsg.hide();\n return $();\n },\n\n /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */\n $scrollContainer: function($where) {\n // override or set via attributes.$scrollContainer\n return this.$list($where);\n },\n\n // ------------------------------------------------------------------------ subviews\n _toggleContentsLoadingIndicator: function(show) {\n if (!show) {\n this.$list()\n .find(\".contents-loading-indicator\")\n .remove();\n } else {\n this.$list().html(\n '' +\n ''\n );\n }\n },\n\n /** override to render pagination also */\n renderItems: function($whereTo) {\n // console.log( this + '.renderItems-----------------', new Date() );\n $whereTo = $whereTo || this.$el;\n var self = this;\n var $list = self.$list($whereTo);\n\n // TODO: bootstrap hack to remove orphaned tooltips\n $(\".tooltip\").remove();\n\n $list.empty();\n self.views = [];\n\n var models = self._filterCollection();\n if (models.length) {\n self._renderPagination($whereTo);\n self.views = self._renderSomeItems(models, $list);\n } else {\n // TODO: consolidate with _renderPagination above by (???) passing in models/length?\n $whereTo.find(\"> .controls .list-pagination\").empty();\n }\n self._renderEmptyMessage($whereTo).toggle(!models.length);\n\n self.trigger(\"views:ready\", self.views);\n return self.views;\n },\n\n /** render pagination controls if not searching and contents says we're paginating */\n _renderPagination: function($whereTo) {\n var $paginationControls = $whereTo.find(\n \"> .controls .list-pagination\"\n );\n if (this.searchFor || !this.model.contents.shouldPaginate())\n return $paginationControls.empty();\n\n $paginationControls.html(\n this.templates.pagination(\n {\n // pagination is 1-based for the user\n current: this.model.contents.currentPage + 1,\n last: this.model.contents.getLastPage() + 1\n },\n this\n )\n );\n $paginationControls.find(\"select.pages\").tooltip();\n return $paginationControls;\n },\n\n /** render a subset of the entire collection (client-side pagination) */\n _renderSomeItems: function(models, $list) {\n var self = this;\n var views = [];\n $list.append(\n models.map(function(m) {\n var view = self._createItemView(m);\n views.push(view);\n return self._renderItemView$el(view);\n })\n );\n return views;\n },\n\n // ------------------------------------------------------------------------ sub-views\n /** in this override, check if the contents would also display based on includeDeleted/hidden */\n _filterItem: function(model) {\n var self = this;\n var contents = self.model.contents;\n return (\n (contents.includeHidden || !model.hidden()) &&\n (contents.includeDeleted || !model.isDeletedOrPurged()) &&\n _super.prototype._filterItem.call(self, model)\n );\n },\n\n /** In this override, since history contents are mixed,\n * get the appropo view class based on history_content_type\n */\n _getItemViewClass: function(model) {\n var contentType = model.get(\"history_content_type\");\n switch (contentType) {\n case \"dataset\":\n return this.HDAViewClass;\n case \"dataset_collection\":\n return this.HDCAViewClass;\n }\n throw new TypeError(\"Unknown history_content_type: \" + contentType);\n },\n\n /** in this override, add a linktarget, and expand if id is in web storage */\n _getItemViewOptions: function(model) {\n var options = _super.prototype._getItemViewOptions.call(\n this,\n model\n );\n return _.extend(options, {\n linkTarget: this.linkTarget,\n expanded: this.model.contents.storage.isExpanded(model.id),\n hasUser: this.model.ownedByCurrUser()\n });\n },\n\n /** In this override, add/remove expanded/collapsed model ids to/from web storage */\n _setUpItemViewListeners: function(view) {\n var panel = this;\n _super.prototype._setUpItemViewListeners.call(panel, view);\n //TODO: send from content view: this.model.collection.storage.addExpanded\n // maintain a list of items whose bodies are expanded\n return panel.listenTo(view, {\n expanded: function(v) {\n panel.model.contents.storage.addExpanded(v.model);\n },\n collapsed: function(v) {\n panel.model.contents.storage.removeExpanded(v.model);\n }\n });\n },\n\n /** override to remove expandedIds from webstorage */\n collapseAll: function() {\n this.model.contents.storage.clearExpanded();\n _super.prototype.collapseAll.call(this);\n },\n\n // ------------------------------------------------------------------------ selection\n /** Override to correctly set the historyId of the new collection */\n getSelectedModels: function() {\n var collection = _super.prototype.getSelectedModels.call(this);\n collection.historyId = this.collection.historyId;\n return collection;\n },\n\n // ------------------------------------------------------------------------ panel events\n /** event map */\n events: _.extend(_.clone(_super.prototype.events), {\n \"click .show-selectors-btn\": \"toggleSelectors\",\n \"click > .controls .prev\": \"_clickPrevPage\",\n \"click > .controls .next\": \"_clickNextPage\",\n \"change > .controls .pages\": \"_changePageSelect\",\n // allow (error) messages to be clicked away\n \"click .messages [class$=message]\": \"clearMessages\"\n }),\n\n _clickPrevPage: function(ev) {\n this.model.clearUpdateTimeout();\n this.model.contents.fetchPrevPage();\n },\n\n _clickNextPage: function(ev) {\n this.model.clearUpdateTimeout();\n this.model.contents.fetchNextPage();\n },\n\n _changePageSelect: function(ev) {\n this.model.clearUpdateTimeout();\n var page = $(ev.currentTarget).val();\n this.model.contents.fetchPage(page);\n },\n\n /** Toggle and store the deleted visibility and re-render items\n * @returns {Boolean} new setting\n */\n toggleShowDeleted: function(show, options) {\n show =\n show !== undefined ? show : !this.model.contents.includeDeleted;\n var self = this;\n var contents = self.model.contents;\n contents.setIncludeDeleted(show, options);\n self.trigger(\"show-deleted\", show);\n\n contents.fetchCurrentPage({ renderAll: true });\n return show;\n },\n\n /** Toggle and store whether to render explicity hidden contents\n * @returns {Boolean} new setting\n */\n toggleShowHidden: function(show, store, options) {\n // console.log( 'toggleShowHidden', show, store );\n show =\n show !== undefined ? show : !this.model.contents.includeHidden;\n var self = this;\n var contents = self.model.contents;\n contents.setIncludeHidden(show, options);\n self.trigger(\"show-hidden\", show);\n\n contents.fetchCurrentPage({ renderAll: true });\n return show;\n },\n\n /** On the first search, if there are no details - load them, then search */\n _firstSearch: function(searchFor) {\n var self = this;\n var inputSelector = \"> .controls .search-input\";\n this.log(\"onFirstSearch\", searchFor);\n\n // if the contents already have enough details to search, search and return now\n if (self.model.contents.haveSearchDetails()) {\n self.searchItems(searchFor);\n return;\n }\n\n // otherwise, load the details progressively here\n self.$(inputSelector).searchInput(\"toggle-loading\");\n // set this now so that only results will show during progress\n self.searchFor = searchFor;\n var xhr = self.model.contents\n .progressivelyFetchDetails({ silent: true })\n .progress(function(response, limit, offset) {\n self.renderItems();\n self.trigger(\"search:loading-progress\", limit, offset);\n })\n .always(function() {\n self.$el.find(inputSelector).searchInput(\"toggle-loading\");\n })\n .done(function() {\n self.searchItems(searchFor, \"force\");\n });\n },\n\n /** clear the search filters and show all views that are normally shown */\n clearSearch: function(searchFor) {\n var self = this;\n if (!self.searchFor) return self;\n //self.log( 'onSearchClear', self );\n self.searchFor = \"\";\n self.trigger(\"search:clear\", self);\n self.$(\"> .controls .search-query\").val(\"\");\n // NOTE: silent + render prevents collection update event with merge only\n // - which causes an empty page due to event handler above\n self.model.contents\n .fetchCurrentPage({ silent: true })\n .done(function() {\n self.renderItems();\n });\n return self;\n },\n\n // ........................................................................ error handling\n /** Event handler for errors (from the panel, the history, or the history's contents)\n * Alternately use two strings for model and xhr to use custom message and title (respectively)\n * @param {Model or View} model the (Backbone) source of the error\n * @param {XMLHTTPRequest} xhr any ajax obj. assoc. with the error\n * @param {Object} options the options map commonly used with bbone ajax\n */\n errorHandler: function(model, xhr, options) {\n //TODO: to mixin or base model\n // interrupted ajax or no connection\n if (xhr && xhr.status === 0 && xhr.readyState === 0) {\n // return ERROR_MODAL.offlineErrorModal();\n // fail silently\n return;\n }\n // otherwise, leave something to report in the console\n this.error(model, xhr, 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LIST_VIEW from \"mvc/list/list-view\";\nimport HISTORY_MODEL from \"mvc/history/history-model\";\nimport HISTORY_CONTENTS from \"mvc/history/history-contents\";\nimport HISTORY_PREFS from \"mvc/history/history-preferences\";\nimport HDA_LI from \"mvc/history/hda-li\";\nimport HDCA_LI from \"mvc/history/hdca-li\";\nimport USER from \"mvc/user/user-model\";\nimport ERROR_MODAL from \"mvc/ui/error-modal\";\nimport faIconButton from \"ui/fa-icon-button\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\nimport \"ui/search-input\";\n\n/* =============================================================================\nTODO:\n\n============================================================================= */\n/** @class non-editable, read-only View/Controller for a history model.\n * Allows:\n * changing the loaded history\n * displaying data, info, and download\n * tracking history attrs: size, tags, annotations, name, etc.\n * Does not allow:\n * changing the name\n */\nvar _super = LIST_VIEW.ModelListPanel;\nvar HistoryView = _super.extend(\n /** @lends HistoryView.prototype */ {\n _logNamespace: \"history\",\n\n /** class to use for constructing the HDA views */\n HDAViewClass: HDA_LI.HDAListItemView,\n /** class to use for constructing the HDCA views */\n HDCAViewClass: HDCA_LI.HDCAListItemView,\n /** class to used for constructing collection of sub-view models */\n collectionClass: HISTORY_CONTENTS.HistoryContents,\n /** key of attribute in model to assign to this.collection */\n modelCollectionKey: \"contents\",\n\n tagName: \"div\",\n className: _super.prototype.className + \" history-panel\",\n\n /** string to display when the collection is empty */\n emptyMsg: _l(\"This history is empty\"),\n /** displayed when no items match the search terms */\n noneFoundMsg: _l(\"No matching datasets found\"),\n /** string used for search placeholder */\n searchPlaceholder: _l(\"search datasets\"),\n\n /** @type {Number} ms to wait after history load to fetch/decorate hdcas with element_count */\n FETCH_COLLECTION_COUNTS_DELAY: 2000,\n\n // ......................................................................... SET UP\n /** Set up the view, bind listeners.\n * @param {Object} attributes optional settings for the panel\n */\n initialize: function(attributes) {\n _super.prototype.initialize.call(this, attributes);\n // ---- instance vars\n // control contents/behavior based on where (and in what context) the panel is being used\n /** where should pages from links be displayed? (default to new tab/window) */\n this.linkTarget = attributes.linkTarget || \"_blank\";\n\n /** timeout id for detailed fetch of collection counts, etc... */\n this.detailedFetchTimeoutId = null;\n },\n\n /** create and return a collection for when none is initially passed */\n _createDefaultCollection: function() {\n // override\n return new this.collectionClass([], {\n history: this.model\n });\n },\n\n /** In this override, clear the update timer on the model */\n freeModel: function() {\n _super.prototype.freeModel.call(this);\n if (this.model) {\n this.model.clearUpdateTimeout();\n }\n this._clearDetailedFetchTimeout();\n return this;\n },\n\n /** clear the timeout and the cached timeout id */\n _clearDetailedFetchTimeout: function() {\n if (this.detailedFetchTimeoutId) {\n clearTimeout(this.detailedFetchTimeoutId);\n this.detailedFetchTimeoutId = null;\n }\n },\n\n /** create any event listeners for the panel\n * @fires: rendered:initial on the first render\n * @fires: empty-history when switching to a history with no contents or creating a new history\n */\n _setUpListeners: function() {\n _super.prototype._setUpListeners.call(this);\n this.on({\n error: function(model, xhr, options, msg, details) {\n this.errorHandler(model, xhr, options, msg, details);\n },\n \"loading-done\": function() {\n var self = this;\n // after the initial load, decorate with more time consuming fields (like HDCA element_counts)\n self.detailedFetchTimeoutId = _.delay(function() {\n self.detailedFetchTimeoutId = null;\n self.model.contents.fetchCollectionCounts();\n }, self.FETCH_COLLECTION_COUNTS_DELAY);\n },\n \"views:ready view:attached view:removed\": function(view) {\n this._renderSelectButton();\n },\n \"view:attached\": function(view) {\n this.scrollTo(0);\n }\n });\n // this.on( 'all', function(){ console.debug( arguments ); });\n },\n\n // ------------------------------------------------------------------------ loading history/hda models\n /** load the history with the given id then it's contents, sending ajax options to both */\n loadHistory: function(historyId, options, contentsOptions) {\n contentsOptions = _.extend(contentsOptions || { silent: true });\n this.info(\"loadHistory:\", historyId, options, contentsOptions);\n var self = this;\n self.setModel(new HISTORY_MODEL.History({ id: historyId }));\n\n contentsOptions.silent = true;\n self.trigger(\"loading\");\n return self.model\n .fetchWithContents(options, contentsOptions)\n .always(function() {\n self.render();\n self.trigger(\"loading-done\");\n });\n },\n\n /** convenience alias to the model. Updates the item list only (not the history) */\n refreshContents: function(options) {\n if (this.model) {\n return this.model.refresh(options);\n }\n // may have callbacks - so return an empty promise\n return $.when();\n },\n\n /** Override to reset web storage when the id changes (since it needs the id) */\n _setUpCollectionListeners: function() {\n _super.prototype._setUpCollectionListeners.call(this);\n return this.listenTo(this.collection, {\n // 'all' : function(){ console.log( this.collection + ':', arguments ); },\n \"fetching-more\": function() {\n this._toggleContentsLoadingIndicator(true);\n this.$emptyMessage().hide();\n },\n \"fetching-more-done\": function() {\n this._toggleContentsLoadingIndicator(false);\n }\n });\n },\n\n // ------------------------------------------------------------------------ panel rendering\n /** hide the $el and display a loading indicator (in the $el's parent) when loading new data */\n _showLoadingIndicator: function(msg, speed, callback) {\n var $indicator = $('',\n '\",\n '',\n '<%- history.name %>',\n \"<%- history.nice_size %>',\n\n '',\n\n '\",\n\n // add tags and annotations\n '',\n '',\n\n '',\n '',\n \"\",\n\n '',\n '\",\n '',\n \"',\n '\",\n '\",\n \"\",\n '\",\n \"');\n this.$el.html(\n $indicator\n .text(msg)\n .slideDown(!_.isUndefined(speed) ? speed : this.fxSpeed)\n );\n },\n\n /** hide the loading indicator */\n _hideLoadingIndicator: function(speed) {\n // make speed a bit slower to compensate for slow rendering of up to 500 contents\n this.$(\".loading-indicator\").slideUp(\n !_.isUndefined(speed) ? speed : this.fxSpeed + 200,\n function() {\n $(this).remove();\n }\n );\n },\n\n /** In this override, add a btn to toggle the selectors */\n _buildNewRender: function() {\n var $newRender = _super.prototype._buildNewRender.call(this);\n this._renderSelectButton($newRender);\n return $newRender;\n },\n\n /** button for starting select mode */\n _renderSelectButton: function($where) {\n $where = $where || this.$el;\n // do not render selector option if no actions\n if (!this.multiselectActions().length) {\n return null;\n }\n // do not render (and remove even) if nothing to select\n if (!this.views.length) {\n this.hideSelectors();\n $where.find(\".controls .actions .show-selectors-btn\").remove();\n return null;\n }\n // don't bother rendering if there's one already\n var $existing = $where.find(\n \".controls .actions .show-selectors-btn\"\n );\n if ($existing.length) {\n return $existing;\n }\n\n return faIconButton({\n title: _l(\"Operations on multiple datasets\"),\n classes: \"show-selectors-btn\",\n faIcon: \"fa-check-square-o\"\n }).prependTo($where.find(\".controls .actions\"));\n },\n\n /** override to avoid showing intial empty message using contents_active */\n _renderEmptyMessage: function($whereTo) {\n var self = this;\n var $emptyMsg = self.$emptyMessage($whereTo);\n\n var empty = self.model.get(\"contents_active\").active <= 0;\n if (empty) {\n return $emptyMsg\n .empty()\n .append(self.emptyMsg)\n .show();\n } else if (\n self.searchFor &&\n self.model.contents.haveSearchDetails() &&\n !self.views.length\n ) {\n return $emptyMsg\n .empty()\n .append(self.noneFoundMsg)\n .show();\n }\n $emptyMsg.hide();\n return $();\n },\n\n /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */\n $scrollContainer: function($where) {\n // override or set via attributes.$scrollContainer\n return this.$list($where);\n },\n\n // ------------------------------------------------------------------------ subviews\n _toggleContentsLoadingIndicator: function(show) {\n if (!show) {\n this.$list()\n .find(\".contents-loading-indicator\")\n .remove();\n } else {\n this.$list().html(\n '' +\n ''\n );\n }\n },\n\n /** override to render pagination also */\n renderItems: function($whereTo) {\n // console.log( this + '.renderItems-----------------', new Date() );\n $whereTo = $whereTo || this.$el;\n var self = this;\n var $list = self.$list($whereTo);\n\n // TODO: bootstrap hack to remove orphaned tooltips\n $(\".tooltip\").remove();\n\n $list.empty();\n self.views = [];\n\n var models = self._filterCollection();\n if (models.length) {\n self._renderPagination($whereTo);\n self.views = self._renderSomeItems(models, $list);\n } else {\n // TODO: consolidate with _renderPagination above by (???) passing in models/length?\n $whereTo.find(\"> .controls .list-pagination\").empty();\n }\n self._renderEmptyMessage($whereTo).toggle(!models.length);\n\n self.trigger(\"views:ready\", self.views);\n return self.views;\n },\n\n /** render pagination controls if not searching and contents says we're paginating */\n _renderPagination: function($whereTo) {\n var $paginationControls = $whereTo.find(\n \"> .controls .list-pagination\"\n );\n if (this.searchFor || !this.model.contents.shouldPaginate())\n return $paginationControls.empty();\n\n $paginationControls.html(\n this.templates.pagination(\n {\n // pagination is 1-based for the user\n current: this.model.contents.currentPage + 1,\n last: this.model.contents.getLastPage() + 1\n },\n this\n )\n );\n $paginationControls.find(\"select.pages\").tooltip();\n return $paginationControls;\n },\n\n /** render a subset of the entire collection (client-side pagination) */\n _renderSomeItems: function(models, $list) {\n var self = this;\n var views = [];\n $list.append(\n models.map(function(m) {\n var view = self._createItemView(m);\n views.push(view);\n return self._renderItemView$el(view);\n })\n );\n return views;\n },\n\n // ------------------------------------------------------------------------ sub-views\n /** in this override, check if the contents would also display based on includeDeleted/hidden */\n _filterItem: function(model) {\n var self = this;\n var contents = self.model.contents;\n return (\n (contents.includeHidden || !model.hidden()) &&\n (contents.includeDeleted || !model.isDeletedOrPurged()) &&\n _super.prototype._filterItem.call(self, model)\n );\n },\n\n /** In this override, since history contents are mixed,\n * get the appropo view class based on history_content_type\n */\n _getItemViewClass: function(model) {\n var contentType = model.get(\"history_content_type\");\n switch (contentType) {\n case \"dataset\":\n return this.HDAViewClass;\n case \"dataset_collection\":\n return this.HDCAViewClass;\n }\n throw new TypeError(\"Unknown history_content_type: \" + contentType);\n },\n\n /** in this override, add a linktarget, and expand if id is in web storage */\n _getItemViewOptions: function(model) {\n var options = _super.prototype._getItemViewOptions.call(\n this,\n model\n );\n return _.extend(options, {\n linkTarget: this.linkTarget,\n expanded: this.model.contents.storage.isExpanded(model.id),\n hasUser: this.model.ownedByCurrUser()\n });\n },\n\n /** In this override, add/remove expanded/collapsed model ids to/from web storage */\n _setUpItemViewListeners: function(view) {\n var panel = this;\n _super.prototype._setUpItemViewListeners.call(panel, view);\n //TODO: send from content view: this.model.collection.storage.addExpanded\n // maintain a list of items whose bodies are expanded\n return panel.listenTo(view, {\n expanded: function(v) {\n panel.model.contents.storage.addExpanded(v.model);\n },\n collapsed: function(v) {\n panel.model.contents.storage.removeExpanded(v.model);\n }\n });\n },\n\n /** override to remove expandedIds from webstorage */\n collapseAll: function() {\n this.model.contents.storage.clearExpanded();\n _super.prototype.collapseAll.call(this);\n },\n\n // ------------------------------------------------------------------------ selection\n /** Override to correctly set the historyId of the new collection */\n getSelectedModels: function() {\n var collection = _super.prototype.getSelectedModels.call(this);\n collection.historyId = this.collection.historyId;\n return collection;\n },\n\n // ------------------------------------------------------------------------ panel events\n /** event map */\n events: _.extend(_.clone(_super.prototype.events), {\n \"click .show-selectors-btn\": \"toggleSelectors\",\n \"click > .controls .prev\": \"_clickPrevPage\",\n \"click > .controls .next\": \"_clickNextPage\",\n \"change > .controls .pages\": \"_changePageSelect\",\n // allow (error) messages to be clicked away\n \"click .messages [class$=message]\": \"clearMessages\"\n }),\n\n _clickPrevPage: function(ev) {\n this.model.clearUpdateTimeout();\n this.model.contents.fetchPrevPage();\n },\n\n _clickNextPage: function(ev) {\n this.model.clearUpdateTimeout();\n this.model.contents.fetchNextPage();\n },\n\n _changePageSelect: function(ev) {\n this.model.clearUpdateTimeout();\n var page = $(ev.currentTarget).val();\n this.model.contents.fetchPage(page);\n },\n\n /** Toggle and store the deleted visibility and re-render items\n * @returns {Boolean} new setting\n */\n toggleShowDeleted: function(show, options) {\n show =\n show !== undefined ? show : !this.model.contents.includeDeleted;\n var self = this;\n var contents = self.model.contents;\n contents.setIncludeDeleted(show, options);\n self.trigger(\"show-deleted\", show);\n\n contents.fetchCurrentPage({ renderAll: true });\n return show;\n },\n\n /** Toggle and store whether to render explicity hidden contents\n * @returns {Boolean} new setting\n */\n toggleShowHidden: function(show, store, options) {\n // console.log( 'toggleShowHidden', show, store );\n show =\n show !== undefined ? show : !this.model.contents.includeHidden;\n var self = this;\n var contents = self.model.contents;\n contents.setIncludeHidden(show, options);\n self.trigger(\"show-hidden\", show);\n\n contents.fetchCurrentPage({ renderAll: true });\n return show;\n },\n\n /** On the first search, if there are no details - load them, then search */\n _firstSearch: function(searchFor) {\n var self = this;\n var inputSelector = \"> .controls .search-input\";\n this.log(\"onFirstSearch\", searchFor);\n\n // if the contents already have enough details to search, search and return now\n if (self.model.contents.haveSearchDetails()) {\n self.searchItems(searchFor);\n return;\n }\n\n // otherwise, load the details progressively here\n self.$(inputSelector).searchInput(\"toggle-loading\");\n // set this now so that only results will show during progress\n self.searchFor = searchFor;\n var xhr = self.model.contents\n .progressivelyFetchDetails({ silent: true })\n .progress(function(response, limit, offset) {\n self.renderItems();\n self.trigger(\"search:loading-progress\", limit, offset);\n })\n .always(function() {\n self.$el.find(inputSelector).searchInput(\"toggle-loading\");\n })\n .done(function() {\n self.searchItems(searchFor, \"force\");\n });\n },\n\n /** clear the search filters and show all views that are normally shown */\n clearSearch: function(searchFor) {\n var self = this;\n if (!self.searchFor) return self;\n //self.log( 'onSearchClear', self );\n self.searchFor = \"\";\n self.trigger(\"search:clear\", self);\n self.$(\"> .controls .search-query\").val(\"\");\n // NOTE: silent + render prevents collection update event with merge only\n // - which causes an empty page due to event handler above\n self.model.contents\n .fetchCurrentPage({ silent: true })\n .done(function() {\n self.renderItems();\n });\n return self;\n },\n\n // ........................................................................ error handling\n /** Event handler for errors (from the panel, the history, or the history's contents)\n * Alternately use two strings for model and xhr to use custom message and title (respectively)\n * @param {Model or View} model the (Backbone) source of the error\n * @param {XMLHTTPRequest} xhr any ajax obj. assoc. with the error\n * @param {Object} options the options map commonly used with bbone ajax\n */\n errorHandler: function(model, xhr, options) {\n //TODO: to mixin or base model\n // interrupted ajax or no connection\n if (xhr && xhr.status === 0 && xhr.readyState === 0) {\n // return ERROR_MODAL.offlineErrorModal();\n // fail silently\n return;\n }\n // otherwise, leave something to report in the console\n this.error(model, xhr, options);\n // and feedback to a modal\n // if sent two strings (and possibly details as 'options'), use those as message and title\n if (_.isString(model) && _.isString(xhr)) {\n var message = model;\n var title = xhr;\n return ERROR_MODAL.errorModal(message, title, options);\n }\n // bad gateway\n // TODO: possibly to global handler\n if (xhr && xhr.status === 502) {\n return ERROR_MODAL.badGatewayErrorModal();\n }\n return ERROR_MODAL.ajaxErrorModal(model, xhr, options);\n },\n\n /** Remove all messages from the panel. */\n clearMessages: function(ev) {\n var $target = !_.isUndefined(ev)\n ? $(ev.currentTarget)\n : this.$messages().children('[class$=\"message\"]');\n $target.fadeOut(this.fxSpeed, function() {\n $(this).remove();\n });\n return this;\n },\n\n // ........................................................................ scrolling\n /** Scrolls the panel to show the content sub-view with the given hid.\n * @param {Integer} hid the hid of item to scroll into view\n * @returns {HistoryView} the panel\n */\n scrollToHid: function(hid) {\n return this.scrollToItem(\n _.first(this.viewsWhereModel({ hid: hid }))\n );\n },\n\n // ........................................................................ misc\n /** utility for adding -st, -nd, -rd, -th to numbers */\n ordinalIndicator: function(number) {\n var numStr = number + \"\";\n switch (numStr.charAt(numStr.length - 1)) {\n case \"1\":\n return numStr + \"st\";\n case \"2\":\n return numStr + \"nd\";\n case \"3\":\n return numStr + \"rd\";\n default:\n return numStr + \"th\";\n }\n },\n\n /** Return a string rep of the history */\n toString: function() {\n return (\n \"HistoryView(\" +\n (this.model ? this.model.get(\"name\") : \"\") +\n \")\"\n );\n }\n 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GRAPH from \"utils/graph\";\nimport addLogging from \"utils/add-logging\";\n\n// ============================================================================\nvar _super = GRAPH.Graph;\n/** A Directed acyclic Graph built from a history's job data.\n * Reads in job json, filters and process that json, and builds a graph\n * using the connections between job inputs and outputs.\n */\nvar JobDAG = function(options) {\n options = options || {};\n var self = this;\n //this.logger = console;\n\n self.filters = [];\n\n // instance vars\n //TODO: needed?\n self._jobsData = [];\n self._historyContentsMap = {};\n self._toolMap = {};\n\n self._outputIdToJobMap = {};\n self.noInputJobs = [];\n self.noOutputJobs = [];\n\n //TODO: save these?\n self.filteredSetMetadata = [];\n self.filteredErroredJobs = [];\n\n self.dataKeys = [\"jobs\", \"historyContents\", \"tools\"];\n _super.call(\n self,\n true,\n _.pick(options, self.dataKeys),\n _.omit(options, self.dataKeys)\n );\n};\nJobDAG.prototype = new 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false;\n });\n }\n\n if (self.options.excludeErroredJobs) {\n self.filteredErroredJobs = [];\n filters.push(function filterErrored(jobData) {\n if (jobData.job.state !== \"error\") {\n return true;\n }\n self.filteredErroredJobs.push(jobData.job.id);\n return false;\n });\n }\n\n // all outputs deleted\n // all outputs hidden\n\n if (_.isArray(self.options.filters)) {\n filters = filters.concat(self.options.filters);\n }\n self.debug(\"filters len:\", filters.length);\n return filters;\n};\n\n/** */\nJobDAG.prototype.read = function _read(data) {\n var self = this;\n if (\n _.has(data, \"historyContents\") &&\n _.has(data, \"jobs\") &&\n _.has(data, \"tools\")\n ) {\n // a job dag is composed of these three elements:\n // clone the 3 data sources into the DAG, processing the jobs finally using the history and tools\n self\n .preprocessHistoryContents(data.historyContents || [])\n .preprocessTools(data.tools || {})\n .preprocessJobs(data.jobs || []);\n\n // filter jobs and create the vertices and edges of the job DAG\n self.createGraph(self._filterJobs());\n return self;\n }\n return _super.prototype.read.call(this, data);\n};\n\n/** */\nJobDAG.prototype.preprocessHistoryContents = function _preprocessHistoryContents(\n historyContents\n) {\n this.info(\"processing history\");\n var self = this;\n self._historyContentsMap = {};\n\n historyContents.forEach(function(content, i) {\n self._historyContentsMap[content.id] = _.clone(content);\n });\n return self;\n};\n\n/** */\nJobDAG.prototype.preprocessTools = function _preprocessTools(tools) {\n this.info(\"processing tools\");\n var self = this;\n self._toolMap = {};\n\n _.each(tools, function(tool, id) {\n self._toolMap[id] = _.clone(tool);\n });\n return self;\n};\n\n/** sort the cloned jobs, decorate with tool and history contents info, and store in prop array */\nJobDAG.prototype.preprocessJobs = function _preprocessJobs(jobs) {\n this.info(\"processing jobs\");\n var self = this;\n self._outputIdToJobMap = {};\n\n self._jobsData = self.sort(jobs).map(function(job) {\n return self.preprocessJob(_.clone(job));\n });\n //console.debug( JSON.stringify( self._jobsData, null, ' ' ) );\n //console.debug( JSON.stringify( self._outputIdToJobMap, null, ' ' ) );\n return self;\n};\n\n/** sort the jobs based on update time */\nJobDAG.prototype.sort = function _sort(jobs) {\n function cmpCreate(a, b) {\n if (a.create_time > b.create_time) {\n return 1;\n }\n if (a.create_time < b.create_time) {\n return -1;\n }\n return 0;\n }\n return jobs.sort(cmpCreate);\n};\n\n/** decorate with input/output datasets and tool */\nJobDAG.prototype.preprocessJob = function _preprocessJob(job, index) {\n //this.info( 'preprocessJob', job, index );\n var self = this,\n jobData = { job: job };\n\n jobData.inputs = self._processInputs(job);\n if (_.size(jobData.inputs) === 0) {\n self.noInputJobs.push(job.id);\n }\n jobData.outputs = self._processOutputs(job);\n if (_.size(jobData.outputs) === 0) {\n 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{};\n\n self._jobsData = self.sort(jobs).map(function(job) {\n return self.preprocessJob(_.clone(job));\n });\n //console.debug( JSON.stringify( self._jobsData, null, ' ' ) );\n //console.debug( JSON.stringify( self._outputIdToJobMap, null, ' ' ) );\n return self;\n};\n\n/** sort the jobs based on update time */\nJobDAG.prototype.sort = function _sort(jobs) {\n function cmpCreate(a, b) {\n if (a.create_time > b.create_time) {\n return 1;\n }\n if (a.create_time < b.create_time) {\n return -1;\n }\n return 0;\n }\n return jobs.sort(cmpCreate);\n};\n\n/** decorate with input/output datasets and tool */\nJobDAG.prototype.preprocessJob = function _preprocessJob(job, index) {\n //this.info( 'preprocessJob', job, index );\n var self = this,\n jobData = { job: job };\n\n jobData.inputs = self._processInputs(job);\n if (_.size(jobData.inputs) === 0) {\n self.noInputJobs.push(job.id);\n }\n jobData.outputs = self._processOutputs(job);\n if (_.size(jobData.outputs) === 0) {\n self.noOutputJobs.push(job.id);\n }\n\n jobData.tool = self._toolMap[job.tool_id];\n\n //self.info( '\\t jobData:', jobData );\n return jobData;\n};\n\n/**\n */\nJobDAG.prototype._processInputs = function __processInputs(job) {\n var self = this,\n inputs = job.inputs,\n inputMap = {};\n _.each(inputs, function(input, nameInJob) {\n input = _.clone(self._validateInputOutput(input));\n input.name = nameInJob;\n // since this is a DAG and we're processing in order of create time,\n // the inputs for this job will already be listed in _outputIdToJobMap\n // TODO: we can possibly exploit this\n //console.debug( 'input in _outputIdToJobMap', self._outputIdToJobMap[ input.id ] );\n input.content = self._historyContentsMap[input.id];\n inputMap[input.id] = input;\n });\n return inputMap;\n};\n\n/**\n */\nJobDAG.prototype._validateInputOutput = function __validateInputOutput(\n inputOutput\n) {\n if (!inputOutput.id) {\n throw new Error(\n \"No id on job input/output: \",\n 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access to the additional data above inside the filters\n var self = this;\n for (var i = 0; i < self.filters.length; i++) {\n if (!self.filters[i].call(self, jobData)) {\n self.debug(\n \"\\t job\",\n jobData.job.id,\n \" has been filtered out by function:\\n\",\n self.filters[i]\n );\n return false;\n }\n }\n return true;\n};\n\n/** Walk all the jobs (vertices), attempting to find connections\n * between datasets used as both inputs and outputs (edges)\n */\nJobDAG.prototype.createGraph = function _createGraph(jobsData) {\n var self = this;\n self.debug(\"connections:\");\n //console.debug( jobsData );\n\n _.each(jobsData, function(jobData) {\n var id = jobData.job.id;\n self.debug(\"\\t\", id, jobData);\n self.createVertex(id, jobData);\n });\n _.each(jobsData, function(jobData) {\n var targetId = jobData.job.id;\n _.each(jobData.inputs, function(input, inputId) {\n //console.debug( '\\t\\t target input:', inputId, input );\n var sourceId = self._outputIdToJobMap[inputId];\n 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_l from \"utils/localization\";\nimport HISTORY_MODEL from \"mvc/history/history-model\";\nimport HISTORY_VIEW_EDIT from \"mvc/history/history-view-edit\";\nimport historyCopyDialog from \"mvc/history/copy-dialog\";\nimport ERROR_MODAL from \"mvc/ui/error-modal\";\nimport baseMVC from \"mvc/base-mvc\";\nimport ajaxQueue from \"utils/ajax-queue\";\nimport \"ui/mode-button\";\nimport \"ui/search-input\";\n\nvar logNamespace = \"history\";\n/* ==============================================================================\nTODO:\n\n============================================================================== */\n/** @class A container for a history panel that renders controls for that history (delete, copy, etc.) */\nvar HistoryViewColumn = Backbone.View.extend(baseMVC.LoggableMixin).extend({\n _logNamespace: logNamespace,\n\n tagName: \"div\",\n className: \"history-column flex-column flex-row-container\",\n id: function id() {\n if (!this.model) {\n return \"\";\n }\n return \"history-column-\" + this.model.get(\"id\");\n },\n\n // ------------------------------------------------------------------------ set up\n /** set up passed-in panel (if any) and listeners */\n initialize: function initialize(options) {\n options = options || {};\n this.purgeAllowed = !_.isUndefined(options.purgeAllowed)\n ? options.purgeAllowed\n : false;\n this.panel = options.panel || this.createPanel(options);\n\n this.setUpListeners();\n },\n\n /** create a history panel for this column */\n createPanel: function createPanel(panelOptions) {\n return new HISTORY_VIEW_EDIT.HistoryViewEdit(\n _.defaults(panelOptions, {\n model: this.model,\n // non-current panels should set their hdas to draggable\n purgeAllowed: this.purgeAllowed,\n dragItems: true,\n $scrollContainer: function() {\n return this.$el;\n }\n })\n );\n },\n\n /** set up reflexive listeners */\n setUpListeners: function setUpListeners() {\n var column = this;\n //this.log( 'setUpListeners', this );\n this.once(\"rendered\", function() {\n column.trigger(\"rendered:initial\", column);\n });\n this.setUpPanelListeners();\n },\n\n /** set listeners needed for panel */\n setUpPanelListeners: function setUpPanelListeners() {\n var column = this;\n this.listenTo(\n this.panel,\n {\n //'all': function(){ console.info( 'panel of ' + this, arguments ); },\n\n // assumes panel will take the longest to render\n rendered: function() {\n column.trigger(\"rendered\", column);\n },\n // when a panel's view expands turn off the click handler on the rerun button so that it uses it's href\n // this allows the button to open the tool rerun form in a new tab (instead of erroring)\n // TODO: hack\n \"view:expanded view:rendered\": function(view) {\n view.$(\".rerun-btn\").off();\n }\n },\n this\n );\n },\n\n /** do the dimensions of this column overlap the given (horizontal) browser coords? */\n inView: function(viewLeft, viewRight) {\n var columnLeft = this.$el.offset().left,\n columnRight = columnLeft + this.$el.width();\n if (columnRight < viewLeft) {\n return false;\n }\n if (columnLeft > viewRight) {\n return false;\n }\n return true;\n },\n\n /** shortcut to the panel */\n $panel: function $panel() {\n return this.$(\".history-panel\");\n },\n\n // ------------------------------------------------------------------------ render\n /** render ths column, its panel, and set up plugins */\n render: function render(speed) {\n speed = speed !== undefined ? speed : \"fast\";\n //this.log( this + '.render', this.$el, this.el );\n //TODO: not needed\n var modelData = this.model ? this.model.toJSON() : {};\n this.$el.html(this.template(modelData));\n this.renderPanel(speed);\n // jq 1.12 doesn't fade/show properly when display: flex, re-set here\n this.panel.$el.css(\"display\", \"flex\");\n // if model and not children\n // template\n // render controls\n this.setUpBehaviors();\n // add panel\n return this;\n },\n\n /** set up plugins */\n setUpBehaviors: function setUpBehaviors() {\n //this.log( 'setUpBehaviors:', this );\n //var column = this;\n // on panel size change, ...\n },\n\n /** column body template with inner div for panel based on data (model json) */\n template: function template(data) {\n data = _.extend(data || {}, {\n isCurrentHistory: this.currentHistory\n });\n return $(\n [\n '',\n '\",\n '',\n '<%- history.name %>',\n \"<%- history.nice_size %>',\n\n '',\n\n '\",\n\n // add tags and annotations\n '',\n '',\n\n '',\n '',\n \"\",\n\n '',\n '\",\n '',\n \"',\n '\",\n '\",\n \"\",\n '\",\n \"',\n this.controlsLeftTemplate({\n history: data,\n view: this\n }),\n //'',\n this.controlsRightTemplate({\n history: data,\n view: this\n }),\n \"\",\n '',\n '',\n \"\"\n ].join(\"\")\n );\n },\n\n /** render the panel contained in the column using speed for fx speed */\n renderPanel: function renderPanel(speed) {\n speed = speed !== undefined ? speed : \"fast\";\n this.panel.setElement(this.$panel()).render(speed);\n if (this.currentHistory) {\n this.panel.$list().before(this.panel._renderDropTargetHelp());\n }\n return this;\n },\n\n // ------------------------------------------------------------------------ behaviors and events\n /** event map */\n events: {\n // will make this the current history\n \"click .switch-to.btn\": function() {\n this.model.setAsCurrent();\n },\n //TODO: remove boiler plate from next 3\n \"click .delete-history\": function() {\n var column = this;\n this.model._delete().done(function(data) {\n column.render();\n });\n },\n \"click .undelete-history\": function() {\n var column = this;\n this.model.undelete().done(function(data) {\n column.render();\n });\n },\n \"click .purge-history\": function() {\n if (\n confirm(\n _l(\"This will permanently remove the data. Are you sure?\")\n )\n ) {\n var column = this;\n this.model.purge().done(function(data) {\n column.render();\n });\n }\n },\n // will copy this history and make the copy the current history\n \"click .copy-history\": \"copy\"\n },\n\n // ------------------------------------------------------------------------ non-current controls\n /** Open a modal to get a new history name, copy it (if not canceled), and makes the copy current */\n copy: function copy() {\n historyCopyDialog(this.model);\n },\n\n // ------------------------------------------------------------------------ templates\n /** controls template displaying controls above the panel based on this.currentHistory */\n controlsLeftTemplate: _.template(\n [\n '',\n \"<% if( data.history.isCurrentHistory ){ %>\",\n '',\n _l(\"Current History\"),\n \"\",\n \"<% } else { %>\",\n '\",\n \"<% } %>\",\n \"\"\n ].join(\"\"),\n { variable: \"data\" }\n ),\n\n /** controls template displaying controls above the panel based on this.currentHistory */\n controlsRightTemplate: _.template(\n [\n '',\n \"<% if( !data.history.purged ){ %>\",\n '\",\n \"<% } %>\",\n \"\"\n ].join(\"\"),\n { variable: \"data\" }\n ),\n\n // ------------------------------------------------------------------------ misc\n /** String rep */\n toString: function() {\n return \"HistoryViewColumn(\" + (this.panel ? this.panel : \"\") + \")\";\n }\n});\n\n//==============================================================================\n/** @class A view of a HistoryCollection and displays histories similarly to the current history panel.\n */\nvar MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({\n _logNamespace: logNamespace,\n\n className: \"multi-panel-history\",\n\n // ------------------------------------------------------------------------ set up\n /** Set up internals, history collection, and columns to display the history */\n initialize: function initialize(options) {\n options = options || {};\n this.log(this + \".init\", options);\n\n // add the className here (since we gen. pass the el in options)\n this.$el.addClass(this.className);\n\n // --- instance vars\n //TODO: move these to some defaults\n this.options = {\n columnWidth: 312,\n borderWidth: 1,\n columnGap: 8,\n headerHeight: 29,\n footerHeight: 0,\n controlsHeight: 20\n };\n\n /** how many histories to get when fetching a new batch/page */\n this.perPage = options.perPage || 10;\n\n /** named ajax queue for loading hdas */\n this.hdaQueue = new ajaxQueue.NamedAjaxQueue([], false);\n\n // --- set up models, sub-views, and listeners\n /** the original unfiltered and unordered collection of histories */\n this.collection = null;\n /** model id to column map */\n this.columnMap = {};\n /** model id to column map */\n this.columnOptions = options.columnOptions || {};\n\n /** what to search for within all histories */\n this.historySearch = null;\n /** what to search for within all datasets */\n this.datasetSearch = null;\n\n this.setCollection(options.histories);\n this.setUpListeners();\n },\n\n /** Set up reflexive listeners */\n setUpListeners: function setUpListeners() {\n var multipanel = this;\n //multipanel.log( 'setUpListeners', multipanel );\n this.on(\"end-of-scroll\", function() {\n multipanel.collection.fetchMore();\n });\n },\n\n // ------------------------------------------------------------------------ collection\n /** Set up a (new) history collection, sorting and adding listeners\n * @fires 'new-collection' when set with this view as the arg\n */\n setCollection: function setCollection(collection) {\n // console.log( 'setCollection:', collection );\n this.stopListening(this.collection);\n\n this.collection = collection || new HISTORY_MODEL.HistoryCollection();\n this.setUpCollectionListeners();\n\n this.createColumns();\n this.hdaQueue.clear();\n\n this.trigger(\"new-collection\", this);\n return this;\n },\n\n /** Set up a (new) history collection, sorting and adding listeners\n * @fires 'new-collection' when set with this view as the arg\n */\n addModels: function addModels(models, collection, options) {\n // console.log( 'addModels:', models, collection, options );\n options = options || {};\n var multipanel = this;\n models = _.isArray(models) ? models : [models];\n models.forEach(function(model) {\n multipanel.addColumn(model, false);\n // if this is from a fetch, sort will be called and it will call render\n });\n return this;\n },\n\n /** Set up listeners for the collection - handling: added histories, change of current, deletion, and sorting */\n setUpCollectionListeners: function() {\n var multipanel = this;\n multipanel.listenTo(multipanel.collection, {\n // handle ajax errors from the collection\n error: multipanel.errorHandler,\n // add multiple models\n add: multipanel.addModels,\n // when all the histories a user has have been fetched\n \"all-fetched\": multipanel._postFetchAll,\n // handle addition of histories, triggered by column copy and create new\n \"new-current\": multipanel.addAsCurrentColumn,\n // handle setting a history as current, triggered by history.setAsCurrent\n \"set-as-current\": multipanel.setCurrentHistory,\n // handle deleting a history (depends on whether panels is including deleted or not)\n \"change:deleted change:purged\": multipanel.handleDeletedHistory,\n // re-render columns after a sort\n sort: function() {\n multipanel.renderColumns(0);\n }\n });\n },\n\n _postFetchAll: function(fetchData) {\n // console.log( '_postFetchAll' );\n this.$(\".histories-loading-indicator\").remove();\n // when new histories is fetched and the indicator is not required,\n // the panel will jump slightly left - totally aesthetic but jarring\n // TODO: this probably would be best handled elsewhere during a refinement cycle (if any)\n if (!this.historySearch) {\n var $scrollContainer = this.$(\".outer-middle\");\n $scrollContainer.scrollLeft($scrollContainer.scrollLeft() + 24);\n }\n },\n\n /** Re-render and set currentHistoryId to reflect a new current history */\n setCurrentHistory: function setCurrentHistory(history) {\n this.log(\"setCurrentHistory:\", history);\n var oldCurrentColumn = _.findWhere(this.columnMap, {\n currentHistory: true\n });\n if (oldCurrentColumn) {\n oldCurrentColumn.currentHistory = false;\n oldCurrentColumn.$el.height(\"\");\n }\n\n var newCurrentColumn = this.columnMap[this.collection.currentHistoryId];\n newCurrentColumn.currentHistory = true;\n this.collection.sort();\n this._recalcFirstColumnHeight();\n return newCurrentColumn;\n },\n\n /** Either remove a deleted history or re-render it to show the deleted message\n * based on collection.includeDeleted\n */\n handleDeletedHistory: function handleDeletedHistory(history) {\n if (history.get(\"deleted\") || history.get(\"purged\")) {\n this.log(\n \"handleDeletedHistory\",\n this.collection.includeDeleted,\n history\n );\n var multipanel = this,\n column = multipanel.columnMap[history.id];\n if (!column) {\n return;\n }\n\n // if it's the current column, create a new, empty history as the new current\n if (column.model.id === this.collection.currentHistoryId) {\n //TODO: figuring out the order of async here is tricky\n // - for now let the user handle the two step process\n //multipanel.collection.create().done( function(){\n // if( !multipanel.collection.includeDeleted ){ multipanel.removeColumn( column, false ); }\n //});\n } else if (!multipanel.collection.includeDeleted) {\n multipanel.removeColumn(column);\n }\n }\n },\n\n // ........................................................................ error handling\n /** Event handler for errors (from the history collection mainly)\n * Alternately use two strings for model and xhr to use custom message and title (respectively)\n * (e.g. this.trigger( 'error', 'Heres a message', 'Heres a title' ))\n * @param {Model or View} model the (Backbone) source of the error\n * @param {XMLHTTPRequest} xhr any ajax obj. assoc. with the error\n * @param {Object} options the options map commonly used with bbone ajax\n */\n errorHandler: function(model, xhr, options) {\n // interrupted ajax or no connection\n if (xhr && xhr.status === 0 && xhr.readyState === 0) {\n // return ERROR_MODAL.offlineErrorModal();\n // fail silently\n return;\n }\n // otherwise, leave something to report in the console\n this.error(model, xhr, options);\n // and feedback to a modal\n // if sent two strings (and possibly details as 'options'), use those as message and title\n if (_.isString(model) && _.isString(xhr)) {\n var message = model;\n var title = xhr;\n return ERROR_MODAL.errorModal(message, title, options);\n }\n // bad gateway\n // TODO: possibly to global handler\n if (xhr && xhr.status === 502) {\n return ERROR_MODAL.badGatewayErrorModal();\n }\n return ERROR_MODAL.ajaxErrorModal(model, xhr, options);\n },\n\n /** If Galaxy object is available handle error there, otherwise, locally (and crudely) */\n _ajaxErrorHandler: function() {\n ERROR_MODAL.ajaxErrorModal.apply(null, _.toArray(arguments));\n },\n\n /** create a new history and set it to current */\n create: function(ev) {\n return this.collection.create({ current: true });\n },\n\n // ------------------------------------------------------------------------ columns\n /** create columns from collection */\n createColumns: function createColumns(models, columnOptions) {\n columnOptions = columnOptions || this.options.columnOptions;\n var multipanel = this;\n // clear column map\n // TODO: make cummulative\n multipanel.columnMap = {};\n multipanel.collection.each(function(model, i) {\n var column = multipanel.createColumn(model, columnOptions);\n multipanel.columnMap[model.id] = column;\n });\n },\n\n /** create a column and its panel and set up any listeners to them */\n createColumn: function createColumn(history, options) {\n // options passed can be re-used, so extend them before adding the model to prevent pollution for the next\n options = _.extend({}, options, {\n model: history,\n purgeAllowed: Galaxy.config.allow_user_dataset_purge\n });\n var column = new HistoryViewColumn(options);\n if (history.id === this.collection.currentHistoryId) {\n column.currentHistory = true;\n }\n this.setUpColumnListeners(column);\n if (this.datasetSearch) {\n column.panel.searchItems(this.datasetSearch);\n this.queueHdaFetchDetails(column);\n }\n return column;\n },\n\n /** add a new column for history and render all columns if render is true */\n addColumn: function add(history, render) {\n // console.debug( 'adding column for:', history, render );\n render = render !== undefined ? render : true;\n var newColumn = this.createColumn(history);\n this.columnMap[history.id] = newColumn;\n if (render) {\n this.renderColumns();\n }\n return newColumn;\n },\n\n /** add a new column for history and make it the current history/column */\n addAsCurrentColumn: function add(history, collection, options) {\n //this.log( 'adding current column for:', history );\n var multipanel = this,\n newColumn = this.addColumn(history, false);\n this.setCurrentHistory(history);\n newColumn.once(\"rendered\", function() {\n multipanel.queueHdaFetch(newColumn);\n });\n return newColumn;\n },\n\n /** remove the given column, it's listeners, and optionally render */\n removeColumn: function remove(column, render) {\n render = render !== undefined ? render : true;\n this.log(\"removeColumn\", column);\n if (!column) {\n return;\n }\n var multipanel = this,\n widthToRemove = this.options.columnWidth + this.options.columnGap;\n column.$el.fadeOut(\"fast\", function() {\n if (render) {\n $(this).remove();\n multipanel\n .$(\".middle\")\n .width(multipanel.$(\".middle\").width() - widthToRemove);\n multipanel.checkColumnsInView();\n multipanel._recalcFirstColumnHeight();\n }\n\n //TODO: to freeColumn (where Columns have freePanel)\n multipanel.stopListening(column.panel);\n multipanel.stopListening(column);\n delete multipanel.columnMap[column.model.id];\n column.remove();\n });\n },\n\n /** set up listeners for a column and it's panel - handling: hda lazy-loading, drag and drop */\n setUpColumnListeners: function setUpColumnListeners(column) {\n var multipanel = this;\n multipanel.listenTo(column, {\n //'all': function(){ console.info( 'column ' + column + ':', arguments ) },\n \"in-view\": multipanel.queueHdaFetch\n });\n\n multipanel.listenTo(column.panel, {\n //'all': function(){ console.info( 'panel ' + column.panel + ':', arguments ) },\n\n \"view:draggable:dragstart\": function(ev, view, panel, column) {\n multipanel._dropData = JSON.parse(\n ev.dataTransfer.getData(\"text\")\n );\n multipanel.currentColumnDropTargetOn();\n },\n \"view:draggable:dragend\": function(ev, view, panel, column) {\n multipanel._dropData = null;\n multipanel.currentColumnDropTargetOff();\n },\n \"droptarget:drop\": function(ev, data, panel) {\n //note: bad copy sources fail silently\n var toCopy = multipanel._dropData.filter(function(json) {\n return panel.model.contents.isCopyable(json);\n });\n multipanel._dropData = null;\n\n var queue = new ajaxQueue.NamedAjaxQueue();\n if (panel.model.contents.currentPage !== 0) {\n queue.add({\n name: \"fetch-front-page\",\n fn: function() {\n return panel.model.contents.fetchPage(0);\n }\n });\n }\n // need to reverse to better match expected order\n // TODO: reconsider order in list-view._setUpItemViewListeners, dragstart (instead of here)\n toCopy.reverse().forEach(function(content) {\n queue.add({\n name: \"copy-\" + content.id,\n fn: function() {\n return panel.model.contents.copy(content);\n }\n });\n });\n queue.start();\n queue.done(function(responses) {\n panel.model.fetch();\n });\n }\n });\n },\n\n /** conv. fn to count the columns in columnMap */\n columnMapLength: function() {\n return Object.keys(this.columnMap).length;\n },\n\n /** return array of Columns filtered by filters and sorted to match the collection\n * @param: filters Function[] array of filter fns\n */\n sortedFilteredColumns: function(filters) {\n filters = filters || this.filters;\n if (!filters || !filters.length) {\n return this.sortedColumns();\n }\n var multipanel = this;\n return multipanel.sortedColumns().filter(function(column, index) {\n var filtered =\n column.currentHistory ||\n _.every(\n filters.map(function(filter) {\n return filter.call(column);\n })\n );\n return filtered;\n });\n },\n\n /** return array of Columns sorted to match the collection */\n sortedColumns: function() {\n var multipanel = this;\n var sorted = this.collection.map(function(history, index) {\n return multipanel.columnMap[history.id];\n });\n return sorted;\n },\n\n // ------------------------------------------------------------------------ render\n /** Render this view, columns, and set up view plugins */\n render: function render(speed) {\n speed = speed !== undefined ? speed : this.fxSpeed;\n var multipanel = this;\n\n multipanel.log(multipanel + \".render\");\n multipanel.$el.html(multipanel.mainTemplate(multipanel));\n multipanel.renderColumns(speed);\n\n // set the columns to full height allowed and set up behaviors for thie multipanel\n multipanel.setUpBehaviors();\n //TODO: wrong - has to wait for columns to render\n // - create a column listener that fires this when all columns are rendered\n multipanel.trigger(\"rendered\", multipanel);\n return multipanel;\n },\n\n /** Render the columns and panels */\n renderColumns: function renderColumns(speed) {\n speed = _.isNumber(speed) ? speed : this.fxSpeed;\n // console.log( 'renderColumns:', speed );\n // render columns and track the total number rendered, firing an event when all are rendered\n var self = this;\n var sortedAndFiltered = self.sortedFilteredColumns();\n // console.log( '\\t sortedAndFiltered:', sortedAndFiltered );\n var $middle = self.$(\".middle\").empty();\n\n self._addColumns(sortedAndFiltered, speed);\n if (!self.collection.allFetched) {\n $middle.append(self.loadingIndicatorTemplate(self));\n }\n //TODO: sorta - at least their fx queue has started the re-rendering\n self.trigger(\"columns-rendered\", sortedAndFiltered, self);\n\n if (self.datasetSearch && sortedAndFiltered.length <= 1) {\n } else {\n // check for in-view, hda lazy-loading if so\n self.checkColumnsInView();\n // the first, current column has position: fixed and flex css will not apply - adjust height manually\n self._recalcFirstColumnHeight();\n }\n return sortedAndFiltered;\n },\n\n _addColumns: function(columns, speed) {\n speed = _.isNumber(speed) ? speed : this.fxSpeed;\n var $middle = this.$(\".middle\");\n\n var numExisting = $middle.children(\".history-column\").length;\n $middle.width(this._calcMiddleWidth(columns.length + numExisting));\n\n columns.forEach(function(column, i) {\n column\n .delegateEvents()\n .render(speed)\n .$el.appendTo($middle);\n });\n },\n\n _calcMiddleWidth: function(numColumns) {\n var preventStackWidthAdj = 16;\n return (\n numColumns * (this.options.columnWidth + this.options.columnGap) +\n // last column gap\n this.options.columnGap +\n // the amount that safely prevents stacking of columns when adding a new one\n preventStackWidthAdj\n );\n },\n\n //TODO: combine the following two more sensibly\n //TODO: could have HistoryContents.haveDetails return false\n // if column.model.contents.length === 0 && !column.model.get( 'empty' ) then just check that\n /** Get the *summary* contents of a column's history (and details on any expanded contents),\n * queueing the ajax call and using a named queue to prevent the call being sent twice\n */\n queueHdaFetch: function queueHdaFetch(column) {\n // console.log( column.model + '.contentsShown:', column.model.contentsShown() );\n var contents = column.model.contents;\n // console.log( 'queueHdaFetch:', column, column.model.get( 'contents_active' ) );\n // if the history model says it has hdas but none are present, queue an ajax req for them\n if (contents.length === 0 && column.model.contentsShown()) {\n var fetchOptions = { silent: true };\n var ids = _.values(contents.storage.allExpanded()).join();\n if (ids) {\n fetchOptions.details = ids;\n }\n // this uses a 'named' queue so that duplicate requests are ignored\n this.hdaQueue.add({\n name: column.model.id,\n fn: function() {\n return contents\n .fetchCurrentPage(fetchOptions)\n .done(function() {\n column.panel.renderItems();\n });\n }\n });\n // the queue is re-used, so if it's not processing requests - start it again\n if (!this.hdaQueue.running) {\n this.hdaQueue.start();\n }\n }\n },\n\n /** Get the *detailed* json for *all* of a column's history's contents - req'd for searching */\n queueHdaFetchDetails: function(column) {\n var contents = column.model.contents;\n var needsContentsLoaded =\n contents.length === 0 && column.model.contentsShown();\n if (needsContentsLoaded || !contents.haveDetails()) {\n // this uses a 'named' queue so that duplicate requests are ignored\n this.hdaQueue.add({\n name: column.model.id,\n fn: function() {\n return contents\n .progressivelyFetchDetails()\n .done(function() {\n column.panel._renderEmptyMessage();\n });\n }\n });\n // the queue is re-used, so if it's not processing requests - start it again\n if (!this.hdaQueue.running) {\n this.hdaQueue.start();\n }\n }\n },\n\n /** put a text msg in the header */\n renderInfo: function(msg) {\n return this.$(\".header .header-info\").text(msg);\n },\n\n // ------------------------------------------------------------------------ events/behaviors\n events: {\n // will move to the server root (gen. Analyze data)\n \"click .done.btn\": \"close\",\n // creates a new empty history and makes it current\n \"click .create-new.btn\": \"create\",\n \"click #include-deleted\": \"_clickToggleDeletedHistories\",\n // these change the collection and column sort order\n \"click .order .set-order\": \"_chooseOrder\",\n \"click #toggle-deleted\": \"_clickToggleDeletedDatasets\",\n \"click #toggle-hidden\": \"_clickToggleHiddenDatasets\"\n //'dragstart .list-item .title-bar' : function( e ){ console.debug( 'ok' ); }\n },\n\n close: function(ev) {\n //TODO: switch to pushState/router\n window.location = Galaxy.root;\n },\n\n _clickToggleDeletedHistories: function(ev) {\n this.toggleDeletedHistories($(ev.currentTarget).is(\":checked\"));\n this.toggleOptionsPopover();\n },\n /** Include deleted histories in the collection */\n toggleDeletedHistories: function(show) {\n if (show) {\n window.location =\n Galaxy.root +\n \"history/view_multiple?include_deleted_histories=True\";\n } else {\n window.location = Galaxy.root + \"history/view_multiple\";\n }\n },\n\n _clickToggleDeletedDatasets: function(ev) {\n this.toggleDeletedDatasets($(ev.currentTarget).is(\":checked\"));\n this.toggleOptionsPopover();\n },\n toggleDeletedDatasets: function(show) {\n show = show !== undefined ? show : false;\n var multipanel = this;\n multipanel.sortedFilteredColumns().forEach(function(column, i) {\n _.delay(function() {\n column.panel.toggleShowDeleted(show, false);\n }, i * 200);\n });\n },\n\n _clickToggleHiddenDatasets: function(ev) {\n this.toggleHiddenDatasets($(ev.currentTarget).is(\":checked\"));\n this.toggleOptionsPopover();\n },\n toggleHiddenDatasets: function(show) {\n show = show !== undefined ? show : false;\n var multipanel = this;\n multipanel.sortedFilteredColumns().forEach(function(column, i) {\n _.delay(function() {\n column.panel.toggleShowHidden(show, false);\n }, i * 200);\n });\n },\n\n /** change the collection order and re-fetch when the drop down in the options menu is changed */\n _chooseOrder: function(ev) {\n var multipanel = this,\n collection = multipanel.collection,\n orderKey = $(ev.currentTarget).data(\"order\");\n // set the sort order text also\n multipanel\n .$(\".current-order\")\n .text(multipanel.orderDescriptions[orderKey]);\n multipanel.toggleOptionsPopover();\n // set the order and re-fetch using the new order, saving the current history as the first\n collection.setOrder(orderKey);\n var currentHistoryModel = collection.slice(0, 1);\n collection.fetchFirst().done(function() {\n collection.unshift(currentHistoryModel, {\n silent: true\n });\n multipanel.createColumns();\n // need to clear this or previously fetched contents won't refetch now (bc of named queue)\n multipanel.hdaQueue.clear();\n multipanel.render();\n });\n multipanel.once(\"columns-rendered\", multipanel._scrollLeft);\n //TODO: check allFetched and do not reset if so - just sort instead\n },\n\n /** scroll the column container right or left */\n _scrollLeft: function(val) {\n val = _.isNumber(val) ? val : 0;\n this.$(\".outer-middle\").scrollLeft(val);\n },\n\n /** Set up any view plugins */\n setUpBehaviors: function() {\n var multipanel = this;\n multipanel._moreOptionsPopover();\n\n // input to search histories\n multipanel.$(\"#search-histories\").searchInput({\n name: \"search-histories\",\n placeholder: _l(\"search histories\"),\n\n onfirstsearch: function(searchFor) {\n multipanel.$(\"#search-histories\").searchInput(\"toggle-loading\");\n multipanel.renderInfo(_l(\"loading all histories for search\"));\n multipanel.collection.fetchAll().done(function() {\n multipanel\n .$(\"#search-histories\")\n .searchInput(\"toggle-loading\");\n multipanel.renderInfo(\"\");\n });\n },\n onsearch: function(searchFor) {\n multipanel.historySearch = searchFor;\n multipanel.filters = [\n function() {\n return this.model.matchesAll(multipanel.historySearch);\n }\n ];\n multipanel.renderColumns(0);\n },\n onclear: function(searchFor) {\n multipanel.historySearch = null;\n //TODO: remove specifically not just reset\n multipanel.filters = [];\n multipanel.renderColumns(0);\n }\n });\n\n // input to search datasets\n multipanel.$(\"#search-datasets\").searchInput({\n name: \"search-datasets\",\n placeholder: _l(\"search all datasets\"),\n\n onfirstsearch: function(searchFor) {\n multipanel.hdaQueue.clear();\n multipanel.$(\"#search-datasets\").searchInput(\"toggle-loading\");\n multipanel.datasetSearch = searchFor;\n multipanel.sortedFilteredColumns().forEach(function(column) {\n column.panel.searchItems(searchFor);\n // load details for them that need\n multipanel.queueHdaFetchDetails(column);\n });\n multipanel.hdaQueue.progress(function(progress) {\n multipanel.renderInfo(\n [\n _l(\"searching\"),\n progress.curr + 1,\n _l(\"of\"),\n progress.total\n ].join(\" \")\n );\n });\n multipanel.hdaQueue.deferred.done(function() {\n multipanel.renderInfo(\"\");\n multipanel\n .$(\"#search-datasets\")\n 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slight override of dropTargetOff to not erase drop-target-help\n currentColumn.panel.dropTarget = false;\n currentColumn.panel.$(\".history-drop-target\").remove();\n },\n\n // ------------------------------------------------------------------------ misc\n /** String rep */\n toString: function() {\n return (\n \"MultiPanelColumns(\" +\n (this.columns ? this.columns.length : 0) +\n \")\"\n );\n },\n\n // ------------------------------------------------------------------------ templates\n mainTemplate: _.template(\n [\n '',\n '\",\n // middle - where the columns go\n '',\n '\",\n '',\n '',\n '',\n '',\n \"\",\n \"\",\n // feedback\n '',\n '\",\n '',\n \"\",\n \"',\n ' \",\n \"\",\n \"',\n '',\n \"\",\n // footer\n ''\n ].join(\"\"),\n { variable: \"view\" }\n ),\n\n loadingIndicatorTemplate: _.template(\n [\n '',\n '',\n _l(\"Loading histories\"),\n \"...\",\n \"\"\n ].join(\"\"),\n { variable: \"view\" }\n ),\n\n orderDescriptions: {\n update_time: _l(\"most recent first\"),\n 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_l from \"utils/localization\";\nimport HISTORY_MODEL from \"mvc/history/history-model\";\nimport HISTORY_VIEW_EDIT from \"mvc/history/history-view-edit\";\nimport historyCopyDialog from \"mvc/history/copy-dialog\";\nimport ERROR_MODAL from \"mvc/ui/error-modal\";\nimport baseMVC from \"mvc/base-mvc\";\nimport ajaxQueue from \"utils/ajax-queue\";\nimport \"ui/mode-button\";\nimport \"ui/search-input\";\n\nvar logNamespace = \"history\";\n/* ==============================================================================\nTODO:\n\n============================================================================== */\n/** @class A container for a history panel that renders controls for that history (delete, copy, etc.) */\nvar HistoryViewColumn = Backbone.View.extend(baseMVC.LoggableMixin).extend({\n _logNamespace: logNamespace,\n\n tagName: \"div\",\n className: \"history-column flex-column flex-row-container\",\n id: function id() {\n if (!this.model) {\n return \"\";\n }\n return \"history-column-\" + this.model.get(\"id\");\n },\n\n // ------------------------------------------------------------------------ set up\n /** set up passed-in panel (if any) and listeners */\n initialize: function initialize(options) {\n options = options || {};\n this.purgeAllowed = !_.isUndefined(options.purgeAllowed)\n ? options.purgeAllowed\n : false;\n this.panel = options.panel || this.createPanel(options);\n\n this.setUpListeners();\n },\n\n /** create a history panel for this column */\n createPanel: function createPanel(panelOptions) {\n return new HISTORY_VIEW_EDIT.HistoryViewEdit(\n _.defaults(panelOptions, {\n model: this.model,\n // non-current panels should set their hdas to draggable\n purgeAllowed: this.purgeAllowed,\n dragItems: true,\n $scrollContainer: function() {\n return this.$el;\n }\n })\n );\n },\n\n /** set up reflexive listeners */\n setUpListeners: function setUpListeners() {\n var column = this;\n //this.log( 'setUpListeners', this );\n this.once(\"rendered\", function() {\n column.trigger(\"rendered:initial\", column);\n });\n this.setUpPanelListeners();\n },\n\n /** set listeners needed for panel */\n setUpPanelListeners: function setUpPanelListeners() {\n var column = this;\n this.listenTo(\n this.panel,\n {\n //'all': function(){ console.info( 'panel of ' + this, arguments ); },\n\n // assumes panel will take the longest to render\n rendered: function() {\n column.trigger(\"rendered\", column);\n },\n // when a panel's view expands turn off the click handler on the rerun button so that it uses it's href\n // this allows the button to open the tool rerun form in a new tab (instead of erroring)\n // TODO: hack\n \"view:expanded view:rendered\": function(view) {\n view.$(\".rerun-btn\").off();\n }\n },\n this\n );\n },\n\n /** do the dimensions of this column overlap the given (horizontal) browser coords? */\n inView: function(viewLeft, viewRight) {\n var columnLeft = this.$el.offset().left,\n columnRight = columnLeft + this.$el.width();\n if (columnRight < viewLeft) {\n return false;\n }\n if (columnLeft > viewRight) {\n return false;\n }\n return true;\n },\n\n /** shortcut to the panel */\n $panel: function $panel() {\n return this.$(\".history-panel\");\n },\n\n // ------------------------------------------------------------------------ render\n /** render ths column, its panel, and set up plugins */\n render: function render(speed) {\n speed = speed !== undefined ? speed : \"fast\";\n //this.log( this + '.render', this.$el, this.el );\n //TODO: not needed\n var modelData = this.model ? this.model.toJSON() : {};\n this.$el.html(this.template(modelData));\n this.renderPanel(speed);\n // jq 1.12 doesn't fade/show properly when display: flex, re-set here\n this.panel.$el.css(\"display\", \"flex\");\n // if model and not children\n // template\n // render controls\n this.setUpBehaviors();\n // add panel\n return this;\n },\n\n /** set up plugins */\n setUpBehaviors: function setUpBehaviors() {\n //this.log( 'setUpBehaviors:', this );\n //var column = this;\n // on panel size change, ...\n },\n\n /** column body template with inner div for panel based on data (model json) */\n template: function template(data) {\n data = _.extend(data || {}, {\n isCurrentHistory: this.currentHistory\n });\n return $(\n [\n '',\n this.controlsLeftTemplate({\n history: data,\n view: this\n }),\n //'',\n this.controlsRightTemplate({\n history: data,\n view: this\n }),\n \"\",\n '',\n '',\n \"\"\n ].join(\"\")\n );\n },\n\n /** render the panel contained in the column using speed for fx speed */\n renderPanel: function renderPanel(speed) {\n speed = speed !== undefined ? speed : \"fast\";\n this.panel.setElement(this.$panel()).render(speed);\n if (this.currentHistory) {\n this.panel.$list().before(this.panel._renderDropTargetHelp());\n }\n return this;\n },\n\n // ------------------------------------------------------------------------ behaviors and events\n /** event map */\n events: {\n // will make this the current history\n \"click .switch-to.btn\": function() {\n this.model.setAsCurrent();\n },\n //TODO: remove boiler plate from next 3\n \"click .delete-history\": function() {\n var column = this;\n this.model._delete().done(function(data) {\n column.render();\n });\n },\n \"click .undelete-history\": function() {\n var column = this;\n this.model.undelete().done(function(data) {\n column.render();\n });\n },\n \"click .purge-history\": function() {\n if (\n confirm(\n _l(\"This will permanently remove the data. Are you sure?\")\n )\n ) {\n var column = this;\n this.model.purge().done(function(data) {\n column.render();\n });\n }\n },\n // will copy this history and make the copy the current history\n \"click .copy-history\": \"copy\"\n },\n\n // ------------------------------------------------------------------------ non-current controls\n /** Open a modal to get a new history name, copy it (if not canceled), and makes the copy current */\n copy: function copy() {\n historyCopyDialog(this.model);\n },\n\n // ------------------------------------------------------------------------ templates\n /** controls template displaying controls above the panel based on this.currentHistory */\n controlsLeftTemplate: _.template(\n [\n '',\n \"<% if( data.history.isCurrentHistory ){ %>\",\n '',\n _l(\"Current History\"),\n \"\",\n \"<% } else { %>\",\n '\",\n \"<% } %>\",\n \"\"\n ].join(\"\"),\n { variable: \"data\" }\n ),\n\n /** controls template displaying controls above the panel based on this.currentHistory */\n controlsRightTemplate: _.template(\n [\n '',\n \"<% if( !data.history.purged ){ %>\",\n '\",\n \"<% } %>\",\n \"\"\n ].join(\"\"),\n { variable: \"data\" }\n ),\n\n // ------------------------------------------------------------------------ misc\n /** String rep */\n toString: function() {\n return \"HistoryViewColumn(\" + (this.panel ? this.panel : \"\") + \")\";\n }\n});\n\n//==============================================================================\n/** @class A view of a HistoryCollection and displays histories similarly to the current history panel.\n */\nvar MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({\n _logNamespace: logNamespace,\n\n className: \"multi-panel-history\",\n\n // ------------------------------------------------------------------------ set up\n /** Set up internals, history collection, and columns to display the history */\n initialize: function initialize(options) {\n options = options || {};\n this.log(this + \".init\", options);\n\n // add the className here (since we gen. pass the el in options)\n this.$el.addClass(this.className);\n\n // --- instance vars\n //TODO: move these to some defaults\n this.options = {\n columnWidth: 312,\n borderWidth: 1,\n columnGap: 8,\n headerHeight: 29,\n footerHeight: 0,\n controlsHeight: 20\n };\n\n /** how many histories to get when fetching a new batch/page */\n this.perPage = options.perPage || 10;\n\n /** named ajax queue for loading hdas */\n this.hdaQueue = new ajaxQueue.NamedAjaxQueue([], false);\n\n // --- set up models, sub-views, and listeners\n /** the original unfiltered and unordered collection of histories */\n this.collection = null;\n /** model id to column map */\n this.columnMap = {};\n /** model id to column map */\n this.columnOptions = options.columnOptions || {};\n\n /** what to search for within all histories */\n this.historySearch = null;\n /** what to search for within all datasets */\n this.datasetSearch = null;\n\n this.setCollection(options.histories);\n this.setUpListeners();\n },\n\n /** Set up reflexive listeners */\n setUpListeners: function setUpListeners() {\n var multipanel = this;\n //multipanel.log( 'setUpListeners', multipanel );\n this.on(\"end-of-scroll\", function() {\n multipanel.collection.fetchMore();\n });\n },\n\n // ------------------------------------------------------------------------ collection\n /** Set up a (new) history collection, sorting and adding listeners\n * @fires 'new-collection' when set with this view as the arg\n */\n setCollection: function setCollection(collection) {\n // console.log( 'setCollection:', collection );\n this.stopListening(this.collection);\n\n this.collection = collection || new HISTORY_MODEL.HistoryCollection();\n this.setUpCollectionListeners();\n\n this.createColumns();\n this.hdaQueue.clear();\n\n this.trigger(\"new-collection\", this);\n return this;\n },\n\n /** Set up a (new) history collection, sorting and adding listeners\n * @fires 'new-collection' when set with this view as the arg\n */\n addModels: function addModels(models, collection, options) {\n // console.log( 'addModels:', models, collection, options );\n options = options || {};\n var multipanel = this;\n models = _.isArray(models) ? models : [models];\n models.forEach(function(model) {\n multipanel.addColumn(model, false);\n // if this is from a fetch, sort will be called and it will call render\n });\n return this;\n },\n\n /** Set up listeners for the collection - handling: added histories, change of current, deletion, and sorting */\n setUpCollectionListeners: function() {\n var multipanel = this;\n multipanel.listenTo(multipanel.collection, {\n // handle ajax errors from the collection\n error: multipanel.errorHandler,\n // add multiple models\n add: multipanel.addModels,\n // when all the histories a user has have been fetched\n \"all-fetched\": multipanel._postFetchAll,\n // handle addition of histories, triggered by column copy and create new\n \"new-current\": multipanel.addAsCurrentColumn,\n // handle setting a history as current, triggered by history.setAsCurrent\n \"set-as-current\": multipanel.setCurrentHistory,\n // handle deleting a history (depends on whether panels is including deleted or not)\n \"change:deleted change:purged\": multipanel.handleDeletedHistory,\n // re-render columns after a sort\n sort: function() {\n multipanel.renderColumns(0);\n }\n });\n },\n\n _postFetchAll: function(fetchData) {\n // console.log( '_postFetchAll' );\n this.$(\".histories-loading-indicator\").remove();\n // when new histories is fetched and the indicator is not required,\n // the panel will jump slightly left - totally aesthetic but jarring\n // TODO: this probably would be best handled elsewhere during a refinement cycle (if any)\n if (!this.historySearch) {\n var $scrollContainer = this.$(\".outer-middle\");\n $scrollContainer.scrollLeft($scrollContainer.scrollLeft() + 24);\n }\n },\n\n /** Re-render and set currentHistoryId to reflect a new current history */\n setCurrentHistory: function setCurrentHistory(history) {\n this.log(\"setCurrentHistory:\", history);\n var oldCurrentColumn = _.findWhere(this.columnMap, {\n currentHistory: true\n });\n if (oldCurrentColumn) {\n oldCurrentColumn.currentHistory = false;\n oldCurrentColumn.$el.height(\"\");\n }\n\n var newCurrentColumn = this.columnMap[this.collection.currentHistoryId];\n newCurrentColumn.currentHistory = true;\n this.collection.sort();\n this._recalcFirstColumnHeight();\n return newCurrentColumn;\n },\n\n /** Either remove a deleted history or re-render it to show the deleted message\n * based on collection.includeDeleted\n */\n handleDeletedHistory: function handleDeletedHistory(history) {\n if (history.get(\"deleted\") || history.get(\"purged\")) {\n this.log(\n \"handleDeletedHistory\",\n this.collection.includeDeleted,\n history\n );\n var multipanel = this,\n column = multipanel.columnMap[history.id];\n if (!column) {\n return;\n }\n\n // if it's the current column, create a new, empty history as the new current\n if (column.model.id === this.collection.currentHistoryId) {\n //TODO: figuring out the order of async here is tricky\n // - for now let the user handle the two step process\n //multipanel.collection.create().done( function(){\n // if( !multipanel.collection.includeDeleted ){ multipanel.removeColumn( column, false ); }\n //});\n } else if (!multipanel.collection.includeDeleted) {\n multipanel.removeColumn(column);\n }\n }\n },\n\n // ........................................................................ error handling\n /** Event handler for errors (from the history collection mainly)\n * Alternately use two strings for model and xhr to use custom message and title (respectively)\n * (e.g. this.trigger( 'error', 'Heres a message', 'Heres a title' ))\n * @param {Model or View} model the (Backbone) source of the error\n * @param {XMLHTTPRequest} xhr any ajax obj. assoc. with the error\n * @param {Object} options the options map commonly used with bbone ajax\n */\n errorHandler: function(model, xhr, options) {\n // interrupted ajax or no connection\n if (xhr && xhr.status === 0 && xhr.readyState === 0) {\n // return ERROR_MODAL.offlineErrorModal();\n // fail silently\n return;\n }\n // otherwise, leave something to report in the console\n this.error(model, xhr, options);\n // and feedback to a modal\n // if sent two strings (and possibly details as 'options'), use those as message and title\n if (_.isString(model) && _.isString(xhr)) {\n var message = model;\n var title = xhr;\n return ERROR_MODAL.errorModal(message, title, options);\n }\n // bad gateway\n // TODO: possibly to global handler\n if (xhr && xhr.status === 502) {\n return ERROR_MODAL.badGatewayErrorModal();\n }\n return ERROR_MODAL.ajaxErrorModal(model, xhr, options);\n },\n\n /** If Galaxy object is available handle error there, otherwise, locally (and crudely) */\n _ajaxErrorHandler: function() {\n ERROR_MODAL.ajaxErrorModal.apply(null, _.toArray(arguments));\n },\n\n /** create a new history and set it to current */\n create: function(ev) {\n return this.collection.create({ current: true });\n },\n\n // ------------------------------------------------------------------------ columns\n /** create columns from collection */\n createColumns: function createColumns(models, columnOptions) {\n columnOptions = columnOptions || this.options.columnOptions;\n var multipanel = this;\n // clear column map\n // TODO: make cummulative\n multipanel.columnMap = {};\n multipanel.collection.each(function(model, i) {\n var column = multipanel.createColumn(model, columnOptions);\n multipanel.columnMap[model.id] = column;\n });\n },\n\n /** create a column and its panel and set up any listeners to them */\n createColumn: function createColumn(history, options) {\n // options passed can be re-used, so extend them before adding the model to prevent pollution for the next\n options = _.extend({}, options, {\n model: history,\n purgeAllowed: Galaxy.config.allow_user_dataset_purge\n });\n var column = new HistoryViewColumn(options);\n if (history.id === this.collection.currentHistoryId) {\n column.currentHistory = true;\n }\n this.setUpColumnListeners(column);\n if (this.datasetSearch) {\n column.panel.searchItems(this.datasetSearch);\n this.queueHdaFetchDetails(column);\n }\n return column;\n },\n\n /** add a new column for history and render all columns if render is true */\n addColumn: function add(history, render) {\n // console.debug( 'adding column for:', history, render );\n render = render !== undefined ? render : true;\n var newColumn = this.createColumn(history);\n this.columnMap[history.id] = newColumn;\n if (render) {\n this.renderColumns();\n }\n return newColumn;\n },\n\n /** add a new column for history and make it the current history/column */\n addAsCurrentColumn: function add(history, collection, options) {\n //this.log( 'adding current column for:', history );\n var multipanel = this,\n newColumn = this.addColumn(history, false);\n this.setCurrentHistory(history);\n newColumn.once(\"rendered\", function() {\n multipanel.queueHdaFetch(newColumn);\n });\n return newColumn;\n },\n\n /** remove the given column, it's listeners, and optionally render */\n removeColumn: function remove(column, render) {\n render = render !== undefined ? render : true;\n this.log(\"removeColumn\", column);\n if (!column) {\n return;\n }\n var multipanel = this,\n widthToRemove = this.options.columnWidth + this.options.columnGap;\n column.$el.fadeOut(\"fast\", function() {\n if (render) {\n $(this).remove();\n multipanel\n .$(\".middle\")\n .width(multipanel.$(\".middle\").width() - widthToRemove);\n multipanel.checkColumnsInView();\n multipanel._recalcFirstColumnHeight();\n }\n\n //TODO: to freeColumn (where Columns have freePanel)\n multipanel.stopListening(column.panel);\n multipanel.stopListening(column);\n delete multipanel.columnMap[column.model.id];\n column.remove();\n });\n },\n\n /** set up listeners for a column and it's panel - handling: hda lazy-loading, drag and drop */\n setUpColumnListeners: function setUpColumnListeners(column) {\n var multipanel = this;\n multipanel.listenTo(column, {\n //'all': function(){ console.info( 'column ' + column + ':', arguments ) },\n \"in-view\": multipanel.queueHdaFetch\n });\n\n multipanel.listenTo(column.panel, {\n //'all': function(){ console.info( 'panel ' + column.panel + ':', arguments ) },\n\n \"view:draggable:dragstart\": function(ev, view, panel, column) {\n multipanel._dropData = JSON.parse(\n ev.dataTransfer.getData(\"text\")\n );\n multipanel.currentColumnDropTargetOn();\n },\n \"view:draggable:dragend\": function(ev, view, panel, column) {\n multipanel._dropData = null;\n multipanel.currentColumnDropTargetOff();\n },\n \"droptarget:drop\": function(ev, data, panel) {\n //note: bad copy sources fail silently\n var toCopy = multipanel._dropData.filter(function(json) {\n return panel.model.contents.isCopyable(json);\n });\n multipanel._dropData = null;\n\n var queue = new ajaxQueue.NamedAjaxQueue();\n if (panel.model.contents.currentPage !== 0) {\n queue.add({\n name: \"fetch-front-page\",\n fn: function() {\n return panel.model.contents.fetchPage(0);\n }\n });\n }\n // need to reverse to better match expected order\n // TODO: reconsider order in list-view._setUpItemViewListeners, dragstart (instead of here)\n toCopy.reverse().forEach(function(content) {\n queue.add({\n name: \"copy-\" + content.id,\n fn: function() {\n return panel.model.contents.copy(content);\n }\n });\n });\n queue.start();\n queue.done(function(responses) {\n panel.model.fetch();\n });\n }\n });\n },\n\n /** conv. fn to count the columns in columnMap */\n columnMapLength: function() {\n return Object.keys(this.columnMap).length;\n },\n\n /** return array of Columns filtered by filters and sorted to match the collection\n * @param: filters Function[] array of filter fns\n */\n sortedFilteredColumns: function(filters) {\n filters = filters || this.filters;\n if (!filters || !filters.length) {\n return this.sortedColumns();\n }\n var multipanel = this;\n return multipanel.sortedColumns().filter(function(column, index) {\n var filtered =\n column.currentHistory ||\n _.every(\n filters.map(function(filter) {\n return filter.call(column);\n })\n );\n return filtered;\n });\n },\n\n /** return array of Columns sorted to match the collection */\n sortedColumns: function() {\n var multipanel = this;\n var sorted = this.collection.map(function(history, index) {\n return multipanel.columnMap[history.id];\n });\n return sorted;\n },\n\n // ------------------------------------------------------------------------ render\n /** Render this view, columns, and set up view plugins */\n render: function render(speed) {\n speed = speed !== undefined ? speed : this.fxSpeed;\n var multipanel = this;\n\n multipanel.log(multipanel + \".render\");\n multipanel.$el.html(multipanel.mainTemplate(multipanel));\n multipanel.renderColumns(speed);\n\n // set the columns to full height allowed and set up behaviors for thie multipanel\n multipanel.setUpBehaviors();\n //TODO: wrong - has to wait for columns to render\n // - create a column listener that fires this when all columns are rendered\n multipanel.trigger(\"rendered\", multipanel);\n return multipanel;\n },\n\n /** Render the columns and panels */\n renderColumns: function renderColumns(speed) {\n speed = _.isNumber(speed) ? speed : this.fxSpeed;\n // console.log( 'renderColumns:', speed );\n // render columns and track the total number rendered, firing an event when all are rendered\n var self = this;\n var sortedAndFiltered = self.sortedFilteredColumns();\n // console.log( '\\t sortedAndFiltered:', sortedAndFiltered );\n var $middle = self.$(\".middle\").empty();\n\n self._addColumns(sortedAndFiltered, speed);\n if (!self.collection.allFetched) {\n $middle.append(self.loadingIndicatorTemplate(self));\n }\n //TODO: sorta - at least their fx queue has started the re-rendering\n self.trigger(\"columns-rendered\", sortedAndFiltered, self);\n\n if (self.datasetSearch && sortedAndFiltered.length <= 1) {\n } else {\n // check for in-view, hda lazy-loading if so\n self.checkColumnsInView();\n // the first, current column has position: fixed and flex css will not apply - adjust height manually\n self._recalcFirstColumnHeight();\n }\n return sortedAndFiltered;\n },\n\n _addColumns: function(columns, speed) {\n speed = _.isNumber(speed) ? speed : this.fxSpeed;\n var $middle = this.$(\".middle\");\n\n var numExisting = $middle.children(\".history-column\").length;\n $middle.width(this._calcMiddleWidth(columns.length + numExisting));\n\n columns.forEach(function(column, i) {\n column\n .delegateEvents()\n .render(speed)\n .$el.appendTo($middle);\n });\n },\n\n _calcMiddleWidth: function(numColumns) {\n var preventStackWidthAdj = 16;\n return (\n numColumns * (this.options.columnWidth + this.options.columnGap) +\n // last column gap\n this.options.columnGap +\n // the amount that safely prevents stacking of columns when adding a new one\n preventStackWidthAdj\n );\n },\n\n //TODO: combine the following two more sensibly\n //TODO: could have HistoryContents.haveDetails return false\n // if column.model.contents.length === 0 && !column.model.get( 'empty' ) then just check that\n /** Get the *summary* contents of a column's history (and details on any expanded contents),\n * queueing the ajax call and using a named queue to prevent the call being sent twice\n */\n queueHdaFetch: function queueHdaFetch(column) {\n // console.log( column.model + '.contentsShown:', column.model.contentsShown() );\n var contents = column.model.contents;\n // console.log( 'queueHdaFetch:', column, column.model.get( 'contents_active' ) );\n // if the history model says it has hdas but none are present, queue an ajax req for them\n if (contents.length === 0 && column.model.contentsShown()) {\n var fetchOptions = { silent: true };\n var ids = _.values(contents.storage.allExpanded()).join();\n if (ids) {\n fetchOptions.details = ids;\n }\n // this uses a 'named' queue so that duplicate requests are ignored\n this.hdaQueue.add({\n name: column.model.id,\n fn: function() {\n return contents\n .fetchCurrentPage(fetchOptions)\n .done(function() {\n column.panel.renderItems();\n });\n }\n });\n // the queue is re-used, so if it's not processing requests - start it again\n if (!this.hdaQueue.running) {\n this.hdaQueue.start();\n }\n }\n },\n\n /** Get the *detailed* json for *all* of a column's history's contents - req'd for searching */\n queueHdaFetchDetails: function(column) {\n var contents = column.model.contents;\n var needsContentsLoaded =\n contents.length === 0 && column.model.contentsShown();\n if (needsContentsLoaded || !contents.haveDetails()) {\n // this uses a 'named' queue so that duplicate requests are ignored\n this.hdaQueue.add({\n name: column.model.id,\n fn: function() {\n return contents\n .progressivelyFetchDetails()\n .done(function() {\n column.panel._renderEmptyMessage();\n });\n }\n });\n // the queue is re-used, so if it's not processing requests - start it again\n if (!this.hdaQueue.running) {\n this.hdaQueue.start();\n }\n }\n },\n\n /** put a text msg in the header */\n renderInfo: function(msg) {\n return this.$(\".header .header-info\").text(msg);\n },\n\n // ------------------------------------------------------------------------ events/behaviors\n events: {\n // will move to the server root (gen. Analyze data)\n \"click .done.btn\": \"close\",\n // creates a new empty history and makes it current\n \"click .create-new.btn\": \"create\",\n \"click #include-deleted\": \"_clickToggleDeletedHistories\",\n // these change the collection and column sort order\n \"click .order .set-order\": \"_chooseOrder\",\n \"click #toggle-deleted\": \"_clickToggleDeletedDatasets\",\n \"click #toggle-hidden\": \"_clickToggleHiddenDatasets\"\n //'dragstart .list-item .title-bar' : function( e ){ console.debug( 'ok' ); }\n },\n\n close: function(ev) {\n //TODO: switch to pushState/router\n window.location = Galaxy.root;\n },\n\n _clickToggleDeletedHistories: function(ev) {\n this.toggleDeletedHistories($(ev.currentTarget).is(\":checked\"));\n this.toggleOptionsPopover();\n },\n /** Include deleted histories in the collection */\n toggleDeletedHistories: function(show) {\n if (show) {\n window.location =\n Galaxy.root +\n \"history/view_multiple?include_deleted_histories=True\";\n } else {\n window.location = Galaxy.root + \"history/view_multiple\";\n }\n },\n\n _clickToggleDeletedDatasets: function(ev) {\n this.toggleDeletedDatasets($(ev.currentTarget).is(\":checked\"));\n this.toggleOptionsPopover();\n },\n toggleDeletedDatasets: function(show) {\n show = show !== undefined ? show : false;\n var multipanel = this;\n multipanel.sortedFilteredColumns().forEach(function(column, i) {\n _.delay(function() {\n column.panel.toggleShowDeleted(show, false);\n }, i * 200);\n });\n },\n\n _clickToggleHiddenDatasets: function(ev) {\n this.toggleHiddenDatasets($(ev.currentTarget).is(\":checked\"));\n this.toggleOptionsPopover();\n },\n toggleHiddenDatasets: function(show) {\n show = show !== undefined ? show : false;\n var multipanel = this;\n multipanel.sortedFilteredColumns().forEach(function(column, i) {\n _.delay(function() {\n column.panel.toggleShowHidden(show, false);\n }, i * 200);\n });\n },\n\n /** change the collection order and re-fetch when the drop down in the options menu is changed */\n _chooseOrder: function(ev) {\n var multipanel = this,\n collection = multipanel.collection,\n orderKey = $(ev.currentTarget).data(\"order\");\n // set the sort order text also\n multipanel\n .$(\".current-order\")\n .text(multipanel.orderDescriptions[orderKey]);\n multipanel.toggleOptionsPopover();\n // set the order and re-fetch using the new order, saving the current history as the first\n collection.setOrder(orderKey);\n var currentHistoryModel = collection.slice(0, 1);\n collection.fetchFirst().done(function() {\n collection.unshift(currentHistoryModel, {\n silent: true\n });\n multipanel.createColumns();\n // need to clear this or previously fetched contents won't refetch now (bc of named queue)\n multipanel.hdaQueue.clear();\n multipanel.render();\n });\n multipanel.once(\"columns-rendered\", multipanel._scrollLeft);\n //TODO: check allFetched and do not reset if so - just sort instead\n },\n\n /** scroll the column container right or left */\n _scrollLeft: function(val) {\n val = _.isNumber(val) ? val : 0;\n this.$(\".outer-middle\").scrollLeft(val);\n },\n\n /** Set up any view plugins */\n setUpBehaviors: function() {\n var multipanel = this;\n multipanel._moreOptionsPopover();\n\n // input to search histories\n multipanel.$(\"#search-histories\").searchInput({\n name: \"search-histories\",\n placeholder: _l(\"search histories\"),\n\n onfirstsearch: function(searchFor) {\n multipanel.$(\"#search-histories\").searchInput(\"toggle-loading\");\n multipanel.renderInfo(_l(\"loading all histories for search\"));\n multipanel.collection.fetchAll().done(function() {\n multipanel\n .$(\"#search-histories\")\n .searchInput(\"toggle-loading\");\n multipanel.renderInfo(\"\");\n });\n },\n onsearch: function(searchFor) {\n multipanel.historySearch = searchFor;\n multipanel.filters = [\n function() {\n return this.model.matchesAll(multipanel.historySearch);\n }\n ];\n multipanel.renderColumns(0);\n },\n onclear: function(searchFor) {\n multipanel.historySearch = null;\n //TODO: remove specifically not just reset\n multipanel.filters = [];\n multipanel.renderColumns(0);\n }\n });\n\n // input to search datasets\n multipanel.$(\"#search-datasets\").searchInput({\n name: \"search-datasets\",\n placeholder: _l(\"search all datasets\"),\n\n onfirstsearch: function(searchFor) {\n multipanel.hdaQueue.clear();\n multipanel.$(\"#search-datasets\").searchInput(\"toggle-loading\");\n multipanel.datasetSearch = searchFor;\n multipanel.sortedFilteredColumns().forEach(function(column) {\n column.panel.searchItems(searchFor);\n // load details for them that need\n multipanel.queueHdaFetchDetails(column);\n });\n multipanel.hdaQueue.progress(function(progress) {\n multipanel.renderInfo(\n [\n _l(\"searching\"),\n progress.curr + 1,\n _l(\"of\"),\n progress.total\n ].join(\" \")\n );\n });\n multipanel.hdaQueue.deferred.done(function() {\n multipanel.renderInfo(\"\");\n multipanel\n .$(\"#search-datasets\")\n .searchInput(\"toggle-loading\");\n });\n },\n onsearch: function(searchFor) {\n multipanel.datasetSearch = searchFor;\n multipanel.sortedFilteredColumns().forEach(function(column) {\n column.panel.searchItems(searchFor);\n });\n },\n onclear: function(searchFor) {\n multipanel.datasetSearch = null;\n multipanel.sortedFilteredColumns().forEach(function(column) {\n column.panel.clearSearch();\n });\n }\n });\n\n // resize first (fixed position) column on page resize\n $(window).resize(function() {\n multipanel._recalcFirstColumnHeight();\n });\n\n // when scrolling - check for histories now in view: they will fire 'in-view' and queueHdaLoading if necc.\n //TODO:?? might be able to simplify and not use pub-sub\n var debouncedInView = _.debounce(function _debouncedInner() {\n var viewport = multipanel._viewport();\n multipanel.checkColumnsInView(viewport);\n multipanel.checkForEndOfScroll(viewport);\n }, 100);\n this.$(\".middle\")\n .parent()\n .scroll(debouncedInView);\n },\n\n /** create the options popover */\n _moreOptionsPopover: function() {\n return this.$(\".open-more-options.btn\").popover({\n container: \".header\",\n placement: \"bottom\",\n html: true,\n content: $(this.optionsPopoverTemplate(this))\n });\n },\n\n /** change the collection order and re-fetch when the drop down in the options menu is changed */\n toggleOptionsPopover: function(ev) {\n // hide seems broken in our version\n this.$(\".open-more-options.btn\").popover(\"toggle\");\n },\n\n /** Adjust the height of the first, current column since flex-boxes won't work with fixed postiion elements */\n _recalcFirstColumnHeight: function() {\n var $firstColumn = this.$(\".history-column\").first(),\n middleHeight = this.$(\".middle\").height(),\n controlHeight = $firstColumn.find(\".panel-controls\").height();\n $firstColumn\n .height(middleHeight)\n .find(\".inner\")\n .height(middleHeight - controlHeight);\n },\n\n /** Get the left and right pixel coords of the middle element */\n _viewport: 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fully to the right? */\n checkForEndOfScroll: function(viewport) {\n viewport = viewport || this._viewport();\n var END_PADDING = 16,\n $middle = this.$(\".middle\"),\n scrollRight = $middle.parent().scrollLeft() + viewport.right;\n if (scrollRight >= $middle.width() - END_PADDING) {\n this.trigger(\"end-of-scroll\");\n }\n },\n\n /** Show and enable the current columns drop target */\n currentColumnDropTargetOn: function() {\n var currentColumn = this.columnMap[this.collection.currentHistoryId];\n if (!currentColumn) {\n return;\n }\n //TODO: fix this - shouldn't need monkeypatch\n currentColumn.panel.dataDropped = function(data) {};\n currentColumn.panel.dropTargetOn();\n },\n\n /** Hide and disable the current columns drop target */\n currentColumnDropTargetOff: function() {\n var currentColumn = this.columnMap[this.collection.currentHistoryId];\n if (!currentColumn) {\n return;\n }\n currentColumn.panel.dataDropped =\n HISTORY_VIEW_EDIT.HistoryViewEdit.prototype.dataDrop;\n // 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PopupMenu from \"mvc/ui/popup-menu\";\nimport historyCopyDialog from \"mvc/history/copy-dialog\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\nimport Webhooks from \"mvc/webhooks\";\n\n// ============================================================================\nvar menu = [\n {\n html: _l(\"History Lists\"),\n header: true\n },\n {\n html: _l(\"Saved Histories\"),\n href: \"histories/list\",\n target: \"_top\"\n },\n {\n html: _l(\"Histories Shared with Me\"),\n href: \"histories/list_shared\",\n target: \"_top\"\n },\n {\n html: _l(\"Current History\"),\n header: true,\n anon: true\n },\n {\n html: _l(\"Create New\"),\n func: function() {\n if (Galaxy && Galaxy.currHistoryPanel) {\n Galaxy.currHistoryPanel.createNewHistory();\n }\n }\n },\n {\n html: _l(\"Copy History\"),\n func: function() {\n historyCopyDialog(Galaxy.currHistoryPanel.model).done(function() {\n Galaxy.currHistoryPanel.loadCurrentHistory();\n });\n }\n },\n {\n html: _l(\"Share or Publish\"),\n href: \"history/sharing\"\n },\n {\n html: _l(\"Show Structure\"),\n href: \"history/display_structured\",\n anon: true\n },\n {\n html: _l(\"Extract Workflow\"),\n href: \"workflow/build_from_current_history\"\n },\n {\n html: _l(\"Delete\"),\n anon: true,\n func: function() {\n if (\n Galaxy &&\n Galaxy.currHistoryPanel &&\n confirm(_l(\"Really delete the current history?\"))\n ) {\n Galaxy.currHistoryPanel.model._delete().done(function() {\n Galaxy.currHistoryPanel.loadCurrentHistory();\n });\n }\n }\n },\n {\n html: _l(\"Delete Permanently\"),\n purge: true,\n anon: true,\n func: function() {\n if (\n Galaxy &&\n Galaxy.currHistoryPanel &&\n confirm(\n _l(\n \"Really delete the current history permanently? 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PopupMenu from \"mvc/ui/popup-menu\";\nimport historyCopyDialog from \"mvc/history/copy-dialog\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\nimport Webhooks from \"mvc/webhooks\";\n\n// ============================================================================\nvar menu = [\n {\n html: _l(\"History Lists\"),\n header: true\n },\n {\n html: _l(\"Saved Histories\"),\n href: \"histories/list\",\n target: \"_top\"\n },\n {\n html: _l(\"Histories Shared with Me\"),\n href: \"histories/list_shared\",\n target: \"_top\"\n },\n {\n html: _l(\"Current History\"),\n header: true,\n anon: true\n },\n {\n html: _l(\"Create New\"),\n func: function() {\n if (Galaxy && Galaxy.currHistoryPanel) {\n Galaxy.currHistoryPanel.createNewHistory();\n }\n }\n },\n {\n html: _l(\"Copy History\"),\n func: function() {\n historyCopyDialog(Galaxy.currHistoryPanel.model).done(function() {\n Galaxy.currHistoryPanel.loadCurrentHistory();\n });\n }\n },\n {\n html: _l(\"Share or Publish\"),\n href: \"history/sharing\"\n },\n {\n html: _l(\"Show Structure\"),\n href: \"history/display_structured\",\n anon: true\n },\n {\n html: _l(\"Extract Workflow\"),\n href: \"workflow/build_from_current_history\"\n },\n {\n html: _l(\"Delete\"),\n anon: true,\n func: function() {\n if (\n Galaxy &&\n Galaxy.currHistoryPanel &&\n confirm(_l(\"Really delete the current history?\"))\n ) {\n Galaxy.currHistoryPanel.model._delete().done(function() {\n Galaxy.currHistoryPanel.loadCurrentHistory();\n });\n }\n }\n },\n {\n html: _l(\"Delete Permanently\"),\n purge: true,\n anon: true,\n func: function() {\n if (\n Galaxy &&\n Galaxy.currHistoryPanel &&\n confirm(\n _l(\n \"Really delete the current history permanently? This cannot be undone.\"\n )\n )\n ) {\n Galaxy.currHistoryPanel.model.purge().done(function() {\n Galaxy.currHistoryPanel.loadCurrentHistory();\n });\n }\n }\n },\n\n {\n html: _l(\"Dataset Actions\"),\n header: true,\n anon: true\n },\n {\n html: _l(\"Copy Datasets\"),\n href: \"dataset/copy_datasets\"\n },\n {\n html: _l(\"Dataset Security\"),\n func: function() {\n if (Galaxy && Galaxy.currHistoryPanel && Galaxy.router) {\n Galaxy.router.push(\n \"/histories/permissions?id=\" +\n Galaxy.currHistoryPanel.model.id\n );\n }\n }\n },\n {\n html: _l(\"Resume Paused Jobs\"),\n href: \"history/resume_paused_jobs?current=True\",\n anon: true\n },\n {\n html: _l(\"Collapse Expanded Datasets\"),\n func: function() {\n if (Galaxy && Galaxy.currHistoryPanel) {\n Galaxy.currHistoryPanel.collapseAll();\n }\n }\n },\n {\n html: _l(\"Unhide Hidden Datasets\"),\n anon: true,\n func: function() {\n // TODO: Deprecate this functionality and replace with group dataset selector and action combination\n if (\n Galaxy &&\n Galaxy.currHistoryPanel &&\n confirm(_l(\"Really unhide all hidden datasets?\"))\n ) {\n $.post(\n Galaxy.root + \"history/adjust_hidden\",\n { user_action: \"unhide\" },\n function() {\n Galaxy.currHistoryPanel.loadCurrentHistory();\n }\n );\n }\n }\n },\n {\n html: _l(\"Delete Hidden Datasets\"),\n anon: true,\n func: function() {\n // TODO: Deprecate this functionality and replace with group dataset selector and action combination\n if (\n Galaxy &&\n Galaxy.currHistoryPanel &&\n confirm(_l(\"Really delete all hidden datasets?\"))\n ) {\n $.post(\n Galaxy.root + \"history/adjust_hidden\",\n { user_action: \"delete\" },\n function() {\n Galaxy.currHistoryPanel.loadCurrentHistory();\n }\n );\n }\n }\n },\n {\n html: _l(\"Purge Deleted Datasets\"),\n confirm: _l(\n \"Really delete all deleted datasets permanently? This cannot be undone.\"\n ),\n href: \"history/purge_deleted_datasets\",\n purge: true,\n anon: true\n },\n\n {\n html: _l(\"Downloads\"),\n header: true\n },\n {\n html: _l(\"Export Tool Citations\"),\n href: \"history/citations\",\n anon: true\n },\n {\n html: _l(\"Export History to File\"),\n href: \"history/export_archive?preview=True\",\n anon: true\n },\n\n {\n html: _l(\"Other Actions\"),\n header: true\n },\n {\n html: _l(\"Import from File\"),\n href: \"history/import_archive\"\n }\n];\n\n// Webhooks\nWebhooks.add({\n url: \"api/webhooks/history-menu/all\",\n async: false, // (hypothetically) slows down the performance\n callback: function(webhooks) {\n var webhooks_menu = [];\n\n $.each(webhooks.models, function(index, model) {\n var webhook = model.toJSON();\n if (webhook.activate) {\n webhooks_menu.push({\n html: _l(webhook.config.title),\n // func: function() {},\n anon: true\n });\n }\n });\n\n if (webhooks_menu.length > 0) {\n webhooks_menu.unshift({\n html: 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LIST_ITEM from \"mvc/list/list-item\";\nimport DATASET_LIST from \"mvc/dataset/dataset-list\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n//==============================================================================\nvar _super = LIST_ITEM.FoldoutListItemView;\n/** @class A job view used from within a larger list of jobs.\n * Each job itself is a foldout panel of history contents displaying the outputs of this job.\n */\nvar JobListItemView = _super.extend(\n /** @lends JobListItemView.prototype */ {\n /** logger used to record this.log messages, commonly set to console */\n //logger : console,\n\n className: _super.prototype.className + \" job\",\n id: function() {\n return [\"job\", this.model.get(\"id\")].join(\"-\");\n },\n\n foldoutPanelClass: DATASET_LIST.DatasetList,\n\n /** Set up: instance vars, options, and event handlers */\n initialize: function(attributes) {\n if (attributes.logger) {\n this.logger = this.model.logger = attributes.logger;\n }\n this.log(this + \".initialize:\", attributes);\n _super.prototype.initialize.call(this, attributes);\n\n this.tool = attributes.tool || {};\n this.jobData = attributes.jobData || {};\n\n /** where should pages from links be displayed? (default to new tab/window) */\n this.linkTarget = attributes.linkTarget || \"_blank\";\n },\n\n /** In this override, add the state as a class for use with state-based CSS */\n _swapNewRender: function($newRender) {\n _super.prototype._swapNewRender.call(this, $newRender);\n if (this.model.has(\"state\")) {\n this.$el.addClass(\"state-\" + this.model.get(\"state\"));\n }\n return this.$el;\n },\n\n /** Stub to return proper foldout panel options */\n _getFoldoutPanelOptions: function() {\n var options = _super.prototype._getFoldoutPanelOptions.call(this);\n return _.extend(options, {\n collection: this.model.outputCollection,\n selecting: false\n });\n },\n\n // ........................................................................ template helpers\n // all of these are ADAPTERs - in other words, it might be better if the API returned the final form\n // or something similar in order to remove some of the complexity here\n\n /** Return tool.inputs that should/can be safely displayed */\n _labelParamMap: function() {\n //ADAPTER\n var params = this.model.get(\"params\"),\n labelParamMap = {};\n _.each(this.tool.inputs, function(i) {\n //console.debug( i.label, i.model_class );\n if (i.label && i.model_class !== \"DataToolParameter\") {\n labelParamMap[i.label] = params[i.name];\n }\n });\n return labelParamMap;\n },\n\n _labelInputMap: function() {\n //ADAPTER\n var view = this,\n labelInputMap = {};\n _.each(this.jobData.inputs, function(input) {\n var toolInput = view._findToolInput(input.name);\n if (toolInput) {\n labelInputMap[toolInput.label] = input;\n }\n });\n return labelInputMap;\n },\n\n /** Return a tool.inputs object that matches (or partially matches) the given (job input) name */\n _findToolInput: function(name) {\n //ADAPTER\n var toolInputs = this.tool.inputs,\n exactMatch = _.findWhere(toolInputs, { name: name });\n if (exactMatch) {\n return exactMatch;\n }\n return this._findRepeatToolInput(name, toolInputs);\n },\n\n /** Return a tool.inputs object that partially matches the given (job input) name (for repeat dataset inputs)*/\n _findRepeatToolInput: function(name, toolInputs) {\n //ADAPTER\n toolInputs = toolInputs || this.tool.inputs;\n var partialMatch = _.find(toolInputs, function(i) {\n return name.indexOf(i.name) === 0;\n });\n if (!partialMatch) {\n return undefined;\n }\n\n var subMatch = _.find(partialMatch.inputs, function(i) {\n return name.indexOf(i.name) !== -1;\n });\n return subMatch;\n },\n\n // ........................................................................ misc\n /** String representation */\n toString: function() {\n return \"JobListItemView(\" + this.model + \")\";\n }\n }\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nJobListItemView.prototype.templates = (function() {\n //TODO: move to require text! plugin\n\n var elTemplate = BASE_MVC.wrapTemplate([\n '',\n '\"\n ]);\n\n var titleBarTemplate = BASE_MVC.wrapTemplate(\n [\n // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display\n '<%- model.id %>',\n // errors, messages, etc.\n '',\n\n // multi-select checkbox\n '',\n '',\n \"\",\n // space for title bar buttons - gen. floated to the right\n '',\n '',\n\n // expandable area for more details\n '',\n \"',\n //'',\n '',\n '<%- view.tool.name %>',\n \"\",\n '',\n '<%- view.tool.description %>',\n \" \",\n _l(\"Created\"),\n \": <%= new Date( job.create_time ).toString() %>, \",\n \"\",\n \"\"\n ],\n \"job\"\n );\n\n var subtitleTemplate = BASE_MVC.wrapTemplate(\n [\n '',\n '<%- view.tool.description %>',\n // ' ', _l( 'Created' ), ': <%= new Date( job.create_time ).toString() %>, ',\n //'',\n // ' (', _l( 'version' ), ': <%- view.tool.version %>)',\n //'\"\n ],\n \"job\"\n );\n\n var detailsTemplate = BASE_MVC.wrapTemplate(\n [\n '',\n //'\"\n ],\n \"job\"\n );\n\n return _.extend({}, _super.prototype.templates, {\n //el : elTemplate,\n titleBar: titleBarTemplate,\n subtitle: subtitleTemplate,\n details: detailsTemplate\n });\n})();\n\n//=============================================================================\nexport default {\n JobListItemView: JobListItemView\n};\n"]} \ No newline at end of file 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LIST_ITEM from \"mvc/list/list-item\";\nimport DATASET_LIST from \"mvc/dataset/dataset-list\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n//==============================================================================\nvar _super = LIST_ITEM.FoldoutListItemView;\n/** @class A job view used from within a larger list of jobs.\n * Each job itself is a foldout panel of history contents displaying the outputs of this job.\n */\nvar JobListItemView = _super.extend(\n /** @lends JobListItemView.prototype */ {\n /** logger used to record this.log messages, commonly set to console */\n //logger : console,\n\n className: _super.prototype.className + \" job\",\n id: function() {\n return [\"job\", this.model.get(\"id\")].join(\"-\");\n },\n\n foldoutPanelClass: DATASET_LIST.DatasetList,\n\n /** Set up: instance vars, options, and event handlers */\n initialize: function(attributes) {\n if (attributes.logger) {\n this.logger = this.model.logger = attributes.logger;\n }\n this.log(this + \".initialize:\", attributes);\n _super.prototype.initialize.call(this, attributes);\n\n this.tool = attributes.tool || {};\n this.jobData = attributes.jobData || {};\n\n /** where should pages from links be displayed? 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TEMPLATES\n/** underscore templates */\nJobListItemView.prototype.templates = (function() {\n //TODO: move to require text! plugin\n\n var elTemplate = BASE_MVC.wrapTemplate([\n '',\n // '',\n // '<%- view.tool.version %>',\n //'',\n '',\n \"<% _.each( view._labelInputMap(), function( input, label ){ %>\",\n '\",\n \"\" data-input-id=\"<%- input.id %>\">',\n '',\n //TODO: input dataset name\n '<%- input.content.name %>',\n \"\",\n \"<% }) %>\",\n \"<% _.each( view._labelParamMap(), function( param, label ){ %>\",\n '\">',\n '',\n '<%- param %>',\n \"\",\n \"<% }) %>\",\n \"',\n '\"\n ]);\n\n var titleBarTemplate = BASE_MVC.wrapTemplate(\n [\n // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display\n '<%- model.id %>',\n // errors, messages, etc.\n '',\n\n // multi-select checkbox\n '',\n '',\n \"\",\n // space for title bar buttons - gen. floated to the right\n '',\n '',\n\n // expandable area for more details\n '',\n \"',\n //'',\n 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HISTORY_CONTENTS from \"mvc/history/history-contents\";\nimport STATES from \"mvc/dataset/states\";\nimport AJAX_QUEUE from \"utils/ajax-queue\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\nvar logNamespace = \"jobs\";\n//==============================================================================\nvar searchableMixin = BASE_MVC.SearchableModelMixin;\n/** @class Represents a job running or ran on the server job handlers.\n */\nvar Job = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(\n BASE_MVC.mixin(\n searchableMixin,\n /** @lends Job.prototype */ {\n _logNamespace: logNamespace,\n\n /** default attributes for a model */\n defaults: {\n model_class: \"Job\",\n\n tool_id: null,\n exit_code: null,\n\n inputs: {},\n outputs: {},\n params: {},\n\n create_time: null,\n update_time: null,\n state: STATES.NEW\n },\n\n /** override to parse params on incomming */\n parse: function(response, options) {\n response.params = this.parseParams(response.params);\n return response;\n },\n\n /** override to treat param values as json */\n parseParams: function(params) {\n var newParams = {};\n _.each(params, function(value, key) {\n newParams[key] = JSON.parse(value);\n });\n return newParams;\n },\n\n /** instance vars and listeners */\n initialize: function(attributes, options) {\n this.debug(this + \"(Job).initialize\", attributes, options);\n\n this.set(\"params\", this.parseParams(this.get(\"params\")), {\n silent: true\n });\n\n this.outputCollection =\n attributes.outputCollection ||\n new HISTORY_CONTENTS.HistoryContents([]);\n this._setUpListeners();\n },\n\n /** set up any event listeners\n * event: state:ready fired when this DA moves into/is already in a ready state\n */\n _setUpListeners: function() {\n // if the state has changed and the new state is a ready state, fire an event\n this.on(\"change:state\", function(currModel, newState) {\n this.log(this + \" has changed state:\", currModel, newState);\n if (this.inReadyState()) {\n this.trigger(\n \"state:ready\",\n currModel,\n newState,\n this.previous(\"state\")\n );\n }\n });\n },\n\n // ........................................................................ common queries\n /** Is this job in a 'ready' state; where 'Ready' states are states where no\n * processing is left to do on the server.\n */\n inReadyState: function() {\n return _.contains(STATES.READY_STATES, this.get(\"state\"));\n },\n\n /** Does this model already contain detailed data (as opposed to just summary level data)? */\n hasDetails: function() {\n //?? this may not be reliable\n return !_.isEmpty(this.get(\"outputs\"));\n },\n\n // ........................................................................ ajax\n /** root api url */\n urlRoot: Galaxy.root + \"api/jobs\",\n //url : function(){ return this.urlRoot; },\n\n // ........................................................................ searching\n // see base-mvc, SearchableModelMixin\n /** what attributes of an Job will be used in a text search */\n //searchAttributes : [\n // 'tool'\n //],\n\n // ........................................................................ misc\n /** String representation */\n toString: function() {\n return [\n \"Job(\",\n this.get(\"id\"),\n \":\",\n this.get(\"tool_id\"),\n \")\"\n ].join(\"\");\n }\n }\n )\n);\n\n//==============================================================================\n/** @class Backbone collection for Jobs.\n */\nvar JobCollection = Backbone.Collection.extend(BASE_MVC.LoggableMixin).extend(\n /** @lends JobCollection.prototype */ {\n _logNamespace: logNamespace,\n\n model: Job,\n\n /** root api url */\n urlRoot: Galaxy.root + \"api/jobs\",\n url: function() {\n return this.urlRoot;\n },\n\n intialize: function(models, options) {\n console.debug(models, options);\n },\n\n // ........................................................................ common queries\n /** Get the ids of every item in this collection\n * @returns array of encoded ids\n */\n ids: function() {\n return this.map(function(item) {\n return item.get(\"id\");\n });\n },\n\n /** Get jobs that are not ready\n * @returns array of content models\n */\n notReady: function() {\n return this.filter(function(job) {\n return !job.inReadyState();\n });\n },\n\n /** return true if any jobs don't have details */\n haveDetails: function() {\n return this.all(function(job) {\n return job.hasDetails();\n });\n },\n\n // ........................................................................ ajax\n /** fetches all details for each job in the collection using a queue */\n queueDetailFetching: function() {\n var collection = this,\n queue = new AJAX_QUEUE.AjaxQueue(\n this.map(function(job) {\n return function() {\n return job.fetch({ silent: true });\n };\n })\n );\n queue.done(function() {\n collection.trigger(\"details-loaded\");\n });\n return queue;\n },\n\n //toDAG : function(){\n // return new JobDAG( this.toJSON() );\n //},\n\n // ........................................................................ sorting/filtering\n /** return a new collection of jobs whose attributes contain the substring matchesWhat */\n matches: function(matchesWhat) {\n return this.filter(function(job) {\n return job.matches(matchesWhat);\n });\n },\n\n // ........................................................................ misc\n /** String representation. */\n toString: function() {\n return [\"JobCollection(\", this.length, \")\"].join(\"\");\n }\n\n //----------------------------------------------------------------------------- class vars\n },\n {\n /** class level fn for fetching the job details for all jobs in a history */\n fromHistory: function(historyId) {\n console.debug(this);\n var Collection = this,\n collection = new Collection([]);\n collection\n .fetch({ data: { history_id: historyId } })\n .done(function() {\n window.queue = collection.queueDetailFetching();\n });\n return collection;\n }\n 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HISTORY_CONTENTS from \"mvc/history/history-contents\";\nimport STATES from \"mvc/dataset/states\";\nimport AJAX_QUEUE from \"utils/ajax-queue\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\nvar logNamespace = \"jobs\";\n//==============================================================================\nvar searchableMixin = BASE_MVC.SearchableModelMixin;\n/** @class Represents a job running or ran on the server job handlers.\n */\nvar Job = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(\n BASE_MVC.mixin(\n searchableMixin,\n /** @lends Job.prototype */ {\n _logNamespace: logNamespace,\n\n /** default attributes for a model */\n defaults: {\n model_class: \"Job\",\n\n tool_id: null,\n exit_code: null,\n\n inputs: {},\n outputs: {},\n params: {},\n\n create_time: null,\n update_time: null,\n state: STATES.NEW\n },\n\n /** override to parse params on incomming */\n parse: function(response, options) {\n response.params = this.parseParams(response.params);\n return response;\n },\n\n /** override to treat param values as json */\n parseParams: function(params) {\n var newParams = {};\n _.each(params, function(value, key) {\n newParams[key] = JSON.parse(value);\n });\n return newParams;\n },\n\n /** instance vars and listeners */\n initialize: function(attributes, options) {\n this.debug(this + \"(Job).initialize\", attributes, options);\n\n this.set(\"params\", this.parseParams(this.get(\"params\")), {\n silent: true\n });\n\n this.outputCollection =\n attributes.outputCollection ||\n new HISTORY_CONTENTS.HistoryContents([]);\n this._setUpListeners();\n },\n\n /** set up any event listeners\n * event: state:ready fired when this DA moves into/is already in a ready state\n */\n _setUpListeners: function() {\n // if the state has changed and the new state is a ready state, fire an event\n this.on(\"change:state\", function(currModel, newState) {\n this.log(this + \" has changed state:\", currModel, newState);\n if (this.inReadyState()) {\n this.trigger(\n \"state:ready\",\n currModel,\n newState,\n this.previous(\"state\")\n );\n }\n });\n },\n\n // ........................................................................ common queries\n /** Is this job in a 'ready' state; where 'Ready' states are states where no\n * processing is left to do on the server.\n */\n inReadyState: function() {\n return _.contains(STATES.READY_STATES, this.get(\"state\"));\n },\n\n /** Does this model already contain detailed data (as opposed to just summary level data)? */\n hasDetails: function() {\n //?? this may not be reliable\n return !_.isEmpty(this.get(\"outputs\"));\n },\n\n // ........................................................................ ajax\n /** root api url */\n urlRoot: Galaxy.root + \"api/jobs\",\n //url : function(){ return this.urlRoot; },\n\n // ........................................................................ searching\n // see base-mvc, SearchableModelMixin\n /** what attributes of an Job will be used in a text search */\n //searchAttributes : [\n // 'tool'\n //],\n\n // ........................................................................ misc\n /** String representation */\n toString: function() {\n return [\n \"Job(\",\n this.get(\"id\"),\n \":\",\n this.get(\"tool_id\"),\n \")\"\n ].join(\"\");\n }\n }\n )\n);\n\n//==============================================================================\n/** @class Backbone collection for Jobs.\n */\nvar JobCollection = Backbone.Collection.extend(BASE_MVC.LoggableMixin).extend(\n /** @lends JobCollection.prototype */ {\n _logNamespace: logNamespace,\n\n model: Job,\n\n /** root api url */\n urlRoot: Galaxy.root + \"api/jobs\",\n url: function() {\n return this.urlRoot;\n },\n\n intialize: function(models, options) {\n console.debug(models, options);\n },\n\n // ........................................................................ common queries\n /** Get the ids of every item in this collection\n * @returns array of encoded ids\n */\n ids: function() {\n return this.map(function(item) {\n return item.get(\"id\");\n });\n },\n\n /** Get jobs that are not ready\n * @returns array of content models\n */\n notReady: function() {\n return this.filter(function(job) {\n return !job.inReadyState();\n });\n },\n\n /** return true if any jobs don't have details */\n haveDetails: function() {\n return this.all(function(job) {\n return job.hasDetails();\n });\n },\n\n // ........................................................................ ajax\n /** fetches all details for each job in the collection using a queue */\n queueDetailFetching: function() {\n var collection = this,\n queue = new AJAX_QUEUE.AjaxQueue(\n this.map(function(job) {\n return function() {\n return job.fetch({ silent: true });\n };\n })\n );\n queue.done(function() {\n collection.trigger(\"details-loaded\");\n });\n return queue;\n },\n\n //toDAG : function(){\n // return new JobDAG( this.toJSON() );\n //},\n\n // ........................................................................ sorting/filtering\n /** return a new collection of jobs whose attributes contain the substring matchesWhat */\n matches: function(matchesWhat) {\n return this.filter(function(job) {\n return job.matches(matchesWhat);\n });\n },\n\n // ........................................................................ misc\n /** String representation. */\n toString: function() {\n return [\"JobCollection(\", this.length, \")\"].join(\"\");\n }\n\n //----------------------------------------------------------------------------- class vars\n },\n {\n /** class level fn for fetching the job details for all jobs in a history */\n fromHistory: function(historyId) {\n console.debug(this);\n var Collection = this,\n collection = new Collection([]);\n collection\n .fetch({ data: { history_id: historyId } })\n .done(function() {\n window.queue = collection.queueDetailFetching();\n });\n return collection;\n }\n 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[\n \"libs/toastr\",\n \"mvc/library/library-model\",\n \"utils/utils\",\n \"mvc/ui/ui-select\"\n ],\n function(mod_toastr, mod_library_model, mod_utils, mod_select) {\n var LibraryDatasetView = Backbone.View.extend({\n el: \"#center\",\n\n model: null,\n\n options: {},\n\n defaults: {\n edit_mode: false\n },\n\n events: {\n \"click .toolbtn_modify_dataset\": \"enableModification\",\n \"click .toolbtn_cancel_modifications\": \"render\",\n \"click .toolbtn-download-dataset\": \"downloadDataset\",\n \"click .toolbtn-import-dataset\": \"importIntoHistory\",\n \"click .copy-link-to-clipboard\": \"copyToClipboard\",\n \"click .make-private\": \"makeDatasetPrivate\",\n \"click .remove-restrictions\": \"removeDatasetRestrictions\",\n \"click .toolbtn_save_permissions\": \"savePermissions\",\n \"click .toolbtn_save_modifications\": \"saveModifications\"\n },\n\n // genome select\n select_genome: null,\n\n // extension select\n select_extension: null,\n\n // extension types\n list_extensions: [],\n\n // datatype placeholder for extension auto-detection\n auto: {\n id: \"auto\",\n text: \"Auto-detect\",\n description:\n \"This system will try to detect the file type automatically.\" +\n \" If your file is not detected properly as one of the known formats,\" +\n \" it most likely means that it has some format problems (e.g., different\" +\n \" number of columns on different rows). You can still coerce the system\" +\n \" to set your data to the format you think it should be.\" +\n \" You can also upload compressed files, which will automatically be decompressed.\"\n },\n\n // genomes\n list_genomes: [],\n\n initialize: function(options) {\n this.options = _.extend(this.options, options);\n this.fetchExtAndGenomes();\n if (this.options.id) {\n this.fetchDataset();\n }\n },\n\n fetchDataset: function(options) {\n this.options = _.extend(this.options, options);\n this.model = new mod_library_model.Item({\n id: this.options.id\n });\n var that = this;\n this.model.fetch({\n success: function() {\n if (that.options.show_permissions) {\n that.showPermissions();\n } else if (that.options.show_version) {\n that.fetchVersion();\n } else {\n that.render();\n }\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(\n response.responseJSON.err_msg +\n \" Click this to go back.\",\n \"\",\n {\n onclick: function() {\n Galaxy.libraries.library_router.back();\n }\n }\n );\n } else {\n mod_toastr.error(\n \"An error occurred. Click this to go back.\",\n \"\",\n {\n onclick: function() {\n Galaxy.libraries.library_router.back();\n }\n }\n );\n }\n }\n });\n },\n\n render: function(options) {\n this.options = _.extend(this.options, options);\n $(\".tooltip\").remove();\n var template = this.templateDataset();\n this.$el.html(template({ item: this.model }));\n $(\".peek\").html(this.model.get(\"peek\"));\n $(\"#center [data-toggle]\").tooltip();\n },\n\n fetchVersion: function(options) {\n this.options = _.extend(this.options, options);\n that = this;\n if (!this.options.ldda_id) {\n this.render();\n mod_toastr.error(\n \"Library dataset version requested but no id provided.\"\n );\n } else {\n this.ldda = new mod_library_model.Ldda({\n id: this.options.ldda_id\n });\n this.ldda.url =\n this.ldda.urlRoot +\n this.model.id +\n \"/versions/\" +\n this.ldda.id;\n this.ldda.fetch({\n success: function() {\n that.renderVersion();\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n }\n });\n }\n },\n\n renderVersion: function() {\n $(\".tooltip\").remove();\n var template = this.templateVersion();\n this.$el.html(template({ item: this.model, ldda: this.ldda }));\n $(\".peek\").html(this.ldda.get(\"peek\"));\n },\n\n enableModification: function() {\n $(\".tooltip\").remove();\n var template = this.templateModifyDataset();\n this.$el.html(template({ item: this.model }));\n this.renderSelectBoxes({\n genome_build: this.model.get(\"genome_build\"),\n file_ext: this.model.get(\"file_ext\")\n });\n $(\".peek\").html(this.model.get(\"peek\"));\n $(\"#center [data-toggle]\").tooltip();\n },\n\n downloadDataset: function() {\n var url =\n Galaxy.root +\n \"api/libraries/datasets/download/uncompressed\";\n var data = { ld_ids: this.id };\n this.processDownload(url, data);\n },\n\n processDownload: function(url, data, method) {\n //url and data options required\n if (url && data) {\n //data can be string of parameters or array/object\n data = typeof data == \"string\" ? data : $.param(data);\n //split params into form inputs\n var inputs = \"\";\n $.each(data.split(\"&\"), function() {\n var pair = this.split(\"=\");\n inputs +=\n '';\n });\n //send request\n $(\n '\"\n )\n .appendTo(\"body\")\n .submit()\n .remove();\n\n mod_toastr.info(\"Your download will begin soon.\");\n }\n },\n\n importIntoHistory: function() {\n this.refreshUserHistoriesList(function(self) {\n var template = self.templateBulkImportInModal();\n self.modal = Galaxy.modal;\n self.modal.show({\n closing_events: true,\n title: \"Import into History\",\n body: template({ histories: self.histories.models }),\n buttons: {\n Import: function() {\n self.importCurrentIntoHistory();\n },\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n });\n },\n\n refreshUserHistoriesList: function(callback) {\n var self = this;\n this.histories = new mod_library_model.GalaxyHistories();\n this.histories.fetch({\n success: function(histories) {\n if (histories.length === 0) {\n mod_toastr.warning(\n \"You have to create history first. Click this to do so.\",\n \"\",\n {\n onclick: function() {\n window.location = Galaxy.root;\n }\n }\n );\n } else {\n callback(self);\n }\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n }\n });\n },\n\n importCurrentIntoHistory: function() {\n this.modal.disableButton(\"Import\");\n var new_history_name = this.modal\n .$(\"input[name=history_name]\")\n .val();\n var that = this;\n if (new_history_name !== \"\") {\n $.post(Galaxy.root + \"api/histories\", {\n name: new_history_name\n })\n .done(function(new_history) {\n that.processImportToHistory(new_history.id);\n })\n .fail(function(xhr, status, error) {\n mod_toastr.error(\"An error occurred.\");\n })\n .always(function() {\n that.modal.enableButton(\"Import\");\n });\n } else {\n var history_id = $(this.modal.$el)\n .find(\n \"select[name=dataset_import_single] option:selected\"\n )\n .val();\n this.processImportToHistory(history_id);\n this.modal.enableButton(\"Import\");\n }\n },\n\n processImportToHistory: function(history_id) {\n var historyItem = new mod_library_model.HistoryItem();\n historyItem.url =\n historyItem.urlRoot + history_id + \"/contents\";\n // set the used history as current so user will see the last one\n // that he imported into in the history panel on the 'analysis' page\n jQuery.getJSON(\n Galaxy.root + \"history/set_as_current?id=\" + history_id\n );\n // save the dataset into selected history\n historyItem.save(\n { content: this.id, source: \"library\" },\n {\n success: function() {\n Galaxy.modal.hide();\n mod_toastr.success(\n \"Dataset imported. Click this to start analyzing it.\",\n \"\",\n {\n onclick: function() {\n window.location = Galaxy.root;\n }\n }\n );\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(\n \"Dataset not imported. \" +\n response.responseJSON.err_msg\n );\n } else {\n mod_toastr.error(\n \"An error occured. Dataset not imported. Please try again.\"\n );\n }\n }\n }\n );\n },\n\n showPermissions: function(options) {\n var template = this.templateDatasetPermissions();\n var self = this;\n this.options = _.extend(this.options, options);\n $(\".tooltip\").remove();\n if (this.options.fetched_permissions !== undefined) {\n if (\n this.options.fetched_permissions.access_dataset_roles\n .length === 0\n ) {\n this.model.set({ is_unrestricted: true });\n } else {\n this.model.set({ is_unrestricted: false });\n }\n }\n this.$el.html(\n template({\n item: this.model,\n is_admin: Galaxy.config.is_admin_user\n })\n );\n $.get(\n Galaxy.root +\n \"api/libraries/datasets/\" +\n self.id +\n \"/permissions?scope=current\"\n )\n .done(function(fetched_permissions) {\n self.prepareSelectBoxes({\n fetched_permissions: fetched_permissions,\n is_admin: Galaxy.config.is_admin_user\n });\n })\n .fail(function() {\n mod_toastr.error(\n \"An error occurred while attempting to fetch dataset permissions.\"\n );\n });\n $(\"#center [data-toggle]\").tooltip();\n $(\"#center\").css(\"overflow\", \"auto\");\n },\n\n _serializeRoles: function(role_list) {\n var selected_roles = [];\n for (var i = 0; i < role_list.length; i++) {\n // Replace the : and , in role's name since these are select2 separators for initialData\n selected_roles.push(\n role_list[i][1] +\n \":\" +\n role_list[i][0].replace(\":\", \" \").replace(\",\", \" &\")\n );\n }\n return selected_roles;\n },\n\n prepareSelectBoxes: function(options) {\n this.options = _.extend(this.options, options);\n this.accessSelectObject = new mod_select.View(\n this._generate_select_options({\n selector: \"access_perm\",\n initialData: this._serializeRoles(\n this.options.fetched_permissions\n .access_dataset_roles\n )\n })\n );\n this.modifySelectObject = new mod_select.View(\n this._generate_select_options({\n selector: \"modify_perm\",\n initialData: this._serializeRoles(\n this.options.fetched_permissions.modify_item_roles\n )\n })\n );\n this.manageSelectObject = new mod_select.View(\n this._generate_select_options({\n selector: \"manage_perm\",\n initialData: this._serializeRoles(\n this.options.fetched_permissions\n .manage_dataset_roles\n )\n })\n );\n },\n\n _generate_select_options: function(options) {\n var select_options = {\n minimumInputLength: 0,\n multiple: true,\n placeholder: \"Click to select a role\",\n formatResult: function roleFormatResult(role) {\n return role.name + \" type: \" + role.type;\n },\n formatSelection: function roleFormatSelection(role) {\n return role.name;\n },\n initSelection: function(element, callback) {\n // the input tag has a value attribute preloaded that points to a preselected role's id\n // this function resolves that id attribute to an object that select2 can render\n // using its formatResult renderer - that way the role name is shown preselected\n var data = [];\n $(element.val().split(\",\")).each(function() {\n var item = this.split(\":\");\n data.push({\n id: item[0],\n name: item[1]\n });\n });\n callback(data);\n },\n dropdownCssClass: \"bigdrop\" // apply css that makes the dropdown taller\n };\n select_options.container = this.$el.find(\n \"#\" + options.selector\n );\n select_options.css = options.selector;\n select_options.initialData = options.initialData.join(\",\");\n select_options.ajax = {\n url:\n Galaxy.root +\n \"api/libraries/datasets/\" +\n this.id +\n \"/permissions?scope=available\",\n dataType: \"json\",\n quietMillis: 100,\n data: function(term, page) {\n // page is the one-based page number tracked by Select2\n return {\n q: term, //search term\n page_limit: 10, // page size, should be same as used in 'more' variable below\n page: page // page number\n };\n },\n results: function(data, page) {\n var more = page * 10 < data.total; // whether or not there are more results available\n // notice we return the value of more so Select2 knows if more results can be loaded\n return { results: data.roles, more: more };\n }\n };\n return select_options;\n },\n\n /**\n * Save the changes made to the library dataset.\n */\n saveModifications: function(options) {\n var is_changed = false;\n var ld = this.model;\n var new_name = this.$el.find(\".input_dataset_name\").val();\n if (\n typeof new_name !== \"undefined\" &&\n new_name !== ld.get(\"name\")\n ) {\n if (new_name.length > 0) {\n ld.set(\"name\", new_name);\n is_changed = true;\n } else {\n mod_toastr.warning(\n \"Library dataset name has to be at least 1 character long.\"\n );\n return;\n }\n }\n var new_info = this.$el.find(\".input_dataset_misc_info\").val();\n if (\n typeof new_info !== \"undefined\" &&\n new_info !== ld.get(\"misc_info\")\n ) {\n ld.set(\"misc_info\", new_info);\n is_changed = true;\n }\n var new_genome_build = this.select_genome.$el.select2(\"data\")\n .id;\n if (\n typeof new_genome_build !== \"undefined\" &&\n new_genome_build !== ld.get(\"genome_build\")\n ) {\n ld.set(\"genome_build\", new_genome_build);\n is_changed = true;\n }\n var new_ext = this.select_extension.$el.select2(\"data\").id;\n if (\n typeof new_ext !== \"undefined\" &&\n new_ext !== ld.get(\"file_ext\")\n ) {\n ld.set(\"file_ext\", new_ext);\n is_changed = true;\n }\n var dataset_view = this;\n if (is_changed) {\n ld.save(null, {\n patch: true,\n success: function(ld) {\n dataset_view.render();\n mod_toastr.success(\n \"Changes to library dataset saved.\"\n );\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\n \"An error occured while attempting to update the library dataset.\"\n );\n }\n }\n });\n } else {\n dataset_view.render();\n mod_toastr.info(\"Nothing has changed.\");\n }\n },\n\n copyToClipboard: function() {\n var href = Backbone.history.location.href;\n if (href.lastIndexOf(\"/permissions\") !== -1) {\n href = href.substr(0, href.lastIndexOf(\"/permissions\"));\n }\n window.prompt(\"Copy to clipboard: Ctrl+C, Enter\", href);\n },\n\n makeDatasetPrivate: function() {\n var self = this;\n $.post(\n Galaxy.root +\n \"api/libraries/datasets/\" +\n self.id +\n \"/permissions?action=make_private\"\n )\n .done(function(fetched_permissions) {\n self.model.set({ is_unrestricted: false });\n self.showPermissions({\n fetched_permissions: fetched_permissions\n });\n mod_toastr.success(\n \"The dataset is now private to you.\"\n );\n })\n .fail(function() {\n mod_toastr.error(\n \"An error occurred while attempting to make dataset private.\"\n );\n });\n },\n\n removeDatasetRestrictions: function() {\n var self = this;\n $.post(\n Galaxy.root +\n \"api/libraries/datasets/\" +\n self.id +\n \"/permissions?action=remove_restrictions\"\n )\n .done(function(fetched_permissions) {\n self.model.set({ is_unrestricted: true });\n self.showPermissions({\n fetched_permissions: fetched_permissions\n });\n mod_toastr.success(\n \"Access to this dataset is now unrestricted.\"\n );\n })\n .fail(function() {\n mod_toastr.error(\n \"An error occurred while attempting to make dataset unrestricted.\"\n );\n });\n },\n\n /**\n * Extract the role ids from Select2 elements's 'data'\n */\n _extractIds: function(roles_list) {\n var ids_list = [];\n for (var i = roles_list.length - 1; i >= 0; i--) {\n ids_list.push(roles_list[i].id);\n }\n return ids_list;\n },\n\n /**\n * Save the permissions for roles entered in the select boxes.\n */\n savePermissions: function(event) {\n var self = this;\n var access_ids = this._extractIds(\n this.accessSelectObject.$el.select2(\"data\")\n );\n var manage_ids = this._extractIds(\n this.manageSelectObject.$el.select2(\"data\")\n );\n var modify_ids = this._extractIds(\n this.modifySelectObject.$el.select2(\"data\")\n );\n $.post(\n Galaxy.root +\n \"api/libraries/datasets/\" +\n self.id +\n \"/permissions?action=set_permissions\",\n {\n \"access_ids[]\": access_ids,\n \"manage_ids[]\": manage_ids,\n \"modify_ids[]\": modify_ids\n }\n )\n .done(function(fetched_permissions) {\n self.showPermissions({\n fetched_permissions: fetched_permissions\n });\n mod_toastr.success(\"Permissions saved.\");\n })\n .fail(function() {\n mod_toastr.error(\n \"An error occurred while attempting to set dataset permissions.\"\n );\n });\n },\n\n /**\n * If needed request all extensions and/or genomes from Galaxy\n * and save them in sorted arrays.\n */\n fetchExtAndGenomes: function() {\n var that = this;\n if (this.list_genomes.length == 0) {\n mod_utils.get({\n url: Galaxy.root + \"api/datatypes?extension_only=False\",\n success: function(datatypes) {\n for (var key in datatypes) {\n that.list_extensions.push({\n id: datatypes[key].extension,\n text: datatypes[key].extension,\n description: datatypes[key].description,\n description_url:\n datatypes[key].description_url\n });\n }\n that.list_extensions.sort(function(a, b) {\n return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;\n });\n that.list_extensions.unshift(that.auto);\n }\n });\n }\n if (this.list_extensions.length == 0) {\n mod_utils.get({\n url: Galaxy.root + \"api/genomes\",\n success: function(genomes) {\n for (var key in genomes) {\n that.list_genomes.push({\n id: genomes[key][1],\n text: genomes[key][0]\n });\n }\n that.list_genomes.sort(function(a, b) {\n return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;\n });\n }\n });\n }\n },\n\n renderSelectBoxes: function(options) {\n // This won't work properly unlesss we already have the data fetched.\n // See this.fetchExtAndGenomes()\n // TODO switch to common resources:\n // https://trello.com/c/dIUE9YPl/1933-ui-common-resources-and-data-into-galaxy-object\n var that = this;\n var current_genome = \"?\";\n var current_ext = \"auto\";\n if (typeof options !== \"undefined\") {\n if (typeof options.genome_build !== \"undefined\") {\n current_genome = options.genome_build;\n }\n if (typeof options.file_ext !== \"undefined\") {\n current_ext = options.file_ext;\n }\n }\n this.select_genome = new mod_select.View({\n css: \"dataset-genome-select\",\n data: that.list_genomes,\n container: that.$el.find(\"#dataset_genome_select\"),\n value: current_genome\n });\n this.select_extension = new mod_select.View({\n css: \"dataset-extension-select\",\n data: that.list_extensions,\n container: that.$el.find(\"#dataset_extension_select\"),\n value: current_ext\n });\n },\n\n templateDataset: function() {\n return _.template(\n [\n // CONTAINER START\n '',\n '\"\n ].join(\"\")\n );\n },\n\n templateVersion: function() {\n return _.template(\n [\n // CONTAINER START\n '',\n '\",\n '\",\n '<% if (item.get(\"can_user_modify\")) { %>',\n '\",\n \"<% } %>\",\n '<% if (item.get(\"can_user_manage\")) { %>',\n '/datasets/<%- item.id %>/permissions\">',\n '\",\n \"\",\n \"<% } %>\",\n \"\",\n\n // BREADCRUMBS\n '\",\n\n '<% if (item.get(\"is_unrestricted\")) { %>',\n \"\",\n 'This dataset is unrestricted so everybody with the link can access it. Just share this page.',\n \"\",\n \"<% } %>\",\n\n // TABLE START\n '',\n '\",\n // CONTAINER END\n \"',\n \"
\",\n\n \"\",\n ' \",\n '<% if (item.get(\"file_ext\")) { %>',\n \"\">Name ',\n '<%= _.escape(item.get(\"name\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"genome_build\")) { %>',\n \"Data type ',\n '<%= _.escape(item.get(\"file_ext\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"file_size\")) { %>',\n \"Genome build ',\n '<%= _.escape(item.get(\"genome_build\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"date_uploaded\")) { %>',\n \"Size ',\n '<%= _.escape(item.get(\"file_size\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"uploaded_by\")) { %>',\n \"Date uploaded (UTC) ',\n '<%= _.escape(item.get(\"date_uploaded\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"metadata_data_lines\")) { %>',\n \"Uploaded by ',\n '<%= _.escape(item.get(\"uploaded_by\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"metadata_comment_lines\")) { %>',\n \"Data Lines ',\n '<%= _.escape(item.get(\"metadata_data_lines\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"metadata_columns\")) { %>',\n \"Comment Lines ',\n '<%= _.escape(item.get(\"metadata_comment_lines\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"metadata_column_types\")) { %>',\n \"Number of Columns ',\n '<%= _.escape(item.get(\"metadata_columns\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"message\")) { %>',\n \"Column Types ',\n '<%= _.escape(item.get(\"metadata_column_types\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"misc_blurb\")) { %>',\n \"Message ',\n '<%= _.escape(item.get(\"message\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"misc_info\")) { %>',\n \"Misc. blurb ',\n '<%= _.escape(item.get(\"misc_blurb\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"tags\")) { %>',\n \"Misc. info ',\n '<%= _.escape(item.get(\"misc_info\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n \"Tags ',\n '<%= _.escape(item.get(\"tags\")) %> ',\n \"\",\n '\",\n\n '<% if (item.get(\"has_versions\")) { %>',\n \"',\n \"
\",\n \"\",\n \"\",\n \"<% } %>\",\n // TABLE END\n \"Expired versions:
\",\n \"- \",\n '<% _.each(item.get(\"expired_versions\"), function(version) { %>',\n '
- \",\n \"
',\n '\",\n\n // BREADCRUMBS\n '\",\n\n '\"\n ].join(\"\")\n );\n },\n\n templateModifyDataset: function() {\n return _.template(\n [\n // CONTAINER START\n 'This is an expired version of the library dataset: <%= _.escape(item.get(\"name\")) %>',\n // DATASET START\n '',\n '\",\n // CONTAINER END\n \"',\n \"
\",\n \"\",\n ' \",\n '<% if (ldda.get(\"file_ext\")) { %>',\n \"\">Name ',\n '<%= _.escape(ldda.get(\"name\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"genome_build\")) { %>',\n \"Data type ',\n '<%= _.escape(ldda.get(\"file_ext\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"file_size\")) { %>',\n \"Genome build ',\n '<%= _.escape(ldda.get(\"genome_build\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"date_uploaded\")) { %>',\n \"Size ',\n '<%= _.escape(ldda.get(\"file_size\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"uploaded_by\")) { %>',\n \"Date uploaded (UTC) ',\n '<%= _.escape(ldda.get(\"date_uploaded\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"metadata_data_lines\")) { %>',\n \"Uploaded by ',\n '<%= _.escape(ldda.get(\"uploaded_by\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"metadata_comment_lines\")) { %>',\n \"Data Lines ',\n '<%= _.escape(ldda.get(\"metadata_data_lines\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"metadata_columns\")) { %>',\n \"Comment Lines ',\n '<%= _.escape(ldda.get(\"metadata_comment_lines\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"metadata_column_types\")) { %>',\n \"Number of Columns ',\n '<%= _.escape(ldda.get(\"metadata_columns\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"message\")) { %>',\n \"Column Types ',\n '<%= _.escape(ldda.get(\"metadata_column_types\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"misc_blurb\")) { %>',\n \"Message ',\n '<%= _.escape(ldda.get(\"message\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"misc_info\")) { %>',\n \"Miscellaneous blurb ',\n '<%= _.escape(ldda.get(\"misc_blurb\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"tags\")) { %>',\n \"Miscellaneous information ',\n '<%= _.escape(ldda.get(\"misc_info\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n \"Tags ',\n '<%= _.escape(item.get(\"tags\")) %> ',\n \"\",\n '\",\n // DATASET END\n \"',\n \"
\",\n \"',\n '\"\n ].join(\"\")\n );\n },\n\n templateDatasetPermissions: function() {\n return _.template(\n [\n // CONTAINER START\n '',\n '\",\n '\",\n \"\",\n\n // BREADCRUMBS\n '\",\n\n '',\n '\",\n // CONTAINER END\n \"',\n \"
\",\n \"\",\n ' \",\n \"\">Name ',\n '\"> ',\n \"\",\n ' \",\n \"Data type ',\n \"\",\n '',\n \" \",\n \"\",\n ' \",\n \"Genome build ',\n \"\",\n '',\n \" \",\n \"\",\n ' \",\n \"Size ',\n '<%= _.escape(item.get(\"file_size\")) %> ',\n \"\",\n ' \",\n \"Date uploaded (UTC) ',\n '<%= _.escape(item.get(\"date_uploaded\")) %> ',\n \"\",\n ' \",\n 'Uploaded by ',\n '<%= _.escape(item.get(\"uploaded_by\")) %> ',\n \"',\n ' \",\n 'Data Lines ',\n '<%= _.escape(item.get(\"metadata_data_lines\")) %> ',\n \"Comment Lines ',\n '<% if (item.get(\"metadata_comment_lines\") === \"\") { %>',\n '<%= _.escape(item.get(\"metadata_comment_lines\")) %> ',\n \"<% } else { %>\",\n 'unknown ',\n \"<% } %>\",\n \"\",\n \"\",\n ' \",\n \"Number of Columns ',\n '<%= _.escape(item.get(\"metadata_columns\")) %> ',\n \"\",\n ' \",\n \"Column Types ',\n '<%= _.escape(item.get(\"metadata_column_types\")) %> ',\n \"\",\n ' \",\n \"Message ',\n '<%= _.escape(item.get(\"message\")) %> ',\n \"\",\n ' \",\n \"Misc. blurb ',\n '<%= _.escape(item.get(\"misc_blurb\")) %> ',\n \"\",\n ' \",\n //TODO: add functionality to modify tags here\n '<% if (item.get(\"tags\")) { %>',\n \"Misc. information ',\n '\"> ',\n \"\",\n ' \",\n \"<% } %>\",\n \"Tags ',\n '<%= _.escape(item.get(\"tags\")) %> ',\n \"\",\n '\",\n \"',\n \"
\",\n \"',\n '\",\n\n // BREADCRUMBS\n '\",\n\n '\"\n ].join(\"\")\n );\n },\n\n templateBulkImportInModal: function() {\n return _.template(\n [\n \"Dataset: <%= _.escape(item.get(\"name\")) %>
',\n '',\n \"<% if (is_admin) { %>\",\n \"You are logged in as an administrator therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.\",\n \"<% } else { %>\",\n \"You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.\",\n \"<% } %>\",\n \"\",\n '',\n \"\",\n // CONTAINER END\n \"Library-related permissions
\",\n \"Roles that can modify the library item
\",\n '',\n 'User with any of these roles can modify name, metadata, and other information about this library item.',\n \"
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\",\n '',\n '',\n \"User has to have all these roles in order to access this dataset.\",\n \" Users without access permission cannot have other permissions on this dataset.\",\n \" If there are no access roles set on the dataset it is considered unrestricted.\",\n \"\",\n \"Roles that can manage permissions on the dataset
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[\n \"libs/toastr\",\n \"mvc/library/library-model\",\n \"utils/utils\",\n \"mvc/ui/ui-select\"\n ],\n function(mod_toastr, mod_library_model, mod_utils, mod_select) {\n var LibraryDatasetView = Backbone.View.extend({\n el: \"#center\",\n\n model: null,\n\n options: {},\n\n defaults: {\n edit_mode: false\n },\n\n events: {\n \"click .toolbtn_modify_dataset\": \"enableModification\",\n \"click .toolbtn_cancel_modifications\": \"render\",\n \"click .toolbtn-download-dataset\": \"downloadDataset\",\n \"click .toolbtn-import-dataset\": \"importIntoHistory\",\n \"click .copy-link-to-clipboard\": \"copyToClipboard\",\n \"click .make-private\": \"makeDatasetPrivate\",\n \"click .remove-restrictions\": \"removeDatasetRestrictions\",\n \"click .toolbtn_save_permissions\": \"savePermissions\",\n \"click .toolbtn_save_modifications\": \"saveModifications\"\n },\n\n // genome select\n select_genome: null,\n\n // extension select\n select_extension: null,\n\n // extension types\n list_extensions: [],\n\n // datatype placeholder for extension auto-detection\n auto: {\n id: \"auto\",\n text: \"Auto-detect\",\n description:\n \"This system will try to detect the file type automatically.\" +\n \" If your file is not detected properly as one of the known formats,\" +\n \" it most likely means that it has some format problems (e.g., different\" +\n \" number of columns on different rows). You can still coerce the system\" +\n \" to set your data to the format you think it should be.\" +\n \" You can also upload compressed files, which will automatically be decompressed.\"\n },\n\n // genomes\n list_genomes: [],\n\n initialize: function(options) {\n this.options = _.extend(this.options, options);\n this.fetchExtAndGenomes();\n if (this.options.id) {\n this.fetchDataset();\n }\n },\n\n fetchDataset: function(options) {\n this.options = _.extend(this.options, options);\n this.model = new mod_library_model.Item({\n id: this.options.id\n });\n var that = this;\n this.model.fetch({\n success: function() {\n if (that.options.show_permissions) {\n that.showPermissions();\n } else if (that.options.show_version) {\n that.fetchVersion();\n } else {\n that.render();\n }\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(\n response.responseJSON.err_msg +\n \" Click this to go back.\",\n \"\",\n {\n onclick: function() {\n Galaxy.libraries.library_router.back();\n }\n }\n );\n } else {\n mod_toastr.error(\n \"An error occurred. Click this to go back.\",\n \"\",\n {\n onclick: function() {\n Galaxy.libraries.library_router.back();\n }\n }\n );\n }\n }\n });\n },\n\n render: function(options) {\n this.options = _.extend(this.options, options);\n $(\".tooltip\").remove();\n var template = this.templateDataset();\n this.$el.html(template({ item: this.model }));\n $(\".peek\").html(this.model.get(\"peek\"));\n $(\"#center [data-toggle]\").tooltip();\n },\n\n fetchVersion: function(options) {\n this.options = _.extend(this.options, options);\n that = this;\n if (!this.options.ldda_id) {\n this.render();\n mod_toastr.error(\n \"Library dataset version requested but no id provided.\"\n );\n } else {\n this.ldda = new mod_library_model.Ldda({\n id: this.options.ldda_id\n });\n this.ldda.url =\n this.ldda.urlRoot +\n this.model.id +\n \"/versions/\" +\n this.ldda.id;\n this.ldda.fetch({\n success: function() {\n that.renderVersion();\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n }\n });\n }\n },\n\n renderVersion: function() {\n $(\".tooltip\").remove();\n var template = this.templateVersion();\n this.$el.html(template({ item: this.model, ldda: this.ldda }));\n $(\".peek\").html(this.ldda.get(\"peek\"));\n },\n\n enableModification: function() {\n $(\".tooltip\").remove();\n var template = this.templateModifyDataset();\n this.$el.html(template({ item: this.model }));\n this.renderSelectBoxes({\n genome_build: this.model.get(\"genome_build\"),\n file_ext: this.model.get(\"file_ext\")\n });\n $(\".peek\").html(this.model.get(\"peek\"));\n $(\"#center [data-toggle]\").tooltip();\n },\n\n downloadDataset: function() {\n var url =\n Galaxy.root +\n \"api/libraries/datasets/download/uncompressed\";\n var data = { ld_ids: this.id };\n this.processDownload(url, data);\n },\n\n processDownload: function(url, data, method) {\n //url and data options required\n if (url && data) {\n //data can be string of parameters or array/object\n data = typeof data == \"string\" ? data : $.param(data);\n //split params into form inputs\n var inputs = \"\";\n $.each(data.split(\"&\"), function() {\n var pair = this.split(\"=\");\n inputs +=\n '';\n });\n //send request\n $(\n '\"\n )\n .appendTo(\"body\")\n .submit()\n .remove();\n\n mod_toastr.info(\"Your download will begin soon.\");\n }\n },\n\n importIntoHistory: function() {\n this.refreshUserHistoriesList(function(self) {\n var template = self.templateBulkImportInModal();\n self.modal = Galaxy.modal;\n self.modal.show({\n closing_events: true,\n title: \"Import into History\",\n body: template({ histories: self.histories.models }),\n buttons: {\n Import: function() {\n self.importCurrentIntoHistory();\n },\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n });\n },\n\n refreshUserHistoriesList: function(callback) {\n var self = this;\n this.histories = new mod_library_model.GalaxyHistories();\n this.histories.fetch({\n success: function(histories) {\n if (histories.length === 0) {\n mod_toastr.warning(\n \"You have to create history first. Click this to do so.\",\n \"\",\n {\n onclick: function() {\n window.location = Galaxy.root;\n }\n }\n );\n } else {\n callback(self);\n }\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n }\n });\n },\n\n importCurrentIntoHistory: function() {\n this.modal.disableButton(\"Import\");\n var new_history_name = this.modal\n .$(\"input[name=history_name]\")\n .val();\n var that = this;\n if (new_history_name !== \"\") {\n $.post(Galaxy.root + \"api/histories\", {\n name: new_history_name\n })\n .done(function(new_history) {\n that.processImportToHistory(new_history.id);\n })\n .fail(function(xhr, status, error) {\n mod_toastr.error(\"An error occurred.\");\n })\n .always(function() {\n that.modal.enableButton(\"Import\");\n });\n } else {\n var history_id = $(this.modal.$el)\n .find(\n \"select[name=dataset_import_single] option:selected\"\n )\n .val();\n this.processImportToHistory(history_id);\n this.modal.enableButton(\"Import\");\n }\n },\n\n processImportToHistory: function(history_id) {\n var historyItem = new mod_library_model.HistoryItem();\n historyItem.url =\n historyItem.urlRoot + history_id + \"/contents\";\n // set the used history as current so user will see the last one\n // that he imported into in the history panel on the 'analysis' page\n jQuery.getJSON(\n Galaxy.root + \"history/set_as_current?id=\" + history_id\n );\n // save the dataset into selected history\n historyItem.save(\n { content: this.id, source: \"library\" },\n {\n success: function() {\n Galaxy.modal.hide();\n mod_toastr.success(\n \"Dataset imported. Click this to start analyzing it.\",\n \"\",\n {\n onclick: function() {\n window.location = Galaxy.root;\n }\n }\n );\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(\n \"Dataset not imported. \" +\n response.responseJSON.err_msg\n );\n } else {\n mod_toastr.error(\n \"An error occured. Dataset not imported. Please try again.\"\n );\n }\n }\n }\n );\n },\n\n showPermissions: function(options) {\n var template = this.templateDatasetPermissions();\n var self = this;\n this.options = _.extend(this.options, options);\n $(\".tooltip\").remove();\n if (this.options.fetched_permissions !== undefined) {\n if (\n this.options.fetched_permissions.access_dataset_roles\n .length === 0\n ) {\n this.model.set({ is_unrestricted: true });\n } else {\n this.model.set({ is_unrestricted: false });\n }\n }\n this.$el.html(\n template({\n item: this.model,\n is_admin: Galaxy.config.is_admin_user\n })\n );\n $.get(\n Galaxy.root +\n \"api/libraries/datasets/\" +\n self.id +\n \"/permissions?scope=current\"\n )\n .done(function(fetched_permissions) {\n self.prepareSelectBoxes({\n fetched_permissions: fetched_permissions,\n is_admin: Galaxy.config.is_admin_user\n });\n })\n .fail(function() {\n mod_toastr.error(\n \"An error occurred while attempting to fetch dataset permissions.\"\n );\n });\n $(\"#center [data-toggle]\").tooltip();\n $(\"#center\").css(\"overflow\", \"auto\");\n },\n\n _serializeRoles: function(role_list) {\n var selected_roles = [];\n for (var i = 0; i < role_list.length; i++) {\n // Replace the : and , in role's name since these are select2 separators for initialData\n selected_roles.push(\n role_list[i][1] +\n \":\" +\n role_list[i][0].replace(\":\", \" \").replace(\",\", \" &\")\n );\n }\n return selected_roles;\n },\n\n prepareSelectBoxes: function(options) {\n this.options = _.extend(this.options, options);\n this.accessSelectObject = new mod_select.View(\n this._generate_select_options({\n selector: \"access_perm\",\n initialData: this._serializeRoles(\n this.options.fetched_permissions\n .access_dataset_roles\n )\n })\n );\n this.modifySelectObject = new mod_select.View(\n this._generate_select_options({\n selector: \"modify_perm\",\n initialData: this._serializeRoles(\n this.options.fetched_permissions.modify_item_roles\n )\n })\n );\n this.manageSelectObject = new mod_select.View(\n this._generate_select_options({\n selector: \"manage_perm\",\n initialData: this._serializeRoles(\n this.options.fetched_permissions\n .manage_dataset_roles\n )\n })\n );\n },\n\n _generate_select_options: function(options) {\n var select_options = {\n minimumInputLength: 0,\n multiple: true,\n placeholder: \"Click to select a role\",\n formatResult: function roleFormatResult(role) {\n return role.name + \" type: \" + role.type;\n },\n formatSelection: function roleFormatSelection(role) {\n return role.name;\n },\n initSelection: function(element, callback) {\n // the input tag has a value attribute preloaded that points to a preselected role's id\n // this function resolves that id attribute to an object that select2 can render\n // using its formatResult renderer - that way the role name is shown preselected\n var data = [];\n $(element.val().split(\",\")).each(function() {\n var item = this.split(\":\");\n data.push({\n id: item[0],\n name: item[1]\n });\n });\n callback(data);\n },\n dropdownCssClass: \"bigdrop\" // apply css that makes the dropdown taller\n };\n select_options.container = this.$el.find(\n \"#\" + options.selector\n );\n select_options.css = options.selector;\n select_options.initialData = options.initialData.join(\",\");\n select_options.ajax = {\n url:\n Galaxy.root +\n \"api/libraries/datasets/\" +\n this.id +\n \"/permissions?scope=available\",\n dataType: \"json\",\n quietMillis: 100,\n data: function(term, page) {\n // page is the one-based page number tracked by Select2\n return {\n q: term, //search term\n page_limit: 10, // page size, should be same as used in 'more' variable below\n page: page // page number\n };\n },\n results: function(data, page) {\n var more = page * 10 < data.total; // whether or not there are more results available\n // notice we return the value of more so Select2 knows if more results can be loaded\n return { results: data.roles, more: more };\n }\n };\n return select_options;\n },\n\n /**\n * Save the changes made to the library dataset.\n */\n saveModifications: function(options) {\n var is_changed = false;\n var ld = this.model;\n var new_name = this.$el.find(\".input_dataset_name\").val();\n if (\n typeof new_name !== \"undefined\" &&\n new_name !== ld.get(\"name\")\n ) {\n if (new_name.length > 0) {\n ld.set(\"name\", new_name);\n is_changed = true;\n } else {\n mod_toastr.warning(\n \"Library dataset name has to be at least 1 character long.\"\n );\n return;\n }\n }\n var new_info = this.$el.find(\".input_dataset_misc_info\").val();\n if (\n typeof new_info !== \"undefined\" &&\n new_info !== ld.get(\"misc_info\")\n ) {\n ld.set(\"misc_info\", new_info);\n is_changed = true;\n }\n var new_genome_build = this.select_genome.$el.select2(\"data\")\n .id;\n if (\n typeof new_genome_build !== \"undefined\" &&\n new_genome_build !== ld.get(\"genome_build\")\n ) {\n ld.set(\"genome_build\", new_genome_build);\n is_changed = true;\n }\n var new_ext = this.select_extension.$el.select2(\"data\").id;\n if (\n typeof new_ext !== \"undefined\" &&\n new_ext !== ld.get(\"file_ext\")\n ) {\n ld.set(\"file_ext\", new_ext);\n is_changed = true;\n }\n var dataset_view = this;\n if (is_changed) {\n ld.save(null, {\n patch: true,\n success: function(ld) {\n dataset_view.render();\n mod_toastr.success(\n \"Changes to library dataset saved.\"\n );\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\n \"An error occured while attempting to update the library dataset.\"\n );\n }\n }\n });\n } else {\n dataset_view.render();\n mod_toastr.info(\"Nothing has changed.\");\n }\n },\n\n copyToClipboard: function() {\n var href = Backbone.history.location.href;\n if (href.lastIndexOf(\"/permissions\") !== -1) {\n href = href.substr(0, href.lastIndexOf(\"/permissions\"));\n }\n window.prompt(\"Copy to clipboard: Ctrl+C, Enter\", href);\n },\n\n makeDatasetPrivate: function() {\n var self = this;\n $.post(\n Galaxy.root +\n \"api/libraries/datasets/\" +\n self.id +\n \"/permissions?action=make_private\"\n )\n .done(function(fetched_permissions) {\n self.model.set({ is_unrestricted: false });\n self.showPermissions({\n fetched_permissions: fetched_permissions\n });\n mod_toastr.success(\n \"The dataset is now private to you.\"\n );\n })\n .fail(function() {\n mod_toastr.error(\n \"An error occurred while attempting to make dataset private.\"\n );\n });\n },\n\n removeDatasetRestrictions: function() {\n var self = this;\n $.post(\n Galaxy.root +\n \"api/libraries/datasets/\" +\n self.id +\n \"/permissions?action=remove_restrictions\"\n )\n .done(function(fetched_permissions) {\n self.model.set({ is_unrestricted: true });\n self.showPermissions({\n fetched_permissions: fetched_permissions\n });\n mod_toastr.success(\n \"Access to this dataset is now unrestricted.\"\n );\n })\n .fail(function() {\n mod_toastr.error(\n \"An error occurred while attempting to make dataset unrestricted.\"\n );\n });\n },\n\n /**\n * Extract the role ids from Select2 elements's 'data'\n */\n _extractIds: function(roles_list) {\n var ids_list = [];\n for (var i = roles_list.length - 1; i >= 0; i--) {\n ids_list.push(roles_list[i].id);\n }\n return ids_list;\n },\n\n /**\n * Save the permissions for roles entered in the select boxes.\n */\n savePermissions: function(event) {\n var self = this;\n var access_ids = this._extractIds(\n this.accessSelectObject.$el.select2(\"data\")\n );\n var manage_ids = this._extractIds(\n this.manageSelectObject.$el.select2(\"data\")\n );\n var modify_ids = this._extractIds(\n this.modifySelectObject.$el.select2(\"data\")\n );\n $.post(\n Galaxy.root +\n \"api/libraries/datasets/\" +\n self.id +\n \"/permissions?action=set_permissions\",\n {\n \"access_ids[]\": access_ids,\n \"manage_ids[]\": manage_ids,\n \"modify_ids[]\": modify_ids\n }\n )\n .done(function(fetched_permissions) {\n self.showPermissions({\n fetched_permissions: fetched_permissions\n });\n mod_toastr.success(\"Permissions saved.\");\n })\n .fail(function() {\n mod_toastr.error(\n \"An error occurred while attempting to set dataset permissions.\"\n );\n });\n },\n\n /**\n * If needed request all extensions and/or genomes from Galaxy\n * and save them in sorted arrays.\n */\n fetchExtAndGenomes: function() {\n var that = this;\n if (this.list_genomes.length == 0) {\n mod_utils.get({\n url: Galaxy.root + \"api/datatypes?extension_only=False\",\n success: function(datatypes) {\n for (var key in datatypes) {\n that.list_extensions.push({\n id: datatypes[key].extension,\n text: datatypes[key].extension,\n description: datatypes[key].description,\n description_url:\n datatypes[key].description_url\n });\n }\n that.list_extensions.sort(function(a, b) {\n return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;\n });\n that.list_extensions.unshift(that.auto);\n }\n });\n }\n if (this.list_extensions.length == 0) {\n mod_utils.get({\n url: Galaxy.root + \"api/genomes\",\n success: function(genomes) {\n for (var key in genomes) {\n that.list_genomes.push({\n id: genomes[key][1],\n text: genomes[key][0]\n });\n }\n that.list_genomes.sort(function(a, b) {\n return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;\n });\n }\n });\n }\n },\n\n renderSelectBoxes: function(options) {\n // This won't work properly unlesss we already have the data fetched.\n // See this.fetchExtAndGenomes()\n // TODO switch to common resources:\n // https://trello.com/c/dIUE9YPl/1933-ui-common-resources-and-data-into-galaxy-object\n var that = this;\n var current_genome = \"?\";\n var current_ext = \"auto\";\n if (typeof options !== \"undefined\") {\n if (typeof options.genome_build !== \"undefined\") {\n current_genome = options.genome_build;\n }\n if (typeof options.file_ext !== \"undefined\") {\n current_ext = options.file_ext;\n }\n }\n this.select_genome = new mod_select.View({\n css: \"dataset-genome-select\",\n data: that.list_genomes,\n container: that.$el.find(\"#dataset_genome_select\"),\n value: current_genome\n });\n this.select_extension = new mod_select.View({\n css: \"dataset-extension-select\",\n data: that.list_extensions,\n container: that.$el.find(\"#dataset_extension_select\"),\n value: current_ext\n });\n },\n\n templateDataset: function() {\n return _.template(\n [\n // CONTAINER START\n '',\n \"Select history: \",\n '\",\n \"\",\n '',\n \"or create new: \",\n '',\n \"\",\n \"\",\n \"',\n '\"\n ].join(\"\")\n );\n },\n\n templateVersion: function() {\n return _.template(\n [\n // CONTAINER START\n '',\n '\",\n '\",\n '<% if (item.get(\"can_user_modify\")) { %>',\n '\",\n \"<% } %>\",\n '<% if (item.get(\"can_user_manage\")) { %>',\n '/datasets/<%- item.id %>/permissions\">',\n '\",\n \"\",\n \"<% } %>\",\n \"\",\n\n // BREADCRUMBS\n '\",\n\n '<% if (item.get(\"is_unrestricted\")) { %>',\n \"\",\n 'This dataset is unrestricted so everybody with the link can access it. Just share this page.',\n \"\",\n \"<% } %>\",\n\n // TABLE START\n '',\n '\",\n // CONTAINER END\n \"',\n \"
\",\n\n \"\",\n ' \",\n '<% if (item.get(\"file_ext\")) { %>',\n \"\">Name ',\n '<%= _.escape(item.get(\"name\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"genome_build\")) { %>',\n \"Data type ',\n '<%= _.escape(item.get(\"file_ext\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"file_size\")) { %>',\n \"Genome build ',\n '<%= _.escape(item.get(\"genome_build\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"date_uploaded\")) { %>',\n \"Size ',\n '<%= _.escape(item.get(\"file_size\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"uploaded_by\")) { %>',\n \"Date uploaded (UTC) ',\n '<%= _.escape(item.get(\"date_uploaded\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"metadata_data_lines\")) { %>',\n \"Uploaded by ',\n '<%= _.escape(item.get(\"uploaded_by\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"metadata_comment_lines\")) { %>',\n \"Data Lines ',\n '<%= _.escape(item.get(\"metadata_data_lines\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"metadata_columns\")) { %>',\n \"Comment Lines ',\n '<%= _.escape(item.get(\"metadata_comment_lines\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"metadata_column_types\")) { %>',\n \"Number of Columns ',\n '<%= _.escape(item.get(\"metadata_columns\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"message\")) { %>',\n \"Column Types ',\n '<%= _.escape(item.get(\"metadata_column_types\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"misc_blurb\")) { %>',\n \"Message ',\n '<%= _.escape(item.get(\"message\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"misc_info\")) { %>',\n \"Misc. blurb ',\n '<%= _.escape(item.get(\"misc_blurb\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"tags\")) { %>',\n \"Misc. info ',\n '<%= _.escape(item.get(\"misc_info\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n \"Tags ',\n '<%= _.escape(item.get(\"tags\")) %> ',\n \"\",\n '\",\n\n '<% if (item.get(\"has_versions\")) { %>',\n \"',\n \"
\",\n \"\",\n \"\",\n \"<% } %>\",\n // TABLE END\n \"Expired versions:
\",\n \"- \",\n '<% _.each(item.get(\"expired_versions\"), function(version) { %>',\n '
- \",\n \"
',\n '\",\n\n // BREADCRUMBS\n '\",\n\n '\"\n ].join(\"\")\n );\n },\n\n templateModifyDataset: function() {\n return _.template(\n [\n // CONTAINER START\n 'This is an expired version of the library dataset: <%= _.escape(item.get(\"name\")) %>',\n // DATASET START\n '',\n '\",\n // CONTAINER END\n \"',\n \"
\",\n \"\",\n ' \",\n '<% if (ldda.get(\"file_ext\")) { %>',\n \"\">Name ',\n '<%= _.escape(ldda.get(\"name\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"genome_build\")) { %>',\n \"Data type ',\n '<%= _.escape(ldda.get(\"file_ext\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"file_size\")) { %>',\n \"Genome build ',\n '<%= _.escape(ldda.get(\"genome_build\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"date_uploaded\")) { %>',\n \"Size ',\n '<%= _.escape(ldda.get(\"file_size\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"uploaded_by\")) { %>',\n \"Date uploaded (UTC) ',\n '<%= _.escape(ldda.get(\"date_uploaded\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"metadata_data_lines\")) { %>',\n \"Uploaded by ',\n '<%= _.escape(ldda.get(\"uploaded_by\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"metadata_comment_lines\")) { %>',\n \"Data Lines ',\n '<%= _.escape(ldda.get(\"metadata_data_lines\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"metadata_columns\")) { %>',\n \"Comment Lines ',\n '<%= _.escape(ldda.get(\"metadata_comment_lines\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"metadata_column_types\")) { %>',\n \"Number of Columns ',\n '<%= _.escape(ldda.get(\"metadata_columns\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"message\")) { %>',\n \"Column Types ',\n '<%= _.escape(ldda.get(\"metadata_column_types\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"misc_blurb\")) { %>',\n \"Message ',\n '<%= _.escape(ldda.get(\"message\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (ldda.get(\"misc_info\")) { %>',\n \"Miscellaneous blurb ',\n '<%= _.escape(ldda.get(\"misc_blurb\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n '<% if (item.get(\"tags\")) { %>',\n \"Miscellaneous information ',\n '<%= _.escape(ldda.get(\"misc_info\")) %> ',\n \"\",\n ' \",\n \"<% } %>\",\n \"Tags ',\n '<%= _.escape(item.get(\"tags\")) %> ',\n \"\",\n '\",\n // DATASET END\n \"',\n \"
\",\n \"',\n '\"\n ].join(\"\")\n );\n },\n\n templateDatasetPermissions: function() {\n return _.template(\n [\n // CONTAINER START\n '',\n '\",\n '\",\n \"\",\n\n // BREADCRUMBS\n '\",\n\n '',\n '\",\n // CONTAINER END\n \"',\n \"
\",\n \"\",\n ' \",\n \"\">Name ',\n '\"> ',\n \"\",\n ' \",\n \"Data type ',\n \"\",\n '',\n \" \",\n \"\",\n ' \",\n \"Genome build ',\n \"\",\n '',\n \" \",\n \"\",\n ' \",\n \"Size ',\n '<%= _.escape(item.get(\"file_size\")) %> ',\n \"\",\n ' \",\n \"Date uploaded (UTC) ',\n '<%= _.escape(item.get(\"date_uploaded\")) %> ',\n \"\",\n ' \",\n 'Uploaded by ',\n '<%= _.escape(item.get(\"uploaded_by\")) %> ',\n \"',\n ' \",\n 'Data Lines ',\n '<%= _.escape(item.get(\"metadata_data_lines\")) %> ',\n \"Comment Lines ',\n '<% if (item.get(\"metadata_comment_lines\") === \"\") { %>',\n '<%= _.escape(item.get(\"metadata_comment_lines\")) %> ',\n \"<% } else { %>\",\n 'unknown ',\n \"<% } %>\",\n \"\",\n \"\",\n ' \",\n \"Number of Columns ',\n '<%= _.escape(item.get(\"metadata_columns\")) %> ',\n \"\",\n ' \",\n \"Column Types ',\n '<%= _.escape(item.get(\"metadata_column_types\")) %> ',\n \"\",\n ' \",\n \"Message ',\n '<%= _.escape(item.get(\"message\")) %> ',\n \"\",\n ' \",\n \"Misc. blurb ',\n '<%= _.escape(item.get(\"misc_blurb\")) %> ',\n \"\",\n ' \",\n //TODO: add functionality to modify tags here\n '<% if (item.get(\"tags\")) { %>',\n \"Misc. information ',\n '\"> ',\n \"\",\n ' \",\n \"<% } %>\",\n \"Tags ',\n '<%= _.escape(item.get(\"tags\")) %> ',\n \"\",\n '\",\n \"',\n \"
\",\n \"',\n '\",\n\n // BREADCRUMBS\n '\",\n\n '\"\n ].join(\"\")\n );\n },\n\n templateBulkImportInModal: function() {\n return _.template(\n [\n \"Dataset: <%= _.escape(item.get(\"name\")) %>
',\n '',\n \"<% if (is_admin) { %>\",\n \"You are logged in as an administrator therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.\",\n \"<% } else { %>\",\n \"You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.\",\n \"<% } %>\",\n \"\",\n '',\n \"\",\n // CONTAINER END\n \"Library-related permissions
\",\n \"Roles that can modify the library item
\",\n '',\n 'User with any of these roles can modify name, metadata, and other information about this library item.',\n \"
\",\n \"Dataset-related permissions
\",\n 'Changes made below will affect every library item that was created from this dataset and also every history this dataset is part of.',\n '<% if (!item.get(\"is_unrestricted\")) { %>',\n 'You can remove all access restrictions on this dataset.
',\n \"<% } else { %>\",\n 'You can make this dataset private to you.
',\n \"<% } %>\",\n \"Roles that can access the dataset
\",\n '',\n '',\n \"User has to have all these roles in order to access this dataset.\",\n \" Users without access permission cannot have other permissions on this dataset.\",\n \" If there are no access roles set on the dataset it is considered unrestricted.\",\n \"\",\n \"Roles that can manage permissions on the dataset
\",\n '',\n '',\n \"User with any of these roles can manage permissions of this dataset. If you remove yourself you will lose the ability manage this dataset unless you are an admin.\",\n \"\",\n '\",\n \"\",\n '\"\n ].join(\"\")\n );\n }\n });\n\n return {\n LibraryDatasetView: LibraryDatasetView\n };\n }\n);\n"]} \ No newline at end of file diff --git a/static/maps/mvc/library/library-folder-view.js.map b/static/maps/mvc/library/library-folder-view.js.map index 420616fa6cf..17e8cec435c 100644 --- a/static/maps/mvc/library/library-folder-view.js.map +++ b/static/maps/mvc/library/library-folder-view.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/library/library-folder-view.js"],"names":["define","mod_toastr","mod_library_model","mod_select","FolderView","Backbone","View","extend","el","model","options","events","click 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[\"libs/toastr\", \"mvc/library/library-model\", \"mvc/ui/ui-select\"],\n function(mod_toastr, mod_library_model, mod_select) {\n var FolderView = Backbone.View.extend({\n el: \"#center\",\n\n model: null,\n\n options: {},\n\n events: {\n \"click .toolbtn_save_permissions\": \"savePermissions\"\n },\n\n initialize: function(options) {\n this.options = _.extend(this.options, options);\n if (this.options.id) {\n this.fetchFolder();\n }\n },\n\n fetchFolder: function(options) {\n this.options = _.extend(this.options, options);\n this.model = new mod_library_model.FolderAsModel({\n id: this.options.id\n });\n var that = this;\n this.model.fetch({\n success: function() {\n if (that.options.show_permissions) {\n that.showPermissions();\n }\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(\n response.responseJSON.err_msg +\n \" Click this to go back.\",\n \"\",\n {\n onclick: function() {\n Galaxy.libraries.library_router.back();\n }\n }\n );\n } else {\n mod_toastr.error(\n \"An error occurred. Click this to go back.\",\n \"\",\n {\n onclick: function() {\n Galaxy.libraries.library_router.back();\n }\n }\n );\n }\n }\n });\n },\n\n showPermissions: function(options) {\n this.options = _.extend(this.options, options);\n $(\".tooltip\").remove();\n\n var is_admin = false;\n if (Galaxy.user) {\n is_admin = Galaxy.user.isAdmin();\n }\n var template = this.templateFolderPermissions();\n this.$el.html(\n template({ folder: this.model, is_admin: is_admin })\n );\n\n var self = this;\n $.get(\n Galaxy.root +\n \"api/folders/\" +\n self.id +\n \"/permissions?scope=current\"\n )\n .done(function(fetched_permissions) {\n self.prepareSelectBoxes({\n fetched_permissions: fetched_permissions\n });\n })\n .fail(function() {\n mod_toastr.error(\n \"An error occurred while attempting to fetch folder permissions.\"\n );\n });\n\n $(\"#center [data-toggle]\").tooltip();\n //hack to show scrollbars\n $(\"#center\").css(\"overflow\", \"auto\");\n },\n\n _serializeRoles: function(role_list) {\n var selected_roles = [];\n for (var i = 0; i < role_list.length; i++) {\n selected_roles.push(\n role_list[i][1] + \":\" + role_list[i][0]\n );\n }\n return selected_roles;\n },\n\n prepareSelectBoxes: function(options) {\n this.options = _.extend(this.options, options);\n var fetched_permissions = this.options.fetched_permissions;\n var self = this;\n\n var selected_add_item_roles = this._serializeRoles(\n fetched_permissions.add_library_item_role_list\n );\n var selected_manage_folder_roles = this._serializeRoles(\n fetched_permissions.manage_folder_role_list\n );\n var selected_modify_folder_roles = this._serializeRoles(\n fetched_permissions.modify_folder_role_list\n );\n\n self.addSelectObject = new mod_select.View(\n this._createSelectOptions(\n this,\n \"add_perm\",\n selected_add_item_roles,\n false\n )\n );\n self.manageSelectObject = new mod_select.View(\n this._createSelectOptions(\n this,\n \"manage_perm\",\n selected_manage_folder_roles,\n false\n )\n );\n self.modifySelectObject = new mod_select.View(\n this._createSelectOptions(\n this,\n \"modify_perm\",\n selected_modify_folder_roles,\n false\n )\n );\n },\n\n _createSelectOptions: function(self, id, init_data) {\n var select_options = {\n minimumInputLength: 0,\n css: id,\n multiple: true,\n placeholder: \"Click to select a role\",\n container: self.$el.find(\"#\" + id),\n ajax: {\n url:\n Galaxy.root +\n \"api/folders/\" +\n self.id +\n \"/permissions?scope=available\",\n dataType: \"json\",\n quietMillis: 100,\n data: function(term, page) {\n // page is the one-based page number tracked by Select2\n return {\n q: term, //search term\n page_limit: 10, // page size\n page: page // page number\n };\n },\n results: function(data, page) {\n var more = page * 10 < data.total; // whether or not there are more results available\n // notice we return the value of more so Select2 knows if more results can be loaded\n return { results: data.roles, more: more };\n }\n },\n formatResult: function roleFormatResult(role) {\n return role.name + \" type: \" + role.type;\n },\n\n formatSelection: function roleFormatSelection(role) {\n return role.name;\n },\n initSelection: function(element, callback) {\n // the input tag has a value attribute preloaded that points to a preselected role's id\n // this function resolves that id attribute to an object that select2 can render\n // using its formatResult renderer - that way the role name is shown preselected\n var data = [];\n $(element.val().split(\",\")).each(function() {\n var item = this.split(\":\");\n data.push({\n id: item[0],\n name: item[1]\n });\n });\n callback(data);\n },\n initialData: init_data.join(\",\"),\n dropdownCssClass: \"bigdrop\" // apply css that makes the dropdown taller\n };\n\n return select_options;\n },\n\n /**\n * Extract the role ids from Select2 elements's 'data'\n */\n _extractIds: function(roles_list) {\n var ids_list = [];\n for (var i = roles_list.length - 1; i >= 0; i--) {\n ids_list.push(roles_list[i].id);\n }\n return ids_list;\n },\n\n /**\n * Save the permissions for roles entered in the select boxes.\n */\n savePermissions: function(event) {\n var self = this;\n var add_ids = this._extractIds(\n this.addSelectObject.$el.select2(\"data\")\n );\n var manage_ids = this._extractIds(\n this.manageSelectObject.$el.select2(\"data\")\n );\n var modify_ids = this._extractIds(\n this.modifySelectObject.$el.select2(\"data\")\n );\n $.post(\n Galaxy.root +\n \"api/folders/\" +\n self.id +\n \"/permissions?action=set_permissions\",\n {\n \"add_ids[]\": add_ids,\n \"manage_ids[]\": manage_ids,\n \"modify_ids[]\": modify_ids\n }\n )\n .done(function(fetched_permissions) {\n self.showPermissions({\n fetched_permissions: fetched_permissions\n });\n mod_toastr.success(\"Permissions saved.\");\n })\n .fail(function() {\n mod_toastr.error(\n \"An error occurred while attempting to set folder permissions.\"\n );\n });\n },\n\n templateFolderPermissions: function() {\n return _.template(\n [\n '',\n \"Select history: \",\n '\",\n \"\",\n '',\n \"or create new: \",\n '',\n \"\",\n \"\",\n \"',\n '\"\n ].join(\"\")\n );\n }\n });\n\n return {\n FolderView: FolderView\n };\n }\n);\n"]} \ No newline at end of file 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[\"libs/toastr\", \"mvc/library/library-model\", \"mvc/ui/ui-select\"],\n function(mod_toastr, mod_library_model, mod_select) {\n var FolderView = Backbone.View.extend({\n el: \"#center\",\n\n model: null,\n\n options: {},\n\n events: {\n \"click .toolbtn_save_permissions\": \"savePermissions\"\n },\n\n initialize: function(options) {\n this.options = _.extend(this.options, options);\n if (this.options.id) {\n this.fetchFolder();\n }\n },\n\n fetchFolder: function(options) {\n this.options = _.extend(this.options, options);\n this.model = new mod_library_model.FolderAsModel({\n id: this.options.id\n });\n var that = this;\n this.model.fetch({\n success: function() {\n if (that.options.show_permissions) {\n that.showPermissions();\n }\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(\n response.responseJSON.err_msg +\n \" Click this to go back.\",\n \"\",\n {\n onclick: function() {\n Galaxy.libraries.library_router.back();\n }\n }\n );\n } else {\n mod_toastr.error(\n \"An error occurred. Click this to go back.\",\n \"\",\n {\n onclick: function() {\n Galaxy.libraries.library_router.back();\n }\n }\n );\n }\n }\n });\n },\n\n showPermissions: function(options) {\n this.options = _.extend(this.options, options);\n $(\".tooltip\").remove();\n\n var is_admin = false;\n if (Galaxy.user) {\n is_admin = Galaxy.user.isAdmin();\n }\n var template = this.templateFolderPermissions();\n this.$el.html(\n template({ folder: this.model, is_admin: is_admin })\n );\n\n var self = this;\n $.get(\n Galaxy.root +\n \"api/folders/\" +\n self.id +\n \"/permissions?scope=current\"\n )\n .done(function(fetched_permissions) {\n self.prepareSelectBoxes({\n fetched_permissions: fetched_permissions\n });\n })\n .fail(function() {\n mod_toastr.error(\n \"An error occurred while attempting to fetch folder permissions.\"\n );\n });\n\n $(\"#center [data-toggle]\").tooltip();\n //hack to show scrollbars\n $(\"#center\").css(\"overflow\", \"auto\");\n },\n\n _serializeRoles: function(role_list) {\n var selected_roles = [];\n for (var i = 0; i < role_list.length; i++) {\n selected_roles.push(\n role_list[i][1] + \":\" + role_list[i][0]\n );\n }\n return selected_roles;\n },\n\n prepareSelectBoxes: function(options) {\n this.options = _.extend(this.options, options);\n var fetched_permissions = this.options.fetched_permissions;\n var self = this;\n\n var selected_add_item_roles = this._serializeRoles(\n fetched_permissions.add_library_item_role_list\n );\n var selected_manage_folder_roles = this._serializeRoles(\n fetched_permissions.manage_folder_role_list\n );\n var selected_modify_folder_roles = this._serializeRoles(\n fetched_permissions.modify_folder_role_list\n );\n\n self.addSelectObject = new mod_select.View(\n this._createSelectOptions(\n this,\n \"add_perm\",\n selected_add_item_roles,\n false\n )\n );\n self.manageSelectObject = new mod_select.View(\n this._createSelectOptions(\n this,\n \"manage_perm\",\n selected_manage_folder_roles,\n false\n )\n );\n self.modifySelectObject = new mod_select.View(\n this._createSelectOptions(\n this,\n \"modify_perm\",\n selected_modify_folder_roles,\n false\n )\n );\n },\n\n _createSelectOptions: function(self, id, init_data) {\n var select_options = {\n minimumInputLength: 0,\n css: id,\n multiple: true,\n placeholder: \"Click to select a role\",\n container: self.$el.find(\"#\" + id),\n ajax: {\n url:\n Galaxy.root +\n \"api/folders/\" +\n self.id +\n \"/permissions?scope=available\",\n dataType: \"json\",\n quietMillis: 100,\n data: function(term, page) {\n // page is the one-based page number tracked by Select2\n return {\n q: term, //search term\n page_limit: 10, // page size\n page: page // page number\n };\n },\n results: function(data, page) {\n var more = page * 10 < data.total; // whether or not there are more results available\n // notice we return the value of more so Select2 knows if more results can be loaded\n return { results: data.roles, more: more };\n }\n },\n formatResult: function roleFormatResult(role) {\n return role.name + \" type: \" + role.type;\n },\n\n formatSelection: function roleFormatSelection(role) {\n return role.name;\n },\n initSelection: function(element, callback) {\n // the input tag has a value attribute preloaded that points to a preselected role's id\n // this function resolves that id attribute to an object that select2 can render\n // using its formatResult renderer - that way the role name is shown preselected\n var data = [];\n $(element.val().split(\",\")).each(function() {\n var item = this.split(\":\");\n data.push({\n id: item[0],\n name: item[1]\n });\n });\n callback(data);\n },\n initialData: init_data.join(\",\"),\n dropdownCssClass: \"bigdrop\" // apply css that makes the dropdown taller\n };\n\n return select_options;\n },\n\n /**\n * Extract the role ids from Select2 elements's 'data'\n */\n _extractIds: function(roles_list) {\n var ids_list = [];\n for (var i = roles_list.length - 1; i >= 0; i--) {\n ids_list.push(roles_list[i].id);\n }\n return ids_list;\n },\n\n /**\n * Save the permissions for roles entered in the select boxes.\n */\n savePermissions: function(event) {\n var self = this;\n var add_ids = this._extractIds(\n this.addSelectObject.$el.select2(\"data\")\n );\n var manage_ids = this._extractIds(\n this.manageSelectObject.$el.select2(\"data\")\n );\n var modify_ids = this._extractIds(\n this.modifySelectObject.$el.select2(\"data\")\n );\n $.post(\n Galaxy.root +\n \"api/folders/\" +\n self.id +\n \"/permissions?action=set_permissions\",\n {\n \"add_ids[]\": add_ids,\n \"manage_ids[]\": manage_ids,\n \"modify_ids[]\": modify_ids\n }\n )\n .done(function(fetched_permissions) {\n self.showPermissions({\n fetched_permissions: fetched_permissions\n });\n mod_toastr.success(\"Permissions saved.\");\n })\n .fail(function() {\n mod_toastr.error(\n \"An error occurred while attempting to set folder permissions.\"\n );\n });\n },\n\n templateFolderPermissions: function() {\n return _.template(\n [\n '',\n '\">',\n '\",\n \"\",\n \"\",\n \"\",\n 'Folder: <%= _.escape(folder.get(\"name\")) %>',\n \"
\",\n '',\n \"<% if (is_admin) { %>\",\n \"You are logged in as an administrator therefore you can manage any folder on this Galaxy instance. Please make sure you understand the consequences.\",\n \"<% } else { %>\",\n \"You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.\",\n \"<% }%>\",\n \"\",\n '',\n \"\",\n \"Folder permissions
\",\n \"\",\n \"Roles that can manage permissions on this folder\",\n \"
\",\n '',\n '',\n \"User with any of these roles can manage permissions on this folder.\",\n \"\",\n \"\",\n \"Roles that can add items to this folder\",\n \"
\",\n '',\n '',\n \"User with any of these roles can add items to this folder (folders and datasets).\",\n \"\",\n \"\",\n \"Roles that can modify this folder\",\n \"
\",\n '',\n '',\n \"User with any of these roles can modify this folder (name, etc.).\",\n \"\",\n '\",\n \"',\n '\"\n ].join(\"\")\n );\n }\n });\n\n return {\n FolderView: FolderView\n };\n }\n);\n"]} \ No newline at end of file diff --git a/static/maps/mvc/library/library-folderlist-view.js.map b/static/maps/mvc/library/library-folderlist-view.js.map index 6b0b70b4ff2..5f2421933ba 100644 --- a/static/maps/mvc/library/library-folderlist-view.js.map +++ b/static/maps/mvc/library/library-folderlist-view.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/library/library-folderlist-view.js"],"names":["define","FolderListView","el","progress","folderContainer","mod_utils","sort","mod_library_model","events","mod_library_dataset_view","Backbone","View","extend","progressStep","include_deleted","show_page","click #select-all-checkboxes","click .dataset_row","click .folder_row","click 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[\n \"layout/masthead\",\n \"utils/utils\",\n \"libs/toastr\",\n \"mvc/library/library-model\",\n \"mvc/library/library-folderrow-view\",\n \"mvc/library/library-dataset-view\"\n ],\n function(\n mod_masthead,\n mod_utils,\n mod_toastr,\n mod_library_model,\n mod_library_folderrow_view,\n mod_library_dataset_view\n ) {\n var FolderListView = Backbone.View.extend({\n el: \"#folder_items_element\",\n // progress percentage\n progress: 0,\n // progress rate per one item\n progressStep: 1,\n\n folderContainer: null,\n\n sort: \"asc\",\n\n events: {\n \"click #select-all-checkboxes\": \"selectAll\",\n \"click .dataset_row\": \"selectClickedRow\",\n \"click .folder_row\": \"selectClickedRow\",\n \"click .sort-folder-link\": \"sortColumnClicked\"\n },\n\n collection: null,\n\n defaults: {\n include_deleted: false,\n page_count: null,\n show_page: null\n },\n\n /**\n * Initialize and fetch the folder from the server.\n * @param {object} options an object with options\n */\n initialize: function(options) {\n this.options = _.defaults(\n this.options || {},\n this.defaults,\n options\n );\n this.modal = null;\n // map of folder item ids to item views = cache\n this.rowViews = {};\n\n // create a collection of folder items for this view\n this.collection = new mod_library_model.Folder();\n\n // start to listen if someone modifies the collection\n this.listenTo(this.collection, \"add\", this.renderOne);\n this.listenTo(this.collection, \"remove\", this.removeOne);\n this.listenTo(this.collection, \"sort\", this.rePaint);\n this.listenTo(this.collection, \"reset\", this.rePaint);\n\n this.fetchFolder();\n },\n\n fetchFolder: function(options) {\n var options = options || {};\n this.options.include_deleted = options.include_deleted;\n var that = this;\n\n this.folderContainer = new mod_library_model.FolderContainer({\n id: this.options.id\n });\n this.folderContainer.url =\n this.folderContainer.attributes.urlRoot +\n this.options.id +\n \"/contents\";\n\n if (this.options.include_deleted) {\n this.folderContainer.url =\n this.folderContainer.url + \"?include_deleted=true\";\n }\n this.folderContainer.fetch({\n success: function(folder_container) {\n that.folder_container = folder_container;\n that.render();\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(\n response.responseJSON.err_msg +\n \" Click this to go back.\",\n \"\",\n {\n onclick: function() {\n Galaxy.libraries.library_router.back();\n }\n }\n );\n } else {\n mod_toastr.error(\n \"An error occurred. Click this to go back.\",\n \"\",\n {\n onclick: function() {\n Galaxy.libraries.library_router.back();\n }\n }\n );\n }\n }\n });\n },\n\n render: function(options) {\n this.options = _.extend(this.options, options);\n var template = this.templateFolder();\n $(\".tooltip\").hide();\n\n // find the upper id in the full path\n var path = this.folderContainer.attributes.metadata.full_path;\n var upper_folder_id;\n if (path.length === 1) {\n // the library is above us\n upper_folder_id = 0;\n } else {\n upper_folder_id = path[path.length - 2][0];\n }\n\n this.$el.html(\n template({\n path: this.folderContainer.attributes.metadata\n .full_path,\n parent_library_id: this.folderContainer.attributes\n .metadata.parent_library_id,\n id: this.options.id,\n upper_folder_id: upper_folder_id,\n order: this.sort\n })\n );\n\n // when dataset_id is present render its details too\n if (this.options.dataset_id) {\n var row = _.findWhere(that.rowViews, {\n id: this.options.dataset_id\n });\n if (row) {\n row.showDatasetDetails();\n } else {\n mod_toastr.error(\n \"Requested dataset not found. Showing folder instead.\"\n );\n }\n } else {\n if (\n this.options.show_page === null ||\n this.options.show_page < 1\n ) {\n this.options.show_page = 1;\n }\n this.paginate();\n }\n $(\"#center [data-toggle]\").tooltip();\n $(\"#center\").css(\"overflow\", \"auto\");\n },\n\n paginate: function(options) {\n this.options = _.extend(this.options, options);\n\n if (\n this.options.show_page === null ||\n this.options.show_page < 1\n ) {\n this.options.show_page = 1;\n }\n this.options.total_items_count = this.folder_container.get(\n \"folder\"\n ).models.length;\n this.options.page_count = Math.ceil(\n this.options.total_items_count /\n Galaxy.libraries.preferences.get(\"folder_page_size\")\n );\n var page_start =\n Galaxy.libraries.preferences.get(\"folder_page_size\") *\n (this.options.show_page - 1);\n var items_to_render = null;\n items_to_render = this.folder_container\n .get(\"folder\")\n .models.slice(\n page_start,\n page_start +\n Galaxy.libraries.preferences.get(\"folder_page_size\")\n );\n this.options.items_shown = items_to_render.length;\n // User requests page with no items\n if (\n Galaxy.libraries.preferences.get(\"folder_page_size\") *\n this.options.show_page >\n this.options.total_items_count +\n Galaxy.libraries.preferences.get(\"folder_page_size\")\n ) {\n items_to_render = [];\n }\n Galaxy.libraries.folderToolbarView.renderPaginator(\n this.options\n );\n this.collection.reset(items_to_render);\n },\n\n rePaint: function(options) {\n this.options = _.extend(this.options, options);\n this.removeAllRows();\n this.renderAll();\n this.checkEmptiness();\n },\n\n /**\n * Adds all given models to the collection.\n * @param {array of Item or FolderAsModel} array of models that should\n * be added to the view's collection.\n */\n addAll: function(models) {\n _.each(models, function(model) {\n Galaxy.libraries.folderListView.collection.add(model, {\n sort: false\n });\n });\n $(\"#center [data-toggle]\").tooltip();\n this.checkEmptiness();\n this.postRender();\n },\n\n /**\n * Call this after all models are added to the collection\n * to ensure that the folder toolbar will show proper options\n * and that event will be bound on all subviews.\n */\n postRender: function() {\n var fetched_metadata = this.folderContainer.attributes.metadata;\n fetched_metadata.contains_file_or_folder =\n typeof this.collection.findWhere({ type: \"file\" }) !==\n \"undefined\" ||\n typeof this.collection.findWhere({ type: \"folder\" }) !==\n \"undefined\";\n Galaxy.libraries.folderToolbarView.configureElements(\n fetched_metadata\n );\n },\n\n /**\n * Iterates this view's collection and calls the render\n * function for each. Also binds the hover behavior.\n */\n renderAll: function() {\n var that = this;\n _.each(this.collection.models.reverse(), function(model) {\n that.renderOne(model);\n });\n this.postRender();\n },\n\n /**\n * Creates a view for the given model and adds it to the folder view.\n * @param {Item or FolderAsModel} model of the view that will be rendered\n */\n renderOne: function(model) {\n this.options.contains_file_or_folder = true;\n //if (model.get('type') !== 'folder'){\n // model.set('readable_size', this.size_to_string(model.get('file_size')));\n //}\n model.set(\"folder_id\", this.id);\n var rowView = new mod_library_folderrow_view.FolderRowView({\n model: model\n });\n\n // save new rowView to cache\n this.rowViews[model.get(\"id\")] = rowView;\n\n this.$el.find(\"#first_folder_item\").after(rowView.el);\n },\n\n /**\n * Remove the view of the given model from the DOM.\n * @param {Item or FolderAsModel} model of the view that will be removed\n */\n removeOne: function(model) {\n this.$el\n .find(\"tr\")\n .filter(function() {\n return (\n $(this).data(\"id\") &&\n $(this).data(\"id\") === model.id\n );\n })\n .remove();\n },\n\n /**\n * Remove all dataset and folder row elements from the DOM.\n */\n removeAllRows: function() {\n $(\".library-row\").remove();\n },\n\n /** Checks whether the list is empty and adds/removes the message */\n checkEmptiness: function() {\n if (\n this.$el.find(\".dataset_row\").length === 0 &&\n this.$el.find(\".folder_row\").length === 0\n ) {\n this.$el.find(\".empty-folder-message\").show();\n } else {\n this.$el.find(\".empty-folder-message\").hide();\n }\n },\n\n /** User clicked the table heading = he wants to sort stuff */\n sortColumnClicked: function(event) {\n event.preventDefault();\n if (this.sort === \"asc\") {\n this.sortFolder(\"name\", \"desc\");\n this.sort = \"desc\";\n } else {\n this.sortFolder(\"name\", \"asc\");\n this.sort = \"asc\";\n }\n this.renderSortIcon();\n },\n\n /**\n * Sorts the underlying collection according to the parameters received.\n * Currently supports only sorting by name.\n */\n sortFolder: function(sort_by, order) {\n // default to asc sort by name\n if (sort_by === \"undefined\" && order === \"undefined\") {\n return this.collection.sortByNameAsc();\n }\n if (sort_by === \"name\") {\n if (order === \"asc\") {\n return this.collection.sortByNameAsc();\n } else if (order === \"desc\") {\n return this.collection.sortByNameDesc();\n }\n }\n },\n\n /**\n * User clicked the checkbox in the table heading\n * @param {context} event\n */\n selectAll: function(event) {\n var selected = event.target.checked;\n that = this;\n // Iterate each checkbox\n $(\":checkbox\", \"#folder_list_body\").each(function() {\n this.checked = selected;\n var $row = $(this).closest(\"tr\");\n // Change color of selected/unselected\n if (selected) {\n that.makeDarkRow($row);\n } else {\n that.makeWhiteRow($row);\n }\n });\n },\n\n /**\n * Check checkbox if user clicks on the whole row or\n * on the checkbox itself\n */\n selectClickedRow: function(event) {\n var checkbox = \"\";\n var $row;\n var source;\n $row = $(event.target).closest(\"tr\");\n if (event.target.localName === \"input\") {\n checkbox = event.target;\n source = \"input\";\n } else if (event.target.localName === \"td\") {\n checkbox = $row.find(\":checkbox\")[0];\n source = \"td\";\n }\n if (checkbox.checked) {\n if (source === \"td\") {\n checkbox.checked = \"\";\n this.makeWhiteRow($row);\n } else if (source === \"input\") {\n this.makeDarkRow($row);\n }\n } else {\n if (source === \"td\") {\n checkbox.checked = \"selected\";\n this.makeDarkRow($row);\n } else if (source === \"input\") {\n this.makeWhiteRow($row);\n }\n }\n },\n\n makeDarkRow: function($row) {\n $row.removeClass(\"light\").addClass(\"dark\");\n $row\n .find(\"a\")\n .removeClass(\"light\")\n .addClass(\"dark\");\n $row\n .find(\".fa-file-o\")\n .removeClass(\"fa-file-o\")\n .addClass(\"fa-file\");\n $row\n .find(\".fa-folder-o\")\n .removeClass(\"fa-folder-o\")\n .addClass(\"fa-folder\");\n },\n\n makeWhiteRow: function($row) {\n $row.removeClass(\"dark\").addClass(\"light\");\n $row\n .find(\"a\")\n .removeClass(\"dark\")\n .addClass(\"light\");\n $row\n .find(\".fa-file\")\n .removeClass(\"fa-file\")\n .addClass(\"fa-file-o\");\n $row\n .find(\".fa-folder\")\n .removeClass(\"fa-folder\")\n .addClass(\"fa-folder-o\");\n },\n\n renderSortIcon: function() {\n if (this.sort === \"asc\") {\n $(\".sort-icon\")\n .removeClass(\"fa-sort-alpha-desc\")\n .addClass(\"fa-sort-alpha-asc\");\n } else {\n $(\".sort-icon\")\n .removeClass(\"fa-sort-alpha-asc\")\n .addClass(\"fa-sort-alpha-desc\");\n }\n },\n\n templateFolder: function() {\n return _.template(\n [\n // BREADCRUMBS\n '\",\n\n // FOLDER CONTENT\n '',\n '\">',\n '\",\n \"\",\n \"\",\n \"\",\n 'Folder: <%= _.escape(folder.get(\"name\")) %>',\n \"
\",\n '',\n \"<% if (is_admin) { %>\",\n \"You are logged in as an administrator therefore you can manage any folder on this Galaxy instance. Please make sure you understand the consequences.\",\n \"<% } else { %>\",\n \"You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.\",\n \"<% }%>\",\n \"\",\n '',\n \"\",\n \"Folder permissions
\",\n \"\",\n \"Roles that can manage permissions on this folder\",\n \"
\",\n '',\n '',\n \"User with any of these roles can manage permissions on this folder.\",\n \"\",\n \"\",\n \"Roles that can add items to this folder\",\n \"
\",\n '',\n '',\n \"User with any of these roles can add items to this folder (folders and datasets).\",\n \"\",\n \"\",\n \"Roles that can modify this folder\",\n \"
\",\n '',\n '',\n \"User with any of these roles can modify this folder (name, etc.).\",\n \"\",\n '\",\n \"\" class=\"grid table table-condensed\">',\n \"\",\n '
\",\n '\"\n ].join(\"\")\n );\n }\n });\n\n return {\n FolderListView: FolderListView\n };\n }\n);\n"]} \ No newline at end of file +{"version":3,"sources":["mvc/library/library-folderlist-view.js"],"names":["define","el","progress","progressStep","mod_masthead","folderContainer","mod_toastr","sort","mod_library_folderrow_view","events","FolderListView","Backbone","View","extend","collection","defaults","page_count","click #select-all-checkboxes","click .dataset_row","click .folder_row","click 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[\n \"layout/masthead\",\n \"utils/utils\",\n \"libs/toastr\",\n \"mvc/library/library-model\",\n \"mvc/library/library-folderrow-view\",\n \"mvc/library/library-dataset-view\"\n ],\n function(\n mod_masthead,\n mod_utils,\n mod_toastr,\n mod_library_model,\n mod_library_folderrow_view,\n mod_library_dataset_view\n ) {\n var FolderListView = Backbone.View.extend({\n el: \"#folder_items_element\",\n // progress percentage\n progress: 0,\n // progress rate per one item\n progressStep: 1,\n\n folderContainer: null,\n\n sort: \"asc\",\n\n events: {\n \"click #select-all-checkboxes\": \"selectAll\",\n \"click .dataset_row\": \"selectClickedRow\",\n \"click .folder_row\": \"selectClickedRow\",\n \"click .sort-folder-link\": \"sortColumnClicked\"\n },\n\n collection: null,\n\n defaults: {\n include_deleted: false,\n page_count: null,\n show_page: null\n },\n\n /**\n * Initialize and fetch the folder from the server.\n * @param {object} options an object with options\n */\n initialize: function(options) {\n this.options = _.defaults(\n this.options || {},\n this.defaults,\n options\n );\n this.modal = null;\n // map of folder item ids to item views = cache\n this.rowViews = {};\n\n // create a collection of folder items for this view\n this.collection = new mod_library_model.Folder();\n\n // start to listen if someone modifies the collection\n this.listenTo(this.collection, \"add\", this.renderOne);\n this.listenTo(this.collection, \"remove\", this.removeOne);\n this.listenTo(this.collection, \"sort\", this.rePaint);\n this.listenTo(this.collection, \"reset\", this.rePaint);\n\n this.fetchFolder();\n },\n\n fetchFolder: function(options) {\n var options = options || {};\n this.options.include_deleted = options.include_deleted;\n var that = this;\n\n this.folderContainer = new mod_library_model.FolderContainer({\n id: this.options.id\n });\n this.folderContainer.url =\n this.folderContainer.attributes.urlRoot +\n this.options.id +\n \"/contents\";\n\n if (this.options.include_deleted) {\n this.folderContainer.url =\n this.folderContainer.url + \"?include_deleted=true\";\n }\n this.folderContainer.fetch({\n success: function(folder_container) {\n that.folder_container = folder_container;\n that.render();\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(\n response.responseJSON.err_msg +\n \" Click this to go back.\",\n \"\",\n {\n onclick: function() {\n Galaxy.libraries.library_router.back();\n }\n }\n );\n } else {\n mod_toastr.error(\n \"An error occurred. Click this to go back.\",\n \"\",\n {\n onclick: function() {\n Galaxy.libraries.library_router.back();\n }\n }\n );\n }\n }\n });\n },\n\n render: function(options) {\n this.options = _.extend(this.options, options);\n var template = this.templateFolder();\n $(\".tooltip\").hide();\n\n // find the upper id in the full path\n var path = this.folderContainer.attributes.metadata.full_path;\n var upper_folder_id;\n if (path.length === 1) {\n // the library is above us\n upper_folder_id = 0;\n } else {\n upper_folder_id = path[path.length - 2][0];\n }\n\n this.$el.html(\n template({\n path: this.folderContainer.attributes.metadata\n .full_path,\n parent_library_id: this.folderContainer.attributes\n .metadata.parent_library_id,\n id: this.options.id,\n upper_folder_id: upper_folder_id,\n order: this.sort\n })\n );\n\n // when dataset_id is present render its details too\n if (this.options.dataset_id) {\n var row = _.findWhere(that.rowViews, {\n id: this.options.dataset_id\n });\n if (row) {\n row.showDatasetDetails();\n } else {\n mod_toastr.error(\n \"Requested dataset not found. Showing folder instead.\"\n );\n }\n } else {\n if (\n this.options.show_page === null ||\n this.options.show_page < 1\n ) {\n this.options.show_page = 1;\n }\n this.paginate();\n }\n $(\"#center [data-toggle]\").tooltip();\n $(\"#center\").css(\"overflow\", \"auto\");\n },\n\n paginate: function(options) {\n this.options = _.extend(this.options, options);\n\n if (\n this.options.show_page === null ||\n this.options.show_page < 1\n ) {\n this.options.show_page = 1;\n }\n this.options.total_items_count = this.folder_container.get(\n \"folder\"\n ).models.length;\n this.options.page_count = Math.ceil(\n this.options.total_items_count /\n Galaxy.libraries.preferences.get(\"folder_page_size\")\n );\n var page_start =\n Galaxy.libraries.preferences.get(\"folder_page_size\") *\n (this.options.show_page - 1);\n var items_to_render = null;\n items_to_render = this.folder_container\n .get(\"folder\")\n .models.slice(\n page_start,\n page_start +\n Galaxy.libraries.preferences.get(\"folder_page_size\")\n );\n this.options.items_shown = items_to_render.length;\n // User requests page with no items\n if (\n Galaxy.libraries.preferences.get(\"folder_page_size\") *\n this.options.show_page >\n this.options.total_items_count +\n Galaxy.libraries.preferences.get(\"folder_page_size\")\n ) {\n items_to_render = [];\n }\n Galaxy.libraries.folderToolbarView.renderPaginator(\n this.options\n );\n this.collection.reset(items_to_render);\n },\n\n rePaint: function(options) {\n this.options = _.extend(this.options, options);\n this.removeAllRows();\n this.renderAll();\n this.checkEmptiness();\n },\n\n /**\n * Adds all given models to the collection.\n * @param {array of Item or FolderAsModel} array of models that should\n * be added to the view's collection.\n */\n addAll: function(models) {\n _.each(models, function(model) {\n Galaxy.libraries.folderListView.collection.add(model, {\n sort: false\n });\n });\n $(\"#center [data-toggle]\").tooltip();\n this.checkEmptiness();\n this.postRender();\n },\n\n /**\n * Call this after all models are added to the collection\n * to ensure that the folder toolbar will show proper options\n * and that event will be bound on all subviews.\n */\n postRender: function() {\n var fetched_metadata = this.folderContainer.attributes.metadata;\n fetched_metadata.contains_file_or_folder =\n typeof this.collection.findWhere({ type: \"file\" }) !==\n \"undefined\" ||\n typeof this.collection.findWhere({ type: \"folder\" }) !==\n \"undefined\";\n Galaxy.libraries.folderToolbarView.configureElements(\n fetched_metadata\n );\n },\n\n /**\n * Iterates this view's collection and calls the render\n * function for each. Also binds the hover behavior.\n */\n renderAll: function() {\n var that = this;\n _.each(this.collection.models.reverse(), function(model) {\n that.renderOne(model);\n });\n this.postRender();\n },\n\n /**\n * Creates a view for the given model and adds it to the folder view.\n * @param {Item or FolderAsModel} model of the view that will be rendered\n */\n renderOne: function(model) {\n this.options.contains_file_or_folder = true;\n //if (model.get('type') !== 'folder'){\n // model.set('readable_size', this.size_to_string(model.get('file_size')));\n //}\n model.set(\"folder_id\", this.id);\n var rowView = new mod_library_folderrow_view.FolderRowView({\n model: model\n });\n\n // save new rowView to cache\n this.rowViews[model.get(\"id\")] = rowView;\n\n this.$el.find(\"#first_folder_item\").after(rowView.el);\n },\n\n /**\n * Remove the view of the given model from the DOM.\n * @param {Item or FolderAsModel} model of the view that will be removed\n */\n removeOne: function(model) {\n this.$el\n .find(\"tr\")\n .filter(function() {\n return (\n $(this).data(\"id\") &&\n $(this).data(\"id\") === model.id\n );\n })\n .remove();\n },\n\n /**\n * Remove all dataset and folder row elements from the DOM.\n */\n removeAllRows: function() {\n $(\".library-row\").remove();\n },\n\n /** Checks whether the list is empty and adds/removes the message */\n checkEmptiness: function() {\n if (\n this.$el.find(\".dataset_row\").length === 0 &&\n this.$el.find(\".folder_row\").length === 0\n ) {\n this.$el.find(\".empty-folder-message\").show();\n } else {\n this.$el.find(\".empty-folder-message\").hide();\n }\n },\n\n /** User clicked the table heading = he wants to sort stuff */\n sortColumnClicked: function(event) {\n event.preventDefault();\n if (this.sort === \"asc\") {\n this.sortFolder(\"name\", \"desc\");\n this.sort = \"desc\";\n } else {\n this.sortFolder(\"name\", \"asc\");\n this.sort = \"asc\";\n }\n this.renderSortIcon();\n },\n\n /**\n * Sorts the underlying collection according to the parameters received.\n * Currently supports only sorting by name.\n */\n sortFolder: function(sort_by, order) {\n // default to asc sort by name\n if (sort_by === \"undefined\" && order === \"undefined\") {\n return this.collection.sortByNameAsc();\n }\n if (sort_by === \"name\") {\n if (order === \"asc\") {\n return this.collection.sortByNameAsc();\n } else if (order === \"desc\") {\n return this.collection.sortByNameDesc();\n }\n }\n },\n\n /**\n * User clicked the checkbox in the table heading\n * @param {context} event\n */\n selectAll: function(event) {\n var selected = event.target.checked;\n that = this;\n // Iterate each checkbox\n $(\":checkbox\", \"#folder_list_body\").each(function() {\n this.checked = selected;\n var $row = $(this).closest(\"tr\");\n // Change color of selected/unselected\n if (selected) {\n that.makeDarkRow($row);\n } else {\n that.makeWhiteRow($row);\n }\n });\n },\n\n /**\n * Check checkbox if user clicks on the whole row or\n * on the checkbox itself\n */\n selectClickedRow: function(event) {\n var checkbox = \"\";\n var $row;\n var source;\n $row = $(event.target).closest(\"tr\");\n if (event.target.localName === \"input\") {\n checkbox = event.target;\n source = \"input\";\n } else if (event.target.localName === \"td\") {\n checkbox = $row.find(\":checkbox\")[0];\n source = \"td\";\n }\n if (checkbox.checked) {\n if (source === \"td\") {\n checkbox.checked = \"\";\n this.makeWhiteRow($row);\n } else if (source === \"input\") {\n this.makeDarkRow($row);\n }\n } else {\n if (source === \"td\") {\n checkbox.checked = \"selected\";\n this.makeDarkRow($row);\n } else if (source === \"input\") {\n this.makeWhiteRow($row);\n }\n }\n },\n\n makeDarkRow: function($row) {\n $row.removeClass(\"light\").addClass(\"dark\");\n $row\n .find(\"a\")\n .removeClass(\"light\")\n .addClass(\"dark\");\n $row\n .find(\".fa-file-o\")\n .removeClass(\"fa-file-o\")\n .addClass(\"fa-file\");\n $row\n .find(\".fa-folder-o\")\n .removeClass(\"fa-folder-o\")\n .addClass(\"fa-folder\");\n },\n\n makeWhiteRow: function($row) {\n $row.removeClass(\"dark\").addClass(\"light\");\n $row\n .find(\"a\")\n .removeClass(\"dark\")\n .addClass(\"light\");\n $row\n .find(\".fa-file\")\n .removeClass(\"fa-file\")\n .addClass(\"fa-file-o\");\n $row\n .find(\".fa-folder\")\n .removeClass(\"fa-folder\")\n .addClass(\"fa-folder-o\");\n },\n\n renderSortIcon: function() {\n if (this.sort === \"asc\") {\n $(\".sort-icon\")\n .removeClass(\"fa-sort-alpha-desc\")\n .addClass(\"fa-sort-alpha-asc\");\n } else {\n $(\".sort-icon\")\n .removeClass(\"fa-sort-alpha-asc\")\n .addClass(\"fa-sort-alpha-desc\");\n }\n },\n\n templateFolder: function() {\n return _.template(\n [\n // BREADCRUMBS\n '\",\n\n // FOLDER CONTENT\n '',\n ' ',\n ' name ',\n 'description ',\n 'data type ',\n 'size ',\n 'time updated (UTC) ',\n '',\n \"\",\n '',\n ' ',\n \" \",\n \"\",\n \"\",\n '\" title=\"Go to parent folder\" class=\"btn_open_folder btn btn-default 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\",\n '\"\n ].join(\"\")\n );\n }\n });\n\n return {\n FolderListView: FolderListView\n };\n }\n);\n"]} \ No newline at end of file diff --git a/static/maps/mvc/library/library-folderrow-view.js.map b/static/maps/mvc/library/library-folderrow-view.js.map index 47408f267ef..f4b7c14bfbb 100644 --- a/static/maps/mvc/library/library-folderrow-view.js.map +++ b/static/maps/mvc/library/library-folderrow-view.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/library/library-folderrow-view.js"],"names":["define","FolderRowView","events","mod_toastr","mod_library_model","mod_library_dataset_view","Backbone","View","extend","click .undelete_dataset_btn","click .undelete_folder_btn","click 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[\n \"libs/toastr\",\n \"mvc/library/library-model\",\n \"mvc/library/library-dataset-view\"\n ],\n function(mod_toastr, mod_library_model, mod_library_dataset_view) {\n var FolderRowView = Backbone.View.extend({\n events: {\n \"click .undelete_dataset_btn\": \"undeleteDataset\",\n \"click .undelete_folder_btn\": \"undeleteFolder\",\n \"click .edit_folder_btn\": \"startModifications\",\n \"click .cancel_folder_btn\": \"cancelModifications\",\n \"click .save_folder_btn\": \"saveModifications\"\n },\n\n defaults: {\n type: null,\n visibility_config: {\n edit_folder_btn: true,\n save_folder_btn: false,\n cancel_folder_btn: false,\n permission_folder_btn: true\n },\n edit_mode: false\n },\n\n initialize: function(options) {\n this.options = _.defaults(options || {}, this.defaults);\n this.render(this.options);\n },\n\n render: function(options) {\n this.options = _.extend(this.options, options);\n var folder_item = this.options.model;\n var template = null;\n\n if (\n folder_item.get(\"type\") === \"folder\" ||\n folder_item.get(\"model_class\") === \"LibraryFolder\"\n ) {\n this.options.type = \"folder\";\n this.prepareButtons(folder_item);\n if (folder_item.get(\"deleted\")) {\n template = this.templateRowDeletedFolder();\n } else {\n template = this.templateRowFolder();\n }\n } else if (\n folder_item.get(\"type\") === \"file\" ||\n folder_item.get(\"model_class\") ===\n \"LibraryDatasetDatasetAssociation\" ||\n folder_item.get(\"model_class\") === \"LibraryDataset\"\n ) {\n this.options.type = \"file\";\n if (folder_item.get(\"deleted\")) {\n template = this.templateRowDeletedFile();\n } else {\n template = this.templateRowFile();\n }\n } else {\n Galaxy.emit.error(\"Unknown library item type found.\");\n Galaxy.emit.error(\n folder_item.get(\"type\") ||\n folder_item.get(\"model_class\")\n );\n }\n this.setElement(\n template({\n content_item: folder_item,\n edit_mode: this.options.edit_mode,\n button_config: this.options.visibility_config\n })\n );\n this.$el.show();\n return this;\n },\n\n /**\n * Modify the visibility of buttons for\n * the filling of the row template of a given folder.\n */\n prepareButtons: function(folder) {\n var vis_config = this.options.visibility_config;\n if (this.options.edit_mode === false) {\n vis_config.save_folder_btn = false;\n vis_config.cancel_folder_btn = false;\n if (folder.get(\"deleted\") === true) {\n vis_config.edit_folder_btn = false;\n vis_config.permission_folder_btn = false;\n } else if (folder.get(\"deleted\") === false) {\n vis_config.save_folder_btn = false;\n vis_config.cancel_folder_btn = false;\n if (folder.get(\"can_modify\") === true) {\n vis_config.edit_folder_btn = true;\n }\n if (folder.get(\"can_manage\") === true) {\n vis_config.permission_folder_btn = true;\n }\n }\n } else if (this.options.edit_mode === true) {\n vis_config.edit_folder_btn = false;\n vis_config.permission_folder_btn = false;\n vis_config.save_folder_btn = true;\n vis_config.cancel_folder_btn = true;\n }\n this.options.visibility_config = vis_config;\n },\n\n /* Show the page with dataset details. */\n showDatasetDetails: function() {\n Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView(\n { id: this.id }\n );\n },\n\n /* Undelete the dataset on server and render the row again. */\n undeleteDataset: function(event) {\n $(\".tooltip\").hide();\n var that = this;\n var dataset_id = $(event.target)\n .closest(\"tr\")\n .data(\"id\");\n var dataset = Galaxy.libraries.folderListView.collection.get(\n dataset_id\n );\n dataset.url = dataset.urlRoot + dataset.id + \"?undelete=true\";\n dataset.destroy({\n success: function(model, response) {\n Galaxy.libraries.folderListView.collection.remove(\n dataset_id\n );\n var updated_dataset = new mod_library_model.Item(\n response\n );\n Galaxy.libraries.folderListView.collection.add(\n updated_dataset\n );\n Galaxy.libraries.folderListView.collection.sortByNameAsc();\n mod_toastr.success(\n \"Dataset undeleted. Click this to see it.\",\n \"\",\n {\n onclick: function() {\n var folder_id = that.model.get(\"folder_id\");\n window.location =\n Galaxy.root +\n \"library/list#folders/\" +\n folder_id +\n \"/datasets/\" +\n that.id;\n }\n }\n );\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(\n \"Dataset was not undeleted. \" +\n response.responseJSON.err_msg\n );\n } else {\n mod_toastr.error(\n \"An error occured! Dataset was not undeleted. Please try again.\"\n );\n }\n }\n });\n },\n\n /* Undelete the folder on server and render the row again. */\n undeleteFolder: function(event) {\n $(\".tooltip\").hide();\n var that = this;\n var folder_id = $(event.target)\n .closest(\"tr\")\n .data(\"id\");\n var folder = Galaxy.libraries.folderListView.collection.get(\n folder_id\n );\n folder.url = folder.urlRoot + folder.id + \"?undelete=true\";\n folder.destroy({\n success: function(model, response) {\n Galaxy.libraries.folderListView.collection.remove(\n folder_id\n );\n var updated_folder = new mod_library_model.FolderAsModel(\n response\n );\n Galaxy.libraries.folderListView.collection.add(\n updated_folder\n );\n Galaxy.libraries.folderListView.collection.sortByNameAsc();\n mod_toastr.success(\"Folder undeleted.\");\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(\n \"Folder was not undeleted. \" +\n response.responseJSON.err_msg\n );\n } else {\n mod_toastr.error(\n \"An error occured! Folder was not undeleted. Please try again.\"\n );\n }\n }\n });\n },\n\n /* User clicked the 'edit' button on row so render the row as editable. */\n startModifications: function() {\n this.options.edit_mode = true;\n this.repaint();\n },\n\n /* User clicked the 'cancel' button so render normal row */\n cancelModifications: function() {\n this.options.edit_mode = false;\n this.repaint();\n },\n\n saveModifications: function() {\n var folder = Galaxy.libraries.folderListView.collection.get(\n this.$el.data(\"id\")\n );\n var is_changed = false;\n var new_name = this.$el.find(\".input_folder_name\").val();\n if (\n typeof new_name !== \"undefined\" &&\n new_name !== folder.get(\"name\")\n ) {\n if (new_name.length > 2) {\n folder.set(\"name\", new_name);\n is_changed = true;\n } else {\n mod_toastr.warning(\n \"Folder name has to be at least 3 characters long.\"\n );\n return;\n }\n }\n var new_description = this.$el\n .find(\".input_folder_description\")\n .val();\n if (\n typeof new_description !== \"undefined\" &&\n new_description !== folder.get(\"description\")\n ) {\n folder.set(\"description\", new_description);\n is_changed = true;\n }\n if (is_changed) {\n var row_view = this;\n folder.save(null, {\n patch: true,\n success: function(folder) {\n row_view.options.edit_mode = false;\n row_view.repaint(folder);\n mod_toastr.success(\"Changes to folder saved.\");\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\n \"An error occured while attempting to update the folder.\"\n );\n }\n }\n });\n } else {\n this.options.edit_mode = false;\n this.repaint(folder);\n mod_toastr.info(\"Nothing has changed.\");\n }\n },\n\n repaint: function() {\n /* need to hide manually because of the element removal in setElement\n invoked in render() */\n $(\".tooltip\").hide();\n /* we need to store the old element to be able to replace it with\n new one */\n var old_element = this.$el;\n /* if user canceled the folder param is undefined,\n if user saved and succeeded the updated folder is rendered */\n this.render();\n old_element.replaceWith(this.$el);\n /* now we attach new tooltips to the newly created row element */\n this.$el.find(\"[data-toggle]\").tooltip();\n },\n\n templateRowFolder: function() {\n return _.template(\n [\n '',\n ' ',\n ' name ',\n 'description ',\n 'data type ',\n 'size ',\n 'time updated (UTC) ',\n '',\n \"\",\n '',\n ' ',\n \" \",\n \"\",\n \"\",\n '\" title=\"Go to parent folder\" class=\"btn_open_folder btn btn-default btn-xs\">..',\n \" \",\n \"\",\n \" \",\n \" \",\n \" \",\n \" \",\n \" \",\n \" \",\n \" \">',\n \" \"\n ].join(\"\")\n );\n },\n\n templateRowFile: function() {\n return _.template(\n [\n '\",\n '',\n \" \",\n '',\n \"<% if(!edit_mode) { %>\",\n \" \",\n '\"><%- content_item.get(\"name\") %>',\n \" \",\n \"\",\n '<%- content_item.get(\"description\") %>',\n \" \",\n \"<% } else if(edit_mode){ %>\",\n '',\n ' ',\n \"<% } %>\",\n \" folder \",\n \"\",\n \" \",\n '<%= _.escape(content_item.get(\"update_time\")) %>',\n \" \",\n \"\",\n \"<% if(edit_mode) { %>\", // start edit mode\n '\",\n '\",\n \"<% } else if (!edit_mode){%>\", // start no edit mode\n '\",\n '/permissions\">',\n '\",\n \"\",\n \"<% } %>\", //end no edit mode\n \" \",\n \"\">',\n \" \"\n ].join(\"\")\n );\n },\n\n templateRowDeletedFile: function() {\n return _.template(\n [\n '\",\n '',\n \" \",\n '',\n '',\n \" \",\n \"\",\n '/datasets/<%- content_item.id %>\" class=\"library-dataset\">',\n '<%- content_item.get(\"name\") %>',\n \"\",\n \" \",\n '<%- content_item.get(\"message\") %> ',\n '<%= _.escape(content_item.get(\"file_ext\")) %> ',\n '<%= _.escape(content_item.get(\"file_size\")) %> ',\n '<%= _.escape(content_item.get(\"update_time\")) %> ',\n \"\",\n '<% if (content_item.get(\"is_unrestricted\")) { %>',\n '',\n \"<% } %>\",\n '<% if (content_item.get(\"is_private\")) { %>',\n '',\n \"<% } %>\",\n '<% if ((content_item.get(\"is_unrestricted\") === false) && (content_item.get(\"is_private\") === false)) { %>',\n '',\n \"<% } %>\",\n '<% if (content_item.get(\"can_manage\")) { %>',\n '/datasets/<%- content_item.id %>/permissions\">',\n '\",\n \"\",\n \"<% } %>\",\n \" \",\n \"\">',\n \" \"\n ].join(\"\")\n );\n },\n\n templateRowDeletedFolder: function() {\n return _.template(\n [\n '\",\n '',\n \" \",\n \"\",\n ' ',\n '<%- content_item.get(\"name\") %>',\n \" \",\n \"\",\n '<%- content_item.get(\"message\") %>',\n \" \",\n \"\",\n '<%= _.escape(content_item.get(\"file_ext\")) %>',\n \" \",\n \"\",\n '<%= _.escape(content_item.get(\"file_size\")) %>',\n \" \",\n \"\",\n '<%= _.escape(content_item.get(\"update_time\")) %>',\n \" \",\n \"\",\n '',\n '\",\n \" \",\n \"\">',\n \" \"\n ].join(\"\")\n );\n }\n });\n\n return {\n FolderRowView: FolderRowView\n };\n }\n);\n"]} \ No newline at end of file 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[\n \"libs/toastr\",\n \"mvc/library/library-model\",\n \"mvc/library/library-dataset-view\"\n ],\n function(mod_toastr, mod_library_model, mod_library_dataset_view) {\n var FolderRowView = Backbone.View.extend({\n events: {\n \"click .undelete_dataset_btn\": \"undeleteDataset\",\n \"click .undelete_folder_btn\": \"undeleteFolder\",\n \"click .edit_folder_btn\": \"startModifications\",\n \"click .cancel_folder_btn\": \"cancelModifications\",\n \"click .save_folder_btn\": \"saveModifications\"\n },\n\n defaults: {\n type: null,\n visibility_config: {\n edit_folder_btn: true,\n save_folder_btn: false,\n cancel_folder_btn: false,\n permission_folder_btn: true\n },\n edit_mode: false\n },\n\n initialize: function(options) {\n this.options = _.defaults(options || {}, this.defaults);\n this.render(this.options);\n },\n\n render: function(options) {\n this.options = _.extend(this.options, options);\n var folder_item = this.options.model;\n var template = null;\n\n if (\n folder_item.get(\"type\") === \"folder\" ||\n folder_item.get(\"model_class\") === \"LibraryFolder\"\n ) {\n this.options.type = \"folder\";\n this.prepareButtons(folder_item);\n if (folder_item.get(\"deleted\")) {\n template = this.templateRowDeletedFolder();\n } else {\n template = this.templateRowFolder();\n }\n } else if (\n folder_item.get(\"type\") === \"file\" ||\n folder_item.get(\"model_class\") ===\n \"LibraryDatasetDatasetAssociation\" ||\n folder_item.get(\"model_class\") === \"LibraryDataset\"\n ) {\n this.options.type = \"file\";\n if (folder_item.get(\"deleted\")) {\n template = this.templateRowDeletedFile();\n } else {\n template = this.templateRowFile();\n }\n } else {\n Galaxy.emit.error(\"Unknown library item type found.\");\n Galaxy.emit.error(\n folder_item.get(\"type\") ||\n folder_item.get(\"model_class\")\n );\n }\n this.setElement(\n template({\n content_item: folder_item,\n edit_mode: this.options.edit_mode,\n button_config: this.options.visibility_config\n })\n );\n this.$el.show();\n return this;\n },\n\n /**\n * Modify the visibility of buttons for\n * the filling of the row template of a given folder.\n */\n prepareButtons: function(folder) {\n var vis_config = this.options.visibility_config;\n if (this.options.edit_mode === false) {\n vis_config.save_folder_btn = false;\n vis_config.cancel_folder_btn = false;\n if (folder.get(\"deleted\") === true) {\n vis_config.edit_folder_btn = false;\n vis_config.permission_folder_btn = false;\n } else if (folder.get(\"deleted\") === false) {\n vis_config.save_folder_btn = false;\n vis_config.cancel_folder_btn = false;\n if (folder.get(\"can_modify\") === true) {\n vis_config.edit_folder_btn = true;\n }\n if (folder.get(\"can_manage\") === true) {\n vis_config.permission_folder_btn = true;\n }\n }\n } else if (this.options.edit_mode === true) {\n vis_config.edit_folder_btn = false;\n vis_config.permission_folder_btn = false;\n vis_config.save_folder_btn = true;\n vis_config.cancel_folder_btn = true;\n }\n this.options.visibility_config = vis_config;\n },\n\n /* Show the page with dataset details. */\n showDatasetDetails: function() {\n Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView(\n { id: this.id }\n );\n },\n\n /* Undelete the dataset on server and render the row again. */\n undeleteDataset: function(event) {\n $(\".tooltip\").hide();\n var that = this;\n var dataset_id = $(event.target)\n .closest(\"tr\")\n .data(\"id\");\n var dataset = Galaxy.libraries.folderListView.collection.get(\n dataset_id\n );\n dataset.url = dataset.urlRoot + dataset.id + \"?undelete=true\";\n dataset.destroy({\n success: function(model, response) {\n Galaxy.libraries.folderListView.collection.remove(\n dataset_id\n );\n var updated_dataset = new mod_library_model.Item(\n response\n );\n Galaxy.libraries.folderListView.collection.add(\n updated_dataset\n );\n Galaxy.libraries.folderListView.collection.sortByNameAsc();\n mod_toastr.success(\n \"Dataset undeleted. Click this to see it.\",\n \"\",\n {\n onclick: function() {\n var folder_id = that.model.get(\"folder_id\");\n window.location =\n Galaxy.root +\n \"library/list#folders/\" +\n folder_id +\n \"/datasets/\" +\n that.id;\n }\n }\n );\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(\n \"Dataset was not undeleted. \" +\n response.responseJSON.err_msg\n );\n } else {\n mod_toastr.error(\n \"An error occured! Dataset was not undeleted. Please try again.\"\n );\n }\n }\n });\n },\n\n /* Undelete the folder on server and render the row again. */\n undeleteFolder: function(event) {\n $(\".tooltip\").hide();\n var that = this;\n var folder_id = $(event.target)\n .closest(\"tr\")\n .data(\"id\");\n var folder = Galaxy.libraries.folderListView.collection.get(\n folder_id\n );\n folder.url = folder.urlRoot + folder.id + \"?undelete=true\";\n folder.destroy({\n success: function(model, response) {\n Galaxy.libraries.folderListView.collection.remove(\n folder_id\n );\n var updated_folder = new mod_library_model.FolderAsModel(\n response\n );\n Galaxy.libraries.folderListView.collection.add(\n updated_folder\n );\n Galaxy.libraries.folderListView.collection.sortByNameAsc();\n mod_toastr.success(\"Folder undeleted.\");\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(\n \"Folder was not undeleted. \" +\n response.responseJSON.err_msg\n );\n } else {\n mod_toastr.error(\n \"An error occured! Folder was not undeleted. Please try again.\"\n );\n }\n }\n });\n },\n\n /* User clicked the 'edit' button on row so render the row as editable. */\n startModifications: function() {\n this.options.edit_mode = true;\n this.repaint();\n },\n\n /* User clicked the 'cancel' button so render normal row */\n cancelModifications: function() {\n this.options.edit_mode = false;\n this.repaint();\n },\n\n saveModifications: function() {\n var folder = Galaxy.libraries.folderListView.collection.get(\n this.$el.data(\"id\")\n );\n var is_changed = false;\n var new_name = this.$el.find(\".input_folder_name\").val();\n if (\n typeof new_name !== \"undefined\" &&\n new_name !== folder.get(\"name\")\n ) {\n if (new_name.length > 2) {\n folder.set(\"name\", new_name);\n is_changed = true;\n } else {\n mod_toastr.warning(\n \"Folder name has to be at least 3 characters long.\"\n );\n return;\n }\n }\n var new_description = this.$el\n .find(\".input_folder_description\")\n .val();\n if (\n typeof new_description !== \"undefined\" &&\n new_description !== folder.get(\"description\")\n ) {\n folder.set(\"description\", new_description);\n is_changed = true;\n }\n if (is_changed) {\n var row_view = this;\n folder.save(null, {\n patch: true,\n success: function(folder) {\n row_view.options.edit_mode = false;\n row_view.repaint(folder);\n mod_toastr.success(\"Changes to folder saved.\");\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\n \"An error occured while attempting to update the folder.\"\n );\n }\n }\n });\n } else {\n this.options.edit_mode = false;\n this.repaint(folder);\n mod_toastr.info(\"Nothing has changed.\");\n }\n },\n\n repaint: function() {\n /* need to hide manually because of the element removal in setElement\n invoked in render() */\n $(\".tooltip\").hide();\n /* we need to store the old element to be able to replace it with\n new one */\n var old_element = this.$el;\n /* if user canceled the folder param is undefined,\n if user saved and succeeded the updated folder is rendered */\n this.render();\n old_element.replaceWith(this.$el);\n /* now we attach new tooltips to the newly created row element */\n this.$el.find(\"[data-toggle]\").tooltip();\n },\n\n templateRowFolder: function() {\n return _.template(\n [\n '\",\n '',\n \" \",\n \"\",\n ' ',\n '<%- content_item.get(\"name\") %>',\n \" \",\n \"\",\n '<%- content_item.get(\"description\") %>',\n \" \",\n \"\",\n \"folder\",\n \" \",\n \"\",\n \" \",\n '<%= _.escape(content_item.get(\"update_time\")) %>',\n \" \",\n \"\",\n '',\n '\",\n \" \",\n \"\">',\n \" \"\n ].join(\"\")\n );\n },\n\n templateRowFile: function() {\n return _.template(\n [\n '\",\n '',\n \" \",\n '',\n \"<% if(!edit_mode) { %>\",\n \" \",\n '\"><%- content_item.get(\"name\") %>',\n \" \",\n \"\",\n '<%- content_item.get(\"description\") %>',\n \" \",\n \"<% } else if(edit_mode){ %>\",\n '',\n ' ',\n \"<% } %>\",\n \" folder \",\n \"\",\n \" \",\n '<%= _.escape(content_item.get(\"update_time\")) %>',\n \" \",\n \"\",\n \"<% if(edit_mode) { %>\", // start edit mode\n '\",\n '\",\n \"<% } else if (!edit_mode){%>\", // start no edit mode\n '\",\n '/permissions\">',\n '\",\n \"\",\n \"<% } %>\", //end no edit mode\n \" \",\n \"\">',\n \" \"\n ].join(\"\")\n );\n },\n\n templateRowDeletedFile: function() {\n return _.template(\n [\n '\",\n '',\n \" \",\n '',\n '',\n \" \",\n \"\",\n '/datasets/<%- content_item.id %>\" class=\"library-dataset\">',\n '<%- content_item.get(\"name\") %>',\n \"\",\n \" \",\n '<%- content_item.get(\"message\") %> ',\n '<%= _.escape(content_item.get(\"file_ext\")) %> ',\n '<%= _.escape(content_item.get(\"file_size\")) %> ',\n '<%= _.escape(content_item.get(\"update_time\")) %> ',\n \"\",\n '<% if (content_item.get(\"is_unrestricted\")) { %>',\n '',\n \"<% } %>\",\n '<% if (content_item.get(\"is_private\")) { %>',\n '',\n \"<% } %>\",\n '<% if ((content_item.get(\"is_unrestricted\") === false) && (content_item.get(\"is_private\") === false)) { %>',\n '',\n \"<% } %>\",\n '<% if (content_item.get(\"can_manage\")) { %>',\n '/datasets/<%- content_item.id %>/permissions\">',\n '\",\n \"\",\n \"<% } %>\",\n \" \",\n \"\">',\n \" \"\n ].join(\"\")\n );\n },\n\n templateRowDeletedFolder: function() {\n return _.template(\n [\n '\",\n '',\n \" \",\n \"\",\n ' ',\n '<%- content_item.get(\"name\") %>',\n \" \",\n \"\",\n '<%- content_item.get(\"message\") %>',\n \" \",\n \"\",\n '<%= _.escape(content_item.get(\"file_ext\")) %>',\n \" \",\n \"\",\n '<%= _.escape(content_item.get(\"file_size\")) %>',\n \" \",\n \"\",\n '<%= _.escape(content_item.get(\"update_time\")) %>',\n \" \",\n \"\",\n '',\n '\",\n \" \",\n \"\">',\n \" \"\n ].join(\"\")\n );\n }\n });\n\n return {\n FolderRowView: FolderRowView\n };\n }\n);\n"]} \ No newline at end of file diff --git a/static/maps/mvc/library/library-foldertoolbar-view.js.map 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[\n \"layout/masthead\",\n \"utils/utils\",\n \"libs/toastr\",\n \"mvc/library/library-model\",\n \"mvc/ui/ui-select\"\n ],\n function(\n mod_masthead,\n mod_utils,\n mod_toastr,\n mod_library_model,\n mod_select\n ) {\n var FolderToolbarView = Backbone.View.extend({\n el: \"#center\",\n\n events: {\n \"click #toolbtn_create_folder\": \"createFolderFromModal\",\n \"click #toolbtn_bulk_import\": \"modalBulkImport\",\n \"click #include_deleted_datasets_chk\": \"checkIncludeDeleted\",\n \"click #toolbtn_bulk_delete\": \"deleteSelectedItems\",\n \"click .toolbtn-show-locinfo\": \"showLocInfo\",\n \"click .page_size_prompt\": \"showPageSizePrompt\"\n },\n\n defaults: {\n can_add_library_item: false,\n contains_file_or_folder: false,\n chain_call_control: {\n total_number: 0,\n failed_number: 0\n },\n disabled_jstree_element: \"folders\"\n },\n\n modal: null,\n\n // directory browsing object\n jstree: null,\n\n // user's histories\n histories: null,\n\n // genome select\n select_genome: null,\n\n // extension select\n select_extension: null,\n\n // extension types\n list_extensions: [],\n\n // datatype placeholder for extension auto-detection\n auto: {\n id: \"auto\",\n text: \"Auto-detect\",\n description:\n \"This system will try to detect the file type automatically.\" +\n \" If your file is not detected properly as one of the known formats,\" +\n \" it most likely means that it has some format problems (e.g., different\" +\n \" number of columns on different rows). You can still coerce the system\" +\n \" to set your data to the format you think it should be.\" +\n \" You can also upload compressed files, which will automatically be decompressed.\"\n },\n\n // genomes\n list_genomes: [],\n\n initialize: function(options) {\n this.options = _.defaults(options || {}, this.defaults);\n this.fetchExtAndGenomes();\n this.render();\n },\n\n render: function(options) {\n this.options = _.extend(this.options, options);\n var toolbar_template = this.templateToolBar();\n var template_defaults = {\n id: this.options.id,\n is_admin: false,\n is_anonym: true,\n mutiple_add_dataset_options: false\n };\n if (Galaxy.user) {\n template_defaults.is_admin = Galaxy.user.isAdmin();\n template_defaults.is_anonym = Galaxy.user.isAnonymous();\n if (\n Galaxy.config.user_library_import_dir !== null ||\n Galaxy.config.allow_library_path_paste !== false ||\n Galaxy.config.library_import_dir !== null\n ) {\n template_defaults.mutiple_add_dataset_options = true;\n }\n }\n this.$el.html(toolbar_template(template_defaults));\n },\n\n /**\n * Called from FolderListView when needed.\n * @param {object} options common options\n */\n renderPaginator: function(options) {\n this.options = _.extend(this.options, options);\n var paginator_template = this.templatePaginator();\n $(\"body\")\n .find(\".folder-paginator\")\n .html(\n paginator_template({\n id: this.options.id,\n show_page: parseInt(this.options.show_page),\n page_count: parseInt(this.options.page_count),\n total_items_count: this.options.total_items_count,\n items_shown: this.options.items_shown\n })\n );\n },\n\n configureElements: function(options) {\n this.options = _.extend(this.options, options);\n\n if (this.options.can_add_library_item === true) {\n $(\".add-library-items\").show();\n } else {\n $(\".add-library-items\").hide();\n }\n if (this.options.contains_file_or_folder === true) {\n if (Galaxy.user) {\n if (!Galaxy.user.isAnonymous()) {\n $(\".logged-dataset-manipulation\").show();\n $(\".dataset-manipulation\").show();\n } else {\n $(\".dataset-manipulation\").show();\n $(\".logged-dataset-manipulation\").hide();\n }\n } else {\n $(\".logged-dataset-manipulation\").hide();\n $(\".dataset-manipulation\").hide();\n }\n } else {\n $(\".logged-dataset-manipulation\").hide();\n $(\".dataset-manipulation\").hide();\n }\n this.$el.find(\"[data-toggle]\").tooltip();\n },\n\n // shows modal for creating folder\n createFolderFromModal: function(event) {\n event.preventDefault();\n event.stopPropagation();\n\n // create modal\n var self = this;\n var template = this.templateNewFolderInModal();\n this.modal = Galaxy.modal;\n this.modal.show({\n closing_events: true,\n title: \"Create New Folder\",\n body: template(),\n buttons: {\n Create: function() {\n self.create_new_folder_event();\n },\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n },\n\n // create the new folder from modal\n create_new_folder_event: function() {\n var folderDetails = this.serialize_new_folder();\n if (this.validate_new_folder(folderDetails)) {\n var folder = new mod_library_model.FolderAsModel();\n var url_items = Backbone.history.fragment.split(\"/\"),\n current_folder_id;\n if (url_items.indexOf(\"page\") > -1) {\n current_folder_id = url_items[url_items.length - 3];\n } else {\n current_folder_id = url_items[url_items.length - 1];\n }\n folder.url = folder.urlRoot + current_folder_id;\n\n folder.save(folderDetails, {\n success: function(folder) {\n Galaxy.modal.hide();\n mod_toastr.success(\"Folder created.\");\n folder.set({ type: \"folder\" });\n Galaxy.libraries.folderListView.collection.add(\n folder\n );\n },\n error: function(model, response) {\n Galaxy.modal.hide();\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n }\n });\n } else {\n mod_toastr.error(\"Folder's name is missing.\");\n }\n return false;\n },\n\n // serialize data from the modal\n serialize_new_folder: function() {\n return {\n name: $(\"input[name='Name']\").val(),\n description: $(\"input[name='Description']\").val()\n };\n },\n\n // validate new folder info\n validate_new_folder: function(folderDetails) {\n return folderDetails.name !== \"\";\n },\n\n // show bulk import modal\n modalBulkImport: function() {\n var $checkedValues = this.findCheckedRows();\n if ($checkedValues.length === 0) {\n mod_toastr.info(\"You must select some datasets first.\");\n } else {\n var that = this;\n this.histories = new mod_library_model.GalaxyHistories();\n this.histories\n .fetch()\n .done(function() {\n var template = that.templateBulkImportInModal();\n that.modal = Galaxy.modal;\n that.modal.show({\n closing_events: true,\n title: \"Import into History\",\n body: template({\n histories: that.histories.models\n }),\n buttons: {\n Import: function() {\n that.importAllIntoHistory();\n },\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n })\n .fail(function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n });\n }\n },\n\n /**\n * Import all selected datasets into history.\n */\n importAllIntoHistory: function() {\n this.modal.disableButton(\"Import\");\n var new_history_name = this.modal\n .$(\"input[name=history_name]\")\n .val();\n var that = this;\n if (new_history_name !== \"\") {\n $.post(Galaxy.root + \"api/histories\", {\n name: new_history_name\n })\n .done(function(new_history) {\n that.options.last_used_history_id = new_history.id;\n that.processImportToHistory(\n new_history.id,\n new_history.name\n );\n })\n .fail(function(xhr, status, error) {\n mod_toastr.error(\"An error occurred.\");\n })\n .always(function() {\n that.modal.enableButton(\"Import\");\n });\n } else {\n var history_id = $(\n \"select[name=dataset_import_bulk] option:selected\"\n ).val();\n this.options.last_used_history_id = history_id;\n var history_name = $(\n \"select[name=dataset_import_bulk] option:selected\"\n ).text();\n this.processImportToHistory(history_id, history_name);\n this.modal.enableButton(\"Import\");\n }\n },\n\n processImportToHistory: function(history_id, history_name) {\n var dataset_ids = [];\n var folder_ids = [];\n this.findCheckedRows().each(function() {\n var row_id = $(this)\n .closest(\"tr\")\n .data(\"id\");\n if (row_id.substring(0, 1) == \"F\") {\n folder_ids.push(row_id);\n } else {\n dataset_ids.push(row_id);\n }\n });\n // prepare the dataset objects to be imported\n var datasets_to_import = [];\n for (var i = dataset_ids.length - 1; i >= 0; i--) {\n var library_dataset_id = dataset_ids[i];\n var historyItem = new mod_library_model.HistoryItem();\n historyItem.url =\n historyItem.urlRoot + history_id + \"/contents\";\n historyItem.content = library_dataset_id;\n historyItem.source = \"library\";\n datasets_to_import.push(historyItem);\n }\n\n // prepare the folder objects to be imported\n var folders_to_import = [];\n for (var i = folder_ids.length - 1; i >= 0; i--) {\n var library_folder_id = folder_ids[i];\n var historyItem = new mod_library_model.HistoryItem();\n historyItem.url =\n historyItem.urlRoot + history_id + \"/contents\";\n historyItem.content = library_folder_id;\n historyItem.source = \"library_folder\";\n datasets_to_import.push(historyItem);\n }\n\n this.initChainCallControl({\n length: datasets_to_import.length,\n action: \"to_history\",\n history_name: history_name\n });\n // set the used history as current so user will see the last one\n // that he imported into in the history panel on the 'analysis' page\n jQuery.getJSON(\n Galaxy.root + \"history/set_as_current?id=\" + history_id\n );\n this.chainCallImportingIntoHistory(\n datasets_to_import,\n history_name\n );\n },\n\n /**\n * Update the progress bar in modal window.\n */\n updateProgress: function() {\n this.progress += this.progressStep;\n $(\".progress-bar-import\").width(\n Math.round(this.progress) + \"%\"\n );\n var txt_representation =\n Math.round(this.progress) + \"% Complete\";\n $(\".completion_span\").text(txt_representation);\n },\n\n /**\n * download selected datasets\n * @param {str} folder_id id of the current folder\n * @param {str} format requested archive format\n */\n download: function(folder_id, format) {\n var dataset_ids = [];\n var folder_ids = [];\n this.findCheckedRows().each(function() {\n var row_id = $(this)\n .closest(\"tr\")\n .data(\"id\");\n if (row_id.substring(0, 1) == \"F\") {\n folder_ids.push(row_id);\n } else {\n dataset_ids.push(row_id);\n }\n });\n var url =\n Galaxy.root + \"api/libraries/datasets/download/\" + format;\n var data = { ld_ids: dataset_ids, folder_ids: folder_ids };\n this.processDownload(url, data, \"get\");\n },\n\n /**\n * Create hidden form and submit it through POST\n * to initialize the download.\n * @param {str} url url to call\n * @param {obj} data data to include in the request\n * @param {str} method method of the request\n */\n processDownload: function(url, data, method) {\n if (url && data) {\n // data can be string of parameters or array/object\n data = typeof data === \"string\" ? data : $.param(data);\n // split params into form inputs\n var inputs = \"\";\n $.each(data.split(\"&\"), function() {\n var pair = this.split(\"=\");\n inputs +=\n '';\n });\n // send request\n $(\n '\"\n )\n .appendTo(\"body\")\n .submit()\n .remove();\n mod_toastr.info(\"Your download will begin soon.\");\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n },\n\n addFilesFromHistoryModal: function() {\n this.histories = new mod_library_model.GalaxyHistories();\n var self = this;\n this.histories\n .fetch()\n .done(function() {\n self.modal = Galaxy.modal;\n var template_modal = self.templateAddFilesFromHistory();\n self.modal.show({\n closing_events: true,\n title: \"Adding datasets from your history\",\n body: template_modal({\n histories: self.histories.models\n }),\n buttons: {\n Add: function() {\n self.addAllDatasetsFromHistory();\n },\n Close: function() {\n Galaxy.modal.hide();\n }\n },\n closing_callback: function() {\n Galaxy.libraries.library_router.navigate(\n \"folders/\" + self.id,\n { trigger: true }\n );\n }\n });\n self.fetchAndDisplayHistoryContents(\n self.histories.models[0].id\n );\n $(\"#dataset_add_bulk\").change(function(event) {\n self.fetchAndDisplayHistoryContents(\n event.target.value\n );\n });\n })\n .fail(function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n });\n },\n\n /**\n * Create modal for importing from Galaxy path.\n * This feature is admin-only.\n */\n importFilesFromPathModal: function() {\n var that = this;\n this.modal = Galaxy.modal;\n var template_modal = this.templateImportPathModal();\n this.modal.show({\n closing_events: true,\n title: \"Please enter paths to import\",\n body: template_modal({}),\n buttons: {\n Import: function() {\n that.importFromPathsClicked(that);\n },\n Close: function() {\n Galaxy.modal.hide();\n }\n },\n closing_callback: function() {\n // TODO: should not trigger routes outside of the router\n Galaxy.libraries.library_router.navigate(\n \"folders/\" + that.id,\n { trigger: true }\n );\n }\n });\n this.renderSelectBoxes();\n },\n\n /**\n * Request all extensions and genomes from Galaxy\n * and save them sorted in arrays.\n */\n fetchExtAndGenomes: function() {\n var that = this;\n mod_utils.get({\n url: Galaxy.root + \"api/datatypes?extension_only=False\",\n success: function(datatypes) {\n that.list_extensions = [];\n for (var key in datatypes) {\n that.list_extensions.push({\n id: datatypes[key].extension,\n text: datatypes[key].extension,\n description: datatypes[key].description,\n description_url: datatypes[key].description_url\n });\n }\n that.list_extensions.sort(function(a, b) {\n return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;\n });\n that.list_extensions.unshift(that.auto);\n },\n cache: true\n });\n mod_utils.get({\n url: Galaxy.root + \"api/genomes\",\n success: function(genomes) {\n that.list_genomes = [];\n for (var key in genomes) {\n that.list_genomes.push({\n id: genomes[key][1],\n text: genomes[key][0]\n });\n }\n that.list_genomes.sort(function(a, b) {\n return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;\n });\n },\n cache: true\n });\n },\n\n renderSelectBoxes: function() {\n // This won't work properly unlesss we already have the data fetched.\n // See this.fetchExtAndGenomes()\n // TODO switch to common resources:\n // https://trello.com/c/dIUE9YPl/1933-ui-common-resources-and-data-into-galaxy-object\n var that = this;\n this.select_genome = new mod_select.View({\n css: \"library-genome-select\",\n data: that.list_genomes,\n container: Galaxy.modal.$el.find(\"#library_genome_select\"),\n value: \"?\"\n });\n this.select_extension = new mod_select.View({\n css: \"library-extension-select\",\n data: that.list_extensions,\n container: Galaxy.modal.$el.find(\n \"#library_extension_select\"\n ),\n value: \"auto\"\n });\n },\n\n /**\n * Create modal for importing from given directory\n * on Galaxy. Bind jQuery events.\n */\n importFilesFromGalaxyFolderModal: function(options) {\n var that = this;\n var template_modal = this.templateBrowserModal();\n this.modal = Galaxy.modal;\n this.modal.show({\n closing_events: true,\n title: \"Please select folders or files\",\n body: template_modal({}),\n buttons: {\n Import: function() {\n that.importFromJstreePath(that, options);\n },\n Close: function() {\n Galaxy.modal.hide();\n }\n },\n closing_callback: function() {\n // TODO: should not trigger routes outside of the router\n Galaxy.libraries.library_router.navigate(\n \"folders/\" + that.id,\n { trigger: true }\n );\n }\n });\n\n $(\".libimport-select-all\").bind(\"click\", function() {\n $(\"#jstree_browser\").jstree(\"check_all\");\n });\n $(\".libimport-select-none\").bind(\"click\", function() {\n $(\"#jstree_browser\").jstree(\"uncheck_all\");\n });\n\n this.renderSelectBoxes();\n options.disabled_jstree_element = \"folders\";\n this.renderJstree(options);\n\n $(\"input[type=radio]\").change(function(event) {\n if (event.target.value === \"jstree-disable-folders\") {\n options.disabled_jstree_element = \"folders\";\n that.renderJstree(options);\n $(\".jstree-folders-message\").hide();\n $(\".jstree-preserve-structure\").hide();\n $(\".jstree-files-message\").show();\n } else if (event.target.value === \"jstree-disable-files\") {\n $(\".jstree-files-message\").hide();\n $(\".jstree-folders-message\").show();\n $(\".jstree-preserve-structure\").show();\n options.disabled_jstree_element = \"files\";\n that.renderJstree(options);\n }\n });\n },\n\n /**\n * Fetch the contents of user directory on Galaxy\n * and render jstree component based on received\n * data.\n * @param {[type]} options [description]\n */\n renderJstree: function(options) {\n var that = this;\n this.options = _.extend(this.options, options);\n var target = options.source || \"userdir\";\n var disabled_jstree_element = this.options\n .disabled_jstree_element;\n this.jstree = new mod_library_model.Jstree();\n this.jstree.url =\n this.jstree.urlRoot +\n \"?target=\" +\n target +\n \"&format=jstree\" +\n \"&disable=\" +\n disabled_jstree_element;\n this.jstree.fetch({\n success: function(model, response) {\n // This is to prevent double jquery load. I think. Carl is magician.\n define(\"jquery\", function() {\n return jQuery;\n });\n // Now we need jstree, time to lazy load it.\n require([\"libs/jquery/jstree\"], function(jstree) {\n $(\"#jstree_browser\").jstree(\"destroy\");\n $(\"#jstree_browser\").jstree({\n core: {\n data: model\n },\n plugins: [\"types\", \"checkbox\"],\n types: {\n folder: {\n icon: \"jstree-folder\"\n },\n file: {\n icon: \"jstree-file\"\n }\n },\n checkbox: {\n three_state: false\n }\n });\n });\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n if (response.responseJSON.err_code === 404001) {\n mod_toastr.warning(\n response.responseJSON.err_msg\n );\n } else {\n mod_toastr.error(response.responseJSON.err_msg);\n }\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n }\n });\n },\n\n /**\n * Take the paths from the textarea, split it, create\n * a request queue and call a function that starts sending\n * one by one to be imported on the server.\n */\n importFromPathsClicked: function() {\n var preserve_dirs = this.modal.$el\n .find(\".preserve-checkbox\")\n .is(\":checked\");\n var link_data = this.modal.$el\n .find(\".link-checkbox\")\n .is(\":checked\");\n var space_to_tab = this.modal.$el\n .find(\".spacetab-checkbox\")\n .is(\":checked\");\n var to_posix_lines = this.modal.$el\n .find(\".posix-checkbox\")\n .is(\":checked\");\n var tag_using_filenames = this.modal.$el\n .find(\".tag-files\")\n .is(\":checked\");\n var file_type = this.select_extension.value();\n var dbkey = this.select_genome.value();\n var paths = $(\"textarea#import_paths\").val();\n var valid_paths = [];\n if (!paths) {\n mod_toastr.info(\n \"Please enter a path relative to Galaxy root.\"\n );\n } else {\n this.modal.disableButton(\"Import\");\n paths = paths.split(\"\\n\");\n for (var i = paths.length - 1; i >= 0; i--) {\n var trimmed = paths[i].trim();\n if (trimmed.length !== 0) {\n valid_paths.push(trimmed);\n }\n }\n this.initChainCallControl({\n length: valid_paths.length,\n action: \"adding_datasets\"\n });\n this.chainCallImportingFolders({\n paths: valid_paths,\n preserve_dirs: preserve_dirs,\n link_data: link_data,\n space_to_tab: space_to_tab,\n to_posix_lines: to_posix_lines,\n source: \"admin_path\",\n file_type: file_type,\n tag_using_filenames: tag_using_filenames,\n dbkey: dbkey\n });\n }\n },\n\n /**\n * Initialize the control of chaining requests\n * in the current modal.\n * @param {int} length The number of items in the chain call.\n */\n initChainCallControl: function(options) {\n var template;\n switch (options.action) {\n case \"adding_datasets\":\n template = this.templateAddingDatasetsProgressBar();\n this.modal.$el.find(\".modal-body\").html(\n template({\n folder_name: this.options.folder_name\n })\n );\n break;\n case \"deleting_datasets\":\n template = this.templateDeletingItemsProgressBar();\n this.modal.$el.find(\".modal-body\").html(template());\n break;\n case \"to_history\":\n template = this.templateImportIntoHistoryProgressBar();\n this.modal.$el\n .find(\".modal-body\")\n .html(\n template({ history_name: options.history_name })\n );\n break;\n default:\n Galaxy.emit.error(\n \"Wrong action specified.\",\n \"datalibs\"\n );\n break;\n }\n\n // var progress_bar_tmpl = this.templateAddingDatasetsProgressBar();\n // this.modal.$el.find( '.modal-body' ).html( progress_bar_tmpl( { folder_name : this.options.folder_name } ) );\n this.progress = 0;\n this.progressStep = 100 / options.length;\n this.options.chain_call_control.total_number = options.length;\n this.options.chain_call_control.failed_number = 0;\n },\n\n /**\n * Take the selected items from the jstree, create a request queue\n * and send them one by one to the server for importing into\n * the current folder.\n *\n * jstree.js has to be loaded before\n * @see renderJstree\n */\n importFromJstreePath: function(that, options) {\n var all_nodes = $(\"#jstree_browser\")\n .jstree()\n .get_selected(true);\n // remove the disabled elements that could have been trigerred with the 'select all'\n var selected_nodes = _.filter(all_nodes, function(node) {\n return node.state.disabled == false;\n });\n var preserve_dirs = this.modal.$el\n .find(\".preserve-checkbox\")\n .is(\":checked\");\n var link_data = this.modal.$el\n .find(\".link-checkbox\")\n .is(\":checked\");\n var space_to_tab = this.modal.$el\n .find(\".spacetab-checkbox\")\n .is(\":checked\");\n var to_posix_lines = this.modal.$el\n .find(\".posix-checkbox\")\n .is(\":checked\");\n var file_type = this.select_extension.value();\n var dbkey = this.select_genome.value();\n var tag_using_filenames = this.modal.$el\n .find(\".tag-files\")\n .is(\":checked\");\n var selection_type = selected_nodes[0].type;\n var paths = [];\n if (selected_nodes.length < 1) {\n mod_toastr.info(\"Please select some items first.\");\n } else {\n this.modal.disableButton(\"Import\");\n for (var i = selected_nodes.length - 1; i >= 0; i--) {\n if (selected_nodes[i].li_attr.full_path !== undefined) {\n paths.push(selected_nodes[i].li_attr.full_path);\n }\n }\n this.initChainCallControl({\n length: paths.length,\n action: \"adding_datasets\"\n });\n if (selection_type === \"folder\") {\n var full_source = options.source + \"_folder\";\n this.chainCallImportingFolders({\n paths: paths,\n preserve_dirs: preserve_dirs,\n link_data: link_data,\n space_to_tab: space_to_tab,\n to_posix_lines: to_posix_lines,\n source: full_source,\n file_type: file_type,\n dbkey: dbkey,\n tag_using_filenames: tag_using_filenames\n });\n } else if (selection_type === \"file\") {\n var full_source = options.source + \"_file\";\n this.chainCallImportingUserdirFiles({\n paths: paths,\n file_type: file_type,\n dbkey: dbkey,\n link_data: link_data,\n space_to_tab: space_to_tab,\n to_posix_lines: to_posix_lines,\n source: full_source,\n tag_using_filenames: tag_using_filenames\n });\n }\n }\n },\n\n fetchAndDisplayHistoryContents: function(history_id) {\n var history_contents = new mod_library_model.HistoryContents({\n id: history_id\n });\n var self = this;\n history_contents.fetch({\n success: function(history_contents) {\n var history_contents_template = self.templateHistoryContents();\n self.histories\n .get(history_id)\n .set({ contents: history_contents });\n self.modal.$el.find(\"#selected_history_content\").html(\n history_contents_template({\n history_contents: history_contents.models.reverse()\n })\n );\n self.modal.$el\n .find(\".history-import-select-all\")\n .bind(\"click\", function() {\n $(\n \"#selected_history_content [type=checkbox]\"\n ).prop(\"checked\", true);\n });\n self.modal.$el\n .find(\".history-import-unselect-all\")\n .bind(\"click\", function() {\n $(\n \"#selected_history_content [type=checkbox]\"\n ).prop(\"checked\", false);\n });\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n }\n });\n },\n\n /**\n * Import all selected datasets from history into the current folder.\n */\n addAllDatasetsFromHistory: function() {\n var checked_hdas = this.modal.$el\n .find(\"#selected_history_content\")\n .find(\":checked\");\n var history_item_ids = []; // can be hda or hdca\n var history_item_types = [];\n var items_to_add = [];\n if (checked_hdas.length < 1) {\n mod_toastr.info(\"You must select some datasets first.\");\n } else {\n this.modal.disableButton(\"Add\");\n checked_hdas.each(function() {\n var hid = $(this)\n .closest(\"li\")\n .data(\"id\");\n if (hid) {\n var item_type = $(this)\n .closest(\"li\")\n .data(\"name\");\n history_item_ids.push(hid);\n history_item_types.push(item_type);\n }\n });\n for (var i = history_item_ids.length - 1; i >= 0; i--) {\n var history_item_id = history_item_ids[i];\n var folder_item = new mod_library_model.Item();\n folder_item.url =\n Galaxy.root +\n \"api/folders/\" +\n this.options.id +\n \"/contents\";\n if (history_item_types[i] === \"collection\") {\n folder_item.set({ from_hdca_id: history_item_id });\n } else {\n folder_item.set({ from_hda_id: history_item_id });\n }\n items_to_add.push(folder_item);\n }\n this.initChainCallControl({\n length: items_to_add.length,\n action: \"adding_datasets\"\n });\n this.chainCallAddingHdas(items_to_add);\n }\n },\n\n /**\n * Take array of empty history items and make request for each of them\n * to create it on server. Update progress in between calls.\n * @param {array} history_item_set array of empty history items\n * @param {str} history_name name of the history to import to\n */\n chainCallImportingIntoHistory: function(\n history_item_set,\n history_name\n ) {\n var self = this;\n var popped_item = history_item_set.pop();\n if (typeof popped_item == \"undefined\") {\n if (this.options.chain_call_control.failed_number === 0) {\n mod_toastr.success(\n \"Selected datasets imported into history. Click this to start analyzing it.\",\n \"\",\n {\n onclick: function() {\n window.location = Galaxy.root;\n }\n }\n );\n } else if (\n this.options.chain_call_control.failed_number ===\n this.options.chain_call_control.total_number\n ) {\n mod_toastr.error(\n \"There was an error and no datasets were imported into history.\"\n );\n } else if (\n this.options.chain_call_control.failed_number <\n this.options.chain_call_control.total_number\n ) {\n mod_toastr.warning(\n \"Some of the datasets could not be imported into history. Click this to see what was imported.\",\n \"\",\n {\n onclick: function() {\n window.location = Galaxy.root;\n }\n }\n );\n }\n Galaxy.modal.hide();\n return true;\n }\n var promise = $.when(\n popped_item.save({\n content: popped_item.content,\n source: popped_item.source\n })\n );\n\n promise\n .done(function() {\n self.updateProgress();\n self.chainCallImportingIntoHistory(\n history_item_set,\n history_name\n );\n })\n .fail(function() {\n self.options.chain_call_control.failed_number += 1;\n self.updateProgress();\n self.chainCallImportingIntoHistory(\n history_item_set,\n history_name\n );\n });\n },\n\n /**\n * Take the array of paths and create a request for each of them\n * calling them in chain. Update the progress bar in between each.\n * @param {array} paths paths relative to user folder on Galaxy\n * @param {boolean} tag_using_filenames add tags to datasets using names of files\n */\n chainCallImportingUserdirFiles: function(options) {\n var that = this;\n var popped_item = options.paths.pop();\n if (typeof popped_item === \"undefined\") {\n if (this.options.chain_call_control.failed_number === 0) {\n mod_toastr.success(\n \"Selected files imported into the current folder\"\n );\n Galaxy.modal.hide();\n } else {\n mod_toastr.error(\"An error occured.\");\n }\n return true;\n }\n var promise = $.when(\n $.post(\n Galaxy.root +\n \"api/libraries/datasets?encoded_folder_id=\" +\n that.id +\n \"&source=\" +\n options.source +\n \"&path=\" +\n popped_item +\n \"&file_type=\" +\n options.file_type +\n \"&link_data=\" +\n options.link_data +\n \"&space_to_tab=\" +\n options.space_to_tab +\n \"&to_posix_lines=\" +\n options.to_posix_lines +\n \"&dbkey=\" +\n options.dbkey +\n \"&tag_using_filenames=\" +\n options.tag_using_filenames\n )\n );\n promise\n .done(function(response) {\n that.updateProgress();\n that.chainCallImportingUserdirFiles(options);\n })\n .fail(function() {\n that.options.chain_call_control.failed_number += 1;\n that.updateProgress();\n that.chainCallImportingUserdirFiles(options);\n });\n },\n\n /**\n * Take the array of paths and create a request for each of them\n * calling them in series. Update the progress bar in between each.\n * @param {array} paths paths relative to Galaxy root folder\n * @param {boolean} preserve_dirs indicates whether to preserve folder structure\n * @param {boolean} link_data copy files to Galaxy or link instead\n * @param {boolean} to_posix_lines convert line endings to POSIX standard\n * @param {boolean} space_to_tab convert spaces to tabs\n * @param {str} source string representing what type of folder\n * is the source of import\n * @param {boolean} tag_using_filenames add tags to datasets using names of files\n */\n chainCallImportingFolders: function(options) {\n // TODO need to check which paths to call\n var that = this;\n var popped_item = options.paths.pop();\n if (typeof popped_item == \"undefined\") {\n if (this.options.chain_call_control.failed_number === 0) {\n mod_toastr.success(\n \"Selected folders and their contents imported into the current folder.\"\n );\n Galaxy.modal.hide();\n } else {\n // TODO better error report\n mod_toastr.error(\"An error occured.\");\n }\n return true;\n }\n var promise = $.when(\n $.post(\n Galaxy.root +\n \"api/libraries/datasets?encoded_folder_id=\" +\n that.id +\n \"&source=\" +\n options.source +\n \"&path=\" +\n popped_item +\n \"&preserve_dirs=\" +\n options.preserve_dirs +\n \"&link_data=\" +\n options.link_data +\n \"&to_posix_lines=\" +\n options.to_posix_lines +\n \"&space_to_tab=\" +\n options.space_to_tab +\n \"&file_type=\" +\n options.file_type +\n \"&dbkey=\" +\n options.dbkey +\n \"&tag_using_filenames=\" +\n options.tag_using_filenames\n )\n );\n promise\n .done(function(response) {\n that.updateProgress();\n that.chainCallImportingFolders(options);\n })\n .fail(function() {\n that.options.chain_call_control.failed_number += 1;\n that.updateProgress();\n that.chainCallImportingFolders(options);\n });\n },\n\n /**\n * Take the array of hdas and create a request for each.\n * Call them in chain and update progress bar in between each.\n * @param {array} hdas_set array of empty hda objects\n */\n chainCallAddingHdas: function(hdas_set) {\n var self = this;\n this.added_hdas = new mod_library_model.Folder();\n var popped_item = hdas_set.pop();\n if (typeof popped_item == \"undefined\") {\n if (this.options.chain_call_control.failed_number === 0) {\n mod_toastr.success(\n \"Selected datasets from history added to the folder\"\n );\n } else if (\n this.options.chain_call_control.failed_number ===\n this.options.chain_call_control.total_number\n ) {\n mod_toastr.error(\n \"There was an error and no datasets were added to the folder.\"\n );\n } else if (\n this.options.chain_call_control.failed_number <\n this.options.chain_call_control.total_number\n ) {\n mod_toastr.warning(\n \"Some of the datasets could not be added to the folder\"\n );\n }\n Galaxy.modal.hide();\n return this.added_hdas;\n }\n var promise = $.when(\n popped_item.save({\n from_hda_id: popped_item.get(\"from_hda_id\")\n })\n );\n\n promise\n .done(function(model) {\n Galaxy.libraries.folderListView.collection.add(model);\n self.updateProgress();\n self.chainCallAddingHdas(hdas_set);\n })\n .fail(function() {\n self.options.chain_call_control.failed_number += 1;\n self.updateProgress();\n self.chainCallAddingHdas(hdas_set);\n });\n },\n\n /**\n * Take the array of lddas, create request for each and\n * call them in chain. Update progress bar in between each.\n * @param {array} lddas_set array of lddas to delete\n */\n chainCallDeletingItems: function(items_to_delete) {\n var self = this;\n this.deleted_items = new mod_library_model.Folder();\n var item_to_delete = items_to_delete.pop();\n if (typeof item_to_delete === \"undefined\") {\n if (this.options.chain_call_control.failed_number === 0) {\n mod_toastr.success(\"Selected items were deleted.\");\n } else if (\n this.options.chain_call_control.failed_number ===\n this.options.chain_call_control.total_number\n ) {\n mod_toastr.error(\n \"There was an error and no items were deleted. Please make sure you have sufficient permissions.\"\n );\n } else if (\n this.options.chain_call_control.failed_number <\n this.options.chain_call_control.total_number\n ) {\n mod_toastr.warning(\n \"Some of the items could not be deleted. Please make sure you have sufficient permissions.\"\n );\n }\n Galaxy.modal.hide();\n return this.deleted_items;\n }\n item_to_delete\n .destroy()\n .done(function(item) {\n Galaxy.libraries.folderListView.collection.remove(\n item_to_delete.id\n );\n self.updateProgress();\n // add the deleted item to collection, triggers rendering\n if (\n Galaxy.libraries.folderListView.options\n .include_deleted\n ) {\n var updated_item = null;\n if (\n item.type === \"folder\" ||\n item.model_class === \"LibraryFolder\"\n ) {\n updated_item = new mod_library_model.FolderAsModel(\n item\n );\n } else if (\n item.type === \"file\" ||\n item.model_class === \"LibraryDataset\"\n ) {\n updated_item = new mod_library_model.Item(item);\n } else {\n Galaxy.emit.error(\n \"Unknown library item type found.\",\n \"datalibs\"\n );\n Galaxy.emit.error(\n item.type || item.model_class,\n \"datalibs\"\n );\n }\n Galaxy.libraries.folderListView.collection.add(\n updated_item\n );\n }\n self.chainCallDeletingItems(items_to_delete);\n })\n .fail(function() {\n self.options.chain_call_control.failed_number += 1;\n self.updateProgress();\n self.chainCallDeletingItems(items_to_delete);\n });\n },\n\n /**\n * Handles the click on 'show deleted' checkbox\n */\n checkIncludeDeleted: function(event) {\n if (event.target.checked) {\n Galaxy.libraries.folderListView.fetchFolder({\n include_deleted: true\n });\n } else {\n Galaxy.libraries.folderListView.fetchFolder({\n include_deleted: false\n });\n }\n },\n\n /**\n * Delete the selected items. Atomic. One by one.\n */\n deleteSelectedItems: function() {\n var dataset_ids = [];\n var folder_ids = [];\n var $checkedValues = this.findCheckedRows();\n if ($checkedValues.length === 0) {\n mod_toastr.info(\n \"You must select at least one item for deletion.\"\n );\n } else {\n var template = this.templateDeletingItemsProgressBar();\n this.modal = Galaxy.modal;\n this.modal.show({\n closing_events: true,\n title: \"Deleting selected items\",\n body: template({}),\n buttons: {\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n // init the control counters\n this.options.chain_call_control.total_number = 0;\n this.options.chain_call_control.failed_number = 0;\n $checkedValues.each(function() {\n var row_id = $(this)\n .closest(\"tr\")\n .data(\"id\");\n if (row_id !== undefined) {\n if (row_id.substring(0, 1) == \"F\") {\n folder_ids.push(row_id);\n } else {\n dataset_ids.push(row_id);\n }\n }\n });\n // init the progress bar\n var items_total = dataset_ids.length + folder_ids.length;\n this.progressStep = 100 / items_total;\n this.progress = 0;\n\n // prepare the dataset items to be added\n var items_to_delete = [];\n for (var i = dataset_ids.length - 1; i >= 0; i--) {\n var dataset = new mod_library_model.Item({\n id: dataset_ids[i]\n });\n items_to_delete.push(dataset);\n }\n for (var i = folder_ids.length - 1; i >= 0; i--) {\n var folder = new mod_library_model.FolderAsModel({\n id: folder_ids[i]\n });\n items_to_delete.push(folder);\n }\n\n this.options.chain_call_control.total_number = items_total;\n // call the recursive function to call ajax one after each other (request FIFO queue)\n this.chainCallDeletingItems(items_to_delete);\n }\n },\n\n showLocInfo: function() {\n var library = null;\n var that = this;\n if (Galaxy.libraries.libraryListView !== null) {\n library = Galaxy.libraries.libraryListView.collection.get(\n this.options.parent_library_id\n );\n this.showLocInfoModal(library);\n } else {\n library = new mod_library_model.Library({\n id: this.options.parent_library_id\n });\n library.fetch({\n success: function() {\n that.showLocInfoModal(library);\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n }\n });\n }\n },\n\n showLocInfoModal: function(library) {\n var that = this;\n var template = this.templateLocInfoInModal();\n this.modal = Galaxy.modal;\n this.modal.show({\n closing_events: true,\n title: \"Location Details\",\n body: template({ library: library, options: that.options }),\n buttons: {\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n },\n\n showImportModal: function(options) {\n switch (options.source) {\n case \"history\":\n this.addFilesFromHistoryModal();\n break;\n case \"importdir\":\n this.importFilesFromGalaxyFolderModal({\n source: \"importdir\"\n });\n break;\n case \"path\":\n this.importFilesFromPathModal();\n break;\n case \"userdir\":\n this.importFilesFromGalaxyFolderModal({\n source: \"userdir\"\n });\n break;\n default:\n Galaxy.libraries.library_router.back();\n mod_toastr.error(\"Invalid import source.\");\n break;\n }\n },\n\n /**\n * Show user the prompt to change the number of items shown on page.\n */\n showPageSizePrompt: function() {\n var folder_page_size = prompt(\n \"How many items per page do you want to see?\",\n Galaxy.libraries.preferences.get(\"folder_page_size\")\n );\n if (\n folder_page_size != null &&\n folder_page_size == parseInt(folder_page_size)\n ) {\n Galaxy.libraries.preferences.set({\n folder_page_size: parseInt(folder_page_size)\n });\n Galaxy.libraries.folderListView.render({\n id: this.options.id,\n show_page: 1\n });\n }\n },\n\n findCheckedRows: function() {\n return $(\"#folder_list_body\").find(\":checked\");\n },\n\n templateToolBar: function() {\n return _.template(\n [\n // container start\n '\",\n '',\n \" \",\n \"\",\n ' ',\n '<%- content_item.get(\"name\") %>',\n \" \",\n \"\",\n '<%- content_item.get(\"description\") %>',\n \" \",\n \"\",\n \"folder\",\n \" \",\n \"\",\n \" \",\n '<%= _.escape(content_item.get(\"update_time\")) %>',\n \" \",\n \"\",\n '',\n '\",\n \" \",\n \"',\n // toolbar start\n '\"\n ].join(\"\")\n );\n },\n\n templateLocInfoInModal: function() {\n return _.template(\n [\n \"',\n '\",\n \"\",\n // toolbar end\n '',\n \"\",\n // paginator will append here\n '',\n // container end\n \"\",\n '\"\n ].join(\"\")\n );\n },\n\n templateNewFolderInModal: function() {\n return _.template(\n [\n '',\n \"\",\n '
\",\n 'library ',\n \"\",\n \"\",\n \"\",\n \" \",\n \" \",\n '<% if(library.get(\"description\") !== \"\") { %>',\n \"name \",\n '<%- library.get(\"name\") %> ',\n \"\",\n \" \",\n \"<% } %>\",\n '<% if(library.get(\"synopsis\") !== \"\") { %>',\n \"description \",\n '<%- library.get(\"description\") %> ',\n \"\",\n \" \",\n \"<% } %>\",\n '<% if(library.get(\"create_time_pretty\") !== \"\") { %>',\n \"synopsis \",\n '<%- library.get(\"synopsis\") %> ',\n \"\",\n \" \",\n \"<% } %>\",\n \"created \",\n '\"><%- library.get(\"create_time_pretty\") %> ',\n \"\",\n \" \",\n \"\",\n \"id \",\n '<%- library.get(\"id\") %> ',\n \"',\n \"\",\n '
\",\n \"folder ',\n \"\",\n \"\",\n \"\",\n \" \",\n \" \",\n '<% if(options.folder_description !== \"\") { %>',\n \"name \",\n \"<%- options.folder_name %> \",\n \"\",\n \" \",\n \"<% } %>\",\n \"description \",\n \"<%- options.folder_description %> \",\n \"\",\n \" \",\n \"\",\n \"id \",\n \"<%- options.id %> \",\n \"',\n \"\",\n \"\"\n ].join(\"\")\n );\n },\n\n templateBulkImportInModal: function() {\n return _.template(\n [\n \"\",\n '\"\n ].join(\"\")\n );\n },\n\n templateImportIntoHistoryProgressBar: function() {\n return _.template(\n [\n '',\n \"Select history: \",\n '\",\n \"\",\n '',\n \"or create new: \",\n '',\n \"\",\n \"\",\n \"',\n \"Importing selected items to history <%= _.escape(history_name) %>\",\n \"\",\n '',\n '\",\n \"\"\n ].join(\"\")\n );\n },\n\n templateAddingDatasetsProgressBar: function() {\n return _.template(\n [\n '',\n \"Adding selected datasets to library folder <%= _.escape(folder_name) %>\",\n \"\",\n '',\n '\",\n \"\"\n ].join(\"\")\n );\n },\n\n templateDeletingItemsProgressBar: function() {\n return _.template(\n [\n '',\n \"\",\n '',\n '\",\n \"\"\n ].join(\"\")\n );\n },\n\n templateBrowserModal: function() {\n return _.template(\n [\n '',\n '\"\n ].join(\"\")\n );\n },\n\n templateImportPathModal: function() {\n return _.template(\n [\n 'All files you select will be imported into the current folder ignoring their folder structure.',\n '',\n '',\n '\",\n '\",\n \"\",\n '',\n '\",\n '\",\n '\",\n '\",\n \"\",\n '\",\n '\",\n \"
\",\n // append jstree object here\n '',\n \"\",\n \"
\",\n \"You can set extension type and genome for all imported datasets at once:
\",\n \"\",\n 'Type: ',\n 'Genome: ',\n \"\",\n \"
\",\n \"\",\n '\",\n \"\",\n \"',\n '\"\n ].join(\"\")\n );\n },\n\n templateAddFilesFromHistory: function() {\n return _.template(\n [\n 'All files within the given folders and their subfolders will be imported into the current folder.',\n '',\n '\",\n '\",\n \"\",\n '',\n \"
\",\n '\",\n '\",\n \"
\",\n \"You can set extension type and genome for all imported datasets at once:
\",\n \"\",\n 'Type: ',\n 'Genome: ',\n \"\",\n \"\",\n '\",\n \"\",\n \"',\n \"\"\n ].join(\"\")\n );\n },\n\n templateHistoryContents: function() {\n return _.template(\n [\n \"\",\n \"1. Select history: \",\n '\",\n \"\",\n \"
\",\n '',\n \"\",\n \"2. Choose the datasets to import:
\",\n \"\",\n '\",\n '\",\n \"\",\n \"
\",\n \"- \",\n \"<% _.each(history_contents, function(history_item) { %>\",\n '<% if (history_item.get(\"deleted\") != true ) { %>',\n '<% var item_name = history_item.get(\"name\") %>',\n '<% if (history_item.get(\"type\") === \"collection\") { %>',\n '<% var collection_type = history_item.get(\"collection_type\") %>',\n '<% if (collection_type === \"list\") { %>',\n '
- ',\n \"<% if ( ( show_page - 1 ) > 0 ) { %>\",\n \"<% if ( ( show_page - 1 ) > page_count ) { %>\", // we are on higher page than total page count\n '
',\n // toolbar start\n '\"\n ].join(\"\")\n );\n },\n\n templateLocInfoInModal: function() {\n return _.template(\n [\n \"',\n '\",\n \"\",\n // toolbar end\n '',\n \"\",\n // paginator will append here\n '',\n // container end\n \"\",\n '\"\n ].join(\"\")\n );\n },\n\n templateNewFolderInModal: function() {\n return _.template(\n [\n '',\n \"\",\n '
\",\n 'library ',\n \"\",\n \"\",\n \"\",\n \" \",\n \" \",\n '<% if(library.get(\"description\") !== \"\") { %>',\n \"name \",\n '<%- library.get(\"name\") %> ',\n \"\",\n \" \",\n \"<% } %>\",\n '<% if(library.get(\"synopsis\") !== \"\") { %>',\n \"description \",\n '<%- library.get(\"description\") %> ',\n \"\",\n \" \",\n \"<% } %>\",\n '<% if(library.get(\"create_time_pretty\") !== \"\") { %>',\n \"synopsis \",\n '<%- library.get(\"synopsis\") %> ',\n \"\",\n \" \",\n \"<% } %>\",\n \"created \",\n '\"><%- library.get(\"create_time_pretty\") %> ',\n \"\",\n \" \",\n \"\",\n \"id \",\n '<%- library.get(\"id\") %> ',\n \"',\n \"\",\n '
\",\n \"folder ',\n \"\",\n \"\",\n \"\",\n \" \",\n \" \",\n '<% if(options.folder_description !== \"\") { %>',\n \"name \",\n \"<%- options.folder_name %> \",\n \"\",\n \" \",\n \"<% } %>\",\n \"description \",\n \"<%- options.folder_description %> \",\n \"\",\n \" \",\n \"\",\n \"id \",\n \"<%- options.id %> \",\n \"',\n \"\",\n \"\"\n ].join(\"\")\n );\n },\n\n templateBulkImportInModal: function() {\n return _.template(\n [\n \"\",\n '\"\n ].join(\"\")\n );\n },\n\n templateImportIntoHistoryProgressBar: function() {\n return _.template(\n [\n '',\n \"Select history: \",\n '\",\n \"\",\n '',\n \"or create new: \",\n '',\n \"\",\n \"\",\n \"',\n \"Importing selected items to history <%= _.escape(history_name) %>\",\n \"\",\n '',\n '\",\n \"\"\n ].join(\"\")\n );\n },\n\n templateAddingDatasetsProgressBar: function() {\n return _.template(\n [\n '',\n \"Adding selected datasets to library folder <%= _.escape(folder_name) %>\",\n \"\",\n '',\n '\",\n \"\"\n ].join(\"\")\n );\n },\n\n templateDeletingItemsProgressBar: function() {\n return _.template(\n [\n '',\n \"\",\n '',\n '\",\n \"\"\n ].join(\"\")\n );\n },\n\n templateBrowserModal: function() {\n return _.template(\n [\n '',\n '\"\n ].join(\"\")\n );\n },\n\n templateImportPathModal: function() {\n return _.template(\n [\n 'All files you select will be imported into the current folder ignoring their folder structure.',\n '',\n '',\n '\",\n '\",\n \"\",\n '',\n '\",\n '\",\n '\",\n '\",\n \"\",\n '\",\n '\",\n \"
\",\n // append jstree object here\n '',\n \"\",\n \"
\",\n \"You can set extension type and genome for all imported datasets at once:
\",\n \"\",\n 'Type: ',\n 'Genome: ',\n \"\",\n \"
\",\n \"\",\n '\",\n \"\",\n \"',\n '\"\n ].join(\"\")\n );\n },\n\n templateAddFilesFromHistory: function() {\n return _.template(\n [\n 'All files within the given folders and their subfolders will be imported into the current folder.',\n '',\n '\",\n '\",\n \"\",\n '',\n \"
\",\n '\",\n '\",\n \"
\",\n \"You can set extension type and genome for all imported datasets at once:
\",\n \"\",\n 'Type: ',\n 'Genome: ',\n \"\",\n \"\",\n '\",\n \"\",\n \"',\n \"\"\n ].join(\"\")\n );\n },\n\n templateHistoryContents: function() {\n return _.template(\n [\n \"\",\n \"1. Select history: \",\n '\",\n \"\",\n \"
\",\n '',\n \"\",\n \"2. Choose the datasets to import:
\",\n \"\",\n '\",\n '\",\n \"\",\n \"
\",\n \"- \",\n \"<% _.each(history_contents, function(history_item) { %>\",\n '<% if (history_item.get(\"deleted\") != true ) { %>',\n '<% var item_name = history_item.get(\"name\") %>',\n '<% if (history_item.get(\"type\") === \"collection\") { %>',\n '<% var collection_type = history_item.get(\"collection_type\") %>',\n '<% if (collection_type === \"list\") { %>',\n '
- ',\n \"<% if ( ( show_page - 1 ) > 0 ) { %>\",\n \"<% if ( ( show_page - 1 ) > page_count ) { %>\", // we are on higher page than total page count\n '
',\n '\"\n ].join(\"\")\n );\n }\n });\n\n return {\n LibraryView: LibraryView\n };\n }\n);\n"]} \ No newline at end of file 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[\"libs/toastr\", \"mvc/library/library-model\", \"mvc/ui/ui-select\"],\n function(mod_toastr, mod_library_model, mod_select) {\n var LibraryView = Backbone.View.extend({\n el: \"#center\",\n\n model: null,\n\n options: {},\n\n events: {\n \"click .toolbtn_save_permissions\": \"savePermissions\"\n },\n\n initialize: function(options) {\n this.options = _.extend(this.options, options);\n if (this.options.id) {\n this.fetchLibrary();\n }\n },\n\n fetchLibrary: function(options) {\n this.options = _.extend(this.options, options);\n this.model = new mod_library_model.Library({\n id: this.options.id\n });\n var that = this;\n this.model.fetch({\n success: function() {\n if (that.options.show_permissions) {\n that.showPermissions();\n }\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(\n response.responseJSON.err_msg +\n \" Click this to go back.\",\n \"\",\n {\n onclick: function() {\n Galaxy.libraries.library_router.back();\n }\n }\n );\n } else {\n mod_toastr.error(\n \"An error occurred. Click this to go back.\",\n \"\",\n {\n onclick: function() {\n Galaxy.libraries.library_router.back();\n }\n }\n );\n }\n }\n });\n },\n\n showPermissions: function(options) {\n this.options = _.extend(this.options, options);\n $(\".tooltip\").remove();\n\n if (this.options.fetched_permissions !== undefined) {\n if (\n this.options.fetched_permissions\n .access_library_role_list.length === 0\n ) {\n this.model.set({ is_unrestricted: true });\n } else {\n this.model.set({ is_unrestricted: false });\n }\n }\n var is_admin = false;\n if (Galaxy.user) {\n is_admin = Galaxy.user.isAdmin();\n }\n var template = this.templateLibraryPermissions();\n this.$el.html(\n template({ library: this.model, is_admin: is_admin })\n );\n\n var self = this;\n $.get(\n Galaxy.root +\n \"api/libraries/\" +\n self.id +\n \"/permissions?scope=current\"\n )\n .done(function(fetched_permissions) {\n self.prepareSelectBoxes({\n fetched_permissions: fetched_permissions\n });\n })\n .fail(function() {\n mod_toastr.error(\n \"An error occurred while attempting to fetch library permissions.\"\n );\n });\n\n $(\"#center [data-toggle]\").tooltip();\n //hack to show scrollbars\n $(\"#center\").css(\"overflow\", \"auto\");\n },\n\n _serializeRoles: function(role_list) {\n var selected_roles = [];\n for (var i = 0; i < role_list.length; i++) {\n selected_roles.push(\n role_list[i][1] + \":\" + role_list[i][0]\n );\n }\n return selected_roles;\n },\n\n prepareSelectBoxes: function(options) {\n this.options = _.extend(this.options, options);\n var fetched_permissions = this.options.fetched_permissions;\n var self = this;\n\n var selected_access_library_roles = this._serializeRoles(\n fetched_permissions.access_library_role_list\n );\n var selected_add_item_roles = this._serializeRoles(\n fetched_permissions.add_library_item_role_list\n );\n var selected_manage_library_roles = this._serializeRoles(\n fetched_permissions.manage_library_role_list\n );\n var selected_modify_library_roles = this._serializeRoles(\n fetched_permissions.modify_library_role_list\n );\n\n self.accessSelectObject = new mod_select.View(\n this._createSelectOptions(\n this,\n \"access_perm\",\n selected_access_library_roles,\n true\n )\n );\n self.addSelectObject = new mod_select.View(\n this._createSelectOptions(\n this,\n \"add_perm\",\n selected_add_item_roles,\n false\n )\n );\n self.manageSelectObject = new mod_select.View(\n this._createSelectOptions(\n this,\n \"manage_perm\",\n selected_manage_library_roles,\n false\n )\n );\n self.modifySelectObject = new mod_select.View(\n this._createSelectOptions(\n this,\n \"modify_perm\",\n selected_modify_library_roles,\n false\n )\n );\n },\n\n _createSelectOptions: function(\n self,\n id,\n init_data,\n is_library_access\n ) {\n is_library_access =\n is_library_access === true ? is_library_access : false;\n var select_options = {\n minimumInputLength: 0,\n css: id,\n multiple: true,\n placeholder: \"Click to select a role\",\n container: self.$el.find(\"#\" + id),\n ajax: {\n url:\n Galaxy.root +\n \"api/libraries/\" +\n self.id +\n \"/permissions?scope=available&is_library_access=\" +\n is_library_access,\n dataType: \"json\",\n quietMillis: 100,\n data: function(term, page) {\n // page is the one-based page number tracked by Select2\n return {\n q: term, //search term\n page_limit: 10, // page size\n page: page // page number\n };\n },\n results: function(data, page) {\n var more = page * 10 < data.total; // whether or not there are more results available\n // notice we return the value of more so Select2 knows if more results can be loaded\n return { results: data.roles, more: more };\n }\n },\n formatResult: function roleFormatResult(role) {\n return role.name + \" type: \" + role.type;\n },\n\n formatSelection: function roleFormatSelection(role) {\n return role.name;\n },\n initSelection: function(element, callback) {\n // the input tag has a value attribute preloaded that points to a preselected role's id\n // this function resolves that id attribute to an object that select2 can render\n // using its formatResult renderer - that way the role name is shown preselected\n var data = [];\n $(element.val().split(\",\")).each(function() {\n var item = this.split(\":\");\n data.push({\n id: item[0],\n name: item[1]\n });\n });\n callback(data);\n },\n // initialData: init_data.join(','),\n initialData: init_data,\n dropdownCssClass: \"bigdrop\" // apply css that makes the dropdown taller\n };\n\n return select_options;\n },\n\n makeDatasetPrivate: function() {\n var self = this;\n $.post(\n Galaxy.root +\n \"api/libraries/datasets/\" +\n self.id +\n \"/permissions?action=make_private\"\n )\n .done(function(fetched_permissions) {\n self.model.set({ is_unrestricted: false });\n self.showPermissions({\n fetched_permissions: fetched_permissions\n });\n mod_toastr.success(\n \"The dataset is now private to you.\"\n );\n })\n .fail(function() {\n mod_toastr.error(\n \"An error occurred while attempting to make dataset private.\"\n );\n });\n },\n\n removeDatasetRestrictions: function() {\n var self = this;\n $.post(\n Galaxy.root +\n \"api/libraries/datasets/\" +\n self.id +\n \"/permissions?action=remove_restrictions\"\n )\n .done(function(fetched_permissions) {\n self.model.set({ is_unrestricted: true });\n self.showPermissions({\n fetched_permissions: fetched_permissions\n });\n mod_toastr.success(\n \"Access to this dataset is now unrestricted.\"\n );\n })\n .fail(function() {\n mod_toastr.error(\n \"An error occurred while attempting to make dataset unrestricted.\"\n );\n });\n },\n\n _extractIds: function(roles_list) {\n var ids_list = [];\n for (var i = roles_list.length - 1; i >= 0; i--) {\n ids_list.push(roles_list[i].id);\n }\n return ids_list;\n },\n savePermissions: function(event) {\n var self = this;\n\n var access_ids = this._extractIds(\n this.accessSelectObject.$el.select2(\"data\")\n );\n var add_ids = this._extractIds(\n this.addSelectObject.$el.select2(\"data\")\n );\n var manage_ids = this._extractIds(\n this.manageSelectObject.$el.select2(\"data\")\n );\n var modify_ids = this._extractIds(\n this.modifySelectObject.$el.select2(\"data\")\n );\n\n $.post(\n Galaxy.root +\n \"api/libraries/\" +\n self.id +\n \"/permissions?action=set_permissions\",\n {\n \"access_ids[]\": access_ids,\n \"add_ids[]\": add_ids,\n \"manage_ids[]\": manage_ids,\n \"modify_ids[]\": modify_ids\n }\n )\n .done(function(fetched_permissions) {\n //fetch dataset again\n self.showPermissions({\n fetched_permissions: fetched_permissions\n });\n mod_toastr.success(\"Permissions saved.\");\n })\n .fail(function() {\n mod_toastr.error(\n \"An error occurred while attempting to set library permissions.\"\n );\n });\n },\n\n templateLibraryPermissions: function() {\n return _.template(\n [\n '',\n '',\n '\",\n \"\",\n \"\",\n \"\",\n 'Library: <%= _.escape(library.get(\"name\")) %>',\n \"
\",\n '',\n \"<% if (is_admin) { %>\",\n \"You are logged in as an administrator therefore you can manage any library on this Galaxy instance. Please make sure you understand the consequences.\",\n \"<% } else { %>\",\n \"You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.\",\n \"<% }%>\",\n \"\",\n '',\n \"\",\n \"Library permissions
\",\n \"Roles that can access the library
\",\n '',\n '',\n \"User with any of these roles can access this library. If there are no access roles set on the library it is considered unrestricted.\",\n \"\",\n \"Roles that can manage permissions on this library
\",\n '',\n '',\n \"User with any of these roles can manage permissions on this library (includes giving access).\",\n \"\",\n \"Roles that can add items to this library
\",\n '',\n '',\n \"User with any of these roles can add items to this library (folders and datasets).\",\n \"\",\n \"Roles that can modify this library
\",\n '',\n '',\n \"User with any of these roles can modify this library (name, synopsis, etc.).\",\n \"\",\n '\",\n \"',\n '\"\n ].join(\"\")\n );\n }\n });\n\n return {\n LibraryView: LibraryView\n };\n }\n);\n"]} \ No newline at end of file diff --git a/static/maps/mvc/library/library-librarylist-view.js.map b/static/maps/mvc/library/library-librarylist-view.js.map index 9bee19d84e0..9ae4940f9ea 100644 --- a/static/maps/mvc/library/library-librarylist-view.js.map +++ b/static/maps/mvc/library/library-librarylist-view.js.map @@ -1 +1 @@ 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[\n \"libs/toastr\",\n \"mvc/library/library-model\",\n \"mvc/library/library-libraryrow-view\",\n \"libs/underscore\"\n ],\n function(mod_toastr, mod_library_model, mod_library_libraryrow_view, _) {\n var LibraryListView = Backbone.View.extend({\n el: \"#libraries_element\",\n\n events: {\n \"click .sort-libraries-link\": \"sort_clicked\"\n },\n\n defaults: {\n page_count: null,\n show_page: null,\n all_fetched: false\n },\n\n /**\n * Initialize and fetch the libraries from server.\n * Async render afterwards.\n * @param {object} options an object with options\n */\n initialize: function(options) {\n this.options = _.defaults(\n this.options || {},\n options,\n this.defaults\n );\n var that = this;\n this.modal = null;\n // collection of {Item}s\n this.collection = new mod_library_model.Libraries();\n this.collection.url =\n this.collection.urlRoot + \"?deleted=false\";\n this.collection.fetch({\n success: function() {\n that.render();\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n }\n });\n },\n\n /**\n * Render the libraries table either from the object's own collection,\n * or from a given array of library models,\n * or render an empty list in case no data is given.\n */\n render: function(options) {\n this.options = _.extend(this.options, options);\n this.setElement(\"#libraries_element\");\n var template = this.templateLibraryList();\n var libraries_to_render = null;\n var models = null;\n var is_public = function(model) {\n return model.get(\"public\") === true;\n };\n $(\".tooltip\").hide();\n if (typeof options !== \"undefined\") {\n models =\n typeof options.models !== \"undefined\"\n ? options.models\n : null;\n }\n if (this.collection !== null && models === null) {\n this.sortLibraries();\n if (Galaxy.libraries.preferences.get(\"with_deleted\")) {\n libraries_to_render = this.collection.models;\n } else {\n libraries_to_render = this.collection.where({\n deleted: false\n });\n }\n if (\n Galaxy.libraries.preferences.get(\"without_restricted\")\n ) {\n libraries_to_render = _.filter(\n libraries_to_render,\n is_public\n );\n }\n } else if (models !== null) {\n if (Galaxy.libraries.preferences.get(\"with_deleted\")) {\n libraries_to_render = models;\n } else {\n var is_deleted = function(model) {\n return model.get(\"deleted\") === false;\n };\n libraries_to_render = _.filter(models, is_deleted);\n }\n if (\n Galaxy.libraries.preferences.get(\"without_restricted\")\n ) {\n libraries_to_render = _.filter(\n libraries_to_render,\n is_public\n );\n }\n } else {\n libraries_to_render = [];\n }\n\n // pagination\n if (\n this.options.show_page === null ||\n this.options.show_page < 1\n ) {\n this.options.show_page = 1;\n }\n this.options.total_libraries_count = libraries_to_render.length;\n var page_start =\n Galaxy.libraries.preferences.get(\"library_page_size\") *\n (this.options.show_page - 1);\n this.options.page_count = Math.ceil(\n this.options.total_libraries_count /\n Galaxy.libraries.preferences.get(\"library_page_size\")\n );\n if (\n this.options.total_libraries_count > 0 &&\n page_start < this.options.total_libraries_count\n ) {\n libraries_to_render = libraries_to_render.slice(\n page_start,\n page_start +\n Galaxy.libraries.preferences.get(\n \"library_page_size\"\n )\n );\n this.options.libraries_shown = libraries_to_render.length;\n // User requests page with no libraries\n if (\n Galaxy.libraries.preferences.get(\"library_page_size\") *\n this.options.show_page >\n this.options.total_libraries_count +\n Galaxy.libraries.preferences.get(\n \"library_page_size\"\n )\n ) {\n libraries_to_render = [];\n }\n this.$el.html(\n template({\n length: 1,\n order: Galaxy.libraries.preferences.get(\n \"sort_order\"\n ),\n search_term:\n Galaxy.libraries.libraryToolbarView.options\n .search_term\n })\n );\n Galaxy.libraries.libraryToolbarView.renderPaginator(\n this.options\n );\n this.renderRows(libraries_to_render);\n } else {\n this.$el.html(\n template({\n length: 0,\n order: Galaxy.libraries.preferences.get(\n \"sort_order\"\n ),\n search_term:\n Galaxy.libraries.libraryToolbarView.options\n .search_term\n })\n );\n Galaxy.libraries.libraryToolbarView.renderPaginator(\n this.options\n );\n }\n $(\"#center [data-toggle]\").tooltip();\n $(\"#center\").css(\"overflow\", \"auto\");\n },\n\n fetchDeleted: function() {\n if (this.options.all_fetched) {\n this.render();\n } else {\n var that = this;\n this.collection.url =\n this.collection.urlRoot + \"?deleted=true\";\n this.collection.fetch({\n remove: false,\n success: function() {\n that.options.all_fetched = true;\n that.render();\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n }\n });\n }\n },\n\n /**\n * Render all given models as rows in the library list\n * @param {array} libraries_to_render array of library models to render\n */\n renderRows: function(libraries_to_render) {\n for (var i = 0; i < libraries_to_render.length; i++) {\n var library = libraries_to_render[i];\n this.renderOne({ library: library });\n }\n },\n\n /**\n * Create a view for the given model and add it to the libraries view.\n * @param {Library} model of the view that will be rendered\n */\n renderOne: function(options) {\n var library = options.library;\n var rowView = new mod_library_libraryrow_view.LibraryRowView(\n library\n );\n this.$el.find(\"#library_list_body\").append(rowView.el);\n },\n\n /**\n * Table heading was clicked, update sorting preferences and re-render.\n * @return {[type]} [description]\n */\n sort_clicked: function() {\n if (Galaxy.libraries.preferences.get(\"sort_order\") === \"asc\") {\n Galaxy.libraries.preferences.set({ sort_order: \"desc\" });\n } else {\n Galaxy.libraries.preferences.set({ sort_order: \"asc\" });\n }\n this.render();\n },\n\n /**\n * Sort the underlying collection according to the parameters received.\n * Currently supports only sorting by name.\n */\n sortLibraries: function() {\n if (Galaxy.libraries.preferences.get(\"sort_by\") === \"name\") {\n if (\n Galaxy.libraries.preferences.get(\"sort_order\") === \"asc\"\n ) {\n this.collection.sortByNameAsc();\n } else if (\n Galaxy.libraries.preferences.get(\"sort_order\") ===\n \"desc\"\n ) {\n this.collection.sortByNameDesc();\n }\n }\n },\n\n /**\n * In case the search_term is not empty perform the search and render\n * the result. Render all visible libraries otherwise.\n * @param {string} search_term string to search for\n */\n searchLibraries: function(search_term) {\n var trimmed_term = $.trim(search_term);\n if (trimmed_term !== \"\") {\n var results = null;\n results = this.collection.search(search_term);\n this.options.searching = true;\n this.render({ models: results, show_page: 1 });\n } else {\n this.options.searching = false;\n this.render();\n }\n },\n\n // MMMMMMMMMMMMMMMMMM\n // === TEMPLATES ====\n // MMMMMMMMMMMMMMMMMM\n\n templateLibraryList: function() {\n return _.template(\n [\n '',\n '',\n '\",\n \"\",\n \"\",\n \"\",\n 'Library: <%= _.escape(library.get(\"name\")) %>',\n \"
\",\n '',\n \"<% if (is_admin) { %>\",\n \"You are logged in as an administrator therefore you can manage any library on this Galaxy instance. Please make sure you understand the consequences.\",\n \"<% } else { %>\",\n \"You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.\",\n \"<% }%>\",\n \"\",\n '',\n \"\",\n \"Library permissions
\",\n \"Roles that can access the library
\",\n '',\n '',\n \"User with any of these roles can access this library. If there are no access roles set on the library it is considered unrestricted.\",\n \"\",\n \"Roles that can manage permissions on this library
\",\n '',\n '',\n \"User with any of these roles can manage permissions on this library (includes giving access).\",\n \"\",\n \"Roles that can add items to this library
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[\n \"libs/toastr\",\n \"mvc/library/library-model\",\n \"mvc/library/library-libraryrow-view\",\n \"libs/underscore\"\n ],\n function(mod_toastr, mod_library_model, mod_library_libraryrow_view, _) {\n var LibraryListView = Backbone.View.extend({\n el: \"#libraries_element\",\n\n events: {\n \"click .sort-libraries-link\": \"sort_clicked\"\n },\n\n defaults: {\n page_count: null,\n show_page: null,\n all_fetched: false\n },\n\n /**\n * Initialize and fetch the libraries from server.\n * Async render afterwards.\n * @param {object} options an object with options\n */\n initialize: function(options) {\n this.options = _.defaults(\n this.options || {},\n options,\n this.defaults\n );\n var that = this;\n this.modal = null;\n // collection of {Item}s\n this.collection = new mod_library_model.Libraries();\n this.collection.url =\n this.collection.urlRoot + \"?deleted=false\";\n this.collection.fetch({\n success: function() {\n that.render();\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n }\n });\n },\n\n /**\n * Render the libraries table either from the object's own collection,\n * or from a given array of library models,\n * or render an empty list in case no data is given.\n */\n render: function(options) {\n this.options = _.extend(this.options, options);\n this.setElement(\"#libraries_element\");\n var template = this.templateLibraryList();\n var libraries_to_render = null;\n var models = null;\n var is_public = function(model) {\n return model.get(\"public\") === true;\n };\n $(\".tooltip\").hide();\n if (typeof options !== \"undefined\") {\n models =\n typeof options.models !== \"undefined\"\n ? options.models\n : null;\n }\n if (this.collection !== null && models === null) {\n this.sortLibraries();\n if (Galaxy.libraries.preferences.get(\"with_deleted\")) {\n libraries_to_render = this.collection.models;\n } else {\n libraries_to_render = this.collection.where({\n deleted: false\n });\n }\n if (\n Galaxy.libraries.preferences.get(\"without_restricted\")\n ) {\n libraries_to_render = _.filter(\n libraries_to_render,\n is_public\n );\n }\n } else if (models !== null) {\n if (Galaxy.libraries.preferences.get(\"with_deleted\")) {\n libraries_to_render = models;\n } else {\n var is_deleted = function(model) {\n return model.get(\"deleted\") === false;\n };\n libraries_to_render = _.filter(models, is_deleted);\n }\n if (\n Galaxy.libraries.preferences.get(\"without_restricted\")\n ) {\n libraries_to_render = _.filter(\n libraries_to_render,\n is_public\n );\n }\n } else {\n libraries_to_render = [];\n }\n\n // pagination\n if (\n this.options.show_page === null ||\n this.options.show_page < 1\n ) {\n this.options.show_page = 1;\n }\n this.options.total_libraries_count = libraries_to_render.length;\n var page_start =\n Galaxy.libraries.preferences.get(\"library_page_size\") *\n (this.options.show_page - 1);\n this.options.page_count = Math.ceil(\n this.options.total_libraries_count /\n Galaxy.libraries.preferences.get(\"library_page_size\")\n );\n if (\n this.options.total_libraries_count > 0 &&\n page_start < this.options.total_libraries_count\n ) {\n libraries_to_render = libraries_to_render.slice(\n page_start,\n page_start +\n Galaxy.libraries.preferences.get(\n \"library_page_size\"\n )\n );\n this.options.libraries_shown = libraries_to_render.length;\n // User requests page with no libraries\n if (\n Galaxy.libraries.preferences.get(\"library_page_size\") *\n this.options.show_page >\n this.options.total_libraries_count +\n Galaxy.libraries.preferences.get(\n \"library_page_size\"\n )\n ) {\n libraries_to_render = [];\n }\n this.$el.html(\n template({\n length: 1,\n order: Galaxy.libraries.preferences.get(\n \"sort_order\"\n ),\n search_term:\n Galaxy.libraries.libraryToolbarView.options\n .search_term\n })\n );\n Galaxy.libraries.libraryToolbarView.renderPaginator(\n this.options\n );\n this.renderRows(libraries_to_render);\n } else {\n this.$el.html(\n template({\n length: 0,\n order: Galaxy.libraries.preferences.get(\n \"sort_order\"\n ),\n search_term:\n Galaxy.libraries.libraryToolbarView.options\n .search_term\n })\n );\n Galaxy.libraries.libraryToolbarView.renderPaginator(\n this.options\n );\n }\n $(\"#center [data-toggle]\").tooltip();\n $(\"#center\").css(\"overflow\", \"auto\");\n },\n\n fetchDeleted: function() {\n if (this.options.all_fetched) {\n this.render();\n } else {\n var that = this;\n this.collection.url =\n this.collection.urlRoot + \"?deleted=true\";\n this.collection.fetch({\n remove: false,\n success: function() {\n that.options.all_fetched = true;\n that.render();\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n }\n });\n }\n },\n\n /**\n * Render all given models as rows in the library list\n * @param {array} libraries_to_render array of library models to render\n */\n renderRows: function(libraries_to_render) {\n for (var i = 0; i < libraries_to_render.length; i++) {\n var library = libraries_to_render[i];\n this.renderOne({ library: library });\n }\n },\n\n /**\n * Create a view for the given model and add it to the libraries view.\n * @param {Library} model of the view that will be rendered\n */\n renderOne: function(options) {\n var library = options.library;\n var rowView = new mod_library_libraryrow_view.LibraryRowView(\n library\n );\n this.$el.find(\"#library_list_body\").append(rowView.el);\n },\n\n /**\n * Table heading was clicked, update sorting preferences and re-render.\n * @return {[type]} [description]\n */\n sort_clicked: function() {\n if (Galaxy.libraries.preferences.get(\"sort_order\") === \"asc\") {\n Galaxy.libraries.preferences.set({ sort_order: \"desc\" });\n } else {\n Galaxy.libraries.preferences.set({ sort_order: \"asc\" });\n }\n this.render();\n },\n\n /**\n * Sort the underlying collection according to the parameters received.\n * Currently supports only sorting by name.\n */\n sortLibraries: function() {\n if (Galaxy.libraries.preferences.get(\"sort_by\") === \"name\") {\n if (\n Galaxy.libraries.preferences.get(\"sort_order\") === \"asc\"\n ) {\n this.collection.sortByNameAsc();\n } else if (\n Galaxy.libraries.preferences.get(\"sort_order\") ===\n \"desc\"\n ) {\n this.collection.sortByNameDesc();\n }\n }\n },\n\n /**\n * In case the search_term is not empty perform the search and render\n * the result. Render all visible libraries otherwise.\n * @param {string} search_term string to search for\n */\n searchLibraries: function(search_term) {\n var trimmed_term = $.trim(search_term);\n if (trimmed_term !== \"\") {\n var results = null;\n results = this.collection.search(search_term);\n this.options.searching = true;\n this.render({ models: results, show_page: 1 });\n } else {\n this.options.searching = false;\n this.render();\n }\n },\n\n // MMMMMMMMMMMMMMMMMM\n // === TEMPLATES ====\n // MMMMMMMMMMMMMMMMMM\n\n templateLibraryList: function() {\n return _.template(\n [\n '\",\n \"There are no libraries matching your search. Try different keyword.\",\n \"\",\n \"<% } else{ %>\",\n \"\",\n \"There are no libraries visible to you here. If you expected some to show up please consult the\",\n ' library security wikipage',\n ' or visit the Galaxy support site.',\n \"\",\n \"<% }%>\",\n \"<% } else{ %>\",\n '',\n \"\",\n '
\",\n \"<% }%>\",\n \"',\n '',\n \"name\",\n \"\",\n '\"/>',\n \" \",\n 'description ',\n 'synopsis ',\n '',\n \"\",\n '',\n // library item views will attach here\n \"\",\n \" ',\n \"<% if(length === 0) { %>\",\n \"<% if(search_term.length > 0) { %>\",\n \"\"\n ].join(\"\")\n );\n }\n });\n\n return {\n LibraryListView: LibraryListView\n };\n }\n);\n"]} \ No newline at end of file diff --git a/static/maps/mvc/library/library-libraryrow-view.js.map b/static/maps/mvc/library/library-libraryrow-view.js.map index 057e133e578..5ce71e062fb 100644 --- a/static/maps/mvc/library/library-libraryrow-view.js.map +++ b/static/maps/mvc/library/library-libraryrow-view.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/library/library-libraryrow-view.js"],"names":["define","mod_masthead","mod_toastr","LibraryRowView","Backbone","View","extend","events","click .edit_library_btn","click .cancel_library_btn","click .save_library_btn","click .delete_library_btn","click 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dependencies\ndefine([\"layout/masthead\", \"utils/utils\", \"libs/toastr\"], function(\n mod_masthead,\n mod_utils,\n mod_toastr\n) {\n // galaxy library row view\n var LibraryRowView = Backbone.View.extend({\n events: {\n \"click .edit_library_btn\": \"edit_button_clicked\",\n \"click .cancel_library_btn\": \"cancel_library_modification\",\n \"click .save_library_btn\": \"save_library_modification\",\n \"click .delete_library_btn\": \"delete_library\",\n \"click .undelete_library_btn\": \"undelete_library\"\n },\n\n edit_mode: false,\n\n element_visibility_config: {\n upload_library_btn: false,\n edit_library_btn: false,\n permission_library_btn: false,\n save_library_btn: false,\n cancel_library_btn: false,\n delete_library_btn: false,\n undelete_library_btn: false\n },\n\n initialize: function(library) {\n this.render(library);\n },\n\n render: function(library) {\n if (typeof library === \"undefined\") {\n library = Galaxy.libraries.libraryListView.collection.get(\n this.$el.data(\"id\")\n );\n }\n this.prepareButtons(library);\n var tmpl = this.templateRow();\n this.setElement(\n tmpl({\n library: library,\n button_config: this.element_visibility_config,\n edit_mode: this.edit_mode\n })\n );\n this.$el.show();\n return this;\n },\n\n repaint: function(library) {\n /* need to hide manually because of the element removal in setElement\n invoked in render() */\n $(\".tooltip\").hide();\n /* we need to store the old element to be able to replace it with\n new one */\n var old_element = this.$el;\n /* if user canceled the library param is undefined,\n if user saved and succeeded the updated library is rendered */\n this.render();\n old_element.replaceWith(this.$el);\n /* now we attach new tooltips to the newly created row element */\n this.$el.find(\"[data-toggle]\").tooltip();\n },\n\n /**\n * Function modifies the visibility of buttons for\n * the filling of the row template of given library.\n */\n prepareButtons: function(library) {\n var vis_config = this.element_visibility_config;\n\n if (this.edit_mode === false) {\n vis_config.save_library_btn = false;\n vis_config.cancel_library_btn = false;\n vis_config.delete_library_btn = false;\n if (library.get(\"deleted\") === true) {\n vis_config.undelete_library_btn = true;\n vis_config.upload_library_btn = false;\n vis_config.edit_library_btn = false;\n vis_config.permission_library_btn = false;\n } else if (library.get(\"deleted\") === false) {\n vis_config.save_library_btn = false;\n vis_config.cancel_library_btn = false;\n vis_config.undelete_library_btn = false;\n if (library.get(\"can_user_add\") === true) {\n vis_config.upload_library_btn = true;\n }\n if (library.get(\"can_user_modify\") === true) {\n vis_config.edit_library_btn = true;\n }\n if (library.get(\"can_user_manage\") === true) {\n vis_config.permission_library_btn = true;\n }\n }\n } else if (this.edit_mode === true) {\n vis_config.upload_library_btn = false;\n vis_config.edit_library_btn = false;\n vis_config.permission_library_btn = false;\n vis_config.save_library_btn = true;\n vis_config.cancel_library_btn = true;\n vis_config.delete_library_btn = true;\n vis_config.undelete_library_btn = false;\n }\n\n this.element_visibility_config = vis_config;\n },\n\n /* User clicked the 'edit' button on row so we render a new row\n that allows editing */\n edit_button_clicked: function() {\n this.edit_mode = true;\n this.repaint();\n },\n\n /* User clicked the 'cancel' button so we render normal rowView */\n cancel_library_modification: function() {\n // mod_toastr.info('Modifications canceled');\n this.edit_mode = false;\n this.repaint();\n },\n\n save_library_modification: function() {\n var library = Galaxy.libraries.libraryListView.collection.get(\n this.$el.data(\"id\")\n );\n var is_changed = false;\n\n var new_name = this.$el.find(\".input_library_name\").val();\n if (\n typeof new_name !== \"undefined\" &&\n new_name !== library.get(\"name\")\n ) {\n if (new_name.length > 2) {\n library.set(\"name\", new_name);\n is_changed = true;\n } else {\n mod_toastr.warning(\n \"Library name has to be at least 3 characters long.\"\n );\n return;\n }\n }\n\n var new_description = this.$el\n .find(\".input_library_description\")\n .val();\n if (\n typeof new_description !== \"undefined\" &&\n new_description !== library.get(\"description\")\n ) {\n library.set(\"description\", new_description);\n is_changed = true;\n }\n\n var new_synopsis = this.$el.find(\".input_library_synopsis\").val();\n if (\n typeof new_synopsis !== \"undefined\" &&\n new_synopsis !== library.get(\"synopsis\")\n ) {\n library.set(\"synopsis\", new_synopsis);\n is_changed = true;\n }\n\n if (is_changed) {\n var row_view = this;\n library.save(null, {\n patch: true,\n success: function(library) {\n row_view.edit_mode = false;\n row_view.repaint(library);\n mod_toastr.success(\"Changes to library saved.\");\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\n \"An error occured while attempting to update the library.\"\n );\n }\n }\n });\n } else {\n this.edit_mode = false;\n this.repaint(library);\n mod_toastr.info(\"Nothing has changed.\");\n }\n },\n\n delete_library: function() {\n var library = Galaxy.libraries.libraryListView.collection.get(\n this.$el.data(\"id\")\n );\n var row_view = this;\n // mark the library deleted\n library.destroy({\n success: function(library) {\n library.set(\"deleted\", true);\n // add the new deleted library back to the collection (Galaxy specialty)\n Galaxy.libraries.libraryListView.collection.add(library);\n row_view.edit_mode = false;\n if (\n Galaxy.libraries.preferences.get(\"with_deleted\") ===\n false\n ) {\n $(\".tooltip\").hide();\n row_view.repaint(library);\n row_view.$el.remove();\n } else if (\n Galaxy.libraries.preferences.get(\"with_deleted\") ===\n true\n ) {\n row_view.repaint(library);\n }\n mod_toastr.success(\"Library has been marked deleted.\");\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\n \"An error occured during deleting the library.\"\n );\n }\n }\n });\n },\n\n undelete_library: function() {\n var library = Galaxy.libraries.libraryListView.collection.get(\n this.$el.data(\"id\")\n );\n var row_view = this;\n\n // mark the library undeleted\n library.url = library.urlRoot + library.id + \"?undelete=true\";\n library.destroy({\n success: function(library) {\n // add the newly undeleted library back to the collection\n // backbone does not accept changes through destroy, so update it too\n library.set(\"deleted\", false);\n Galaxy.libraries.libraryListView.collection.add(library);\n row_view.edit_mode = false;\n row_view.repaint(library);\n mod_toastr.success(\"Library has been undeleted.\");\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\n \"An error occured while undeleting the library.\"\n );\n }\n }\n });\n },\n\n templateRow: function() {\n return _.template(\n [\n '\",\n \"There are no libraries matching your search. Try different keyword.\",\n \"\",\n \"<% } else{ %>\",\n \"\",\n \"There are no libraries visible to you here. If you expected some to show up please consult the\",\n ' library security wikipage',\n ' or visit the Galaxy support site.',\n \"\",\n \"<% }%>\",\n \"<% } else{ %>\",\n '',\n \"\",\n '
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dependencies\ndefine([\"layout/masthead\", \"utils/utils\", \"libs/toastr\"], function(\n mod_masthead,\n mod_utils,\n mod_toastr\n) {\n // galaxy library row view\n var LibraryRowView = Backbone.View.extend({\n events: {\n \"click .edit_library_btn\": \"edit_button_clicked\",\n \"click .cancel_library_btn\": \"cancel_library_modification\",\n \"click .save_library_btn\": \"save_library_modification\",\n \"click .delete_library_btn\": \"delete_library\",\n \"click .undelete_library_btn\": \"undelete_library\"\n },\n\n edit_mode: false,\n\n element_visibility_config: {\n upload_library_btn: false,\n edit_library_btn: false,\n permission_library_btn: false,\n save_library_btn: false,\n cancel_library_btn: false,\n delete_library_btn: false,\n undelete_library_btn: false\n },\n\n initialize: function(library) {\n this.render(library);\n },\n\n render: function(library) {\n if (typeof library === \"undefined\") {\n library = Galaxy.libraries.libraryListView.collection.get(\n this.$el.data(\"id\")\n );\n }\n this.prepareButtons(library);\n var tmpl = this.templateRow();\n this.setElement(\n tmpl({\n library: library,\n button_config: this.element_visibility_config,\n edit_mode: this.edit_mode\n })\n );\n this.$el.show();\n return this;\n },\n\n repaint: function(library) {\n /* need to hide manually because of the element removal in setElement\n invoked in render() */\n $(\".tooltip\").hide();\n /* we need to store the old element to be able to replace it with\n new one */\n var old_element = this.$el;\n /* if user canceled the library param is undefined,\n if user saved and succeeded the updated library is rendered */\n this.render();\n old_element.replaceWith(this.$el);\n /* now we attach new tooltips to the newly created row element */\n this.$el.find(\"[data-toggle]\").tooltip();\n },\n\n /**\n * Function modifies the visibility of buttons for\n * the filling of the row template of given library.\n */\n prepareButtons: function(library) {\n var vis_config = this.element_visibility_config;\n\n if (this.edit_mode === false) {\n vis_config.save_library_btn = false;\n vis_config.cancel_library_btn = false;\n vis_config.delete_library_btn = false;\n if (library.get(\"deleted\") === true) {\n vis_config.undelete_library_btn = true;\n vis_config.upload_library_btn = false;\n vis_config.edit_library_btn = false;\n vis_config.permission_library_btn = false;\n } else if (library.get(\"deleted\") === false) {\n vis_config.save_library_btn = false;\n vis_config.cancel_library_btn = false;\n vis_config.undelete_library_btn = false;\n if (library.get(\"can_user_add\") === true) {\n vis_config.upload_library_btn = true;\n }\n if (library.get(\"can_user_modify\") === true) {\n vis_config.edit_library_btn = true;\n }\n if (library.get(\"can_user_manage\") === true) {\n vis_config.permission_library_btn = true;\n }\n }\n } else if (this.edit_mode === true) {\n vis_config.upload_library_btn = false;\n vis_config.edit_library_btn = false;\n vis_config.permission_library_btn = false;\n vis_config.save_library_btn = true;\n vis_config.cancel_library_btn = true;\n vis_config.delete_library_btn = true;\n vis_config.undelete_library_btn = false;\n }\n\n this.element_visibility_config = vis_config;\n },\n\n /* User clicked the 'edit' button on row so we render a new row\n that allows editing */\n edit_button_clicked: function() {\n this.edit_mode = true;\n this.repaint();\n },\n\n /* User clicked the 'cancel' button so we render normal rowView */\n cancel_library_modification: function() {\n // mod_toastr.info('Modifications canceled');\n this.edit_mode = false;\n this.repaint();\n },\n\n save_library_modification: function() {\n var library = Galaxy.libraries.libraryListView.collection.get(\n this.$el.data(\"id\")\n );\n var is_changed = false;\n\n var new_name = this.$el.find(\".input_library_name\").val();\n if (\n typeof new_name !== \"undefined\" &&\n new_name !== library.get(\"name\")\n ) {\n if (new_name.length > 2) {\n library.set(\"name\", new_name);\n is_changed = true;\n } else {\n mod_toastr.warning(\n \"Library name has to be at least 3 characters long.\"\n );\n return;\n }\n }\n\n var new_description = this.$el\n .find(\".input_library_description\")\n .val();\n if (\n typeof new_description !== \"undefined\" &&\n new_description !== library.get(\"description\")\n ) {\n library.set(\"description\", new_description);\n is_changed = true;\n }\n\n var new_synopsis = this.$el.find(\".input_library_synopsis\").val();\n if (\n typeof new_synopsis !== \"undefined\" &&\n new_synopsis !== library.get(\"synopsis\")\n ) {\n library.set(\"synopsis\", new_synopsis);\n is_changed = true;\n }\n\n if (is_changed) {\n var row_view = this;\n library.save(null, {\n patch: true,\n success: function(library) {\n row_view.edit_mode = false;\n row_view.repaint(library);\n mod_toastr.success(\"Changes to library saved.\");\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\n \"An error occured while attempting to update the library.\"\n );\n }\n }\n });\n } else {\n this.edit_mode = false;\n this.repaint(library);\n mod_toastr.info(\"Nothing has changed.\");\n }\n },\n\n delete_library: function() {\n var library = Galaxy.libraries.libraryListView.collection.get(\n this.$el.data(\"id\")\n );\n var row_view = this;\n // mark the library deleted\n library.destroy({\n success: function(library) {\n library.set(\"deleted\", true);\n // add the new deleted library back to the collection (Galaxy specialty)\n Galaxy.libraries.libraryListView.collection.add(library);\n row_view.edit_mode = false;\n if (\n Galaxy.libraries.preferences.get(\"with_deleted\") ===\n false\n ) {\n $(\".tooltip\").hide();\n row_view.repaint(library);\n row_view.$el.remove();\n } else if (\n Galaxy.libraries.preferences.get(\"with_deleted\") ===\n true\n ) {\n row_view.repaint(library);\n }\n mod_toastr.success(\"Library has been marked deleted.\");\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\n \"An error occured during deleting the library.\"\n );\n }\n }\n });\n },\n\n undelete_library: function() {\n var library = Galaxy.libraries.libraryListView.collection.get(\n this.$el.data(\"id\")\n );\n var row_view = this;\n\n // mark the library undeleted\n library.url = library.urlRoot + library.id + \"?undelete=true\";\n library.destroy({\n success: function(library) {\n // add the newly undeleted library back to the collection\n // backbone does not accept changes through destroy, so update it too\n library.set(\"deleted\", false);\n Galaxy.libraries.libraryListView.collection.add(library);\n row_view.edit_mode = false;\n row_view.repaint(library);\n mod_toastr.success(\"Library has been undeleted.\");\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\n \"An error occured while undeleting the library.\"\n );\n }\n }\n });\n },\n\n templateRow: function() {\n return _.template(\n [\n '<%- library.get(\"name\") %> ',\n \"<% } else { %>\",\n '\"><%- library.get(\"name\") %> ',\n \"<% } %>\",\n '<% if(library.get(\"description\")) { %>',\n '<% if( (library.get(\"description\")).length> 80 ) { %>',\n '\"><%= _.escape(library.get(\"description\")).substring(0, 80) + \"...\" %> ',\n \"<% } else { %>\",\n '<%= _.escape(library.get(\"description\"))%> ',\n \"<% } %>\",\n \"<% } else { %>\",\n \"\",\n \"<% } %>\",\n '<% if(library.get(\"synopsis\")) { %>',\n '<% if( (library.get(\"synopsis\")).length> 120 ) { %>',\n ' \"><%= _.escape(library.get(\"synopsis\")).substring(0, 120) + \"...\" %> ',\n \"<% } else { %>\",\n '<%= _.escape(library.get(\"synopsis\"))%> ',\n \"<% } %>\",\n \"<% } else { %>\",\n \"\",\n \"<% } %>\",\n \"<% } else if(edit_mode){ %>\",\n ' ',\n ' ',\n ' ',\n \"<% } %>\",\n ' ',\n '<% if( (library.get(\"public\")) && (library.get(\"deleted\") === false) ) { %>',\n ' ',\n \"<% }%>\",\n '',\n '/permissions\">',\n '',\n '',\n '',\n '',\n \" \",\n \"\" style=\"display:none;\" data-id=\"<%- library.get(\"id\") %>\">',\n \"<% if(!edit_mode) { %>\",\n '<% if(library.get(\"deleted\")) { %>',\n ' \"\n ].join(\"\")\n );\n }\n });\n\n return {\n LibraryRowView: LibraryRowView\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/library/library-librarytoolbar-view.js.map b/static/maps/mvc/library/library-librarytoolbar-view.js.map index 3824955f195..bc5e25dffa6 100644 --- a/static/maps/mvc/library/library-librarytoolbar-view.js.map +++ b/static/maps/mvc/library/library-librarytoolbar-view.js.map @@ -1 +1 @@ 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\"mvc/library/library-model\"], function(\n mod_toastr,\n mod_library_model\n) {\n /**\n * This view represents the top part of the library page.\n * It contains the tool bar with controls.\n */\n var LibraryToolbarView = Backbone.View.extend({\n el: \"#center\",\n\n defaults: {\n search_term: \"\"\n },\n\n events: {\n \"click #create_new_library_btn\": \"createLibraryFromModal\",\n \"click #include_deleted_chk\": \"includeDeletedChecked\",\n \"click #exclude_restricted_chk\": \"excludeRestrictedChecked\",\n \"click #lib_page_size_prompt\": \"showPageSizePrompt\",\n \"keyup .library-search-input\": \"searchLibraries\"\n },\n\n initialize: function(options) {\n this.options = _.defaults(\n this.options || {},\n options,\n this.defaults\n );\n this.render();\n },\n\n render: function() {\n var toolbar_template = this.templateToolBar();\n var is_admin = false;\n var is_anonym = true;\n if (Galaxy.user) {\n is_admin = Galaxy.user.isAdmin();\n is_anonym = Galaxy.user.isAnonymous();\n }\n 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\"mvc/library/library-model\"], function(\n mod_toastr,\n mod_library_model\n) {\n /**\n * This view represents the top part of the library page.\n * It contains the tool bar with controls.\n */\n var LibraryToolbarView = Backbone.View.extend({\n el: \"#center\",\n\n defaults: {\n search_term: \"\"\n },\n\n events: {\n \"click #create_new_library_btn\": \"createLibraryFromModal\",\n \"click #include_deleted_chk\": \"includeDeletedChecked\",\n \"click #exclude_restricted_chk\": \"excludeRestrictedChecked\",\n \"click #lib_page_size_prompt\": \"showPageSizePrompt\",\n \"keyup .library-search-input\": \"searchLibraries\"\n },\n\n initialize: function(options) {\n this.options = _.defaults(\n this.options || {},\n options,\n this.defaults\n );\n this.render();\n },\n\n render: function() {\n var toolbar_template = this.templateToolBar();\n var is_admin = false;\n var is_anonym = true;\n if (Galaxy.user) {\n is_admin = Galaxy.user.isAdmin();\n is_anonym = Galaxy.user.isAnonymous();\n }\n this.$el.html(\n toolbar_template({ admin_user: is_admin, anon_user: is_anonym })\n );\n if (is_admin) {\n this.$el.find(\n \"#include_deleted_chk\"\n )[0].checked = Galaxy.libraries.preferences.get(\"with_deleted\");\n this.$el.find(\n \"#exclude_restricted_chk\"\n )[0].checked = Galaxy.libraries.preferences.get(\n \"without_restricted\"\n );\n }\n },\n\n /**\n * Renders the element that shows pages into its div within the toolbar.\n */\n renderPaginator: function(options) {\n this.options = _.extend(this.options, options);\n var paginator_template = this.templatePaginator();\n this.$el.find(\"#library_paginator\").html(\n paginator_template({\n show_page: parseInt(this.options.show_page),\n page_count: parseInt(this.options.page_count),\n total_libraries_count: this.options.total_libraries_count,\n libraries_shown: this.options.libraries_shown\n })\n );\n },\n\n /**\n * User clicked on 'New library' button. Show modal to\n * satisfy the wish.\n */\n createLibraryFromModal: function(event) {\n event.preventDefault();\n event.stopPropagation();\n var self = this;\n this.modal = Galaxy.modal;\n this.modal.show({\n closing_events: true,\n title: \"Create New Library\",\n body: this.templateNewLibraryInModal(),\n buttons: {\n Create: function() {\n self.createNewLibrary();\n },\n Close: function() {\n self.modal.hide();\n }\n }\n });\n },\n\n /**\n * Create the new library using the API asynchronously.\n */\n createNewLibrary: function() {\n var libraryDetails = this.serializeNewLibrary();\n if (this.validateNewLibrary(libraryDetails)) {\n var library = new mod_library_model.Library();\n var self = this;\n library.save(libraryDetails, {\n success: function(library) {\n Galaxy.libraries.libraryListView.collection.add(\n library\n );\n self.modal.hide();\n self.clearLibraryModal();\n Galaxy.libraries.libraryListView.render();\n mod_toastr.success(\"Library created.\");\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\"An error occured.\");\n }\n }\n });\n } else {\n mod_toastr.error(\"Library's name is missing.\");\n }\n return false;\n },\n\n /**\n * Show user the propmpt to change the number of libs shown on page.\n */\n showPageSizePrompt: function() {\n var library_page_size = prompt(\n \"How many libraries per page do you want to see?\",\n Galaxy.libraries.preferences.get(\"library_page_size\")\n );\n if (\n library_page_size != null &&\n library_page_size == parseInt(library_page_size)\n ) {\n Galaxy.libraries.preferences.set({\n library_page_size: parseInt(library_page_size)\n });\n Galaxy.libraries.libraryListView.render({ show_page: 1 });\n }\n },\n\n /**\n * Clear the library modal once it is saved.\n */\n clearLibraryModal: function() {\n $(\"input[name='Name']\").val(\"\");\n $(\"input[name='Description']\").val(\"\");\n $(\"input[name='Synopsis']\").val(\"\");\n },\n\n /**\n * Prepare new library variables to be submitted to API.\n */\n serializeNewLibrary: function() {\n return {\n name: $(\"input[name='Name']\").val(),\n description: $(\"input[name='Description']\").val(),\n synopsis: $(\"input[name='Synopsis']\").val()\n };\n },\n\n /**\n * Check whether entered values are valid.\n */\n validateNewLibrary: function(libraryDetails) {\n return libraryDetails.name !== \"\";\n },\n\n /**\n * Include or exclude deleted libraries in the view.\n */\n includeDeletedChecked: function(event) {\n if (event.target.checked) {\n Galaxy.libraries.preferences.set({ with_deleted: true });\n Galaxy.libraries.libraryListView.fetchDeleted();\n } else {\n Galaxy.libraries.preferences.set({ with_deleted: false });\n Galaxy.libraries.libraryListView.render();\n }\n },\n\n /**\n * Include or exclude restricted libraries in the view.\n */\n excludeRestrictedChecked: function(event) {\n if (event.target.checked) {\n Galaxy.libraries.preferences.set({ without_restricted: true });\n } else {\n Galaxy.libraries.preferences.set({ without_restricted: false });\n }\n Galaxy.libraries.libraryListView.render();\n },\n\n /**\n * Take the contents of the search field and send it to the list view\n * to query the collection of libraries.\n */\n searchLibraries: function(event) {\n var search_term = $(\".library-search-input\").val();\n this.options.search_term = search_term;\n Galaxy.libraries.libraryListView.searchLibraries(search_term);\n },\n\n templateToolBar: function() {\n return _.template(\n [\n '',\n '\"\n ].join(\"\")\n );\n },\n\n templatePaginator: function() {\n return _.template(\n [\n '',\n '\",\n '',\n '\",\n \"\",\n \"',\n // table with libraries will append here\n \"\",\n \"- ',\n \"<% if ( ( show_page - 1 ) > 0 ) { %>\",\n \"<% if ( ( show_page - 1 ) > page_count ) { %>\", // we are on higher page than total page count\n '
',\n \"\",\n \"\"\n ].join(\"\")\n );\n }\n });\n\n return {\n LibraryToolbarView: LibraryToolbarView\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/library/library-model.js.map b/static/maps/mvc/library/library-model.js.map index 40c35c01426..a2d5fff0f34 100644 --- a/static/maps/mvc/library/library-model.js.map +++ b/static/maps/mvc/library/library-model.js.map @@ -1 +1 @@ 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function() {\n // ============================================================================\n // LIBRARY RELATED MODELS\n\n var Library = Backbone.Model.extend({\n urlRoot: Galaxy.root + \"api/libraries/\",\n\n /** based on show_deleted would this lib show in the list of lib's?\n * @param {Boolean} show_deleted are we including deleted libraries?\n */\n isVisible: function(show_deleted) {\n var isVisible = true;\n if (!show_deleted && this.get(\"deleted\")) {\n isVisible = false;\n }\n return isVisible;\n }\n });\n\n var Libraries = Backbone.Collection.extend({\n urlRoot: Galaxy.root + \"api/libraries\",\n\n model: Library,\n\n sort_key: \"name\", // default\n\n sort_order: null, // default\n\n initialize: function(options) {\n options = options || {};\n },\n\n search: function(search_term) {\n /**\n * Search the collection and return only the models that have\n * the search term in their names.\n * [the term to search]\n * @type {string}\n */\n if (search_term == \"\") return this;\n var lowercase_term = search_term.toLowerCase();\n return this.filter(function(data) {\n var lowercase_name = data.get(\"name\").toLowerCase();\n return lowercase_name.indexOf(lowercase_term) !== -1;\n });\n },\n\n /** Get every 'shown' library in this collection based on deleted filter\n * @param {Boolean} show_deleted are we including deleted libraries?\n * @returns array of library models\n */\n getVisible: function(show_deleted, filters) {\n filters = filters || [];\n var filteredLibraries = new Libraries(\n this.filter(function(item) {\n return item.isVisible(show_deleted);\n })\n );\n\n return filteredLibraries;\n },\n\n /** Sort collection by library name (ascending) and return the sorted\n * collection\n */\n sortByNameAsc: function() {\n this.comparator = function(libraryA, libraryB) {\n if (\n libraryA.get(\"name\").toLowerCase() >\n libraryB.get(\"name\").toLowerCase()\n ) {\n return 1; // after\n }\n if (\n libraryB.get(\"name\").toLowerCase() >\n libraryA.get(\"name\").toLowerCase()\n ) {\n return -1; // before\n }\n return 0; // equal\n };\n this.sort();\n return this;\n },\n\n /** Sort collection by library name (descending) and return the sorted\n * collection\n */\n sortByNameDesc: function() {\n this.comparator = function(libraryA, libraryB) {\n if (\n libraryA.get(\"name\").toLowerCase() >\n libraryB.get(\"name\").toLowerCase()\n ) {\n return -1; // before\n }\n if (\n libraryB.get(\"name\").toLowerCase() >\n libraryA.get(\"name\").toLowerCase()\n ) {\n return 1; // after\n }\n return 0; // equal\n };\n this.sort();\n return this;\n }\n });\n\n // ============================================================================\n // FOLDER RELATED MODELS\n\n var LibraryItem = Backbone.Model.extend({});\n\n var Ldda = LibraryItem.extend({\n urlRoot: Galaxy.root + \"api/libraries/datasets/\"\n });\n\n var FolderAsModel = LibraryItem.extend({\n urlRoot: Galaxy.root + \"api/folders/\"\n });\n\n var Folder = Backbone.Collection.extend({\n model: LibraryItem,\n\n /** Sort collection by item name (ascending) and return the sorted\n * collection. Folders go before datasets.\n */\n sortByNameAsc: function() {\n this.comparator = function(itemA, itemB) {\n if (itemA.get(\"type\") === itemB.get(\"type\")) {\n if (\n itemA.get(\"name\").toLowerCase() >\n itemB.get(\"name\").toLowerCase()\n ) {\n return 1; // after\n }\n if (\n itemB.get(\"name\").toLowerCase() >\n itemA.get(\"name\").toLowerCase()\n ) {\n return -1; // before\n }\n return 0; // equal\n } else {\n if (itemA.get(\"type\") === \"folder\") {\n return -1; // folder is always before dataset\n } else {\n return 1;\n }\n }\n };\n this.sort();\n return this;\n },\n\n /** Sort collection by item name (descending) and return the sorted\n * collection. Folders go before datasets.\n */\n sortByNameDesc: function() {\n this.comparator = function(itemA, itemB) {\n if (itemA.get(\"type\") === itemB.get(\"type\")) {\n if (\n itemA.get(\"name\").toLowerCase() >\n itemB.get(\"name\").toLowerCase()\n ) {\n return -1; // after\n }\n if (\n itemB.get(\"name\").toLowerCase() >\n itemA.get(\"name\").toLowerCase()\n ) {\n return 1; // before\n }\n return 0; // equal\n } else {\n if (itemA.get(\"type\") === \"folder\") {\n return -1; // folder is always before dataset\n } else {\n return 1;\n }\n }\n };\n this.sort();\n return this;\n }\n });\n\n var FolderContainer = Backbone.Model.extend({\n defaults: {\n folder: new Folder(),\n urlRoot: Galaxy.root + \"api/folders/\",\n id: \"unknown\"\n },\n parse: function(obj) {\n // empty the collection\n this.get(\"folder\").reset();\n // response is not a simple array, it contains metadata\n // this will update the inner collection\n for (var i = 0; i < obj.folder_contents.length; i++) {\n if 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function() {\n // ============================================================================\n // LIBRARY RELATED MODELS\n\n var Library = Backbone.Model.extend({\n urlRoot: Galaxy.root + \"api/libraries/\",\n\n /** based on show_deleted would this lib show in the list of lib's?\n * @param {Boolean} show_deleted are we including deleted libraries?\n */\n isVisible: function(show_deleted) {\n var isVisible = true;\n if (!show_deleted && this.get(\"deleted\")) {\n isVisible = false;\n }\n return isVisible;\n }\n });\n\n var Libraries = Backbone.Collection.extend({\n urlRoot: Galaxy.root + \"api/libraries\",\n\n model: Library,\n\n sort_key: \"name\", // default\n\n sort_order: null, // default\n\n initialize: function(options) {\n options = options || {};\n },\n\n search: function(search_term) {\n /**\n * Search the collection and return only the models that have\n * the search term in their names.\n * [the term to search]\n * @type {string}\n */\n if (search_term == \"\") return this;\n var lowercase_term = search_term.toLowerCase();\n return this.filter(function(data) {\n var lowercase_name = data.get(\"name\").toLowerCase();\n return lowercase_name.indexOf(lowercase_term) !== -1;\n });\n },\n\n /** Get every 'shown' library in this collection based on deleted filter\n * @param {Boolean} show_deleted are we including deleted libraries?\n * @returns array of library models\n */\n getVisible: function(show_deleted, filters) {\n filters = filters || [];\n var filteredLibraries = new Libraries(\n this.filter(function(item) {\n return item.isVisible(show_deleted);\n })\n );\n\n return filteredLibraries;\n },\n\n /** Sort collection by library name (ascending) and return the sorted\n * collection\n */\n sortByNameAsc: function() {\n this.comparator = function(libraryA, libraryB) {\n if (\n libraryA.get(\"name\").toLowerCase() >\n libraryB.get(\"name\").toLowerCase()\n ) {\n return 1; // after\n }\n if (\n libraryB.get(\"name\").toLowerCase() >\n libraryA.get(\"name\").toLowerCase()\n ) {\n return -1; // before\n }\n return 0; // equal\n };\n this.sort();\n return this;\n },\n\n /** Sort collection by library name (descending) and return the sorted\n * collection\n */\n sortByNameDesc: function() {\n this.comparator = function(libraryA, libraryB) {\n if (\n libraryA.get(\"name\").toLowerCase() >\n libraryB.get(\"name\").toLowerCase()\n ) {\n return -1; // before\n }\n if (\n libraryB.get(\"name\").toLowerCase() >\n libraryA.get(\"name\").toLowerCase()\n ) {\n return 1; // after\n }\n return 0; // equal\n };\n this.sort();\n return this;\n }\n });\n\n // ============================================================================\n // FOLDER RELATED MODELS\n\n var LibraryItem = Backbone.Model.extend({});\n\n var Ldda = LibraryItem.extend({\n urlRoot: Galaxy.root + \"api/libraries/datasets/\"\n });\n\n var FolderAsModel = LibraryItem.extend({\n urlRoot: Galaxy.root + \"api/folders/\"\n });\n\n var Folder = Backbone.Collection.extend({\n model: LibraryItem,\n\n /** Sort collection by item name (ascending) and return the sorted\n * collection. Folders go before datasets.\n */\n sortByNameAsc: function() {\n this.comparator = function(itemA, itemB) {\n if (itemA.get(\"type\") === itemB.get(\"type\")) {\n if (\n itemA.get(\"name\").toLowerCase() >\n itemB.get(\"name\").toLowerCase()\n ) {\n return 1; // after\n }\n if (\n itemB.get(\"name\").toLowerCase() >\n itemA.get(\"name\").toLowerCase()\n ) {\n return -1; // before\n }\n return 0; // equal\n } else {\n if (itemA.get(\"type\") === \"folder\") {\n return -1; // folder is always before dataset\n } else {\n return 1;\n }\n }\n };\n this.sort();\n return this;\n },\n\n /** Sort collection by item name (descending) and return the sorted\n * collection. Folders go before datasets.\n */\n sortByNameDesc: function() {\n this.comparator = function(itemA, itemB) {\n if (itemA.get(\"type\") === itemB.get(\"type\")) {\n if (\n itemA.get(\"name\").toLowerCase() >\n itemB.get(\"name\").toLowerCase()\n ) {\n return -1; // after\n }\n if (\n itemB.get(\"name\").toLowerCase() >\n itemA.get(\"name\").toLowerCase()\n ) {\n return 1; // before\n }\n return 0; // equal\n } else {\n if (itemA.get(\"type\") === \"folder\") {\n return -1; // folder is always before dataset\n } else {\n return 1;\n }\n }\n };\n this.sort();\n return this;\n }\n });\n\n var FolderContainer = Backbone.Model.extend({\n defaults: {\n folder: new Folder(),\n urlRoot: Galaxy.root + \"api/folders/\",\n id: \"unknown\"\n },\n parse: function(obj) {\n // empty the collection\n this.get(\"folder\").reset();\n // response is not a simple array, it contains metadata\n // this will update the inner collection\n for (var i = 0; i < obj.folder_contents.length; i++) {\n if (obj.folder_contents[i].type === \"folder\") {\n var folder_item = new FolderAsModel(obj.folder_contents[i]);\n this.get(\"folder\").add(folder_item);\n } else if (obj.folder_contents[i].type === \"file\") {\n var file_item = new Ldda(obj.folder_contents[i]);\n this.get(\"folder\").add(file_item);\n } else {\n Galaxy.emit.error(\n \"Unknown folder item type encountered while parsing response.\"\n );\n }\n }\n return obj;\n }\n });\n\n // ============================================================================\n // HISTORY RELATED MODELS\n // TODO UNITE\n\n var HistoryItem = Backbone.Model.extend({\n urlRoot: Galaxy.root + \"api/histories/\"\n });\n\n var HistoryContents = Backbone.Collection.extend({\n urlRoot: Galaxy.root + \"api/histories/\",\n initialize: function(options) {\n this.id = options.id;\n },\n url: function() {\n return this.urlRoot + this.id + \"/contents\";\n },\n model: HistoryItem\n });\n\n var GalaxyHistory = Backbone.Model.extend({\n urlRoot: Galaxy.root + 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BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\nvar logNamespace = \"list\";\n//==============================================================================\n/** A view which, when first rendered, shows only summary data/attributes, but\n * can be expanded to show further details (and optionally fetch those\n * details from the server).\n */\nvar ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({\n _logNamespace: logNamespace,\n\n //TODO: Although the reasoning behind them is different, this shares a lot with HiddenUntilActivated above: combine them\n //PRECONDITION: model must have method hasDetails\n //PRECONDITION: subclasses must have templates.el and templates.details\n\n initialize: function(attributes) {\n /** are the details of this view expanded/shown or not? */\n this.expanded = attributes.expanded || false;\n this.log(\"\\t expanded:\", this.expanded);\n this.fxSpeed =\n attributes.fxSpeed !== undefined\n ? attributes.fxSpeed\n : this.fxSpeed;\n },\n\n // ........................................................................ render main\n /** jq fx speed */\n fxSpeed: \"fast\",\n\n /** Render this content, set up ui.\n * @param {Number or String} speed the speed of the render\n */\n render: function(speed) {\n var $newRender = this._buildNewRender();\n this._setUpBehaviors($newRender);\n this._queueNewRender($newRender, speed);\n return this;\n },\n\n /** Build a temp div containing the new children for the view's $el.\n * If the view is already expanded, build the details as well.\n */\n _buildNewRender: function() {\n // create a new render using a skeleton template, render title buttons, render body, and set up events, etc.\n var $newRender = $(this.templates.el(this.model.toJSON(), this));\n if (this.expanded) {\n this.$details($newRender).replaceWith(this._renderDetails().show());\n }\n return $newRender;\n },\n\n /** Fade out the old el, swap in the new contents, then fade in.\n * @param {Number or String} speed jq speed to use for rendering effects\n * @fires rendered when rendered\n */\n _queueNewRender: function($newRender, speed) {\n speed = speed === undefined ? this.fxSpeed : speed;\n var view = this;\n\n if (speed === 0) {\n view._swapNewRender($newRender);\n view.trigger(\"rendered\", view);\n } else {\n $(view).queue(\"fx\", [\n function(next) {\n view.$el.fadeOut(speed, next);\n },\n function(next) {\n view._swapNewRender($newRender);\n next();\n },\n function(next) {\n view.$el.fadeIn(speed, next);\n },\n function(next) {\n view.trigger(\"rendered\", view);\n next();\n }\n ]);\n }\n },\n\n /** empty out the current el, move the $newRender's children in */\n _swapNewRender: function($newRender) {\n return this.$el\n .empty()\n .attr(\n \"class\",\n _.isFunction(this.className) ? this.className() : this.className\n )\n .append($newRender.children());\n },\n\n /** set up js behaviors, event handlers for elements within the given container\n * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el)\n */\n _setUpBehaviors: function($where) {\n $where = $where || this.$el;\n // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.)\n //make_popup_menus( $where );\n $where.find(\"[title]\").tooltip({ placement: \"bottom\" });\n },\n\n // ......................................................................... details\n /** shortcut to details DOM (as jQ) */\n $details: function($where) {\n $where = $where || this.$el;\n return $where.find(\"> .details\");\n },\n\n /** build the DOM for the details and set up behaviors on it */\n _renderDetails: function() {\n var $newDetails = $(this.templates.details(this.model.toJSON(), this));\n this._setUpBehaviors($newDetails);\n return $newDetails;\n },\n\n // ......................................................................... expansion/details\n /** Show or hide the details\n * @param {Boolean} expand if true, expand; if false, collapse\n */\n toggleExpanded: function(expand) {\n expand = expand === undefined ? !this.expanded : expand;\n if (expand) {\n this.expand();\n } else {\n this.collapse();\n }\n return this;\n },\n\n /** Render and show the full, detailed body of this view including extra data and controls.\n * note: if the model does not have detailed data, fetch that data before showing the body\n * @fires expanded when a body has been expanded\n */\n expand: function() {\n var view = this;\n return view._fetchModelDetails().always(function() {\n view._expand();\n });\n },\n\n /** Check for model details and, if none, fetch them.\n * @returns {jQuery.promise} the model.fetch.xhr if details are being fetched, an empty promise if not\n */\n _fetchModelDetails: function() {\n if (!this.model.hasDetails()) {\n return this.model.fetch();\n }\n return jQuery.when();\n },\n\n /** Inner fn called when expand (public) has fetched the details */\n _expand: function() {\n var view = this,\n $newDetails = view._renderDetails();\n view.$details().replaceWith($newDetails);\n // needs to be set after the above or the slide will not show\n view.expanded = true;\n view.$details().slideDown(view.fxSpeed, function() {\n view.trigger(\"expanded\", view);\n });\n },\n\n /** Hide the body/details of an HDA.\n * @fires collapsed when a body has been collapsed\n */\n collapse: function() {\n this.debug(this + \"(ExpandableView).collapse\");\n var view = this;\n view.expanded = false;\n this.$details().slideUp(view.fxSpeed, function() {\n view.trigger(\"collapsed\", view);\n });\n }\n});\n\n//==============================================================================\n/** A view that is displayed in some larger list/grid/collection.\n * Inherits from Expandable, Selectable, Draggable.\n * The DOM contains warnings, a title bar, and a series of primary action controls.\n * Primary actions are meant to be easily accessible item functions (such as delete)\n * that are rendered in the title bar.\n *\n * Details are rendered when the user clicks the title bar or presses enter/space when\n * the title bar is in focus.\n *\n * Designed as a base class for history panel contents - but usable elsewhere (I hope).\n */\nvar ListItemView = ExpandableView.extend(\n BASE_MVC.mixin(BASE_MVC.SelectableViewMixin, BASE_MVC.DraggableViewMixin, {\n tagName: \"div\",\n className: \"list-item\",\n\n /** Set up the base class and all mixins */\n initialize: function(attributes) {\n ExpandableView.prototype.initialize.call(this, attributes);\n BASE_MVC.SelectableViewMixin.initialize.call(this, attributes);\n BASE_MVC.DraggableViewMixin.initialize.call(this, attributes);\n this._setUpListeners();\n },\n\n /** event listeners */\n _setUpListeners: function() {\n // hide the primary actions in the title bar when selectable and narrow\n this.on(\n \"selectable\",\n function(isSelectable) {\n if (isSelectable) {\n this.$(\".primary-actions\").hide();\n } else {\n this.$(\".primary-actions\").show();\n }\n },\n this\n );\n return this;\n },\n\n // ........................................................................ rendering\n /** In this override, call methods to build warnings, titlebar and primary actions */\n _buildNewRender: function() {\n var $newRender = ExpandableView.prototype._buildNewRender.call(\n this\n );\n $newRender\n .children(\".warnings\")\n .replaceWith(this._renderWarnings());\n $newRender\n .children(\".title-bar\")\n .replaceWith(this._renderTitleBar());\n $newRender\n .children(\".primary-actions\")\n .append(this._renderPrimaryActions());\n $newRender\n .find(\"> .title-bar .subtitle\")\n .replaceWith(this._renderSubtitle());\n return $newRender;\n },\n\n /** In this override, render the selector controls and set up dragging before the swap */\n _swapNewRender: function($newRender) {\n ExpandableView.prototype._swapNewRender.call(this, $newRender);\n if (this.selectable) {\n this.showSelector(0);\n }\n if (this.draggable) {\n this.draggableOn();\n }\n return this.$el;\n },\n\n /** Render any warnings the item may need to show (e.g. \"I'm deleted\") */\n _renderWarnings: function() {\n var view = this,\n $warnings = $(''),\n json = view.model.toJSON();\n //TODO:! unordered (map)\n _.each(view.templates.warnings, function(templateFn) {\n $warnings.append($(templateFn(json, view)));\n });\n return $warnings;\n },\n\n /** Render the title bar (the main/exposed SUMMARY dom element) */\n _renderTitleBar: function() {\n return $(this.templates.titleBar(this.model.toJSON(), this));\n },\n\n /** Return an array of jQ objects containing common/easily-accessible item controls */\n _renderPrimaryActions: function() {\n // override this\n return [];\n },\n\n /** Render the title bar (the main/exposed SUMMARY dom element) */\n _renderSubtitle: function() {\n return $(this.templates.subtitle(this.model.toJSON(), this));\n },\n\n // ......................................................................... events\n /** event map */\n events: {\n // expand the body when the title is clicked or when in focus and space or enter is pressed\n \"click .title-bar\": \"_clickTitleBar\",\n \"keydown .title-bar\": \"_keyDownTitleBar\",\n \"click .selector\": \"toggleSelect\"\n },\n\n /** expand when the title bar is clicked */\n _clickTitleBar: function(event) {\n event.stopPropagation();\n if (event.altKey) {\n this.toggleSelect(event);\n if (!this.selectable) {\n this.showSelector();\n }\n } else {\n this.toggleExpanded();\n }\n },\n\n /** expand when the title bar is in focus and enter or space is pressed */\n _keyDownTitleBar: function(event) {\n // bail (with propagation) if keydown and not space or enter\n var KEYCODE_SPACE = 32,\n KEYCODE_RETURN = 13;\n if (\n event &&\n event.type === \"keydown\" &&\n (event.keyCode === KEYCODE_SPACE ||\n event.keyCode === KEYCODE_RETURN)\n ) {\n this.toggleExpanded();\n event.stopPropagation();\n return false;\n }\n return true;\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"ListItemView(\" + modelString + \")\";\n }\n })\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nListItemView.prototype.templates = (function() {\n var elTemplato = BASE_MVC.wrapTemplate([\n '',\n // errors, messages, etc.\n '',\n\n // multi-select checkbox\n '\"\n ]);\n\n var warnings = {};\n\n var titleBarTemplate = BASE_MVC.wrapTemplate(\n [\n // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display\n '\"\n ],\n \"element\"\n );\n\n var subtitleTemplate = BASE_MVC.wrapTemplate([\n // override this\n ''\n ]);\n\n var detailsTemplate = BASE_MVC.wrapTemplate([\n // override this\n ''\n ]);\n\n return {\n el: elTemplato,\n warnings: warnings,\n titleBar: titleBarTemplate,\n subtitle: subtitleTemplate,\n details: detailsTemplate\n };\n})();\n\n//==============================================================================\n/** A view that is displayed in some larger list/grid/collection.\n * *AND* can display some sub-list of it's own when expanded (e.g. dataset collections).\n * This list will 'foldout' when the item is expanded depending on this.foldoutStyle:\n * If 'foldout': will expand vertically to show the nested list\n * If 'drilldown': will overlay the parent list\n *\n * Inherits from ListItemView.\n *\n * _renderDetails does the work of creating this.details: a sub-view that shows the nested list\n */\nvar FoldoutListItemView = ListItemView.extend({\n /** If 'foldout': show the sub-panel inside the expanded item\n * If 'drilldown': only fire events and handle by pub-sub\n * (allow the panel containing this item to attach it, hide itself, etc.)\n */\n foldoutStyle: \"foldout\",\n /** Panel view class to instantiate for the sub-panel */\n foldoutPanelClass: null,\n\n /** override to:\n * add attributes foldoutStyle and foldoutPanelClass for config poly\n * disrespect attributes.expanded if drilldown\n */\n initialize: function(attributes) {\n if (this.foldoutStyle === \"drilldown\") {\n this.expanded = false;\n }\n this.foldoutStyle = attributes.foldoutStyle || this.foldoutStyle;\n this.foldoutPanelClass =\n attributes.foldoutPanelClass || this.foldoutPanelClass;\n\n ListItemView.prototype.initialize.call(this, attributes);\n this.foldout = this._createFoldoutPanel();\n },\n\n /** in this override, attach the foldout panel when rendering details */\n _renderDetails: function() {\n if (this.foldoutStyle === \"drilldown\") {\n return $();\n }\n var $newDetails = ListItemView.prototype._renderDetails.call(this);\n return this._attachFoldout(this.foldout, $newDetails);\n },\n\n /** In this override, handle collection expansion. */\n _createFoldoutPanel: function() {\n var model = this.model;\n var FoldoutClass = this._getFoldoutPanelClass(model),\n options = this._getFoldoutPanelOptions(model),\n foldout = new FoldoutClass(\n _.extend(options, {\n model: model\n })\n );\n return foldout;\n },\n\n /** Stub to return proper foldout panel class */\n _getFoldoutPanelClass: function() {\n // override\n return this.foldoutPanelClass;\n },\n\n /** Stub to return proper foldout panel options */\n _getFoldoutPanelOptions: function() {\n return {\n // propagate foldout style down\n foldoutStyle: this.foldoutStyle,\n fxSpeed: this.fxSpeed\n };\n },\n\n /** Render the foldout panel inside the view, hiding controls */\n _attachFoldout: function(foldout, $whereTo) {\n $whereTo = $whereTo || this.$(\"> .details\");\n this.foldout = foldout.render(0);\n foldout.$(\"> .controls\").hide();\n return $whereTo.append(foldout.$el);\n },\n\n /** In this override, branch on foldoutStyle to show expanded */\n expand: function() {\n var view = this;\n return view._fetchModelDetails().always(function() {\n if (view.foldoutStyle === \"foldout\") {\n view._expand();\n } else if (view.foldoutStyle === \"drilldown\") {\n view._expandByDrilldown();\n }\n });\n },\n\n /** For drilldown, set up close handler and fire expanded:drilldown\n * containing views can listen to this and handle other things\n * (like hiding themselves) by listening for expanded/collapsed:drilldown\n */\n _expandByDrilldown: function() {\n var view = this;\n // attachment and rendering done by listener\n view.listenTo(view.foldout, \"close\", function() {\n view.trigger(\"collapsed:drilldown\", view, view.foldout);\n });\n view.trigger(\"expanded:drilldown\", view, view.foldout);\n }\n});\n\n// ............................................................................ 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BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\nvar logNamespace = \"list\";\n//==============================================================================\n/** A view which, when first rendered, shows only summary data/attributes, but\n * can be expanded to show further details (and optionally fetch those\n * details from the server).\n */\nvar ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({\n _logNamespace: logNamespace,\n\n //TODO: Although the reasoning behind them is different, this shares a lot with HiddenUntilActivated above: combine them\n //PRECONDITION: model must have method hasDetails\n //PRECONDITION: subclasses must have templates.el and templates.details\n\n initialize: function(attributes) {\n /** are the details of this view expanded/shown or not? */\n this.expanded = attributes.expanded || false;\n this.log(\"\\t expanded:\", this.expanded);\n this.fxSpeed =\n attributes.fxSpeed !== undefined\n ? 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}\n },\n this\n );\n return this;\n },\n\n // ........................................................................ rendering\n /** In this override, call methods to build warnings, titlebar and primary actions */\n _buildNewRender: function() {\n var $newRender = ExpandableView.prototype._buildNewRender.call(\n this\n );\n $newRender\n .children(\".warnings\")\n .replaceWith(this._renderWarnings());\n $newRender\n .children(\".title-bar\")\n .replaceWith(this._renderTitleBar());\n $newRender\n .children(\".primary-actions\")\n .append(this._renderPrimaryActions());\n $newRender\n .find(\"> .title-bar .subtitle\")\n .replaceWith(this._renderSubtitle());\n return $newRender;\n },\n\n /** In this override, render the selector controls and set up dragging before the swap */\n _swapNewRender: function($newRender) {\n ExpandableView.prototype._swapNewRender.call(this, $newRender);\n if (this.selectable) {\n this.showSelector(0);\n }\n if (this.draggable) {\n this.draggableOn();\n }\n return this.$el;\n },\n\n /** Render any warnings the item may need to show (e.g. \"I'm deleted\") */\n _renderWarnings: function() {\n var view = this,\n $warnings = $(''),\n json = view.model.toJSON();\n //TODO:! unordered (map)\n _.each(view.templates.warnings, function(templateFn) {\n $warnings.append($(templateFn(json, view)));\n });\n return $warnings;\n },\n\n /** Render the title bar (the main/exposed SUMMARY dom element) */\n _renderTitleBar: function() {\n return $(this.templates.titleBar(this.model.toJSON(), this));\n },\n\n /** Return an array of jQ objects containing common/easily-accessible item controls */\n _renderPrimaryActions: function() {\n // override this\n return [];\n },\n\n /** Render the title bar (the main/exposed SUMMARY dom element) */\n _renderSubtitle: function() {\n return $(this.templates.subtitle(this.model.toJSON(), this));\n },\n\n // ......................................................................... events\n /** event map */\n events: {\n // expand the body when the title is clicked or when in focus and space or enter is pressed\n \"click .title-bar\": \"_clickTitleBar\",\n \"keydown .title-bar\": \"_keyDownTitleBar\",\n \"click .selector\": \"toggleSelect\"\n },\n\n /** expand when the title bar is clicked */\n _clickTitleBar: function(event) {\n event.stopPropagation();\n if (event.altKey) {\n this.toggleSelect(event);\n if (!this.selectable) {\n this.showSelector();\n }\n } else {\n this.toggleExpanded();\n }\n },\n\n /** expand when the title bar is in focus and enter or space is pressed */\n _keyDownTitleBar: function(event) {\n // bail (with propagation) if keydown and not space or enter\n var KEYCODE_SPACE = 32,\n KEYCODE_RETURN = 13;\n if (\n event &&\n event.type === \"keydown\" &&\n (event.keyCode === KEYCODE_SPACE ||\n event.keyCode === KEYCODE_RETURN)\n ) {\n this.toggleExpanded();\n event.stopPropagation();\n return false;\n }\n return true;\n },\n\n // ......................................................................... misc\n /** String representation */\n toString: function() {\n var modelString = this.model ? this.model + \"\" : \"(no model)\";\n return \"ListItemView(\" + modelString + \")\";\n }\n })\n);\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nListItemView.prototype.templates = (function() {\n var elTemplato = BASE_MVC.wrapTemplate([\n '',\n // errors, messages, etc.\n '',\n\n // multi-select checkbox\n '\"\n ]);\n\n var warnings = {};\n\n var titleBarTemplate = BASE_MVC.wrapTemplate(\n [\n // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display\n '\"\n ],\n \"element\"\n );\n\n var subtitleTemplate = BASE_MVC.wrapTemplate([\n // override this\n ''\n ]);\n\n var detailsTemplate = BASE_MVC.wrapTemplate([\n // override this\n ''\n ]);\n\n return {\n el: elTemplato,\n warnings: warnings,\n titleBar: titleBarTemplate,\n subtitle: subtitleTemplate,\n details: detailsTemplate\n };\n})();\n\n//==============================================================================\n/** A view that is displayed in some larger list/grid/collection.\n * *AND* can display some sub-list of it's own when expanded (e.g. dataset collections).\n * This list will 'foldout' when the item is expanded depending on this.foldoutStyle:\n * If 'foldout': will expand vertically to show the nested list\n * If 'drilldown': will overlay the parent list\n *\n * Inherits from ListItemView.\n *\n * _renderDetails does the work of creating this.details: a sub-view that shows the nested list\n */\nvar FoldoutListItemView = ListItemView.extend({\n /** If 'foldout': show the sub-panel inside the expanded item\n * If 'drilldown': only fire events and handle by pub-sub\n * (allow the panel containing this item to attach it, hide itself, etc.)\n */\n foldoutStyle: \"foldout\",\n /** Panel view class to instantiate for the sub-panel */\n foldoutPanelClass: null,\n\n /** override to:\n * add attributes foldoutStyle and foldoutPanelClass for config poly\n * disrespect attributes.expanded if drilldown\n */\n initialize: function(attributes) {\n if (this.foldoutStyle === \"drilldown\") {\n this.expanded = false;\n }\n this.foldoutStyle = attributes.foldoutStyle || this.foldoutStyle;\n this.foldoutPanelClass =\n attributes.foldoutPanelClass || this.foldoutPanelClass;\n\n ListItemView.prototype.initialize.call(this, attributes);\n this.foldout = this._createFoldoutPanel();\n },\n\n /** in this override, attach the foldout panel when rendering details */\n _renderDetails: function() {\n if (this.foldoutStyle === \"drilldown\") {\n return $();\n }\n var $newDetails = ListItemView.prototype._renderDetails.call(this);\n return this._attachFoldout(this.foldout, $newDetails);\n },\n\n /** In this override, handle collection expansion. */\n _createFoldoutPanel: function() {\n var model = this.model;\n var FoldoutClass = this._getFoldoutPanelClass(model),\n options = this._getFoldoutPanelOptions(model),\n foldout = new FoldoutClass(\n _.extend(options, {\n model: model\n })\n );\n return foldout;\n },\n\n /** Stub to return proper foldout panel class */\n _getFoldoutPanelClass: function() {\n // override\n return this.foldoutPanelClass;\n },\n\n /** Stub to return proper foldout panel options */\n _getFoldoutPanelOptions: function() {\n return {\n // propagate foldout style down\n foldoutStyle: this.foldoutStyle,\n fxSpeed: this.fxSpeed\n };\n },\n\n /** Render the foldout panel inside the view, hiding controls */\n _attachFoldout: function(foldout, $whereTo) {\n $whereTo = $whereTo || this.$(\"> .details\");\n this.foldout = foldout.render(0);\n foldout.$(\"> .controls\").hide();\n return $whereTo.append(foldout.$el);\n },\n\n /** In this override, branch on foldoutStyle to show expanded */\n expand: function() {\n var view = this;\n return view._fetchModelDetails().always(function() {\n if (view.foldoutStyle === \"foldout\") {\n view._expand();\n } else if (view.foldoutStyle === \"drilldown\") {\n view._expandByDrilldown();\n }\n });\n },\n\n /** For drilldown, set up close handler and fire expanded:drilldown\n * containing views can listen to this and handle other things\n * (like hiding themselves) by listening for expanded/collapsed:drilldown\n */\n _expandByDrilldown: function() {\n var view = this;\n // attachment and rendering done by listener\n view.listenTo(view.foldout, \"close\", function() {\n view.trigger(\"collapsed:drilldown\", view, view.foldout);\n });\n view.trigger(\"expanded:drilldown\", view, view.foldout);\n }\n});\n\n// ............................................................................ 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LIST_ITEM from \"mvc/list/list-item\";\nimport LoadingIndicator from \"ui/loading-indicator\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\nimport \"ui/search-input\";\n\nvar logNamespace = \"list\";\n/* ============================================================================\nTODO:\n\n============================================================================ */\n/** @class View for a list/collection of models and the sub-views of those models.\n * Sub-views must (at least have the interface if not) inherit from ListItemView.\n * (For a list panel that also includes some 'container' model (History->HistoryContents)\n * use ModelWithListPanel)\n *\n * Allows for:\n * searching collection/sub-views\n * selecting/multi-selecting sub-views\n *\n * Currently used:\n * for dataset/dataset-choice\n * as superclass of ModelListPanel\n */\nvar ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(\n /** @lends ListPanel.prototype */ {\n _logNamespace: logNamespace,\n\n /** class to use for constructing the sub-views */\n viewClass: LIST_ITEM.ListItemView,\n /** class to used for constructing collection of sub-view models */\n collectionClass: Backbone.Collection,\n\n tagName: \"div\",\n className: \"list-panel\",\n\n /** (in ms) that jquery effects will use */\n fxSpeed: \"fast\",\n\n /** string to display when the collection has no contents */\n emptyMsg: _l(\"This list is empty\"),\n /** displayed when no items match the search terms */\n noneFoundMsg: _l(\"No matching items found\"),\n /** string used for search placeholder */\n searchPlaceholder: _l(\"search\"),\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events\n * @param {Object} attributes optional settings for the list\n */\n initialize: function(attributes, options) {\n attributes = attributes || {};\n // set the logger if requested\n if (attributes.logger) {\n this.logger = attributes.logger;\n }\n this.log(this + \".initialize:\", attributes);\n\n // ---- instance vars\n /** how quickly should jquery fx run? */\n this.fxSpeed = _.has(attributes, \"fxSpeed\")\n ? attributes.fxSpeed\n : this.fxSpeed;\n\n /** filters for displaying subviews */\n this.filters = [];\n /** current search terms */\n this.searchFor = attributes.searchFor || \"\";\n\n /** loading indicator */\n // this.indicator = new LoadingIndicator( this.$el );\n\n /** currently showing selectors on items? */\n this.selecting =\n attributes.selecting !== undefined\n ? attributes.selecting\n : true;\n //this.selecting = false;\n\n /** cached selected item.model.ids to persist btwn renders */\n this.selected = attributes.selected || [];\n /** the last selected item.model.id */\n this.lastSelected = null;\n\n /** are sub-views draggable */\n this.dragItems = attributes.dragItems || false;\n\n /** list item view class (when passed models) */\n this.viewClass = attributes.viewClass || this.viewClass;\n\n /** list item views */\n this.views = [];\n /** list item models */\n this.collection =\n attributes.collection || this._createDefaultCollection();\n\n /** filter fns run over collection items to see if they should show in the list */\n this.filters = attributes.filters || [];\n\n /** override $scrollContainer fn via attributes - fn should return jq for elem to call scrollTo on */\n this.$scrollContainer =\n attributes.$scrollContainer || this.$scrollContainer;\n\n /** @type {String} generic title */\n this.title = attributes.title || \"\";\n /** @type {String} generic subtitle */\n this.subtitle = attributes.subtitle || \"\";\n\n this._setUpListeners();\n },\n\n // ------------------------------------------------------------------------ listeners\n /** create any event listeners for the list */\n _setUpListeners: function() {\n this.off();\n\n //TODO: move errorHandler down into list-view from history-view or\n // pass to global error handler (Galaxy)\n this.on({\n error: function(model, xhr, options, msg, details) {\n //this.errorHandler( model, xhr, options, msg, details );\n console.error(model, xhr, options, msg, details);\n },\n // show hide the loading indicator\n loading: function() {\n this._showLoadingIndicator(\"loading...\", 40);\n },\n \"loading-done\": function() {\n this._hideLoadingIndicator(40);\n }\n });\n\n // throw the first render up as a diff namespace using once (for outside consumption)\n this.once(\"rendered\", function() {\n this.trigger(\"rendered:initial\", this);\n });\n\n this._setUpCollectionListeners();\n this._setUpViewListeners();\n return this;\n },\n\n /** create and return a collection for when none is initially passed */\n _createDefaultCollection: function() {\n // override\n return new this.collectionClass([]);\n },\n\n /** listening for collection events */\n _setUpCollectionListeners: function() {\n this.log(this + \"._setUpCollectionListeners\", this.collection);\n this.stopListening(this.collection);\n\n // bubble up error events\n this.listenTo(this.collection, {\n error: function(model, xhr, options, msg, details) {\n this.trigger(\"error\", model, xhr, options, msg, details);\n },\n update: function(collection, options) {\n var changes = options.changes;\n // console.info( collection + ', update:', changes, '\\noptions:', options );\n // more than one: render everything\n if (\n options.renderAll ||\n changes.added.length + changes.removed.length > 1\n ) {\n return this.renderItems();\n }\n // otherwise, let the single add/remove handlers do it\n if (changes.added.length === 1) {\n return this.addItemView(\n _.first(changes.added),\n collection,\n options\n );\n }\n if (changes.removed.length === 1) {\n return this.removeItemView(\n _.first(changes.removed),\n collection,\n options\n );\n }\n }\n });\n return this;\n },\n\n /** listening for sub-view events that bubble up with the 'view:' prefix */\n _setUpViewListeners: function() {\n this.log(this + \"._setUpViewListeners\");\n\n // shift to select a range\n this.on({\n \"view:selected\": function(view, ev) {\n if (ev && ev.shiftKey && this.lastSelected) {\n var lastSelectedView = this.viewFromModelId(\n this.lastSelected\n );\n if (lastSelectedView) {\n this.selectRange(view, lastSelectedView);\n }\n } else if (ev && ev.altKey && !this.selecting) {\n this.showSelectors();\n }\n this.selected.push(view.model.id);\n this.lastSelected = view.model.id;\n },\n\n \"view:de-selected\": function(view, ev) {\n this.selected = _.without(this.selected, view.model.id);\n }\n });\n },\n\n // ------------------------------------------------------------------------ rendering\n /** Render this content, set up ui.\n * @param {Number or String} speed the speed of the render\n */\n render: function(speed) {\n this.log(this + \".render\", speed);\n var $newRender = this._buildNewRender();\n this._setUpBehaviors($newRender);\n this._queueNewRender($newRender, speed);\n return this;\n },\n\n /** Build a temp div containing the new children for the view's $el. */\n _buildNewRender: function() {\n this.debug(this + \"(ListPanel)._buildNewRender\");\n var $newRender = $(this.templates.el({}, this));\n this._renderControls($newRender);\n this._renderTitle($newRender);\n this._renderSubtitle($newRender);\n this._renderSearch($newRender);\n this.renderItems($newRender);\n return $newRender;\n },\n\n /** Build a temp div containing the new children for the view's $el. */\n _renderControls: function($newRender) {\n this.debug(this + \"(ListPanel)._renderControls\");\n var $controls = $(this.templates.controls({}, this));\n $newRender.find(\".controls\").replaceWith($controls);\n return $controls;\n },\n\n /** return a jQuery object containing the title DOM */\n _renderTitle: function($where) {\n //$where = $where || this.$el;\n //$where.find( '.title' ).replaceWith( ... )\n },\n\n /** return a jQuery object containing the subtitle DOM (if any) */\n _renderSubtitle: function($where) {\n //$where = $where || this.$el;\n //$where.find( '.title' ).replaceWith( ... )\n },\n\n /** Fade out the old el, swap in the new contents, then fade in.\n * @param {Number or String} speed jq speed to use for rendering effects\n * @fires rendered when rendered\n */\n _queueNewRender: function($newRender, speed) {\n speed = speed === undefined ? this.fxSpeed : speed;\n var panel = this;\n panel.log(\"_queueNewRender:\", $newRender, speed);\n\n $(panel).queue(\"fx\", [\n function(next) {\n panel.$el.fadeOut(speed, next);\n },\n function(next) {\n panel._swapNewRender($newRender);\n next();\n },\n function(next) {\n panel.$el.fadeIn(speed, next);\n },\n function(next) {\n panel.trigger(\"rendered\", panel);\n next();\n }\n ]);\n },\n\n /** empty out the current el, move the $newRender's children in */\n _swapNewRender: function($newRender) {\n this.$el\n .empty()\n .attr(\"class\", this.className)\n .append($newRender.children());\n if (this.selecting) {\n this.showSelectors(0);\n }\n return this;\n },\n\n /** Set up any behaviors, handlers (ep. plugins) that need to be called when the entire view has been built but\n * not attached to the page yet.\n */\n _setUpBehaviors: function($where) {\n $where = $where || this.$el;\n this.$controls($where)\n .find(\"[title]\")\n .tooltip();\n // set up the pupup for actions available when multi selecting\n this._renderMultiselectActionMenu($where);\n return this;\n },\n\n /** render a menu containing the actions available to sets of selected items */\n _renderMultiselectActionMenu: function($where) {\n $where = $where || this.$el;\n var $menu = $where.find(\".list-action-menu\"),\n actions = this.multiselectActions();\n if (!actions.length) 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TEMPLATES\n/** underscore templates */\nModelListPanel.prototype.templates = (function() {\n var controlsTemplate = BASE_MVC.wrapTemplate([\n '',\n '\",\n '<%- view.title %>',\n \"<%- view.subtitle %>',\n // buttons, controls go here\n '',\n // deleted msg, etc.\n '',\n\n '',\n '',\n \"\",\n\n // show when selectors are shown\n '',\n '\",\n \"',\n '\",\n '\",\n \"\",\n '\",\n \"',\n '\"\n ]);\n\n return _.extend(_.clone(ListPanel.prototype.templates), {\n controls: controlsTemplate\n });\n})();\n\n//=============================================================================\nexport default {\n ListPanel: ListPanel,\n ModelListPanel: ModelListPanel\n};\n"]} \ No newline at end of file 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LIST_ITEM from \"mvc/list/list-item\";\nimport LoadingIndicator from \"ui/loading-indicator\";\nimport BASE_MVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\nimport \"ui/search-input\";\n\nvar logNamespace = \"list\";\n/* ============================================================================\nTODO:\n\n============================================================================ */\n/** @class View for a list/collection of models and the sub-views of those models.\n * Sub-views must (at least have the interface if not) inherit from ListItemView.\n * (For a list panel that also includes some 'container' model (History->HistoryContents)\n * use ModelWithListPanel)\n *\n * Allows for:\n * searching collection/sub-views\n * selecting/multi-selecting sub-views\n *\n * Currently used:\n * for dataset/dataset-choice\n * as superclass of ModelListPanel\n */\nvar ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(\n /** @lends ListPanel.prototype */ {\n _logNamespace: logNamespace,\n\n /** class to use for constructing the sub-views */\n viewClass: LIST_ITEM.ListItemView,\n /** class to used for constructing collection of sub-view models */\n collectionClass: Backbone.Collection,\n\n tagName: \"div\",\n className: \"list-panel\",\n\n /** (in ms) that jquery effects will use */\n fxSpeed: \"fast\",\n\n /** string to display when the collection has no contents */\n emptyMsg: _l(\"This list is empty\"),\n /** displayed when no items match the search terms */\n noneFoundMsg: _l(\"No matching items found\"),\n /** string used for search placeholder */\n searchPlaceholder: _l(\"search\"),\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events\n * @param {Object} attributes optional settings for the list\n */\n initialize: function(attributes, options) {\n attributes = attributes || {};\n // set the logger if requested\n if (attributes.logger) {\n this.logger = attributes.logger;\n }\n this.log(this + \".initialize:\", attributes);\n\n // ---- instance vars\n /** how quickly should jquery fx run? */\n this.fxSpeed = _.has(attributes, \"fxSpeed\")\n ? attributes.fxSpeed\n : this.fxSpeed;\n\n /** filters for displaying subviews */\n this.filters = [];\n /** current search terms */\n this.searchFor = attributes.searchFor || \"\";\n\n /** loading indicator */\n // this.indicator = new LoadingIndicator( this.$el );\n\n /** currently showing selectors on items? */\n this.selecting =\n attributes.selecting !== undefined\n ? attributes.selecting\n : true;\n //this.selecting = false;\n\n /** cached selected item.model.ids to persist btwn renders */\n this.selected = attributes.selected || [];\n /** the last selected item.model.id */\n this.lastSelected = null;\n\n /** are sub-views draggable */\n this.dragItems = attributes.dragItems || false;\n\n /** list item view class (when passed models) */\n this.viewClass = attributes.viewClass || this.viewClass;\n\n /** list item views */\n this.views = [];\n /** list item models */\n this.collection =\n attributes.collection || this._createDefaultCollection();\n\n /** filter fns run over collection items to see if they should show in the list */\n this.filters = attributes.filters || [];\n\n /** override $scrollContainer fn via attributes - fn should return jq for elem to call scrollTo on */\n this.$scrollContainer =\n attributes.$scrollContainer || this.$scrollContainer;\n\n /** @type {String} generic title */\n this.title = attributes.title || \"\";\n /** @type {String} generic subtitle */\n this.subtitle = attributes.subtitle || \"\";\n\n this._setUpListeners();\n },\n\n // ------------------------------------------------------------------------ listeners\n /** create any event listeners for the list */\n _setUpListeners: function() {\n this.off();\n\n //TODO: move errorHandler down into list-view from history-view or\n // pass to global error handler (Galaxy)\n this.on({\n error: function(model, xhr, options, msg, details) {\n //this.errorHandler( model, xhr, options, msg, details );\n console.error(model, xhr, options, msg, details);\n },\n // show hide the loading indicator\n loading: function() {\n this._showLoadingIndicator(\"loading...\", 40);\n },\n \"loading-done\": function() {\n this._hideLoadingIndicator(40);\n }\n });\n\n // throw the first render up as a diff namespace using once (for outside consumption)\n this.once(\"rendered\", function() {\n this.trigger(\"rendered:initial\", this);\n });\n\n this._setUpCollectionListeners();\n this._setUpViewListeners();\n return this;\n },\n\n /** create and return a collection for when none is initially passed */\n _createDefaultCollection: function() {\n // override\n return new this.collectionClass([]);\n },\n\n /** listening for collection events */\n _setUpCollectionListeners: function() {\n this.log(this + \"._setUpCollectionListeners\", this.collection);\n this.stopListening(this.collection);\n\n // bubble up error events\n this.listenTo(this.collection, {\n error: function(model, xhr, options, msg, details) {\n this.trigger(\"error\", model, xhr, options, msg, details);\n },\n update: function(collection, options) {\n var changes = options.changes;\n // console.info( collection + ', update:', changes, '\\noptions:', options );\n // more than one: render everything\n if (\n options.renderAll ||\n changes.added.length + changes.removed.length > 1\n ) {\n return this.renderItems();\n }\n // otherwise, let the single add/remove handlers do it\n if (changes.added.length === 1) {\n return this.addItemView(\n _.first(changes.added),\n collection,\n options\n );\n }\n if (changes.removed.length === 1) {\n return this.removeItemView(\n _.first(changes.removed),\n collection,\n options\n );\n }\n }\n });\n return this;\n },\n\n /** listening for sub-view events that bubble up with the 'view:' prefix */\n _setUpViewListeners: function() {\n this.log(this + \"._setUpViewListeners\");\n\n // shift to select a range\n this.on({\n \"view:selected\": function(view, ev) {\n if (ev && ev.shiftKey && this.lastSelected) {\n var lastSelectedView = this.viewFromModelId(\n this.lastSelected\n );\n if (lastSelectedView) {\n this.selectRange(view, lastSelectedView);\n }\n } else if (ev && ev.altKey && !this.selecting) {\n this.showSelectors();\n }\n this.selected.push(view.model.id);\n this.lastSelected = view.model.id;\n },\n\n \"view:de-selected\": function(view, ev) {\n this.selected = _.without(this.selected, view.model.id);\n }\n });\n },\n\n // ------------------------------------------------------------------------ rendering\n /** Render this content, set up ui.\n * @param {Number or String} speed the speed of the render\n */\n render: function(speed) {\n this.log(this + \".render\", speed);\n var $newRender = this._buildNewRender();\n this._setUpBehaviors($newRender);\n this._queueNewRender($newRender, speed);\n return this;\n },\n\n /** Build a temp div containing the new children for the view's $el. */\n _buildNewRender: function() {\n this.debug(this + \"(ListPanel)._buildNewRender\");\n var $newRender = $(this.templates.el({}, this));\n this._renderControls($newRender);\n this._renderTitle($newRender);\n this._renderSubtitle($newRender);\n this._renderSearch($newRender);\n this.renderItems($newRender);\n return $newRender;\n },\n\n /** Build a temp div containing the new children for the view's $el. */\n _renderControls: function($newRender) {\n this.debug(this + \"(ListPanel)._renderControls\");\n var $controls = $(this.templates.controls({}, this));\n $newRender.find(\".controls\").replaceWith($controls);\n return $controls;\n },\n\n /** return a jQuery object containing the title DOM */\n _renderTitle: function($where) {\n //$where = $where || this.$el;\n //$where.find( '.title' ).replaceWith( ... )\n },\n\n /** return a jQuery object containing the subtitle DOM (if any) */\n _renderSubtitle: function($where) {\n //$where = $where || this.$el;\n //$where.find( '.title' ).replaceWith( ... )\n },\n\n /** Fade out the old el, swap in the new contents, then fade in.\n * @param {Number or String} speed jq speed to use for rendering effects\n * @fires rendered when rendered\n */\n _queueNewRender: function($newRender, speed) {\n speed = speed === undefined ? this.fxSpeed : speed;\n var panel = this;\n panel.log(\"_queueNewRender:\", $newRender, speed);\n\n $(panel).queue(\"fx\", [\n function(next) {\n panel.$el.fadeOut(speed, next);\n },\n function(next) {\n panel._swapNewRender($newRender);\n next();\n },\n function(next) {\n panel.$el.fadeIn(speed, next);\n },\n function(next) {\n panel.trigger(\"rendered\", panel);\n next();\n }\n ]);\n },\n\n /** empty out the current el, move the $newRender's children in */\n _swapNewRender: function($newRender) {\n this.$el\n .empty()\n .attr(\"class\", this.className)\n .append($newRender.children());\n if (this.selecting) {\n this.showSelectors(0);\n }\n return this;\n },\n\n /** Set up any behaviors, handlers (ep. plugins) that need to be called when the entire view has been built but\n * not attached to the page yet.\n */\n _setUpBehaviors: function($where) {\n $where = $where || this.$el;\n this.$controls($where)\n .find(\"[title]\")\n .tooltip();\n // set up the pupup for actions available when multi selecting\n this._renderMultiselectActionMenu($where);\n return this;\n },\n\n /** render a menu containing the actions available to sets of selected items */\n _renderMultiselectActionMenu: function($where) {\n $where = $where || this.$el;\n var $menu = $where.find(\".list-action-menu\"),\n actions = this.multiselectActions();\n if (!actions.length) 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this.stopListening(this.collection);\n this.collection =\n this.model[this.modelCollectionKey] ||\n attributes.collection ||\n this._createDefaultCollection();\n this._setUpCollectionListeners();\n\n if (oldModelId && model.get(\"id\") !== oldModelId) {\n this.trigger(\"new-model\", this);\n }\n }\n return this;\n },\n\n /** free the current model and all listeners for it, free any views for the model */\n freeModel: function() {\n // stop/release the previous model, and clear cache to sub-views\n if (this.model) {\n this.stopListening(this.model);\n //TODO: see base-mvc\n //this.model.free();\n //this.model = null;\n }\n return this;\n },\n\n // ------------------------------------------------------------------------ listening\n /** listening for model events */\n _setUpModelListeners: function() {\n // override\n this.log(this + \"._setUpModelListeners\", this.model);\n // bounce model errors up to the panel\n this.listenTo(\n this.model,\n \"error\",\n function() {\n var args = Array.prototype.slice.call(arguments, 0);\n //args.unshift( 'model:error' );\n args.unshift(\"error\");\n this.trigger.apply(this, args);\n },\n this\n );\n\n // debugging\n if (this.logger) {\n this.listenTo(this.model, \"all\", function(event) {\n this.info(this + \"(model)\", event, arguments);\n });\n }\n return this;\n },\n\n /** Build a temp div containing the new children for the view's $el.\n */\n _renderControls: function($newRender) {\n this.debug(this + \"(ModelListPanel)._renderControls\");\n var json = this.model ? this.model.toJSON() : {},\n $controls = $(this.templates.controls(json, this));\n $newRender.find(\".controls\").replaceWith($controls);\n return $controls;\n },\n\n // ------------------------------------------------------------------------ misc\n /** Return a string rep of the panel */\n toString: function() {\n return \"ModelListPanel(\" + this.model + \")\";\n }\n});\n\n// ............................................................................ 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baseMVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n// =============================================================================\n/** A view on any model that has a 'tags' attribute (a list of tag strings)\n * Incorporates the select2 jQuery plugin for tags display/editing:\n * http://ivaynberg.github.io/select2/\n */\nvar TagsEditor = Backbone.View\n .extend(baseMVC.LoggableMixin)\n .extend(baseMVC.HiddenUntilActivatedViewMixin)\n .extend({\n tagName: \"div\",\n className: \"tags-display\",\n select_width: \"100%\",\n events: {},\n\n /** Set up listeners, parse options */\n initialize: function(options) {\n //console.debug( this, options );\n // only listen to the model only for changes to tags - re-render\n this.show_editor = false;\n if (options.usePrompt === false) {\n this.label = \"\";\n } else {\n this.label = '\";\n }\n this.workflow_mode = options.workflow_mode || false;\n if (this.workflow_mode) {\n this.events.click = \"showEditor\";\n 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tag.slice(5) : tag;\n var renderString =\n '' + tag + \"\";\n renderedArray.push(renderString);\n });\n if (renderedArray.length === 0) {\n // If there are no tags to render we just show the add-tag-button\n renderedArray.push(\n \"',\n //TODO: this is really the only difference - consider factoring titlebar out\n '\",\n '<%- model.name %>',\n \"<%- view.subtitle %>',\n '',\n '',\n\n '',\n '',\n \"\",\n\n '',\n '\",\n \"',\n '\",\n '\",\n \"\",\n '\",\n \"'\n );\n }\n return renderedArray.join(\" \");\n },\n\n /** @returns {String} the sorted, comma-separated tags from the model */\n tagsToCSV: function() {\n var self = this;\n var tagsArray = this.model.get(\"tags\");\n if (!_.isArray(tagsArray) || _.isEmpty(tagsArray)) {\n return \"\";\n }\n return tagsArray\n .map(function(tag) {\n return _.escape(self._nameToHash(tag));\n })\n .sort()\n .join(\",\");\n },\n\n /** @returns {jQuery} the input for this view */\n $input: function() {\n return this.$el.find(\"input.tags-input\");\n 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* Model, view, and controller objects for Galaxy tools and tool panel.\n */\n\nimport _ from \"libs/underscore\";\nimport util from \"viz/trackster/util\";\nimport data from \"mvc/dataset/data\";\nimport ToolForm from \"mvc/tool/tool-form\";\n\n/**\n * Mixin for tracking model visibility.\n */\nvar VisibilityMixin = {\n hidden: false,\n\n show: function() {\n this.set(\"hidden\", false);\n },\n\n hide: function() {\n this.set(\"hidden\", true);\n },\n\n toggle: function() {\n this.set(\"hidden\", !this.get(\"hidden\"));\n },\n\n is_visible: function() {\n return !this.attributes.hidden;\n }\n};\n\n/**\n * A tool parameter.\n */\nvar ToolParameter = Backbone.Model.extend({\n defaults: {\n name: null,\n label: null,\n type: null,\n value: null,\n html: null,\n num_samples: 5\n },\n\n initialize: function(options) {\n this.attributes.html = unescape(this.attributes.html);\n },\n\n copy: function() {\n return new ToolParameter(this.toJSON());\n },\n\n set_value: function(value) {\n this.set(\"value\", value || \"\");\n }\n});\n\nvar ToolParameterCollection = Backbone.Collection.extend({\n model: ToolParameter\n});\n\n/**\n * A data tool parameter.\n */\nvar DataToolParameter = ToolParameter.extend({});\n\n/**\n * An integer tool parameter.\n */\nvar IntegerToolParameter = ToolParameter.extend({\n set_value: function(value) {\n this.set(\"value\", parseInt(value, 10));\n },\n\n /**\n * Returns samples from a tool input.\n */\n get_samples: function() {\n return d3.scale\n .linear()\n .domain([this.get(\"min\"), this.get(\"max\")])\n .ticks(this.get(\"num_samples\"));\n }\n});\n\nvar FloatToolParameter = IntegerToolParameter.extend({\n set_value: function(value) {\n this.set(\"value\", parseFloat(value));\n }\n});\n\n/**\n * A select tool parameter.\n */\nvar SelectToolParameter = ToolParameter.extend({\n /**\n * Returns tool options.\n */\n get_samples: function() {\n return _.map(this.get(\"options\"), function(option) {\n return option[0];\n });\n }\n});\n\n// Set up dictionary of parameter types.\nToolParameter.subModelTypes = {\n integer: IntegerToolParameter,\n float: FloatToolParameter,\n data: DataToolParameter,\n select: SelectToolParameter\n};\n\n/**\n * A Galaxy tool.\n */\nvar Tool = Backbone.Model.extend({\n // Default attributes.\n defaults: {\n id: null,\n name: null,\n description: null,\n target: null,\n inputs: [],\n outputs: []\n },\n\n urlRoot: Galaxy.root + \"api/tools\",\n\n initialize: function(options) {\n // Set parameters.\n this.set(\n \"inputs\",\n new ToolParameterCollection(\n _.map(options.inputs, function(p) {\n var p_class =\n ToolParameter.subModelTypes[p.type] || ToolParameter;\n return new p_class(p);\n })\n )\n );\n },\n\n /**\n *\n */\n toJSON: function() {\n var rval = Backbone.Model.prototype.toJSON.call(this);\n\n // Convert inputs to JSON manually.\n rval.inputs = this.get(\"inputs\").map(function(i) {\n return i.toJSON();\n });\n return rval;\n },\n\n /**\n * Removes inputs of a particular type; this is useful because not all inputs can be handled by\n * client and server yet.\n */\n remove_inputs: function(types) {\n var tool = this,\n incompatible_inputs = tool.get(\"inputs\").filter(function(input) {\n return types.indexOf(input.get(\"type\")) !== -1;\n });\n tool.get(\"inputs\").remove(incompatible_inputs);\n },\n\n /**\n * Returns object copy, optionally including only inputs that can be sampled.\n */\n copy: function(only_samplable_inputs) {\n var copy = new Tool(this.toJSON());\n\n // Return only samplable inputs if flag is set.\n if (only_samplable_inputs) {\n var valid_inputs = new Backbone.Collection();\n copy.get(\"inputs\").each(function(input) {\n if (input.get_samples()) {\n valid_inputs.push(input);\n }\n });\n copy.set(\"inputs\", valid_inputs);\n }\n\n return copy;\n },\n\n apply_search_results: function(results) {\n _.indexOf(results, this.attributes.id) !== -1\n ? this.show()\n : this.hide();\n return this.is_visible();\n },\n\n /**\n * Set a tool input's value.\n */\n set_input_value: function(name, value) {\n this.get(\"inputs\")\n .find(function(input) {\n return input.get(\"name\") === name;\n })\n .set(\"value\", value);\n },\n\n /**\n * Set many input values at once.\n */\n set_input_values: function(inputs_dict) {\n var self = this;\n _.each(_.keys(inputs_dict), function(input_name) {\n self.set_input_value(input_name, inputs_dict[input_name]);\n });\n },\n\n /**\n * Run tool; returns a Deferred that resolves to the tool's output(s).\n */\n run: function() {\n return this._run();\n },\n\n /**\n * Rerun tool using regions and a target dataset.\n */\n rerun: function(target_dataset, regions) {\n return this._run({\n action: \"rerun\",\n target_dataset_id: target_dataset.id,\n regions: regions\n });\n },\n\n /**\n * Returns input dict for tool's inputs.\n */\n get_inputs_dict: function() {\n var input_dict = {};\n this.get(\"inputs\").each(function(input) {\n input_dict[input.get(\"name\")] = input.get(\"value\");\n });\n return input_dict;\n },\n\n /**\n * Run tool; returns a Deferred that resolves to the tool's output(s).\n * NOTE: this method is a helper method and should not be called directly.\n */\n _run: function(additional_params) {\n // Create payload.\n var payload = _.extend(\n {\n tool_id: this.id,\n inputs: this.get_inputs_dict()\n },\n additional_params\n );\n\n // Because job may require indexing datasets, use server-side\n // deferred to ensure that job is run. Also use deferred that\n // resolves to outputs from tool.\n var run_deferred = $.Deferred(),\n ss_deferred = new util.ServerStateDeferred({\n ajax_settings: {\n url: this.urlRoot,\n data: JSON.stringify(payload),\n dataType: \"json\",\n contentType: \"application/json\",\n type: \"POST\"\n },\n interval: 2000,\n success_fn: function(response) {\n return response !== \"pending\";\n }\n });\n\n // Run job and resolve run_deferred to tool outputs.\n $.when(ss_deferred.go()).then(function(result) {\n run_deferred.resolve(new data.DatasetCollection(result));\n });\n return run_deferred;\n }\n});\n_.extend(Tool.prototype, VisibilityMixin);\n\n/**\n * Tool view.\n */\nvar ToolView = Backbone.View.extend({});\n\n/**\n * Wrap collection of tools for fast access/manipulation.\n */\nvar ToolCollection = Backbone.Collection.extend({\n model: Tool\n});\n\n/**\n * Label or section header in tool panel.\n */\nvar ToolSectionLabel = Backbone.Model.extend(VisibilityMixin);\n\n/**\n * Section of tool panel with elements (labels and tools).\n */\nvar ToolSection = Backbone.Model.extend({\n defaults: {\n elems: [],\n open: false\n },\n\n clear_search_results: function() {\n _.each(this.attributes.elems, function(elt) {\n elt.show();\n });\n\n this.show();\n this.set(\"open\", false);\n },\n\n apply_search_results: function(results) {\n var all_hidden = true,\n cur_label;\n _.each(this.attributes.elems, function(elt) {\n if (elt instanceof ToolSectionLabel) {\n cur_label = elt;\n cur_label.hide();\n } else if (elt instanceof Tool) {\n if (elt.apply_search_results(results)) {\n all_hidden = false;\n if (cur_label) {\n cur_label.show();\n }\n }\n }\n });\n\n if (all_hidden) {\n this.hide();\n } else {\n this.show();\n this.set(\"open\", true);\n }\n }\n});\n_.extend(ToolSection.prototype, VisibilityMixin);\n\n/**\n * Tool search that updates results when query is changed. Result value of null\n * indicates that query was not run; if not null, results are from search using\n * query.\n */\nvar ToolSearch = Backbone.Model.extend({\n defaults: {\n search_hint_string: \"search tools\",\n min_chars_for_search: 3,\n clear_btn_url: \"\",\n visible: true,\n query: \"\",\n results: null,\n // ESC (27) will clear the input field and tool search filters\n clear_key: 27\n },\n\n urlRoot: Galaxy.root + \"api/tools\",\n\n initialize: function() {\n this.on(\"change:query\", this.do_search);\n },\n\n /**\n * Do the search and update the results.\n */\n do_search: function() {\n var query = this.attributes.query;\n\n // If query is too short, do not search.\n if (query.length < this.attributes.min_chars_for_search) {\n this.set(\"results\", null);\n return;\n }\n\n // Do search via AJAX.\n var q = query;\n // Stop previous ajax-request\n if (this.timer) {\n clearTimeout(this.timer);\n }\n // Start a new ajax-request in X ms\n $(\"#search-clear-btn\").hide();\n $(\"#search-spinner\").show();\n var self = this;\n this.timer = setTimeout(function() {\n // log the search to analytics if present\n if (typeof ga !== \"undefined\") {\n ga(\"send\", \"pageview\", Galaxy.root + \"?q=\" + q);\n }\n $.get(\n self.urlRoot,\n { q: q },\n function(data) {\n self.set(\"results\", data);\n $(\"#search-spinner\").hide();\n $(\"#search-clear-btn\").show();\n },\n \"json\"\n );\n }, 400);\n },\n\n clear_search: function() {\n this.set(\"query\", \"\");\n this.set(\"results\", null);\n }\n});\n_.extend(ToolSearch.prototype, VisibilityMixin);\n\n/**\n * Tool Panel.\n */\nvar ToolPanel = Backbone.Model.extend({\n initialize: function(options) {\n this.attributes.tool_search = options.tool_search;\n this.attributes.tool_search.on(\n \"change:results\",\n this.apply_search_results,\n this\n );\n this.attributes.tools = options.tools;\n this.attributes.layout = new Backbone.Collection(\n this.parse(options.layout)\n );\n },\n\n /**\n * Parse tool panel dictionary and return collection of tool panel elements.\n */\n parse: function(response) {\n // Recursive function to parse tool panel elements.\n var self = this,\n // Helper to recursively parse tool panel.\n parse_elt = function(elt_dict) {\n var type = elt_dict.model_class;\n // There are many types of tools; for now, anything that ends in 'Tool'\n // is treated as a generic tool.\n if (type.indexOf(\"Tool\") === type.length - 4) {\n return self.attributes.tools.get(elt_dict.id);\n } else if (type === \"ToolSection\") {\n // Parse elements.\n var elems = _.map(elt_dict.elems, parse_elt);\n elt_dict.elems = elems;\n return new ToolSection(elt_dict);\n } else if (type === \"ToolSectionLabel\") {\n return new ToolSectionLabel(elt_dict);\n }\n };\n\n return _.map(response, parse_elt);\n },\n\n clear_search_results: function() {\n this.get(\"layout\").each(function(panel_elt) {\n if (panel_elt instanceof ToolSection) {\n panel_elt.clear_search_results();\n } else {\n // Label or tool, so just show.\n panel_elt.show();\n }\n });\n },\n\n apply_search_results: function() {\n var results = this.get(\"tool_search\").get(\"results\");\n if (results === null) {\n this.clear_search_results();\n return;\n }\n\n var cur_label = null;\n this.get(\"layout\").each(function(panel_elt) {\n if (panel_elt instanceof ToolSectionLabel) {\n cur_label = panel_elt;\n cur_label.hide();\n } else if (panel_elt instanceof Tool) {\n if (panel_elt.apply_search_results(results)) {\n if (cur_label) {\n cur_label.show();\n }\n }\n } else {\n // Starting new section, so clear current label.\n cur_label = null;\n panel_elt.apply_search_results(results);\n }\n });\n }\n});\n\n/**\n * View classes for Galaxy tools and tool panel.\n *\n * Views use the templates defined below for rendering. Views update as needed\n * based on (a) model/collection events and (b) user interactions; in this sense,\n * they are controllers are well and the HTML is the real view in the MVC architecture.\n */\n\n/**\n * Base view that handles visibility based on model's hidden attribute.\n */\nvar BaseView = Backbone.View.extend({\n initialize: function() {\n this.model.on(\"change:hidden\", this.update_visible, this);\n this.update_visible();\n },\n update_visible: function() {\n this.model.attributes.hidden ? this.$el.hide() : this.$el.show();\n }\n});\n\n/**\n * Link to a tool.\n */\nvar ToolLinkView = BaseView.extend({\n tagName: \"div\",\n\n render: function() {\n // create element\n var $link = $(\"\");\n $link.append(templates.tool_link(this.model.toJSON()));\n\n var formStyle = this.model.get(\"form_style\", null);\n // open upload dialog for upload tool\n if (this.model.id === \"upload1\") {\n $link.find(\"a\").on(\"click\", function(e) {\n e.preventDefault();\n Galaxy.upload.show();\n });\n } else if (formStyle === \"regular\") {\n // regular tools\n var self = this;\n $link.find(\"a\").on(\"click\", function(e) {\n e.preventDefault();\n Galaxy.router.push(\"/\", {\n tool_id: self.model.id,\n version: self.model.get(\"version\")\n });\n });\n }\n\n // add element\n this.$el.append($link);\n return this;\n }\n});\n\n/**\n * Panel label/section header.\n */\nvar ToolSectionLabelView = BaseView.extend({\n tagName: \"div\",\n className: \"toolPanelLabel\",\n\n render: function() {\n this.$el.append($(\"\").text(this.model.attributes.text));\n return this;\n }\n});\n\n/**\n * Panel section.\n */\nvar ToolSectionView = BaseView.extend({\n tagName: \"div\",\n className: \"toolSectionWrapper\",\n\n initialize: function() {\n BaseView.prototype.initialize.call(this);\n this.model.on(\"change:open\", this.update_open, this);\n },\n\n render: function() {\n // Build using template.\n this.$el.append(templates.panel_section(this.model.toJSON()));\n\n // Add tools to section.\n var section_body = this.$el.find(\".toolSectionBody\");\n _.each(this.model.attributes.elems, function(elt) {\n if (elt instanceof Tool) {\n var tool_view = new ToolLinkView({\n model: elt,\n className: \"toolTitle\"\n });\n tool_view.render();\n section_body.append(tool_view.$el);\n } else if (elt instanceof ToolSectionLabel) {\n var label_view = new ToolSectionLabelView({\n model: elt\n });\n label_view.render();\n section_body.append(label_view.$el);\n } else {\n // TODO: handle nested section bodies?\n }\n });\n return this;\n },\n\n events: {\n \"click .toolSectionTitle > a\": \"toggle\"\n },\n\n /**\n * Toggle visibility of tool section.\n */\n toggle: function() {\n this.model.set(\"open\", !this.model.attributes.open);\n },\n\n /**\n * Update whether section is open or close.\n */\n update_open: function() {\n this.model.attributes.open\n ? this.$el.children(\".toolSectionBody\").slideDown(\"fast\")\n : this.$el.children(\".toolSectionBody\").slideUp(\"fast\");\n }\n});\n\nvar ToolSearchView = Backbone.View.extend({\n tagName: \"div\",\n id: \"tool-search\",\n className: \"bar\",\n\n events: {\n click: \"focus_and_select\",\n \"keyup :input\": \"query_changed\",\n \"change :input\": \"query_changed\",\n \"click #search-clear-btn\": \"clear\"\n },\n\n render: function() {\n this.$el.append(templates.tool_search(this.model.toJSON()));\n if (!this.model.is_visible()) {\n this.$el.hide();\n }\n\n // Adjust top for issue 2907 depending on whether the messagebox is visible.\n if ($(\"#messagebox\").is(\":visible\")) {\n this.$el.css(\"top\", \"95px\");\n }\n\n this.$el.find(\"[title]\").tooltip();\n return this;\n },\n\n focus_and_select: function() {\n this.$el\n .find(\":input\")\n .focus()\n .select();\n },\n\n clear: function() {\n this.model.clear_search();\n this.$el.find(\":input\").val(\"\");\n this.focus_and_select();\n return false;\n },\n\n query_changed: function(evData) {\n // check for the 'clear key' (ESC) first\n if (\n this.model.attributes.clear_key &&\n this.model.attributes.clear_key === evData.which\n ) {\n this.clear();\n return false;\n }\n this.model.set(\"query\", this.$el.find(\":input\").val());\n }\n});\n\n/**\n * Tool panel view. Events triggered include:\n * tool_link_click(click event, tool_model)\n */\nvar ToolPanelView = Backbone.View.extend({\n tagName: \"div\",\n className: \"toolMenu\",\n\n /**\n * Set up view.\n */\n initialize: function() {\n this.model\n .get(\"tool_search\")\n .on(\"change:results\", this.handle_search_results, this);\n },\n\n render: function() {\n var self = this;\n\n // Render search.\n var search_view = new ToolSearchView({\n model: this.model.get(\"tool_search\")\n });\n search_view.render();\n self.$el.append(search_view.$el);\n\n // Render panel.\n this.model.get(\"layout\").each(function(panel_elt) {\n if (panel_elt instanceof ToolSection) {\n var section_title_view = new ToolSectionView({\n model: panel_elt\n });\n section_title_view.render();\n self.$el.append(section_title_view.$el);\n } else if (panel_elt instanceof Tool) {\n var tool_view = new ToolLinkView({\n model: panel_elt,\n className: \"toolTitleNoSection\"\n });\n tool_view.render();\n self.$el.append(tool_view.$el);\n } else if (panel_elt instanceof ToolSectionLabel) {\n var label_view = new ToolSectionLabelView({\n model: panel_elt\n });\n label_view.render();\n self.$el.append(label_view.$el);\n }\n });\n\n // Setup tool link click eventing.\n self.$el.find(\"a.tool-link\").click(function(e) {\n // Tool id is always the first class.\n var tool_id = $(this)\n .attr(\"class\")\n .split(/\\s+/)[0],\n tool = self.model.get(\"tools\").get(tool_id);\n\n self.trigger(\"tool_link_click\", e, tool);\n });\n\n return this;\n },\n\n handle_search_results: function() {\n var results = this.model.get(\"tool_search\").get(\"results\");\n if (results && results.length === 0) {\n $(\"#search-no-results\").show();\n } else {\n $(\"#search-no-results\").hide();\n }\n }\n});\n\n/**\n * View for working with a tool: setting parameters and inputs and executing the tool.\n */\nvar ToolFormView = Backbone.View.extend({\n className: \"toolForm\",\n\n render: function() {\n this.$el.children().remove();\n this.$el.append(templates.tool_form(this.model.toJSON()));\n }\n});\n\n/**\n * Integrated tool menu + tool execution.\n */\nvar IntegratedToolMenuAndView = Backbone.View.extend({\n className: \"toolMenuAndView\",\n\n initialize: function() {\n this.tool_panel_view = new ToolPanelView({\n collection: this.collection\n });\n this.tool_form_view = new ToolFormView();\n },\n\n render: function() {\n // Render and append tool panel.\n this.tool_panel_view.render();\n this.tool_panel_view.$el.css(\"float\", \"left\");\n this.$el.append(this.tool_panel_view.$el);\n\n // Append tool form view.\n this.tool_form_view.$el.hide();\n this.$el.append(this.tool_form_view.$el);\n\n // On tool link click, show tool.\n var self = this;\n this.tool_panel_view.on(\"tool_link_click\", function(e, tool) {\n // Prevents click from activating link:\n e.preventDefault();\n // Show tool that was clicked on:\n self.show_tool(tool);\n });\n },\n\n /**\n * Fetch and display tool.\n */\n show_tool: function(tool) {\n var self = this;\n tool.fetch().done(function() {\n self.tool_form_view.model = tool;\n self.tool_form_view.render();\n self.tool_form_view.$el.show();\n $(\"#left\").width(\"650px\");\n });\n }\n});\n\n// TODO: move into relevant views\nvar templates = {\n // the search bar at the top of the tool panel\n tool_search: _.template(\n [\n '\" autocomplete=\"off\" type=\"text\" />',\n ' ',\n //TODO: replace with icon\n ''\n ].join(\"\")\n ),\n\n // the category level container in the tool panel (e.g. 'Get Data', 'Text Manipulation')\n panel_section: _.template(\n [\n '<% tool.help %>',\n \"\">',\n '<%- name %>',\n \"\",\n '\" class=\"toolSectionBody\" style=\"display: none;\">',\n '',\n \"\"\n ].join(\"\")\n ),\n\n // a single tool's link in the tool panel; will load the tool form in the center panel\n tool_link: _.template(\n [\n ' tool-link\" href=\"<%= link %>\" target=\"<%- target %>\" minsizehint=\"<%- min_width %>\">',\n '',\n \"<% _.each( labels, function( label ){ %>\",\n '\">',\n \"<%- label %>\",\n \"\",\n \"<% }); %>\",\n \"\",\n '',\n \"<%- name %>\",\n \"\",\n \" <%- description %>\",\n \"\"\n ].join(\"\")\n ),\n\n // the tool form for entering tool parameters, viewing help and executing the tool\n // loaded when a tool link is clicked in the tool panel\n tool_form: _.template(\n [\n '<%- tool.name %> (version <%- tool.version %>)',\n '',\n \"<% _.each( tool.inputs, function( input ){ %>\",\n '\",\n '',\n '',\n '\",\n \"<% }); %>\",\n \"',\n \"<%= input.html %>\",\n \"\",\n '',\n \"<%- input.help %>\",\n \"\",\n '',\n \"',\n '',\n \"\",\n '',\n '\"\n // TODO: we need scoping here because 'help' is the dom for the help menu in the masthead\n // which implies a leaky variable that I can't find\n ].join(\"\"),\n { variable: \"tool\" }\n )\n};\n\n// Exports\nexport default {\n ToolParameter: ToolParameter,\n IntegerToolParameter: IntegerToolParameter,\n SelectToolParameter: SelectToolParameter,\n Tool: Tool,\n ToolCollection: ToolCollection,\n ToolSearch: ToolSearch,\n ToolPanel: ToolPanel,\n ToolPanelView: ToolPanelView,\n ToolFormView: ToolFormView\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/toolshed/categories-view.js.map b/static/maps/mvc/toolshed/categories-view.js.map index d94760a1ec0..a3c583262ad 100644 --- a/static/maps/mvc/toolshed/categories-view.js.map +++ b/static/maps/mvc/toolshed/categories-view.js.map @@ -1 +1 @@ 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\"mvc/toolshed/util\"], function(\n toolshed_model,\n toolshed_util\n) {\n var ToolShedCategories = Backbone.View.extend({\n el: \"#center\",\n\n defaults: {\n tool_shed: \"https://toolshed.g2.bx.psu.edu/\"\n },\n\n initialize: function(options) {\n var self = this;\n var shed = options.tool_shed.replace(/\\//g, \"%2f\");\n this.options = _.defaults(this.options || options, this.defaults);\n this.model = new toolshed_model.Categories();\n this.listenTo(this.model, \"sync\", this.render);\n this.model.url =\n this.model.url + \"?tool_shed_url=\" + this.options.tool_shed;\n this.model.tool_shed = shed;\n this.model.fetch();\n },\n\n render: function(options) {\n this.options = _.extend(this.options, options);\n this.options.categories = this.model.models;\n this.options.queue = toolshed_util.queueLength();\n var category_list_template = this.templateCategoryList;\n this.$el.html(category_list_template(this.options));\n $(\"#center\").css(\"overflow\", \"auto\");\n this.bindEvents();\n },\n\n bindEvents: function() {\n var that = this;\n require([\"libs/jquery/jquery-ui\"], function() {\n $(\"#search_box\").autocomplete({\n source: function(request, response) {\n var shed_url = that.model.tool_shed.replace(\n /%2f/g,\n \"/\"\n );\n var base_url = Galaxy.root + \"api/tool_shed/search\";\n var params = {\n term: request.term,\n tool_shed_url: shed_url\n };\n $.post(base_url, params, function(data) {\n console.log(data);\n var result_list = toolshed_util.shedParser(data);\n response(result_list);\n });\n },\n minLength: 3,\n select: function(event, ui) {\n var tsr_id = ui.item.value;\n var api_url = Galaxy.root + \"api/tool_shed/repository\";\n var params = {\n tool_shed_url: that.model.tool_shed,\n tsr_id: tsr_id\n };\n var new_route =\n \"repository/s/\" +\n that.model.tool_shed +\n \"/r/\" +\n tsr_id;\n Backbone.history.navigate(new_route, {\n trigger: true,\n replace: true\n });\n }\n });\n });\n },\n\n reDraw: function(options) {\n this.$el.empty();\n 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\"mvc/toolshed/util\"], function(\n toolshed_model,\n toolshed_util\n) {\n var ToolShedCategories = Backbone.View.extend({\n el: \"#center\",\n\n defaults: {\n tool_shed: \"https://toolshed.g2.bx.psu.edu/\"\n },\n\n initialize: function(options) {\n var self = this;\n var shed = options.tool_shed.replace(/\\//g, \"%2f\");\n this.options = _.defaults(this.options || options, this.defaults);\n this.model = new toolshed_model.Categories();\n this.listenTo(this.model, \"sync\", this.render);\n this.model.url =\n this.model.url + \"?tool_shed_url=\" + this.options.tool_shed;\n this.model.tool_shed = shed;\n this.model.fetch();\n },\n\n render: function(options) {\n this.options = _.extend(this.options, options);\n this.options.categories = this.model.models;\n this.options.queue = toolshed_util.queueLength();\n var category_list_template = this.templateCategoryList;\n this.$el.html(category_list_template(this.options));\n $(\"#center\").css(\"overflow\", \"auto\");\n this.bindEvents();\n },\n\n bindEvents: function() {\n var that = this;\n require([\"libs/jquery/jquery-ui\"], function() {\n $(\"#search_box\").autocomplete({\n source: function(request, response) {\n var shed_url = that.model.tool_shed.replace(\n /%2f/g,\n \"/\"\n );\n var base_url = Galaxy.root + \"api/tool_shed/search\";\n var params = {\n term: request.term,\n tool_shed_url: shed_url\n };\n $.post(base_url, params, function(data) {\n console.log(data);\n var result_list = toolshed_util.shedParser(data);\n response(result_list);\n });\n },\n minLength: 3,\n select: function(event, ui) {\n var tsr_id = ui.item.value;\n var api_url = Galaxy.root + \"api/tool_shed/repository\";\n var params = {\n tool_shed_url: that.model.tool_shed,\n tsr_id: tsr_id\n };\n var new_route =\n \"repository/s/\" +\n that.model.tool_shed +\n \"/r/\" +\n tsr_id;\n Backbone.history.navigate(new_route, {\n trigger: true,\n replace: true\n });\n }\n });\n });\n },\n\n reDraw: function(options) {\n this.$el.empty();\n 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',\n '\"\n ].join(\"\")\n ),\n\n workflows_missing_tools: _.template(\n [\n '',\n '',\n \"
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\",\n ' \",\n \"\",\n \"\",\n \"<% _.each(Object.keys(workflows), function(workflow_key) { %>\",\n '<% var workflow_details = workflow_key.split(\"/\"); %>',\n \"<% var workflow = workflows[workflow_key]; %>\",\n \"Workflows ',\n 'Tool IDs ',\n 'Shed ',\n 'Name ',\n 'Owner ',\n 'Actions ',\n \"\",\n ' \",\n \"<% }); %>\",\n \"\",\n \"\"\n ].join(\"\")\n )\n });\n\n return {\n RepoQueue: ToolShedRepositoryQueue\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/toolshed/repo-status-view.js.map b/static/maps/mvc/toolshed/repo-status-view.js.map index 4825f223d81..8ec76ae285c 100644 --- a/static/maps/mvc/toolshed/repo-status-view.js.map +++ b/static/maps/mvc/toolshed/repo-status-view.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/toolshed/repo-status-view.js"],"names":["define","toolshed_model","RepoStatus","Backbone","View","extend","el","initialize","self","options","this","model","_","listenTo","terminal_states","all_done","render","repo_id","repository","repositories","join","fetch","timer","some","models","get","clearInterval","indexOf","repo_status","title","$","bindEvents","that","repo_status_template","templateRepoStatus","$el","html","queue","toolshed_util","queueLength","css","reDraw","empty","template"],"mappings":"aAAAA,QAAQ,8BAA+B,qBAAsB,SACzDC,EADJD,GAoJI,OACIE,WAjJ8CC,SAAAC,KAAAC,QAC9CC,GAAI,UAGAC,WAAIC,SAAJC,GAMAC,KAAKC,QAAQC,EAAIX,SACjBS,KAAKG,cACLJ,EAEAC,KAAKC,UAGGD,KAAAC,MAAIG,IAAAA,EAAmBZ,WACvBQ,KAAAG,SAAIE,KAAWJ,MAAf,OAAAD,KAAAM,QACAJ,KAAAA,MAAOJ,KACHS,iBAAUC,KAAAA,QAAeC,aAAzBC,KAAA,KACAV,KAAAC,MAAAU,QAGAX,KAAAY,MAAIR,YACAC,SAAAA,GACA,IAAAD,GAAA,YAAA,SACHC,GAAA,EARLH,EAAAW,KAAAf,EAAAG,MAAAa,OAAA,SAAAN,GAUIH,QAAUG,EAAAO,IAAA,MACVC,IAAAA,EAAmBJ,EAChBG,IAAA,UACEd,cACR,IAAA,IAAAG,EAAAa,QAAAC,GAjCiC,OAe1Cb,GAAA,GAf0C,IAyC1CW,EAzC0CA,cAAAlB,EAAAc,OA4CtCd,EAAAG,MAASF,SAGb,IAEQoB,OAKRC,MAAE,WACFJ,cAAKK,KAALT,QAGJS,OAAAA,SAAYtB,GACRC,KAAIsB,QAAJpB,EAAAP,OAAAK,KAAAD,QAAAA,GA3D0C,IAAAwB,EAAAvB,KAAAwB,mBA+C1CxB,KAAKyB,IAAIC,KAeLH,GACJJ,MAAA,oBACKtB,aAAWE,KAAhBE,MAAAa,OAhE0Ca,MAAAC,EAAAC,iBAAlDT,EAAA,WAAAU,IAAA,WAAA,QAuDQ9B,KAAKqB,cAyFbA,WAAA,aAlFIU,OAAQ,SAAShC,GACbC,KAAKyB,IAAIO,QACThC,KAAKH,WAAWE,IAGpByB,mBAAoBtB,EAAE+B,UAEd,yEACA,6DACA,wJACA,SACA,0BACA,oBACA,4BACA,qEACA,wBACA,sCACA,mDACA,6CACA,0FACA,sEACA,kEACA,WACA,uCACA,iCACA,OACA,iEACA,wEACA,kEACA,qEACA,gFACA,QACA,WACA,+BACA,oDACA,OACA,OACA,uBACA,uFACA,gCACA,WACA,SACA,QACA,OACA,uBACA,uFACA,uCACA,WACA,SACA,QACA,OACA,uBACA,uFACA,iCACA,WACA,SACA,QACA,OACA,uBACA,4FACA,8CACA,WACA,SACA,QACA,OACA,uBACA,8FACA,qKACA,kCACA,SACA,WACA,SACA,QACA,QACA,YACA,WACA,yCACA,YACFvB,KAAK","file":"../../../scripts/mvc/toolshed/repo-status-view.js","sourcesContent":["define([\"mvc/toolshed/toolshed-model\", \"mvc/toolshed/util\"], function(\n toolshed_model,\n toolshed_util\n) {\n var ToolShedRepoStatusView = Backbone.View.extend({\n el: \"#center\",\n\n initialize: function(options) {\n var self = this;\n this.options = _.defaults(\n this.options || [{}],\n options,\n this.defaults\n );\n this.model = new toolshed_model.RepoStatus();\n this.listenTo(this.model, \"sync\", this.render);\n this.model.url +=\n \"?repositories=\" + this.options.repositories.join(\"|\");\n this.model.fetch();\n this.timer = setInterval(\n function(self) {\n var terminal_states = [\"installed\", \"error\"];\n var all_done = true;\n _.some(self.model.models, function(repository) {\n repo_id = repository.get(\"id\");\n var repo_status = repository\n .get(\"status\")\n .toLowerCase();\n if (terminal_states.indexOf(repo_status) === -1) {\n all_done = false;\n return true;\n }\n });\n if (all_done) {\n clearInterval(self.timer);\n } else {\n self.model.fetch();\n }\n },\n 2000,\n this\n );\n },\n\n close: function() {\n clearInterval(this.timer);\n },\n\n render: function(options) {\n this.options = _.extend(this.options, options);\n var repo_status_template = this.templateRepoStatus;\n this.$el.html(\n repo_status_template({\n title: \"Repository Status\",\n repositories: this.model.models,\n queue: toolshed_util.queueLength()\n })\n );\n $(\"#center\").css(\"overflow\", \"auto\");\n this.bindEvents();\n },\n\n bindEvents: function() {\n var that = this;\n },\n\n reDraw: function(options) {\n this.$el.empty();\n this.initialize(options);\n },\n\n templateRepoStatus: _.template(\n [\n '',\n ' \",\n '- ',\n \"<% _.each(workflow.workflows.sort(), function(wf) { %>\",\n '
',\n ' \",\n '- ',\n \"<% _.each(workflow.tools.sort(), function(tool) { %>\",\n '
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',\n '\",\n '\",\n '<%= title %>',\n '',\n \"',\n '',\n \"
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\"mvc/toolshed/util\"], function(\n toolshed_model,\n toolshed_util\n) {\n var View = Backbone.View.extend({\n el: \"#center\",\n\n defaults: [{}],\n\n initialize: function(options) {\n var that = this;\n this.model = new toolshed_model.RepoQueue();\n this.listenTo(this.model, \"sync\", this.render);\n this.model.fetch();\n that.render();\n },\n\n render: function(options) {\n var that = this;\n var repo_queue_template = that.templateRepoQueue;\n var repositories = that.model.models;\n that.$el.html(\n repo_queue_template({\n title: \"Repository Installation Queue\",\n repositories: repositories,\n queue: toolshed_util.queueLength()\n })\n );\n $(\"#center\").css(\"overflow\", \"auto\");\n that.bindEvents();\n },\n\n bindEvents: function() {\n var that = this;\n $(\".install_one\").on(\"click\", function() {\n var repository_metadata = that.loadFromQueue(\n $(this).attr(\"data-repokey\")\n );\n that.installFromQueue(\n repository_metadata,\n $(this).attr(\"data-repokey\")\n );\n });\n $(\".remove_one\").on(\"click\", function() {\n var queue_key = $(this).attr(\"data-repokey\");\n var repo_queue = JSON.parse(localStorage.repositories);\n if (repo_queue.hasOwnProperty(queue_key)) {\n var repository_id = repo_queue[queue_key].repository.id;\n delete repo_queue[queue_key];\n $(\"#queued_repository_\" + repository_id).remove();\n }\n localStorage.repositories = JSON.stringify(repo_queue);\n });\n $(\"#clear_queue\").on(\"click\", function() {\n localStorage.repositories = \"{}\";\n });\n $(\"#from_workflow\").on(\"click\", function() {\n Backbone.history.navigate(\"workflows\", {\n trigger: true,\n replace: true\n });\n });\n },\n\n installFromQueue: function(repository_metadata, queue_key) {\n var that = this;\n var params = Object();\n params.install_tool_dependencies =\n repository_metadata.install_tool_dependencies;\n params.install_repository_dependencies =\n repository_metadata.install_repository_dependencies;\n params.install_resolver_dependencies =\n 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\"mvc/toolshed/util\"], function(\n toolshed_model,\n toolshed_util\n) {\n var View = Backbone.View.extend({\n el: \"#center\",\n\n defaults: [{}],\n\n initialize: function(options) {\n var that = this;\n this.model = new toolshed_model.RepoQueue();\n this.listenTo(this.model, \"sync\", this.render);\n this.model.fetch();\n that.render();\n },\n\n render: function(options) {\n var that = this;\n var repo_queue_template = that.templateRepoQueue;\n var repositories = that.model.models;\n that.$el.html(\n repo_queue_template({\n title: \"Repository Installation Queue\",\n repositories: repositories,\n queue: toolshed_util.queueLength()\n })\n );\n $(\"#center\").css(\"overflow\", \"auto\");\n that.bindEvents();\n },\n\n bindEvents: function() {\n var that = this;\n $(\".install_one\").on(\"click\", function() {\n var repository_metadata = that.loadFromQueue(\n $(this).attr(\"data-repokey\")\n );\n that.installFromQueue(\n repository_metadata,\n $(this).attr(\"data-repokey\")\n );\n });\n $(\".remove_one\").on(\"click\", function() {\n var queue_key = $(this).attr(\"data-repokey\");\n var repo_queue = JSON.parse(localStorage.repositories);\n if (repo_queue.hasOwnProperty(queue_key)) {\n var repository_id = repo_queue[queue_key].repository.id;\n delete repo_queue[queue_key];\n $(\"#queued_repository_\" + repository_id).remove();\n }\n localStorage.repositories = JSON.stringify(repo_queue);\n });\n $(\"#clear_queue\").on(\"click\", function() {\n localStorage.repositories = \"{}\";\n });\n $(\"#from_workflow\").on(\"click\", function() {\n Backbone.history.navigate(\"workflows\", {\n trigger: true,\n replace: true\n });\n });\n },\n\n installFromQueue: function(repository_metadata, queue_key) {\n var that = this;\n var params = Object();\n params.install_tool_dependencies =\n repository_metadata.install_tool_dependencies;\n params.install_repository_dependencies =\n repository_metadata.install_repository_dependencies;\n params.install_resolver_dependencies =\n repository_metadata.install_resolver_dependencies;\n params.tool_panel_section = repository_metadata.tool_panel_section;\n params.shed_tool_conf = repository_metadata.shed_tool_conf;\n params.repositories = JSON.stringify([\n [\n repository_metadata.repository.id,\n repository_metadata.changeset_revision\n ]\n ]);\n params.tool_shed_repository_ids = JSON.stringify([\n repository_metadata.repository.id\n ]);\n params.tool_shed_url = queue_key.split(\"|\")[0];\n params.changeset = repository_metadata.changeset_revision;\n var url =\n Galaxy.root + \"api/tool_shed_repositories/install?async=True\";\n $(\n \"#queued_repository_\" + repository_metadata.repository.id\n ).remove();\n if (localStorage.repositories) {\n if (queue_key === undefined) {\n queue_key = toolshed_util.queueKey(repository_metadata);\n }\n var repository_queue = JSON.parse(localStorage.repositories);\n if (repository_queue.hasOwnProperty(queue_key)) {\n delete repository_queue[queue_key];\n localStorage.repositories = JSON.stringify(\n repository_queue\n );\n }\n }\n\n $.post(url, params, function(data) {\n var iri_params = JSON.parse(data);\n var repositories = iri_params.repositories;\n var new_route = \"status/r/\" + repositories.join(\"|\");\n $.post(\n Galaxy.root + \"admin_toolshed/manage_repositories\",\n iri_params,\n function(data) {\n console.log(\n \"Initializing repository installation succeeded\"\n );\n }\n );\n Backbone.history.navigate(new_route, {\n trigger: true,\n replace: true\n });\n });\n },\n\n loadFromQueue: function(queue_key) {\n var repository_queue = JSON.parse(localStorage.repositories);\n if (repository_queue.hasOwnProperty(queue_key)) {\n return repository_queue[queue_key];\n }\n return undefined;\n },\n\n reDraw: function(options) {\n this.$el.empty();\n this.initialize(options);\n this.model.fetch();\n this.render(options);\n },\n\n templateRepoQueue: _.template(\n [\n '',\n '',\n \"
\",\n '',\n \"\",\n ' \",\n \"\",\n \"\",\n \"<% _.each(repositories, function(repository) { %>\",\n 'Name ',\n 'Owner ',\n 'Revision ',\n 'ToolShed ',\n 'Install ',\n '',\n \" \">',\n ' \",\n \"<% }); %>\",\n \"\",\n \"<%= repository.get(\"repository\").name %> ',\n '<%= repository.get(\"repository\").owner %> ',\n '<%= repository.get(\"changeset_revision\") %> ',\n '<%= repository.get(\"tool_shed_url\") %> ',\n '',\n '\" type=\"submit\" id=\"install_repository_<%= repository.get(\"id\") %>\" name=\"install_repository\" value=\"Install now\" />',\n \" \",\n '',\n '\" type=\"submit\" id=\"unqueue_repository_<%= repository.get(\"id\") %>\" name=\"unqueue_repository\" value=\"Remove from queue\" />',\n \" \",\n \"',\n '\",\n '<%= title %>',\n '',\n \"',\n '\"\n ].join(\"\")\n )\n });\n\n return {\n RepoQueueView: View\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/toolshed/repository-view.js.map b/static/maps/mvc/toolshed/repository-view.js.map index 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[\n \"mvc/toolshed/toolshed-model\",\n \"libs/jquery/jstree\",\n \"utils/utils\",\n \"mvc/ui/ui-modal\",\n \"mvc/form/form-view\",\n \"mvc/toolshed/util\"\n ],\n function(toolshed_model, jstree, Utils, Modal, FormView, toolshed_util) {\n var ToolShedRepositoryView = Backbone.View.extend({\n el: \"#center\",\n\n initialize: function(params) {\n var self = this;\n this.options = _.defaults(this.options || {}, this.defaults);\n this.model = new toolshed_model.RepositoryCollection();\n this.listenTo(this.model, \"sync\", this.render);\n var shed = params.tool_shed.replace(/\\//g, \"%2f\");\n this.model.url +=\n \"?tool_shed_url=\" +\n shed +\n \"&repository_id=\" +\n params.repository_id;\n this.model.tool_shed_url = params.tool_shed.replace(\n /%2f/g,\n \"/\"\n );\n this.model.tool_shed = shed;\n this.model.category = params.repository_id;\n this.model.fetch();\n },\n\n render: function(options) {\n var repo_details_template = this.templateRepoDetails;\n var models = this.model.models[0];\n this.options = {\n repository: models.get(\"repository\"),\n tool_shed: this.model.tool_shed,\n queue: toolshed_util.queueLength()\n };\n var changesets = Object.keys(this.options.repository.metadata);\n this.options.current_changeset =\n this.options.current_changeset ||\n changesets[changesets.length - 1];\n this.options.current_metadata = this.options.repository.metadata[\n this.options.current_changeset\n ];\n this.options.current_metadata.tool_shed_url = this.model.tool_shed_url;\n this.options.tools = this.options.current_metadata.tools;\n this.options.repository_dependencies_template = this.templateRepoDependencies;\n this.options.repository_dependency_template = this.templateRepoDependency;\n this.options.tps_template_global_select = this.templateGlobalSectionSelect;\n this.options.tps_template_tool_select = this.templateToolSectionSelect;\n this.options.tps_select_options = this.templatePanelSelectOptions;\n this.options.tool_dependencies = models.get(\n \"tool_dependencies\"\n );\n this.options.shed_tool_conf = this.templateShedToolConf({\n stc_html: models.get(\"shed_conf\")\n });\n this.options.panel_section_dict = models.get(\n \"panel_section_dict\"\n );\n this.options.api_url =\n Galaxy.root +\n \"api/tool_shed_repositories/install?async=True\";\n this.options = _.extend(this.options, options);\n this.$el.html(repo_details_template(this.options));\n this.checkInstalled(this.options.current_metadata);\n this.bindEvents();\n $(\"#center\").css(\"overflow\", \"auto\");\n },\n\n bindEvents: function() {\n var that = this;\n $(\"#changeset\").on(\"change\", function() {\n that.options.current_changeset = $(\"#changeset\")\n .find(\"option:selected\")\n .text();\n that.options.current_metadata =\n that.options.repository.metadata[\n that.options.current_changeset\n ];\n that.checkInstalled(that.options.current_metadata);\n that.reDraw();\n });\n $(\"#tool_panel_section_select\").on(\"change\", function() {\n that.tpsSelection();\n });\n $(\"#install_repository\").on(\"click\", function(ev) {\n var form = $(\"#repository_installation\");\n ev.preventDefault();\n var params = {};\n params.repositories = JSON.stringify([\n [\n $(\"#install_repository\").attr(\"data-tsrid\"),\n $(\"#changeset\")\n .find(\"option:selected\")\n .val()\n ]\n ]);\n params.tool_shed_repository_ids = JSON.stringify([\n $(\"#install_repository\").attr(\"data-tsrid\")\n ]);\n params.tool_shed_url = that.model.tool_shed_url;\n params.install_tool_dependencies = $(\n \"#install_tool_dependencies\"\n ).val();\n params.install_repository_dependencies = $(\n \"#install_repository_dependencies\"\n ).val();\n params.install_resolver_dependencies = $(\n \"#install_resolver_dependencies\"\n ).val();\n var tps = that.panelSelect(params);\n params.tool_panel_section = JSON.stringify(\n that.panelSelect(params)\n );\n params.shed_tool_conf = $(\"select[name='shed_tool_conf']\")\n .find(\"option:selected\")\n .val();\n params.changeset = $(\"#changeset\")\n .find(\"option:selected\")\n .val();\n var url = $(\"#repository_installation\").attr(\"action\");\n that.prepareInstall(params, url);\n });\n $(\"#queue_install\").on(\"click\", function(ev) {\n that.options.current_changeset = $(\"#changeset\")\n .find(\"option:selected\")\n .text();\n that.options.current_metadata =\n that.options.repository.metadata[\n that.options.current_changeset\n ];\n var changeset = that.options.current_changeset;\n var repository_metadata = {};\n _.each(Object.keys(that.options.current_metadata), function(\n key\n ) {\n if (!repository_metadata[key]) {\n repository_metadata[key] =\n that.options.current_metadata[key];\n }\n });\n repository_metadata.install_tool_dependencies = $(\n \"#install_tool_dependencies\"\n ).val();\n repository_metadata.install_repository_dependencies = $(\n \"#install_repository_dependencies\"\n ).val();\n repository_metadata.install_resolver_dependencies = $(\n \"#install_resolver_dependencies\"\n ).val();\n repository_metadata.tool_panel_section = JSON.stringify(\n that.panelSelect({})\n );\n repository_metadata.shed_tool_conf = $(\n \"select[name='shed_tool_conf']\"\n )\n .find(\"option:selected\")\n .val();\n repository_metadata.tool_shed_url =\n that.model.tool_shed_url;\n if (repository_metadata.tool_shed_url.substr(-1) == \"/\") {\n repository_metadata.tool_shed_url = repository_metadata.tool_shed_url.substr(\n 0,\n repository_metadata.tool_shed_url.length - 1\n );\n }\n toolshed_util.addToQueue(repository_metadata);\n that.checkInstalled(repository_metadata);\n });\n $(\".tool_panel_section_picker\").on(\"change\", function() {\n var new_value = $(this)\n .find(\"option:selected\")\n .val();\n var default_tps = $(\"#tool_panel_section_select\")\n .find(\"option:selected\")\n .val();\n if (new_value == default_tps) {\n $(this).attr(\"default\", \"active\");\n } else {\n $(this).removeAttr(\"default\");\n }\n });\n $(function() {\n $(\"#repository_dependencies\").jstree();\n });\n $(\".tool_form\").on(\"click\", function() {\n var guid = $(this).attr(\"data-guid\");\n var clean = $(this).attr(\"data-clean\");\n var name = $(this).attr(\"data-name\");\n var desc = $(this).attr(\"data-desc\");\n var tool_shed_url = that.model.tool_shed_url;\n var tsr_id = $(\"#repository_details\").attr(\"data-tsrid\");\n var changeset = $(\"#changeset\")\n .find(\"option:selected\")\n .val();\n var api_url = Galaxy.root + \"api/tool_shed/tool_json\";\n var params = {\n guid: guid,\n tool_shed_url: tool_shed_url,\n tsr_id: tsr_id,\n changeset: changeset\n };\n $.get(api_url, params, function(data) {\n data.cls = \"ui-portlet-plain\";\n var toolform = new FormView(data);\n Utils.deepeach(data.inputs, function(input) {\n if (input.type) {\n if (\n [\"data\", \"data_collection\"].indexOf(\n input.type\n ) != -1\n ) {\n input.type = \"hidden\";\n input.info =\n \"Data input '\" +\n input.name +\n \"' (\" +\n Utils.textify(input.extensions) +\n \")\";\n }\n }\n });\n var modal = new Modal.View();\n var modal_title = \"\" + name + \" \" + desc;\n modal.show({\n closing_events: true,\n title: modal_title,\n body: toolform.$el,\n buttons: {\n Close: function() {\n modal.hide();\n }\n }\n });\n });\n });\n },\n\n checkInstalled: function(metadata) {\n var that = this;\n var params = { name: metadata.name, owner: metadata.owner };\n var already_installed = false;\n var queued = that.repoQueued(metadata);\n $.get(\n Galaxy.root + \"api/tool_shed_repositories\",\n params,\n function(data) {\n for (var index = 0; index < data.length; index++) {\n var repository = data[index];\n var installed =\n !repository.deleted && !repository.uninstalled;\n var changeset_match =\n repository.changeset_revision ==\n metadata.changeset_revision ||\n repository.installed_changeset_revision ==\n metadata.changeset_revision;\n if (\n repository.name == metadata.repository.name &&\n repository.owner == metadata.repository.owner &&\n installed &&\n changeset_match\n ) {\n already_installed = true;\n }\n if (already_installed) {\n $(\"#install_repository\").prop(\"disabled\", true);\n $(\"#install_repository\").val(\n \"This revision is already installed\"\n );\n } else {\n $(\"#install_repository\").prop(\n \"disabled\",\n false\n );\n $(\"#install_repository\").val(\n \"Install this revision\"\n );\n }\n }\n if (that.repoQueued(metadata) || already_installed) {\n $(\"#queue_install\").hide();\n $(\"#queue_install\").val(\n \"This revision is already in the queue\"\n );\n } else {\n $(\"#queue_install\").show();\n $(\"#queue_install\").val(\n \"Install this revision later\"\n );\n }\n }\n );\n },\n\n panelSelect: function(params) {\n var tool_panel_section = {};\n if ($(\"#tool_panel_section_select\").length) {\n params.tool_panel_section_id = $(\n \"#tool_panel_section_select\"\n )\n .find(\"option:selected\")\n .val();\n } else {\n params.new_tool_panel_section = $(\n \"#new_tool_panel_section\"\n ).val();\n }\n $(\".tool_panel_section_picker\").each(function() {\n var element_name = $(this).attr(\"name\");\n var tool_guid = $(this).attr(\"data-toolguid\");\n if (element_name === \"tool_panel_section_id\") {\n tool_panel_section[tool_guid] = {\n tool_panel_section: $(this)\n .find(\"option:selected\")\n .val(),\n action: \"append\"\n };\n } else {\n tool_panel_section[tool_guid] = {\n tool_panel_section: $(this).val(),\n action: \"create\"\n };\n }\n });\n return tool_panel_section;\n },\n\n reDraw: function(options) {\n this.$el.empty();\n this.initialize(options);\n },\n\n repoQueued: function(metadata) {\n var that = this;\n if (!localStorage.repositories) {\n return;\n }\n var repository_queue = JSON.parse(localStorage.repositories);\n var changeset = metadata.changeset_revision;\n var queue_key = that.queueKey(metadata);\n if (localStorage.repositories) {\n queued_repos = JSON.parse(localStorage.repositories);\n }\n if (queued_repos.hasOwnProperty(queue_key)) {\n return true;\n }\n return false;\n },\n\n queueKey: function(metadata) {\n var shed_url = this.model.tool_shed_url;\n // Make sure there is never a trailing slash on the shed URL.\n if (shed_url.substr(-1) == \"/\") {\n shed_url = shed_url.substr(0, shed_url.length - 1);\n }\n return (\n shed_url +\n \"|\" +\n metadata.repository_id +\n \"|\" +\n metadata.changeset_revision\n );\n },\n\n tpsSelection: function() {\n new_tps = $(\"#tool_panel_section_select\")\n .find(\"option:selected\")\n .val();\n $(\n '.tool_panel_section_picker[default=\"active\"]'\n ).each(function() {\n $(this).val(new_tps);\n });\n },\n\n prepareInstall: function(params, api_url) {\n var that = this;\n $.post(api_url, params, function(data) {\n var iri_parameters = JSON.parse(data);\n that.doInstall(iri_parameters);\n });\n },\n\n doInstall: function(params) {\n var controller_url =\n Galaxy.root + \"admin_toolshed/manage_repositories\";\n var repositories = params.repositories;\n var new_route = \"status/r/\" + repositories.join(\"|\");\n $.post(controller_url, params, function(data) {\n console.log(\n \"Initializing repository installation succeeded\"\n );\n });\n Backbone.history.navigate(new_route, {\n trigger: true,\n replace: true\n });\n },\n\n templateRepoDetails: _.template(\n [\n '',\n '',\n \"
\",\n '',\n \"\",\n ' \",\n \"\",\n \"\",\n \"<% _.each(repositories, function(repository) { %>\",\n 'Name ',\n 'Owner ',\n 'Revision ',\n 'ToolShed ',\n 'Install ',\n '',\n \" \">',\n ' \",\n \"<% }); %>\",\n \"\",\n \"<%= repository.get(\"repository\").name %> ',\n '<%= repository.get(\"repository\").owner %> ',\n '<%= repository.get(\"changeset_revision\") %> ',\n '<%= repository.get(\"tool_shed_url\") %> ',\n '',\n '\" type=\"submit\" id=\"install_repository_<%= repository.get(\"id\") %>\" name=\"install_repository\" value=\"Install now\" />',\n \" \",\n '',\n '\" type=\"submit\" id=\"unqueue_repository_<%= repository.get(\"id\") %>\" name=\"unqueue_repository\" value=\"Remove from queue\" />',\n \" \",\n \"',\n '\",\n 'Repository information for <%= repository.name %> from <%= repository.owner %>',\n '',\n \"\">',\n '\",\n \"\"\n ].join(\"\")\n ),\n\n templateRepoDependencies: _.template(\n [\n 'Repository Dependencies',\n '',\n \"\"\n ].join(\"\")\n ),\n\n templateRepoDependency: _.template(\n [\n '- \",\n \"
Shed tool configuration file:',\n '',\n '\"\n ].join(\"\")\n ),\n\n templateToolDependency: _.template(\n [\n \"<% if (has_repository_dependencies) { %>\",\n \"<% _.each(repository_dependencies, function(dependency) { %>\",\n \"<% if (dependency.includes_tool_dependencies) { %>\",\n \"<% dependency.tool_dependency_template = tool_dependency_template %>\",\n \"<%= tool_dependency_template(dependency) %>\",\n \"<% } %>\",\n \"<% }); %>\",\n \"<% } %>\"\n ].join(\"\")\n ),\n\n templateGlobalSectionCreate: _.template(\n [\n '',\n \"<%= stc_html %>\",\n '\",\n \"Select the file whose tool_path setting you want used for installing repositories.',\n \"',\n '\"\n ].join(\"\")\n ),\n\n templateGlobalSectionSelect: _.template(\n [\n '',\n '',\n '',\n '\",\n \"',\n \"Add a new tool panel section to contain the installed tools (optional).\",\n \"\",\n \"',\n '\"\n ].join(\"\")\n ),\n\n templateToolSectionCreate: _.template(\n [\n 'Tool Panel Section',\n '',\n '\",\n \"',\n '\",\n '',\n '\",\n 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[\n \"mvc/toolshed/toolshed-model\",\n \"libs/jquery/jstree\",\n \"utils/utils\",\n \"mvc/ui/ui-modal\",\n \"mvc/form/form-view\",\n \"mvc/toolshed/util\"\n ],\n function(toolshed_model, jstree, Utils, Modal, FormView, toolshed_util) {\n var ToolShedRepositoryView = Backbone.View.extend({\n el: \"#center\",\n\n initialize: function(params) {\n var self = this;\n this.options = _.defaults(this.options || {}, this.defaults);\n this.model = new toolshed_model.RepositoryCollection();\n this.listenTo(this.model, \"sync\", this.render);\n var shed = params.tool_shed.replace(/\\//g, \"%2f\");\n this.model.url +=\n \"?tool_shed_url=\" +\n shed +\n \"&repository_id=\" +\n params.repository_id;\n this.model.tool_shed_url = params.tool_shed.replace(\n /%2f/g,\n \"/\"\n );\n this.model.tool_shed = shed;\n this.model.category = params.repository_id;\n this.model.fetch();\n },\n\n render: function(options) {\n var repo_details_template = this.templateRepoDetails;\n var models = this.model.models[0];\n this.options = {\n repository: models.get(\"repository\"),\n tool_shed: this.model.tool_shed,\n queue: toolshed_util.queueLength()\n };\n var changesets = Object.keys(this.options.repository.metadata);\n this.options.current_changeset =\n this.options.current_changeset ||\n changesets[changesets.length - 1];\n this.options.current_metadata = this.options.repository.metadata[\n this.options.current_changeset\n ];\n this.options.current_metadata.tool_shed_url = this.model.tool_shed_url;\n this.options.tools = this.options.current_metadata.tools;\n this.options.repository_dependencies_template = this.templateRepoDependencies;\n this.options.repository_dependency_template = this.templateRepoDependency;\n this.options.tps_template_global_select = this.templateGlobalSectionSelect;\n this.options.tps_template_tool_select = this.templateToolSectionSelect;\n this.options.tps_select_options = this.templatePanelSelectOptions;\n this.options.tool_dependencies = models.get(\n \"tool_dependencies\"\n );\n this.options.shed_tool_conf = this.templateShedToolConf({\n stc_html: models.get(\"shed_conf\")\n });\n this.options.panel_section_dict = models.get(\n \"panel_section_dict\"\n );\n this.options.api_url =\n Galaxy.root +\n \"api/tool_shed_repositories/install?async=True\";\n this.options = _.extend(this.options, options);\n this.$el.html(repo_details_template(this.options));\n this.checkInstalled(this.options.current_metadata);\n this.bindEvents();\n $(\"#center\").css(\"overflow\", \"auto\");\n },\n\n bindEvents: function() {\n var that = this;\n $(\"#changeset\").on(\"change\", function() {\n that.options.current_changeset = $(\"#changeset\")\n .find(\"option:selected\")\n .text();\n that.options.current_metadata =\n that.options.repository.metadata[\n that.options.current_changeset\n ];\n that.checkInstalled(that.options.current_metadata);\n that.reDraw();\n });\n $(\"#tool_panel_section_select\").on(\"change\", function() {\n that.tpsSelection();\n });\n $(\"#install_repository\").on(\"click\", function(ev) {\n var form = $(\"#repository_installation\");\n ev.preventDefault();\n var params = {};\n params.repositories = JSON.stringify([\n [\n $(\"#install_repository\").attr(\"data-tsrid\"),\n $(\"#changeset\")\n .find(\"option:selected\")\n .val()\n ]\n ]);\n params.tool_shed_repository_ids = JSON.stringify([\n $(\"#install_repository\").attr(\"data-tsrid\")\n ]);\n params.tool_shed_url = that.model.tool_shed_url;\n params.install_tool_dependencies = $(\n \"#install_tool_dependencies\"\n ).val();\n params.install_repository_dependencies = $(\n \"#install_repository_dependencies\"\n ).val();\n params.install_resolver_dependencies = $(\n \"#install_resolver_dependencies\"\n ).val();\n var tps = that.panelSelect(params);\n params.tool_panel_section = JSON.stringify(\n that.panelSelect(params)\n );\n params.shed_tool_conf = $(\"select[name='shed_tool_conf']\")\n .find(\"option:selected\")\n .val();\n params.changeset = $(\"#changeset\")\n .find(\"option:selected\")\n .val();\n var url = $(\"#repository_installation\").attr(\"action\");\n that.prepareInstall(params, url);\n });\n $(\"#queue_install\").on(\"click\", function(ev) {\n that.options.current_changeset = $(\"#changeset\")\n .find(\"option:selected\")\n .text();\n that.options.current_metadata =\n that.options.repository.metadata[\n that.options.current_changeset\n ];\n var changeset = that.options.current_changeset;\n var repository_metadata = {};\n _.each(Object.keys(that.options.current_metadata), function(\n key\n ) {\n if (!repository_metadata[key]) {\n repository_metadata[key] =\n that.options.current_metadata[key];\n }\n });\n repository_metadata.install_tool_dependencies = $(\n \"#install_tool_dependencies\"\n ).val();\n repository_metadata.install_repository_dependencies = $(\n \"#install_repository_dependencies\"\n ).val();\n repository_metadata.install_resolver_dependencies = $(\n \"#install_resolver_dependencies\"\n ).val();\n repository_metadata.tool_panel_section = JSON.stringify(\n that.panelSelect({})\n );\n repository_metadata.shed_tool_conf = $(\n \"select[name='shed_tool_conf']\"\n )\n .find(\"option:selected\")\n .val();\n repository_metadata.tool_shed_url =\n that.model.tool_shed_url;\n if (repository_metadata.tool_shed_url.substr(-1) == \"/\") {\n repository_metadata.tool_shed_url = repository_metadata.tool_shed_url.substr(\n 0,\n repository_metadata.tool_shed_url.length - 1\n );\n }\n toolshed_util.addToQueue(repository_metadata);\n that.checkInstalled(repository_metadata);\n });\n $(\".tool_panel_section_picker\").on(\"change\", function() {\n var new_value = $(this)\n .find(\"option:selected\")\n .val();\n var default_tps = $(\"#tool_panel_section_select\")\n .find(\"option:selected\")\n .val();\n if (new_value == default_tps) {\n $(this).attr(\"default\", \"active\");\n } else {\n $(this).removeAttr(\"default\");\n }\n });\n $(function() {\n $(\"#repository_dependencies\").jstree();\n });\n $(\".tool_form\").on(\"click\", function() {\n var guid = $(this).attr(\"data-guid\");\n var clean = $(this).attr(\"data-clean\");\n var name = $(this).attr(\"data-name\");\n var desc = $(this).attr(\"data-desc\");\n var tool_shed_url = that.model.tool_shed_url;\n var tsr_id = $(\"#repository_details\").attr(\"data-tsrid\");\n var changeset = $(\"#changeset\")\n .find(\"option:selected\")\n .val();\n var api_url = Galaxy.root + \"api/tool_shed/tool_json\";\n var params = {\n guid: guid,\n tool_shed_url: tool_shed_url,\n tsr_id: tsr_id,\n changeset: changeset\n };\n $.get(api_url, params, function(data) {\n data.cls = \"ui-portlet-plain\";\n var toolform = new FormView(data);\n Utils.deepeach(data.inputs, function(input) {\n if (input.type) {\n if (\n [\"data\", \"data_collection\"].indexOf(\n input.type\n ) != -1\n ) {\n input.type = \"hidden\";\n input.info =\n \"Data input '\" +\n input.name +\n \"' (\" +\n Utils.textify(input.extensions) +\n \")\";\n }\n }\n });\n var modal = new Modal.View();\n var modal_title = \"\" + name + \" \" + desc;\n modal.show({\n closing_events: true,\n title: modal_title,\n body: toolform.$el,\n buttons: {\n Close: function() {\n modal.hide();\n }\n }\n });\n });\n });\n },\n\n checkInstalled: function(metadata) {\n var that = this;\n var params = { name: metadata.name, owner: metadata.owner };\n var already_installed = false;\n var queued = that.repoQueued(metadata);\n $.get(\n Galaxy.root + \"api/tool_shed_repositories\",\n params,\n function(data) {\n for (var index = 0; index < data.length; index++) {\n var repository = data[index];\n var installed =\n !repository.deleted && !repository.uninstalled;\n var changeset_match =\n repository.changeset_revision ==\n metadata.changeset_revision ||\n repository.installed_changeset_revision ==\n metadata.changeset_revision;\n if (\n repository.name == metadata.repository.name &&\n repository.owner == metadata.repository.owner &&\n installed &&\n changeset_match\n ) {\n already_installed = true;\n }\n if (already_installed) {\n $(\"#install_repository\").prop(\"disabled\", true);\n $(\"#install_repository\").val(\n \"This revision is already installed\"\n );\n } else {\n $(\"#install_repository\").prop(\n \"disabled\",\n false\n );\n $(\"#install_repository\").val(\n \"Install this revision\"\n );\n }\n }\n if (that.repoQueued(metadata) || already_installed) {\n $(\"#queue_install\").hide();\n $(\"#queue_install\").val(\n \"This revision is already in the queue\"\n );\n } else {\n $(\"#queue_install\").show();\n $(\"#queue_install\").val(\n \"Install this revision later\"\n );\n }\n }\n );\n },\n\n panelSelect: function(params) {\n var tool_panel_section = {};\n if ($(\"#tool_panel_section_select\").length) {\n params.tool_panel_section_id = $(\n \"#tool_panel_section_select\"\n )\n .find(\"option:selected\")\n .val();\n } else {\n params.new_tool_panel_section = $(\n \"#new_tool_panel_section\"\n ).val();\n }\n $(\".tool_panel_section_picker\").each(function() {\n var element_name = $(this).attr(\"name\");\n var tool_guid = $(this).attr(\"data-toolguid\");\n if (element_name === \"tool_panel_section_id\") {\n tool_panel_section[tool_guid] = {\n tool_panel_section: $(this)\n .find(\"option:selected\")\n .val(),\n action: \"append\"\n };\n } else {\n tool_panel_section[tool_guid] = {\n tool_panel_section: $(this).val(),\n action: \"create\"\n };\n }\n });\n return tool_panel_section;\n },\n\n reDraw: function(options) {\n this.$el.empty();\n this.initialize(options);\n },\n\n repoQueued: function(metadata) {\n var that = this;\n if (!localStorage.repositories) {\n return;\n }\n var repository_queue = JSON.parse(localStorage.repositories);\n var changeset = metadata.changeset_revision;\n var queue_key = that.queueKey(metadata);\n if (localStorage.repositories) {\n queued_repos = JSON.parse(localStorage.repositories);\n }\n if (queued_repos.hasOwnProperty(queue_key)) {\n return true;\n }\n return false;\n },\n\n queueKey: function(metadata) {\n var shed_url = this.model.tool_shed_url;\n // Make sure there is never a trailing slash on the shed URL.\n if (shed_url.substr(-1) == \"/\") {\n shed_url = shed_url.substr(0, shed_url.length - 1);\n }\n return (\n shed_url +\n \"|\" +\n metadata.repository_id +\n \"|\" +\n metadata.changeset_revision\n );\n },\n\n tpsSelection: function() {\n new_tps = $(\"#tool_panel_section_select\")\n .find(\"option:selected\")\n .val();\n $(\n '.tool_panel_section_picker[default=\"active\"]'\n ).each(function() {\n $(this).val(new_tps);\n });\n },\n\n prepareInstall: function(params, api_url) {\n var that = this;\n $.post(api_url, params, function(data) {\n var iri_parameters = JSON.parse(data);\n that.doInstall(iri_parameters);\n });\n },\n\n doInstall: function(params) {\n var controller_url =\n Galaxy.root + \"admin_toolshed/manage_repositories\";\n var repositories = params.repositories;\n var new_route = \"status/r/\" + repositories.join(\"|\");\n $.post(controller_url, params, function(data) {\n console.log(\n \"Initializing repository installation succeeded\"\n );\n });\n Backbone.history.navigate(new_route, {\n trigger: true,\n replace: true\n });\n },\n\n templateRepoDetails: _.template(\n [\n '',\n '\",\n 'Repository information for <%= repository.name %> from <%= repository.owner %>',\n '',\n \"\">',\n '\",\n \"\"\n ].join(\"\")\n ),\n\n templateRepoDependencies: _.template(\n [\n 'Repository Dependencies',\n '',\n \"\"\n ].join(\"\")\n ),\n\n templateRepoDependency: _.template(\n [\n '- \",\n \"
Shed tool configuration file:',\n '',\n '\"\n ].join(\"\")\n ),\n\n templateToolDependency: _.template(\n [\n \"<% if (has_repository_dependencies) { %>\",\n \"<% _.each(repository_dependencies, function(dependency) { %>\",\n \"<% if (dependency.includes_tool_dependencies) { %>\",\n \"<% dependency.tool_dependency_template = tool_dependency_template %>\",\n \"<%= tool_dependency_template(dependency) %>\",\n \"<% } %>\",\n \"<% }); %>\",\n \"<% } %>\"\n ].join(\"\")\n ),\n\n templateGlobalSectionCreate: _.template(\n [\n '',\n \"<%= stc_html %>\",\n '\",\n \"Select the file whose tool_path setting you want used for installing repositories.',\n \"',\n '\"\n ].join(\"\")\n ),\n\n templateGlobalSectionSelect: _.template(\n [\n '',\n '',\n '',\n '\",\n \"',\n \"Add a new tool panel section to contain the installed tools (optional).\",\n \"\",\n \"',\n '\"\n ].join(\"\")\n ),\n\n templateToolSectionCreate: _.template(\n [\n 'Tool Panel Section',\n '',\n '\",\n \"',\n '\",\n '',\n '\",\n \"',\n \"Select an existing tool panel section to contain the installed tools (optional).\",\n \"\",\n \"\" data-clean=\"<%= tool.clean %>\" class=\"form-row\">',\n '\" class=\"tool_panel_section_picker\" size=\"40\" name=\"new_tool_panel_section\" id=\"new_tool_panel_section_<%= tool.clean %>\" type=\"text\">',\n '\" class=\"btn btn-primary\" data-toolguid=\"<%= tool.guid %>\" value=\"Select existing\" id=\"select_existing_<%= tool.clean %>\" type=\"button\">',\n \"\"\n ].join(\"\")\n ),\n\n templateToolSectionSelect: _.template(\n [\n '\" data-clean=\"<%= tool.clean %>\" class=\"tps_creator\">',\n '\",\n '\" data-clean=\"<%= tool.clean %>\" class=\"btn btn-primary create-tps-button\" data-toolguid=\"<%= tool.guid %>\" value=\"Create new\" id=\"create_new_<%= tool.clean %>\" type=\"button\">',\n '',\n \"\"\n ].join(\"\")\n ),\n\n templatePanelSelectOptions: _.template(\n [\n \"<% _.each(sections, function(section) { %>\",\n '',\n \"<% }); 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function() {\n var ToolShedModel = Backbone.Model.extend({\n defaults: {\n url: \"https://toolshed.g2.bx.psu.edu/\",\n name: \"Galaxy Main Tool Shed\"\n },\n urlRoot: Galaxy.root + \"api/tool_shed\"\n });\n\n var ToolShedsCollection = Backbone.Collection.extend({\n url: Galaxy.root + \"api/tool_shed\",\n model: ToolShedModel\n });\n\n var ToolShedCategoriesModel = Backbone.Model.extend({\n defaults: [{}],\n urlRoot: Galaxy.root + \"api/tool_shed/contents\"\n });\n\n var ToolShedCategoriesCollection = Backbone.Collection.extend({\n url: Galaxy.root + \"api/tool_shed/contents\",\n model: ToolShedCategoriesModel\n });\n\n var ToolShedCategoryModel = Backbone.Model.extend({\n defaults: [{}],\n urlRoot: Galaxy.root + \"api/tool_shed/category\"\n });\n\n var ToolShedCategoryCollection = Backbone.Collection.extend({\n url: Galaxy.root + \"api/tool_shed/category\",\n model: ToolShedCategoryModel\n });\n\n var ToolShedRepositoryModel = Backbone.Model.extend({\n defaults: [{}],\n urlRoot: 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\"mvc/toolshed/util\"], function(\n toolshed_model,\n toolshed_util\n) {\n var View = Backbone.View.extend({\n el: \"#center\",\n\n defaults: [{}],\n\n initialize: function(options) {\n var that = this;\n this.model = new toolshed_model.WorkflowTools();\n this.listenTo(this.model, \"sync\", this.render);\n this.model.fetch();\n that.render();\n },\n\n render: function(options) {\n var that = this;\n var workflows_missing_tools = that.templateWorkflows;\n var workflows = that.model.models;\n that.$el.html(\n workflows_missing_tools({\n title: \"Workflows Missing Tools\",\n workflows: workflows,\n queue: toolshed_util.queueLength()\n })\n );\n $(\"#center\").css(\"overflow\", \"auto\");\n that.bindEvents();\n },\n\n bindEvents: function() {\n var that = this,\n repository_id;\n $(\".show_wf_repo\").on(\"click\", function() {\n var tool_ids = $(this).attr(\"data-toolids\");\n var toolshed = $(this).attr(\"data-shed\");\n var api_url = Galaxy.root + \"api/tool_shed/repository\";\n var params = { tool_ids: tool_ids };\n $.get(api_url, params, function(data) {\n repository_id = data.repository.id;\n var new_route =\n \"repository/s/\" +\n toolshed.replace(/:/g, \"%3a\").replace(/\\//g, \"%2f\") +\n \"/r/\" +\n data.repository.id;\n Backbone.history.navigate(new_route, {\n trigger: true,\n replace: true\n });\n });\n });\n $(\".queue_wf_repo\").on(\"click\", function() {\n var elem = $(this);\n var tool_ids = elem.attr(\"data-toolids\");\n var toolshed = elem.attr(\"data-shed\");\n var api_url = Galaxy.root + \"api/tool_shed/repository\";\n var params = { tool_ids: tool_ids };\n $.get(api_url, params, function(data) {\n repository_id = data.repository.id;\n params = {\n tool_shed_url: toolshed,\n repository_id: repository_id\n };\n $.get(api_url, params, function(data) {\n var changesets = Object.keys(data.repository.metadata);\n var current_changeset = changesets[0];\n var current_metadata =\n data.repository.metadata[current_changeset];\n current_metadata.tool_shed_url = toolshed;\n toolshed_util.addToQueue(current_metadata);\n elem.remove();\n });\n });\n });\n $(\"#from_workflow\").on(\"click\", that.loadWorkflows);\n },\n\n reDraw: function(options) {\n this.$el.empty();\n this.initialize(options);\n },\n\n templateWorkflows: _.template(\n [\n '',\n ' \",\n '- ',\n '<% _.each(workflow.get(\"workflows\"), function(name) { %>',\n '
',\n ' \",\n '- ',\n '<% _.each(workflow.get(\"tools\"), function(tool) { %>',\n '
<%= workflow.get(\"shed\") %> ',\n '<%= workflow.get(\"repository\") %> ',\n '<%= workflow.get(\"owner\") %> ',\n '',\n ' \",\n \"- ',\n '
',\n '\",\n '\",\n '<%= title %>',\n '',\n \"',\n '',\n \"
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',\n ' \",\n '- ',\n '<% _.each(workflow.get(\"tools\"), function(tool) { %>',\n '
<%= workflow.get(\"shed\") %> ',\n '<%= workflow.get(\"repository\") %> ',\n '<%= workflow.get(\"owner\") %> ',\n '',\n ' \",\n \"- ',\n '
Galaxy Tours
\nThis page presents a list of interactive tours available on this Galaxy server.\nSelect any tour to get started (and remember, you can click 'End Tour' at any time).
\n- \n<% _.each(tours, function(tour) { %>\n
Galaxy Tours
\nThis page presents a list of interactive tours available on this Galaxy server.\nSelect any tour to get started (and remember, you can click 'End Tour' at any time).
\n- \n<% _.each(tours, function(tour) { %>\n
' +\n '' +\n \"\"\n );\n },\n\n /** Box template */\n _templateBox: function(color) {\n return (\n ''\n );\n },\n\n /** Main template */\n _template: function() {\n return (\n '' +\n '' +\n '' +\n '\" +\n 'Select a color' +\n \"' +\n '\");\n }\n });\n});\n"]} \ No newline at end of file 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Renders the color picker used e.g. in the tool form **/\ndefine([\"utils/utils\"], function(Utils) {\n return Backbone.View.extend({\n colors: {\n standard: [\n \"c00000\",\n \"ff0000\",\n \"ffc000\",\n \"ffff00\",\n \"92d050\",\n \"00b050\",\n \"00b0f0\",\n \"0070c0\",\n \"002060\",\n \"7030a0\"\n ],\n base: [\n \"ffffff\",\n \"000000\",\n \"eeece1\",\n \"1f497d\",\n \"4f81bd\",\n \"c0504d\",\n \"9bbb59\",\n \"8064a2\",\n \"4bacc6\",\n \"f79646\"\n ],\n theme: [\n [\n \"f2f2f2\",\n \"7f7f7f\",\n \"ddd9c3\",\n \"c6d9f0\",\n \"dbe5f1\",\n \"f2dcdb\",\n \"ebf1dd\",\n \"e5e0ec\",\n \"dbeef3\",\n \"fdeada\"\n ],\n [\n \"d8d8d8\",\n \"595959\",\n \"c4bd97\",\n \"8db3e2\",\n \"b8cce4\",\n \"e5b9b7\",\n \"d7e3bc\",\n \"ccc1d9\",\n \"b7dde8\",\n \"fbd5b5\"\n ],\n [\n \"bfbfbf\",\n \"3f3f3f\",\n \"938953\",\n \"548dd4\",\n \"95b3d7\",\n \"d99694\",\n \"c3d69b\",\n \"b2a2c7\",\n \"92cddc\",\n \"fac08f\"\n ],\n [\n \"a5a5a5\",\n \"262626\",\n \"494429\",\n \"17365d\",\n \"366092\",\n \"953734\",\n \"76923c\",\n \"5f497a\",\n \"31859b\",\n \"e36c09\"\n ],\n [\n \"7f7f7e\",\n \"0c0c0c\",\n \"1d1b10\",\n \"0f243e\",\n \"244061\",\n \"632423\",\n \"4f6128\",\n \"3f3151\",\n \"205867\",\n \"974806\"\n ]\n ]\n },\n\n initialize: function(options) {\n this.options = Utils.merge(options, {});\n this.setElement(this._template());\n this.$panel = this.$(\".ui-color-picker-panel\");\n this.$view = this.$(\".ui-color-picker-view\");\n this.$value = this.$(\".ui-color-picker-value\");\n this.$header = this.$(\".ui-color-picker-header\");\n this._build();\n this.visible = false;\n this.value(this.options.value);\n this.$boxes = this.$(\".ui-color-picker-box\");\n var self = this;\n this.$boxes.on(\"click\", function() {\n self.value($(this).css(\"background-color\"));\n self.$header.trigger(\"click\");\n });\n this.$header.on(\"click\", function() {\n self.visible = !self.visible;\n if (self.visible) {\n self.$view.fadeIn(\"fast\");\n } else {\n self.$view.fadeOut(\"fast\");\n }\n });\n },\n\n /** Get/set value */\n value: function(new_val) {\n if (new_val !== undefined && new_val !== null) {\n this.$value.css(\"background-color\", new_val);\n this.$(\".ui-color-picker-box\").empty();\n this.$(this._getValue()).html(this._templateCheck());\n this.options.onchange && this.options.onchange(new_val);\n }\n return this._getValue();\n },\n\n /** Get value from dom */\n _getValue: function() {\n var rgb = this.$value.css(\"background-color\");\n rgb = rgb.match(/^rgb\\((\\d+),\\s*(\\d+),\\s*(\\d+)\\)$/);\n if (rgb) {\n function hex(x) {\n return (\"0\" + parseInt(x).toString(16)).slice(-2);\n }\n return \"#\" + hex(rgb[1]) + hex(rgb[2]) + hex(rgb[3]);\n } else {\n return null;\n }\n },\n\n /** Build color panel */\n _build: function() {\n this._content({ colors: this.colors.base });\n for (var i in this.colors.theme) {\n var line_def = {};\n if (i == 0) {\n line_def[\"bottom\"] = true;\n } else if (i != this.colors.theme.length - 1) {\n line_def[\"top\"] = true;\n line_def[\"bottom\"] = true;\n } else {\n line_def[\"top\"] = true;\n }\n line_def[\"colors\"] = this.colors.theme[i];\n this._content(line_def);\n }\n this._content({ colors: this.colors.standard });\n },\n\n /** Create content */\n _content: function(options) {\n var colors = options.colors;\n var $content = $(this._templateContent());\n var $line = $content.find(\".line\");\n this.$panel.append($content);\n for (var i in colors) {\n var $box = $(this._templateBox(colors[i]));\n if (options.top) {\n $box.css(\"border-top\", \"none\");\n $box.css(\"border-top-left-radius\", \"0px\");\n $box.css(\"border-top-right-radius\", \"0px\");\n }\n if (options.bottom) {\n $box.css(\"border-bottom\", \"none\");\n $box.css(\"border-bottom-left-radius\", \"0px\");\n $box.css(\"border-bottom-right-radius\", \"0px\");\n }\n $line.append($box);\n }\n return $content;\n },\n\n /** Check icon */\n _templateCheck: function() {\n return '';\n },\n\n /** Content template */\n _templateContent: function() {\n return (\n '' +\n \"\"\n );\n (\"' +\n '' +\n \"\"\n );\n },\n\n /** Box template */\n _templateBox: function(color) {\n return (\n ''\n );\n },\n\n /** Main template */\n _template: function() {\n return (\n '' +\n '' +\n '' +\n '\" +\n 'Select a color' +\n \"' +\n '\");\n }\n });\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/ui/ui-drilldown.js.map b/static/maps/mvc/ui/ui-drilldown.js.map index 105e9349c7b..e38f4d72056 100644 --- a/static/maps/mvc/ui/ui-drilldown.js.map +++ b/static/maps/mvc/ui/ui-drilldown.js.map @@ -1 +1 @@ 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This class creates/wraps a drill down element. */\ndefine([\"utils/utils\", \"mvc/ui/ui-options\"], function(Utils, Options) {\n var View = Options.BaseIcons.extend({\n initialize: function(options) {\n options.type = options.display || \"checkbox\";\n options.multiple = options.type == \"checkbox\";\n Options.BaseIcons.prototype.initialize.call(this, options);\n },\n\n /** Set states for selected values */\n _setValue: function(new_value) {\n Options.BaseIcons.prototype._setValue.call(this, new_value);\n if (\n new_value !== undefined &&\n new_value !== null &&\n this.header_index\n ) {\n var self = this;\n var values = $.isArray(new_value) ? new_value : [new_value];\n _.each(values, function(v) {\n var list = self.header_index[v];\n _.each(list, function(element) {\n self._setState(element, true);\n });\n });\n }\n },\n\n /** Expand/collapse a sub group */\n _setState: function(header_id, is_expanded) {\n var $button = this.$(\".button-\" + header_id);\n var $subgroup = this.$(\".subgroup-\" + header_id);\n $button.data(\"is_expanded\", is_expanded);\n if (is_expanded) {\n $subgroup.show();\n $button\n .removeClass(\"fa-plus-square\")\n .addClass(\"fa-minus-square\");\n } else {\n $subgroup.hide();\n $button\n .removeClass(\"fa-minus-square\")\n .addClass(\"fa-plus-square\");\n }\n },\n\n /** Template to create options tree */\n _templateOptions: function() {\n var self = this;\n this.header_index = {};\n\n // attach event handler\n function attach($el, header_id) {\n var $button = $el.find(\".button-\" + header_id);\n $button.on(\"click\", function() {\n self._setState(header_id, !$button.data(\"is_expanded\"));\n });\n }\n\n // recursive function which iterates through options\n function iterate($tmpl, options, header) {\n header = header || [];\n for (var i in options) {\n var level = options[i];\n var has_options = level.options && level.options.length > 0;\n var new_header = header.slice(0);\n self.header_index[level.value] = 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drilldown-container\")\n .attr(\"id\", this.model.id);\n }\n });\n\n return {\n View: View\n };\n});\n"]} \ No newline at end of file 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This class creates/wraps a drill down element. */\ndefine([\"utils/utils\", \"mvc/ui/ui-options\"], function(Utils, Options) {\n var View = Options.BaseIcons.extend({\n initialize: function(options) {\n options.type = options.display || \"checkbox\";\n options.multiple = options.type == \"checkbox\";\n Options.BaseIcons.prototype.initialize.call(this, options);\n },\n\n /** Set states for selected values */\n _setValue: function(new_value) {\n Options.BaseIcons.prototype._setValue.call(this, new_value);\n if (\n new_value !== undefined &&\n new_value !== null &&\n this.header_index\n ) {\n var self = this;\n var values = $.isArray(new_value) ? new_value : [new_value];\n _.each(values, function(v) {\n var list = self.header_index[v];\n _.each(list, function(element) {\n self._setState(element, true);\n });\n });\n }\n },\n\n /** Expand/collapse a sub group */\n _setState: function(header_id, is_expanded) {\n var $button = this.$(\".button-\" + header_id);\n var $subgroup = this.$(\".subgroup-\" + header_id);\n $button.data(\"is_expanded\", is_expanded);\n if (is_expanded) {\n $subgroup.show();\n $button\n .removeClass(\"fa-plus-square\")\n .addClass(\"fa-minus-square\");\n } else {\n $subgroup.hide();\n $button\n .removeClass(\"fa-minus-square\")\n .addClass(\"fa-plus-square\");\n }\n },\n\n /** Template to create options tree */\n _templateOptions: function() {\n var self = this;\n this.header_index = {};\n\n // attach event handler\n function attach($el, header_id) {\n var $button = $el.find(\".button-\" + header_id);\n $button.on(\"click\", function() {\n self._setState(header_id, !$button.data(\"is_expanded\"));\n });\n }\n\n // recursive function which iterates through options\n function iterate($tmpl, options, header) {\n header = header || [];\n for (var i in options) {\n var level = options[i];\n var has_options = level.options && level.options.length > 0;\n var new_header = header.slice(0);\n self.header_index[level.value] = new_header.slice(0);\n var $group = $(\"\");\n if (has_options) {\n var header_id = Utils.uid();\n var $button = $(\"\")\n .addClass(\"button-\" + header_id)\n .addClass(\"ui-drilldown-button fa fa-plus-square\");\n var $subgroup = $(\"\")\n .addClass(\"subgroup-\" + header_id)\n .addClass(\"ui-drilldown-subgroup\");\n $group.append(\n $(\"\")\n .append($button)\n .append(\n self._templateOption({\n label: level.name,\n value: level.value\n })\n )\n );\n new_header.push(header_id);\n iterate($subgroup, level.options, new_header);\n $group.append($subgroup);\n attach($group, header_id);\n } else {\n $group.append(\n self._templateOption({\n label: level.name,\n value: level.value\n })\n );\n }\n $tmpl.append($group);\n }\n }\n\n // iterate through options and create dom\n var $tmpl = $(\"\");\n iterate($tmpl, this.model.get(\"data\"));\n return $tmpl;\n },\n\n /** Template for drill down view */\n _template: function() {\n return $(\"\")\n .addClass(\"ui-options-list drilldown-container\")\n .attr(\"id\", this.model.id);\n }\n });\n\n return {\n View: View\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/ui/ui-frames.js.map b/static/maps/mvc/ui/ui-frames.js.map index 875bded27de..895cad2970d 100644 --- a/static/maps/mvc/ui/ui-frames.js.map +++ b/static/maps/mvc/ui/ui-frames.js.map @@ -1 +1 @@ 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function() {\n /** Frame view */\n var FrameView = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.model =\n (options && options.model) || new Backbone.Model(options);\n this.setElement($(\"\").addClass(\"corner frame\"));\n this.$el\n .append(\n $(\"\")\n .addClass(\"f-header corner\")\n .append($(\"\").addClass(\"f-title\"))\n .append(\n $(\"\")\n .addClass(\"f-icon f-close fa fa-close\")\n .tooltip({\n title: \"Close\",\n placement: \"bottom\"\n })\n )\n )\n .append($(\"\").addClass(\"f-content\"))\n .append(\n $(\"\")\n .addClass(\"f-resize f-icon corner fa fa-expand\")\n .tooltip({ title: \"Resize\" })\n )\n .append($(\"\").addClass(\"f-cover\"));\n this.$header = this.$(\".f-header\");\n this.$title = this.$(\".f-title\");\n this.$content = this.$(\".f-content\");\n this.render();\n this.listenTo(this.model, \"change\", this.render, this);\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$title.html(options.title || \"\");\n this.$header.find(\".f-icon-left\").remove();\n _.each(options.menu, function(option) {\n var $option = $(\"\")\n .addClass(\"f-icon-left\")\n .addClass(option.icon);\n if (_.isFunction(option.disabled) && option.disabled()) {\n $option.attr(\"disabled\", true);\n } else {\n $option\n .on(\"click\", function() {\n option.onclick(self);\n })\n .tooltip({\n title: option.tooltip,\n placement: \"bottom\"\n });\n }\n self.$header.append($option);\n });\n if (options.url) {\n this.$content.html(\n $(\"\")\n .addClass(\"f-iframe\")\n .attr(\"scrolling\", \"auto\")\n .attr(\n \"src\",\n options.url +\n (options.url.indexOf(\"?\") === -1 ? \"?\" : \"&\") +\n \"widget=True\"\n )\n );\n } else if (options.content) {\n _.isFunction(options.content)\n ? options.content(self.$content)\n : self.$content.html(options.content);\n }\n }\n });\n\n /** Scratchbook viewer */\n var View = Backbone.View.extend({\n defaultOptions: {\n frame: {\n // default frame size in cells\n cols: 6,\n rows: 3\n },\n rows: 1000, // maximum number of rows\n cell: 130, // cell size in px\n margin: 5, // margin between frames\n scroll: 5, // scroll speed\n top_min: 40, // top margin\n frame_max: 9, // maximum number of frames\n visible: true // initial visibility\n },\n\n cols: 0, // number of columns\n top: 0, // scroll/element top\n top_max: 0, // viewport scrolling state\n frame_z: 0, // frame z-index\n frame_counter: 0, // frame counter\n frame_uid: 0, // unique frame id counter\n frame_list: {}, // list of all frames\n frame_shadow: null, // frame shown as placeholder when moving active frames\n visible: false, // flag indicating if scratchbook viewer is visible or not\n event: {}, // dictionary keeping track of current event\n\n initialize: function(options) {\n var self = this;\n this.options = _.defaults(options || {}, this.defaultOptions);\n this.visible = this.options.visible;\n this.top = this.top_max = this.options.top_min;\n this.setElement(\n $(\"\")\n .addClass(\"galaxy-frame\")\n .append($(\"\").addClass(\"frame-background\"))\n .append(\n $(\"\").addClass(\n \"frame-menu frame-scroll-up fa fa-chevron-up fa-2x\"\n )\n )\n .append(\n $(\"\").addClass(\n \"frame-menu frame-scroll-down fa fa-chevron-down fa-2x\"\n )\n )\n );\n\n // initialize shadow to guiding drag/resize events\n this.frame_shadow = new Backbone.View({\n el: $(\"\").addClass(\"corner frame-shadow\")\n });\n this.$el.append(this.frame_shadow.$el);\n this._frameInit(this.frame_shadow, \"#frame-shadow\");\n this._frameResize(this.frame_shadow, { width: 0, height: 0 });\n this.frame_list[\"#frame-shadow\"] = this.frame_shadow;\n\n // initialize panel\n this.visible ? this.show() : this.hide();\n this._panelRefresh();\n $(window).resize(function() {\n self.visible && self._panelRefresh();\n });\n },\n\n /** Render */\n render: function() {\n this.$(\".frame-scroll-up\")[\n (this.top != this.options.top_min && \"show\") || \"hide\"\n ]();\n this.$(\".frame-scroll-down\")[\n (this.top != this.top_max && \"show\") || \"hide\"\n ]();\n },\n\n /**\n * Adds and displays a new frame.\n *\n * options:\n * url : loaded into an iframe\n * content : content is treated as a function or raw HTML, function is passed a single\n * argument that is the frame's content DOM element\n */\n add: function(options) {\n if (this.frame_counter >= this.options.frame_max) {\n Galaxy.modal.show({\n title: \"Warning\",\n body:\n \"You have reached the maximum number of allowed frames (\" +\n this.options.frame_max +\n \").\",\n buttons: {\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n } else {\n var frame_id = \"#frame-\" + this.frame_uid++;\n if ($(frame_id).length !== 0) {\n Galaxy.modal.show({\n title: \"Error\",\n body:\n \"This frame already exists. This page might contain multiple frame managers.\",\n buttons: {\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n } else {\n // initialize new frame elements\n this.top = this.options.top_min;\n var frame = new FrameView(options);\n this.$el.append(frame.$el);\n\n // set dimensions\n options.width = this._toPixelCoord(\n \"width\",\n this.options.frame.cols\n );\n options.height = this._toPixelCoord(\n \"height\",\n this.options.frame.rows\n );\n\n // set default z-index and add to ui and frame list\n this.frame_z = parseInt(frame.$el.css(\"z-index\"));\n this.frame_list[frame_id] = frame;\n this.frame_counter++;\n this._frameInit(frame, frame_id);\n this._frameResize(frame, {\n width: options.width,\n height: options.height\n });\n this._frameInsert(frame, { top: 0, left: 0 }, true);\n !this.visible && this.show();\n this.trigger(\"add\");\n }\n }\n },\n\n /** Remove a frame */\n del: function(frame) {\n var self = this;\n var $frame = frame.$el;\n $frame.fadeOut(\"fast\", function() {\n $frame.remove();\n delete self.frame_list[frame.id];\n self.frame_counter--;\n self._panelRefresh(true);\n self._panelAnimationComplete();\n self.trigger(\"remove\");\n });\n },\n\n /** Show panel */\n show: function() {\n this.visible = true;\n this.$el.fadeIn(\"fast\");\n this.trigger(\"show\");\n },\n\n /** Hide panel */\n hide: function() {\n if (!this.event.type) {\n this.visible = false;\n this.$el.fadeOut(\"fast\", function() {\n $(this).hide();\n });\n this.trigger(\"hide\");\n }\n },\n\n /** Returns the number of frames */\n length: function() {\n return this.frame_counter;\n },\n\n /*\n EVENT HANDLING\n */\n events: {\n // global frame events\n mousemove: \"_eventFrameMouseMove\",\n mouseup: \"_eventFrameMouseUp\",\n mouseleave: \"_eventFrameMouseUp\",\n mousewheel: \"_eventPanelScroll\",\n DOMMouseScroll: \"_eventPanelScroll\",\n\n // events fixed to elements\n \"mousedown .frame\": \"_eventFrameMouseDown\",\n \"mousedown .frame-background\": \"_eventHide\",\n \"mousedown .frame-scroll-up\": \"_eventPanelScroll_up\",\n \"mousedown .frame-scroll-down\": \"_eventPanelScroll_down\",\n \"mousedown .f-close\": \"_eventFrameClose\"\n },\n\n /** Start drag/resize event */\n _eventFrameMouseDown: function(e) {\n $(\".tooltip\").hide();\n if (!this.event.type) {\n if (\n $(e.target).hasClass(\"f-header\") ||\n $(e.target).hasClass(\"f-title\")\n ) {\n this.event.type = \"drag\";\n }\n if ($(e.target).hasClass(\"f-resize\")) {\n this.event.type = \"resize\";\n }\n if (this.event.type) {\n e.preventDefault();\n this.event.target = this._frameIdentify(e.target);\n this.event.xy = {\n x: e.originalEvent.pageX,\n y: e.originalEvent.pageY\n };\n this._frameDragStart(this.event.target);\n }\n }\n },\n\n /** Processes drag/resize events */\n _eventFrameMouseMove: function(e) {\n if (this.event.type) {\n // get mouse motion and delta\n var event_xy_new = {\n x: e.originalEvent.pageX,\n y: e.originalEvent.pageY\n };\n var event_xy_delta = {\n x: event_xy_new.x - this.event.xy.x,\n y: event_xy_new.y - this.event.xy.y\n };\n this.event.xy = event_xy_new;\n\n // get current screen position and size of frame\n var p = this._frameScreen(this.event.target);\n\n // drag/resize event\n if (this.event.type == \"resize\") {\n p.width += event_xy_delta.x;\n p.height += event_xy_delta.y;\n var min_dim = this.options.cell - this.options.margin - 1;\n p.width = Math.max(p.width, min_dim);\n p.height = Math.max(p.height, min_dim);\n this._frameResize(this.event.target, p);\n p.width = this._toGridCoord(\"width\", p.width) + 1;\n p.height = this._toGridCoord(\"height\", p.height) + 1;\n p.width = this._toPixelCoord(\"width\", p.width);\n p.height = this._toPixelCoord(\"height\", p.height);\n this._frameResize(this.frame_shadow, p);\n this._frameInsert(this.frame_shadow, {\n top: this._toGridCoord(\"top\", p.top),\n left: this._toGridCoord(\"left\", p.left)\n });\n } else if (this.event.type == \"drag\") {\n p.left += event_xy_delta.x;\n p.top += event_xy_delta.y;\n this._frameOffset(this.event.target, p);\n var l = {\n top: this._toGridCoord(\"top\", p.top),\n left: this._toGridCoord(\"left\", p.left)\n };\n l.left !== 0 && l.left++;\n this._frameInsert(this.frame_shadow, l);\n }\n }\n },\n\n /** Stop drag/resize events */\n _eventFrameMouseUp: function(e) {\n if (this.event.type) {\n this._frameDragStop(this.event.target);\n this.event.type = null;\n }\n },\n\n /** Destroy a frame */\n _eventFrameClose: function(e) {\n if (!this.event.type) {\n e.preventDefault();\n this.del(this._frameIdentify(e.target));\n }\n },\n\n /** Hide all frames */\n _eventHide: function(e) {\n !this.event.type && this.hide();\n },\n\n /** Fired when scrolling occurs on panel */\n _eventPanelScroll: function(e) {\n if (!this.event.type && this.visible) {\n // Stop propagation if scrolling is happening inside a frame.\n // TODO: could propagate scrolling if at top/bottom of frame.\n var frames = $(e.srcElement).parents(\".frame\");\n if (frames.length !== 0) {\n e.stopPropagation();\n } else {\n e.preventDefault();\n this._panelScroll(\n e.originalEvent.detail\n ? e.originalEvent.detail\n : e.originalEvent.wheelDelta / -3\n );\n }\n }\n },\n\n /** Handle scroll up event */\n _eventPanelScroll_up: function(e) {\n if (!this.event.type) {\n e.preventDefault();\n this._panelScroll(-this.options.scroll);\n }\n },\n\n /** Handle scroll down */\n _eventPanelScroll_down: function(e) {\n if (!this.event.type) {\n e.preventDefault();\n this._panelScroll(this.options.scroll);\n }\n },\n\n /*\n FRAME EVENTS SUPPORT\n */\n\n /** Identify the target frame */\n _frameIdentify: function(target) {\n return this.frame_list[\n \"#\" +\n $(target)\n .closest(\".frame\")\n .attr(\"id\")\n ];\n },\n\n /** Provides drag support */\n _frameDragStart: function(frame) {\n this._frameFocus(frame, true);\n var p = this._frameScreen(frame);\n this._frameResize(this.frame_shadow, p);\n this._frameGrid(this.frame_shadow, frame.grid_location);\n frame.grid_location = null;\n this.frame_shadow.$el.show();\n $(\".f-cover\").show();\n },\n\n /** Removes drag support */\n _frameDragStop: function(frame) {\n this._frameFocus(frame, false);\n var p = this._frameScreen(this.frame_shadow);\n this._frameResize(frame, p);\n this._frameGrid(frame, this.frame_shadow.grid_location, true);\n this.frame_shadow.grid_location = null;\n this.frame_shadow.$el.hide();\n $(\".f-cover\").hide();\n this._panelAnimationComplete();\n },\n\n /*\n GRID/PIXEL CONVERTER\n */\n\n /** Converts a pixel to a grid dimension */\n _toGridCoord: function(type, px) {\n var sign = type == \"width\" || type == \"height\" ? 1 : -1;\n type == \"top\" && (px -= this.top);\n return parseInt(\n (px + sign * this.options.margin) / this.options.cell,\n 10\n );\n },\n\n /** Converts a grid to a pixels dimension */\n _toPixelCoord: function(type, g) {\n var sign = type == \"width\" || type == \"height\" ? 1 : -1;\n var px = g * this.options.cell - sign * this.options.margin;\n type == \"top\" && (px += this.top);\n return px;\n },\n\n /** Converts a pixel to a grid coordinate set */\n _toGrid: function(px) {\n return {\n top: this._toGridCoord(\"top\", px.top),\n left: this._toGridCoord(\"left\", px.left),\n width: this._toGridCoord(\"width\", px.width),\n height: this._toGridCoord(\"height\", px.height)\n };\n },\n\n /** Converts a pixel to a grid coordinate set */\n _toPixel: function(g) {\n return {\n top: this._toPixelCoord(\"top\", g.top),\n left: this._toPixelCoord(\"left\", g.left),\n width: this._toPixelCoord(\"width\", g.width),\n height: this._toPixelCoord(\"height\", g.height)\n };\n },\n\n /* \n COLLISION DETECTION\n */\n\n /** Check collisions for a grid coordinate set */\n _isCollision: function(g) {\n function is_collision_pair(a, b) {\n return !(\n a.left > b.left + b.width - 1 ||\n a.left + a.width - 1 < b.left ||\n a.top > b.top + b.height - 1 ||\n a.top + a.height - 1 < b.top\n );\n }\n for (var i in this.frame_list) 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frame = this.frame_list[i];\n if (frame.grid_location !== null) {\n var screen_location = {\n top:\n frame.screen_location.top -\n (this.top - top_new),\n left: frame.screen_location.left\n };\n this._frameOffset(frame, screen_location, animate);\n }\n }\n this.top = top_new;\n }\n this.render();\n },\n\n /*\n FRAME FUNCTIONS\n */\n\n /** Initialize a new frame */\n _frameInit: function(frame, id) {\n frame.id = id;\n frame.screen_location = {};\n frame.grid_location = {};\n frame.grid_rank = null;\n frame.$el.attr(\"id\", id.substring(1));\n },\n\n /** Insert frame at given location */\n _frameInsert: function(frame, new_loc, animate) {\n var self = this;\n var place_list = [];\n if (frame) {\n frame.grid_location = null;\n place_list.push([frame, this._locationRank(new_loc)]);\n }\n _.each(this.frame_list, function(f) {\n if (f.grid_location !== null) {\n f.grid_location = null;\n place_list.push([f, f.grid_rank]);\n }\n });\n place_list.sort(function(a, b) {\n return a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0;\n });\n _.each(place_list, function(place) {\n self._framePlace(place[0], animate);\n });\n this.top_max = 0;\n _.each(this.frame_list, function(f) {\n if (f.grid_location !== null) {\n self.top_max = Math.max(\n self.top_max,\n f.grid_location.top + f.grid_location.height\n );\n }\n });\n this.top_max =\n $(window).height() -\n this.top_max * this.options.cell -\n 2 * this.options.margin;\n this.top_max = Math.min(this.top_max, this.options.top_min);\n this.render();\n },\n\n /** Naive frame placement */\n _framePlace: function(frame, animate) {\n frame.grid_location = null;\n var g = this._toGrid(this._frameScreen(frame));\n var done = false;\n for (var i = 0; i < this.options.rows; i++) {\n for (var j = 0; j < Math.max(1, this.cols - g.width); j++) {\n g.top = i;\n g.left = j;\n if (!this._isCollision(g)) {\n done = true;\n break;\n }\n }\n if (done) {\n break;\n }\n }\n if (done) {\n this._frameGrid(frame, g, animate);\n } else {\n console.log(\"Grid dimensions exceeded.\");\n }\n },\n\n /** Handle frame focussing */\n _frameFocus: function(frame, has_focus) {\n frame.$el.css(\"z-index\", this.frame_z + (has_focus ? 1 : 0));\n },\n\n /** New left/top position frame */\n _frameOffset: function(frame, p, animate) {\n frame.screen_location.left = p.left;\n frame.screen_location.top = p.top;\n if (animate) {\n this._frameFocus(frame, true);\n var self = this;\n frame.$el.animate(\n { top: p.top, left: p.left },\n \"fast\",\n function() {\n self._frameFocus(frame, false);\n }\n );\n } else {\n frame.$el.css({ top: p.top, left: p.left });\n }\n },\n\n /** Resize frame */\n _frameResize: function(frame, p) {\n frame.$el.css({ width: p.width, height: p.height });\n frame.screen_location.width = p.width;\n frame.screen_location.height = p.height;\n },\n\n /** Push frame to new grid location */\n _frameGrid: function(frame, l, animate) {\n frame.grid_location = l;\n this._frameOffset(frame, this._toPixel(l), animate);\n frame.grid_rank = 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function() {\n /** Frame view */\n var FrameView = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.model =\n (options && options.model) || new Backbone.Model(options);\n this.setElement($(\"\").addClass(\"corner frame\"));\n this.$el\n .append(\n $(\"\")\n .addClass(\"f-header corner\")\n .append($(\"\").addClass(\"f-title\"))\n .append(\n $(\"\")\n .addClass(\"f-icon f-close fa fa-close\")\n .tooltip({\n title: \"Close\",\n placement: \"bottom\"\n })\n )\n )\n .append($(\"\").addClass(\"f-content\"))\n .append(\n $(\"\")\n .addClass(\"f-resize f-icon corner fa fa-expand\")\n .tooltip({ title: \"Resize\" })\n )\n .append($(\"\").addClass(\"f-cover\"));\n this.$header = this.$(\".f-header\");\n this.$title = this.$(\".f-title\");\n this.$content = this.$(\".f-content\");\n this.render();\n this.listenTo(this.model, \"change\", this.render, this);\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$title.html(options.title || \"\");\n this.$header.find(\".f-icon-left\").remove();\n _.each(options.menu, function(option) {\n var $option = $(\"\")\n .addClass(\"f-icon-left\")\n .addClass(option.icon);\n if (_.isFunction(option.disabled) && option.disabled()) {\n $option.attr(\"disabled\", true);\n } else {\n $option\n .on(\"click\", function() {\n option.onclick(self);\n })\n .tooltip({\n title: option.tooltip,\n placement: \"bottom\"\n });\n }\n self.$header.append($option);\n });\n if (options.url) {\n this.$content.html(\n $(\"\")\n .addClass(\"f-iframe\")\n .attr(\"scrolling\", \"auto\")\n .attr(\n \"src\",\n options.url +\n (options.url.indexOf(\"?\") === -1 ? \"?\" : \"&\") +\n \"widget=True\"\n )\n );\n } else if (options.content) {\n _.isFunction(options.content)\n ? options.content(self.$content)\n : self.$content.html(options.content);\n }\n }\n });\n\n /** Scratchbook viewer */\n var View = Backbone.View.extend({\n defaultOptions: {\n frame: {\n // default frame size in cells\n cols: 6,\n rows: 3\n },\n rows: 1000, // maximum number of rows\n cell: 130, // cell size in px\n margin: 5, // margin between frames\n scroll: 5, // scroll speed\n top_min: 40, // top margin\n frame_max: 9, // maximum number of frames\n visible: true // initial visibility\n },\n\n cols: 0, // number of columns\n top: 0, // scroll/element top\n top_max: 0, // viewport scrolling state\n frame_z: 0, // frame z-index\n frame_counter: 0, // frame counter\n frame_uid: 0, // unique frame id counter\n frame_list: {}, // list of all frames\n frame_shadow: null, // frame shown as placeholder when moving active frames\n visible: false, // flag indicating if scratchbook viewer is visible or not\n event: {}, // dictionary keeping track of current event\n\n initialize: function(options) {\n var self = this;\n this.options = _.defaults(options || {}, this.defaultOptions);\n this.visible = this.options.visible;\n this.top = this.top_max = this.options.top_min;\n this.setElement(\n $(\"\")\n .addClass(\"galaxy-frame\")\n .append($(\"\").addClass(\"frame-background\"))\n .append(\n $(\"\").addClass(\n \"frame-menu frame-scroll-up fa fa-chevron-up fa-2x\"\n )\n )\n .append(\n $(\"\").addClass(\n \"frame-menu frame-scroll-down fa fa-chevron-down fa-2x\"\n )\n )\n );\n\n // initialize shadow to guiding drag/resize events\n this.frame_shadow = new Backbone.View({\n el: $(\"\").addClass(\"corner frame-shadow\")\n });\n this.$el.append(this.frame_shadow.$el);\n this._frameInit(this.frame_shadow, \"#frame-shadow\");\n this._frameResize(this.frame_shadow, { width: 0, height: 0 });\n this.frame_list[\"#frame-shadow\"] = this.frame_shadow;\n\n // initialize panel\n this.visible ? this.show() : this.hide();\n this._panelRefresh();\n $(window).resize(function() {\n self.visible && self._panelRefresh();\n });\n },\n\n /** Render */\n render: function() {\n this.$(\".frame-scroll-up\")[\n (this.top != this.options.top_min && \"show\") || \"hide\"\n ]();\n this.$(\".frame-scroll-down\")[\n (this.top != this.top_max && \"show\") || \"hide\"\n ]();\n },\n\n /**\n * Adds and displays a new frame.\n *\n * options:\n * url : loaded into an iframe\n * content : content is treated as a function or raw HTML, function is passed a single\n * argument that is the frame's content DOM element\n */\n add: function(options) {\n if (this.frame_counter >= this.options.frame_max) {\n Galaxy.modal.show({\n title: \"Warning\",\n body:\n \"You have reached the maximum number of allowed frames (\" +\n this.options.frame_max +\n \").\",\n buttons: {\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n } else {\n var frame_id = \"#frame-\" + this.frame_uid++;\n if ($(frame_id).length !== 0) {\n Galaxy.modal.show({\n title: \"Error\",\n body:\n \"This frame already exists. This page might contain multiple frame managers.\",\n buttons: {\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n } else {\n // initialize new frame elements\n this.top = this.options.top_min;\n var frame = new FrameView(options);\n this.$el.append(frame.$el);\n\n // set dimensions\n options.width = this._toPixelCoord(\n \"width\",\n this.options.frame.cols\n );\n options.height = this._toPixelCoord(\n \"height\",\n this.options.frame.rows\n );\n\n // set default z-index and add to ui and frame list\n this.frame_z = parseInt(frame.$el.css(\"z-index\"));\n this.frame_list[frame_id] = frame;\n this.frame_counter++;\n this._frameInit(frame, frame_id);\n this._frameResize(frame, {\n width: options.width,\n height: options.height\n });\n this._frameInsert(frame, { top: 0, left: 0 }, true);\n !this.visible && this.show();\n this.trigger(\"add\");\n }\n }\n },\n\n /** Remove a frame */\n del: function(frame) {\n var self = this;\n var $frame = frame.$el;\n $frame.fadeOut(\"fast\", function() {\n $frame.remove();\n delete self.frame_list[frame.id];\n self.frame_counter--;\n self._panelRefresh(true);\n self._panelAnimationComplete();\n self.trigger(\"remove\");\n });\n },\n\n /** Show panel */\n show: function() {\n this.visible = true;\n this.$el.fadeIn(\"fast\");\n this.trigger(\"show\");\n },\n\n /** Hide panel */\n hide: function() {\n if (!this.event.type) {\n this.visible = false;\n this.$el.fadeOut(\"fast\", function() {\n $(this).hide();\n });\n this.trigger(\"hide\");\n }\n },\n\n /** Returns the number of frames */\n length: function() {\n return this.frame_counter;\n },\n\n /*\n EVENT HANDLING\n */\n events: {\n // global frame events\n mousemove: \"_eventFrameMouseMove\",\n mouseup: \"_eventFrameMouseUp\",\n mouseleave: \"_eventFrameMouseUp\",\n mousewheel: \"_eventPanelScroll\",\n DOMMouseScroll: \"_eventPanelScroll\",\n\n // events fixed to elements\n \"mousedown .frame\": \"_eventFrameMouseDown\",\n \"mousedown .frame-background\": \"_eventHide\",\n \"mousedown .frame-scroll-up\": \"_eventPanelScroll_up\",\n \"mousedown .frame-scroll-down\": \"_eventPanelScroll_down\",\n \"mousedown .f-close\": \"_eventFrameClose\"\n },\n\n /** Start drag/resize event */\n _eventFrameMouseDown: function(e) {\n $(\".tooltip\").hide();\n if (!this.event.type) {\n if (\n $(e.target).hasClass(\"f-header\") ||\n $(e.target).hasClass(\"f-title\")\n ) {\n this.event.type = \"drag\";\n }\n if ($(e.target).hasClass(\"f-resize\")) {\n this.event.type = \"resize\";\n }\n if (this.event.type) {\n e.preventDefault();\n this.event.target = this._frameIdentify(e.target);\n this.event.xy = {\n x: e.originalEvent.pageX,\n y: e.originalEvent.pageY\n };\n this._frameDragStart(this.event.target);\n }\n }\n },\n\n /** Processes drag/resize events */\n _eventFrameMouseMove: function(e) {\n if (this.event.type) {\n // get mouse motion and delta\n var event_xy_new = {\n x: e.originalEvent.pageX,\n y: e.originalEvent.pageY\n };\n var event_xy_delta = {\n x: event_xy_new.x - this.event.xy.x,\n y: event_xy_new.y - this.event.xy.y\n };\n this.event.xy = event_xy_new;\n\n // get current screen position and size of frame\n var p = this._frameScreen(this.event.target);\n\n // drag/resize event\n if (this.event.type == \"resize\") {\n p.width += event_xy_delta.x;\n p.height += event_xy_delta.y;\n var min_dim = this.options.cell - this.options.margin - 1;\n p.width = Math.max(p.width, min_dim);\n p.height = Math.max(p.height, min_dim);\n this._frameResize(this.event.target, p);\n p.width = this._toGridCoord(\"width\", p.width) + 1;\n p.height = this._toGridCoord(\"height\", p.height) + 1;\n p.width = this._toPixelCoord(\"width\", p.width);\n p.height = this._toPixelCoord(\"height\", p.height);\n this._frameResize(this.frame_shadow, p);\n this._frameInsert(this.frame_shadow, {\n top: this._toGridCoord(\"top\", p.top),\n left: this._toGridCoord(\"left\", p.left)\n });\n } else if (this.event.type == \"drag\") {\n p.left += event_xy_delta.x;\n p.top += event_xy_delta.y;\n this._frameOffset(this.event.target, p);\n var l = {\n top: this._toGridCoord(\"top\", p.top),\n left: this._toGridCoord(\"left\", p.left)\n };\n l.left !== 0 && l.left++;\n this._frameInsert(this.frame_shadow, l);\n }\n }\n },\n\n /** Stop drag/resize events */\n _eventFrameMouseUp: function(e) {\n if (this.event.type) {\n this._frameDragStop(this.event.target);\n this.event.type = null;\n }\n },\n\n /** Destroy a frame */\n _eventFrameClose: function(e) {\n if (!this.event.type) {\n e.preventDefault();\n this.del(this._frameIdentify(e.target));\n }\n },\n\n /** Hide all frames */\n _eventHide: function(e) {\n !this.event.type && this.hide();\n },\n\n /** Fired when scrolling occurs on panel */\n _eventPanelScroll: function(e) {\n if (!this.event.type && this.visible) {\n // Stop propagation if scrolling is happening inside a frame.\n // TODO: could propagate scrolling if at top/bottom of frame.\n var frames = $(e.srcElement).parents(\".frame\");\n if (frames.length !== 0) {\n e.stopPropagation();\n } else {\n e.preventDefault();\n this._panelScroll(\n e.originalEvent.detail\n ? e.originalEvent.detail\n : e.originalEvent.wheelDelta / -3\n );\n }\n }\n },\n\n /** Handle scroll up event */\n _eventPanelScroll_up: function(e) {\n if (!this.event.type) {\n e.preventDefault();\n this._panelScroll(-this.options.scroll);\n }\n },\n\n /** Handle scroll down */\n _eventPanelScroll_down: function(e) {\n if (!this.event.type) {\n e.preventDefault();\n this._panelScroll(this.options.scroll);\n }\n },\n\n /*\n FRAME EVENTS SUPPORT\n */\n\n /** Identify the target frame */\n _frameIdentify: function(target) {\n return this.frame_list[\n \"#\" +\n $(target)\n .closest(\".frame\")\n .attr(\"id\")\n ];\n },\n\n /** Provides drag support */\n _frameDragStart: function(frame) {\n this._frameFocus(frame, true);\n var p = this._frameScreen(frame);\n this._frameResize(this.frame_shadow, p);\n this._frameGrid(this.frame_shadow, frame.grid_location);\n frame.grid_location = null;\n this.frame_shadow.$el.show();\n $(\".f-cover\").show();\n },\n\n /** Removes drag support */\n _frameDragStop: function(frame) {\n this._frameFocus(frame, false);\n var p = this._frameScreen(this.frame_shadow);\n this._frameResize(frame, p);\n this._frameGrid(frame, this.frame_shadow.grid_location, true);\n this.frame_shadow.grid_location = null;\n this.frame_shadow.$el.hide();\n $(\".f-cover\").hide();\n this._panelAnimationComplete();\n },\n\n /*\n GRID/PIXEL CONVERTER\n */\n\n /** Converts a pixel to a grid dimension */\n _toGridCoord: function(type, px) {\n var sign = type == \"width\" || type == \"height\" ? 1 : -1;\n type == \"top\" && (px -= this.top);\n return parseInt(\n (px + sign * this.options.margin) / this.options.cell,\n 10\n );\n },\n\n /** Converts a grid to a pixels dimension */\n _toPixelCoord: function(type, g) {\n var sign = type == \"width\" || type == \"height\" ? 1 : -1;\n var px = g * this.options.cell - sign * this.options.margin;\n type == \"top\" && (px += this.top);\n return px;\n },\n\n /** Converts a pixel to a grid coordinate set */\n _toGrid: function(px) {\n return {\n top: this._toGridCoord(\"top\", px.top),\n left: this._toGridCoord(\"left\", px.left),\n width: this._toGridCoord(\"width\", px.width),\n height: this._toGridCoord(\"height\", px.height)\n };\n },\n\n /** Converts a pixel to a grid coordinate set */\n _toPixel: function(g) {\n return {\n top: this._toPixelCoord(\"top\", g.top),\n left: this._toPixelCoord(\"left\", g.left),\n width: this._toPixelCoord(\"width\", g.width),\n height: this._toPixelCoord(\"height\", g.height)\n };\n },\n\n /* \n COLLISION DETECTION\n */\n\n /** Check collisions for a grid coordinate set */\n _isCollision: function(g) {\n function is_collision_pair(a, b) {\n return !(\n a.left > b.left + b.width - 1 ||\n a.left + a.width - 1 < b.left ||\n a.top > b.top + b.height - 1 ||\n a.top + a.height - 1 < b.top\n );\n }\n for (var i in this.frame_list) {\n var frame = this.frame_list[i];\n if (\n frame.grid_location !== null &&\n is_collision_pair(g, frame.grid_location)\n ) {\n return true;\n }\n }\n return false;\n },\n\n /** Return location/grid rank */\n _locationRank: function(loc) {\n return loc.top * this.cols + loc.left;\n },\n\n /*\n PANEL/WINDOW FUNCTIONS\n */\n\n /** Refresh panel */\n _panelRefresh: function(animate) {\n this.cols = parseInt($(window).width() / this.options.cell, 10) + 1;\n this._frameInsert(null, null, animate);\n },\n\n /** Complete panel animation / frames not moving */\n _panelAnimationComplete: function() {\n var self = this;\n $(\".frame\")\n .promise()\n .done(function() {\n self._panelScroll(0, true);\n });\n },\n\n /** Scroll panel */\n _panelScroll: function(delta, animate) {\n var top_new = this.top - this.options.scroll * delta;\n top_new = Math.max(top_new, this.top_max);\n top_new = Math.min(top_new, this.options.top_min);\n if (this.top != top_new) {\n for (var i in this.frame_list) {\n var frame = this.frame_list[i];\n if (frame.grid_location !== null) {\n var screen_location = {\n top:\n frame.screen_location.top -\n (this.top - top_new),\n left: frame.screen_location.left\n };\n this._frameOffset(frame, screen_location, animate);\n }\n }\n this.top = top_new;\n }\n this.render();\n },\n\n /*\n FRAME FUNCTIONS\n */\n\n /** Initialize a new frame */\n _frameInit: function(frame, id) {\n frame.id = id;\n frame.screen_location = {};\n frame.grid_location = {};\n frame.grid_rank = null;\n frame.$el.attr(\"id\", id.substring(1));\n },\n\n /** Insert frame at given location */\n _frameInsert: function(frame, new_loc, animate) {\n var self = this;\n var place_list = [];\n if (frame) {\n frame.grid_location = null;\n place_list.push([frame, this._locationRank(new_loc)]);\n }\n _.each(this.frame_list, function(f) {\n if (f.grid_location !== null) {\n f.grid_location = null;\n place_list.push([f, f.grid_rank]);\n }\n });\n place_list.sort(function(a, b) {\n return a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0;\n });\n _.each(place_list, function(place) {\n self._framePlace(place[0], animate);\n });\n this.top_max = 0;\n _.each(this.frame_list, function(f) {\n if (f.grid_location !== null) {\n self.top_max = Math.max(\n self.top_max,\n f.grid_location.top + f.grid_location.height\n );\n }\n });\n this.top_max =\n $(window).height() -\n this.top_max * this.options.cell -\n 2 * this.options.margin;\n this.top_max = Math.min(this.top_max, this.options.top_min);\n this.render();\n },\n\n /** Naive frame placement */\n _framePlace: function(frame, animate) {\n frame.grid_location = null;\n var g = this._toGrid(this._frameScreen(frame));\n var done = false;\n for (var i = 0; i < this.options.rows; i++) {\n for (var j = 0; j < Math.max(1, this.cols - g.width); j++) {\n g.top = i;\n g.left = j;\n if (!this._isCollision(g)) {\n done = true;\n break;\n }\n }\n if (done) {\n break;\n }\n }\n if (done) {\n this._frameGrid(frame, g, animate);\n } else {\n console.log(\"Grid dimensions exceeded.\");\n }\n },\n\n /** Handle frame focussing */\n _frameFocus: function(frame, has_focus) {\n frame.$el.css(\"z-index\", this.frame_z + (has_focus ? 1 : 0));\n },\n\n /** New left/top position frame */\n _frameOffset: function(frame, p, animate) {\n frame.screen_location.left = p.left;\n frame.screen_location.top = p.top;\n if (animate) {\n this._frameFocus(frame, true);\n var self = this;\n frame.$el.animate(\n { top: p.top, left: p.left },\n \"fast\",\n function() {\n self._frameFocus(frame, false);\n }\n );\n } else {\n frame.$el.css({ top: p.top, left: p.left });\n }\n },\n\n /** Resize frame */\n _frameResize: function(frame, p) {\n frame.$el.css({ width: p.width, height: p.height });\n frame.screen_location.width = p.width;\n frame.screen_location.height = p.height;\n },\n\n /** Push frame to new grid location */\n _frameGrid: function(frame, l, animate) {\n frame.grid_location = l;\n this._frameOffset(frame, this._toPixel(l), animate);\n frame.grid_rank = this._locationRank(l);\n },\n\n /** Get frame dimensions */\n _frameScreen: function(frame) {\n var p = frame.screen_location;\n return {\n top: p.top,\n left: p.left,\n width: p.width,\n height: p.height\n };\n }\n });\n\n return {\n View: View\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/ui/ui-list.js.map b/static/maps/mvc/ui/ui-list.js.map index af91ff6b1d5..283d0747c55 100644 --- a/static/maps/mvc/ui/ui-list.js.map +++ b/static/maps/mvc/ui/ui-list.js.map @@ -1 +1 @@ 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dependencies\ndefine([\"utils/utils\", \"mvc/ui/ui-portlet\", \"mvc/ui/ui-misc\"], function(\n Utils,\n Portlet,\n Ui\n) {\n // ui list element\n var View = Backbone.View.extend({\n // create portlet to keep track of selected list elements\n initialize: function(options) {\n // link this\n var self = this;\n\n // initialize options\n this.options = options;\n this.name = options.name || \"element\";\n this.multiple = options.multiple || false;\n\n // create message handler\n this.message = new Ui.Message();\n\n // create portlet\n this.portlet = new Portlet.View({ cls: \"ui-portlet-section\" });\n\n // create select field containing the options which can be inserted into the list\n this.select = new Ui.Select.View({ optional: options.optional });\n\n // create insert new list element button\n this.button = new Ui.ButtonIcon({\n icon: \"fa fa-sign-in\",\n tooltip: \"Insert new \" + this.name,\n onclick: function() {\n self.add({\n id: self.select.value(),\n name: self.select.text()\n });\n }\n });\n\n // build main element\n this.setElement(this._template(options));\n this.$(\".ui-list-message\").append(this.message.$el);\n this.$(\".ui-list-portlet\").append(this.portlet.$el);\n this.$(\".ui-list-button\").append(this.button.$el);\n this.$(\".ui-list-select\").append(this.select.$el);\n },\n\n /** Return/Set currently selected list elements */\n value: function(val) {\n // set new value\n if (val !== undefined) {\n this.portlet.empty();\n if ($.isArray(val)) {\n for (var i in val) {\n var v = val[i];\n var v_id = null;\n var v_name = null;\n if ($.type(v) != \"string\") {\n v_id = v.id;\n v_name = v.name;\n } else {\n v_id = v_name = v;\n }\n if (v_id != null) {\n this.add({\n id: v_id,\n name: v_name\n });\n }\n }\n }\n this._refresh();\n }\n // get current value\n var lst = [];\n this.$(\".ui-list-id\").each(function() {\n lst.push({\n id: $(this).prop(\"id\"),\n name: $(this)\n .find(\".ui-list-name\")\n .html()\n });\n });\n if (lst.length == 0) {\n return null;\n }\n return lst;\n },\n\n /** Add row */\n add: function(options) {\n var self = this;\n if (this.$('[id=\"' + options.id + '\"]').length === 0) {\n if (!Utils.isEmpty(options.id)) {\n var $el = $(\n this._templateRow({\n id: options.id,\n name: options.name\n })\n );\n $el.on(\"click\", function() {\n $el.remove();\n self._refresh();\n });\n $el.on(\"mouseover\", function() {\n $el.addClass(\"portlet-highlight\");\n });\n $el.on(\"mouseout\", function() {\n $el.removeClass(\"portlet-highlight\");\n });\n this.portlet.append($el);\n this._refresh();\n } else {\n this.message.update({\n message: \"Please select a valid \" + this.name + \".\",\n status: \"danger\"\n });\n }\n } else {\n this.message.update({\n message: \"This \" + this.name + \" is already in the list.\"\n });\n }\n },\n\n /** Update available options */\n update: function(options) {\n this.select.update(options);\n },\n\n /** Refresh view */\n _refresh: function() {\n if (this.$(\".ui-list-id\").length > 0) {\n 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dependencies\ndefine([\"utils/utils\", \"mvc/ui/ui-portlet\", \"mvc/ui/ui-misc\"], function(\n Utils,\n Portlet,\n Ui\n) {\n // ui list element\n var View = Backbone.View.extend({\n // create portlet to keep track of selected list elements\n initialize: function(options) {\n // link this\n var self = this;\n\n // initialize options\n this.options = options;\n this.name = options.name || \"element\";\n this.multiple = options.multiple || false;\n\n // create message handler\n this.message = new Ui.Message();\n\n // create portlet\n this.portlet = new Portlet.View({ cls: \"ui-portlet-section\" });\n\n // create select field containing the options which can be inserted into the list\n this.select = new Ui.Select.View({ optional: options.optional });\n\n // create insert new list element button\n this.button = new Ui.ButtonIcon({\n icon: \"fa fa-sign-in\",\n tooltip: \"Insert new \" + this.name,\n onclick: function() {\n self.add({\n id: self.select.value(),\n name: self.select.text()\n });\n }\n });\n\n // build main element\n this.setElement(this._template(options));\n this.$(\".ui-list-message\").append(this.message.$el);\n this.$(\".ui-list-portlet\").append(this.portlet.$el);\n this.$(\".ui-list-button\").append(this.button.$el);\n this.$(\".ui-list-select\").append(this.select.$el);\n },\n\n /** Return/Set currently selected list elements */\n value: function(val) {\n // set new value\n if (val !== undefined) {\n this.portlet.empty();\n if ($.isArray(val)) {\n for (var i in val) {\n var v = val[i];\n var v_id = null;\n var v_name = null;\n if ($.type(v) != \"string\") {\n v_id = v.id;\n v_name = v.name;\n } else {\n v_id = v_name = v;\n }\n if (v_id != null) {\n this.add({\n id: v_id,\n name: v_name\n });\n }\n }\n }\n this._refresh();\n }\n // get current value\n var lst = [];\n this.$(\".ui-list-id\").each(function() {\n lst.push({\n id: $(this).prop(\"id\"),\n name: $(this)\n .find(\".ui-list-name\")\n .html()\n });\n });\n if (lst.length == 0) {\n return null;\n }\n return lst;\n },\n\n /** Add row */\n add: function(options) {\n var self = this;\n if (this.$('[id=\"' + options.id + '\"]').length === 0) {\n if (!Utils.isEmpty(options.id)) {\n var $el = $(\n this._templateRow({\n id: options.id,\n name: options.name\n })\n );\n $el.on(\"click\", function() {\n $el.remove();\n self._refresh();\n });\n $el.on(\"mouseover\", function() {\n $el.addClass(\"portlet-highlight\");\n });\n $el.on(\"mouseout\", function() {\n $el.removeClass(\"portlet-highlight\");\n });\n this.portlet.append($el);\n this._refresh();\n } else {\n this.message.update({\n message: \"Please select a valid \" + this.name + \".\",\n status: \"danger\"\n });\n }\n } else {\n this.message.update({\n message: \"This \" + this.name + \" is already in the list.\"\n });\n }\n },\n\n /** Update available options */\n update: function(options) {\n this.select.update(options);\n },\n\n /** Refresh view */\n _refresh: function() {\n if (this.$(\".ui-list-id\").length > 0) {\n 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this.$el.html(this.messageForDisplay());\n this.$el[this.model.get(\"fade\") ? \"fadeIn\" : \"show\"]();\n this.timeout && window.clearTimeout(this.timeout);\n if (!this.model.get(\"persistent\")) {\n var self = this;\n this.timeout = window.setTimeout(function() {\n self.model.set(\"message\", \"\");\n }, 3000);\n }\n } else {\n this.$el.fadeOut();\n }\n return this;\n },\n messageForDisplay: function() {\n return _.escape(this.model.get(\"message\"));\n }\n });\n\n var UnescapedMessage = Message.extend({\n messageForDisplay: function() {\n return this.model.get(\"message\");\n }\n });\n\n /** Renders an input element used e.g. in the tool form */\n var Input = Backbone.View.extend({\n initialize: function(options) {\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n type: \"text\",\n placeholder: \"\",\n disabled: false,\n readonly: false,\n visible: true,\n cls: \"\",\n area: false,\n color: null,\n style: null\n }).set(options);\n this.tagName = this.model.get(\"area\") ? \"textarea\" : \"input\";\n this.setElement($(\"<\" + this.tagName + \"/>\"));\n this.listenTo(this.model, \"change\", this.render, this);\n this.render();\n },\n events: {\n input: \"_onchange\"\n },\n value: function(new_val) {\n new_val !== undefined &&\n this.model.set(\n \"value\",\n typeof new_val === \"string\" ? new_val : \"\"\n );\n return this.model.get(\"value\");\n },\n render: function() {\n var self = this;\n this.$el\n .removeClass()\n .addClass(\"ui-\" + this.tagName)\n .addClass(this.model.get(\"cls\"))\n .addClass(this.model.get(\"style\"))\n .attr(\"id\", this.model.id)\n .attr(\"type\", this.model.get(\"type\"))\n .attr(\"placeholder\", this.model.get(\"placeholder\"))\n .css(\"color\", this.model.get(\"color\") || \"\")\n .css(\"border-color\", this.model.get(\"color\") || \"\");\n var datalist = this.model.get(\"datalist\");\n if ($.isArray(datalist) && datalist.length > 0) {\n this.$el.autocomplete({\n source: function(request, response) {\n response(self.model.get(\"datalist\"));\n },\n change: function() {\n self._onchange();\n }\n });\n }\n if (this.model.get(\"value\") !== this.$el.val()) {\n this.$el.val(this.model.get(\"value\"));\n }\n _.each([\"readonly\", \"disabled\"], function(attr_name) {\n self.model.get(attr_name)\n ? self.$el.attr(attr_name, true)\n : self.$el.removeAttr(attr_name);\n });\n this.$el[this.model.get(\"visible\") ? \"show\" : \"hide\"]();\n return this;\n },\n _onchange: function() {\n this.value(this.$el.val());\n this.model.get(\"onchange\") &&\n this.model.get(\"onchange\")(this.model.get(\"value\"));\n }\n });\n\n /** Creates a hidden element input field used e.g. in the tool form */\n var Hidden = Backbone.View.extend({\n initialize: function(options) {\n this.model =\n (options && options.model) || new Backbone.Model(options);\n this.setElement(\n $(\"\")\n .append((this.$info = $(\"\")))\n .append((this.$hidden = $(\"\")))\n );\n this.listenTo(this.model, \"change\", this.render, this);\n this.render();\n },\n value: function(new_val) {\n new_val !== undefined && this.model.set(\"value\", new_val);\n return this.model.get(\"value\");\n },\n render: function() {\n this.$el.attr(\"id\", this.model.id);\n this.$hidden.val(this.model.get(\"value\"));\n this.model.get(\"info\")\n ? this.$info.show().text(this.model.get(\"info\"))\n : this.$info.hide();\n return this;\n }\n });\n\n /** Creates a upload element input field */\n var Upload = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.model =\n (options && options.model) || new Backbone.Model(options);\n this.setElement(\n $(\"\")\n .append((this.$info = $(\"\")))\n .append(\n (this.$file = $(\"\")\n .attr(\"type\", \"file\")\n .addClass(\"ui-margin-bottom\"))\n )\n .append(\n (this.$text = $(\"\")\n .addClass(\"ui-textarea\")\n .attr(\"disabled\", true))\n )\n .append(\n (this.$wait = $(\"\").addClass(\n \"fa fa-spinner fa-spin\"\n ))\n )\n );\n 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* This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc.\n */\ndefine(\n [\n \"utils/utils\",\n \"mvc/ui/ui-select-default\",\n \"mvc/ui/ui-slider\",\n \"mvc/ui/ui-options\",\n \"mvc/ui/ui-drilldown\",\n \"mvc/ui/ui-buttons\",\n \"mvc/ui/ui-modal\"\n ],\n function(Utils, Select, Slider, Options, Drilldown, Buttons, Modal) {\n /** Label wrapper */\n var Label = Backbone.View.extend({\n tagName: \"label\",\n initialize: function(options) {\n this.model =\n (options && options.model) || new Backbone.Model(options);\n this.tagName = options.tagName || this.tagName;\n this.setElement($(\"<\" + this.tagName + \"/>\"));\n this.listenTo(this.model, \"change\", this.render, this);\n this.render();\n },\n title: function(new_title) {\n this.model.set(\"title\", new_title);\n },\n value: function() {\n return this.model.get(\"title\");\n },\n render: function() {\n this.$el\n .removeClass()\n .addClass(\"ui-label\")\n .addClass(this.model.get(\"cls\"))\n .html(this.model.get(\"title\"));\n return this;\n }\n });\n\n /** Displays messages used e.g. in the tool form */\n var Message = Backbone.View.extend({\n initialize: function(options) {\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n message: null,\n status: \"info\",\n cls: \"\",\n persistent: false,\n fade: true\n }).set(options);\n this.listenTo(this.model, \"change\", this.render, this);\n this.render();\n },\n update: function(options) {\n this.model.set(options);\n },\n render: function() {\n this.$el\n .removeClass()\n .addClass(\"ui-message\")\n .addClass(this.model.get(\"cls\"));\n var status = this.model.get(\"status\");\n if (this.model.get(\"large\")) {\n this.$el.addClass(\n ((status == \"success\" && \"done\") ||\n (status == \"danger\" && \"error\") ||\n status) + \"messagelarge\"\n );\n } else {\n this.$el.addClass(\"alert\").addClass(\"alert-\" + status);\n }\n if (this.model.get(\"message\")) {\n this.$el.html(this.messageForDisplay());\n this.$el[this.model.get(\"fade\") ? \"fadeIn\" : \"show\"]();\n this.timeout && window.clearTimeout(this.timeout);\n if (!this.model.get(\"persistent\")) {\n var self = this;\n this.timeout = window.setTimeout(function() {\n self.model.set(\"message\", \"\");\n }, 3000);\n }\n } else {\n this.$el.fadeOut();\n }\n return this;\n },\n messageForDisplay: function() {\n return _.escape(this.model.get(\"message\"));\n }\n });\n\n var UnescapedMessage = Message.extend({\n messageForDisplay: function() {\n return this.model.get(\"message\");\n }\n });\n\n /** Renders an input element used e.g. in the tool form */\n var Input = Backbone.View.extend({\n initialize: function(options) {\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n type: \"text\",\n placeholder: \"\",\n disabled: false,\n readonly: false,\n visible: true,\n cls: \"\",\n area: false,\n color: null,\n style: null\n }).set(options);\n this.tagName = this.model.get(\"area\") ? \"textarea\" : \"input\";\n this.setElement($(\"<\" + this.tagName + \"/>\"));\n this.listenTo(this.model, \"change\", this.render, this);\n this.render();\n },\n events: {\n input: \"_onchange\"\n },\n value: function(new_val) {\n new_val !== undefined &&\n this.model.set(\n \"value\",\n typeof new_val === \"string\" ? new_val : \"\"\n );\n return this.model.get(\"value\");\n },\n render: function() {\n var self = this;\n this.$el\n .removeClass()\n .addClass(\"ui-\" + this.tagName)\n .addClass(this.model.get(\"cls\"))\n .addClass(this.model.get(\"style\"))\n .attr(\"id\", this.model.id)\n .attr(\"type\", this.model.get(\"type\"))\n .attr(\"placeholder\", this.model.get(\"placeholder\"))\n .css(\"color\", this.model.get(\"color\") || \"\")\n .css(\"border-color\", this.model.get(\"color\") || \"\");\n var datalist = this.model.get(\"datalist\");\n if ($.isArray(datalist) && datalist.length > 0) {\n this.$el.autocomplete({\n source: function(request, response) {\n response(self.model.get(\"datalist\"));\n },\n change: function() {\n self._onchange();\n }\n });\n }\n if (this.model.get(\"value\") !== this.$el.val()) {\n this.$el.val(this.model.get(\"value\"));\n }\n _.each([\"readonly\", \"disabled\"], function(attr_name) {\n self.model.get(attr_name)\n ? self.$el.attr(attr_name, true)\n : self.$el.removeAttr(attr_name);\n });\n this.$el[this.model.get(\"visible\") ? \"show\" : \"hide\"]();\n return this;\n },\n _onchange: function() {\n this.value(this.$el.val());\n this.model.get(\"onchange\") &&\n this.model.get(\"onchange\")(this.model.get(\"value\"));\n }\n });\n\n /** Creates a hidden element input field used e.g. in the tool form */\n var Hidden = Backbone.View.extend({\n initialize: function(options) {\n this.model =\n (options && options.model) || new Backbone.Model(options);\n this.setElement(\n $(\"\")\n .append((this.$info = $(\"\")))\n .append((this.$hidden = $(\"\")))\n );\n this.listenTo(this.model, \"change\", this.render, this);\n this.render();\n },\n value: function(new_val) {\n new_val !== undefined && this.model.set(\"value\", new_val);\n return this.model.get(\"value\");\n },\n render: function() {\n this.$el.attr(\"id\", this.model.id);\n this.$hidden.val(this.model.get(\"value\"));\n this.model.get(\"info\")\n ? this.$info.show().text(this.model.get(\"info\"))\n : this.$info.hide();\n return this;\n }\n });\n\n /** Creates a upload element input field */\n var Upload = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.model =\n (options && options.model) || new Backbone.Model(options);\n this.setElement(\n $(\"\")\n .append((this.$info = $(\"\")))\n .append(\n (this.$file = $(\"\")\n .attr(\"type\", \"file\")\n .addClass(\"ui-margin-bottom\"))\n )\n .append(\n (this.$text = $(\"\")\n .addClass(\"ui-textarea\")\n .attr(\"disabled\", true))\n )\n .append(\n (this.$wait = $(\"\").addClass(\n \"fa fa-spinner fa-spin\"\n ))\n )\n );\n this.listenTo(this.model, \"change\", this.render, this);\n this.$file.on(\"change\", function(e) {\n self._readFile(e);\n });\n this.render();\n },\n value: function(new_val) {\n new_val !== undefined && this.model.set(\"value\", new_val);\n return this.model.get(\"value\");\n },\n render: function() {\n this.$el.attr(\"id\", this.model.id);\n this.model.get(\"info\")\n ? this.$info.show().text(this.model.get(\"info\"))\n : this.$info.hide();\n this.model.get(\"value\")\n ? this.$text.text(this.model.get(\"value\")).show()\n : this.$text.hide();\n this.model.get(\"wait\") ? this.$wait.show() : this.$wait.hide();\n return this;\n },\n _readFile: function(e) {\n var self = this;\n var file = e.target.files && e.target.files[0];\n if (file) {\n var reader = new FileReader();\n reader.onload = function() {\n self.model.set({ wait: false, value: this.result });\n };\n this.model.set({ wait: true, value: null });\n reader.readAsText(file);\n }\n }\n });\n\n return {\n Button: 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function() {\n var View = Backbone.View.extend({\n className: \"ui-modal\",\n\n // defaults\n optionsDefault: {\n container: \"body\",\n title: \"ui-modal\",\n cls: \"ui-modal\",\n body: \"\",\n backdrop: true,\n height: null,\n width: null,\n closing_events: false,\n closing_callback: null,\n title_separator: true\n },\n\n // button list\n buttonList: {},\n\n // initialize\n initialize: function(options) {\n this.options = _.defaults(options || {}, this.optionsDefault);\n $(this.options.container).prepend(this.el);\n // optional render\n if (options) {\n this.render();\n }\n },\n\n /**\n * Displays modal\n */\n show: function(options) {\n if (options) {\n this.options = _.defaults(options, this.optionsDefault);\n this.render();\n }\n if (!this.visible) {\n this.visible = true;\n this.$el.fadeIn(\"fast\");\n if (this.options.closing_events) {\n var self = this;\n $(document).on(\"keyup.ui-modal\", function(e) {\n if (e.keyCode == 27) {\n self.hide(true);\n }\n });\n this.$backdrop.on(\"click\", function() {\n self.hide(true);\n });\n }\n }\n },\n\n /**\n * Hide modal\n */\n hide: function(canceled) {\n this.visible = false;\n this.$el.fadeOut(\"fast\");\n if (this.options.closing_callback) {\n this.options.closing_callback(canceled);\n }\n $(document).off(\"keyup.ui-modal\");\n this.$backdrop.off(\"click\");\n },\n\n /**\n * Render modal\n */\n render: function() {\n var self = this;\n this.$el.html(this._template());\n\n // link elements\n this.$header = this.$(\".modal-header\");\n this.$dialog = this.$(\".modal-dialog\");\n this.$body = this.$(\".modal-body\");\n this.$footer = this.$(\".modal-footer\");\n this.$backdrop = this.$(\".modal-backdrop\");\n this.$buttons = this.$(\".buttons\");\n\n if (this.options.body == \"progress\") {\n this.options.body = $(\n '' +\n '\"\n );\n }\n\n // fix main content\n this.$el\n .removeClass()\n .addClass(\"modal\")\n .addClass(this.options.cls);\n this.$header.find(\".title\").html(this.options.title);\n this.$body.html(this.options.body);\n\n // append buttons\n this.$buttons.empty();\n this.buttonList = {};\n if (this.options.buttons) {\n var counter = 0;\n $.each(this.options.buttons, function(name, callback) {\n var $button = $(\"\")\n .attr(\"id\", \"button-\" + counter++)\n .text(name)\n .click(callback);\n self.$buttons.append($button).append(\" \");\n self.buttonList[name] = $button;\n });\n } else {\n this.$footer.hide();\n }\n\n // configure background, separator line\n this.$backdrop[\n (this.options.backdrop && \"addClass\") || \"removeClass\"\n ](\"in\");\n this.$header[\n (!this.options.title_separator && \"addClass\") || \"removeClass\"\n ](\"no-separator\");\n\n // fix dimensions\n // note: because this is a singleton, we need to clear inline styles from any previous invocations\n this.$body.removeAttr(\"style\");\n if (this.options.height) {\n this.$body.css(\"height\", this.options.height);\n this.$body.css(\"overflow\", \"hidden\");\n } else {\n 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function() {\n var View = Backbone.View.extend({\n className: \"ui-modal\",\n\n // defaults\n optionsDefault: {\n container: \"body\",\n title: \"ui-modal\",\n cls: \"ui-modal\",\n body: \"\",\n backdrop: true,\n height: null,\n width: null,\n closing_events: false,\n closing_callback: null,\n title_separator: true\n },\n\n // button list\n buttonList: {},\n\n // initialize\n initialize: function(options) {\n this.options = _.defaults(options || {}, this.optionsDefault);\n $(this.options.container).prepend(this.el);\n // optional render\n if (options) {\n this.render();\n }\n },\n\n /**\n * Displays modal\n */\n show: function(options) {\n if (options) {\n this.options = _.defaults(options, this.optionsDefault);\n this.render();\n }\n if (!this.visible) {\n this.visible = true;\n this.$el.fadeIn(\"fast\");\n if (this.options.closing_events) {\n var self = this;\n $(document).on(\"keyup.ui-modal\", function(e) {\n if (e.keyCode == 27) {\n self.hide(true);\n }\n });\n this.$backdrop.on(\"click\", function() {\n self.hide(true);\n });\n }\n }\n },\n\n /**\n * Hide modal\n */\n hide: function(canceled) {\n this.visible = false;\n this.$el.fadeOut(\"fast\");\n if (this.options.closing_callback) {\n this.options.closing_callback(canceled);\n }\n $(document).off(\"keyup.ui-modal\");\n this.$backdrop.off(\"click\");\n },\n\n /**\n * Render modal\n */\n render: function() {\n var self = this;\n this.$el.html(this._template());\n\n // link elements\n this.$header = this.$(\".modal-header\");\n this.$dialog = this.$(\".modal-dialog\");\n this.$body = this.$(\".modal-body\");\n this.$footer = this.$(\".modal-footer\");\n this.$backdrop = this.$(\".modal-backdrop\");\n this.$buttons = this.$(\".buttons\");\n\n if (this.options.body == \"progress\") {\n this.options.body = $(\n '' +\n '\"\n );\n }\n\n // fix main content\n this.$el\n .removeClass()\n .addClass(\"modal\")\n .addClass(this.options.cls);\n this.$header.find(\".title\").html(this.options.title);\n this.$body.html(this.options.body);\n\n // append buttons\n this.$buttons.empty();\n this.buttonList = {};\n if (this.options.buttons) {\n var counter = 0;\n $.each(this.options.buttons, function(name, callback) {\n var $button = $(\"\")\n .attr(\"id\", \"button-\" + counter++)\n .text(name)\n .click(callback);\n self.$buttons.append($button).append(\" \");\n self.buttonList[name] = $button;\n });\n } else {\n this.$footer.hide();\n }\n\n // configure background, separator line\n this.$backdrop[\n (this.options.backdrop && \"addClass\") || \"removeClass\"\n ](\"in\");\n this.$header[\n (!this.options.title_separator && \"addClass\") || \"removeClass\"\n ](\"no-separator\");\n\n // fix dimensions\n // note: because this is a singleton, we need to clear inline styles from any previous invocations\n this.$body.removeAttr(\"style\");\n if (this.options.height) {\n this.$body.css(\"height\", this.options.height);\n this.$body.css(\"overflow\", \"hidden\");\n } else {\n this.$body.css(\"max-height\", $(window).height() / 2);\n }\n if (this.options.width) {\n this.$dialog.css(\"width\", this.options.width);\n }\n },\n\n /**\n * Returns the button dom\n * @param{String} name - Button name/title\n */\n getButton: function(name) {\n return this.buttonList[name];\n },\n\n /**\n * Enables a button\n * @param{String} name - Button name/title\n */\n enableButton: function(name) {\n this.getButton(name).prop(\"disabled\", false);\n },\n\n /**\n * Disables a button\n * @param{String} name - Button name/title\n */\n disableButton: function(name) {\n this.getButton(name).prop(\"disabled\", true);\n },\n\n /**\n * Show a button\n * @param{String} name - Button name/title\n */\n showButton: function(name) {\n this.getButton(name).show();\n },\n\n /**\n * Hide a button\n * @param{String} name - Button name/title\n */\n hideButton: function(name) {\n this.getButton(name).hide();\n },\n\n /**\n * Returns scroll top for body element\n */\n scrollTop: function() {\n return this.$body.scrollTop();\n },\n\n /**\n * Returns the modal template\n */\n _template: function() {\n return (\n '' +\n '' +\n '' +\n '' +\n '\" +\n '' +\n \"
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Base class for options based ui elements **/\ndefine([\"utils/utils\", \"mvc/ui/ui-buttons\"], function(Utils, Buttons) {\n var Base = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n visible: true,\n data: [],\n id: Utils.uid(),\n error_text: \"No options available.\",\n wait_text: \"Please wait...\",\n multiple: false,\n optional: false,\n onchange: function() {}\n }).set(options);\n this.listenTo(this.model, \"change:value\", this._changeValue, this);\n this.listenTo(this.model, \"change:wait\", this._changeWait, this);\n this.listenTo(this.model, \"change:data\", this._changeData, this);\n this.listenTo(\n this.model,\n \"change:visible\",\n this._changeVisible,\n this\n );\n this.on(\"change\", function() {\n self.model.get(\"onchange\")(self.value());\n });\n this.render();\n },\n\n render: function() {\n var self = this;\n this.$el\n .empty()\n .removeClass()\n .addClass(\"ui-options\")\n .append((this.$message = $(\"\")))\n .append((this.$menu = $(\"\").addClass(\"ui-options-menu\")))\n .append((this.$options = $(this._template())));\n\n // add select/unselect all button\n this.all_button = null;\n if (this.model.get(\"multiple\")) {\n this.all_button = new Buttons.ButtonCheck({\n onclick: function() {\n self\n .$(\"input\")\n .prop(\"checked\", self.all_button.value() !== 0);\n self.value(self._getValue());\n self.trigger(\"change\");\n }\n });\n this.$menu.append(this.all_button.$el);\n }\n\n // finalize dom\n this._changeData();\n this._changeWait();\n this._changeVisible();\n },\n\n /** Update available options */\n update: function(options) {\n this.model.set(\"data\", options);\n },\n\n _changeData: function() {\n var self = this;\n this.$options.empty();\n if (this._templateOptions) {\n this.$options.append(\n this._templateOptions(this.model.get(\"data\"))\n );\n } else {\n _.each(this.model.get(\"data\"), function(option) {\n self.$options.append(\n $(self._templateOption(option))\n .addClass(\"ui-option\")\n .tooltip({\n title: option.tooltip,\n placement: \"bottom\"\n })\n );\n });\n }\n var self = this;\n this.$(\"input\").on(\"change\", function() {\n self.value(self._getValue());\n self.trigger(\"change\");\n });\n this._changeValue();\n this._changeWait();\n },\n\n _changeVisible: function() {\n this.$el[this.model.get(\"visible\") ? \"show\" : \"hide\"]();\n },\n\n _changeWait: function() {\n if (this.model.get(\"wait\")) {\n if (this.length() === 0) {\n this._messageShow(this.model.get(\"wait_text\"), \"info\");\n this.$options.hide();\n this.$menu.hide();\n }\n } else {\n if (this.length() === 0) {\n this._messageShow(this.model.get(\"error_text\"), \"danger\");\n this.$options.hide();\n this.$menu.hide();\n } else {\n this.$message.hide();\n this.$options.css(\"display\", \"inline-block\");\n this.$menu.show();\n }\n }\n },\n\n _changeValue: function() {\n this._setValue(this.model.get(\"value\"));\n if (\n this._getValue() === null &&\n !this.model.get(\"multiple\") &&\n !this.model.get(\"optional\")\n ) {\n this._setValue(this.first());\n }\n this.all_button &&\n this.all_button.value(\n $.isArray(this._getValue()) ? this._getValue().length : 0,\n this.length()\n );\n },\n\n /** Return/Set current selection */\n value: function(new_value) {\n new_value !== undefined && this.model.set(\"value\", new_value);\n return this._getValue();\n },\n\n /** Return first available option */\n first: function() {\n var options = this.$(\"input\").first();\n return options.length > 0 ? options.val() : null;\n },\n\n /** Show a spinner indicating that the select options are currently loaded */\n wait: function() {\n this.model.set(\"wait\", true);\n },\n\n /** Hide spinner indicating that the request has been completed */\n unwait: function() {\n this.model.set(\"wait\", false);\n },\n\n /** Returns the number of options */\n length: function() {\n return this.$(\".ui-option\").length;\n },\n\n /** Set value to dom */\n _setValue: function(new_value) {\n var self = this;\n if (new_value !== undefined) {\n this.$(\"input\").prop(\"checked\", false);\n if (new_value !== null) {\n var values = $.isArray(new_value) ? new_value : [new_value];\n _.each(values, function(v) {\n self\n .$('input[value=\"' + v + '\"]')\n .first()\n .prop(\"checked\", true);\n });\n }\n }\n },\n\n /** Return current selection */\n _getValue: function() {\n var selected = [];\n this.$(\":checked\").each(function() {\n selected.push($(this).val());\n });\n if (Utils.isEmpty(selected)) {\n return null;\n }\n return this.model.get(\"multiple\") ? selected : selected[0];\n },\n\n /** Show message instead if options */\n _messageShow: function(text, status) {\n this.$message\n .show()\n .removeClass()\n .addClass(\"ui-message alert alert-\" + status)\n .html(text);\n },\n\n /** Main template function */\n _template: function() {\n return $(\"\").addClass(\"ui-options-list\");\n }\n });\n\n /** Iconized **/\n var BaseIcons = Base.extend({\n _templateOption: function(pair) {\n var id = Utils.uid();\n return $(\"\")\n .addClass(\"ui-option\")\n .append(\n $(\"\").attr({\n id: id,\n type: this.model.get(\"type\"),\n name: this.model.id,\n value: pair.value\n })\n )\n .append(\n $(\"\")\n .addClass(\"ui-options-label\")\n .attr(\"for\", id)\n .html(pair.label)\n );\n }\n });\n\n /** Radio button field **/\n var Radio = {};\n Radio.View = BaseIcons.extend({\n initialize: function(options) {\n options.type = \"radio\";\n BaseIcons.prototype.initialize.call(this, options);\n }\n });\n\n /** Checkbox options field **/\n var Checkbox = {};\n Checkbox.View = BaseIcons.extend({\n initialize: function(options) {\n options.type = \"checkbox\";\n options.multiple = true;\n BaseIcons.prototype.initialize.call(this, options);\n }\n });\n\n /** Radio button options field styled as classic buttons **/\n var RadioButton = {};\n 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Base class for options based ui elements **/\ndefine([\"utils/utils\", \"mvc/ui/ui-buttons\"], function(Utils, Buttons) {\n var Base = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n visible: true,\n data: [],\n id: Utils.uid(),\n error_text: \"No options available.\",\n wait_text: \"Please wait...\",\n multiple: false,\n optional: false,\n onchange: function() {}\n }).set(options);\n this.listenTo(this.model, \"change:value\", this._changeValue, this);\n this.listenTo(this.model, \"change:wait\", this._changeWait, this);\n this.listenTo(this.model, \"change:data\", this._changeData, this);\n this.listenTo(\n this.model,\n \"change:visible\",\n this._changeVisible,\n this\n );\n this.on(\"change\", function() {\n self.model.get(\"onchange\")(self.value());\n });\n this.render();\n },\n\n render: function() {\n var self = this;\n this.$el\n .empty()\n .removeClass()\n .addClass(\"ui-options\")\n .append((this.$message = $(\"\")))\n .append((this.$menu = $(\"\").addClass(\"ui-options-menu\")))\n .append((this.$options = $(this._template())));\n\n // add select/unselect all button\n this.all_button = null;\n if (this.model.get(\"multiple\")) {\n this.all_button = new Buttons.ButtonCheck({\n onclick: function() {\n self\n .$(\"input\")\n .prop(\"checked\", self.all_button.value() !== 0);\n self.value(self._getValue());\n self.trigger(\"change\");\n }\n });\n this.$menu.append(this.all_button.$el);\n }\n\n // finalize dom\n this._changeData();\n this._changeWait();\n this._changeVisible();\n },\n\n /** Update available options */\n update: function(options) {\n this.model.set(\"data\", options);\n },\n\n _changeData: function() {\n var self = this;\n this.$options.empty();\n if (this._templateOptions) {\n this.$options.append(\n this._templateOptions(this.model.get(\"data\"))\n );\n } else {\n _.each(this.model.get(\"data\"), function(option) {\n 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return this.$(\".ui-option\").length;\n },\n\n /** Set value to dom */\n _setValue: function(new_value) {\n var self = this;\n if (new_value !== undefined) {\n this.$(\"input\").prop(\"checked\", false);\n if (new_value !== null) {\n var values = $.isArray(new_value) ? new_value : [new_value];\n _.each(values, function(v) {\n self\n .$('input[value=\"' + v + '\"]')\n .first()\n .prop(\"checked\", true);\n });\n }\n }\n },\n\n /** Return current selection */\n _getValue: function() {\n var selected = [];\n this.$(\":checked\").each(function() {\n selected.push($(this).val());\n });\n if (Utils.isEmpty(selected)) {\n return null;\n }\n return this.model.get(\"multiple\") ? selected : selected[0];\n },\n\n /** Show message instead if options */\n _messageShow: function(text, status) {\n this.$message\n .show()\n .removeClass()\n .addClass(\"ui-message alert alert-\" + status)\n .html(text);\n },\n\n /** Main template function */\n _template: function() {\n return $(\"\").addClass(\"ui-options-list\");\n }\n });\n\n /** Iconized **/\n var BaseIcons = Base.extend({\n _templateOption: function(pair) {\n var id = Utils.uid();\n return $(\"\")\n .addClass(\"ui-option\")\n .append(\n $(\"\").attr({\n id: id,\n type: this.model.get(\"type\"),\n name: this.model.id,\n value: pair.value\n })\n )\n .append(\n $(\"\")\n .addClass(\"ui-options-label\")\n .attr(\"for\", id)\n .html(pair.label)\n );\n }\n });\n\n /** Radio button field **/\n var Radio = {};\n Radio.View = BaseIcons.extend({\n initialize: function(options) {\n options.type = \"radio\";\n BaseIcons.prototype.initialize.call(this, options);\n }\n });\n\n /** Checkbox options field **/\n var Checkbox = {};\n Checkbox.View = BaseIcons.extend({\n initialize: function(options) {\n options.type = \"checkbox\";\n options.multiple = true;\n BaseIcons.prototype.initialize.call(this, options);\n }\n });\n\n /** Radio button options field styled as classic buttons **/\n var RadioButton = {};\n 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!$(self.el).is(e.target) &&\n $(self.el).has(e.target).length === 0 &&\n self.hide();\n });\n },\n\n /**\n * Render popover\n */\n render: function() {\n this.$title.html(this.options.title);\n this.$el\n .removeClass()\n .addClass(\"ui-popover popover fade in\")\n .addClass(this.options.placement);\n this.$el.css(this._get_placement(this.options.placement));\n\n // configure close option\n var self = this;\n if (this.options.with_close) {\n this.$close\n .on(\"click\", function() {\n self.hide();\n })\n .show();\n } else {\n this.$close.off().hide();\n }\n },\n\n /**\n * Set the popover title\n * @params{ String } newTitle - New popover title\n */\n title: function(newTitle) {\n if (newTitle !== undefined) {\n this.options.title = newTitle;\n this.$title.html(newTitle);\n }\n },\n\n /**\n * Show popover\n */\n show: function() {\n this.render();\n this.$el.show();\n this.visible = true;\n },\n\n /**\n * Hide popover\n */\n hide: function() {\n this.$el.hide();\n this.visible = 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!$(self.el).is(e.target) &&\n $(self.el).has(e.target).length === 0 &&\n self.hide();\n });\n },\n\n /**\n * Render popover\n */\n render: function() {\n this.$title.html(this.options.title);\n this.$el\n .removeClass()\n .addClass(\"ui-popover popover fade in\")\n .addClass(this.options.placement);\n this.$el.css(this._get_placement(this.options.placement));\n\n // configure close option\n var self = this;\n if (this.options.with_close) {\n this.$close\n .on(\"click\", function() {\n self.hide();\n })\n .show();\n } else {\n this.$close.off().hide();\n }\n },\n\n /**\n * Set the popover title\n * @params{ String } newTitle - New popover title\n */\n title: function(newTitle) {\n if (newTitle !== undefined) {\n this.options.title = newTitle;\n this.$title.html(newTitle);\n }\n },\n\n /**\n * Show popover\n */\n show: function() {\n this.render();\n this.$el.show();\n this.visible = true;\n },\n\n /**\n * Hide popover\n */\n hide: function() {\n this.$el.hide();\n this.visible = false;\n },\n\n /**\n * Append new content to the popover\n * @params{ Object } $el - Dom element\n */\n append: function($el) {\n this.$body.append($el);\n },\n\n /**\n * Remove all content\n */\n empty: function() {\n this.$body.empty();\n },\n\n /**\n * Remove popover\n */\n remove: function() {\n $(\"body\").off(\"mousedown.\" + this.uid);\n this.$el.remove();\n },\n\n /**\n * Improve popover location/placement\n */\n _get_placement: function(placement) {\n // get popover dimensions\n var width = this._get_width(this.$el);\n var height = this.$el.height();\n\n // get container details\n var $container = this.options.container;\n var container_width = this._get_width($container);\n var container_height = this._get_height($container);\n var container_position = $container.position();\n\n // get position\n var top, left;\n top = left = 0;\n if ([\"top\", \"bottom\"].indexOf(placement) != -1) {\n left =\n container_position.left -\n width +\n (container_width + width) / 2;\n switch (placement) {\n case \"top\":\n top = container_position.top - height - 5;\n break;\n case \"bottom\":\n top = container_position.top + container_height + 5;\n break;\n }\n } else {\n top =\n container_position.top -\n height +\n (container_height + height) / 2;\n switch (placement) {\n case \"right\":\n left = container_position.left + container_width;\n break;\n }\n }\n return { top: top, left: left };\n },\n\n /**\n * Returns padding/margin corrected width\n */\n _get_width: function($el) {\n return (\n $el.width() +\n parseInt($el.css(\"padding-left\")) +\n parseInt($el.css(\"margin-left\")) +\n parseInt($el.css(\"padding-right\")) +\n parseInt($el.css(\"margin-right\"))\n );\n },\n\n /**\n * Returns padding corrected height\n */\n _get_height: function($el) {\n return (\n $el.height() +\n parseInt($el.css(\"padding-top\")) +\n parseInt($el.css(\"padding-bottom\"))\n );\n },\n\n /**\n * Return the popover template\n */\n _template: function(options) {\n return (\n '' +\n '' +\n '' +\n '' +\n '' +\n \"\" +\n '' +\n \"\"\n );\n }\n });\n\n return {\n View: View\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/ui/ui-portlet.js.map b/static/maps/mvc/ui/ui-portlet.js.map index 17d5e144ed3..1af0bca6631 100644 --- a/static/maps/mvc/ui/ui-portlet.js.map +++ b/static/maps/mvc/ui/ui-portlet.js.map @@ -1 +1 @@ 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\"mvc/ui/ui-misc\"], function(Utils, Ui) {\n var View = Backbone.View.extend({\n visible: false,\n initialize: function(options) {\n var self = this;\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n id: Utils.uid(),\n cls: \"ui-portlet\",\n title: \"\",\n icon: \"\",\n buttons: null,\n body: null,\n scrollable: true,\n nopadding: false,\n operations: null,\n collapsible: false,\n collapsible_button: false,\n collapsed: false,\n onchange_title: null\n }).set(options);\n this.setElement(this._template());\n\n // link all dom elements\n this.$body = this.$(\".portlet-body\");\n this.$title_text = this.$(\".portlet-title-text\");\n this.$title_icon = this.$(\".portlet-title-icon\");\n this.$header = this.$(\".portlet-header\");\n this.$content = this.$(\".portlet-content\");\n this.$backdrop = this.$(\".portlet-backdrop\");\n this.$buttons = this.$(\".portlet-buttons\");\n this.$operations = this.$(\".portlet-operations\");\n\n // add body to component list\n 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this.$title_text\n [options.collapsible ? \"addClass\" : \"removeClass\"](\n \"no-highlight collapsible\"\n )\n .off();\n if (options.collapsible) {\n this.$title_text.on(\"click\", function() {\n self[self.collapsed ? \"expand\" : \"collapse\"]();\n });\n options.collapsed ? this.collapse() : this.expand();\n }\n\n // allow title editing\n this.$title_text.prop(\"disabled\", !options.onchange_title);\n options.onchange_title &&\n this.$title_text.make_text_editable({\n on_finish: function(new_title) {\n options.onchange_title(new_title);\n }\n });\n\n // render buttons\n if (options.buttons) {\n this.$buttons.empty().show();\n $.each(this.model.get(\"buttons\"), function(name, item) {\n item.$el.prop(\"id\", name);\n self.$buttons.append(item.$el);\n });\n } else {\n this.$buttons.hide();\n }\n\n // render operations\n this.$operations.empty;\n if (options.collapsible_button) {\n this.$operations.append(this.collapsible_button.$el);\n }\n if (options.operations) {\n 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\"mvc/ui/ui-misc\", \"mvc/ui/ui-select-default\"], function(\n Utils,\n Ui,\n Select\n) {\n /** Batch mode variations */\n var Batch = { DISABLED: \"disabled\", ENABLED: \"enabled\", LINKED: \"linked\" };\n\n /** List of available content selectors options */\n var Configurations = {\n data: [\n {\n src: \"hda\",\n icon: \"fa-file-o\",\n tooltip: \"Single dataset\",\n multiple: false,\n batch: Batch.DISABLED\n },\n {\n src: \"hda\",\n icon: \"fa-files-o\",\n tooltip: \"Multiple datasets\",\n multiple: true,\n batch: Batch.LINKED\n },\n {\n src: \"hdca\",\n icon: \"fa-folder-o\",\n tooltip: \"Dataset collection\",\n multiple: false,\n batch: Batch.LINKED\n }\n ],\n data_multiple: [\n {\n src: \"hda\",\n icon: \"fa-files-o\",\n tooltip: \"Multiple datasets\",\n multiple: true,\n batch: Batch.DISABLED\n },\n {\n src: \"hdca\",\n icon: \"fa-folder-o\",\n tooltip: \"Dataset collections\",\n multiple: true,\n batch: Batch.DISABLED\n }\n ],\n data_collection: [\n {\n src: \"hdca\",\n icon: \"fa-folder-o\",\n tooltip: \"Dataset collection\",\n multiple: false,\n batch: Batch.DISABLED\n }\n ],\n workflow_data: [\n {\n src: \"hda\",\n icon: \"fa-file-o\",\n tooltip: \"Single dataset\",\n multiple: false,\n batch: Batch.DISABLED\n }\n ],\n workflow_data_multiple: [\n {\n src: \"hda\",\n icon: \"fa-files-o\",\n tooltip: \"Multiple datasets\",\n multiple: true,\n batch: Batch.DISABLED\n }\n ],\n workflow_data_collection: [\n {\n src: \"hdca\",\n icon: \"fa-folder-o\",\n tooltip: \"Dataset collection\",\n multiple: false,\n batch: Batch.DISABLED\n }\n ],\n module_data: [\n {\n src: \"hda\",\n icon: \"fa-file-o\",\n tooltip: \"Single dataset\",\n multiple: false,\n batch: Batch.DISABLED\n },\n {\n src: \"hda\",\n icon: \"fa-files-o\",\n tooltip: \"Multiple datasets\",\n multiple: true,\n batch: Batch.ENABLED\n }\n ],\n module_data_collection: [\n {\n src: \"hdca\",\n icon: \"fa-folder-o\",\n tooltip: \"Dataset collection\",\n multiple: false,\n batch: Batch.DISABLED\n },\n {\n src: \"hdca\",\n icon: \"fa-folder\",\n tooltip: \"Multiple collections\",\n multiple: true,\n batch: Batch.ENABLED\n }\n ]\n };\n\n /** View for hda and hdca content selector ui elements */\n var View = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n src_labels: { hda: \"dataset\", hdca: \"dataset collection\" },\n pagelimit: 100,\n statustimer: 1000\n }).set(options);\n this.setElement($(\"\").addClass(\"ui-select-content\"));\n this.button_product = new Ui.RadioButton.View({\n value: \"false\",\n data: [\n {\n icon: \"fa fa-chain\",\n value: \"false\",\n tooltip:\n \"Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads.\"\n },\n {\n icon: \"fa fa-chain-broken\",\n value: \"true\",\n tooltip:\n \"Unlinked dataset inputs will be run against *all* other inputs.\"\n }\n ]\n });\n var $batch_div = $(\"\")\n .addClass(\"ui-form-info\")\n .append($(\"\").addClass(\"fa fa-sitemap\"))\n .append(\n $(\"\").html(\n \"This is a batch mode input field. Separate jobs will be triggered for each dataset selection.\"\n )\n );\n this.$batch = {\n linked: $batch_div.clone(),\n enabled: $batch_div\n .clone()\n .append(\n $(\"\")\n .append(\n $(\"\")\n .addClass(\"ui-form-title\")\n .html(\"Batch options:\")\n )\n .append(this.button_product.$el)\n )\n .append($(\"\").css(\"clear\", \"both\"))\n };\n\n // add drag-drop event handlers\n this.$el\n .on(\"dragenter\", function(e) {\n this.lastenter = e.target;\n self.$el.addClass(\"ui-dragover\");\n })\n .on(\"dragover\", function(e) {\n e.preventDefault();\n })\n .on(\"dragleave\", function(e) {\n this.lastenter === e.target &&\n self.$el.removeClass(\"ui-dragover\");\n })\n .on(\"drop\", function(e) {\n self._handleDrop(e);\n });\n\n // track current history elements\n this.history = {};\n\n // add listeners\n this.listenTo(this.model, \"change:data\", this._changeData, this);\n this.listenTo(this.model, \"change:wait\", this._changeWait, this);\n this.listenTo(\n this.model,\n \"change:current\",\n this._changeCurrent,\n this\n );\n this.listenTo(this.model, \"change:value\", this._changeValue, this);\n this.listenTo(\n this.model,\n \"change:type change:optional change:multiple change:extensions\",\n this._changeType,\n this\n );\n this.render();\n\n // add change event\n this.on(\"change\", function() {\n options.onchange && options.onchange(self.value());\n });\n },\n\n render: function() {\n this._changeType();\n this._changeValue();\n this._changeWait();\n },\n\n /** Indicate that select fields are being updated */\n wait: function() {\n this.model.set(\"wait\", true);\n },\n\n /** Indicate that the options update has been completed */\n unwait: function() {\n this.model.set(\"wait\", false);\n },\n\n /** Update data representing selectable options */\n update: function(options) {\n this.model.set(\"data\", options);\n },\n\n /** Return the currently selected dataset values */\n value: function(new_value) {\n new_value !== undefined && this.model.set(\"value\", new_value);\n var current = this.model.get(\"current\");\n if (this.config[current]) {\n var id_list = this.fields[current].value();\n if (id_list !== null) {\n id_list = $.isArray(id_list) ? id_list : [id_list];\n if (id_list.length > 0) {\n var result = this._batch({ values: [] });\n for (var i in id_list) {\n var details = this.history[\n id_list[i] + \"_\" + this.config[current].src\n ];\n if (details) {\n result.values.push(details);\n } else {\n Galaxy.emit.debug(\n \"ui-select-content::value()\",\n \"Requested details not found for '\" +\n id_list[i] +\n \"'.\"\n );\n return null;\n }\n }\n result.values.sort(function(a, b) {\n return a.hid - b.hid;\n });\n return result;\n }\n }\n } else {\n Galaxy.emit.debug(\n \"ui-select-content::value()\",\n \"Invalid value/source '\" + new_value + \"'.\"\n );\n }\n return null;\n },\n\n /** Change of current select field */\n _changeCurrent: function() {\n var self = this;\n _.each(this.fields, function(field, i) {\n if (self.model.get(\"current\") == i) {\n field.$el.show();\n _.each(self.$batch, function($batchfield, batchmode) {\n $batchfield[\n self.config[i].batch == batchmode ? \"show\" : \"hide\"\n ]();\n });\n self.button_type.value(i);\n } else {\n field.$el.hide();\n }\n });\n },\n\n /** Change of type */\n _changeType: function() {\n var self = this;\n\n // identify selector type identifier i.e. [ flavor ]_[ type ]_[ multiple ]\n var config_id =\n (this.model.get(\"flavor\")\n ? this.model.get(\"flavor\") + \"_\"\n : \"\") +\n String(this.model.get(\"type\")) +\n (this.model.get(\"multiple\") ? \"_multiple\" : \"\");\n if (Configurations[config_id]) {\n this.config = Configurations[config_id];\n } else {\n this.config = Configurations[\"data\"];\n Galaxy.emit.debug(\n \"ui-select-content::_changeType()\",\n \"Invalid configuration/type id '\" + config_id + \"'.\"\n );\n }\n\n // prepare extension component of error message\n var data = self.model.get(\"data\");\n var extensions = Utils.textify(this.model.get(\"extensions\"));\n var src_labels = this.model.get(\"src_labels\");\n\n // build views\n this.fields = [];\n this.button_data = [];\n _.each(this.config, function(c, i) {\n self.button_data.push({\n value: i,\n icon: c.icon,\n tooltip: c.tooltip\n });\n self.fields.push(\n new Select.View({\n optional: self.model.get(\"optional\"),\n multiple: c.multiple,\n searchable:\n !c.multiple ||\n (data &&\n data[c.src] &&\n data[c.src].length >\n self.model.get(\"pagelimit\")),\n individual: true,\n error_text:\n \"No \" +\n (extensions ? extensions + \" \" : \"\") +\n (src_labels[c.src] || \"content\") +\n \" available.\",\n onchange: function() {\n self.trigger(\"change\");\n }\n })\n );\n });\n this.button_type = new Ui.RadioButton.View({\n value: this.model.get(\"current\"),\n data: this.button_data,\n onchange: function(value) {\n self.model.set(\"current\", value);\n self.trigger(\"change\");\n }\n });\n\n // append views\n this.$el.empty();\n var button_width = 0;\n if (this.fields.length > 1) {\n this.$el.append(this.button_type.$el);\n button_width = Math.max(0, this.fields.length * 36) + \"px\";\n }\n _.each(this.fields, function(field) {\n self.$el.append(field.$el.css({ \"margin-left\": button_width }));\n });\n _.each(this.$batch, function($batchfield, batchmode) {\n self.$el.append(\n $batchfield.css({ \"margin-left\": button_width })\n );\n });\n this.model.set(\"current\", 0);\n this._changeCurrent();\n this._changeData();\n },\n\n /** Change of wait flag */\n _changeWait: function() {\n var self = this;\n _.each(this.fields, function(field) {\n field[self.model.get(\"wait\") ? \"wait\" : \"unwait\"]();\n });\n },\n\n /** Change of available options */\n _changeData: function() {\n var options = this.model.get(\"data\");\n var self = this;\n var select_options = {};\n _.each(options, function(items, src) {\n select_options[src] = [];\n _.each(items, function(item) {\n select_options[src].push({\n hid: item.hid,\n keep: item.keep,\n label: item.hid + \": \" + item.name,\n value: item.id,\n tags: item.tags\n });\n self.history[item.id + \"_\" + src] = item;\n });\n });\n _.each(this.config, function(c, i) {\n select_options[c.src] &&\n self.fields[i].add(select_options[c.src], function(a, b) {\n return b.hid - a.hid;\n });\n });\n },\n\n /** Change of incoming value */\n _changeValue: function() {\n var new_value = this.model.get(\"value\");\n if (new_value && new_value.values && new_value.values.length > 0) {\n // create list with content ids\n var list = [];\n _.each(new_value.values, function(value) {\n list.push(value.id);\n });\n // sniff first suitable field type from config list\n var src = new_value.values[0].src;\n var multiple = new_value.values.length > 1;\n for (var i = 0; i < this.config.length; i++) {\n var field = this.fields[i];\n var c = this.config[i];\n if (\n c.src == src &&\n [multiple, true].indexOf(c.multiple) !== -1\n ) {\n this.model.set(\"current\", i);\n field.value(list);\n break;\n }\n }\n } else {\n _.each(this.fields, function(field) {\n field.value(null);\n });\n }\n },\n\n /** Handles drop events e.g. from history panel */\n _handleDrop: function(ev) {\n try {\n var data = this.model.get(\"data\");\n var current = this.model.get(\"current\");\n var config = this.config[current];\n var field = this.fields[current];\n var drop_data = JSON.parse(\n ev.originalEvent.dataTransfer.getData(\"text\")\n )[0];\n var new_id = drop_data.id;\n var new_src =\n drop_data.history_content_type == \"dataset\"\n ? \"hda\"\n : \"hdca\";\n var new_value = { id: new_id, src: new_src };\n if (data && _.findWhere(data[new_src], new_value)) {\n if (config.src == new_src) {\n var current_value = field.value();\n if (current_value && config.multiple) {\n if (current_value.indexOf(new_id) == -1) {\n current_value.push(new_id);\n }\n } else {\n current_value = new_id;\n }\n field.value(current_value);\n } else {\n this.model.set(\"value\", { values: [new_value] });\n 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\"change:current\",\n this._changeCurrent,\n this\n );\n this.listenTo(this.model, \"change:value\", this._changeValue, this);\n this.listenTo(\n this.model,\n \"change:type change:optional change:multiple change:extensions\",\n this._changeType,\n this\n );\n this.render();\n\n // add change event\n this.on(\"change\", function() {\n options.onchange && options.onchange(self.value());\n });\n },\n\n render: function() {\n this._changeType();\n this._changeValue();\n this._changeWait();\n },\n\n /** Indicate that select fields are being updated */\n wait: function() {\n this.model.set(\"wait\", true);\n },\n\n /** Indicate that the options update has been completed */\n unwait: function() {\n this.model.set(\"wait\", false);\n },\n\n /** Update data representing selectable options */\n update: function(options) {\n this.model.set(\"data\", options);\n },\n\n /** Return the currently selected dataset values */\n value: function(new_value) {\n new_value !== undefined && 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{\n if (self.model.get(\"current\") == i) {\n field.$el.show();\n _.each(self.$batch, function($batchfield, batchmode) {\n $batchfield[\n self.config[i].batch == batchmode ? \"show\" : \"hide\"\n ]();\n });\n self.button_type.value(i);\n } else {\n field.$el.hide();\n }\n });\n },\n\n /** Change of type */\n _changeType: function() {\n var self = this;\n\n // identify selector type identifier i.e. [ flavor ]_[ type ]_[ multiple ]\n var config_id =\n (this.model.get(\"flavor\")\n ? this.model.get(\"flavor\") + \"_\"\n : \"\") +\n String(this.model.get(\"type\")) +\n (this.model.get(\"multiple\") ? \"_multiple\" : \"\");\n if (Configurations[config_id]) {\n this.config = Configurations[config_id];\n } else {\n this.config = Configurations[\"data\"];\n Galaxy.emit.debug(\n \"ui-select-content::_changeType()\",\n \"Invalid configuration/type id '\" + config_id + \"'.\"\n );\n }\n\n // prepare extension component of error message\n var data = self.model.get(\"data\");\n var extensions = Utils.textify(this.model.get(\"extensions\"));\n var src_labels = this.model.get(\"src_labels\");\n\n // build views\n this.fields = [];\n this.button_data = [];\n _.each(this.config, function(c, i) {\n self.button_data.push({\n value: i,\n icon: c.icon,\n tooltip: c.tooltip\n });\n self.fields.push(\n new Select.View({\n optional: self.model.get(\"optional\"),\n multiple: c.multiple,\n searchable:\n !c.multiple ||\n (data &&\n data[c.src] &&\n data[c.src].length >\n self.model.get(\"pagelimit\")),\n individual: true,\n error_text:\n \"No \" +\n (extensions ? extensions + \" \" : \"\") +\n (src_labels[c.src] || \"content\") +\n \" available.\",\n onchange: function() {\n self.trigger(\"change\");\n }\n })\n );\n });\n this.button_type = new Ui.RadioButton.View({\n value: this.model.get(\"current\"),\n data: this.button_data,\n onchange: function(value) {\n self.model.set(\"current\", value);\n self.trigger(\"change\");\n }\n });\n\n // append views\n this.$el.empty();\n var button_width = 0;\n if (this.fields.length > 1) {\n this.$el.append(this.button_type.$el);\n button_width = Math.max(0, this.fields.length * 36) + \"px\";\n }\n _.each(this.fields, function(field) {\n self.$el.append(field.$el.css({ \"margin-left\": button_width }));\n });\n _.each(this.$batch, function($batchfield, batchmode) {\n self.$el.append(\n $batchfield.css({ \"margin-left\": button_width })\n );\n });\n this.model.set(\"current\", 0);\n this._changeCurrent();\n this._changeData();\n },\n\n /** Change of wait flag */\n _changeWait: function() {\n var self = this;\n _.each(this.fields, function(field) {\n field[self.model.get(\"wait\") ? \"wait\" : \"unwait\"]();\n });\n },\n\n /** Change of available options */\n _changeData: function() {\n var options = this.model.get(\"data\");\n var self = this;\n var select_options = {};\n _.each(options, function(items, src) {\n select_options[src] = [];\n _.each(items, function(item) {\n select_options[src].push({\n hid: item.hid,\n keep: item.keep,\n label: item.hid + \": \" + item.name,\n value: item.id,\n tags: item.tags\n });\n self.history[item.id + \"_\" + src] = item;\n });\n });\n _.each(this.config, function(c, i) {\n select_options[c.src] &&\n self.fields[i].add(select_options[c.src], function(a, b) {\n return b.hid - a.hid;\n });\n });\n },\n\n /** Change of incoming value */\n _changeValue: function() {\n var new_value = this.model.get(\"value\");\n if (new_value && new_value.values && new_value.values.length > 0) {\n // create list with content ids\n var list = [];\n _.each(new_value.values, function(value) {\n list.push(value.id);\n });\n // sniff first suitable field type from config list\n var src = new_value.values[0].src;\n var multiple = new_value.values.length > 1;\n for (var i = 0; i < this.config.length; i++) {\n var field = this.fields[i];\n var c = this.config[i];\n if (\n c.src == src &&\n [multiple, true].indexOf(c.multiple) !== -1\n ) {\n this.model.set(\"current\", i);\n field.value(list);\n break;\n }\n }\n } else {\n _.each(this.fields, function(field) {\n field.value(null);\n });\n }\n },\n\n /** Handles drop events e.g. from history panel */\n _handleDrop: function(ev) {\n try {\n var data = this.model.get(\"data\");\n var current = this.model.get(\"current\");\n var config = this.config[current];\n var field = this.fields[current];\n var drop_data = JSON.parse(\n ev.originalEvent.dataTransfer.getData(\"text\")\n )[0];\n var new_id = drop_data.id;\n var new_src =\n drop_data.history_content_type == \"dataset\"\n ? \"hda\"\n : \"hdca\";\n var new_value = { id: new_id, src: new_src };\n if (data && _.findWhere(data[new_src], new_value)) {\n if (config.src == new_src) {\n var current_value = field.value();\n if (current_value && config.multiple) {\n if (current_value.indexOf(new_id) == -1) {\n current_value.push(new_id);\n }\n } else {\n current_value = new_id;\n }\n field.value(current_value);\n } else {\n this.model.set(\"value\", { values: [new_value] });\n this.model.trigger(\"change:value\");\n }\n this.trigger(\"change\");\n this._handleDropStatus(\"success\");\n } else {\n this._handleDropStatus(\"danger\");\n }\n } catch (e) {\n this._handleDropStatus(\"danger\");\n }\n ev.preventDefault();\n },\n\n /** Highlight drag result */\n _handleDropStatus: function(status) {\n var self = this;\n this.$el\n .removeClass(\"ui-dragover\")\n .addClass(\"ui-dragover-\" + status);\n setTimeout(function() {\n self.$el.removeClass(\"ui-dragover-\" + status);\n }, this.model.get(\"statustimer\"));\n },\n\n /** Assists in identifying the batch mode */\n _batch: function(result) {\n result[\"batch\"] = false;\n var current = this.model.get(\"current\");\n var config = this.config[current];\n if (config.src == \"hdca\" && !config.multiple) {\n var hdca = this.history[this.fields[current].value() + \"_hdca\"];\n if (hdca && hdca.map_over_type) {\n result[\"batch\"] = true;\n }\n }\n if (config.batch == Batch.LINKED || config.batch == Batch.ENABLED) {\n result[\"batch\"] = true;\n if (\n config.batch == Batch.ENABLED &&\n this.button_product.value() === \"true\"\n ) {\n result[\"product\"] = true;\n }\n }\n return result;\n }\n });\n\n return {\n View: View\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/ui/ui-select-default.js.map b/static/maps/mvc/ui/ui-select-default.js.map index 89830ec6938..4c20d3b27fa 100644 --- a/static/maps/mvc/ui/ui-select-default.js.map +++ b/static/maps/mvc/ui/ui-select-default.js.map @@ -1 +1 @@ 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* This class creates/wraps a default html select field as backbone class.\n */\ndefine([\"utils/utils\", \"mvc/ui/ui-buttons\"], function(Utils, Buttons) {\n var View = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.data = [];\n this.data2 = [];\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n id: Utils.uid(),\n cls: \"ui-select\",\n error_text: \"No options available\",\n empty_text: \"Nothing selected\",\n visible: true,\n wait: false,\n multiple: false,\n searchable: true,\n optional: false,\n disabled: false,\n readonly: false,\n onchange: function() {},\n value: null,\n individual: false,\n pagesize: 20\n }).set(options);\n this.on(\"change\", function() {\n self.model.get(\"onchange\") &&\n self.model.get(\"onchange\")(self.value());\n });\n this.listenTo(this.model, \"change:data\", this._changeData, this);\n this.listenTo(\n this.model,\n \"change:disabled\",\n this._changeDisabled,\n this\n );\n this.listenTo(this.model, \"change:wait\", this._changeWait, this);\n this.listenTo(\n this.model,\n \"change:visible\",\n this._changeVisible,\n this\n );\n this.listenTo(this.model, \"change:value\", this._changeValue, this);\n this.listenTo(\n this.model,\n \"change:multiple change:searchable change:cls change:id\",\n this.render,\n this\n );\n this.render();\n },\n\n render: function() {\n var self = this;\n this.model.get(\"searchable\")\n ? this._renderSearchable()\n : this._renderClassic();\n this.$el\n .addClass(this.model.get(\"cls\"))\n .attr(\"id\", this.model.get(\"id\"));\n this.$select\n .empty()\n .addClass(\"select\")\n .attr(\"id\", this.model.get(\"id\") + \"_select\")\n .prop(\"multiple\", this.model.get(\"multiple\"))\n .on(\"change\", function() {\n self.value(self._getValue());\n self.trigger(\"change\");\n });\n this._changeData();\n this._changeWait();\n this._changeVisible();\n this._changeDisabled();\n },\n\n /** Renders the classic selection field */\n _renderClassic: function() {\n var self = this;\n this.$el\n .addClass(\n this.model.get(\"multiple\")\n ? \"ui-select-multiple\"\n : \"ui-select\"\n )\n .append((this.$select = $(\"\")))\n .append((this.$dropdown = $(\"\")))\n .append(\n (this.$resize = $(\"\").append(\n (this.$resize_icon = $(\"\"))\n ))\n );\n if (this.model.get(\"multiple\")) {\n this.$dropdown.hide();\n this.$resize_icon\n .addClass(\"fa fa-angle-double-right fa-rotate-45\")\n .show();\n this.$resize\n .removeClass()\n .addClass(\"icon-resize\")\n .show()\n .off(\"mousedown\")\n .on(\"mousedown\", function(event) {\n var currentY = event.pageY;\n var currentHeight = self.$select.height();\n self.minHeight = self.minHeight || currentHeight;\n $(\"#dd-helper\")\n .show()\n .on(\"mousemove\", function(event) {\n self.$select.height(\n Math.max(\n currentHeight +\n (event.pageY - currentY),\n self.minHeight\n )\n );\n })\n .on(\"mouseup mouseleave\", function() {\n $(\"#dd-helper\")\n .hide()\n .off();\n });\n });\n } else {\n this.$dropdown.show();\n this.$resize.hide();\n this.$resize_icon.hide();\n }\n },\n\n /** Renders the default select2 field */\n _renderSearchable: function() {\n var self = this;\n this.$el\n .append((this.$select = $(\"\")))\n .append((this.$dropdown = $(\"\")));\n this.$dropdown.hide();\n if (!this.model.get(\"multiple\")) {\n this.$dropdown.show().on(\"click\", function() {\n self.$select.select2 && self.$select.select2(\"open\");\n });\n }\n this.all_button = null;\n if (\n this.model.get(\"multiple\") &&\n !this.model.get(\"individual\") &&\n !this.model.get(\"readonly\")\n ) {\n this.all_button = new Buttons.ButtonCheck({\n onclick: function() {\n var new_value = [];\n self.all_button.value() !== 0 &&\n _.each(self.model.get(\"data\"), function(option) {\n new_value.push(option.value);\n });\n self.value(new_value);\n self.trigger(\"change\");\n }\n });\n this.$el.prepend(this.all_button.$el);\n }\n },\n\n /** Matches a search term with a given text */\n _match: function(term, text) {\n return (\n !term ||\n term == \"\" ||\n String(text)\n .toUpperCase()\n .indexOf(term.toUpperCase()) >= 0\n );\n },\n\n /** Updates the selection options */\n _changeData: function() {\n var self = this;\n this.data = [];\n if (!this.model.get(\"multiple\") && this.model.get(\"optional\")) {\n this.data.push({\n value: \"__null__\",\n label: self.model.get(\"empty_text\")\n });\n }\n _.each(this.model.get(\"data\"), function(option) {\n self.data.push(option);\n });\n if (this.length() == 0) {\n this.data.push({\n value: \"__null__\",\n label: this.model.get(\"error_text\")\n });\n }\n if (this.model.get(\"searchable\")) {\n this.data2 = [];\n _.each(this.data, function(option, index) {\n self.data2.push({\n order: index,\n id: option.value,\n text: option.label,\n tags: option.tags\n });\n });\n this.$select.data(\"select2\") && this.$select.select2(\"destroy\");\n this.matched_tags = {};\n this.$select.select2({\n data: self.data2,\n closeOnSelect: !this.model.get(\"multiple\"),\n multiple: this.model.get(\"multiple\"),\n query: function(q) {\n self.matched_tags = {};\n var pagesize = self.model.get(\"pagesize\");\n var results = _.filter(self.data2, function(e) {\n var found = false;\n _.each(e.tags, function(tag) {\n if (self._match(q.term, tag)) {\n found = self.matched_tags[tag] = true;\n }\n });\n return found || self._match(q.term, e.text);\n });\n q.callback({\n results: results.slice(\n (q.page - 1) * pagesize,\n q.page * pagesize\n ),\n more: results.length >= q.page * pagesize\n });\n },\n formatResult: function(result) {\n return (\n _.escape(result.text) +\n '\"\n );\n }\n });\n this.$(\".select2-container .select2-search input\").off(\"blur\");\n } else {\n this.$select.find(\"option\").remove();\n _.each(this.data, function(option) {\n self.$select.append(\n $(\"\")\n .attr(\"value\", option.value)\n .html(_.escape(option.label))\n );\n });\n }\n this.model.set(\n \"disabled\",\n this.model.get(\"readonly\") || this.length() == 0\n );\n this._changeValue();\n },\n\n /** Handles field enabling/disabling, usually used when no options are available */\n _changeDisabled: function() {\n if (this.model.get(\"searchable\")) {\n this.$select.select2(\n this.model.get(\"disabled\") ? \"disable\" : \"enable\"\n );\n } else {\n this.$select.prop(\"disabled\", this.model.get(\"disabled\"));\n }\n },\n\n /** Searchable fields may display a spinner e.g. while waiting for a server response */\n _changeWait: function() {\n this.$dropdown\n .removeClass()\n .addClass(\"icon-dropdown fa\")\n .addClass(\n this.model.get(\"wait\")\n ? \"fa-spinner fa-spin\"\n : \"fa-caret-down\"\n );\n },\n\n /** Handles field visibility */\n _changeVisible: function() {\n this.$el[this.model.get(\"visible\") ? \"show\" : \"hide\"]();\n this.$select[this.model.get(\"visible\") ? \"show\" : \"hide\"]();\n },\n\n /** Synchronizes the model value with the actually selected field value */\n _changeValue: function() {\n this._setValue(this.model.get(\"value\"));\n if (this.model.get(\"multiple\")) {\n if (this.all_button) {\n var value = this._getValue();\n this.all_button.value(\n $.isArray(value) ? value.length : 0,\n this.length()\n );\n }\n } else if (\n this._getValue() === null &&\n !this.model.get(\"optional\")\n ) {\n this._setValue(this.first());\n }\n },\n\n /** Return/Set current selection */\n value: function(new_value) {\n new_value !== undefined && this.model.set(\"value\", new_value);\n return this._getValue();\n },\n\n /** Return the first select option */\n first: function() {\n return this.data.length > 0 ? this.data[0].value : null;\n },\n\n /** Check if a value is an existing option */\n exists: function(value) {\n return _.findWhere(this.data, { value: value });\n },\n\n /** Return the label/text of the current selection */\n text: function() {\n var v = this._getValue();\n var d = this.exists($.isArray(v) ? v[0] : v);\n return d ? d.label : \"\";\n },\n\n /** Show the select 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* This class creates/wraps a default html select field as backbone class.\n */\ndefine([\"utils/utils\", \"mvc/ui/ui-buttons\"], function(Utils, Buttons) {\n var View = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.data = [];\n this.data2 = [];\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n id: Utils.uid(),\n cls: \"ui-select\",\n error_text: \"No options available\",\n empty_text: \"Nothing selected\",\n visible: true,\n wait: false,\n multiple: false,\n searchable: true,\n optional: false,\n disabled: false,\n readonly: false,\n onchange: function() {},\n value: null,\n individual: false,\n pagesize: 20\n }).set(options);\n this.on(\"change\", function() {\n self.model.get(\"onchange\") &&\n self.model.get(\"onchange\")(self.value());\n });\n this.listenTo(this.model, \"change:data\", this._changeData, this);\n this.listenTo(\n this.model,\n \"change:disabled\",\n this._changeDisabled,\n this\n );\n this.listenTo(this.model, \"change:wait\", this._changeWait, this);\n this.listenTo(\n this.model,\n \"change:visible\",\n this._changeVisible,\n this\n );\n this.listenTo(this.model, \"change:value\", this._changeValue, this);\n this.listenTo(\n this.model,\n \"change:multiple change:searchable change:cls change:id\",\n this.render,\n this\n );\n this.render();\n },\n\n render: function() {\n var self = this;\n this.model.get(\"searchable\")\n ? this._renderSearchable()\n : this._renderClassic();\n this.$el\n .addClass(this.model.get(\"cls\"))\n .attr(\"id\", this.model.get(\"id\"));\n this.$select\n .empty()\n .addClass(\"select\")\n .attr(\"id\", this.model.get(\"id\") + \"_select\")\n .prop(\"multiple\", this.model.get(\"multiple\"))\n .on(\"change\", function() {\n self.value(self._getValue());\n self.trigger(\"change\");\n });\n this._changeData();\n this._changeWait();\n this._changeVisible();\n this._changeDisabled();\n },\n\n /** Renders the classic selection field */\n _renderClassic: function() {\n var self = this;\n this.$el\n .addClass(\n this.model.get(\"multiple\")\n ? \"ui-select-multiple\"\n : \"ui-select\"\n )\n .append((this.$select = $(\"\")))\n .append((this.$dropdown = $(\"\")))\n .append(\n (this.$resize = $(\"\").append(\n (this.$resize_icon = $(\"\"))\n ))\n );\n if (this.model.get(\"multiple\")) {\n this.$dropdown.hide();\n this.$resize_icon\n .addClass(\"fa fa-angle-double-right fa-rotate-45\")\n .show();\n this.$resize\n .removeClass()\n .addClass(\"icon-resize\")\n .show()\n .off(\"mousedown\")\n .on(\"mousedown\", function(event) {\n var currentY = event.pageY;\n var currentHeight = self.$select.height();\n self.minHeight = self.minHeight || currentHeight;\n $(\"#dd-helper\")\n .show()\n .on(\"mousemove\", function(event) {\n self.$select.height(\n Math.max(\n currentHeight +\n (event.pageY - currentY),\n self.minHeight\n )\n );\n })\n .on(\"mouseup mouseleave\", function() {\n $(\"#dd-helper\")\n .hide()\n .off();\n });\n });\n } else {\n this.$dropdown.show();\n this.$resize.hide();\n this.$resize_icon.hide();\n }\n },\n\n /** Renders the default select2 field */\n _renderSearchable: function() {\n var self = this;\n this.$el\n .append((this.$select = $(\"\")))\n .append((this.$dropdown = $(\"\")));\n this.$dropdown.hide();\n if (!this.model.get(\"multiple\")) {\n this.$dropdown.show().on(\"click\", function() {\n self.$select.select2 && self.$select.select2(\"open\");\n });\n }\n this.all_button = null;\n if (\n this.model.get(\"multiple\") &&\n !this.model.get(\"individual\") &&\n !this.model.get(\"readonly\")\n ) {\n this.all_button = new Buttons.ButtonCheck({\n onclick: function() {\n var new_value = [];\n self.all_button.value() !== 0 &&\n _.each(self.model.get(\"data\"), function(option) {\n new_value.push(option.value);\n });\n self.value(new_value);\n self.trigger(\"change\");\n }\n });\n this.$el.prepend(this.all_button.$el);\n }\n },\n\n /** Matches a search term with a given text */\n _match: function(term, text) {\n return (\n !term ||\n term == \"\" ||\n String(text)\n .toUpperCase()\n .indexOf(term.toUpperCase()) >= 0\n );\n },\n\n /** Updates the selection options */\n _changeData: function() {\n var self = this;\n this.data = [];\n if (!this.model.get(\"multiple\") && this.model.get(\"optional\")) {\n this.data.push({\n value: \"__null__\",\n label: self.model.get(\"empty_text\")\n });\n }\n _.each(this.model.get(\"data\"), function(option) {\n self.data.push(option);\n });\n if (this.length() == 0) {\n this.data.push({\n value: \"__null__\",\n label: this.model.get(\"error_text\")\n });\n }\n if (this.model.get(\"searchable\")) {\n this.data2 = [];\n _.each(this.data, function(option, index) {\n self.data2.push({\n order: index,\n id: option.value,\n text: option.label,\n tags: option.tags\n });\n });\n this.$select.data(\"select2\") && this.$select.select2(\"destroy\");\n this.matched_tags = {};\n this.$select.select2({\n data: self.data2,\n closeOnSelect: !this.model.get(\"multiple\"),\n multiple: this.model.get(\"multiple\"),\n query: function(q) {\n self.matched_tags = {};\n var pagesize = self.model.get(\"pagesize\");\n var results = _.filter(self.data2, function(e) {\n var found = false;\n _.each(e.tags, function(tag) {\n if (self._match(q.term, tag)) {\n found = self.matched_tags[tag] = true;\n }\n });\n return found || self._match(q.term, e.text);\n });\n q.callback({\n results: results.slice(\n (q.page - 1) * pagesize,\n q.page * pagesize\n ),\n more: results.length >= q.page * pagesize\n });\n },\n formatResult: function(result) {\n return (\n _.escape(result.text) +\n '\"\n );\n }\n });\n this.$(\".select2-container .select2-search input\").off(\"blur\");\n } else {\n this.$select.find(\"option\").remove();\n _.each(this.data, function(option) {\n self.$select.append(\n $(\"\")\n .attr(\"value\", option.value)\n .html(_.escape(option.label))\n );\n });\n }\n this.model.set(\n \"disabled\",\n this.model.get(\"readonly\") || this.length() == 0\n );\n this._changeValue();\n },\n\n /** Handles field enabling/disabling, usually used when no options are available */\n _changeDisabled: function() {\n if (this.model.get(\"searchable\")) {\n this.$select.select2(\n this.model.get(\"disabled\") ? \"disable\" : \"enable\"\n );\n } else {\n this.$select.prop(\"disabled\", this.model.get(\"disabled\"));\n }\n },\n\n /** Searchable fields may display a spinner e.g. while waiting for a server response */\n _changeWait: function() {\n this.$dropdown\n .removeClass()\n .addClass(\"icon-dropdown fa\")\n .addClass(\n this.model.get(\"wait\")\n ? \"fa-spinner fa-spin\"\n : \"fa-caret-down\"\n );\n },\n\n /** Handles field visibility */\n _changeVisible: function() {\n this.$el[this.model.get(\"visible\") ? \"show\" : \"hide\"]();\n this.$select[this.model.get(\"visible\") ? \"show\" : \"hide\"]();\n },\n\n /** Synchronizes the model value with the actually selected field value */\n _changeValue: function() {\n this._setValue(this.model.get(\"value\"));\n if (this.model.get(\"multiple\")) {\n if (this.all_button) {\n var value = this._getValue();\n this.all_button.value(\n $.isArray(value) ? value.length : 0,\n this.length()\n );\n }\n } else if (\n this._getValue() === null &&\n !this.model.get(\"optional\")\n ) {\n this._setValue(this.first());\n }\n },\n\n /** Return/Set current selection */\n value: function(new_value) {\n new_value !== undefined && this.model.set(\"value\", new_value);\n return this._getValue();\n },\n\n /** Return the first select option */\n first: function() {\n return this.data.length > 0 ? this.data[0].value : null;\n },\n\n /** Check if a value is an existing option */\n exists: function(value) {\n return _.findWhere(this.data, { value: value });\n },\n\n /** Return the label/text of the current selection */\n text: function() {\n var v = this._getValue();\n var d = this.exists($.isArray(v) ? v[0] : v);\n return d ? d.label : \"\";\n },\n\n /** Show the select field */\n show: function() {\n this.model.set(\"visible\", true);\n },\n\n /** Hide the select field */\n hide: function() {\n this.model.set(\"visible\", false);\n },\n\n /** Show a spinner indicating that the select options are currently loaded */\n wait: function() {\n this.model.set(\"wait\", true);\n },\n\n /** Hide spinner indicating that the request has been completed */\n unwait: function() {\n this.model.set(\"wait\", false);\n },\n\n /** Returns true if the field is disabled */\n disabled: function() {\n return this.model.get(\"disabled\");\n },\n\n /** Enable the select field */\n enable: function() {\n this.model.set(\"disabled\", false);\n },\n\n /** Disable the select field */\n disable: function() {\n this.model.set(\"disabled\", true);\n },\n\n /** Update all available options at once */\n add: function(options, sorter) {\n _.each(this.model.get(\"data\"), function(v) {\n v.keep &&\n !_.findWhere(options, { value: v.value }) &&\n options.push(v);\n });\n sorter && options && options.sort(sorter);\n this.model.set(\"data\", options);\n },\n\n /** Update available options */\n update: function(options) {\n this.model.set(\"data\", options);\n },\n\n /** Set the custom onchange callback function */\n setOnChange: function(callback) {\n this.model.set(\"onchange\", callback);\n },\n\n /** Number of available options */\n length: function() {\n return $.isArray(this.model.get(\"data\"))\n ? this.model.get(\"data\").length\n : 0;\n },\n\n /** Set value to dom */\n _setValue: function(new_value) {\n var self = this;\n if (new_value === null || new_value === undefined) {\n new_value = \"__null__\";\n }\n if (this.model.get(\"multiple\")) {\n new_value = $.isArray(new_value) ? new_value : [new_value];\n } else if ($.isArray(new_value)) {\n if (new_value.length > 0) {\n new_value = new_value[0];\n } else {\n new_value = \"__null__\";\n }\n }\n if (this.model.get(\"searchable\")) {\n if ($.isArray(new_value)) {\n var val = [];\n _.each(new_value, function(v) {\n var d = _.findWhere(self.data2, { id: v });\n d && val.push(d);\n });\n new_value = val;\n } else {\n var d = _.findWhere(this.data2, { id: new_value });\n new_value = d;\n }\n this.$select.select2(\"data\", new_value);\n } else {\n this.$select.val(new_value);\n }\n },\n\n /** Get value from dom */\n _getValue: function() {\n var val = null;\n if (this.model.get(\"searchable\")) {\n var selected = this.$select.select2(\"data\");\n if (selected) {\n if ($.isArray(selected)) {\n val = [];\n selected.sort(function(a, b) {\n return a.order - b.order;\n });\n _.each(selected, function(v) {\n val.push(v.id);\n });\n } else {\n val = selected.id;\n }\n }\n } else {\n val = this.$select.val();\n }\n return Utils.isEmpty(val) ? null : val;\n }\n });\n\n return {\n View: View\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/ui/ui-select-ftp.js.map b/static/maps/mvc/ui/ui-select-ftp.js.map index 1474371f6f8..cc7b9f02691 100644 --- a/static/maps/mvc/ui/ui-select-ftp.js.map +++ b/static/maps/mvc/ui/ui-select-ftp.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/ui/ui-select-ftp.js"],"names":["define","Utils","List","View","Backbone","extend","initialize","this","ftpfile_list","name","optional","options","multiple","onchange","self","value","setElement","$el","get","url","Galaxy","root","response","success","i","data","update","val"],"mappings":"aACAA,QAAQ,cAAe,kBAAmB,SAASC,EAAOC,GAItB,OA0C5BC,KA1COC,SAASD,KAAKE,QAArBF,WAAOC,SAAcC,GAErBC,IAAAA,EAAYC,KAKRA,KAAKC,aAAe,IAAIN,EAAKC,MAD7BM,KAAA,OACAC,SAAKF,EAAeE,SAChBD,SAAME,EADwBC,SAE9BF,SAAUC,WACVC,EAAUD,UAAQC,EAHYC,SAAAC,EAAAC,YAUlCR,KAAKS,WAAWT,KAAKC,aAAaS,KAGlChB,EAAMiB,KADNC,IAAAC,OAAAC,KAAA,mBACApB,QAAU,SAAAqB,GACNH,IAAKC,KACLG,IAAS,IAAAC,KAAAF,EACDG,EAAAA,MACCV,MAASO,EAAUE,GAAVF,KACVG,MAAUH,EAAAE,GAAA,OAAAV,EAAVN,aAAAkB,OAAAD,OAWhBV,MAAO,SAASY,GADhB,OAAApB,KAAAC,aAAAO,MAAAY","file":"../../../scripts/mvc/ui/ui-select-ftp.js","sourcesContent":["// dependencies\ndefine([\"utils/utils\", \"mvc/ui/ui-list\"], function(Utils, List) {\n /**\n * FTP file selector\n */\n var View = Backbone.View.extend({\n // initialize\n initialize: function(options) {\n // link this\n var self = this;\n\n // create ui-list view to keep track of selected ftp files\n this.ftpfile_list = new List.View({\n name: \"file\",\n optional: options.optional,\n multiple: options.multiple,\n onchange: function() {\n options.onchange && options.onchange(self.value());\n }\n });\n\n // create elements\n this.setElement(this.ftpfile_list.$el);\n\n // initial fetch of ftps\n Utils.get({\n url: Galaxy.root + \"api/remote_files\",\n success: function(response) {\n var data = [];\n for (var i in response) {\n data.push({\n value: response[i][\"path\"],\n label: response[i][\"path\"]\n });\n }\n self.ftpfile_list.update(data);\n }\n });\n },\n\n /** Return/Set currently selected ftp datasets */\n value: function(val) {\n return this.ftpfile_list.value(val);\n }\n });\n\n return {\n View: View\n };\n});\n"]} \ No newline at end of file +{"version":3,"sources":["mvc/ui/ui-select-ftp.js"],"names":["define","Utils","List","View","Backbone","extend","initialize","options","self","this","ftpfile_list","name","optional","multiple","onchange","value","setElement","$el","get","url","Galaxy","root","success","response","push","data","i","label","val"],"mappings":"kCACAA,QAAQ,cAAe,kBAAmB,SAASC,EAAOC,GA0CjD,OAtC2BC,KAHhCC,SAAAD,KAAAE,QAKIC,WAAY,SAASC,GADrB,IAAAC,EAAAC,KAGIA,KAAAC,aAAA,IAAAR,EAAAC,MAIIQ,KAAM,OAFVC,SAAAL,EAAAK,SACAC,SAAKH,EAALG,SACIF,SAAM,WACNC,EAAAA,UAAkBA,EAFYE,SAAAN,EAAAO,YAAAN,KAAdO,WAApBP,KAAAC,aAAAO,KAUAhB,EAAAiB,KAIIC,IAAKC,OAAOC,KAAO,mBAFvBC,QAAA,SAAAC,GACAtB,IAAMiB,KACFC,IAAKC,IAAAA,KAAOC,EACZC,EAASE,MACDC,MAAOF,EAAXG,GAAW,KACXC,MAAAJ,EAAcA,GAAd,OAGQI,EAAAA,aAAAA,OAAOJ,OAM1BR,MAjC2B,SAAAa,GAqCxB,OAAOnB,KAAKC,aAAaK,MAAMa","file":"../../../scripts/mvc/ui/ui-select-ftp.js","sourcesContent":["// dependencies\ndefine([\"utils/utils\", \"mvc/ui/ui-list\"], function(Utils, List) {\n /**\n * FTP file selector\n */\n var View = Backbone.View.extend({\n // initialize\n initialize: function(options) {\n // link this\n var self = this;\n\n // create ui-list view to keep track of selected ftp files\n this.ftpfile_list = new List.View({\n name: \"file\",\n optional: options.optional,\n multiple: options.multiple,\n onchange: function() {\n options.onchange && options.onchange(self.value());\n }\n });\n\n // create elements\n this.setElement(this.ftpfile_list.$el);\n\n // initial fetch of ftps\n Utils.get({\n url: Galaxy.root + \"api/remote_files\",\n success: function(response) {\n var data = [];\n for (var i in response) {\n data.push({\n value: response[i][\"path\"],\n label: response[i][\"path\"]\n });\n }\n self.ftpfile_list.update(data);\n }\n });\n },\n\n /** Return/Set currently selected ftp datasets */\n value: function(val) {\n return this.ftpfile_list.value(val);\n }\n });\n\n return {\n View: View\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/ui/ui-select-genomespace.js.map b/static/maps/mvc/ui/ui-select-genomespace.js.map index 5c6a4d84ad4..853ea1ec5be 100644 --- a/static/maps/mvc/ui/ui-select-genomespace.js.map +++ b/static/maps/mvc/ui/ui-select-genomespace.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/ui/ui-select-genomespace.js"],"names":["define","Utils","GenomespaceBrowser","View","initialize","extend","self","options","this","icon","Ui","ButtonIcon","tooltip","onclick","browseGenomeSpace","filename_textbox","Input","token_textbox","type","$","_template","append","$el","openFileBrowser","successCallback","data","value","destination","token","new_value","_setValue","undefined","_getValue","values","split"],"mappings":"aACAA,QAAQ,cAAe,iBAAkB,6BAA8B,SADvEC,EACAD,EAKIE,GAuFA,OACIC,KAnFAC,SAAYD,KAAAE,QAERD,WAAIE,SAAJC,GAEA,IAAAD,EAAAE,KAGIC,KAAAA,cAAM,IAF6BC,EAAAC,YAGnCC,MAAAA,SACAC,KAAAA,gBACIP,QAAKQ,qBACRD,QAAA,WANLP,EAAAQ,uBAYAN,KAAAO,iBAAA,IAAAL,EAAAM,MACkCR,KAAlCS,cAAA,IAAAP,EAAAM,OACIE,KAAM,aAMVV,KAAKW,WAAEX,KAAAY,UAAAb,IACPC,KAAKW,EAAE,wBAAwBE,OAAOb,KAAKS,cAAcK,KA5BjCd,KAAAW,EAAA,2BAAAE,OAAAb,KAAAO,iBAAAO,KA4BxBd,KAAKW,EAAE,wBAAwBE,OAAOb,KAAKS,cAAcK,MAMzDpB,kBAAAA,SAAmBqB,GACfC,IAAAA,EAAAA,KACIlB,EAAWmB,iBACdD,gBAAA,SAAAC,GAHLnB,EAAAoB,MAAAD,EAAAE,YAAA,IAAAF,EAAAG,WAqBHR,UAvD2B,SAAAb,GA2CxB,MAcJ,6SACAmB,MAAO,SAASG,GAiBhBC,QAAWC,IAAXD,EAGQ,OAAKf,KAAAA,YAFLc,KAAAA,UAAWA,IARnBG,UAAW,WAgBR,OACG7B,KAAAA,iBAAAA,QAAAA,IAAAA,KAAAA,cAAAA,SAVN2B,UAAW,SAASD,GACZA,IACAI,OAASJ,EAAUK,MAAM,KACzB1B,KAAKO,iBAAiBW,MAAMO,OAAO,IACnCzB,KAAKS,cAAcS,MAAMO,OAAO","file":"../../../scripts/mvc/ui/ui-select-genomespace.js","sourcesContent":["// dependencies\ndefine([\"utils/utils\", \"mvc/ui/ui-misc\", \"mvc/tool/tool-genomespace\"], function(\n Utils,\n Ui,\n GenomespaceBrowser\n) {\n /**\n * GenomeSpace file selector\n */\n var View = Backbone.View.extend({\n // initialize\n initialize: function(options) {\n // link this\n var self = this;\n\n // create insert new list element button\n this.browse_button = new Ui.ButtonIcon({\n title: \"Browse\",\n icon: \"fa fa-sign-in\",\n tooltip: \"Browse GenomeSpace\",\n onclick: function() {\n self.browseGenomeSpace();\n }\n });\n\n // create genomespace filepath textbox\n this.filename_textbox = new Ui.Input();\n\n // create genomespace token textbox\n this.token_textbox = new Ui.Input({\n type: \"password\"\n });\n\n // create elements\n this.setElement(this._template(options));\n this.$(\".ui-gs-browse-button\").append(this.browse_button.$el);\n this.$(\".ui-gs-filename-textbox\").append(this.filename_textbox.$el);\n this.$(\".ui-gs-token-textbox\").append(this.token_textbox.$el);\n },\n\n /** Browse GenomeSpace */\n browseGenomeSpace: function(options) {\n var self = this;\n GenomespaceBrowser.openFileBrowser({\n successCallback: function(data) {\n self.value(data.destination + \"^\" + data.token);\n }\n });\n },\n\n /** Main Template */\n _template: function(options) {\n return (\n '' +\n '\"\n );\n },\n\n /** Return/Set currently selected genomespace filename/token */\n value: function(new_value) {\n // check if new_value is defined\n if (new_value !== undefined) {\n this._setValue(new_value);\n } else {\n return this._getValue();\n }\n },\n\n // get value\n _getValue: function() {\n return (\n this.filename_textbox.value() + \"^\" + this.token_textbox.value()\n );\n },\n\n // set value\n _setValue: function(new_value) {\n if (new_value) {\n values = new_value.split(\"^\");\n this.filename_textbox.value(values[0]);\n this.token_textbox.value(values[1]);\n }\n }\n });\n\n return {\n View: View\n };\n});\n"]} \ No newline at end of file +{"version":3,"sources":["mvc/ui/ui-select-genomespace.js"],"names":["define","Utils","Ui","View","Backbone","extend","initialize","options","self","this","title","ButtonIcon","icon","tooltip","onclick","browseGenomeSpace","filename_textbox","Input","type","setElement","_template","$","append","$el","token_textbox","GenomespaceBrowser","successCallback","value","destination","data","token","new_value","undefined","values","_setValue","_getValue","split"],"mappings":"kCACAA,QAAQ,cAAe,iBAAkB,6BAA8B,SACnEC,EAFJC,EACAF,GA4FI,OACIG,KApFAC,SAAAD,KAAAE,QAEIC,WAAA,SAAAC,GACA,IAAIC,EAAOC,KAIPC,KAAAA,cAAO,IAD4BR,EAAAS,YAEnCC,MAAAA,SACAC,KAAAA,gBACAC,QAAAA,qBACIN,QAAAA,WACHA,EAAAO,uBAILN,KAAKO,iBAAmB,IAAId,EAAGe,MAI3BC,KAAAA,cAAM,IAAAhB,EAAAe,OADwBC,KAAlC,aAMAT,KAAAU,WAAOV,KAAAW,UAAAb,IACPE,KAAAY,EAAA,wBAAOC,OAA2BA,KAAAA,cAAYN,KAC9CP,KAAAY,EAAA,2BAAAC,OAAAb,KAAsCO,iBAAmBO,KAC5Dd,KA7B2BY,EAAA,wBAAAC,OAAAb,KAAAe,cAAAD,MAiCxBR,kBAAW,SAAXR,GACAkB,IAAAA,EAAAA,KACIC,EAAAA,iBACIlB,gBAAKmB,SAAWC,GACnBpB,EAAAmB,MAAAE,EAAAD,YAAA,IAAAC,EAAAC,WAMLV,UAAA,SACIb,GAWP,MAXO,6SA4BPoB,MAxE2B,SAAAI,GA0E5B,QAAAC,IAAAD,EAGQE,OAAAA,KAAAA,YAFRC,KAAAA,UAAWH,IA3EiBI,UAAhC,WAqEQ,OAeD1B,KAAAO,iBAAAW,QAAA,IAAAlB,KAAAe,cAAAG,SATHO,UAAW,SAASH,GACZA,IACAE,OAASF,EAAUK,MAAM,KACzB3B,KAAKO,iBAAiBW,MAAMM,OAAO,IACnCxB,KAAKe,cAAcG,MAAMM,OAAO","file":"../../../scripts/mvc/ui/ui-select-genomespace.js","sourcesContent":["// dependencies\ndefine([\"utils/utils\", \"mvc/ui/ui-misc\", \"mvc/tool/tool-genomespace\"], function(\n Utils,\n Ui,\n GenomespaceBrowser\n) {\n /**\n * GenomeSpace file selector\n */\n var View = Backbone.View.extend({\n // initialize\n initialize: function(options) {\n // link this\n var self = this;\n\n // create insert new list element button\n this.browse_button = new Ui.ButtonIcon({\n title: \"Browse\",\n icon: \"fa fa-sign-in\",\n tooltip: \"Browse GenomeSpace\",\n onclick: function() {\n self.browseGenomeSpace();\n }\n });\n\n // create genomespace filepath textbox\n this.filename_textbox = new Ui.Input();\n\n // create genomespace token textbox\n this.token_textbox = new Ui.Input({\n type: \"password\"\n });\n\n // create elements\n this.setElement(this._template(options));\n this.$(\".ui-gs-browse-button\").append(this.browse_button.$el);\n this.$(\".ui-gs-filename-textbox\").append(this.filename_textbox.$el);\n this.$(\".ui-gs-token-textbox\").append(this.token_textbox.$el);\n },\n\n /** Browse GenomeSpace */\n browseGenomeSpace: function(options) {\n var self = this;\n GenomespaceBrowser.openFileBrowser({\n successCallback: function(data) {\n self.value(data.destination + \"^\" + data.token);\n }\n });\n },\n\n /** Main Template */\n _template: function(options) {\n return (\n '' +\n '' +\n '' +\n \"\" +\n '' +\n '\" +\n \"Token' +\n '' +\n \"' +\n '\"\n );\n },\n\n /** Return/Set currently selected genomespace filename/token */\n value: function(new_value) {\n // check if new_value is defined\n if (new_value !== undefined) {\n this._setValue(new_value);\n } else {\n return this._getValue();\n }\n },\n\n // get value\n _getValue: function() {\n return (\n this.filename_textbox.value() + \"^\" + this.token_textbox.value()\n );\n },\n\n // set value\n _setValue: function(new_value) {\n if (new_value) {\n values = new_value.split(\"^\");\n this.filename_textbox.value(values[0]);\n this.token_textbox.value(values[1]);\n }\n }\n });\n\n return {\n View: View\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/ui/ui-select-library.js.map b/static/maps/mvc/ui/ui-select-library.js.map index e5cef77b695..90a4f9f68cb 100644 --- a/static/maps/mvc/ui/ui-select-library.js.map +++ b/static/maps/mvc/ui/ui-select-library.js.map @@ -1 +1 @@ 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dependencies\ndefine(\n [\"utils/utils\", \"mvc/ui/ui-misc\", \"mvc/ui/ui-table\", \"mvc/ui/ui-list\"],\n function(Utils, Ui, Table, List) {\n // collection of libraries\n var Libraries = Backbone.Collection.extend({\n url: Galaxy.root + \"api/libraries?deleted=false\"\n });\n\n // collection of dataset\n var LibraryDatasets = Backbone.Collection.extend({\n initialize: function() {\n var self = this;\n this.config = new Backbone.Model({ library_id: null });\n this.config.on(\"change\", function() {\n self.fetch({ reset: true });\n });\n },\n url: function() {\n return (\n Galaxy.root +\n \"api/libraries/\" +\n this.config.get(\"library_id\") +\n \"/contents\"\n );\n }\n });\n\n // hda/hdca content selector ui element\n var View = Backbone.View.extend({\n // initialize\n initialize: function(options) {\n // link this\n var self = this;\n\n // collections\n this.libraries = new Libraries();\n this.datasets = new LibraryDatasets();\n\n // link app and options\n this.options = options;\n\n 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dependencies\ndefine(\n [\"utils/utils\", \"mvc/ui/ui-misc\", \"mvc/ui/ui-table\", \"mvc/ui/ui-list\"],\n function(Utils, Ui, Table, List) {\n // collection of libraries\n var Libraries = Backbone.Collection.extend({\n url: Galaxy.root + \"api/libraries?deleted=false\"\n });\n\n // collection of dataset\n var LibraryDatasets = Backbone.Collection.extend({\n initialize: function() {\n var self = this;\n this.config = new Backbone.Model({ library_id: null });\n this.config.on(\"change\", function() {\n self.fetch({ reset: true });\n });\n },\n url: function() {\n return (\n Galaxy.root +\n \"api/libraries/\" +\n this.config.get(\"library_id\") +\n \"/contents\"\n );\n }\n });\n\n // hda/hdca content selector ui element\n var View = Backbone.View.extend({\n // initialize\n initialize: function(options) {\n // link this\n var self = this;\n\n // collections\n this.libraries = new Libraries();\n this.datasets = new LibraryDatasets();\n\n // link app and options\n this.options = options;\n\n // select field for the library\n // TODO: Remove this once the library API supports searching for library datasets\n this.library_select = new Ui.Select.View({\n onchange: function(value) {\n self.datasets.config.set(\"library_id\", value);\n }\n });\n\n // create ui-list view to keep track of selected data libraries\n this.dataset_list = new List.View({\n name: \"dataset\",\n optional: options.optional,\n multiple: options.multiple,\n onchange: function() {\n self.trigger(\"change\");\n }\n });\n\n // add reset handler for fetched libraries\n this.libraries.on(\"reset\", function() {\n var data = [];\n self.libraries.each(function(model) {\n data.push({\n value: model.id,\n label: model.get(\"name\")\n });\n });\n self.library_select.update(data);\n });\n\n // add reset handler for fetched library datasets\n this.datasets.on(\"reset\", function() {\n var data = [];\n var library_current = self.library_select.text();\n if (library_current !== null) {\n 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dependencies\ndefine([\"utils/utils\"], function(Utils) {\n /**\n * A plugin for initializing select2 input items.\n * Make sure the select2 library itself is loaded beforehand.\n * Also the element to which select2 will be appended has to \n * be created before select2 initialization (and passed as option).\n */\n var View = Backbone.View.extend({\n // options\n optionsDefault: {\n css: \"\",\n placeholder: \"No data available\",\n data: [],\n value: null,\n multiple: false,\n minimumInputLength: 0,\n // example format of initial data: \"id:name,55:anotherrole@role.com,27:role@role.com\"\n initialData: \"\"\n },\n\n // initialize\n initialize: function(options) {\n // configure options\n this.options = Utils.merge(options, this.optionsDefault);\n\n // create new element\n this.setElement(this._template(this.options));\n\n // check if container exists\n if (!this.options.container) {\n console.log(\n \"ui-select::initialize() : container not specified.\"\n );\n return;\n }\n\n // add to dom\n this.options.container.append(this.$el);\n\n // link selection dictionary\n this.select_data = this.options.data;\n\n // refresh\n this._refresh();\n\n if (!this.options.multiple) {\n // initial value\n if (this.options.value) {\n this._setValue(this.options.value);\n }\n\n // add change event\n var self = this;\n if (this.options.onchange) {\n this.$el.on(\"change\", function() {\n self.options.onchange(self.value());\n });\n }\n }\n },\n\n // value\n value: function(new_value) {\n // get current id/value\n var before = this._getValue();\n\n // check if new_value is defined\n if (new_value !== undefined) {\n this._setValue(new_value);\n }\n\n // get current id/value\n var after = this._getValue();\n\n // fire onchange\n if (after != before && this.options.onchange) {\n this.options.onchange(after);\n }\n\n // return current value\n return after;\n },\n\n // label\n text: function() {\n return this.$el.select2(\"data\").text;\n },\n\n // disabled\n disabled: function() {\n return !this.$el.select2(\"enable\");\n },\n\n // enable\n enable: function() {\n this.$el.select2(\"enable\", true);\n },\n\n // disable\n disable: function() {\n this.$el.select2(\"enable\", false);\n },\n\n // add\n add: function(options) {\n // add options\n this.select_data.push({\n id: options.id,\n text: options.text\n });\n\n // refresh\n this._refresh();\n },\n\n // remove\n del: function(id) {\n // search option\n var index = this._getIndex(id);\n\n // check if found\n if (index != -1) {\n // remove options\n this.select_data.splice(index, 1);\n\n // refresh\n this._refresh();\n }\n },\n\n // remove\n remove: function() {\n this.$el.select2(\"destroy\");\n },\n\n // update\n update: function(options) {\n // copy options\n this.select_data = [];\n for (var key in options.data) {\n this.select_data.push(options.data[key]);\n }\n\n // refresh\n this._refresh();\n },\n\n // refresh\n _refresh: function() {\n // add select2 data based on type of input\n if (!this.options.multiple) 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dependencies\ndefine([\"utils/utils\"], function(Utils) {\n /**\n * A plugin for initializing select2 input items.\n * Make sure the select2 library itself is loaded beforehand.\n * Also the element to which select2 will be appended has to \n * be created before select2 initialization (and passed as option).\n */\n var View = Backbone.View.extend({\n // options\n optionsDefault: {\n css: \"\",\n placeholder: \"No data available\",\n data: [],\n value: null,\n multiple: false,\n minimumInputLength: 0,\n // example format of initial data: \"id:name,55:anotherrole@role.com,27:role@role.com\"\n initialData: \"\"\n },\n\n // initialize\n initialize: function(options) {\n // configure options\n this.options = Utils.merge(options, this.optionsDefault);\n\n // create new element\n this.setElement(this._template(this.options));\n\n // check if container exists\n if (!this.options.container) {\n console.log(\n \"ui-select::initialize() : container not specified.\"\n );\n return;\n }\n\n // add to dom\n this.options.container.append(this.$el);\n\n // link selection dictionary\n this.select_data = this.options.data;\n\n // refresh\n this._refresh();\n\n if (!this.options.multiple) {\n // initial value\n if (this.options.value) {\n this._setValue(this.options.value);\n }\n\n // add change event\n var self = this;\n if (this.options.onchange) {\n this.$el.on(\"change\", function() {\n self.options.onchange(self.value());\n });\n }\n }\n },\n\n // value\n value: function(new_value) {\n // get current id/value\n var before = this._getValue();\n\n // check if new_value is defined\n if (new_value !== undefined) {\n this._setValue(new_value);\n }\n\n // get current id/value\n var after = this._getValue();\n\n // fire onchange\n if (after != before && this.options.onchange) {\n this.options.onchange(after);\n }\n\n // return current value\n return after;\n },\n\n // label\n text: function() {\n return this.$el.select2(\"data\").text;\n },\n\n // disabled\n disabled: function() {\n return !this.$el.select2(\"enable\");\n },\n\n // enable\n enable: function() {\n this.$el.select2(\"enable\", true);\n },\n\n // disable\n disable: function() {\n this.$el.select2(\"enable\", false);\n },\n\n // add\n add: function(options) {\n // add options\n this.select_data.push({\n id: options.id,\n text: options.text\n });\n\n // refresh\n this._refresh();\n },\n\n // remove\n del: function(id) {\n // search option\n var index = this._getIndex(id);\n\n // check if found\n if (index != -1) {\n // remove options\n this.select_data.splice(index, 1);\n\n // refresh\n this._refresh();\n }\n },\n\n // remove\n remove: function() {\n this.$el.select2(\"destroy\");\n },\n\n // update\n update: function(options) {\n // copy options\n this.select_data = [];\n for (var key in options.data) {\n this.select_data.push(options.data[key]);\n }\n\n // refresh\n this._refresh();\n },\n\n // refresh\n _refresh: function() {\n // add select2 data based on type of input\n if (!this.options.multiple) 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value\n _getValue: function() {\n return this.$el.select2(\"val\");\n },\n\n // set value\n _setValue: function(new_value) {\n var index = this._getIndex(new_value);\n if (index == -1) {\n if (this.select_data.length > 0) {\n new_value = this.select_data[0].id;\n }\n }\n this.$el.select2(\"val\", new_value);\n },\n\n // element\n _template: function(options) {\n return (\n ''\n );\n }\n });\n\n return {\n View: View\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/ui/ui-slider.js.map b/static/maps/mvc/ui/ui-slider.js.map index dbcacbc40c5..abf0d4b6e8d 100644 --- a/static/maps/mvc/ui/ui-slider.js.map +++ b/static/maps/mvc/ui/ui-slider.js.map @@ -1 +1 @@ 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function(Utils) {\n var View = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n id: Utils.uid(),\n min: null,\n max: null,\n step: null,\n precise: false,\n split: 10000,\n value: null,\n onchange: function() {}\n }).set(options);\n\n // create new element\n this.setElement(this._template());\n this.$el.attr(\"id\", this.model.id);\n this.$text = this.$(\".ui-form-slider-text\");\n this.$slider = this.$(\".ui-form-slider-element\");\n\n // add text field event\n var pressed = [];\n this.$text\n .on(\"change\", function() {\n self.value($(this).val());\n })\n .on(\"keyup\", function(e) {\n pressed[e.which] = false;\n })\n .on(\"keydown\", function(e) {\n var v = e.which;\n pressed[v] = true;\n if (\n self.model.get(\"is_workflow\") &&\n pressed[16] &&\n v == 52\n ) {\n self.value(\"$\");\n event.preventDefault();\n } else if (\n !(\n v == 8 ||\n v == 9 ||\n v == 13 ||\n v == 37 ||\n v == 39 ||\n (v >= 48 && v <= 57 && !pressed[16]) ||\n (v >= 96 && v <= 105) ||\n ((v == 190 || v == 110) &&\n $(this)\n .val()\n .indexOf(\".\") == -1 &&\n self.model.get(\"precise\")) ||\n ((v == 189 || v == 109) &&\n $(this)\n .val()\n .indexOf(\"-\") == -1) ||\n self._isParameter($(this).val()) ||\n pressed[91] ||\n pressed[17]\n )\n ) {\n event.preventDefault();\n }\n });\n\n // build slider, cannot be rebuild in render\n var opts = this.model.attributes;\n this.has_slider =\n opts.max !== null && opts.min !== null && opts.max > opts.min;\n var step = opts.step;\n if (!step) {\n if (opts.precise && this.has_slider) {\n step = (opts.max - opts.min) / opts.split;\n } else {\n step = 1.0;\n }\n }\n if (this.has_slider) {\n this.$text.addClass(\"ui-form-slider-left\");\n this.$slider\n .slider({ min: opts.min, max: opts.max, step: step })\n .on(\"slide\", function(event, ui) {\n self.value(ui.value);\n });\n } else {\n this.$slider.hide();\n }\n\n // add listeners\n this.listenTo(this.model, \"change\", this.render, this);\n this.render();\n },\n\n render: function() {\n var value = this.model.get(\"value\");\n this.has_slider && this.$slider.slider(\"value\", value);\n value !== this.$text.val() && this.$text.val(value);\n },\n\n /** Set and return the current value */\n value: function(new_val) {\n var options = this.model.attributes;\n if (new_val !== undefined) {\n if (\n new_val !== null &&\n new_val !== \"\" &&\n !this._isParameter(new_val)\n ) {\n isNaN(new_val) && (new_val = 0);\n !options.precise && (new_val = Math.round(new_val));\n options.max !== null &&\n (new_val = Math.min(new_val, options.max));\n options.min !== null &&\n (new_val = Math.max(new_val, options.min));\n }\n this.model.set(\"value\", new_val);\n this.model.trigger(\"change\");\n options.onchange(new_val);\n }\n return this.model.get(\"value\");\n },\n\n /** Return true if the field contains a workflow parameter i.e. $('name') */\n _isParameter: function(value) {\n 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This class creates a ui table element. */\ndefine([\"utils/utils\"], function(Utils) {\n var View = Backbone.View.extend({\n initialize: function(options) {\n this.options = Utils.merge(options, {\n content: \"No content available.\",\n onchange: null,\n ondblclick: null,\n onconfirm: null,\n cls: \"ui-table\",\n selectable: true,\n cls_tr: \"\"\n });\n this.setElement(this._template());\n this.$thead = this.$(\"thead\");\n this.$tbody = this.$(\"tbody\");\n this.$tmessage = this.$(\"tmessage\");\n this.row = this._row();\n this.row_count = 0;\n },\n\n events: {\n click: \"_onclick\",\n dblclick: \"_ondblclick\"\n },\n\n /** Add cell to header row */\n addHeader: function($el) {\n this.row.append($(\"\").append($el));\n },\n\n /** Append header row to table */\n appendHeader: function() {\n this.$thead.append(this.row);\n this.row = $(\" \");\n },\n\n /** Add cell to row */\n add: function($el, width, align) {\n var wrapper = $(\" \");\n if (width) {\n wrapper.css(\"width\", width);\n }\n if (align) {\n wrapper.css(\"text-align\", align);\n }\n this.row.append(wrapper.append($el));\n },\n\n /** Append row to table */\n append: function(id, fade) {\n this._commit(id, fade, false);\n },\n\n /** Prepend row to table */\n prepend: function(id, fade) {\n this._commit(id, fade, true);\n },\n\n /** Helper to get row element */\n get: function(id) {\n return this.$(\"#\" + id);\n },\n\n /** Delete row by id */\n del: function(id) {\n var item = this.$tbody.find(\"#\" + id);\n if (item.length > 0) {\n item.remove();\n this.row_count--;\n this._refresh();\n }\n },\n\n /** Delete all rows */\n delAll: function() {\n this.$tbody.empty();\n this.row_count = 0;\n this._refresh();\n },\n\n /** Set a value i.e. selects/highlights a particular row by id */\n value: function(new_value) {\n if (this.options.selectable) {\n this.before = this.$tbody.find(\".current\").attr(\"id\");\n if (new_value !== undefined) {\n this.$tbody.find(\"tr\").removeClass(\"current\");\n if (new_value) 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(new_value != \"\") {\n if (new_value && old_value != new_value) {\n if (this.options.onconfirm) {\n this.options.onconfirm(new_value);\n } else {\n this.value(new_value);\n }\n }\n }\n },\n\n /** Handles ondblclick events */\n _ondblclick: function(e) {\n var value = this.value();\n if (value && this.options.ondblclick) {\n this.options.ondblclick(value);\n }\n },\n\n /** Refresh helper */\n _refresh: function() {\n if (this.row_count == 0) {\n this.$tmessage.show();\n } else {\n this.$tmessage.hide();\n }\n },\n\n /** Template */\n _template: function() {\n return (\n \" \" +\n '' +\n \"\" +\n \"\" +\n \"
\" +\n \"\" +\n this.options.content +\n \" \" +\n \"\"\n );\n }\n });\n\n return {\n View: View\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/ui/ui-tabs.js.map b/static/maps/mvc/ui/ui-tabs.js.map index 3b1a83d5ec0..12e8792ecfa 100644 --- a/static/maps/mvc/ui/ui-tabs.js.map +++ b/static/maps/mvc/ui/ui-tabs.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/ui/ui-tabs.js"],"names":["define","Utils","View","Backbone","extend","initialize","options","this","self","collection","model","onchange","visible","setElement","$","_template","$nav","$content","$el","on","hide","render","listenTo","_add","_remove","_change","_reset","id","get","addClass","first","removeClass","size","current","show","set","add","del","remove","delAll","reset","showTab","hideTab","title","placement","container","append","e","preventDefault","_template_tab","tooltip","tab_model","$tmpl","empty","attr","$href","find","icon"],"mappings":"aAGAA,QAAQ,eAAgB,SAASC,GAgL7B,OAASC,KA/KEC,SAASD,KAAKE,QADrBC,WAAA,SAAgBC,GAEhBD,KAAAA,WAAY,IAAAF,SAASG,WACjBC,KAAIC,MACCC,GAALH,EAAsBH,OACtB,IAAKO,SACAJ,OAEGK,SADe,KAEfC,SAAS,IACNN,IAAAA,GACXC,KAAKM,WAAWC,EAAEP,KAAKQ,cACvBR,KAAKS,KAAOT,KAAKO,EAAE,mBACnBP,KAAKU,SAAWV,KAAKO,EAAE,gBACvBP,KAAKW,IAAIC,GAAG,QAAS,WACjBL,EAAE,YAAYM,SAElBb,KAAKc,SACLd,KAAKe,SAASf,KAAKG,MAAO,SAAUH,KAAKc,OAAQd,MACjDA,KAAKe,SAASf,KAAKE,WAAY,MAAOF,KAAKgB,KAAMhB,MACjDA,KAAKe,SAASf,KAAKE,WAAY,SAAUF,KAAKiB,QAASjB,MACvDA,KAAKe,SAASf,KAAKE,WAAY,SAAUF,KAAKkB,QAASlB,MACvDA,KAAKe,SAASf,KAAKE,WAAY,QAASF,KAAKmB,OAAQnB,MACrDA,KAAKe,SAtBmBf,KAAAE,WAwBpB,mBAMAF,KAAAc,OACAM,OAIAN,OAAA,WACA,IAAAM,EAAKb,KAAEJ,MAAAkB,IAAP,YACAD,EAAApB,KAAAO,EAAO,IAAMa,GAAIE,OAAS,EAAAF,EAA1BpB,KAAAuB,WAEJvB,KAASS,KAAKN,WAAUqB,YAAa,UACrCxB,KAAAU,SAAee,WAAaD,YAAS,UAxCbxB,KAAAO,EAAA,QAAAa,GAAAE,SAAA,UAqCpBtB,KAAKO,EAAE,IAAMa,GAAIE,SAAS,WAOlCI,KAASf,IAAAX,KAAAG,MAAAkB,IAAW,WAAA,SAAA,WAAA,QAChBrB,KAAAS,KAAOT,KAAKG,OAAU,EAAA,OAAtB,WAIJwB,QAAM,WACF,OAAA3B,KAAQG,MAAAkB,IAAA,YAIXM,KAtD2B,SAAAP,GAkDpBA,IAMRpB,KAAAG,MAAAyB,KAAAF,QAAAN,EAAAf,SAAA,IACML,KAAAG,MAAAkB,IAAW,aAAArB,KAAAG,MAAAkB,IAAA,WAAArB,CAAAoB,KAKjBG,KAAAA,WACIvB,KAAIG,MAAAA,IAAQ,WAAKD,IAIrBqB,MAAA,WACAE,IAAMtB,EAAAH,KAAAE,WAAWqB,QACb,OAAOpB,GAAKD,EAALkB,IAIXS,KAAK,WACD,OAAK3B,KAAAA,WAAeH,QAIxB+B,IAAK,SAAA/B,GACDC,KAAKE,WAAW6B,IAAAA,IAIpBC,IAAAA,SAAQZ,GACJpB,KAAKE,WAAW+B,OAAhBb,IAIJc,OAAAA,WACIlC,KAAKE,WAAWmB,SAIpBc,QAAS,SAAAf,GACLpB,KAAKE,WAAWmB,IAAID,GAAIQ,IAAI,UAAU,IAI1CZ,QAAM,SAAAI,GACFpB,KAAIC,WAAJoB,IAAAD,GAAAQ,IAAA,UAAA,IAYYQ,KAAAA,SAAOrC,GACPsC,IAAAA,EAAAA,KACAC,EAAAA,EAAgB3B,WAHXX,KAFbU,SAAA6B,OAQQC,EAAEC,UACGd,KAAK5B,KAAAA,EAAVqB,IAVZE,SAAA,YAaSG,OAAL1B,EAAkBY,MAErBX,KAAAS,KAAA8B,OA1HuBhC,EAAAP,KAAA0C,cAAA3C,IA6Gf4B,OAgBbgB,SACSP,MAAArC,EAAS6C,QACPP,UAAUO,SACVN,UAAgBlB,EAAIW,MAblBnB,GAAG,QAAS,SAAS4B,GAgBlCA,EAAAC,iBACQxC,EAAA0B,KAAW5B,EAAAqB,OApIS,GAAApB,KAAAyB,QAyHpBzB,KAAK2B,KAAK5B,EAAQqB,KAK1BH,QAAS,SAAS2B,GAkBlB5C,KAAAO,EAAA,QAAAqC,EAAAxB,IAAAW,SACAvB,KAAAA,EAAW,IAAAoC,EAAAxB,IAAAW,UAOXZ,OAAA,WACAuB,KAAAA,KAAAA,QACI1C,KAAI6C,SAAUC,SAiBd5B,QAAA,SAAA0B,GACH5C,KAAAO,EAAA,QAAAqC,EAAAxB,IA5KLwB,EAAAvB,IAAA,UAAA,OAAA,WAiJIb,UAAW,WACP,OAAOD,EAAE,UACJe,SAAS,8BACTiB,OAAOhC,EAAE,SAASe,SAAS,gCAC3BiB,OAAOhC,EAAE,UAAUe,SAAS,iBAIrCoB,cAAe,SAAS3C,GACpB,IAAI8C,EAAQtC,EAAE,SACTe,SAAS,eACTyB,KAAK,KAAM,OAAShD,EAAQqB,IAC5BmB,OAAOhC,EAAE,QAAQwC,KAAK,KAAM,kBAAoBhD,EAAQqB,KACzD4B,EAAQH,EAAMI,KAAK,KAavB,OAZAlD,EAAQmD,MACJF,EAAMT,OACFhC,EAAE,QACGe,SAAS,eACTA,SAASvB,EAAQmD,OAE9BF,EAAMT,OACFhC,EAAE,WACGwC,KAAK,KAAM,kBAAoBhD,EAAQqB,IACvCE,SAAS,kBACTiB,OAAOxC,EAAQqC,QAEjBS","file":"../../../scripts/mvc/ui/ui-tabs.js","sourcesContent":["/**\n * Renders tabs e.g. used in the charts editor, behaves similar to repeat and section rendering\n */\ndefine([\"utils/utils\"], function(Utils) {\n var View = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.collection = new Backbone.Collection();\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n onchange: null,\n visible: true\n }).set(options);\n this.setElement($(this._template()));\n this.$nav = this.$(\".tab-navigation\");\n this.$content = this.$(\".tab-content\");\n this.$el.on(\"click\", function() {\n $(\".tooltip\").hide();\n });\n this.render();\n this.listenTo(this.model, \"change\", this.render, this);\n this.listenTo(this.collection, \"add\", this._add, this);\n this.listenTo(this.collection, \"remove\", this._remove, this);\n this.listenTo(this.collection, \"change\", this._change, this);\n this.listenTo(this.collection, \"reset\", this._reset, this);\n this.listenTo(\n this.collection,\n \"add remove reset\",\n this.render,\n this\n );\n },\n\n render: function() {\n var id = this.model.get(\"current\");\n id = this.$(\"#\" + id).length > 0 ? id : this.first();\n if (id) {\n this.$nav.children().removeClass(\"active\");\n this.$content.children().removeClass(\"active\");\n this.$(\"#tab-\" + id).addClass(\"active\");\n this.$(\"#\" + id).addClass(\"active\");\n }\n this.$el[this.model.get(\"visible\") ? \"fadeIn\" : \"fadeOut\"](\"fast\");\n this.$nav[this.size() > 1 ? \"show\" : \"hide\"]();\n },\n\n /** Returns tab id for currently shown tab */\n current: function() {\n return this.model.get(\"current\");\n },\n\n /** Show tab view and highlight a tab by id */\n show: function(id) {\n if (id) {\n this.model.set({ current: id, visible: true });\n this.model.get(\"onchange\") && this.model.get(\"onchange\")(id);\n }\n },\n\n /** Hide tab view */\n hide: function() {\n this.model.set(\"visible\", false);\n },\n\n /** Returns first tab */\n first: function() {\n var model = this.collection.first();\n return model && model.id;\n },\n\n /** Returns current number of tabs */\n size: function() {\n return this.collection.length;\n },\n\n /** Adds a new tab */\n add: function(options) {\n this.collection.add(options);\n },\n\n /** Delete tab */\n del: function(id) {\n this.collection.remove(id);\n },\n\n /** Delete all tabs */\n delAll: function() {\n this.collection.reset();\n },\n\n /** Show tab */\n showTab: function(id) {\n this.collection.get(id).set(\"hidden\", false);\n },\n\n /** Hide tab */\n hideTab: function(id) {\n this.collection.get(id).set(\"hidden\", true);\n },\n\n /** Adds a new tab */\n _add: function(tab_model) {\n var self = this;\n var options = tab_model.attributes;\n this.$content.append(\n $(\"\")\n .attr(\"id\", options.id)\n .addClass(\"tab-pane\")\n .append(options.$el)\n );\n this.$nav.append(\n $(this._template_tab(options))\n .show()\n .tooltip({\n title: options.tooltip,\n placement: \"bottom\",\n container: self.$el\n })\n .on(\"click\", function(e) {\n e.preventDefault();\n self.show(options.id);\n })\n );\n if (this.size() == 1) {\n this.show(options.id);\n }\n },\n\n /** Delete tab */\n _remove: function(tab_model) {\n this.$(\"#tab-\" + tab_model.id).remove();\n this.$(\"#\" + tab_model.id).remove();\n },\n\n /** Reset collection */\n _reset: function() {\n this.$nav.empty();\n this.$content.empty();\n },\n\n /** Change tab */\n _change: function(tab_model) {\n this.$(\"#tab-\" + tab_model.id)[\n tab_model.get(\"hidden\") ? \"hide\" : \"show\"\n ]();\n },\n\n /** Main template */\n _template: function() {\n return $(\"\")\n .addClass(\"ui-tabs tabbable tabs-left\")\n .append($(\"' +\n '' +\n '
' +\n '' +\n options.title +\n \"\" +\n \"\"\n );\n },\n\n /* Thumbnail template with image and description */\n _templateRegularItem: function(options) {\n return (\n '' +\n \"\" +\n \"
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title\n : title.substr(0, title_length) + \"...\",\n title_icon: model.get(\"title_icon\"),\n image_src: model.get(\"image_src\")\n })\n ).tooltip({\n title: model.get(\"description\"),\n placement: \"bottom\"\n })\n );\n }\n });\n if ($el.children().length > 0) {\n this.tabs.add({\n id: Utils.uid(),\n title: self.model.get(\"title_default\"),\n $el: $el\n });\n }\n },\n\n _renderList: function() {\n var self = this;\n if (this.collection.length > 0) {\n this.first = this.first || this.collection.first().id;\n var $el = $(\"\").addClass(\"ui-thumbnails-grid\");\n this.collection.each(function(model) {\n $el.append(self._templateRegularItem(model.attributes));\n });\n this.tabs.add({\n id: Utils.uid(),\n title: self.model.get(\"title_list\"),\n $el: $el\n });\n }\n },\n\n /** Set/Get value */\n value: function(new_value) {\n if (new_value !== undefined) {\n new_value = new_value == \"__first\" ? this.first : new_value;\n var before = this.$(\".ui-thumbnail-current\").attr(\"value\");\n this.$(\".ui-thumbnail-current\").removeClass(\n \"ui-thumbnail-current\"\n );\n this.$('[value=\"' + new_value + '\"]').addClass(\n \"ui-thumbnail-current\"\n );\n var after = this.$(\".ui-thumbnail-current\").attr(\"value\");\n var change_handler = this.model.get(\"onchange\");\n after != before && change_handler && change_handler(after);\n }\n return this.$(\".ui-thumbnail-current\").attr(\"value\");\n },\n\n /** Add click handler */\n _onclick: function(e) {\n this.value(\n $(e.target)\n .closest(\".ui-thumbnails-item\")\n .attr(\"value\")\n );\n },\n\n /** Add double click handler */\n _ondblclick: function(e) {\n this.model.get(\"ondblclick\") &&\n this.model.get(\"ondblclick\")(this.value());\n },\n\n /* Thumbnail template with image */\n _templateThumbnailItem: function(options) {\n return (\n '' +\n '' +\n '' +\n options.title +\n \"\" +\n \"\"\n );\n },\n\n /* Thumbnail template with image and description */\n _templateRegularItem: function(options) {\n return (\n '' +\n \"\" +\n \"
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Renders the collection uploader rows */\nimport Utils from \"utils/utils\";\nimport UploadModel from \"mvc/upload/upload-model\";\nimport UploadSettings from \"mvc/upload/upload-settings\";\nimport Popover from \"mvc/ui/ui-popover\";\nimport Select from \"mvc/ui/ui-select\";\nexport default Backbone.View.extend({\n /** Dictionary of upload states and associated icons */\n status_classes: {\n init: \"upload-icon-button fa fa-trash-o\",\n queued: \"upload-icon fa fa-spinner fa-spin\",\n running: \"upload-icon fa fa-spinner fa-spin\",\n success: \"upload-icon-button fa fa-check\",\n error: \"upload-icon-button fa fa-exclamation-triangle\"\n },\n\n initialize: function(app, options) {\n var self = this;\n this.app = app;\n this.model = options.model;\n this.setElement(this._template(options.model));\n this.$mode = this.$(\".upload-mode\");\n this.$title = this.$(\".upload-title-extended\");\n this.$text = this.$(\".upload-text\");\n this.$size = this.$(\".upload-size\");\n this.$info_text = this.$(\".upload-info-text\");\n this.$info_progress = this.$(\".upload-info-progress\");\n this.$text_content = this.$(\".upload-text-content\");\n this.$symbol = this.$(\".upload-symbol\");\n this.$progress_bar = this.$(\".upload-progress-bar\");\n this.$percentage = this.$(\".upload-percentage\");\n\n // append popup to settings icon\n this.settings = new Popover.View({\n title: \"Upload configuration\",\n container: this.$(\".upload-settings\"),\n placement: \"bottom\"\n });\n\n // identify default genome and extension values\n var default_genome = this.app.select_genome.value();\n var default_extension = this.app.select_extension.value();\n\n // handle click event\n this.$symbol.on(\"click\", function() {\n self._removeRow();\n });\n\n // handle text editing event\n this.$text_content.on(\"change input\", function(e) {\n self.model.set({\n url_paste: $(e.target).val(),\n file_size: $(e.target).val().length\n });\n });\n\n // model events\n this.listenTo(this.model, \"change:percentage\", function() {\n self._refreshPercentage();\n });\n this.listenTo(this.model, \"change:status\", function() {\n self._refreshStatus();\n });\n this.listenTo(this.model, \"change:info\", function() {\n self._refreshInfo();\n });\n this.listenTo(this.model, \"change:file_size\", function() {\n self._refreshFileSize();\n });\n this.listenTo(this.model, \"remove\", function() {\n self.remove();\n });\n this.app.collection.on(\"reset\", function() {\n self.remove();\n });\n },\n\n render: function() {\n var options = this.model.attributes;\n this.$title.html(_.escape(options.file_name));\n this.$size.html(Utils.bytesToString(options.file_size));\n this.$mode\n .removeClass()\n .addClass(\"upload-mode\")\n .addClass(\"text-primary\");\n if (options.file_mode == \"new\") {\n this.$text\n .css({\n width: this.$el.width() - 16 + \"px\",\n top: this.$el.height() - 8 + \"px\"\n })\n .show();\n this.$el.height(this.$el.height() - 8 + this.$text.height() + 16);\n 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Renders the collection uploader rows */\nimport Utils from \"utils/utils\";\nimport UploadModel from \"mvc/upload/upload-model\";\nimport UploadSettings from \"mvc/upload/upload-settings\";\nimport Popover from \"mvc/ui/ui-popover\";\nimport Select from \"mvc/ui/ui-select\";\nexport default Backbone.View.extend({\n /** Dictionary of upload states and associated icons */\n status_classes: {\n init: \"upload-icon-button fa fa-trash-o\",\n queued: \"upload-icon fa fa-spinner fa-spin\",\n running: \"upload-icon fa fa-spinner fa-spin\",\n success: \"upload-icon-button fa fa-check\",\n error: \"upload-icon-button fa fa-exclamation-triangle\"\n },\n\n initialize: function(app, options) {\n var self = this;\n this.app = app;\n this.model = options.model;\n this.setElement(this._template(options.model));\n this.$mode = this.$(\".upload-mode\");\n this.$title = this.$(\".upload-title-extended\");\n this.$text = this.$(\".upload-text\");\n this.$size = this.$(\".upload-size\");\n this.$info_text = this.$(\".upload-info-text\");\n this.$info_progress = this.$(\".upload-info-progress\");\n this.$text_content = this.$(\".upload-text-content\");\n this.$symbol = this.$(\".upload-symbol\");\n this.$progress_bar = this.$(\".upload-progress-bar\");\n this.$percentage = this.$(\".upload-percentage\");\n\n // append popup to settings icon\n this.settings = new Popover.View({\n title: \"Upload configuration\",\n container: this.$(\".upload-settings\"),\n placement: \"bottom\"\n });\n\n // identify default genome and extension values\n var default_genome = this.app.select_genome.value();\n var default_extension = this.app.select_extension.value();\n\n // handle click event\n this.$symbol.on(\"click\", function() {\n self._removeRow();\n });\n\n // handle text editing event\n this.$text_content.on(\"change input\", function(e) {\n self.model.set({\n url_paste: $(e.target).val(),\n file_size: $(e.target).val().length\n });\n });\n\n // model events\n this.listenTo(this.model, \"change:percentage\", function() {\n self._refreshPercentage();\n });\n this.listenTo(this.model, \"change:status\", function() {\n self._refreshStatus();\n });\n this.listenTo(this.model, \"change:info\", function() {\n self._refreshInfo();\n });\n this.listenTo(this.model, \"change:file_size\", function() {\n self._refreshFileSize();\n });\n this.listenTo(this.model, \"remove\", function() {\n self.remove();\n });\n this.app.collection.on(\"reset\", function() {\n self.remove();\n });\n },\n\n render: function() {\n var options = this.model.attributes;\n this.$title.html(_.escape(options.file_name));\n this.$size.html(Utils.bytesToString(options.file_size));\n this.$mode\n .removeClass()\n .addClass(\"upload-mode\")\n .addClass(\"text-primary\");\n if (options.file_mode == \"new\") {\n this.$text\n .css({\n width: this.$el.width() - 16 + \"px\",\n top: this.$el.height() - 8 + \"px\"\n })\n .show();\n this.$el.height(this.$el.height() - 8 + this.$text.height() + 16);\n 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this.model.get(\"enabled\");\n this.$text_content.attr(\"disabled\", !enabled);\n if (status == \"success\") {\n this.$el.addClass(\"success\");\n this.$percentage.html(\"100%\");\n }\n if (status == \"error\") {\n this.$el.addClass(\"danger\");\n this.$info_progress.hide();\n }\n },\n\n /** Refresh file size */\n _refreshFileSize: function() {\n this.$size.html(Utils.bytesToString(this.model.get(\"file_size\")));\n },\n\n /** Remove row */\n _removeRow: function() {\n if (\n [\"init\", \"success\", \"error\"].indexOf(this.model.get(\"status\")) !==\n -1\n ) {\n this.app.collection.remove(this.model);\n }\n },\n\n /** Attach file info popup */\n _showSettings: function() {\n if (!this.settings.visible) {\n this.settings.empty();\n this.settings.append(new UploadSettings(this).$el);\n this.settings.show();\n } else {\n this.settings.hide();\n }\n },\n\n /** View template */\n _template: function(options) {\n return (\n '\" +\n ' \" +\n \"' +\n '' +\n '' +\n '\" +\n \"' +\n '\" +\n \"You 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You can also directly paste the contents of a file.' +\n '' +\n \"\" +\n ' \" +\n \"' +\n \"\" +\n ' \" +\n \"' +\n '' +\n '\" +\n \"' +\n '' +\n '\" +\n \"0%' +\n \"\" +\n '' +\n \" \" +\n \"' +\n \" \"\n );\n }\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/upload/collection/collection-view.js.map b/static/maps/mvc/upload/collection/collection-view.js.map index d258aeac65f..c56201602de 100644 --- a/static/maps/mvc/upload/collection/collection-view.js.map +++ b/static/maps/mvc/upload/collection/collection-view.js.map @@ -1 +1 @@ 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Renders contents of the collection uploader */\nimport Utils from \"utils/utils\";\nimport UploadModel from \"mvc/upload/upload-model\";\nimport UploadRow from \"mvc/upload/collection/collection-row\";\nimport UploadFtp from \"mvc/upload/upload-ftp\";\nimport UploadExtension from \"mvc/upload/upload-extension\";\nimport Popover from \"mvc/ui/ui-popover\";\nimport Select from \"mvc/ui/ui-select\";\nimport Ui from \"mvc/ui/ui-misc\";\nimport LIST_COLLECTION_CREATOR from \"mvc/collection/list-collection-creator\";\nimport \"utils/uploadbox\";\nexport default Backbone.View.extend({\n // current upload size in bytes\n upload_size: 0,\n\n // contains upload row models\n collection: new UploadModel.Collection(),\n\n // keeps track of the current uploader state\n counter: {\n announce: 0,\n success: 0,\n error: 0,\n running: 0,\n reset: function() {\n this.announce = this.success = this.error = this.running = 0;\n }\n },\n\n initialize: function(app) {\n var self = this;\n this.app = app;\n this.options = app.options;\n this.list_extensions = app.list_extensions;\n this.list_genomes = app.list_genomes;\n this.ui_button = app.ui_button;\n this.ftp_upload_site = app.currentFtp();\n this.setElement(this._template());\n\n // append buttons to dom\n this.btnLocal = new Ui.Button({\n id: \"btn-local\",\n title: \"Choose local files\",\n onclick: function() {\n self.uploadbox.select();\n },\n icon: \"fa fa-laptop\"\n });\n this.btnFtp = new Ui.Button({\n id: \"btn-ftp\",\n title: \"Choose FTP files\",\n onclick: function() {\n self._eventFtp();\n },\n icon: \"fa fa-folder-open-o\"\n });\n this.btnCreate = new Ui.Button({\n id: \"btn-new\",\n title: \"Paste/Fetch data\",\n onclick: function() {\n self._eventCreate();\n },\n icon: \"fa fa-edit\"\n });\n this.btnStart = new Ui.Button({\n id: \"btn-start\",\n title: \"Start\",\n onclick: function() {\n self._eventStart();\n }\n });\n this.btnBuild = new Ui.Button({\n id: \"btn-build\",\n title: \"Build\",\n onclick: function() {\n self._eventBuild();\n }\n });\n this.btnStop = new Ui.Button({\n id: \"btn-stop\",\n title: \"Pause\",\n onclick: function() {\n self._eventStop();\n }\n });\n this.btnReset = new Ui.Button({\n id: \"btn-reset\",\n title: \"Reset\",\n onclick: function() {\n self._eventReset();\n }\n });\n this.btnClose = new Ui.Button({\n id: \"btn-close\",\n title: \"Close\",\n onclick: function() {\n self.app.modal.hide();\n }\n });\n _.each(\n [\n this.btnLocal,\n this.btnFtp,\n this.btnCreate,\n this.btnStop,\n this.btnReset,\n this.btnStart,\n this.btnBuild,\n this.btnClose\n ],\n function(button) {\n self.$(\".upload-buttons\").prepend(button.$el);\n }\n );\n\n // file upload\n this.uploadbox = this.$(\".upload-box\").uploadbox({\n url: this.app.options.nginx_upload_path,\n announce: function(index, file) {\n self._eventAnnounce(index, file);\n },\n initialize: function(index) {\n return self.app.toData(\n [self.collection.get(index)],\n self.history_id\n );\n },\n progress: function(index, percentage) {\n self._eventProgress(index, percentage);\n },\n success: function(index, message) {\n self._eventSuccess(index, message);\n },\n error: function(index, message) {\n self._eventError(index, message);\n },\n complete: function() {\n self._eventComplete();\n },\n ondragover: function() {\n self.$(\".upload-box\").addClass(\"highlight\");\n },\n ondragleave: function() {\n self.$(\".upload-box\").removeClass(\"highlight\");\n }\n });\n\n // add ftp file viewer\n this.ftp = new Popover.View({\n title: \"FTP files\",\n container: this.btnFtp.$el\n });\n\n // select extension\n this.select_extension = new Select.View({\n css: \"upload-footer-selection-compressed\",\n container: this.$(\".upload-footer-extension\"),\n data: _.filter(this.list_extensions, function(ext) {\n return !ext.composite_files;\n }),\n value: this.options.default_extension,\n onchange: function(extension) {\n self.updateExtension(extension);\n }\n });\n\n this.collectionType = \"list\";\n this.select_collection = new Select.View({\n css: \"upload-footer-selection-compressed\",\n container: this.$(\".upload-footer-collection-type\"),\n data: [\n { id: \"list\", text: \"List\" },\n { id: \"paired\", text: \"Paired\" },\n { id: \"list:paired\", text: \"List of Pairs\" }\n ],\n value: \"list\",\n onchange: function(collectionType) {\n self.updateCollectionType(collectionType);\n }\n });\n\n // handle extension info popover\n this.$(\".upload-footer-extension-info\")\n .on(\"click\", function(e) {\n new UploadExtension({\n $el: $(e.target),\n title: self.select_extension.text(),\n extension: self.select_extension.value(),\n list: self.list_extensions,\n placement: \"top\"\n });\n })\n .on(\"mousedown\", function(e) {\n e.preventDefault();\n });\n\n // genome extension\n this.select_genome = new Select.View({\n css: \"upload-footer-selection\",\n container: this.$(\".upload-footer-genome\"),\n data: this.list_genomes,\n value: this.options.default_genome,\n onchange: function(genome) {\n self.updateGenome(genome);\n }\n });\n\n // events\n this.collection.on(\"remove\", function(model) {\n self._eventRemove(model);\n });\n this._updateScreen();\n },\n\n /** A new file has been dropped/selected through the uploadbox plugin */\n _eventAnnounce: function(index, file) {\n this.counter.announce++;\n var new_model = new UploadModel.Model({\n id: index,\n file_name: file.name,\n file_size: file.size,\n file_mode: file.mode || \"local\",\n file_path: file.path,\n file_data: file,\n extension: this.select_extension.value(),\n genome: this.select_genome.value()\n });\n this.collection.add(new_model);\n var upload_row = new UploadRow(this, { model: new_model });\n this.$(\".upload-table > tbody:first\").append(upload_row.$el);\n this._updateScreen();\n upload_row.render();\n },\n\n /** Progress */\n _eventProgress: function(index, percentage) {\n var it = this.collection.get(index);\n it.set(\"percentage\", percentage);\n this.ui_button.model.set(\n \"percentage\",\n this._uploadPercentage(percentage, it.get(\"file_size\"))\n );\n },\n\n /** Success */\n _eventSuccess: function(index, message) {\n // var hdaId = message[\"outputs\"][0][\"id\"];\n var hids = _.pluck(message[\"outputs\"], \"hid\");\n var it = this.collection.get(index);\n it.set({ percentage: 100, status: \"success\", hids: hids });\n this.ui_button.model.set(\n \"percentage\",\n this._uploadPercentage(100, it.get(\"file_size\"))\n );\n this.upload_completed += it.get(\"file_size\") * 100;\n this.counter.announce--;\n this.counter.success++;\n this._updateScreen();\n Galaxy.currHistoryPanel.refreshContents();\n },\n\n /** Error */\n _eventError: function(index, message) {\n var it = this.collection.get(index);\n it.set({ percentage: 100, status: \"error\", info: message });\n this.ui_button.model.set({\n percentage: this._uploadPercentage(100, it.get(\"file_size\")),\n status: \"danger\"\n });\n this.upload_completed += it.get(\"file_size\") * 100;\n this.counter.announce--;\n this.counter.error++;\n this._updateScreen();\n },\n\n /** Queue is done */\n _eventComplete: function() {\n this.collection.each(function(model) {\n model.get(\"status\") == \"queued\" && model.set(\"status\", \"init\");\n });\n this.counter.running = 0;\n this._updateScreen();\n },\n\n _eventBuild: function() {\n var allHids = [];\n _.forEach(this.collection.models, function(upload) {\n allHids.push.apply(allHids, upload.get(\"hids\"));\n });\n var models = _.map(allHids, function(hid) {\n return Galaxy.currHistoryPanel.collection.getByHid(hid);\n });\n var selection = new Galaxy.currHistoryPanel.collection.constructor(\n models\n );\n // I'm building the selection wrong because I need to set this historyId directly.\n selection.historyId = Galaxy.currHistoryPanel.collection.historyId;\n Galaxy.currHistoryPanel.buildCollection(\n this.collectionType,\n selection,\n true\n );\n this.counter.running = 0;\n this._updateScreen();\n this._eventReset();\n this.app.modal.hide();\n },\n\n /** Remove model from upload list */\n _eventRemove: function(model) {\n var status = model.get(\"status\");\n if (status == \"success\") {\n this.counter.success--;\n } else if (status == \"error\") {\n this.counter.error--;\n } else {\n this.counter.announce--;\n }\n this.uploadbox.remove(model.id);\n this._updateScreen();\n },\n\n //\n // events triggered by this view\n //\n\n /** Show/hide ftp popup */\n _eventFtp: function() {\n if (!this.ftp.visible) {\n this.ftp.empty();\n var self = this;\n this.ftp.append(\n new UploadFtp({\n collection: this.collection,\n ftp_upload_site: this.ftp_upload_site,\n onadd: function(ftp_file) {\n return self.uploadbox.add([\n {\n mode: \"ftp\",\n name: ftp_file.path,\n size: ftp_file.size,\n path: ftp_file.path\n }\n ]);\n },\n onremove: function(model_index) {\n self.collection.remove(model_index);\n }\n }).$el\n );\n this.ftp.show();\n } else {\n this.ftp.hide();\n }\n },\n\n /** Create a new file */\n _eventCreate: function() {\n this.uploadbox.add([{ name: \"New File\", size: 0, mode: \"new\" }]);\n },\n\n /** Start upload process */\n _eventStart: function() {\n if (this.counter.announce == 0 || this.counter.running > 0) {\n return;\n }\n var self = this;\n this.upload_size = 0;\n this.upload_completed = 0;\n this.collection.each(function(model) {\n if (model.get(\"status\") == \"init\") {\n model.set(\"status\", \"queued\");\n self.upload_size += model.get(\"file_size\");\n }\n });\n this.ui_button.model.set({ percentage: 0, status: \"success\" });\n this.counter.running = this.counter.announce;\n this.history_id = this.app.currentHistory();\n this.uploadbox.start();\n this._updateScreen();\n },\n\n /** Pause upload process */\n _eventStop: function() {\n if (this.counter.running > 0) {\n this.ui_button.model.set(\"status\", \"info\");\n $(\".upload-top-info\").html(\n \"Queue will pause after completing the current file...\"\n );\n this.uploadbox.stop();\n }\n },\n\n /** Remove all */\n _eventReset: function() {\n if (this.counter.running == 0) {\n this.collection.reset();\n this.counter.reset();\n this.uploadbox.reset();\n this.select_extension.value(this.options.default_extension);\n this.select_genome.value(this.options.default_genome);\n this.ui_button.model.set(\"percentage\", 0);\n this._updateScreen();\n }\n },\n\n /** Update extension for all models */\n updateExtension: function(extension, defaults_only) {\n var self = this;\n this.collection.each(function(model) {\n if (\n model.get(\"status\") == \"init\" &&\n (model.get(\"extension\") == self.options.default_extension ||\n !defaults_only)\n ) {\n model.set(\"extension\", extension);\n }\n });\n },\n\n /** Update collection type */\n updateCollectionType: function(collectionType) {\n var self = this;\n this.collectionType = collectionType;\n },\n\n /** Update genome for all models */\n updateGenome: function(genome, defaults_only) {\n var self = this;\n this.collection.each(function(model) {\n if (\n model.get(\"status\") == \"init\" &&\n (model.get(\"genome\") == self.options.default_genome ||\n !defaults_only)\n ) {\n model.set(\"genome\", genome);\n }\n });\n },\n\n /** Set screen */\n _updateScreen: function() {\n var message = \"\";\n if (this.counter.announce == 0) {\n if (this.uploadbox.compatible()) {\n message = \" \";\n } else {\n message =\n \"Browser does not support Drag & Drop. Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.\";\n }\n } else {\n if (this.counter.running == 0) {\n message =\n \"You added \" +\n this.counter.announce +\n \" file(s) to the queue. Add more files or click 'Start' to proceed.\";\n } else {\n message =\n \"Please wait...\" +\n this.counter.announce +\n \" out of \" +\n this.counter.running +\n \" remaining.\";\n }\n }\n this.$(\".upload-top-info\").html(message);\n var enable_reset =\n this.counter.running == 0 &&\n this.counter.announce + this.counter.success + this.counter.error >\n 0;\n var enable_start =\n this.counter.running == 0 && this.counter.announce > 0;\n var enable_build =\n this.counter.running == 0 &&\n this.counter.announce == 0 &&\n this.counter.success > 0 &&\n this.counter.error == 0;\n var enable_sources = this.counter.running == 0;\n var show_table =\n this.counter.announce + this.counter.success + this.counter.error >\n 0;\n this.btnReset[enable_reset ? \"enable\" : \"disable\"]();\n this.btnStart[enable_start ? \"enable\" : \"disable\"]();\n this.btnStart.$el[enable_start ? \"addClass\" : \"removeClass\"](\n \"btn-primary\"\n );\n this.btnBuild[enable_build ? \"enable\" : \"disable\"]();\n this.btnBuild.$el[enable_build ? \"addClass\" : \"removeClass\"](\n \"btn-primary\"\n );\n this.btnStop[this.counter.running > 0 ? \"enable\" : \"disable\"]();\n this.btnLocal[enable_sources ? \"enable\" : \"disable\"]();\n this.btnFtp[enable_sources ? \"enable\" : \"disable\"]();\n this.btnCreate[enable_sources ? \"enable\" : \"disable\"]();\n this.btnFtp.$el[this.ftp_upload_site ? \"show\" : \"hide\"]();\n this.$(\".upload-table\")[show_table ? \"show\" : \"hide\"]();\n this.$(\".upload-helper\")[show_table ? \"hide\" : \"show\"]();\n },\n\n /** Calculate percentage of all queued uploads */\n _uploadPercentage: function(percentage, size) {\n return (this.upload_completed + percentage * size) / this.upload_size;\n },\n\n /** Template */\n _template: function() {\n return (\n '\" +\n ' \" +\n \"' +\n '' +\n '' +\n '\" +\n \"' +\n '\" +\n \"You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.' +\n '' +\n \"\" +\n ' \" +\n \"' +\n \"\" +\n ' \" +\n \"' +\n '' +\n '\" +\n \"' +\n '' +\n '\" +\n \"0%' +\n \"\" +\n '' +\n \" \" +\n \"' +\n '' +\n '\" +\n '' +\n \"
' +\n '\" +\n '\" +\n '\"\n );\n }\n});\n"]} \ No newline at end of file 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self._eventBuild();\n }\n });\n this.btnStop = new Ui.Button({\n id: \"btn-stop\",\n title: \"Pause\",\n onclick: function() {\n self._eventStop();\n }\n });\n this.btnReset = new Ui.Button({\n id: \"btn-reset\",\n title: \"Reset\",\n onclick: function() {\n self._eventReset();\n }\n });\n this.btnClose = new Ui.Button({\n id: \"btn-close\",\n title: \"Close\",\n onclick: function() {\n self.app.modal.hide();\n }\n });\n _.each(\n [\n this.btnLocal,\n this.btnFtp,\n this.btnCreate,\n this.btnStop,\n this.btnReset,\n this.btnStart,\n this.btnBuild,\n this.btnClose\n ],\n function(button) {\n self.$(\".upload-buttons\").prepend(button.$el);\n }\n );\n\n // file upload\n this.uploadbox = this.$(\".upload-box\").uploadbox({\n url: this.app.options.nginx_upload_path,\n announce: function(index, file) {\n self._eventAnnounce(index, file);\n },\n initialize: function(index) {\n return self.app.toData(\n [self.collection.get(index)],\n self.history_id\n );\n },\n progress: function(index, percentage) {\n self._eventProgress(index, percentage);\n },\n success: function(index, message) {\n self._eventSuccess(index, message);\n },\n error: function(index, message) {\n self._eventError(index, message);\n },\n complete: function() {\n self._eventComplete();\n },\n ondragover: function() {\n self.$(\".upload-box\").addClass(\"highlight\");\n },\n ondragleave: function() {\n self.$(\".upload-box\").removeClass(\"highlight\");\n }\n });\n\n // add ftp file viewer\n this.ftp = new Popover.View({\n title: \"FTP files\",\n container: this.btnFtp.$el\n });\n\n // select extension\n this.select_extension = new Select.View({\n css: \"upload-footer-selection-compressed\",\n container: this.$(\".upload-footer-extension\"),\n data: _.filter(this.list_extensions, function(ext) {\n return !ext.composite_files;\n }),\n value: this.options.default_extension,\n onchange: function(extension) {\n self.updateExtension(extension);\n }\n });\n\n this.collectionType = \"list\";\n 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function(genome) {\n self.updateGenome(genome);\n }\n });\n\n // events\n this.collection.on(\"remove\", function(model) {\n self._eventRemove(model);\n });\n this._updateScreen();\n },\n\n /** A new file has been dropped/selected through the uploadbox plugin */\n _eventAnnounce: function(index, file) {\n this.counter.announce++;\n var new_model = new UploadModel.Model({\n id: index,\n file_name: file.name,\n file_size: file.size,\n file_mode: file.mode || \"local\",\n file_path: file.path,\n file_data: file,\n extension: this.select_extension.value(),\n genome: this.select_genome.value()\n });\n this.collection.add(new_model);\n var upload_row = new UploadRow(this, { model: new_model });\n this.$(\".upload-table > tbody:first\").append(upload_row.$el);\n this._updateScreen();\n upload_row.render();\n },\n\n /** Progress */\n _eventProgress: function(index, percentage) {\n var it = this.collection.get(index);\n it.set(\"percentage\", percentage);\n this.ui_button.model.set(\n \"percentage\",\n this._uploadPercentage(percentage, it.get(\"file_size\"))\n );\n },\n\n /** Success */\n _eventSuccess: function(index, message) {\n // var hdaId = message[\"outputs\"][0][\"id\"];\n var hids = _.pluck(message[\"outputs\"], \"hid\");\n var it = this.collection.get(index);\n it.set({ percentage: 100, status: \"success\", hids: hids });\n this.ui_button.model.set(\n \"percentage\",\n this._uploadPercentage(100, it.get(\"file_size\"))\n );\n this.upload_completed += it.get(\"file_size\") * 100;\n this.counter.announce--;\n this.counter.success++;\n this._updateScreen();\n Galaxy.currHistoryPanel.refreshContents();\n },\n\n /** Error */\n _eventError: function(index, message) {\n var it = this.collection.get(index);\n it.set({ percentage: 100, status: \"error\", info: message });\n this.ui_button.model.set({\n percentage: this._uploadPercentage(100, it.get(\"file_size\")),\n status: \"danger\"\n });\n this.upload_completed += it.get(\"file_size\") * 100;\n this.counter.announce--;\n this.counter.error++;\n this._updateScreen();\n },\n\n /** Queue is done */\n _eventComplete: function() {\n this.collection.each(function(model) {\n model.get(\"status\") == \"queued\" && model.set(\"status\", \"init\");\n });\n this.counter.running = 0;\n this._updateScreen();\n },\n\n _eventBuild: function() {\n var allHids = [];\n _.forEach(this.collection.models, function(upload) {\n allHids.push.apply(allHids, upload.get(\"hids\"));\n });\n var models = _.map(allHids, function(hid) {\n return Galaxy.currHistoryPanel.collection.getByHid(hid);\n });\n var selection = new Galaxy.currHistoryPanel.collection.constructor(\n models\n );\n // I'm building the selection wrong because I need to set this historyId directly.\n selection.historyId = Galaxy.currHistoryPanel.collection.historyId;\n Galaxy.currHistoryPanel.buildCollection(\n this.collectionType,\n selection,\n true\n );\n this.counter.running = 0;\n this._updateScreen();\n this._eventReset();\n this.app.modal.hide();\n },\n\n /** Remove model from upload list */\n _eventRemove: function(model) {\n var status = model.get(\"status\");\n if (status == \"success\") {\n this.counter.success--;\n } else if (status == \"error\") {\n this.counter.error--;\n } else {\n this.counter.announce--;\n }\n this.uploadbox.remove(model.id);\n this._updateScreen();\n },\n\n //\n // events triggered by this view\n //\n\n /** Show/hide ftp popup */\n _eventFtp: function() {\n if (!this.ftp.visible) {\n this.ftp.empty();\n var self = this;\n this.ftp.append(\n new UploadFtp({\n collection: this.collection,\n ftp_upload_site: this.ftp_upload_site,\n onadd: function(ftp_file) {\n return self.uploadbox.add([\n {\n mode: \"ftp\",\n name: ftp_file.path,\n size: ftp_file.size,\n path: ftp_file.path\n }\n ]);\n },\n onremove: function(model_index) {\n self.collection.remove(model_index);\n }\n }).$el\n );\n this.ftp.show();\n } else {\n this.ftp.hide();\n }\n },\n\n /** Create a new file */\n _eventCreate: function() {\n this.uploadbox.add([{ name: \"New File\", size: 0, mode: \"new\" }]);\n },\n\n /** Start upload process */\n _eventStart: function() {\n if (this.counter.announce == 0 || this.counter.running > 0) {\n return;\n }\n var self = this;\n this.upload_size = 0;\n this.upload_completed = 0;\n this.collection.each(function(model) {\n if (model.get(\"status\") == \"init\") {\n model.set(\"status\", \"queued\");\n self.upload_size += model.get(\"file_size\");\n }\n });\n this.ui_button.model.set({ percentage: 0, status: \"success\" });\n this.counter.running = this.counter.announce;\n this.history_id = this.app.currentHistory();\n this.uploadbox.start();\n this._updateScreen();\n },\n\n /** Pause upload process */\n _eventStop: function() {\n if (this.counter.running > 0) {\n this.ui_button.model.set(\"status\", \"info\");\n $(\".upload-top-info\").html(\n \"Queue will pause after completing the current file...\"\n );\n this.uploadbox.stop();\n }\n },\n\n /** Remove all */\n _eventReset: function() {\n if (this.counter.running == 0) {\n this.collection.reset();\n this.counter.reset();\n this.uploadbox.reset();\n this.select_extension.value(this.options.default_extension);\n this.select_genome.value(this.options.default_genome);\n this.ui_button.model.set(\"percentage\", 0);\n this._updateScreen();\n }\n },\n\n /** Update extension for all models */\n updateExtension: function(extension, defaults_only) {\n var self = this;\n this.collection.each(function(model) {\n if (\n model.get(\"status\") == \"init\" &&\n (model.get(\"extension\") == self.options.default_extension ||\n !defaults_only)\n ) {\n model.set(\"extension\", extension);\n }\n });\n },\n\n /** Update collection type */\n updateCollectionType: function(collectionType) {\n var self = this;\n this.collectionType = collectionType;\n },\n\n /** Update genome for all models */\n updateGenome: function(genome, defaults_only) {\n var self = this;\n this.collection.each(function(model) {\n if (\n model.get(\"status\") == \"init\" &&\n (model.get(\"genome\") == self.options.default_genome ||\n !defaults_only)\n ) {\n model.set(\"genome\", genome);\n }\n });\n },\n\n /** Set screen */\n _updateScreen: function() {\n var message = \"\";\n if (this.counter.announce == 0) {\n if (this.uploadbox.compatible()) {\n message = \" \";\n } else {\n message =\n \"Browser does not support Drag & Drop. 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Add more files or click 'Start' to proceed.\";\n } else {\n message =\n \"Please wait...\" +\n this.counter.announce +\n \" out of \" +\n this.counter.running +\n \" remaining.\";\n }\n }\n this.$(\".upload-top-info\").html(message);\n var enable_reset =\n this.counter.running == 0 &&\n this.counter.announce + this.counter.success + this.counter.error >\n 0;\n var enable_start =\n this.counter.running == 0 && this.counter.announce > 0;\n var enable_build =\n this.counter.running == 0 &&\n this.counter.announce == 0 &&\n this.counter.success > 0 &&\n this.counter.error == 0;\n var enable_sources = this.counter.running == 0;\n var show_table =\n this.counter.announce + this.counter.success + this.counter.error >\n 0;\n this.btnReset[enable_reset ? \"enable\" : \"disable\"]();\n this.btnStart[enable_start ? \"enable\" : \"disable\"]();\n this.btnStart.$el[enable_start ? \"addClass\" : \"removeClass\"](\n \"btn-primary\"\n );\n this.btnBuild[enable_build ? \"enable\" : \"disable\"]();\n this.btnBuild.$el[enable_build ? \"addClass\" : \"removeClass\"](\n \"btn-primary\"\n );\n this.btnStop[this.counter.running > 0 ? \"enable\" : \"disable\"]();\n this.btnLocal[enable_sources ? \"enable\" : \"disable\"]();\n this.btnFtp[enable_sources ? \"enable\" : \"disable\"]();\n this.btnCreate[enable_sources ? \"enable\" : \"disable\"]();\n this.btnFtp.$el[this.ftp_upload_site ? \"show\" : \"hide\"]();\n this.$(\".upload-table\")[show_table ? \"show\" : \"hide\"]();\n this.$(\".upload-helper\")[show_table ? \"hide\" : \"show\"]();\n },\n\n /** Calculate percentage of all queued uploads */\n _uploadPercentage: function(percentage, size) {\n return (this.upload_completed + percentage * size) / this.upload_size;\n },\n\n /** Template */\n _template: function() {\n return (\n 'Drop files here' +\n '' +\n \"\" +\n \"
\" +\n \"\" +\n \" \" +\n \"\" +\n \"\" +\n \"Name \" +\n \"Size \" +\n \"Status \" +\n \"\" +\n \" ' +\n '' +\n '\" +\n '' +\n \"
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Renders the composite upload row view */\nimport Utils from \"utils/utils\";\nimport UploadSettings from \"mvc/upload/upload-settings\";\nimport UploadFtp from \"mvc/upload/upload-ftp\";\nimport Popover from \"mvc/ui/ui-popover\";\nimport Ui from \"mvc/ui/ui-misc\";\nimport Select from \"mvc/ui/ui-select\";\nimport \"utils/uploadbox\";\nexport default Backbone.View.extend({\n /** Dictionary of upload states and associated icons */\n status_classes: {\n init: \"upload-mode fa fa-exclamation text-primary\",\n ready: \"upload-mode fa fa-check text-success\",\n running: \"upload-mode fa fa-spinner fa-spin\",\n success: \"upload-mode fa fa-check\",\n error: \"upload-mode fa fa-exclamation-triangle\"\n },\n\n initialize: function(app, options) {\n var self = this;\n this.app = app;\n this.model = options.model;\n this.setElement(this._template());\n this.$source = this.$(\".upload-source\");\n this.$settings = this.$(\".upload-settings\");\n this.$status = this.$(\".upload-status\");\n this.$text = this.$(\".upload-text\");\n this.$text_content = this.$(\".upload-text-content\");\n this.$info_text = this.$(\".upload-info-text\");\n this.$info_progress = this.$(\".upload-info-progress\");\n this.$file_name = this.$(\".upload-file-name\");\n this.$file_desc = this.$(\".upload-file-desc\");\n this.$file_size = this.$(\".upload-file-size\");\n this.$progress_bar = this.$(\".upload-progress-bar\");\n this.$percentage = this.$(\".upload-percentage\");\n\n // build upload functions\n this.uploadinput = this.$el.uploadinput({\n ondragover: function() {\n self.model.get(\"enabled\") && self.$el.addClass(\"warning\");\n },\n ondragleave: function() {\n self.$el.removeClass(\"warning\");\n },\n onchange: function(files) {\n if (\n self.model.get(\"status\") != \"running\" &&\n files &&\n files.length > 0\n ) {\n self.model.reset({\n file_data: files[0],\n file_name: files[0].name,\n file_size: files[0].size,\n file_mode: files[0].mode || \"local\"\n });\n self._refreshReady();\n }\n }\n });\n\n // source selection popup\n this.button_menu = new Ui.ButtonMenu({\n icon: \"fa-caret-down\",\n title: \"Select\",\n pull: \"left\"\n });\n this.$source.append(this.button_menu.$el);\n this.button_menu.addMenu({\n icon: \"fa-laptop\",\n title: \"Choose local file\",\n onclick: function() {\n self.uploadinput.dialog();\n }\n });\n if (this.app.ftp_upload_site) {\n this.button_menu.addMenu({\n icon: \"fa-folder-open-o\",\n title: \"Choose FTP file\",\n onclick: function() {\n self._showFtp();\n }\n });\n }\n this.button_menu.addMenu({\n icon: \"fa-edit\",\n title: \"Paste/Fetch data\",\n onclick: function() {\n self.model.reset({\n file_mode: \"new\",\n file_name: \"New File\"\n });\n }\n });\n\n // add ftp file viewer\n this.ftp = new Popover.View({\n title: \"Choose FTP file:\",\n container: this.$source.find(\".ui-button-menu\"),\n placement: \"right\"\n });\n\n // append popup to settings icon\n this.settings = new Popover.View({\n title: 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Renders the composite upload row view */\nimport Utils from \"utils/utils\";\nimport UploadSettings from \"mvc/upload/upload-settings\";\nimport UploadFtp from \"mvc/upload/upload-ftp\";\nimport Popover from \"mvc/ui/ui-popover\";\nimport Ui from \"mvc/ui/ui-misc\";\nimport Select from \"mvc/ui/ui-select\";\nimport \"utils/uploadbox\";\nexport default Backbone.View.extend({\n /** Dictionary of upload states and associated icons */\n status_classes: {\n init: \"upload-mode fa fa-exclamation text-primary\",\n ready: \"upload-mode fa fa-check text-success\",\n running: \"upload-mode fa fa-spinner fa-spin\",\n success: \"upload-mode fa fa-check\",\n error: \"upload-mode fa fa-exclamation-triangle\"\n },\n\n initialize: function(app, options) {\n var self = this;\n this.app = app;\n this.model = options.model;\n this.setElement(this._template());\n this.$source = this.$(\".upload-source\");\n this.$settings = this.$(\".upload-settings\");\n this.$status = this.$(\".upload-status\");\n this.$text = this.$(\".upload-text\");\n this.$text_content = this.$(\".upload-text-content\");\n this.$info_text = this.$(\".upload-info-text\");\n this.$info_progress = this.$(\".upload-info-progress\");\n this.$file_name = this.$(\".upload-file-name\");\n this.$file_desc = this.$(\".upload-file-desc\");\n this.$file_size = this.$(\".upload-file-size\");\n this.$progress_bar = this.$(\".upload-progress-bar\");\n this.$percentage = this.$(\".upload-percentage\");\n\n // build upload functions\n this.uploadinput = this.$el.uploadinput({\n ondragover: function() {\n self.model.get(\"enabled\") && self.$el.addClass(\"warning\");\n },\n ondragleave: function() {\n self.$el.removeClass(\"warning\");\n },\n onchange: function(files) {\n if (\n self.model.get(\"status\") != \"running\" &&\n files &&\n files.length > 0\n ) {\n self.model.reset({\n file_data: files[0],\n file_name: files[0].name,\n file_size: files[0].size,\n file_mode: files[0].mode || \"local\"\n });\n self._refreshReady();\n }\n }\n });\n\n // source selection popup\n this.button_menu = new Ui.ButtonMenu({\n icon: \"fa-caret-down\",\n title: \"Select\",\n pull: \"left\"\n });\n this.$source.append(this.button_menu.$el);\n this.button_menu.addMenu({\n icon: \"fa-laptop\",\n title: \"Choose local file\",\n onclick: function() {\n self.uploadinput.dialog();\n }\n });\n if (this.app.ftp_upload_site) {\n this.button_menu.addMenu({\n icon: \"fa-folder-open-o\",\n title: \"Choose FTP file\",\n onclick: function() {\n self._showFtp();\n }\n });\n }\n this.button_menu.addMenu({\n icon: \"fa-edit\",\n title: \"Paste/Fetch data\",\n onclick: function() {\n self.model.reset({\n file_mode: \"new\",\n file_name: \"New File\"\n });\n }\n });\n\n // add ftp file viewer\n this.ftp = new Popover.View({\n title: \"Choose FTP file:\",\n container: this.$source.find(\".ui-button-menu\"),\n placement: \"right\"\n });\n\n // append popup to settings icon\n this.settings = new Popover.View({\n title: \"Upload configuration\",\n container: this.$settings,\n placement: \"bottom\"\n });\n\n // handle text editing event\n this.$text_content.on(\"change input\", function(e) {\n self.model.set({\n url_paste: $(e.target).val(),\n file_size: $(e.target).val().length\n });\n self._refreshReady();\n });\n\n // handle settings popover\n this.$settings\n .on(\"click\", function(e) {\n self._showSettings();\n })\n .on(\"mousedown\", function(e) {\n e.preventDefault();\n });\n\n // model events\n this.listenTo(this.model, \"change:percentage\", function() {\n self._refreshPercentage();\n });\n this.listenTo(this.model, \"change:status\", function() {\n self._refreshStatus();\n });\n this.listenTo(this.model, \"change:info\", function() {\n self._refreshInfo();\n });\n this.listenTo(this.model, \"change:file_name\", function() {\n self._refreshFileName();\n });\n this.listenTo(this.model, \"change:file_mode\", function() {\n self._refreshMode();\n });\n this.listenTo(this.model, \"change:file_size\", function() {\n self._refreshFileSize();\n });\n this.listenTo(this.model, \"remove\", function() {\n self.remove();\n });\n this.app.collection.on(\"reset\", function() {\n self.remove();\n });\n },\n\n render: function() {\n this.$el.attr(\"id\", \"upload-row-\" + this.model.id);\n this.$file_name.html(_.escape(this.model.get(\"file_name\") || \"-\"));\n this.$file_desc.html(this.model.get(\"file_desc\") || \"Unavailable\");\n this.$file_size.html(Utils.bytesToString(this.model.get(\"file_size\")));\n this.$status.removeClass().addClass(this.status_classes.init);\n },\n\n /** Remove view */\n remove: function() {\n // call the base class remove method\n Backbone.View.prototype.remove.apply(this);\n },\n\n //\n // handle model events\n //\n\n /** Refresh ready or not states */\n _refreshReady: function() {\n this.app.collection.each(function(model) {\n model.set(\n \"status\",\n (model.get(\"file_size\") > 0 && \"ready\") || \"init\"\n );\n });\n },\n\n /** 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Renders contents of the composite uploader */\nimport Utils from \"utils/utils\";\nimport UploadModel from \"mvc/upload/upload-model\";\nimport UploadRow from \"mvc/upload/composite/composite-row\";\nimport UploadExtension from \"mvc/upload/upload-extension\";\nimport Popover from \"mvc/ui/ui-popover\";\nimport Select from \"mvc/ui/ui-select\";\nimport Ui from \"mvc/ui/ui-misc\";\nexport default Backbone.View.extend({\n collection: new UploadModel.Collection(),\n initialize: function(app) {\n var self = this;\n this.app = app;\n this.options = app.options;\n this.list_extensions = app.list_extensions;\n this.list_genomes = app.list_genomes;\n this.ftp_upload_site = app.currentFtp();\n this.setElement(this._template());\n\n // create button section\n this.btnStart = new Ui.Button({\n title: \"Start\",\n onclick: function() {\n self._eventStart();\n }\n });\n this.btnClose = new Ui.Button({\n title: \"Close\",\n onclick: function() {\n self.app.modal.hide();\n }\n });\n\n // append 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this.collection.where({ status: \"ready\" }).length ==\n this.collection.length &&\n this.collection.length > 0\n ) {\n this.btnStart.enable();\n this.btnStart.$el.addClass(\"btn-primary\");\n } else {\n this.btnStart.disable();\n this.btnStart.$el.removeClass(\"btn-primary\");\n }\n this.$(\".upload-table\")[this.collection.length > 0 ? \"show\" : \"hide\"]();\n },\n\n //\n // upload events / process pipeline\n //\n\n /** Builds the basic ui with placeholder rows for each composite data type file */\n _eventAnnounce: function(model) {\n var upload_row = new UploadRow(this, { model: model });\n this.$(\".upload-table > tbody:first\").append(upload_row.$el);\n this.$(\".upload-table\")[this.collection.length > 0 ? \"show\" : \"hide\"]();\n upload_row.render();\n },\n\n /** Start upload process */\n _eventStart: function() {\n var self = this;\n this.collection.each(function(model) {\n model.set({\n genome: self.select_genome.value(),\n extension: self.select_extension.value()\n });\n 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this.$(\".upload-info-text\");\n this.$info_progress = this.$(\".upload-info-progress\");\n this.$text_content = this.$(\".upload-text-content\");\n this.$settings = this.$(\".upload-settings\");\n this.$symbol = this.$(\".upload-symbol\");\n this.$progress_bar = this.$(\".upload-progress-bar\");\n this.$percentage = this.$(\".upload-percentage\");\n\n // append popup to settings icon\n this.settings = new Popover.View({\n title: \"Upload configuration\",\n container: this.$(\".upload-settings\"),\n placement: \"bottom\"\n });\n\n // identify default genome and extension values\n var default_genome = this.app.select_genome.value();\n var default_extension = this.app.select_extension.value();\n\n // create select genomes\n this.select_genome = new Select.View({\n css: \"upload-genome\",\n data: self.app.list_genomes,\n container: this.$(\".upload-genome\"),\n value: default_genome,\n onchange: function(genome) {\n self.model.set(\"genome\", genome);\n }\n });\n\n // create select extension\n this.select_extension = new Select.View({\n css: \"upload-extension\",\n data: self.app.list_extensions,\n container: this.$(\".upload-extension\"),\n value: default_extension,\n onchange: function(extension) {\n self.model.set(\"extension\", extension);\n }\n });\n\n // initialize genome and extension values\n this.model.set({\n genome: default_genome,\n extension: default_extension\n });\n\n // handle click event\n this.$symbol.on(\"click\", function() {\n self._removeRow();\n });\n\n // handle extension info popover\n this.$(\".upload-extension-info\")\n .on(\"click\", function(e) {\n self.app.showExtensionInfo({\n $el: $(e.target),\n title: self.select_extension.text(),\n extension: self.select_extension.value()\n });\n })\n .on(\"mousedown\", function(e) {\n e.preventDefault();\n });\n\n // handle settings popover\n this.$settings\n .on(\"click\", function(e) {\n self._showSettings();\n })\n .on(\"mousedown\", function(e) {\n e.preventDefault();\n });\n\n // handle text editing event\n this.$text_content.on(\"change input\", function(e) {\n self.model.set({\n url_paste: $(e.target).val(),\n file_size: $(e.target).val().length\n });\n });\n\n // model events\n this.listenTo(this.model, \"change:percentage\", function() {\n self._refreshPercentage();\n });\n this.listenTo(this.model, \"change:status\", function() {\n self._refreshStatus();\n });\n this.listenTo(this.model, \"change:info\", function() {\n self._refreshInfo();\n });\n this.listenTo(this.model, \"change:genome\", function() {\n self._refreshGenome();\n });\n this.listenTo(this.model, \"change:extension\", function() {\n self._refreshExtension();\n });\n this.listenTo(this.model, \"change:file_size\", function() {\n self._refreshFileSize();\n });\n },\n\n render: function() {\n this._refreshType();\n this._refreshPercentage();\n this._refreshStatus();\n this._refreshInfo();\n this._refreshGenome();\n this._refreshExtension();\n this._refreshFileSize();\n },\n\n /** Remove view */\n remove: function() {\n this.select_genome.remove();\n this.select_extension.remove();\n Backbone.View.prototype.remove.apply(this);\n },\n\n /** Render type */\n _refreshType: function() {\n var options = this.model.attributes;\n this.$title.html(_.escape(options.file_name));\n this.$size.html(Utils.bytesToString(options.file_size));\n this.$mode\n .removeClass()\n .addClass(\"upload-mode\")\n .addClass(\"text-primary\");\n if (options.file_mode == \"new\") {\n this.$text\n .css({\n width: this.$el.width() - 16 + \"px\",\n top: this.$el.height() - 8 + \"px\"\n })\n .show();\n this.$el.height(this.$el.height() - 8 + this.$text.height() + 16);\n this.$mode.addClass(\"fa fa-edit\");\n } else if (options.file_mode == \"local\") {\n this.$mode.addClass(\"fa fa-laptop\");\n } else if (options.file_mode == \"ftp\") {\n this.$mode.addClass(\"fa fa-folder-open-o\");\n }\n },\n\n /** Update extension */\n _refreshExtension: function() {\n this.select_extension.value(this.model.get(\"extension\"));\n },\n\n /** Update genome */\n _refreshGenome: function() {\n this.select_genome.value(this.model.get(\"genome\"));\n },\n\n /** Refresh info text */\n _refreshInfo: function() {\n var info = this.model.get(\"info\");\n if (info) {\n this.$info_text.html(\"Failed: \" + info).show();\n } else {\n this.$info_text.hide();\n }\n },\n\n /** Refresh percentage status */\n _refreshPercentage: function() {\n var percentage = parseInt(this.model.get(\"percentage\"));\n this.$progress_bar.css({ width: percentage + \"%\" });\n this.$percentage.html(\n percentage != 100 ? percentage + \"%\" : \"Adding to history...\"\n );\n },\n\n /** Refresh status */\n _refreshStatus: function() {\n var status = this.model.get(\"status\");\n this.$symbol\n .removeClass()\n .addClass(\"upload-symbol\")\n .addClass(this.status_classes[status]);\n this.model.set(\"enabled\", status == \"init\");\n var enabled = this.model.get(\"enabled\");\n this.$text_content.attr(\"disabled\", !enabled);\n if (enabled) {\n this.select_genome.enable();\n this.select_extension.enable();\n } else {\n this.select_genome.disable();\n this.select_extension.disable();\n }\n if (status == \"success\") {\n this.$el.addClass(\"success\");\n this.$percentage.html(\"100%\");\n }\n if (status == \"error\") {\n this.$el.addClass(\"danger\");\n this.$info_progress.hide();\n }\n },\n\n /** Refresh file size */\n _refreshFileSize: function() {\n this.$size.html(Utils.bytesToString(this.model.get(\"file_size\")));\n },\n\n /** Remove row */\n _removeRow: function() {\n if (\n [\"init\", \"success\", \"error\"].indexOf(this.model.get(\"status\")) !==\n -1\n ) {\n this.app.collection.remove(this.model);\n }\n },\n\n /** Attach file info popup */\n _showSettings: function() {\n if (!this.settings.visible) {\n this.settings.empty();\n this.settings.append(new UploadSettings(this).$el);\n this.settings.show();\n } else {\n this.settings.hide();\n }\n },\n\n 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Renders the default uploader rows */\nimport Utils from \"utils/utils\";\nimport UploadModel from \"mvc/upload/upload-model\";\nimport UploadSettings from \"mvc/upload/upload-settings\";\nimport Popover from \"mvc/ui/ui-popover\";\nimport Select from \"mvc/ui/ui-select\";\nexport default Backbone.View.extend({\n /** Dictionary of upload states and associated icons */\n status_classes: {\n init: \"upload-icon-button fa fa-trash-o\",\n queued: \"upload-icon fa fa-spinner fa-spin\",\n running: \"upload-icon fa fa-spinner fa-spin\",\n success: \"upload-icon-button fa fa-check\",\n error: \"upload-icon-button fa fa-exclamation-triangle\"\n },\n\n initialize: function(app, options) {\n var self = this;\n this.app = app;\n this.model = options.model;\n this.setElement(this._template(options.model));\n this.$mode = this.$(\".upload-mode\");\n this.$title = this.$(\".upload-title\");\n this.$text = this.$(\".upload-text\");\n this.$size = this.$(\".upload-size\");\n this.$info_text = this.$(\".upload-info-text\");\n this.$info_progress = this.$(\".upload-info-progress\");\n this.$text_content = this.$(\".upload-text-content\");\n this.$settings = this.$(\".upload-settings\");\n this.$symbol = this.$(\".upload-symbol\");\n this.$progress_bar = this.$(\".upload-progress-bar\");\n this.$percentage = this.$(\".upload-percentage\");\n\n // append popup to settings icon\n this.settings = new Popover.View({\n title: \"Upload configuration\",\n container: this.$(\".upload-settings\"),\n placement: \"bottom\"\n });\n\n // identify default genome and extension values\n var default_genome = this.app.select_genome.value();\n var default_extension = this.app.select_extension.value();\n\n // create select genomes\n this.select_genome = new Select.View({\n css: \"upload-genome\",\n data: self.app.list_genomes,\n container: this.$(\".upload-genome\"),\n value: default_genome,\n onchange: function(genome) {\n self.model.set(\"genome\", genome);\n }\n });\n\n // create select extension\n this.select_extension = new Select.View({\n css: \"upload-extension\",\n data: self.app.list_extensions,\n container: this.$(\".upload-extension\"),\n value: default_extension,\n onchange: function(extension) {\n self.model.set(\"extension\", extension);\n }\n });\n\n // initialize genome and extension values\n this.model.set({\n genome: default_genome,\n extension: default_extension\n });\n\n // handle click event\n this.$symbol.on(\"click\", function() {\n self._removeRow();\n });\n\n // handle extension info popover\n this.$(\".upload-extension-info\")\n .on(\"click\", function(e) {\n self.app.showExtensionInfo({\n $el: $(e.target),\n title: self.select_extension.text(),\n extension: self.select_extension.value()\n });\n })\n .on(\"mousedown\", function(e) {\n e.preventDefault();\n });\n\n // handle settings popover\n this.$settings\n .on(\"click\", function(e) {\n self._showSettings();\n })\n .on(\"mousedown\", function(e) {\n e.preventDefault();\n });\n\n // handle text editing event\n this.$text_content.on(\"change input\", function(e) {\n self.model.set({\n url_paste: $(e.target).val(),\n file_size: $(e.target).val().length\n });\n });\n\n // model events\n this.listenTo(this.model, \"change:percentage\", function() {\n self._refreshPercentage();\n });\n this.listenTo(this.model, \"change:status\", function() {\n self._refreshStatus();\n });\n this.listenTo(this.model, \"change:info\", function() {\n self._refreshInfo();\n });\n this.listenTo(this.model, \"change:genome\", function() {\n self._refreshGenome();\n });\n this.listenTo(this.model, \"change:extension\", function() {\n self._refreshExtension();\n });\n this.listenTo(this.model, \"change:file_size\", function() {\n self._refreshFileSize();\n });\n },\n\n render: function() {\n this._refreshType();\n this._refreshPercentage();\n this._refreshStatus();\n this._refreshInfo();\n this._refreshGenome();\n this._refreshExtension();\n this._refreshFileSize();\n },\n\n /** Remove view */\n remove: function() {\n this.select_genome.remove();\n this.select_extension.remove();\n Backbone.View.prototype.remove.apply(this);\n },\n\n /** Render type */\n _refreshType: function() {\n var options = this.model.attributes;\n this.$title.html(_.escape(options.file_name));\n this.$size.html(Utils.bytesToString(options.file_size));\n this.$mode\n .removeClass()\n .addClass(\"upload-mode\")\n .addClass(\"text-primary\");\n if (options.file_mode == \"new\") {\n this.$text\n .css({\n width: this.$el.width() - 16 + \"px\",\n top: this.$el.height() - 8 + \"px\"\n })\n .show();\n this.$el.height(this.$el.height() - 8 + this.$text.height() + 16);\n this.$mode.addClass(\"fa fa-edit\");\n } else if (options.file_mode == \"local\") {\n this.$mode.addClass(\"fa fa-laptop\");\n } else if (options.file_mode == \"ftp\") {\n this.$mode.addClass(\"fa fa-folder-open-o\");\n }\n },\n\n /** Update extension */\n _refreshExtension: function() {\n this.select_extension.value(this.model.get(\"extension\"));\n },\n\n /** Update genome */\n _refreshGenome: function() {\n this.select_genome.value(this.model.get(\"genome\"));\n },\n\n /** Refresh info text */\n _refreshInfo: function() {\n var info = this.model.get(\"info\");\n if (info) {\n this.$info_text.html(\"Failed: \" + info).show();\n } else {\n this.$info_text.hide();\n }\n },\n\n /** Refresh percentage status */\n _refreshPercentage: function() {\n var percentage = parseInt(this.model.get(\"percentage\"));\n this.$progress_bar.css({ width: percentage + \"%\" });\n this.$percentage.html(\n percentage != 100 ? percentage + \"%\" : \"Adding to history...\"\n );\n },\n\n /** Refresh status */\n _refreshStatus: function() {\n var status = this.model.get(\"status\");\n this.$symbol\n .removeClass()\n .addClass(\"upload-symbol\")\n .addClass(this.status_classes[status]);\n this.model.set(\"enabled\", status == \"init\");\n var enabled = this.model.get(\"enabled\");\n this.$text_content.attr(\"disabled\", !enabled);\n if (enabled) {\n this.select_genome.enable();\n this.select_extension.enable();\n } else {\n this.select_genome.disable();\n this.select_extension.disable();\n }\n if (status == \"success\") {\n this.$el.addClass(\"success\");\n this.$percentage.html(\"100%\");\n }\n if (status == \"error\") {\n this.$el.addClass(\"danger\");\n this.$info_progress.hide();\n }\n },\n\n /** Refresh file size */\n _refreshFileSize: function() {\n this.$size.html(Utils.bytesToString(this.model.get(\"file_size\")));\n },\n\n /** Remove row */\n _removeRow: function() {\n if (\n [\"init\", \"success\", \"error\"].indexOf(this.model.get(\"status\")) !==\n -1\n ) {\n this.app.collection.remove(this.model);\n }\n },\n\n /** Attach file info popup */\n _showSettings: function() {\n if (!this.settings.visible) {\n this.settings.empty();\n this.settings.append(new UploadSettings(this).$el);\n this.settings.show();\n } else {\n this.settings.hide();\n }\n },\n\n /** View template */\n _template: function(options) {\n return (\n '\" +\n ' \" +\n \"' +\n '' +\n '' +\n '\" +\n \"' +\n '\" +\n \"You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.' +\n '' +\n \"\" +\n ' \" +\n \"' +\n \"\" +\n ' ' +\n '' +\n \" \" +\n \"\" +\n ' \" +\n '' +\n \"' +\n \" \" +\n ' \" +\n \"' +\n '' +\n '\" +\n \"' +\n '' +\n '\" +\n \"0%' +\n \"\" +\n '' +\n \" \" +\n \"' +\n \" \"\n );\n }\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/upload/default/default-view.js.map b/static/maps/mvc/upload/default/default-view.js.map index 3d657f86940..8f5e1914eeb 100644 --- a/static/maps/mvc/upload/default/default-view.js.map +++ b/static/maps/mvc/upload/default/default-view.js.map @@ -1 +1 @@ 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$(e.target),\n title: self.select_extension.text(),\n extension: self.select_extension.value(),\n list: self.list_extensions,\n placement: \"top\"\n });\n })\n .on(\"mousedown\", function(e) {\n e.preventDefault();\n });\n\n // genome extension\n this.select_genome = new Select.View({\n css: \"upload-footer-selection\",\n container: this.$(\".upload-footer-genome\"),\n data: this.list_genomes,\n value: this.options.default_genome,\n onchange: function(genome) {\n self._changeGenome(genome);\n }\n });\n\n // Lazy load helper\n this.loader = new LazyLimited({\n $container: this.$uploadbox,\n collection: this.collection,\n new_content: function(model) {\n var upload_row = new UploadRow(self, { model: model });\n self.$uploadtable.find(\"> tbody:first\").append(upload_row.$el);\n upload_row.render();\n return upload_row;\n }\n });\n\n // events\n this.collection.on(\"remove\", function(model) {\n self._eventRemove(model);\n });\n this.render();\n },\n\n render: function() {\n var message = 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Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.\";\n }\n } else {\n if (this.counter.running == 0) {\n message =\n \"You added \" +\n this.counter.announce +\n \" file(s) to the queue. 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this.btnCreate[enable_sources ? \"enable\" : \"disable\"]();\n this.btnFtp.$el[this.ftp_upload_site ? \"show\" : \"hide\"]();\n this.$(\".upload-table\")[show_table ? \"show\" : \"hide\"]();\n this.$(\".upload-helper\")[show_table ? \"hide\" : \"show\"]();\n },\n\n /** A new file has been dropped/selected through the uploadbox plugin */\n _eventAnnounce: function(index, file) {\n this.counter.announce++;\n var new_model = new UploadModel.Model({\n id: index,\n file_name: file.name,\n file_size: file.size,\n file_mode: file.mode || \"local\",\n file_path: file.path,\n file_data: file\n });\n this.render();\n this.collection.add(new_model);\n },\n\n /** Progress */\n _eventProgress: function(index, percentage) {\n var it = this.collection.get(index);\n it.set(\"percentage\", percentage);\n this.ui_button.model.set(\n \"percentage\",\n this._uploadPercentage(percentage, it.get(\"file_size\"))\n );\n },\n\n /** Success */\n _eventSuccess: function(index, message) {\n var it = this.collection.get(index);\n it.set({ percentage: 100, status: \"success\" });\n this.ui_button.model.set(\n \"percentage\",\n this._uploadPercentage(100, it.get(\"file_size\"))\n );\n this.upload_completed += it.get(\"file_size\") * 100;\n this.counter.announce--;\n this.counter.success++;\n this.render();\n Galaxy.currHistoryPanel.refreshContents();\n },\n\n /** Error */\n _eventError: function(index, message) {\n var it = this.collection.get(index);\n it.set({ percentage: 100, status: \"error\", info: message });\n this.ui_button.model.set({\n percentage: this._uploadPercentage(100, it.get(\"file_size\")),\n status: \"danger\"\n });\n this.upload_completed += it.get(\"file_size\") * 100;\n this.counter.announce--;\n this.counter.error++;\n this.render();\n },\n\n /** Queue is done */\n _eventComplete: function() {\n this.collection.each(function(model) {\n model.get(\"status\") == \"queued\" && model.set(\"status\", \"init\");\n });\n this.counter.running = 0;\n this.render();\n },\n\n /** Remove model from upload list */\n _eventRemove: function(model) {\n var status = model.get(\"status\");\n if (status == \"success\") {\n this.counter.success--;\n } else if (status == \"error\") {\n this.counter.error--;\n } else {\n this.counter.announce--;\n }\n this.uploadbox.remove(model.id);\n this.render();\n },\n\n //\n // events triggered by this view\n //\n\n /** Show/hide ftp popup */\n _eventFtp: function() {\n if (!this.ftp.visible) {\n this.ftp.empty();\n var self = this;\n this.ftp.append(\n new UploadFtp({\n collection: this.collection,\n ftp_upload_site: this.ftp_upload_site,\n onadd: function(ftp_file) {\n return self.uploadbox.add([\n {\n mode: \"ftp\",\n name: ftp_file.path,\n size: ftp_file.size,\n path: ftp_file.path\n }\n ]);\n },\n onremove: function(model_index) {\n self.collection.remove(model_index);\n }\n }).$el\n );\n this.ftp.show();\n } else {\n this.ftp.hide();\n }\n },\n\n /** Create a new file */\n _eventCreate: function() {\n this.uploadbox.add([{ name: \"New File\", size: 0, mode: \"new\" }]);\n },\n\n /** Start upload process */\n _eventStart: function() {\n if (this.counter.announce != 0 && this.counter.running == 0) {\n // prepare upload process\n var self = this;\n this.upload_size = 0;\n this.upload_completed = 0;\n this.collection.each(function(model) {\n if (model.get(\"status\") == \"init\") {\n model.set(\"status\", \"queued\");\n self.upload_size += model.get(\"file_size\");\n }\n });\n this.ui_button.model.set({\n percentage: 0,\n status: \"success\"\n });\n this.counter.running = this.counter.announce;\n this.history_id = this.app.currentHistory();\n\n // package ftp files separately, and remove them from queue\n this._uploadFtp();\n\n // queue remaining files\n this.uploadbox.start();\n this.render();\n }\n },\n\n /** Pause upload process */\n _eventStop: function() {\n if (this.counter.running > 0) {\n this.ui_button.model.set(\"status\", \"info\");\n $(\".upload-top-info\").html(\n \"Queue will pause after completing the current file...\"\n );\n this.uploadbox.stop();\n }\n },\n\n /** Remove all */\n _eventReset: function() {\n if (this.counter.running == 0) {\n var self = this;\n this.collection.reset();\n this.counter.reset();\n this.uploadbox.reset();\n this.select_extension.value(this.options.default_extension);\n this.select_genome.value(this.options.default_genome);\n this.ui_button.model.set(\"percentage\", 0);\n this.render();\n }\n },\n\n /** Update extension for all models */\n _changeExtension: function(extension, defaults_only) {\n var self = this;\n this.collection.each(function(model) {\n if (\n model.get(\"status\") == \"init\" &&\n (model.get(\"extension\") == self.options.default_extension ||\n !defaults_only)\n ) {\n model.set(\"extension\", extension);\n }\n });\n },\n\n /** Update genome for all models */\n _changeGenome: function(genome, defaults_only) {\n var self = this;\n this.collection.each(function(model) {\n if (\n model.get(\"status\") == \"init\" &&\n (model.get(\"genome\") == self.options.default_genome ||\n !defaults_only)\n ) {\n model.set(\"genome\", genome);\n }\n });\n },\n\n /** Package and upload ftp files in a single request */\n _uploadFtp: function() {\n var self = this;\n var list = [];\n this.collection.each(function(model) {\n if (\n model.get(\"status\") == \"queued\" &&\n model.get(\"file_mode\") == \"ftp\"\n ) {\n self.uploadbox.remove(model.id);\n list.push(model);\n }\n });\n if (list.length > 0) {\n $.uploadpost({\n data: this.app.toData(list),\n url: this.app.options.nginx_upload_path,\n success: function(message) {\n _.each(list, function(model) {\n self._eventSuccess(model.id);\n });\n },\n error: function(message) {\n _.each(list, function(model) {\n self._eventError(model.id, message);\n });\n }\n });\n }\n },\n\n /** Calculate percentage of all queued uploads */\n _uploadPercentage: function(percentage, size) {\n return (this.upload_completed + percentage * size) / this.upload_size;\n },\n\n /** Template */\n _template: function() {\n return (\n '\" +\n ' \" +\n \"' +\n '' +\n '' +\n '\" +\n \"' +\n '\" +\n \"You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.' +\n '' +\n \"\" +\n ' \" +\n \"' +\n \"\" +\n ' ' +\n '' +\n \" \" +\n \"\" +\n ' \" +\n '' +\n \"' +\n \" \" +\n ' \" +\n \"' +\n '' +\n '\" +\n \"' +\n '' +\n '\" +\n \"0%' +\n \"\" +\n '' +\n \" \" +\n \"' +\n '' +\n '\" +\n '' +\n \"
' +\n '\" +\n '\" +\n '\"\n );\n }\n});\n"]} \ No newline at end of file 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Renders contents of the default uploader */\nimport Utils from \"utils/utils\";\nimport UploadModel from \"mvc/upload/upload-model\";\nimport UploadRow from \"mvc/upload/default/default-row\";\nimport UploadFtp from \"mvc/upload/upload-ftp\";\nimport UploadExtension from \"mvc/upload/upload-extension\";\nimport Popover from \"mvc/ui/ui-popover\";\nimport Select from \"mvc/ui/ui-select\";\nimport Ui from \"mvc/ui/ui-misc\";\nimport LazyLimited from \"mvc/lazy/lazy-limited\";\nimport \"utils/uploadbox\";\nexport default Backbone.View.extend({\n // current upload size in bytes\n upload_size: 0,\n\n // contains upload row models\n collection: new UploadModel.Collection(),\n\n // keeps track of the current uploader state\n counter: {\n announce: 0,\n success: 0,\n error: 0,\n running: 0,\n reset: function() {\n this.announce = this.success = this.error = this.running = 0;\n }\n },\n\n initialize: function(app) {\n var self = this;\n this.app = app;\n this.options = app.options;\n this.list_extensions = app.list_extensions;\n this.list_genomes = app.list_genomes;\n this.ui_button = app.ui_button;\n this.ftp_upload_site = app.currentFtp();\n\n // build template\n this.setElement(this._template());\n this.$uploadbox = this.$(\".upload-box\");\n this.$uploadtable = this.$(\".upload-table\");\n\n // append buttons to dom\n this.btnLocal = new Ui.Button({\n id: \"btn-local\",\n title: \"Choose local file\",\n onclick: function() {\n self.uploadbox.select();\n },\n icon: \"fa fa-laptop\"\n });\n this.btnFtp = new Ui.Button({\n id: \"btn-ftp\",\n title: \"Choose FTP file\",\n onclick: function() {\n self._eventFtp();\n },\n icon: \"fa fa-folder-open-o\"\n });\n this.btnCreate = new Ui.Button({\n id: \"btn-new\",\n title: \"Paste/Fetch data\",\n onclick: function() {\n self._eventCreate();\n },\n icon: \"fa fa-edit\"\n });\n this.btnStart = new Ui.Button({\n id: \"btn-start\",\n title: \"Start\",\n onclick: function() {\n self._eventStart();\n }\n });\n this.btnStop = new Ui.Button({\n id: \"btn-stop\",\n title: \"Pause\",\n onclick: function() {\n self._eventStop();\n }\n });\n this.btnReset = new Ui.Button({\n id: \"btn-reset\",\n title: \"Reset\",\n onclick: function() {\n self._eventReset();\n }\n });\n this.btnClose = new Ui.Button({\n id: \"btn-close\",\n title: \"Close\",\n onclick: function() {\n self.app.modal.hide();\n }\n });\n _.each(\n [\n this.btnLocal,\n this.btnFtp,\n this.btnCreate,\n this.btnStop,\n this.btnReset,\n this.btnStart,\n this.btnClose\n ],\n function(button) {\n self.$(\".upload-buttons\").prepend(button.$el);\n }\n );\n\n // file upload\n this.uploadbox = this.$uploadbox.uploadbox({\n url: this.app.options.nginx_upload_path,\n announce: function(index, file) {\n self._eventAnnounce(index, file);\n },\n initialize: function(index) {\n return self.app.toData(\n [self.collection.get(index)],\n self.history_id\n );\n },\n progress: function(index, percentage) {\n self._eventProgress(index, percentage);\n },\n success: function(index, message) {\n self._eventSuccess(index, message);\n },\n error: function(index, message) {\n self._eventError(index, message);\n },\n complete: function() {\n self._eventComplete();\n },\n ondragover: function() {\n self.$uploadbox.addClass(\"highlight\");\n },\n ondragleave: function() {\n self.$uploadbox.removeClass(\"highlight\");\n }\n });\n\n // add ftp file viewer\n this.ftp = new Popover.View({\n title: \"FTP files\",\n container: this.btnFtp.$el\n });\n\n // select extension\n this.select_extension = new Select.View({\n css: \"upload-footer-selection\",\n container: this.$(\".upload-footer-extension\"),\n data: _.filter(this.list_extensions, function(ext) {\n return !ext.composite_files;\n }),\n value: this.options.default_extension,\n onchange: function(extension) {\n self._changeExtension(extension);\n }\n });\n\n // handle extension info popover\n this.$(\".upload-footer-extension-info\")\n .on(\"click\", function(e) {\n new UploadExtension({\n $el: $(e.target),\n title: self.select_extension.text(),\n extension: self.select_extension.value(),\n list: self.list_extensions,\n placement: \"top\"\n });\n })\n .on(\"mousedown\", function(e) {\n e.preventDefault();\n });\n\n // genome extension\n this.select_genome = new Select.View({\n css: \"upload-footer-selection\",\n container: this.$(\".upload-footer-genome\"),\n data: this.list_genomes,\n value: this.options.default_genome,\n onchange: function(genome) {\n self._changeGenome(genome);\n }\n });\n\n // Lazy load helper\n this.loader = new LazyLimited({\n $container: this.$uploadbox,\n collection: this.collection,\n new_content: function(model) {\n var upload_row = new UploadRow(self, { model: model });\n self.$uploadtable.find(\"> tbody:first\").append(upload_row.$el);\n upload_row.render();\n return upload_row;\n }\n });\n\n // events\n this.collection.on(\"remove\", function(model) {\n self._eventRemove(model);\n });\n this.render();\n },\n\n render: function() {\n var message = \"\";\n if (this.counter.announce == 0) {\n if (this.uploadbox.compatible()) {\n message = \" \";\n } else {\n message =\n \"Browser does not support Drag & Drop. 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this.btnCreate[enable_sources ? \"enable\" : \"disable\"]();\n this.btnFtp.$el[this.ftp_upload_site ? \"show\" : \"hide\"]();\n this.$(\".upload-table\")[show_table ? \"show\" : \"hide\"]();\n this.$(\".upload-helper\")[show_table ? \"hide\" : \"show\"]();\n },\n\n /** A new file has been dropped/selected through the uploadbox plugin */\n _eventAnnounce: function(index, file) {\n this.counter.announce++;\n var new_model = new UploadModel.Model({\n id: index,\n file_name: file.name,\n file_size: file.size,\n file_mode: file.mode || \"local\",\n file_path: file.path,\n file_data: file\n });\n this.render();\n this.collection.add(new_model);\n },\n\n /** Progress */\n _eventProgress: function(index, percentage) {\n var it = this.collection.get(index);\n it.set(\"percentage\", percentage);\n this.ui_button.model.set(\n \"percentage\",\n this._uploadPercentage(percentage, it.get(\"file_size\"))\n );\n },\n\n /** Success */\n _eventSuccess: function(index, message) {\n var it = this.collection.get(index);\n it.set({ percentage: 100, status: \"success\" });\n this.ui_button.model.set(\n \"percentage\",\n this._uploadPercentage(100, it.get(\"file_size\"))\n );\n this.upload_completed += it.get(\"file_size\") * 100;\n this.counter.announce--;\n this.counter.success++;\n this.render();\n Galaxy.currHistoryPanel.refreshContents();\n },\n\n /** Error */\n _eventError: function(index, message) {\n var it = this.collection.get(index);\n it.set({ percentage: 100, status: \"error\", info: message });\n this.ui_button.model.set({\n percentage: this._uploadPercentage(100, it.get(\"file_size\")),\n status: \"danger\"\n });\n this.upload_completed += it.get(\"file_size\") * 100;\n this.counter.announce--;\n this.counter.error++;\n this.render();\n },\n\n /** Queue is done */\n _eventComplete: function() {\n this.collection.each(function(model) {\n model.get(\"status\") == \"queued\" && model.set(\"status\", \"init\");\n });\n this.counter.running = 0;\n this.render();\n },\n\n /** Remove model from upload list */\n _eventRemove: function(model) {\n var status = model.get(\"status\");\n if (status == \"success\") {\n this.counter.success--;\n } else if (status == \"error\") {\n this.counter.error--;\n } else {\n this.counter.announce--;\n }\n this.uploadbox.remove(model.id);\n this.render();\n },\n\n //\n // events triggered by this view\n //\n\n /** Show/hide ftp popup */\n _eventFtp: function() {\n if (!this.ftp.visible) {\n this.ftp.empty();\n var self = this;\n this.ftp.append(\n new UploadFtp({\n collection: this.collection,\n ftp_upload_site: this.ftp_upload_site,\n onadd: function(ftp_file) {\n return self.uploadbox.add([\n {\n mode: \"ftp\",\n name: ftp_file.path,\n size: ftp_file.size,\n path: ftp_file.path\n }\n ]);\n },\n onremove: function(model_index) {\n self.collection.remove(model_index);\n }\n }).$el\n );\n this.ftp.show();\n } else {\n this.ftp.hide();\n }\n },\n\n /** Create a new file */\n _eventCreate: function() {\n this.uploadbox.add([{ name: \"New File\", size: 0, mode: \"new\" }]);\n },\n\n /** Start upload process */\n _eventStart: function() {\n if (this.counter.announce != 0 && this.counter.running == 0) {\n // prepare upload process\n var self = this;\n this.upload_size = 0;\n this.upload_completed = 0;\n this.collection.each(function(model) {\n if (model.get(\"status\") == \"init\") {\n model.set(\"status\", \"queued\");\n self.upload_size += model.get(\"file_size\");\n }\n });\n this.ui_button.model.set({\n percentage: 0,\n status: \"success\"\n });\n this.counter.running = this.counter.announce;\n this.history_id = this.app.currentHistory();\n\n // package ftp files separately, and remove them from queue\n this._uploadFtp();\n\n // queue remaining files\n this.uploadbox.start();\n this.render();\n }\n },\n\n /** Pause upload process */\n _eventStop: function() {\n if (this.counter.running > 0) {\n this.ui_button.model.set(\"status\", \"info\");\n $(\".upload-top-info\").html(\n \"Queue will pause after completing the current file...\"\n );\n this.uploadbox.stop();\n }\n },\n\n /** Remove all */\n _eventReset: function() {\n if (this.counter.running == 0) {\n var self = this;\n this.collection.reset();\n this.counter.reset();\n this.uploadbox.reset();\n this.select_extension.value(this.options.default_extension);\n this.select_genome.value(this.options.default_genome);\n this.ui_button.model.set(\"percentage\", 0);\n this.render();\n }\n },\n\n /** Update extension for all models */\n _changeExtension: function(extension, defaults_only) {\n var self = this;\n this.collection.each(function(model) {\n if (\n model.get(\"status\") == \"init\" &&\n (model.get(\"extension\") == self.options.default_extension ||\n !defaults_only)\n ) {\n model.set(\"extension\", extension);\n }\n });\n },\n\n /** Update genome for all models */\n _changeGenome: function(genome, defaults_only) {\n var self = this;\n this.collection.each(function(model) {\n if (\n model.get(\"status\") == \"init\" &&\n (model.get(\"genome\") == self.options.default_genome ||\n !defaults_only)\n ) {\n model.set(\"genome\", genome);\n }\n });\n },\n\n /** Package and upload ftp files in a single request */\n _uploadFtp: function() {\n var self = this;\n var list = [];\n this.collection.each(function(model) {\n if (\n model.get(\"status\") == \"queued\" &&\n model.get(\"file_mode\") == \"ftp\"\n ) {\n self.uploadbox.remove(model.id);\n list.push(model);\n }\n });\n if (list.length > 0) {\n $.uploadpost({\n data: this.app.toData(list),\n url: this.app.options.nginx_upload_path,\n success: function(message) {\n _.each(list, function(model) {\n self._eventSuccess(model.id);\n });\n },\n error: function(message) {\n _.each(list, function(model) {\n self._eventError(model.id, message);\n });\n }\n });\n }\n },\n\n /** Calculate percentage of all queued uploads */\n _uploadPercentage: function(percentage, size) {\n return (this.upload_completed + percentage * size) / this.upload_size;\n },\n\n /** Template */\n _template: function() {\n return (\n 'Drop files here' +\n '' +\n \"\" +\n \"
\" +\n \"\" +\n \" \" +\n \"\" +\n \"\" +\n \"Name \" +\n \"Size \" +\n \"Type \" +\n \"Genome \" +\n \"Settings \" +\n \"Status \" +\n \"\" +\n \" ' +\n '' +\n '\" +\n '' +\n \"
' +\n '\" +\n '\" +\n '\"\n );\n }\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/upload/upload-button.js.map b/static/maps/mvc/upload/upload-button.js.map index f4a0042d7da..b948f127f84 100644 --- a/static/maps/mvc/upload/upload-button.js.map +++ b/static/maps/mvc/upload/upload-button.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/upload/upload-button.js"],"names":["View","Backbone","extend","initialize","options","self","this","model","icon","tooltip","label","percentage","status","onunload","_template","onclick","$","set","render","setElement","window","$progress","listenTo","attributes","$el","e","title","get","placement","removeClass","addClass","css","width"],"mappings":"oEAEA,IAAIA,KAAOC,SAASD,KAAKE,QACrBC,WAAY,SAASC,GACjB,IAAIC,EAAOC,KAJnBA,KAAAC,MAMaH,GAAWA,EAAQG,OAJrBN,IAAAA,SAAcC,OACTM,KAAA,YACJH,QAAJ,8CACKE,MACAH,YAEGI,WAAM,EACNC,OAAS,GACTC,SAAO,aACPC,QAJe,eAKfC,IAAAA,GACAC,KAAAA,WAAUP,KAAAQ,aACVC,KAAAA,UAAST,KAAAU,EAAA,iBAPMV,KAQhBW,SARHX,KAFJC,MAAA,SAAAD,KAAAY,OAAAZ,MAWAA,KAAKa,SACLH,EAAAI,QAAKC,GAAAA,eAAmB,WACxB,OAAKC,EAASf,MAAKA,IAAO,WAArBe,MAIJJ,OAFD,WAlBwB,IAyBpBd,EAAUE,KAAKC,MAAMgB,WAF7BL,KAAQM,IACAnB,IAAAA,SACAD,GAAAA,QAAU,SAAWmB,GACzBnB,EACSW,QADTU,KAKKhB,SACGiB,MAAOpB,KAAKC,MAAUoB,IAAA,WACtBC,UAAW,WAEnBtB,KAAKe,UAnCmBQ,cAqCnBC,SAAS,gBAMlBA,SAAA,6BACAhB,SAAsB,IAAXV,EAAAQ,QAAW,gBAAAR,EAAAQ,QAClBmB,KACIC,MAAA5B,EAAAO,WACA,OAHRG,UAAW,WACP,MACI,sOAWKd,KAAMA","file":"../../../scripts/mvc/upload/upload-button.js","sourcesContent":["/** View for upload/progress bar button */\n\nvar View = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n icon: \"fa-upload\",\n tooltip: \"Download from URL or upload files from disk\",\n label: \"Load Data\",\n percentage: 0,\n status: \"\",\n onunload: function() {},\n onclick: function() {}\n }).set(options);\n this.setElement(this._template());\n this.$progress = this.$(\".progress-bar\");\n this.listenTo(this.model, \"change\", this.render, this);\n this.render();\n $(window).on(\"beforeunload\", function() {\n return self.model.get(\"onunload\")();\n });\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el\n .off(\"click\")\n .on(\"click\", function(e) {\n options.onclick(e);\n })\n .tooltip({\n title: this.model.get(\"tooltip\"),\n placement: \"bottom\"\n });\n this.$progress\n .removeClass()\n .addClass(\"progress-bar\")\n .addClass(\"progress-bar-notransition\")\n .addClass(options.status != \"\" && \"progress-bar-\" + options.status)\n .css({ width: options.percentage + \"%\" });\n },\n\n /** Template */\n _template: function() {\n return (\n 'Drop files here' +\n '' +\n \"\" +\n \"
\" +\n \"\" +\n \" \" +\n \"\" +\n \"\" +\n \"Name \" +\n \"Size \" +\n \"Type \" +\n \"Genome \" +\n \"Settings \" +\n \"Status \" +\n \"\" +\n \" ' +\n '' +\n '\" +\n \"\"\n );\n }\n});\nexport default { View: View };\n"]} \ No newline at end of file +{"version":3,"sources":["mvc/upload/upload-button.js"],"names":["View","Backbone","extend","initialize","options","self","this","model","Model","percentage","icon","tooltip","label","status","_template","onunload","$","onclick","render","window","setElement","$progress","get","attributes","$el","on","e","title","removeClass","addClass","width"],"mappings":"6FAEA,IAAIA,EAAOC,SAASD,KAAKE,QACrBC,WAAY,SAASC,GACjB,IAAIC,EAAOC,KACXA,KAAKC,MALbH,GAAAA,EAAAG,OAOY,IAAIN,SAASO,OALdP,KAAAA,YACPE,QAAY,8CACJE,MAAO,YACXI,WACKL,EAEGM,OAAM,GACNC,SAAS,aACTC,QAAO,eACPH,IAAAA,GACAI,KAAAA,WAAQP,KALOQ,aAMfC,KAAAA,UAAAA,KAAUC,EAAA,iBACVC,KAAAA,SAAAA,KAASV,MAAA,SAAWD,KAAEY,OAAAZ,MAPPA,KAAnBY,SASJF,EAAAG,QAAKC,GAAAA,eAAgBN,WACrB,OAAKO,EAAAA,MAAYC,IAAKN,WAAjBK,MAIDH,OAAA,WACH,IApBuBd,EAAAE,KAAAC,MAAAgB,WA0BxBjB,KAAKkB,IAHTN,IAAQ,SACJO,GAAIpB,QAAO,SAAXqB,GACItB,EAAAA,QAAeG,KAIXH,SAEHO,MAAQL,KAAAC,MAAAe,IAAA,WACLK,UAAO,WADFrB,KALbe,UASAO,cAnCwBC,SAAA,gBAsCnBA,SAAS,6BAKlBA,SAAA,IAAAzB,EAAAS,QAAA,gBAAAT,EAAAS,QACAC,KAAWgB,MAAA1B,EAAAK,WAAW,OAAtBK,UAAW,WACP,MACI,gOAWKd,KAAMA","file":"../../../scripts/mvc/upload/upload-button.js","sourcesContent":["/** View for upload/progress bar button */\n\nvar View = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.model =\n (options && options.model) ||\n new Backbone.Model({\n icon: \"fa-upload\",\n tooltip: \"Download from URL or upload files from disk\",\n label: \"Load Data\",\n percentage: 0,\n status: \"\",\n onunload: function() {},\n onclick: function() {}\n }).set(options);\n this.setElement(this._template());\n this.$progress = this.$(\".progress-bar\");\n this.listenTo(this.model, \"change\", this.render, this);\n this.render();\n $(window).on(\"beforeunload\", function() {\n return self.model.get(\"onunload\")();\n });\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el\n .off(\"click\")\n .on(\"click\", function(e) {\n options.onclick(e);\n })\n .tooltip({\n title: this.model.get(\"tooltip\"),\n placement: \"bottom\"\n });\n this.$progress\n .removeClass()\n .addClass(\"progress-bar\")\n .addClass(\"progress-bar-notransition\")\n .addClass(options.status != \"\" && \"progress-bar-\" + options.status)\n .css({ width: options.percentage + \"%\" });\n },\n\n /** Template */\n _template: function() {\n return (\n '' +\n '' +\n '\" +\n \"\"\n );\n }\n});\nexport default { View: View };\n"]} \ No newline at end of file diff --git a/static/maps/mvc/upload/upload-extension.js.map b/static/maps/mvc/upload/upload-extension.js.map index 401b53262b7..5f5f4160ccb 100644 --- a/static/maps/mvc/upload/upload-extension.js.map +++ b/static/maps/mvc/upload/upload-extension.js.map @@ -1 +1 @@ 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This renders a popover with extension details **/\nimport Utils from \"utils/utils\";\nimport Popover from \"mvc/ui/ui-popover\";\nexport default Backbone.View.extend({\n initialize: function(options) {\n this.model = new Backbone.Model(options);\n this.setElement(\"\");\n this.render();\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n var description = _.findWhere(options.list, {\n id: options.extension\n });\n this.extension_popup && this.extension_popup.remove();\n this.extension_popup = new Popover.View({\n placement: options.placement || \"bottom\",\n container: options.$el\n });\n this.extension_popup.title(options.title);\n this.extension_popup.empty();\n this.extension_popup.append(this._templateDescription(description));\n this.extension_popup.show();\n },\n\n /** Template for extensions description */\n _templateDescription: function(options) {\n if (options.description) {\n var tmpl = options.description;\n if (options.description_url) {\n tmpl +=\n ' (read more)';\n }\n return tmpl;\n } else {\n return \"There is no description available for this file extension.\";\n }\n }\n});\n"]} \ No newline at end of file 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This renders a popover with extension details **/\nimport Utils from \"utils/utils\";\nimport Popover from \"mvc/ui/ui-popover\";\nexport default Backbone.View.extend({\n initialize: function(options) {\n this.model = new Backbone.Model(options);\n this.setElement(\"\");\n this.render();\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n var description = _.findWhere(options.list, {\n id: options.extension\n });\n this.extension_popup && this.extension_popup.remove();\n this.extension_popup = new Popover.View({\n placement: options.placement || \"bottom\",\n container: options.$el\n });\n this.extension_popup.title(options.title);\n this.extension_popup.empty();\n this.extension_popup.append(this._templateDescription(description));\n this.extension_popup.show();\n },\n\n /** Template for extensions description */\n _templateDescription: function(options) {\n if (options.description) {\n var tmpl = options.description;\n if (options.description_url) {\n tmpl +=\n ' (read more)';\n }\n return tmpl;\n } else {\n return \"There is no description available for this file extension.\";\n }\n }\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/upload/upload-ftp.js.map b/static/maps/mvc/upload/upload-ftp.js.map index d4f270fc233..0ee124a1299 100644 --- a/static/maps/mvc/upload/upload-ftp.js.map +++ b/static/maps/mvc/upload/upload-ftp.js.map @@ -1 +1 @@ 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This renders the content of the ftp popup **/\nimport Utils from \"utils/utils\";\nexport default Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n this.model = new Backbone.Model({\n cls: \"upload-ftp\",\n class_add: \"upload-icon-button fa fa-square-o\",\n class_remove: \"upload-icon-button fa fa-check-square-o\",\n class_partial: \"upload-icon-button fa fa-minus-square-o\",\n help_enabled: true,\n help_text:\n \"This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at \" +\n options.ftp_upload_site +\n \" using your Galaxy credentials.\",\n collection: null,\n onchange: function() {},\n onadd: function() {},\n onremove: function() {}\n }).set(options);\n this.collection = this.model.get(\"collection\");\n this.setElement(this._template());\n this.$content = this.$(\".upload-ftp-content\");\n this.$wait = this.$(\".upload-ftp-wait\");\n this.$help = this.$(\".upload-ftp-help\");\n this.$number = this.$(\".upload-ftp-number\");\n this.$disk = this.$(\".upload-ftp-disk\");\n this.$body = this.$(\".upload-ftp-body\");\n this.$warning = this.$(\".upload-ftp-warning\");\n this.$select = this.$(\".upload-ftp-select-all\");\n this.render();\n },\n\n render: function() {\n var self = this;\n this.$wait.show();\n this.$content.hide();\n this.$warning.hide();\n this.$help.hide();\n $.ajax({\n url: Galaxy.root + \"api/remote_files\",\n method: \"GET\",\n success: function(ftp_files) {\n self.model.set(\"ftp_files\", ftp_files);\n self._index();\n self._renderTable();\n },\n error: function() {\n self._renderTable();\n }\n });\n },\n\n /** Fill table with ftp entries */\n _renderTable: function() {\n var self = this;\n var ftp_files = this.model.get(\"ftp_files\");\n this.rows = [];\n if (ftp_files && ftp_files.length > 0) {\n this.$body.empty();\n var size = 0;\n _.each(ftp_files, function(ftp_file) {\n self.rows.push(self._renderRow(ftp_file));\n size += ftp_file.size;\n });\n this.$number.html(ftp_files.length + \" files\");\n this.$disk.html(Utils.bytesToString(size, true));\n if (this.collection) {\n this.$(\"._has_collection\").show();\n this.$select\n .addClass(this.model.get(\"class_add\"))\n .off()\n .on(\"click\", function() {\n self._all();\n });\n this._refresh();\n }\n this.$content.show();\n } else {\n this.$warning.show();\n }\n this.model.get(\"help_enabled\") && this.$help.show();\n this.$wait.hide();\n },\n\n /** Add row */\n _renderRow: function(ftp_file) {\n var self = this;\n var options = this.model.attributes;\n var $it = $(this._templateRow(ftp_file));\n var $icon = $it.find(\".icon\");\n this.$body.append($it);\n if (this.collection) {\n var model_index = this.ftp_index[ftp_file.path];\n $icon.addClass(\n model_index === undefined\n ? options.class_add\n : options.class_remove\n );\n $it.on(\"click\", function() {\n self._switch($icon, ftp_file);\n self._refresh();\n });\n } else {\n $it.on(\"click\", function() {\n options.onchange(ftp_file);\n });\n }\n return $icon;\n },\n\n /** Create ftp index */\n _index: function() {\n var self = this;\n this.ftp_index = {};\n this.collection &&\n this.collection.each(function(model) {\n if (model.get(\"file_mode\") == \"ftp\") {\n self.ftp_index[model.get(\"file_path\")] = model.id;\n }\n });\n },\n\n /** Select all event handler */\n _all: function() {\n var options = this.model.attributes;\n var ftp_files = this.model.get(\"ftp_files\");\n var add = this.$select.hasClass(options.class_add);\n for (var index in ftp_files) {\n var ftp_file = ftp_files[index];\n var model_index = this.ftp_index[ftp_file.path];\n if (\n (model_index === undefined && add) ||\n (model_index !== undefined && !add)\n ) {\n this._switch(this.rows[index], ftp_file);\n }\n }\n this._refresh();\n },\n\n /** Handle collection changes */\n _switch: function($icon, ftp_file) {\n $icon.removeClass();\n var options = this.model.attributes;\n var model_index = this.ftp_index[ftp_file.path];\n if (model_index === undefined) {\n var new_index = options.onadd(ftp_file);\n $icon.addClass(options.class_remove);\n this.ftp_index[ftp_file.path] = new_index;\n } else {\n options.onremove(model_index);\n $icon.addClass(options.class_add);\n this.ftp_index[ftp_file.path] = undefined;\n }\n },\n\n /** Refresh select all button state */\n _refresh: function() {\n var counts = _.reduce(\n this.ftp_index,\n function(memo, element) {\n element !== undefined && memo++;\n return memo;\n },\n 0\n );\n this.$select.removeClass();\n if (counts == 0) {\n this.$select.addClass(this.model.get(\"class_add\"));\n } else {\n this.$select.addClass(\n counts == this.rows.length\n ? this.model.get(\"class_remove\")\n : this.model.get(\"class_partial\")\n );\n }\n },\n\n /** Template of row */\n _templateRow: function(options) {\n return (\n '' +\n ' \"\n );\n },\n\n /** Template of main view */\n _template: function() {\n return (\n '' +\n ' ' +\n _.escape(options.path) +\n \" \" +\n '' +\n Utils.bytesToString(options.size) +\n \" \" +\n '' +\n options.ctime +\n \" \" +\n \"' +\n '' +\n '' +\n this.model.get(\"help_text\") +\n \"\" +\n '' +\n 'Available files: ' +\n '' +\n '' +\n ' ' +\n '' +\n '' +\n \"\" +\n '\" +\n '' +\n \"\" +\n \"
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To upload some files, log in to the FTP server at \" +\n options.ftp_upload_site +\n \" using your Galaxy credentials.\",\n collection: null,\n onchange: function() {},\n onadd: function() {},\n onremove: function() {}\n }).set(options);\n this.collection = this.model.get(\"collection\");\n this.setElement(this._template());\n this.$content = this.$(\".upload-ftp-content\");\n this.$wait = this.$(\".upload-ftp-wait\");\n this.$help = this.$(\".upload-ftp-help\");\n this.$number = this.$(\".upload-ftp-number\");\n this.$disk = this.$(\".upload-ftp-disk\");\n this.$body = this.$(\".upload-ftp-body\");\n this.$warning = this.$(\".upload-ftp-warning\");\n this.$select = this.$(\".upload-ftp-select-all\");\n this.render();\n },\n\n render: function() {\n var self = this;\n this.$wait.show();\n this.$content.hide();\n this.$warning.hide();\n this.$help.hide();\n $.ajax({\n url: Galaxy.root + \"api/remote_files\",\n method: \"GET\",\n success: function(ftp_files) {\n self.model.set(\"ftp_files\", ftp_files);\n self._index();\n self._renderTable();\n },\n error: function() {\n self._renderTable();\n }\n });\n },\n\n /** Fill table with ftp entries */\n _renderTable: function() {\n var self = this;\n var ftp_files = this.model.get(\"ftp_files\");\n this.rows = [];\n if (ftp_files && ftp_files.length > 0) {\n this.$body.empty();\n var size = 0;\n _.each(ftp_files, function(ftp_file) {\n self.rows.push(self._renderRow(ftp_file));\n size += ftp_file.size;\n });\n this.$number.html(ftp_files.length + \" files\");\n this.$disk.html(Utils.bytesToString(size, true));\n if (this.collection) {\n this.$(\"._has_collection\").show();\n this.$select\n .addClass(this.model.get(\"class_add\"))\n .off()\n .on(\"click\", function() {\n self._all();\n });\n this._refresh();\n }\n this.$content.show();\n } else {\n this.$warning.show();\n }\n this.model.get(\"help_enabled\") && this.$help.show();\n this.$wait.hide();\n },\n\n /** Add row */\n _renderRow: function(ftp_file) {\n var self = this;\n var options = this.model.attributes;\n var $it = $(this._templateRow(ftp_file));\n var $icon = $it.find(\".icon\");\n this.$body.append($it);\n if (this.collection) {\n var model_index = this.ftp_index[ftp_file.path];\n $icon.addClass(\n model_index === undefined\n ? options.class_add\n : options.class_remove\n );\n $it.on(\"click\", function() {\n self._switch($icon, ftp_file);\n self._refresh();\n });\n } else {\n $it.on(\"click\", function() {\n options.onchange(ftp_file);\n });\n }\n return $icon;\n },\n\n /** Create ftp index */\n _index: function() {\n var self = this;\n this.ftp_index = {};\n this.collection &&\n this.collection.each(function(model) {\n if (model.get(\"file_mode\") == \"ftp\") {\n self.ftp_index[model.get(\"file_path\")] = model.id;\n }\n });\n },\n\n /** Select all event handler */\n _all: function() {\n var options = this.model.attributes;\n var ftp_files = this.model.get(\"ftp_files\");\n var add = this.$select.hasClass(options.class_add);\n for (var index in ftp_files) {\n var ftp_file = ftp_files[index];\n var model_index = this.ftp_index[ftp_file.path];\n if (\n (model_index === undefined && add) ||\n (model_index !== undefined && !add)\n ) {\n this._switch(this.rows[index], ftp_file);\n }\n }\n this._refresh();\n },\n\n /** Handle collection changes */\n _switch: function($icon, ftp_file) {\n $icon.removeClass();\n var options = this.model.attributes;\n var model_index = this.ftp_index[ftp_file.path];\n if (model_index === undefined) {\n var new_index = options.onadd(ftp_file);\n $icon.addClass(options.class_remove);\n this.ftp_index[ftp_file.path] = new_index;\n } else {\n options.onremove(model_index);\n $icon.addClass(options.class_add);\n this.ftp_index[ftp_file.path] = undefined;\n }\n },\n\n /** Refresh select all button state */\n _refresh: function() {\n var counts = _.reduce(\n this.ftp_index,\n function(memo, element) {\n element !== undefined && memo++;\n return memo;\n },\n 0\n );\n this.$select.removeClass();\n if (counts == 0) {\n this.$select.addClass(this.model.get(\"class_add\"));\n } else {\n this.$select.addClass(\n counts == this.rows.length\n ? this.model.get(\"class_remove\")\n : this.model.get(\"class_partial\")\n );\n }\n },\n\n /** Template of row */\n _templateRow: function(options) {\n return (\n '' +\n ' \"\n );\n },\n\n /** Template of main view */\n _template: function() {\n return (\n '' +\n ' ' +\n _.escape(options.path) +\n \" \" +\n '' +\n Utils.bytesToString(options.size) +\n \" \" +\n '' +\n options.ctime +\n \" \" +\n \"' +\n '' +\n '\"\n );\n },\n\n /** Main template */\n _templateHeader: function() {\n return (\n '' +\n this.model.get(\"help_text\") +\n \"\" +\n '' +\n 'Available files: ' +\n '' +\n '' +\n ' ' +\n '' +\n '' +\n \"\" +\n '\" +\n '' +\n \"\" +\n \"
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Upload app contains the upload progress button and upload modal, compiles model data for API request **/\nimport Utils from \"utils/utils\";\nimport Modal from \"mvc/ui/ui-modal\";\nimport Tabs from \"mvc/ui/ui-tabs\";\nimport UploadButton from \"mvc/upload/upload-button\";\nimport UploadViewDefault from \"mvc/upload/default/default-view\";\nimport UploadViewComposite from \"mvc/upload/composite/composite-view\";\nimport UploadViewCollection from \"mvc/upload/collection/collection-view\";\nexport default Backbone.View.extend({\n options: {\n nginx_upload_path: \"\",\n ftp_upload_site: \"n/a\",\n default_genome: \"?\",\n default_extension: \"auto\",\n height: 500,\n width: 900,\n auto: {\n id: \"auto\",\n text: \"Auto-detect\",\n description:\n \"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed.\"\n }\n },\n\n // contains all available dataset extensions/types\n list_extensions: [],\n\n // contains all available genomes\n list_genomes: [],\n\n initialize: function(options) {\n var self = this;\n this.options = Utils.merge(options, this.options);\n\n // create view for upload/progress button\n this.ui_button = new UploadButton.View({\n onclick: function(e) {\n e.preventDefault();\n self.show();\n },\n onunload: function() {\n var percentage = self.ui_button.model.get(\"percentage\", 0);\n if (percentage > 0 && percentage < 100) {\n return \"Several uploads are queued.\";\n }\n }\n });\n\n // set element to button view\n this.setElement(this.ui_button.$el);\n\n // load extensions\n var self = this;\n Utils.get({\n url: Galaxy.root + \"api/datatypes?extension_only=False\",\n success: function(datatypes) {\n for (var key in datatypes) {\n self.list_extensions.push({\n id: datatypes[key].extension,\n 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function() {\n var self = this;\n if (!Galaxy.currHistoryPanel || !Galaxy.currHistoryPanel.model) {\n window.setTimeout(function() {\n self.show();\n }, 500);\n return;\n }\n this.current_user = Galaxy.user.id;\n if (!this.modal) {\n this.tabs = new Tabs.View();\n this.default_view = new UploadViewDefault(this);\n this.tabs.add({\n id: \"regular\",\n title: \"Regular\",\n $el: this.default_view.$el\n });\n this.composite_view = new UploadViewComposite(this);\n this.tabs.add({\n id: \"composite\",\n title: \"Composite\",\n $el: this.composite_view.$el\n });\n this.collection_view = new UploadViewCollection(this);\n this.tabs.add({\n id: \"collection\",\n title: \"Collection\",\n $el: this.collection_view.$el\n });\n this.modal = new Modal.View({\n title: \"Download from web or upload from disk\",\n body: this.tabs.$el,\n height: this.options.height,\n width: this.options.width,\n closing_events: true,\n title_separator: false\n });\n }\n this.modal.show();\n },\n\n /** Refresh user and 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Upload app contains the upload progress button and upload modal, compiles model data for API request **/\nimport Utils from \"utils/utils\";\nimport Modal from \"mvc/ui/ui-modal\";\nimport Tabs from \"mvc/ui/ui-tabs\";\nimport UploadButton from \"mvc/upload/upload-button\";\nimport UploadViewDefault from \"mvc/upload/default/default-view\";\nimport UploadViewComposite from \"mvc/upload/composite/composite-view\";\nimport UploadViewCollection from \"mvc/upload/collection/collection-view\";\nexport default Backbone.View.extend({\n options: {\n nginx_upload_path: \"\",\n ftp_upload_site: \"n/a\",\n default_genome: \"?\",\n default_extension: \"auto\",\n height: 500,\n width: 900,\n auto: {\n id: \"auto\",\n text: \"Auto-detect\",\n description:\n \"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed.\"\n }\n },\n\n // contains all available dataset extensions/types\n list_extensions: [],\n\n // contains all available genomes\n list_genomes: [],\n\n initialize: function(options) {\n var self = this;\n this.options = Utils.merge(options, this.options);\n\n // create view for upload/progress button\n this.ui_button = new UploadButton.View({\n onclick: function(e) {\n e.preventDefault();\n self.show();\n },\n onunload: function() {\n var percentage = self.ui_button.model.get(\"percentage\", 0);\n if (percentage > 0 && percentage < 100) {\n return \"Several uploads are queued.\";\n }\n }\n });\n\n // set element to button view\n this.setElement(this.ui_button.$el);\n\n // load extensions\n var self = this;\n Utils.get({\n url: Galaxy.root + \"api/datatypes?extension_only=False\",\n success: function(datatypes) {\n for (var key in datatypes) {\n self.list_extensions.push({\n id: datatypes[key].extension,\n text: datatypes[key].extension,\n description: datatypes[key].description,\n description_url: datatypes[key].description_url,\n composite_files: datatypes[key].composite_files\n });\n }\n self.list_extensions.sort(function(a, b) {\n var a_text = a.text && a.text.toLowerCase();\n var b_text = b.text && b.text.toLowerCase();\n return a_text > b_text ? 1 : a_text < b_text ? -1 : 0;\n });\n if (!self.options.datatypes_disable_auto) {\n self.list_extensions.unshift(self.options.auto);\n }\n }\n });\n\n // load genomes\n Utils.get({\n url: Galaxy.root + \"api/genomes\",\n success: function(genomes) {\n for (var key in genomes) {\n self.list_genomes.push({\n id: genomes[key][1],\n text: genomes[key][0]\n });\n }\n self.list_genomes.sort(function(a, b) {\n if (a.id == self.options.default_genome) {\n return -1;\n }\n if (b.id == self.options.default_genome) {\n return 1;\n }\n return a.text > b.text ? 1 : a.text < b.text ? -1 : 0;\n });\n }\n });\n },\n\n /** Show/hide upload dialog */\n show: function() {\n var self = this;\n if (!Galaxy.currHistoryPanel || !Galaxy.currHistoryPanel.model) {\n window.setTimeout(function() {\n self.show();\n }, 500);\n return;\n }\n this.current_user = Galaxy.user.id;\n if (!this.modal) {\n this.tabs = new Tabs.View();\n this.default_view = new UploadViewDefault(this);\n this.tabs.add({\n id: \"regular\",\n title: \"Regular\",\n $el: this.default_view.$el\n });\n this.composite_view = new UploadViewComposite(this);\n this.tabs.add({\n id: \"composite\",\n title: \"Composite\",\n $el: this.composite_view.$el\n });\n this.collection_view = new UploadViewCollection(this);\n this.tabs.add({\n id: \"collection\",\n title: \"Collection\",\n $el: this.collection_view.$el\n });\n this.modal = new Modal.View({\n title: \"Download from web or upload from disk\",\n body: this.tabs.$el,\n height: this.options.height,\n width: this.options.width,\n closing_events: true,\n title_separator: false\n });\n }\n this.modal.show();\n },\n\n /** Refresh user and current history */\n currentHistory: function() {\n return this.current_user && Galaxy.currHistoryPanel.model.get(\"id\");\n },\n\n /** Get ftp configuration */\n currentFtp: function() {\n return this.current_user && this.options.ftp_upload_site;\n },\n\n /**\n * Package API data from array of models\n * @param{Array} items - Upload items/rows filtered from a collection\n */\n toData: function(items, history_id) {\n // create dictionary for data submission\n var data = {\n payload: {\n tool_id: \"upload1\",\n history_id: history_id || this.currentHistory(),\n inputs: {}\n },\n files: [],\n error_message: null\n };\n // add upload tools input data\n if (items && items.length > 0) {\n var inputs = {\n file_count: items.length,\n dbkey: items[0].get(\"genome\", \"?\"),\n file_type: items[0].get(\"extension\", \"auto\")\n };\n for (var index in items) {\n var it = items[index];\n it.set(\"status\", \"running\");\n if (it.get(\"file_size\") > 0) {\n var prefix = \"files_\" + index + 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This class renders the chart configuration form. */\nimport Utils from \"utils/utils\";\nimport Ui from \"mvc/ui/ui-misc\";\nimport Form from \"mvc/form/form-view\";\nimport Table from \"mvc/ui/ui-table\";\nvar Collection = Backbone.Collection.extend({\n comparator: function(a, b) {\n a = a.get(\"name\");\n b = b.get(\"name\");\n return a > b ? 1 : a < b ? -1 : 0;\n }\n});\n\nvar View = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n var history_id =\n Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model.id;\n this.model = new Backbone.Model();\n this.model.url =\n Galaxy.root +\n \"api/histories/\" +\n history_id +\n \"/custom_builds_metadata\";\n this.collection = new Collection();\n this.collection.url =\n Galaxy.root + \"api/users/\" + Galaxy.user.id + \"/custom_builds\";\n this.message = new Ui.Message({});\n this.installed_builds = new Ui.Select.View({\n optional: true,\n onchange: function() {\n self.installed_builds.value(null);\n },\n empty_text: \"List of available builds:\",\n error_text: \"No system installed builds available.\"\n });\n this.table = new Table.View({ cls: \"grid\", selectable: false });\n this.table.addHeader(\"Name\");\n this.table.addHeader(\"Key\");\n this.table.addHeader(\"Number of chroms/contigs\");\n this.table.addHeader(\"\");\n this.table.appendHeader();\n this.setElement(\n $(\"\")\n .append($(\"\").text(\"Current Custom Builds\"))\n .append(this.table.$el)\n .append(\n (this.$installed = $(\"\")\n .append(\n $(\"\")\n .text(\"System Installed Builds\")\n .addClass(\"ui-margin-top\")\n )\n .append(this.installed_builds.$el))\n )\n .append(\n $(\"\")\n .text(\"Add a Custom Build\")\n .addClass(\"ui-margin-top\")\n )\n .append(\n $(\"\")\n .addClass(\"ui-column\")\n .append(\n $(\"\")\n .addClass(\"ui-column-left\")\n .append(this.message.$el)\n .append(\n (this.$form = $(\"\").addClass(\n \"ui-margin-top\"\n ))\n )\n )\n .append(\n (this.$help = $(\"\").addClass(\n \"ui-column-right\"\n ))\n )\n )\n );\n this.listenTo(this.collection, \"add remove reset\", function() {\n self._renderTable();\n });\n this.listenTo(this.model, \"change\", function() {\n self._renderForm();\n });\n this.collection.fetch();\n this.model.fetch();\n },\n\n render: function() {\n this._renderTable();\n this._renderForm();\n },\n\n _renderTable: function() {\n var self = this;\n this.table.delAll();\n this.collection.sort();\n this.collection.each(function(model) {\n self.table.add(model.get(\"name\"));\n self.table.add(model.id);\n self.table.add(\n model.get(\"count\") !== undefined\n ? model.get(\"count\")\n : \"Processing...\"\n );\n self.table.add(\n new Ui.ButtonIcon({\n icon: \"fa-trash-o\",\n cls: \"ui-button-icon-plain\",\n tooltip: \"Delete custom build.\",\n onclick: function() {\n model.destroy();\n }\n }).$el\n );\n self.table.append(model.id);\n });\n },\n\n _renderForm: function() {\n var self = this;\n var initial_type = \"fasta\";\n var form = new Form({\n inputs: [\n {\n type: \"text\",\n name: \"name\",\n label: \"Name\",\n help: \"Specify a build name e.g. Hamster.\"\n },\n {\n type: \"text\",\n name: \"id\",\n label: \"Key\",\n help: \"Specify a build key e.g. hamster_v1.\"\n },\n {\n name: \"len\",\n type: \"conditional\",\n test_param: {\n name: \"type\",\n label: \"Definition\",\n help: \"Provide the data source.\",\n type: \"select\",\n value: initial_type,\n data: [\n {\n value: \"fasta\",\n label: \"FASTA-file from history\"\n },\n {\n value: \"file\",\n label: \"Len-file from disk\"\n },\n {\n value: \"text\",\n label: \"Len-file by copy/paste\"\n }\n ]\n },\n cases: [\n {\n value: \"fasta\",\n inputs: [\n {\n type: \"select\",\n name: \"value\",\n label: \"FASTA-file\",\n data: this.model.get(\"fasta_hdas\")\n }\n ]\n },\n {\n value: \"file\",\n inputs: [\n {\n type: \"upload\",\n name: \"value\",\n label: \"Len-file\",\n data: this.model.get(\"len_hdas\")\n }\n ]\n },\n {\n value: \"text\",\n inputs: [\n {\n type: \"text\",\n area: true,\n name: \"value\",\n label: \"Edit/Paste\"\n }\n ]\n }\n ]\n }\n ],\n buttons: {\n save: new Ui.Button({\n icon: \"fa-save\",\n tooltip: \"Create new Build\",\n title: \"Save\",\n cls: \"btn btn-primary ui-clear-float\",\n onclick: function() {\n var data = form.data.create();\n if (!data.id || !data.name) {\n self.message.update({\n message: \"All inputs are required.\",\n status: \"danger\"\n });\n } else {\n self.collection.create(data, {\n wait: true,\n success: function(response) {\n if (response.get(\"message\")) {\n self.message.update({\n message: response.get(\"message\"),\n status: \"warning\"\n });\n } else {\n self.message.update({\n message:\n \"Successfully added a new custom build.\",\n status: \"success\"\n });\n }\n },\n error: function(response, err) {\n var message =\n err &&\n err.responseJSON &&\n err.responseJSON.err_msg;\n self.message.update({\n message:\n message ||\n \"Failed to create custom build.\",\n status: \"danger\"\n });\n }\n });\n }\n }\n })\n },\n onchange: function() {\n var input_id = form.data.match(\"len|type\");\n if (input_id) {\n var input_field = form.field_list[input_id];\n self._renderHelp(input_field.value());\n }\n }\n });\n this.$form.empty().append(form.$el);\n var installed_builds = this.model.get(\"installed_builds\");\n if (installed_builds && installed_builds.length) {\n this.$installed.show();\n this.installed_builds.update(this.model.get(\"installed_builds\"));\n } else {\n this.$installed.hide();\n }\n this._renderHelp(initial_type);\n },\n\n _renderHelp: function(len_type) {\n this.$help\n .empty()\n .addClass(\"alert alert-info\")\n .html(\n len_type == \"fasta\"\n ? this._templateFasta()\n : this._templateLen()\n );\n },\n\n _templateLen: function() {\n return (\n \" Length Format
\" +\n \"\" +\n \"The length format is two-column, separated by whitespace, of the form:\" +\n \"
chrom/contig length of chrom/contig
\" +\n \"\" +\n \"\" +\n \"For example, the first few entries of mm9.len are as follows:\" +\n \"
\" +\n \"chr1 197195432\\n\" +\n \"chr2 181748087\\n\" +\n \"chr3 159599783\\n\" +\n \"chr4 155630120\\n\" +\n \"chr5 152537259\" +\n \"
\" +\n \"\" +\n \"Trackster uses this information to populate the select box for chrom/contig, and\" +\n \"to set the maximum basepair of the track browser. You may either upload a .len file\" +\n \"of this format (Len File option), or directly enter the information into the box \" +\n \"(Len Entry option).
\"\n );\n },\n\n _templateFasta: function() {\n return (\n \"FASTA format
\" +\n \"\" +\n \"This is a multi-fasta file from your current history that provides the genome\" +\n \"sequences for each chromosome/contig in your build.\" +\n \"
\" +\n \"\" +\n \"Here is a snippet from an example multi-fasta file:\" +\n \"
\" +\n \">chr1\\n\" +\n \"ATTATATATAAGACCACAGAGAGAATATTTTGCCCGG...\\n\\n\" +\n \">chr2\\n\" +\n \"GGCGGCCGCGGCGATATAGAACTACTCATTATATATA...\\n\\n\" +\n \"...\" +\n \"
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1 : a < b ? -1 : 0;\n }\n});\n\nvar View = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n var history_id =\n Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model.id;\n this.model = new Backbone.Model();\n this.model.url =\n Galaxy.root +\n \"api/histories/\" +\n history_id +\n \"/custom_builds_metadata\";\n this.collection = new Collection();\n this.collection.url =\n Galaxy.root + \"api/users/\" + Galaxy.user.id + \"/custom_builds\";\n this.message = new Ui.Message({});\n this.installed_builds = new Ui.Select.View({\n optional: true,\n onchange: function() {\n self.installed_builds.value(null);\n },\n empty_text: \"List of available builds:\",\n error_text: \"No system installed builds available.\"\n });\n this.table = new Table.View({ cls: \"grid\", selectable: false });\n this.table.addHeader(\"Name\");\n this.table.addHeader(\"Key\");\n this.table.addHeader(\"Number of chroms/contigs\");\n this.table.addHeader(\"\");\n this.table.appendHeader();\n this.setElement(\n $(\"\")\n .append($(\"\").text(\"Current Custom Builds\"))\n .append(this.table.$el)\n .append(\n (this.$installed = $(\"\")\n .append(\n $(\"\")\n .text(\"System Installed Builds\")\n .addClass(\"ui-margin-top\")\n )\n .append(this.installed_builds.$el))\n )\n .append(\n $(\"\")\n .text(\"Add a Custom Build\")\n .addClass(\"ui-margin-top\")\n )\n .append(\n $(\"\")\n .addClass(\"ui-column\")\n .append(\n $(\"\")\n .addClass(\"ui-column-left\")\n .append(this.message.$el)\n .append(\n (this.$form = $(\"\").addClass(\n \"ui-margin-top\"\n ))\n )\n )\n .append(\n (this.$help = $(\"\").addClass(\n \"ui-column-right\"\n ))\n )\n )\n );\n this.listenTo(this.collection, \"add remove reset\", function() {\n self._renderTable();\n });\n this.listenTo(this.model, \"change\", function() {\n self._renderForm();\n });\n this.collection.fetch();\n this.model.fetch();\n },\n\n render: function() {\n this._renderTable();\n this._renderForm();\n },\n\n _renderTable: function() {\n var self = this;\n this.table.delAll();\n this.collection.sort();\n this.collection.each(function(model) {\n self.table.add(model.get(\"name\"));\n self.table.add(model.id);\n self.table.add(\n model.get(\"count\") !== undefined\n ? model.get(\"count\")\n : \"Processing...\"\n );\n self.table.add(\n new Ui.ButtonIcon({\n icon: \"fa-trash-o\",\n cls: \"ui-button-icon-plain\",\n tooltip: \"Delete custom build.\",\n onclick: function() {\n model.destroy();\n }\n }).$el\n );\n self.table.append(model.id);\n });\n },\n\n _renderForm: function() {\n var self = this;\n var initial_type = \"fasta\";\n var form = new Form({\n inputs: [\n {\n type: \"text\",\n name: \"name\",\n label: \"Name\",\n help: \"Specify a build name e.g. Hamster.\"\n },\n {\n type: \"text\",\n name: \"id\",\n label: \"Key\",\n help: \"Specify a build key e.g. hamster_v1.\"\n },\n {\n name: \"len\",\n type: \"conditional\",\n test_param: {\n name: \"type\",\n label: \"Definition\",\n help: \"Provide the data source.\",\n type: \"select\",\n value: initial_type,\n data: [\n {\n value: \"fasta\",\n label: \"FASTA-file from history\"\n },\n {\n value: \"file\",\n label: \"Len-file from disk\"\n },\n {\n value: \"text\",\n label: \"Len-file by copy/paste\"\n }\n ]\n },\n cases: [\n {\n value: \"fasta\",\n inputs: [\n {\n type: \"select\",\n name: \"value\",\n label: \"FASTA-file\",\n data: this.model.get(\"fasta_hdas\")\n }\n ]\n },\n {\n value: \"file\",\n inputs: [\n {\n type: \"upload\",\n name: \"value\",\n label: \"Len-file\",\n data: this.model.get(\"len_hdas\")\n }\n ]\n },\n {\n value: \"text\",\n inputs: [\n {\n type: \"text\",\n area: true,\n name: \"value\",\n label: \"Edit/Paste\"\n }\n ]\n }\n ]\n }\n ],\n buttons: {\n save: new Ui.Button({\n icon: \"fa-save\",\n tooltip: \"Create new Build\",\n title: \"Save\",\n cls: \"btn btn-primary ui-clear-float\",\n onclick: function() {\n var data = form.data.create();\n if (!data.id || !data.name) {\n self.message.update({\n message: \"All inputs are required.\",\n status: \"danger\"\n });\n } else {\n self.collection.create(data, {\n wait: true,\n success: function(response) {\n if (response.get(\"message\")) {\n self.message.update({\n message: response.get(\"message\"),\n status: \"warning\"\n });\n } else {\n self.message.update({\n message:\n \"Successfully added a new custom build.\",\n status: \"success\"\n });\n }\n },\n error: function(response, err) {\n var message =\n err &&\n err.responseJSON &&\n err.responseJSON.err_msg;\n self.message.update({\n message:\n message ||\n \"Failed to create custom build.\",\n status: \"danger\"\n });\n }\n });\n }\n }\n })\n },\n onchange: function() {\n var input_id = form.data.match(\"len|type\");\n if (input_id) {\n var input_field = form.field_list[input_id];\n self._renderHelp(input_field.value());\n }\n }\n });\n this.$form.empty().append(form.$el);\n var installed_builds = this.model.get(\"installed_builds\");\n if (installed_builds && installed_builds.length) {\n this.$installed.show();\n this.installed_builds.update(this.model.get(\"installed_builds\"));\n } else {\n this.$installed.hide();\n }\n this._renderHelp(initial_type);\n },\n\n _renderHelp: function(len_type) {\n this.$help\n .empty()\n .addClass(\"alert alert-info\")\n .html(\n len_type == \"fasta\"\n ? this._templateFasta()\n : this._templateLen()\n );\n },\n\n _templateLen: function() {\n return (\n \"Length Format
\" +\n \"\" +\n \"The length format is two-column, separated by whitespace, of the form:\" +\n \"
chrom/contig length of chrom/contig
\" +\n \"\" +\n \"\" +\n \"For example, the first few entries of mm9.len are as follows:\" +\n \"
\" +\n \"chr1 197195432\\n\" +\n \"chr2 181748087\\n\" +\n \"chr3 159599783\\n\" +\n \"chr4 155630120\\n\" +\n \"chr5 152537259\" +\n \"
\" +\n \"\" +\n \"Trackster uses this information to populate the select box for chrom/contig, and\" +\n \"to set the maximum basepair of the track browser. You may either upload a .len file\" +\n \"of this format (Len File option), or directly enter the information into the box \" +\n \"(Len Entry option).
\"\n );\n },\n\n _templateFasta: function() {\n return (\n \"FASTA format
\" +\n \"\" +\n \"This is a multi-fasta file from your current history that provides the genome\" +\n \"sequences for each chromosome/contig in your build.\" +\n \"
\" +\n \"\" +\n \"Here is a snippet from an example multi-fasta file:\" +\n \"
\" +\n \">chr1\\n\" +\n \"ATTATATATAAGACCACAGAGAGAATATTTTGCCCGG...\\n\\n\" +\n \">chr2\\n\" +\n \"GGCGGCCGCGGCGATATAGAACTACTCATTATATATA...\\n\\n\" +\n \"...\" +\n \"
\" +\n \"\"\n );\n }\n});\n\nexport default {\n View: View\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/user/user-model.js.map b/static/maps/mvc/user/user-model.js.map index 56611ff9c44..83ab53fbba4 100644 --- a/static/maps/mvc/user/user-model.js.map +++ b/static/maps/mvc/user/user-model.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/user/user-model.js"],"names":["_underscore","require","_backbone","_baseMvc","_localization","logNamespace","User","_backbone2","default","Model","extend","_baseMvc2","LoggableMixin","_logNamespace","urlRoot","Galaxy","root","defaults","username","_localization2","email","total_disk_usage","nice_total_disk_usage","quota_percent","is_admin","initialize","data","this","log","on","model","resp","changes","get","isAdmin","loadFromApi","idOrCurrent","options","CURRENT_ID_STR","isAnonymous","userFn","success","newModel","response","url","prototype","call","clearSessionStorage","key","sessionStorage","trigger","removeItem","toString","userInfo","unshift","push","join","getCurrentUserFromApi","currentUser","Collection"],"mappings":"4IAAA,IAAAA,YAAAC,QAAA,oEACAC,UAAAD,QAAA,8DACAE,SAAAF,QAAA,2DACAG,cAAAH,QAAA,2EAEII,aAAe,OAJnBC,KAAAC,WAAAC,QAAAC,MAAAC,OAAAC,UAAAH,QAAAI,eAAAF,QAWQG,cAAeR,aAGfS,QAAS,WACL,OAAOC,OAAOC,KAAO,aAOzBC,UAlBJZ,GAAAA,KACJa,SAAA,KAAA,EAAAC,eAAAX,SAAA,kBAAA,IACAY,MAAA,GAoBYC,iBAAkB,EAClBC,sBAAuB,GAlBxBC,cAAA,KACPC,UAAA,GAA6BC,WAAA,SAAAC,GA0BrBC,KAAKC,IAAI,mBAAoBF,GAE7BC,KAAKE,GAAG,SAAU,SAASC,EAAOC,GAC9BJ,KAAKC,IAAID,KAAO,eAAgBG,EAAOC,KAjB/Cd,KAAUY,GAAA,SAAA,SAAAC,EAA6BJ,GAAAC,KAAAC,IAAAD,KAAA,gBAAAG,EAAAJ,EAAAM,YAKnCV,YAAAA,WACAC,OAAAA,KAAeU,IANoB,UA4BvCC,QAAS,WAlBT,OAAAP,KAAAM,IAAA,aAUQE,YAAS,SAAOC,EAAhBC,GADJD,EAAAA,GAAA9B,KAAAgC,eAKJC,IAAAA,EAAaZ,KACDa,GAiBRH,EAAUA,OAjBVI,QAcJN,OAXAD,EAASO,QAAA,SAAWC,EAAAC,GACTb,EAAKG,QAAI,SAAhBS,EAAAC,GAzCqBH,GA8DbA,EAAOE,EAAUC,IAKrBP,IAAgB9B,KAAKgC,iBACrBD,EAAQO,IAAMjB,KAAKb,QAAU,IAAMR,KAAKgC,gBAjBnC/B,WAAAC,QAAAC,MAAAoC,UAAST,MAATU,KAAsBT,KAASA,IAIxCU,oBACqBN,WAoBrB,IAAK,IAAIO,KAAOC,eAhBsBN,IAA5BO,EAAAA,QAAQ,YACVV,eAAQW,WAAAH,GACSL,kBAAVD,GACVO,eAAAE,WAAAH,IAMJI,SAAA,WACD,IAAOC,GAAA1B,KAAAM,IAASxB,aAKpBsC,OA3EyBpB,KAAAM,IAAA,QA2FjBoB,EAASC,QAAQ3B,KAAKM,IAAI,OAlBlCoB,EAAAE,KAAA5B,KAAAM,IAAA,WAEAc,QAAqBM,EAAAG,KAAA,KAAA,OAMZlD,KAAAgC,eAAM,UAGVhC,KAAAmD,sBAAA,SAAApB,GACJ,IArFwBqB,EAAA,IAAApD,KAuFzB,OAkBJoD,EAAYvB,YAAY7B,KAAKgC,eAAgBD,GAlBzCqB,GAIQL,IAAAA,eAASC,WAAAA,QAAQK,WAASjD,OAA1BC,UAAAH,QAAAI,eAAAF,QACA2C,MAAAA,KACHvC,QAAA,WACD,OAAOC,OAAAC,KAAUqC,gCAQ7B/C,KAAAA","file":"../../../scripts/mvc/user/user-model.js","sourcesContent":["import _ from \"libs/underscore\";\nimport Backbone from \"libs/backbone\";\nimport baseMVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\nvar logNamespace = \"user\";\n//==============================================================================\n/** @class Model for a Galaxy user (including anonymous users).\n * @name User\n */\nvar User = Backbone.Model.extend(baseMVC.LoggableMixin).extend(\n /** @lends User.prototype */ {\n _logNamespace: logNamespace,\n\n /** API location for this resource */\n urlRoot: function() {\n return Galaxy.root + \"api/users\";\n },\n\n /** Model defaults\n * Note: don't check for anon-users with the username as the default is '(anonymous user)'\n * a safer method is if( !user.get( 'email' ) ) -> anon user\n */\n defaults: /** @lends User.prototype */ {\n id: null,\n username: \"(\" + _l(\"anonymous user\") + \")\",\n email: \"\",\n total_disk_usage: 0,\n nice_total_disk_usage: \"\",\n quota_percent: null,\n is_admin: false\n },\n\n /** Set up and bind events\n * @param {Object} data Initial model data.\n */\n initialize: function(data) {\n this.log(\"User.initialize:\", data);\n\n this.on(\"loaded\", function(model, resp) {\n this.log(this + \" has loaded:\", model, resp);\n });\n this.on(\"change\", function(model, data) {\n this.log(this + \" has changed:\", model, data.changes);\n });\n },\n\n isAnonymous: function() {\n return !this.get(\"email\");\n },\n\n isAdmin: function() {\n return this.get(\"is_admin\");\n },\n\n /** Load a user with the API using an id.\n * If getting an anonymous user or no access to a user id, pass the User.CURRENT_ID_STR\n * (e.g. 'current') and the API will return the current transaction's user data.\n * @param {String} idOrCurrent encoded user id or the User.CURRENT_ID_STR\n * @param {Object} options hash to pass to Backbone.Model.fetch. Can contain success, error fns.\n * @fires loaded when the model has been loaded from the API, passing the newModel and AJAX response.\n */\n loadFromApi: function(idOrCurrent, options) {\n idOrCurrent = idOrCurrent || User.CURRENT_ID_STR;\n\n options = options || {};\n var model = this,\n userFn = options.success;\n\n /** @ignore */\n options.success = function(newModel, response) {\n model.trigger(\"loaded\", newModel, response);\n if (userFn) {\n userFn(newModel, response);\n }\n };\n\n // requests for the current user must have a sep. constructed url (fetch don't work, ma)\n if (idOrCurrent === User.CURRENT_ID_STR) {\n options.url = this.urlRoot + \"/\" + User.CURRENT_ID_STR;\n }\n return Backbone.Model.prototype.fetch.call(this, options);\n },\n\n /** Clears all data from the sessionStorage.\n */\n clearSessionStorage: function() {\n for (var key in sessionStorage) {\n //TODO: store these under the user key so we don't have to do this\n // currently only history\n if (key.indexOf(\"history:\") === 0) {\n sessionStorage.removeItem(key);\n } else if (key === \"history-panel\") {\n sessionStorage.removeItem(key);\n }\n }\n },\n\n /** string representation */\n toString: function() {\n var userInfo = [this.get(\"username\")];\n if (this.get(\"id\")) {\n userInfo.unshift(this.get(\"id\"));\n userInfo.push(this.get(\"email\"));\n }\n return \"User(\" + userInfo.join(\":\") + \")\";\n }\n }\n);\n\n// string to send to tell server to return this transaction's user (see api/users.py)\nUser.CURRENT_ID_STR = \"current\";\n\n// class method to load the current user via the api and return that model\nUser.getCurrentUserFromApi = function(options) {\n var currentUser = new User();\n currentUser.loadFromApi(User.CURRENT_ID_STR, options);\n return currentUser;\n};\n\n// (stub) collection for users (shouldn't be common unless admin UI)\nvar UserCollection = Backbone.Collection.extend(baseMVC.LoggableMixin).extend({\n model: User,\n urlRoot: function() {\n return Galaxy.root + \"api/users\";\n }\n //logger : console,\n});\n\n//==============================================================================\nexport default {\n User: User\n};\n"]} \ No newline at end of file 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up and bind events\n * @param {Object} data Initial model data.\n */\n initialize: function(data) {\n this.log(\"User.initialize:\", data);\n\n this.on(\"loaded\", function(model, resp) {\n this.log(this + \" has loaded:\", model, resp);\n });\n this.on(\"change\", function(model, data) {\n this.log(this + \" has changed:\", model, data.changes);\n });\n },\n\n isAnonymous: function() {\n return !this.get(\"email\");\n },\n\n isAdmin: function() {\n return this.get(\"is_admin\");\n },\n\n /** Load a user with the API using an id.\n * If getting an anonymous user or no access to a user id, pass the User.CURRENT_ID_STR\n * (e.g. 'current') and the API will return the current transaction's user data.\n * @param {String} idOrCurrent encoded user id or the User.CURRENT_ID_STR\n * @param {Object} options hash to pass to Backbone.Model.fetch. 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User Preferences view */\nimport Form from \"mvc/form/form-view\";\nimport Ui from \"mvc/ui/ui-misc\";\nimport QueryStringParsing from \"utils/query-string-parsing\";\n/** Contains descriptive dictionaries describing user forms */\nvar Model = Backbone.Model.extend({\n initialize: function(options) {\n options = options || {};\n options.user_id = options.user_id || Galaxy.user.id;\n this.set({\n user_id: options.user_id,\n information: {\n title: \"Manage information\",\n description:\n \"Edit your email, addresses and custom parameters or change your username.\",\n url: \"api/users/\" + options.user_id + \"/information/inputs\",\n icon: \"fa-user\",\n redirect: \"user\"\n },\n password: {\n title: \"Change password\",\n description: \"Allows you to change your login credentials.\",\n icon: \"fa-unlock-alt\",\n url: \"api/users/\" + options.user_id + \"/password/inputs\",\n submit_title: \"Save password\",\n redirect: \"user\"\n },\n communication: {\n title: \"Change communication 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Changes made here will only affect histories created after these settings have been stored.\",\n url: \"api/users/\" + options.user_id + \"/permissions/inputs\",\n icon: \"fa-users\",\n submit_title: \"Save permissions\",\n redirect: \"user\"\n },\n api_key: {\n title: \"Manage API key\",\n description: \"Access your current API key or create a new one.\",\n url: \"api/users/\" + options.user_id + \"/api_key/inputs\",\n icon: \"fa-key\",\n submit_title: \"Create a new key\",\n submit_icon: \"fa-check\"\n },\n toolbox_filters: {\n title: \"Manage Toolbox filters\",\n description:\n \"Customize your Toolbox by displaying or omitting sets of Tools.\",\n url: \"api/users/\" + options.user_id + \"/toolbox_filters/inputs\",\n icon: \"fa-filter\",\n submit_title: \"Save filters\",\n redirect: \"user\"\n },\n openids: {\n title: \"Manage OpenIDs\",\n description: \"Associate OpenIDs with your account.\",\n icon: \"fa-openid\",\n onclick: function() {\n window.location.href =\n Galaxy.root +\n \"user/openid_manage?cntrller=user&use_panels=True\";\n }\n },\n custom_builds: {\n title: \"Manage custom builds\",\n description:\n \"Add or remove custom builds using history datasets.\",\n icon: \"fa-cubes\",\n onclick: function() {\n window.location.href = Galaxy.root + \"custom_builds\";\n }\n },\n logout: {\n title: \"Sign out\",\n description: \"Click here to sign out of all sessions.\",\n icon: \"fa-sign-out\",\n onclick: function() {\n Galaxy.modal.show({\n title: \"Sign out\",\n body:\n \"Do you want to continue and sign out of all active sessions?\",\n buttons: {\n Cancel: function() {\n Galaxy.modal.hide();\n },\n \"Sign out\": function() {\n window.location.href =\n Galaxy.root +\n \"user/logout?session_csrf_token=\" +\n Galaxy.session_csrf_token;\n }\n }\n });\n }\n }\n });\n }\n});\n\n/** View of the main user preference panel with links to individual user forms */\nvar View = Backbone.View.extend({\n title: \"User Preferences\",\n initialize: function() {\n this.model = new Model();\n this.setElement(\"\");\n this.render();\n },\n\n render: function() {\n var self = this;\n var config = Galaxy.config;\n $.getJSON(Galaxy.root + \"api/users/\" + Galaxy.user.id, function(data) {\n self.$preferences = $(\"\")\n .addClass(\"ui-panel\")\n .append($(\"\").append(\"User preferences\"))\n .append(\n $(\"\").append(\n \"You are logged in as \" +\n _.escape(data.email) +\n \".\"\n )\n )\n .append(\n (self.$table = $(\"\" +\n ' \" +\n \"\" +\n '' +\n options.title +\n \"\" +\n ' \" +\n \"' +\n options.description +\n \"\" +\n \"\").addClass(\"ui-panel-table\"))\n );\n var message = QueryStringParsing.get(\"message\");\n var status = QueryStringParsing.get(\"status\");\n if (message && status) {\n self.$preferences.prepend(\n new Ui.Message({ message: message, status: status }).$el\n );\n }\n if (!config.use_remote_user) {\n self._addLink(\"information\");\n self._addLink(\"password\");\n }\n if (config.enable_communication_server) {\n self._addLink(\"communication\");\n }\n self._addLink(\"custom_builds\");\n self._addLink(\"permissions\");\n self._addLink(\"api_key\");\n if (config.has_user_tool_filters) {\n self._addLink(\"toolbox_filters\");\n }\n if (config.enable_openid && !config.use_remote_user) {\n self._addLink(\"openids\");\n }\n if (Galaxy.session_csrf_token) {\n self._addLink(\"logout\");\n }\n self.$preferences.append(self._templateFooter(data));\n self.$el.empty().append(self.$preferences);\n });\n },\n\n _addLink: function(action) {\n var options = this.model.get(action);\n var $row = $(this._templateLink(options));\n var $a = $row.find(\"a\");\n if (options.onclick) {\n $a.on(\"click\", function() {\n options.onclick();\n });\n } else {\n $a.attr(\"href\", Galaxy.root + \"user/\" + action);\n }\n this.$table.append($row);\n },\n\n _templateLink: function(options) {\n return (\n \"
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Will render as a progress bar\n * with their percentage of that quota in text over the bar.\n * @fires quota:over when user is over quota (>= this.errorAtPercent)\n * @fires quota:under when user is under quota\n * @fires quota:under:approaching when user is >= this.warnAtPercent of their quota\n * @fires quota:under:ok when user is below this.warnAtPercent\n * @returns {jQuery} the rendered meter\n */\n _render_quota: function() {\n var modelJson = this.model.toJSON(),\n //prevPercent = this.model.previous( 'quota_percent' ),\n percent = modelJson.quota_percent,\n //meter = $( UserQuotaMeter.templates.quota( modelJson ) );\n $meter = $(this._templateQuotaMeter(modelJson)),\n $bar = $meter.find(\".progress-bar\");\n //this.log( this + '.rendering quota, percent:', percent, 'meter:', meter );\n\n // OVER QUOTA: color the quota bar and show the quota error message\n if (this.isOverQuota()) {\n //this.log( '\\t over quota' );\n $bar.attr(\"class\", \"progress-bar progress-bar-danger\");\n $meter.find(\".quota-meter-text\").css(\"color\", \"white\");\n //TODO: only trigger event if state has changed\n this.trigger(\"quota:over\", modelJson);\n\n // APPROACHING QUOTA: color the quota bar\n } else if (percent >= this.options.warnAtPercent) {\n //this.log( '\\t approaching quota' );\n $bar.attr(\"class\", \"progress-bar progress-bar-warning\");\n //TODO: only trigger event if state has changed\n this.trigger(\"quota:under quota:under:approaching\", modelJson);\n\n // otherwise, hide/don't use the msg box\n } else {\n $bar.attr(\"class\", \"progress-bar progress-bar-success\");\n //TODO: only trigger event if state has changed\n this.trigger(\"quota:under quota:under:ok\", modelJson);\n }\n return $meter;\n },\n\n /** Render the meter when the user has NO applicable quota. Will render as text\n * showing the human readable sum storage their data is using.\n * @returns {jQuery} the rendered text\n */\n _render_usage: function() {\n //var usage = $( UserQuotaMeter.templates.usage( this.model.toJSON() ) );\n var usage = $(this._templateUsage(this.model.toJSON()));\n this.log(this + \".rendering usage:\", usage);\n return usage;\n },\n\n /** Render either the quota percentage meter or the human readable disk usage\n * depending on whether the user model has quota info (quota_percent === null -> no quota)\n * @returns {Object} this UserQuotaMeter\n */\n render: function() {\n //this.log( this + '.rendering' );\n var meterHtml = null;\n\n // no quota on server ('quota_percent' === null (can be valid at 0)), show usage instead\n this.log(\n this + \".model.quota_percent:\",\n this.model.get(\"quota_percent\")\n );\n if (\n this.model.get(\"quota_percent\") === null ||\n this.model.get(\"quota_percent\") === undefined\n ) {\n meterHtml = this._render_usage();\n\n // otherwise, render percent of quota (and warning, error)\n } else {\n meterHtml = this._render_quota();\n //TODO: add the original text for unregistered quotas\n //tooltip = \"Your disk quota is %s. 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Will render as a progress bar\n * with their percentage of that quota in text over the bar.\n * @fires quota:over when user is over quota (>= this.errorAtPercent)\n * @fires quota:under when user is under quota\n * @fires quota:under:approaching when user is >= this.warnAtPercent of their quota\n * @fires quota:under:ok when user is below this.warnAtPercent\n * @returns {jQuery} the rendered meter\n */\n _render_quota: function() {\n var modelJson = this.model.toJSON(),\n //prevPercent = this.model.previous( 'quota_percent' ),\n percent = modelJson.quota_percent,\n //meter = $( UserQuotaMeter.templates.quota( modelJson ) );\n $meter = $(this._templateQuotaMeter(modelJson)),\n $bar = $meter.find(\".progress-bar\");\n //this.log( this + '.rendering quota, percent:', percent, 'meter:', meter );\n\n // OVER QUOTA: color the quota bar and show the quota error message\n if (this.isOverQuota()) {\n //this.log( '\\t over quota' );\n $bar.attr(\"class\", \"progress-bar progress-bar-danger\");\n $meter.find(\".quota-meter-text\").css(\"color\", \"white\");\n //TODO: only trigger event if state has changed\n this.trigger(\"quota:over\", modelJson);\n\n // APPROACHING QUOTA: color the quota bar\n } else if (percent >= this.options.warnAtPercent) {\n //this.log( '\\t approaching quota' );\n $bar.attr(\"class\", \"progress-bar progress-bar-warning\");\n //TODO: only trigger event if state has changed\n this.trigger(\"quota:under quota:under:approaching\", modelJson);\n\n // otherwise, hide/don't use the msg box\n } else {\n $bar.attr(\"class\", \"progress-bar progress-bar-success\");\n //TODO: only trigger event if state has changed\n this.trigger(\"quota:under quota:under:ok\", modelJson);\n }\n return $meter;\n },\n\n /** Render the meter when the user has NO applicable quota. Will render as text\n * showing the human readable sum storage their data is using.\n * @returns {jQuery} the rendered text\n */\n _render_usage: function() {\n //var usage = $( UserQuotaMeter.templates.usage( this.model.toJSON() ) );\n var usage = $(this._templateUsage(this.model.toJSON()));\n this.log(this + \".rendering usage:\", usage);\n return usage;\n },\n\n /** Render either the quota percentage meter or the human readable disk usage\n * depending on whether the user model has quota info (quota_percent === null -> no quota)\n * @returns {Object} this UserQuotaMeter\n */\n render: function() {\n //this.log( this + '.rendering' );\n var meterHtml = null;\n\n // no quota on server ('quota_percent' === null (can be valid at 0)), show usage instead\n this.log(\n this + \".model.quota_percent:\",\n this.model.get(\"quota_percent\")\n );\n if (\n this.model.get(\"quota_percent\") === null ||\n this.model.get(\"quota_percent\") === undefined\n ) {\n meterHtml = this._render_usage();\n\n // otherwise, render percent of quota (and warning, error)\n } else {\n meterHtml = this._render_quota();\n //TODO: add the original text for unregistered quotas\n //tooltip = \"Your disk quota is %s. You can increase your quota by registering a Galaxy account.\"\n }\n\n this.$el.html(meterHtml);\n this.$el.find(\".quota-meter-text\").tooltip();\n return this;\n },\n\n _templateQuotaMeter: function(data) {\n return [\n '',\n data.nice_total_disk_usage\n ? _l(\"Using \") + data.nice_total_disk_usage\n : \"\",\n \"\",\n \"',\n '',\n '\"\n ].join(\"\");\n },\n\n _templateUsage: function(data) {\n return [\n ''\n : \">\",\n _l(\"Using\"),\n \" \",\n data.quota_percent,\n \"%\",\n \"\",\n \"',\n '\"\n ].join(\"\");\n },\n\n toString: function() {\n return \"UserQuotaMeter(\" + this.model + \")\";\n }\n }\n);\n\n//==============================================================================\nexport default {\n UserQuotaMeter: UserQuotaMeter\n};\n"]} \ No newline at end of file diff --git a/static/maps/mvc/visualization/visualization-model.js.map b/static/maps/mvc/visualization/visualization-model.js.map index 83db0dfb6c7..716438e2947 100644 --- 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function(){\n\n//==============================================================================\n/** @class Model for a saved Galaxy visualization.\n *\n * @augments Backbone.Model\n * @constructs\n */\nvar Visualization = Backbone.Model.extend(\n /** @lends Visualization.prototype */ {\n ///** logger used to record this.log messages, commonly set to console */\n //// comment this out to suppress log output\n //logger : console,\n\n /** default attributes for a model */\n defaults: {\n config: {}\n },\n\n /** override urlRoot to handle prefix */\n urlRoot: function() {\n var apiUrl = \"api/visualizations\";\n return Galaxy.root + apiUrl;\n },\n\n /** Set up the model, determine if accessible, bind listeners\n * @see Backbone.Model#initialize\n */\n initialize: function(data) {\n //this.log( this + '.initialize', data, this.attributes );\n\n // munge config sub-object here since bbone won't handle defaults with this\n if (_.isObject(data.config) && _.isObject(this.defaults.config)) {\n _.defaults(data.config, this.defaults.config);\n }\n\n this._setUpListeners();\n },\n\n /** set up any event listeners\n */\n _setUpListeners: function() {\n //this.on( 'change', function(){\n // console.info( 'change:', arguments );\n //});\n },\n\n // ........................................................................ config\n /** override set to properly allow update and trigger change when setting the sub-obj 'config' */\n set: function(key, val) {\n //TODO: validate config is object\n if (key === \"config\") {\n var oldConfig = this.get(\"config\");\n // extend if already exists (is this correct behavior? no way to eliminate keys or reset entirely)\n // clone in order to trigger change (diff. obj ref)\n if (_.isObject(oldConfig)) {\n val = _.extend(_.clone(oldConfig), val);\n }\n }\n Backbone.Model.prototype.set.call(this, key, val);\n return this;\n },\n\n // ........................................................................ misc\n /** String representation */\n toString: function() {\n var idAndTitle = this.get(\"id\") || \"\";\n if (this.get(\"title\")) {\n idAndTitle += \":\" + this.get(\"title\");\n }\n return \"Visualization(\" + idAndTitle + \")\";\n }\n }\n);\n\n//==============================================================================\n/** @class Backbone collection of visualization models\n *\n * @constructs\n */\nvar VisualizationCollection = Backbone.Collection.extend(\n /** @lends VisualizationCollection.prototype */ {\n model: Visualization,\n\n ///** logger used to record this.log messages, commonly set to console */\n //// comment this out to suppress log output\n //logger : console,\n\n url: function() {\n return Galaxy.root + \"api/visualizations\";\n },\n\n /** Set up.\n * @see Backbone.Collection#initialize\n */\n initialize: function(models, options) {\n options = options || {};\n //this._setUpListeners();\n },\n\n //_setUpListeners : function(){\n //},\n\n // 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text_disable: \"Set at Runtime\",\n narrow: true,\n initial_errors: true,\n cls: \"ui-portlet-narrow\",\n initialmodel: function(process, form) {\n self._customize(form);\n process.resolve();\n },\n buildmodel: function(process, form) {\n form.model.get(\"postchange\")(process, form);\n },\n postchange: function(process, form) {\n var options = form.model.attributes;\n var current_state = {\n tool_id: options.id,\n tool_version: options.version,\n type: \"tool\",\n inputs: $.extend(true, {}, form.data.create())\n };\n Galaxy.emit.debug(\n \"tool-form-workflow::postchange()\",\n \"Sending current state.\",\n current_state\n );\n Utils.request({\n type: \"POST\",\n url: Galaxy.root + \"api/workflows/build_module\",\n data: current_state,\n success: function(data) {\n form.model.set(data.config_form);\n self._customize(form);\n form.update(data.config_form);\n form.errors(data.config_form);\n // This hasn't modified the workflow, just returned\n // module information for the tool to update the workflow\n // state stored on the client with. User needs to save\n // for this to take effect.\n node.update_field_data(data);\n Galaxy.emit.debug(\n \"tool-form-workflow::postchange()\",\n \"Received new model.\",\n data\n );\n process.resolve();\n },\n error: function(response) {\n Galaxy.emit.debug(\n \"tool-form-workflow::postchange()\",\n \"Refresh request failed.\",\n response\n );\n process.reject();\n }\n });\n }\n })\n );\n },\n\n _customize: function(form) {\n var options = form.model.attributes;\n Utils.deepeach(options.inputs, function(input) {\n if (input.type) {\n if (\n [\"data\", \"data_collection\"].indexOf(input.type) !=\n -1\n ) {\n input.type = \"hidden\";\n input.info =\n \"Data input '\" +\n input.name +\n \"' (\" +\n Utils.textify(input.extensions) +\n \")\";\n input.value = { __class__: \"RuntimeValue\" };\n } else if (!input.fixed) {\n input.collapsible_value = {\n __class__: \"RuntimeValue\"\n };\n input.is_workflow =\n (input.options && input.options.length == 0) ||\n [\"integer\", \"float\"].indexOf(input.type) != -1;\n }\n }\n });\n Utils.deepeach(options.inputs, function(input) {\n input.type == \"conditional\" &&\n (input.test_param.collapsible_value = undefined);\n });\n _addSections(form);\n _addLabelAnnotation(form);\n }\n });\n\n /** Augments the module form definition by adding label and annotation fields */\n function _addLabelAnnotation(form) {\n var options = form.model.attributes;\n var workflow = options.workflow;\n var node = options.node;\n options.inputs.unshift({\n type: \"text\",\n name: \"__annotation\",\n label: \"Annotation\",\n fixed: true,\n value: node.annotation,\n area: true,\n help:\n \"Add an annotation or notes to this step. Annotations are available when a workflow is viewed.\"\n });\n options.inputs.unshift({\n type: \"text\",\n name: \"__label\",\n label: \"Label\",\n value: node.label,\n help: \"Add a step label.\",\n fixed: true,\n onchange: function(new_label) {\n var duplicate = false;\n for (var i in workflow.nodes) {\n var n = workflow.nodes[i];\n if (\n n.label &&\n n.label == new_label &&\n n.id != node.id\n ) {\n duplicate = true;\n break;\n }\n }\n var input_id = form.data.match(\"__label\");\n var input_element = form.element_list[input_id];\n input_element.model.set(\n \"error_text\",\n duplicate &&\n \"Duplicate label. Please fix this before saving the workflow.\"\n );\n form.trigger(\"change\");\n }\n });\n }\n\n /** Builds all sub sections */\n function _addSections(form) {\n var options = form.model.attributes;\n var inputs = options.inputs;\n var datatypes = options.datatypes;\n var node = options.node;\n var workflow = options.workflow;\n var post_job_actions = node.post_job_actions;\n var output_id =\n node.output_terminals && Object.keys(node.output_terminals)[0];\n\n /** Visit input nodes and enrich by name/value pairs from server data */\n function visit(head, head_list) {\n head_list = head_list || [];\n head_list.push(head);\n for (var i in head.inputs) {\n var input = head.inputs[i];\n var action = input.action;\n if (action) {\n input.name = \"pja__\" + output_id + \"__\" + input.action;\n if (input.pja_arg) {\n input.name += \"__\" + input.pja_arg;\n }\n if (input.payload) {\n for (var p_id in input.payload) {\n input.payload[input.name + \"__\" + p_id] =\n input.payload[p_id];\n delete input.payload[p_id];\n }\n }\n var d = post_job_actions[input.action + output_id];\n if (d) {\n for (var j in head_list) {\n head_list[j].expanded = true;\n }\n if (input.pja_arg) {\n input.value =\n (d.action_arguments &&\n d.action_arguments[input.pja_arg]) ||\n input.value;\n } else {\n input.value = \"true\";\n }\n }\n }\n input.inputs && visit(input, head_list.slice(0));\n }\n }\n\n /** Builds sub section with step actions/annotation */\n function _makeSection(output_id, datatypes) {\n var extensions = [];\n var input_terminal_names = [];\n for (var key in datatypes) {\n extensions.push({ 0: datatypes[key], 1: datatypes[key] });\n }\n for (key in node.input_terminals) {\n input_terminal_names.push(node.input_terminals[key].name);\n }\n extensions.sort(function(a, b) {\n return a.label > b.label ? 1 : a.label < b.label ? -1 : 0;\n });\n extensions.unshift({\n 0: \"Sequences\",\n 1: \"Sequences\"\n });\n extensions.unshift({\n 0: \"Roadmaps\",\n 1: \"Roadmaps\"\n });\n extensions.unshift({\n 0: \"Leave unchanged\",\n 1: \"__empty__\"\n });\n var output;\n var input_config = {\n title: \"Configure Output: '\" + output_id + \"'\",\n type: \"section\",\n flat: true,\n inputs: [\n {\n label: \"Label\",\n type: \"text\",\n value:\n ((output = node.getWorkflowOutput(output_id)) &&\n output.label) ||\n \"\",\n help:\n \"This will provide a short name to describe the output - this must be unique across workflows.\",\n onchange: function(new_value) {\n workflow.attemptUpdateOutputLabel(\n node,\n output_id,\n new_value\n );\n }\n },\n {\n action: \"RenameDatasetAction\",\n pja_arg: \"newname\",\n label: \"Rename dataset\",\n type: \"text\",\n value: \"\",\n ignore: \"\",\n help:\n 'This action will rename the output dataset. Click here for more information. Valid inputs are: ' +\n input_terminal_names.join(\", \") +\n \".\"\n },\n {\n action: \"ChangeDatatypeAction\",\n pja_arg: \"newtype\",\n label: \"Change datatype\",\n type: \"select\",\n ignore: \"__empty__\",\n value: \"__empty__\",\n options: extensions,\n help:\n \"This action will change the datatype of the output to the indicated value.\"\n },\n {\n action: \"TagDatasetAction\",\n pja_arg: \"tags\",\n label: \"Add Tags\",\n type: \"text\",\n value: \"\",\n ignore: \"\",\n help: \"This action will set tags for the dataset.\"\n },\n {\n action: \"RemoveTagDatasetAction\",\n pja_arg: \"tags\",\n label: \"Remove Tags\",\n type: \"text\",\n value: \"\",\n ignore: \"\",\n help:\n \"This action will remove tags for the dataset.\"\n },\n {\n title: \"Assign columns\",\n type: \"section\",\n flat: true,\n inputs: [\n {\n action: \"ColumnSetAction\",\n pja_arg: \"chromCol\",\n label: \"Chrom column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n },\n {\n action: \"ColumnSetAction\",\n pja_arg: \"startCol\",\n label: \"Start column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n },\n {\n action: \"ColumnSetAction\",\n pja_arg: \"endCol\",\n label: \"End column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n },\n {\n action: \"ColumnSetAction\",\n pja_arg: \"strandCol\",\n label: \"Strand column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n },\n {\n action: \"ColumnSetAction\",\n pja_arg: \"nameCol\",\n label: \"Name column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n }\n ],\n help:\n \"This action will set column assignments in the output dataset. 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Tool: Tool\n };\n }\n);\n"]} \ No newline at end of file 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[\"utils/utils\", \"mvc/form/form-view\", \"mvc/tool/tool-form-base\"],\n function(Utils, Form, ToolFormBase) {\n /** Default form wrapper for non-tool modules in the workflow editor. */\n var Default = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n var node = options.node;\n this.form = new Form(\n Utils.merge(options, {\n onchange: function() {\n Utils.request({\n type: \"POST\",\n url: Galaxy.root + \"api/workflows/build_module\",\n data: {\n id: node.id,\n type: node.type,\n content_id: node.content_id,\n inputs: self.form.data.create()\n },\n success: function(data) {\n node.update_field_data(data);\n }\n });\n }\n })\n );\n _addLabelAnnotation(this.form);\n this.form.render();\n }\n });\n\n /** Tool form wrapper for the workflow editor. */\n var Tool = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n var node = options.node;\n this.form = new ToolFormBase(\n Utils.merge(options, {\n text_enable: \"Set in Advance\",\n text_disable: \"Set at Runtime\",\n narrow: true,\n initial_errors: true,\n cls: \"ui-portlet-narrow\",\n initialmodel: function(process, form) {\n self._customize(form);\n process.resolve();\n },\n buildmodel: function(process, form) {\n form.model.get(\"postchange\")(process, form);\n },\n postchange: function(process, form) {\n var options = form.model.attributes;\n var current_state = {\n tool_id: options.id,\n tool_version: options.version,\n type: \"tool\",\n inputs: $.extend(true, {}, form.data.create())\n };\n Galaxy.emit.debug(\n \"tool-form-workflow::postchange()\",\n \"Sending current state.\",\n current_state\n );\n Utils.request({\n type: \"POST\",\n url: Galaxy.root + \"api/workflows/build_module\",\n data: current_state,\n success: function(data) {\n form.model.set(data.config_form);\n self._customize(form);\n form.update(data.config_form);\n form.errors(data.config_form);\n // This hasn't modified the workflow, just returned\n // module information for the tool to update the workflow\n // state stored on the client with. User needs to save\n // for this to take effect.\n node.update_field_data(data);\n Galaxy.emit.debug(\n \"tool-form-workflow::postchange()\",\n \"Received new model.\",\n data\n );\n process.resolve();\n },\n error: function(response) {\n Galaxy.emit.debug(\n \"tool-form-workflow::postchange()\",\n \"Refresh request failed.\",\n response\n );\n process.reject();\n }\n });\n }\n })\n );\n },\n\n _customize: function(form) {\n var options = form.model.attributes;\n Utils.deepeach(options.inputs, function(input) {\n if (input.type) {\n if (\n [\"data\", \"data_collection\"].indexOf(input.type) !=\n -1\n ) {\n input.type = \"hidden\";\n input.info =\n \"Data input '\" +\n input.name +\n \"' (\" +\n Utils.textify(input.extensions) +\n \")\";\n input.value = { __class__: \"RuntimeValue\" };\n } else if (!input.fixed) {\n input.collapsible_value = {\n __class__: \"RuntimeValue\"\n };\n input.is_workflow =\n (input.options && input.options.length == 0) ||\n [\"integer\", \"float\"].indexOf(input.type) != -1;\n }\n }\n });\n Utils.deepeach(options.inputs, function(input) {\n input.type == \"conditional\" &&\n (input.test_param.collapsible_value = undefined);\n });\n _addSections(form);\n _addLabelAnnotation(form);\n }\n });\n\n /** Augments the module form definition by adding label and annotation fields */\n function _addLabelAnnotation(form) {\n var options = form.model.attributes;\n var workflow = options.workflow;\n var node = options.node;\n options.inputs.unshift({\n type: \"text\",\n name: \"__annotation\",\n label: \"Annotation\",\n fixed: true,\n value: node.annotation,\n area: true,\n help:\n \"Add an annotation or notes to this step. Annotations are available when a workflow is viewed.\"\n });\n options.inputs.unshift({\n type: \"text\",\n name: \"__label\",\n label: \"Label\",\n value: node.label,\n help: \"Add a step label.\",\n fixed: true,\n onchange: function(new_label) {\n var duplicate = false;\n for (var i in workflow.nodes) {\n var n = workflow.nodes[i];\n if (\n n.label &&\n n.label == new_label &&\n n.id != node.id\n ) {\n duplicate = true;\n break;\n }\n }\n var input_id = form.data.match(\"__label\");\n var input_element = form.element_list[input_id];\n input_element.model.set(\n \"error_text\",\n duplicate &&\n \"Duplicate label. Please fix this before saving the workflow.\"\n );\n form.trigger(\"change\");\n }\n });\n }\n\n /** Builds all sub sections */\n function _addSections(form) {\n var options = form.model.attributes;\n var inputs = options.inputs;\n var datatypes = options.datatypes;\n var node = options.node;\n var workflow = options.workflow;\n var post_job_actions = node.post_job_actions;\n var output_id =\n node.output_terminals && Object.keys(node.output_terminals)[0];\n\n /** Visit input nodes and enrich by name/value pairs from server data */\n function visit(head, head_list) {\n head_list = head_list || [];\n head_list.push(head);\n for (var i in head.inputs) {\n var input = head.inputs[i];\n var action = input.action;\n if (action) {\n input.name = \"pja__\" + output_id + \"__\" + input.action;\n if (input.pja_arg) {\n input.name += \"__\" + input.pja_arg;\n }\n if (input.payload) {\n for (var p_id in input.payload) {\n input.payload[input.name + \"__\" + p_id] =\n input.payload[p_id];\n delete input.payload[p_id];\n }\n }\n var d = post_job_actions[input.action + output_id];\n if (d) {\n for (var j in head_list) {\n head_list[j].expanded = true;\n }\n if (input.pja_arg) {\n input.value =\n (d.action_arguments &&\n d.action_arguments[input.pja_arg]) ||\n input.value;\n } else {\n input.value = \"true\";\n }\n }\n }\n input.inputs && visit(input, head_list.slice(0));\n }\n }\n\n /** Builds sub section with step actions/annotation */\n function _makeSection(output_id, datatypes) {\n var extensions = [];\n var input_terminal_names = [];\n for (var key in datatypes) {\n extensions.push({ 0: datatypes[key], 1: datatypes[key] });\n }\n for (key in node.input_terminals) {\n input_terminal_names.push(node.input_terminals[key].name);\n }\n extensions.sort(function(a, b) {\n return a.label > b.label ? 1 : a.label < b.label ? -1 : 0;\n });\n extensions.unshift({\n 0: \"Sequences\",\n 1: \"Sequences\"\n });\n extensions.unshift({\n 0: \"Roadmaps\",\n 1: \"Roadmaps\"\n });\n extensions.unshift({\n 0: \"Leave unchanged\",\n 1: \"__empty__\"\n });\n var output;\n var input_config = {\n title: \"Configure Output: '\" + output_id + \"'\",\n type: \"section\",\n flat: true,\n inputs: [\n {\n label: \"Label\",\n type: \"text\",\n value:\n ((output = node.getWorkflowOutput(output_id)) &&\n output.label) ||\n \"\",\n help:\n \"This will provide a short name to describe the output - this must be unique across workflows.\",\n onchange: function(new_value) {\n workflow.attemptUpdateOutputLabel(\n node,\n output_id,\n new_value\n );\n }\n },\n {\n action: \"RenameDatasetAction\",\n pja_arg: \"newname\",\n label: \"Rename dataset\",\n type: \"text\",\n value: \"\",\n ignore: \"\",\n help:\n 'This action will rename the output dataset. Click here for more information. Valid inputs are: ' +\n input_terminal_names.join(\", \") +\n \".\"\n },\n {\n action: \"ChangeDatatypeAction\",\n pja_arg: \"newtype\",\n label: \"Change datatype\",\n type: \"select\",\n ignore: \"__empty__\",\n value: \"__empty__\",\n options: extensions,\n help:\n \"This action will change the datatype of the output to the indicated value.\"\n },\n {\n action: \"TagDatasetAction\",\n pja_arg: \"tags\",\n label: \"Add Tags\",\n type: \"text\",\n value: \"\",\n ignore: \"\",\n help: \"This action will set tags for the dataset.\"\n },\n {\n action: \"RemoveTagDatasetAction\",\n pja_arg: \"tags\",\n label: \"Remove Tags\",\n type: \"text\",\n value: \"\",\n ignore: \"\",\n help:\n \"This action will remove tags for the dataset.\"\n },\n {\n title: \"Assign columns\",\n type: \"section\",\n flat: true,\n inputs: [\n {\n action: \"ColumnSetAction\",\n pja_arg: \"chromCol\",\n label: \"Chrom column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n },\n {\n action: \"ColumnSetAction\",\n pja_arg: \"startCol\",\n label: \"Start column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n },\n {\n action: \"ColumnSetAction\",\n pja_arg: \"endCol\",\n label: \"End column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n },\n {\n action: \"ColumnSetAction\",\n pja_arg: \"strandCol\",\n label: \"Strand column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n },\n {\n action: \"ColumnSetAction\",\n pja_arg: \"nameCol\",\n label: \"Name column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n }\n ],\n help:\n \"This action will set column assignments in the output dataset. Blank fields are ignored.\"\n }\n ]\n };\n visit(input_config);\n return input_config;\n }\n\n if (output_id) {\n inputs.push({\n name: \"pja__\" + output_id + \"__EmailAction\",\n label: \"Email notification\",\n type: \"boolean\",\n value: String(\n Boolean(post_job_actions[\"EmailAction\" + output_id])\n ),\n ignore: \"false\",\n help:\n \"An email notification will be sent when the job has completed.\",\n payload: {\n host: window.location.host\n }\n });\n inputs.push({\n name: \"pja__\" + output_id + \"__DeleteIntermediatesAction\",\n label: \"Output cleanup\",\n type: \"boolean\",\n value: String(\n Boolean(\n post_job_actions[\n \"DeleteIntermediatesAction\" + output_id\n ]\n )\n ),\n ignore: \"false\",\n help:\n \"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs.\"\n });\n for (var i in node.output_terminals) {\n inputs.push(_makeSection(i, datatypes));\n }\n }\n }\n\n return {\n Default: Default,\n 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Remove all PJAs and recreate based on outputs.\n var self = this;\n $.each(this.nodes, function(k, node) {\n if (node.type === \"tool\") {\n var node_changed = false;\n if (node.post_job_actions === null) {\n node.post_job_actions = {};\n node_changed = true;\n }\n var pjas_to_rem = [];\n $.each(node.post_job_actions, function(pja_id, pja) {\n if (pja.action_type == \"HideDatasetAction\") {\n pjas_to_rem.push(pja_id);\n }\n });\n if (pjas_to_rem.length > 0) {\n $.each(pjas_to_rem, function(i, pja_name) {\n node_changed = true;\n delete node.post_job_actions[pja_name];\n });\n }\n if (using_workflow_outputs) {\n $.each(node.output_terminals, function(ot_id, ot) {\n var create_pja = !node.isWorkflowOutput(\n ot.name\n );\n if (create_pja === true) {\n node_changed = true;\n var pja = {\n action_type: \"HideDatasetAction\",\n output_name: ot.name,\n action_arguments: {}\n };\n node.post_job_actions[\n \"HideDatasetAction\" + ot.name\n ] = null;\n node.post_job_actions[\n \"HideDatasetAction\" + ot.name\n ] = pja;\n }\n });\n }\n // lastly, if this is the active node, and we made changes, reload the display at right.\n if (self.active_node == node && node_changed === true) {\n self.reload_active_node();\n }\n }\n });\n }\n },\n to_simple: function() {\n var nodes = {};\n $.each(this.nodes, function(i, node) {\n var input_connections = {};\n $.each(node.input_terminals, function(k, t) {\n input_connections[t.name] = null;\n // There should only be 0 or 1 connectors, so this is\n // really a sneaky if statement\n var cons = [];\n $.each(t.connectors, function(i, c) {\n if (c.handle1) {\n var con_dict = {\n id: c.handle1.node.id,\n output_name: c.handle1.name\n };\n var input_subworkflow_step_id =\n t.attributes.input.input_subworkflow_step_id;\n if (input_subworkflow_step_id !== undefined) {\n con_dict[\n \"input_subworkflow_step_id\"\n ] = input_subworkflow_step_id;\n }\n cons[i] = con_dict;\n input_connections[t.name] = cons;\n }\n });\n });\n var post_job_actions = {};\n if (node.post_job_actions) {\n $.each(node.post_job_actions, function(i, act) {\n var pja = {\n action_type: act.action_type,\n output_name: act.output_name,\n action_arguments: act.action_arguments\n };\n post_job_actions[\n act.action_type + act.output_name\n ] = null;\n post_job_actions[\n act.action_type + act.output_name\n ] = pja;\n });\n }\n if (!node.workflow_outputs) {\n node.workflow_outputs = [];\n // Just in case.\n }\n var node_data = {\n id: node.id,\n type: node.type,\n content_id: node.content_id,\n tool_version: node.config_form.version,\n tool_state: node.tool_state,\n errors: node.errors,\n input_connections: input_connections,\n position: $(node.element).position(),\n annotation: node.annotation,\n post_job_actions: node.post_job_actions,\n uuid: node.uuid,\n label: node.label,\n workflow_outputs: node.workflow_outputs\n };\n nodes[node.id] = node_data;\n });\n return { steps: nodes };\n },\n from_simple: function(data, initialImport_) {\n var initialImport =\n initialImport_ === undefined ? true : initialImport_;\n var wf = this;\n var offset = 0;\n if (initialImport) {\n wf.name = data.name;\n } else {\n offset = Object.keys(wf.nodes).length;\n }\n var max_id = offset;\n // First pass, nodes\n var using_workflow_outputs = false;\n $.each(data.steps, function(id, step) {\n var node = wf.app.prebuildNode(\n step.type,\n step.name,\n step.content_id\n );\n // If workflow being copied into another, wipe UUID and let\n // Galaxy assign new ones.\n if (!initialImport) {\n step.uuid = null;\n $.each(step.workflow_outputs, function(\n name,\n workflow_output\n ) {\n workflow_output.uuid = null;\n });\n }\n node.init_field_data(step);\n if (step.position) {\n node.element.css({\n top: step.position.top,\n left: step.position.left\n });\n }\n node.id = parseInt(step.id) + offset;\n wf.nodes[node.id] = node;\n max_id = Math.max(max_id, parseInt(id) + offset);\n // For older workflows, it's possible to have HideDataset PJAs, but not WorkflowOutputs.\n // Check for either, and then add outputs in the next pass.\n if (!using_workflow_outputs) {\n if (node.workflow_outputs.length > 0) {\n using_workflow_outputs = true;\n } else {\n $.each(node.post_job_actions || [], function(\n pja_id,\n pja\n ) {\n if (pja.action_type === \"HideDatasetAction\") {\n using_workflow_outputs = true;\n }\n });\n }\n }\n });\n wf.id_counter = max_id + 1;\n // Second pass, connections\n $.each(data.steps, function(id, step) {\n var node = wf.nodes[parseInt(id) + offset];\n $.each(step.input_connections, function(k, v) {\n if (v) {\n if (!$.isArray(v)) {\n v = [v];\n }\n $.each(v, function(l, x) {\n var other_node = wf.nodes[parseInt(x.id) + offset];\n var c = new Connector();\n c.connect(\n other_node.output_terminals[x.output_name],\n node.input_terminals[k]\n );\n c.redraw();\n });\n }\n });\n if (using_workflow_outputs) {\n // Ensure that every output terminal has a WorkflowOutput or HideDatasetAction.\n $.each(node.output_terminals, function(ot_id, ot) {\n if (\n node.post_job_actions[\n \"HideDatasetAction\" + ot.name\n ] === undefined\n ) {\n node.addWorkflowOutput(ot.name);\n var callout = $(node.element).find(\n \".callout.\" + ot.name\n );\n callout\n .find(\"img\")\n .attr(\n \"src\",\n Galaxy.root +\n \"static/images/fugue/asterisk-small.png\"\n );\n wf.has_changes = true;\n }\n });\n }\n });\n },\n check_changes_in_active_form: function() {\n // If active form has changed, save it\n if (this.active_form_has_changes) {\n this.has_changes = true;\n // Submit form.\n $(\"#right-content\")\n .find(\"form\")\n .submit();\n this.active_form_has_changes = false;\n }\n },\n reload_active_node: function() {\n if (this.active_node) {\n var node = this.active_node;\n this.clear_active_node();\n this.activate_node(node);\n }\n },\n clear_active_node: function() {\n if (this.active_node) {\n this.active_node.make_inactive();\n this.active_node = null;\n }\n this.app.showAttributes();\n },\n activate_node: function(node) {\n if (this.active_node != node) {\n this.check_changes_in_active_form();\n this.clear_active_node();\n this.app.showForm(node.config_form, node);\n node.make_active();\n this.active_node = node;\n }\n },\n node_changed: function(node, force) {\n this.has_changes = true;\n if (this.active_node == node && force) {\n // Force changes to be saved even on new connection (previously dumped)\n this.check_changes_in_active_form();\n this.app.showForm(node.config_form, node);\n }\n this.app.showWorkflowParameters();\n },\n layout: function() {\n this.check_changes_in_active_form();\n this.has_changes = true;\n // Prepare predecessor / successor tracking\n var n_pred = {};\n var successors = {};\n // First pass to initialize arrays even for nodes with no connections\n $.each(this.nodes, function(id, node) {\n if (n_pred[id] === undefined) {\n n_pred[id] = 0;\n }\n if (successors[id] === undefined) {\n successors[id] = [];\n }\n });\n // Second pass to count predecessors and successors\n $.each(this.nodes, function(id, node) {\n $.each(node.input_terminals, function(j, t) {\n $.each(t.connectors, function(k, c) {\n // A connection exists from `other` to `node`\n var other = c.handle1.node;\n // node gains a predecessor\n n_pred[node.id] += 1;\n // other gains a successor\n successors[other.id].push(node.id);\n });\n });\n });\n // Assemble order, tracking levels\n var node_ids_by_level = [];\n while (true) {\n // Everything without a predecessor\n var level_parents = [];\n for (var pred_k in n_pred) {\n if (n_pred[pred_k] === 0) {\n level_parents.push(pred_k);\n }\n }\n if (level_parents.length === 0) {\n break;\n }\n node_ids_by_level.push(level_parents);\n // Remove the parents from this level, and decrement the number\n // of predecessors for each successor\n for (var k in level_parents) {\n var v = level_parents[k];\n delete n_pred[v];\n for (var sk in successors[v]) {\n n_pred[successors[v][sk]] -= 1;\n }\n }\n }\n if (n_pred.length) {\n // ERROR: CYCLE! Currently we do nothing\n return;\n }\n // Layout each level\n var all_nodes = this.nodes;\n var h_pad = 80;\n var v_pad = 30;\n var left = h_pad;\n $.each(node_ids_by_level, function(i, ids) {\n // We keep nodes in the same order in a level to give the user\n // some control over ordering\n ids.sort(function(a, b) {\n return (\n $(all_nodes[a].element).position().top -\n $(all_nodes[b].element).position().top\n );\n });\n // Position each node\n var max_width = 0;\n var top = v_pad;\n $.each(ids, function(j, id) {\n var node = all_nodes[id];\n var element = $(node.element);\n $(element).css({ top: top, left: left });\n max_width = Math.max(max_width, $(element).width());\n top += $(element).height() + v_pad;\n });\n left += max_width + h_pad;\n });\n // Need to redraw all connectors\n $.each(all_nodes, function(_, node) {\n node.redraw();\n });\n },\n bounds_for_all_nodes: function() {\n var xmin = Infinity,\n xmax = -Infinity,\n ymin = Infinity,\n ymax = -Infinity,\n p;\n $.each(this.nodes, function(id, node) {\n var e = $(node.element);\n p = e.position();\n xmin = Math.min(xmin, p.left);\n xmax = Math.max(xmax, p.left + e.width());\n ymin = Math.min(ymin, p.top);\n ymax = Math.max(ymax, p.top + e.width());\n });\n return { xmin: xmin, xmax: xmax, ymin: ymin, ymax: ymax };\n },\n fit_canvas_to_nodes: function() {\n // Math utils\n function round_up(x, n) {\n return Math.ceil(x / n) * n;\n }\n function fix_delta(x, n) {\n if (x < n || x > 3 * n) {\n var new_pos = (Math.ceil((x % n) / n) + 1) * n;\n return -(x - new_pos);\n }\n return 0;\n }\n // Span of all elements\n var bounds = this.bounds_for_all_nodes();\n var position = this.canvas_container.position();\n var parent = this.canvas_container.parent();\n // Determine amount we need to expand on top/left\n var xmin_delta = fix_delta(bounds.xmin, 100);\n var ymin_delta = fix_delta(bounds.ymin, 100);\n // May need to expand farther to fill viewport\n xmin_delta = Math.max(xmin_delta, position.left);\n 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labels \" +\n toLabel +\n \". This must be fixed before it can be saved.\"\n );\n }\n if (toLabel) {\n this.registerOutputLabel(toLabel);\n }\n },\n attemptUpdateOutputLabel: function(node, outputName, label) {\n if (this.canLabelOutputWith(label)) {\n node.labelWorkflowOutput(outputName, label);\n node.nodeView.redrawWorkflowOutputs();\n return true;\n } else {\n return false;\n }\n },\n create_node: function(type, title_text, content_id) {\n var node = this.app.prebuildNode(type, title_text, content_id);\n this.add_node(node);\n this.fit_canvas_to_nodes();\n this.app.canvas_manager.draw_overview();\n this.activate_node(node);\n return node;\n },\n add_node: function(node) {\n node.id = this.id_counter;\n node.element.attr(\"id\", \"wf-node-step-\" + node.id);\n this.id_counter++;\n this.nodes[node.id] = node;\n this.has_changes = true;\n node.workflow = this;\n },\n remove_node: function(node) {\n if (this.active_node == node) {\n this.clear_active_node();\n }\n delete this.nodes[node.id];\n this.has_changes = true;\n },\n remove_all: function() {\n var wf = this;\n $.each(this.nodes, function(k, v) {\n v.destroy();\n wf.remove_node(v);\n });\n },\n rectify_workflow_outputs: function() {\n // Find out if we're using workflow_outputs or not.\n var using_workflow_outputs = false;\n var has_existing_pjas = false;\n $.each(this.nodes, function(k, node) {\n if (node.workflow_outputs && node.workflow_outputs.length > 0) {\n using_workflow_outputs = true;\n }\n $.each(node.post_job_actions, function(pja_id, pja) {\n if (pja.action_type === \"HideDatasetAction\") {\n has_existing_pjas = true;\n }\n });\n });\n if (\n using_workflow_outputs !== false ||\n has_existing_pjas !== false\n ) {\n // Using workflow outputs, or has existing pjas. Remove all PJAs and recreate based on outputs.\n var self = this;\n $.each(this.nodes, function(k, node) {\n if (node.type === \"tool\") {\n var node_changed = false;\n if (node.post_job_actions === null) {\n node.post_job_actions = {};\n node_changed = true;\n }\n var pjas_to_rem = [];\n $.each(node.post_job_actions, function(pja_id, pja) {\n if (pja.action_type == \"HideDatasetAction\") {\n pjas_to_rem.push(pja_id);\n }\n });\n if (pjas_to_rem.length > 0) {\n $.each(pjas_to_rem, function(i, pja_name) {\n node_changed = true;\n delete node.post_job_actions[pja_name];\n });\n }\n if (using_workflow_outputs) {\n $.each(node.output_terminals, function(ot_id, ot) {\n var create_pja = !node.isWorkflowOutput(\n ot.name\n );\n if (create_pja === true) {\n node_changed = true;\n var pja = {\n action_type: \"HideDatasetAction\",\n output_name: ot.name,\n action_arguments: {}\n };\n node.post_job_actions[\n \"HideDatasetAction\" + ot.name\n ] = null;\n node.post_job_actions[\n \"HideDatasetAction\" + ot.name\n ] = pja;\n }\n });\n }\n // lastly, if this is the active node, and we made changes, reload the display at right.\n if (self.active_node == node && node_changed === true) {\n self.reload_active_node();\n }\n }\n });\n }\n },\n to_simple: function() {\n var nodes = {};\n $.each(this.nodes, function(i, node) {\n var input_connections = {};\n $.each(node.input_terminals, function(k, t) {\n input_connections[t.name] = null;\n // There should only be 0 or 1 connectors, so this is\n // really a sneaky if statement\n var cons = [];\n $.each(t.connectors, function(i, c) {\n if (c.handle1) {\n var con_dict = {\n id: c.handle1.node.id,\n output_name: c.handle1.name\n };\n var input_subworkflow_step_id =\n t.attributes.input.input_subworkflow_step_id;\n if (input_subworkflow_step_id !== undefined) {\n con_dict[\n \"input_subworkflow_step_id\"\n ] = input_subworkflow_step_id;\n }\n cons[i] = con_dict;\n input_connections[t.name] = cons;\n }\n });\n });\n var post_job_actions = {};\n if (node.post_job_actions) {\n $.each(node.post_job_actions, function(i, act) {\n var pja = {\n action_type: act.action_type,\n output_name: act.output_name,\n action_arguments: act.action_arguments\n };\n post_job_actions[\n act.action_type + act.output_name\n ] = null;\n post_job_actions[\n act.action_type + act.output_name\n ] = pja;\n });\n }\n if (!node.workflow_outputs) {\n node.workflow_outputs = [];\n // Just in case.\n }\n var node_data = {\n id: node.id,\n type: node.type,\n content_id: node.content_id,\n tool_version: node.config_form.version,\n tool_state: node.tool_state,\n errors: node.errors,\n input_connections: input_connections,\n position: $(node.element).position(),\n annotation: node.annotation,\n post_job_actions: node.post_job_actions,\n uuid: node.uuid,\n label: node.label,\n workflow_outputs: node.workflow_outputs\n };\n nodes[node.id] = node_data;\n });\n return { steps: nodes };\n },\n from_simple: function(data, initialImport_) {\n var initialImport =\n initialImport_ === undefined ? true : initialImport_;\n var wf = this;\n var offset = 0;\n if (initialImport) {\n wf.name = data.name;\n } else {\n offset = Object.keys(wf.nodes).length;\n }\n var max_id = offset;\n // First pass, nodes\n var using_workflow_outputs = false;\n $.each(data.steps, function(id, step) {\n var node = wf.app.prebuildNode(\n step.type,\n step.name,\n step.content_id\n );\n // If workflow being copied into another, wipe UUID and let\n // Galaxy assign new ones.\n if (!initialImport) {\n step.uuid = null;\n $.each(step.workflow_outputs, function(\n name,\n workflow_output\n ) {\n workflow_output.uuid = null;\n });\n }\n node.init_field_data(step);\n if (step.position) {\n node.element.css({\n top: step.position.top,\n left: step.position.left\n });\n }\n node.id = parseInt(step.id) + offset;\n wf.nodes[node.id] = node;\n max_id = Math.max(max_id, parseInt(id) + offset);\n // For older workflows, it's possible to have HideDataset PJAs, but not WorkflowOutputs.\n // Check for either, and then add outputs in the next pass.\n if (!using_workflow_outputs) {\n if (node.workflow_outputs.length > 0) {\n using_workflow_outputs = true;\n } else {\n $.each(node.post_job_actions || [], function(\n pja_id,\n pja\n ) {\n if (pja.action_type === \"HideDatasetAction\") {\n using_workflow_outputs = true;\n }\n });\n }\n }\n });\n wf.id_counter = max_id + 1;\n // Second pass, connections\n $.each(data.steps, function(id, step) {\n var node = wf.nodes[parseInt(id) + offset];\n $.each(step.input_connections, function(k, v) {\n if (v) {\n if (!$.isArray(v)) {\n v = [v];\n }\n $.each(v, function(l, x) {\n var other_node = wf.nodes[parseInt(x.id) + offset];\n var c = new Connector();\n c.connect(\n other_node.output_terminals[x.output_name],\n node.input_terminals[k]\n );\n c.redraw();\n });\n }\n });\n if (using_workflow_outputs) {\n // Ensure that every output terminal has a WorkflowOutput or HideDatasetAction.\n $.each(node.output_terminals, function(ot_id, ot) {\n if (\n node.post_job_actions[\n \"HideDatasetAction\" + ot.name\n ] === undefined\n ) {\n node.addWorkflowOutput(ot.name);\n var callout = $(node.element).find(\n \".callout.\" + ot.name\n );\n callout\n .find(\"img\")\n .attr(\n \"src\",\n Galaxy.root +\n \"static/images/fugue/asterisk-small.png\"\n );\n wf.has_changes = true;\n }\n });\n }\n });\n },\n check_changes_in_active_form: function() {\n // If active form has changed, save it\n if (this.active_form_has_changes) {\n this.has_changes = true;\n // Submit form.\n $(\"#right-content\")\n .find(\"form\")\n .submit();\n this.active_form_has_changes = false;\n }\n },\n reload_active_node: function() {\n if (this.active_node) {\n var node = this.active_node;\n this.clear_active_node();\n this.activate_node(node);\n }\n },\n clear_active_node: function() {\n if (this.active_node) {\n this.active_node.make_inactive();\n this.active_node = null;\n }\n this.app.showAttributes();\n },\n activate_node: function(node) {\n if (this.active_node != node) {\n this.check_changes_in_active_form();\n this.clear_active_node();\n this.app.showForm(node.config_form, node);\n node.make_active();\n this.active_node = node;\n }\n },\n node_changed: function(node, force) {\n this.has_changes = true;\n if (this.active_node == node && force) {\n // Force changes to be saved even on new connection (previously dumped)\n this.check_changes_in_active_form();\n this.app.showForm(node.config_form, node);\n }\n this.app.showWorkflowParameters();\n },\n layout: function() {\n this.check_changes_in_active_form();\n this.has_changes = true;\n // Prepare predecessor / successor tracking\n var n_pred = {};\n var successors = {};\n // First pass to initialize arrays even for nodes with no connections\n $.each(this.nodes, function(id, node) {\n if (n_pred[id] === undefined) {\n n_pred[id] = 0;\n }\n if (successors[id] === undefined) {\n successors[id] = [];\n }\n });\n // Second pass to count predecessors and successors\n $.each(this.nodes, function(id, node) {\n $.each(node.input_terminals, function(j, t) {\n $.each(t.connectors, function(k, c) {\n // A connection exists from `other` to `node`\n var other = c.handle1.node;\n // node gains a predecessor\n n_pred[node.id] += 1;\n // other gains a successor\n successors[other.id].push(node.id);\n });\n });\n });\n // Assemble order, tracking levels\n var node_ids_by_level = [];\n while (true) {\n // Everything without a predecessor\n var level_parents = [];\n for (var pred_k in n_pred) {\n if (n_pred[pred_k] === 0) {\n level_parents.push(pred_k);\n }\n }\n if (level_parents.length === 0) {\n break;\n }\n node_ids_by_level.push(level_parents);\n // Remove the parents from this level, and decrement the number\n // of predecessors for each successor\n for (var k in level_parents) {\n var v = level_parents[k];\n delete n_pred[v];\n for (var sk in successors[v]) {\n n_pred[successors[v][sk]] -= 1;\n }\n }\n }\n if (n_pred.length) {\n // ERROR: CYCLE! Currently we do nothing\n return;\n }\n // Layout each level\n var all_nodes = this.nodes;\n var h_pad = 80;\n var v_pad = 30;\n var left = h_pad;\n $.each(node_ids_by_level, function(i, ids) {\n // We keep nodes in the same order in a level to give the user\n // some control over ordering\n ids.sort(function(a, b) {\n return (\n $(all_nodes[a].element).position().top -\n $(all_nodes[b].element).position().top\n );\n });\n // Position each node\n var max_width = 0;\n var top = v_pad;\n $.each(ids, function(j, id) {\n var node = all_nodes[id];\n var element = $(node.element);\n $(element).css({ top: top, left: left });\n max_width = Math.max(max_width, $(element).width());\n top += $(element).height() + v_pad;\n });\n left += max_width + h_pad;\n });\n // Need to redraw all connectors\n $.each(all_nodes, function(_, node) {\n node.redraw();\n });\n },\n bounds_for_all_nodes: function() {\n var xmin = Infinity,\n xmax = -Infinity,\n ymin = Infinity,\n ymax = -Infinity,\n p;\n $.each(this.nodes, function(id, node) {\n var e = $(node.element);\n p = e.position();\n xmin = Math.min(xmin, p.left);\n xmax = Math.max(xmax, p.left + e.width());\n ymin = Math.min(ymin, p.top);\n ymax = Math.max(ymax, p.top + e.width());\n });\n return { xmin: xmin, xmax: xmax, ymin: ymin, ymax: ymax };\n },\n fit_canvas_to_nodes: function() {\n // Math utils\n function round_up(x, n) {\n return Math.ceil(x / n) * n;\n }\n function fix_delta(x, n) {\n if (x < n || x > 3 * n) {\n var new_pos = (Math.ceil((x % n) / n) + 1) * n;\n return -(x - new_pos);\n }\n return 0;\n }\n // Span of all elements\n var bounds = this.bounds_for_all_nodes();\n var position = this.canvas_container.position();\n var parent = this.canvas_container.parent();\n // Determine amount we need to expand on top/left\n var xmin_delta = fix_delta(bounds.xmin, 100);\n var ymin_delta = fix_delta(bounds.ymin, 100);\n // May need to expand farther to fill viewport\n xmin_delta = Math.max(xmin_delta, position.left);\n ymin_delta = Math.max(ymin_delta, position.top);\n var left = position.left - xmin_delta;\n var top = position.top - ymin_delta;\n // Same for width/height\n var width = round_up(bounds.xmax + 100, 100) + xmin_delta;\n var height = round_up(bounds.ymax + 100, 100) + ymin_delta;\n width = Math.max(width, -left + parent.width());\n height = Math.max(height, -top + parent.height());\n // Grow the canvas container\n this.canvas_container.css({\n left: left,\n top: top,\n width: width,\n height: height\n });\n // Move elements back if needed\n this.canvas_container.children().each(function() {\n var p = $(this).position();\n $(this).css(\"left\", p.left + xmin_delta);\n $(this).css(\"top\", p.top + ymin_delta);\n });\n }\n });\n return Workflow;\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/workflow/workflow-model.js.map b/static/maps/mvc/workflow/workflow-model.js.map index 951a1852b04..f5d1a71cecb 100644 --- a/static/maps/mvc/workflow/workflow-model.js.map +++ b/static/maps/mvc/workflow/workflow-model.js.map @@ -1 +1 @@ -{"version":3,"sources":["mvc/workflow/workflow-model.js"],"names":["define","baseMVC","WorkflowItem","Backbone","Model","extend","LoggableMixin","_logNamespace","logNamespace","urlRoot","toJSON","workflow","this","attributes","WorkflowCollection","Collection","model"],"mappings":"aAAAA,QAAQ,gBAAiB,SAASC,GAE9B,IAQIC,EAAeC,SAASC,MAAMC,OAAOJ,EAAQK,eAAeD,QAC5DE,cATJ,WASIA,QAAAA,OAAeC,KAAAA,gBAEfC,OAAAA,WAEAC,OAAQC,SAAAC,KAAWC,eAgBvB,OAGIX,aAAcA,EADlBY,mBAPyBX,SAASY,WAAWV,QACzCW,MAAOd,EADPY,IAAAA,OAAAA,KAAAA","file":"../../../scripts/mvc/workflow/workflow-model.js","sourcesContent":["define([\"mvc/base-mvc\"], function(baseMVC) {\n /* global Backbone */\n // workflow model\n\n var logNamespace = \"workflow\";\n //==============================================================================\n /** @class model for a single workflow.\n * @name WorkflowItem\n * @augments Backbone.Model\n */\n var WorkflowItem = Backbone.Model.extend(baseMVC.LoggableMixin).extend({\n _logNamespace: logNamespace,\n\n urlRoot: Galaxy.root + \"api/workflows\",\n\n toJSON: function() {\n // need to overwrite this as endpoint expects the 'workflow' key in payload\n return { workflow: this.attributes };\n }\n });\n\n //==============================================================================\n /** @class collection for workflows.\n * @name WorkflowCollection\n * @augments Backbone.Collection\n */\n var WorkflowCollection = Backbone.Collection.extend({\n model: WorkflowItem,\n url: Galaxy.root + \"api/workflows\"\n });\n\n //==============================================================================\n\n return {\n WorkflowItem: WorkflowItem,\n WorkflowCollection: WorkflowCollection\n };\n});\n"]} \ No newline at end of file +{"version":3,"sources":["mvc/workflow/workflow-model.js"],"names":["define","baseMVC","WorkflowItem","Backbone","Model","extend","LoggableMixin","_logNamespace","urlRoot","toJSON","workflow","this","attributes","WorkflowCollection","Collection","model","url","Galaxy","root"],"mappings":"kCAAAA,QAAQ,gBAAiB,SAASC,GAC9B,IASIC,EAAeC,SAASC,MAAMC,OAAOJ,EAAQK,eAAeD,QAC5DE,cAVJ,WASAC,QAAIN,OAAAA,KAAeC,gBAKfM,OAAQ,WAEJ,OAASC,SAAUC,KAAKC,eAgBhC,OAFAV,aAAAA,EAIIW,mBATqBV,SAASW,WAAWT,QACzCU,MAAOb,EACPc,IAAKC,OAAOC,KAAO","file":"../../../scripts/mvc/workflow/workflow-model.js","sourcesContent":["define([\"mvc/base-mvc\"], function(baseMVC) {\n /* global Backbone */\n // workflow model\n\n var logNamespace = \"workflow\";\n //==============================================================================\n /** @class model for a single workflow.\n * @name WorkflowItem\n * @augments Backbone.Model\n */\n var WorkflowItem = Backbone.Model.extend(baseMVC.LoggableMixin).extend({\n _logNamespace: logNamespace,\n\n urlRoot: Galaxy.root + \"api/workflows\",\n\n toJSON: function() {\n // need to overwrite this as endpoint expects the 'workflow' key in payload\n return { workflow: this.attributes };\n }\n });\n\n //==============================================================================\n /** @class collection for workflows.\n * @name WorkflowCollection\n * @augments Backbone.Collection\n */\n var WorkflowCollection = Backbone.Collection.extend({\n model: WorkflowItem,\n url: Galaxy.root + \"api/workflows\"\n });\n\n //==============================================================================\n\n return {\n WorkflowItem: WorkflowItem,\n WorkflowCollection: WorkflowCollection\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/workflow/workflow-node.js.map b/static/maps/mvc/workflow/workflow-node.js.map index 8374115f3cd..b84637d0775 100644 --- a/static/maps/mvc/workflow/workflow-node.js.map +++ b/static/maps/mvc/workflow/workflow-node.js.map @@ -1 +1 @@ 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function(NodeView) {\n var Node = Backbone.Model.extend({\n initialize: function(app, attr) {\n this.app = app;\n this.element = attr.element;\n this.input_terminals = {};\n this.output_terminals = {};\n this.errors = {};\n this.workflow_outputs = [];\n },\n getWorkflowOutput: function(outputName) {\n return _.findWhere(this.workflow_outputs, {\n output_name: outputName\n });\n },\n isWorkflowOutput: function(outputName) {\n return this.getWorkflowOutput(outputName) != undefined;\n },\n removeWorkflowOutput: function(outputName) {\n while (this.isWorkflowOutput(outputName)) {\n this.workflow_outputs.splice(\n this.getWorkflowOutput(outputName),\n 1\n );\n }\n },\n addWorkflowOutput: function(outputName, label) {\n if (!this.isWorkflowOutput(outputName)) {\n var output = { output_name: outputName };\n if (label) {\n output[\"label\"] = label;\n }\n this.workflow_outputs.push(output);\n return true;\n }\n return false;\n },\n labelWorkflowOutput: function(outputName, label) {\n var changed = false;\n var oldLabel = null;\n if (this.isWorkflowOutput(outputName)) {\n var workflowOutput = this.getWorkflowOutput(outputName);\n oldLabel = workflowOutput[\"label\"];\n workflowOutput[\"label\"] = label;\n changed = oldLabel != label;\n } else {\n changed = this.addWorkflowOutput(outputName, label);\n }\n if (changed) {\n this.app.workflow.updateOutputLabel(oldLabel, label);\n this.markChanged();\n this.nodeView.redrawWorkflowOutputs();\n }\n return changed;\n },\n connectedOutputTerminals: function() {\n return this._connectedTerminals(this.output_terminals);\n },\n _connectedTerminals: function(terminals) {\n var connectedTerminals = [];\n $.each(terminals, function(_, t) {\n if (t.connectors.length > 0) {\n connectedTerminals.push(t);\n }\n });\n return connectedTerminals;\n },\n hasConnectedOutputTerminals: function() {\n // return this.connectedOutputTerminals().length > 0; <- optimized this\n var outputTerminals = this.output_terminals;\n for (var outputName in outputTerminals) {\n if (outputTerminals[outputName].connectors.length > 0) {\n return true;\n }\n }\n return false;\n },\n connectedMappedInputTerminals: function() {\n return this._connectedMappedTerminals(this.input_terminals);\n },\n hasConnectedMappedInputTerminals: function() {\n // return this.connectedMappedInputTerminals().length > 0; <- optimized this\n var inputTerminals = this.input_terminals;\n for (var inputName in inputTerminals) {\n var inputTerminal = inputTerminals[inputName];\n if (\n inputTerminal.connectors.length > 0 &&\n inputTerminal.isMappedOver()\n ) {\n return true;\n }\n }\n return false;\n },\n _connectedMappedTerminals: function(terminals) {\n var mapped_outputs = [];\n $.each(terminals, function(_, t) {\n var mapOver = t.mapOver();\n if (mapOver.isCollection) {\n if (t.connectors.length > 0) {\n mapped_outputs.push(t);\n }\n }\n });\n return mapped_outputs;\n },\n mappedInputTerminals: function() {\n return this._mappedTerminals(this.input_terminals);\n },\n _mappedTerminals: function(terminals) {\n var mappedTerminals = [];\n $.each(terminals, function(_, t) {\n var mapOver = t.mapOver();\n if (mapOver.isCollection) {\n mappedTerminals.push(t);\n }\n });\n return mappedTerminals;\n },\n hasMappedOverInputTerminals: function() {\n var found = false;\n _.each(this.input_terminals, function(t) {\n var mapOver = t.mapOver();\n if (mapOver.isCollection) {\n found = true;\n }\n });\n return found;\n },\n redraw: function() {\n $.each(this.input_terminals, function(_, t) {\n t.redraw();\n });\n $.each(this.output_terminals, function(_, t) {\n t.redraw();\n });\n },\n destroy: function() {\n $.each(this.input_terminals, function(k, t) {\n t.destroy();\n });\n $.each(this.output_terminals, function(k, t) {\n t.destroy();\n });\n this.app.workflow.remove_node(this);\n $(this.element).remove();\n },\n make_active: function() {\n $(this.element).addClass(\"toolForm-active\");\n },\n make_inactive: function() {\n // Keep inactive nodes stacked from most to least recently active\n // by moving element to the end of parent's node list\n var element = this.element.get(0);\n (function(p) {\n p.removeChild(element);\n p.appendChild(element);\n })(element.parentNode);\n // Remove active class\n $(element).removeClass(\"toolForm-active\");\n },\n init_field_data: function(data) {\n if (data.type) {\n this.type = data.type;\n }\n this.name = data.name;\n this.config_form = data.config_form;\n this.tool_version = this.config_form && this.config_form.version;\n this.tool_state = data.tool_state;\n this.errors = data.errors;\n this.tooltip = data.tooltip ? data.tooltip : \"\";\n this.annotation = data.annotation;\n this.post_job_actions = data.post_job_actions\n ? data.post_job_actions\n : {};\n this.label = data.label;\n this.uuid = data.uuid;\n this.workflow_outputs = data.workflow_outputs\n ? data.workflow_outputs\n : [];\n var node = this;\n var nodeView = new NodeView({\n el: this.element[0],\n node: node\n });\n node.nodeView = nodeView;\n $.each(data.data_inputs, function(i, input) {\n nodeView.addDataInput(input);\n });\n if (data.data_inputs.length > 0 && data.data_outputs.length > 0) {\n nodeView.addRule();\n }\n $.each(data.data_outputs, function(i, output) {\n nodeView.addDataOutput(output);\n });\n nodeView.render();\n this.app.workflow.node_changed(this, true);\n },\n update_field_data: function(data) {\n var node = this;\n var nodeView = node.nodeView;\n // remove unused output views and remove pre-existing output views from data.data_outputs,\n // so that these are not added twice.\n var unused_outputs = [];\n // nodeView.outputViews contains pre-existing outputs,\n // while data.data_output contains what should be displayed.\n // Now we gather the unused outputs\n $.each(nodeView.outputViews, function(i, output_view) {\n var cur_name = output_view.output.name;\n var data_names = data.data_outputs;\n var cur_name_in_data_outputs = false;\n _.each(data_names, function(data_name) {\n if (data_name.name == cur_name) {\n cur_name_in_data_outputs = true;\n }\n });\n if (cur_name_in_data_outputs === false) {\n unused_outputs.push(cur_name);\n }\n });\n\n // Remove the unused outputs\n _.each(unused_outputs, function(unused_output) {\n _.each(\n nodeView.outputViews[unused_output].terminalElement.terminal\n .connectors,\n function(x) {\n if (x) {\n x.destroy(); // Removes the noodle connectors\n }\n }\n );\n nodeView.outputViews[unused_output].remove(); // removes the rendered output\n delete nodeView.outputViews[unused_output]; // removes the reference to the output\n delete node.output_terminals[unused_output]; // removes the output terminal\n });\n $.each(node.workflow_outputs, function(i, wf_output) {\n if (\n wf_output &&\n !node.output_terminals[wf_output.output_name]\n ) {\n node.workflow_outputs.splice(i, 1); // removes output from list of workflow outputs\n }\n });\n $.each(data.data_outputs, function(i, output) {\n if (!nodeView.outputViews[output.name]) {\n nodeView.addDataOutput(output); // add data output if it does not yet exist\n } else {\n // the output already exists, but the output formats may have changed.\n // Therefore we update the datatypes and destroy invalid connections.\n node.output_terminals[output.name].datatypes =\n output.extensions;\n node.output_terminals[\n output.name\n ].destroyInvalidConnections();\n }\n });\n this.tool_state = data.tool_state;\n this.config_form = data.config_form;\n this.tool_version = this.config_form && this.config_form.version;\n this.errors = data.errors;\n this.annotation = data[\"annotation\"];\n this.label = data.label;\n if (\"post_job_actions\" in data) {\n // Won't be present in response for data inputs\n var pja_in = data.post_job_actions;\n this.post_job_actions = pja_in ? pja_in : {};\n }\n node.nodeView.renderToolErrors();\n // Update input rows\n var old_body = nodeView.$(\"div.inputs\");\n var new_body = nodeView.newInputsDiv();\n var newTerminalViews = {};\n _.each(data.data_inputs, function(input) {\n var terminalView = node.nodeView.addDataInput(input, new_body);\n newTerminalViews[input.name] = terminalView;\n });\n // Cleanup any leftover terminals\n _.each(\n _.difference(\n _.values(nodeView.terminalViews),\n _.values(newTerminalViews)\n ),\n function(unusedView) {\n unusedView.el.terminal.destroy();\n }\n );\n nodeView.terminalViews = newTerminalViews;\n node.nodeView.render();\n // In general workflow editor assumes tool outputs don't change in # or\n // type (not really valid right?) but adding special logic here for\n // data collection input parameters that can have their collection\n // change.\n if (\n data.data_outputs.length == 1 &&\n \"collection_type\" in data.data_outputs[0]\n ) {\n nodeView.updateDataOutput(data.data_outputs[0]);\n }\n old_body.replaceWith(new_body);\n if (\"workflow_outputs\" in data) {\n // Won't be present in response for data inputs\n this.workflow_outputs = workflow_outputs\n ? workflow_outputs\n : [];\n }\n // If active, reactivate with new config_form\n this.markChanged();\n this.redraw();\n },\n error: function(text) {\n var b = $(this.element).find(\".toolFormBody\");\n b.find(\"div\").remove();\n var tmp =\n \"',\n data.nice_total_disk_usage\n ? _l(\"Using \") + data.nice_total_disk_usage\n : \"\",\n \"\",\n \"\" +\n text +\n \"\";\n this.config_form = tmp;\n b.html(tmp);\n this.app.workflow.node_changed(this);\n },\n markChanged: function() {\n this.app.workflow.node_changed(this);\n }\n });\n return Node;\n});\n"]} \ No newline at end of file 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function(NodeView) {\n var Node = Backbone.Model.extend({\n initialize: function(app, attr) {\n this.app = app;\n this.element = attr.element;\n this.input_terminals = {};\n this.output_terminals = {};\n this.errors = {};\n this.workflow_outputs = [];\n },\n getWorkflowOutput: function(outputName) {\n return _.findWhere(this.workflow_outputs, {\n output_name: outputName\n });\n },\n isWorkflowOutput: function(outputName) {\n return this.getWorkflowOutput(outputName) != undefined;\n },\n removeWorkflowOutput: function(outputName) {\n while (this.isWorkflowOutput(outputName)) {\n this.workflow_outputs.splice(\n this.getWorkflowOutput(outputName),\n 1\n );\n }\n },\n addWorkflowOutput: function(outputName, label) {\n if (!this.isWorkflowOutput(outputName)) {\n var output = { output_name: outputName };\n if (label) {\n output[\"label\"] = label;\n }\n this.workflow_outputs.push(output);\n return true;\n }\n return false;\n },\n labelWorkflowOutput: function(outputName, label) {\n var changed = false;\n var oldLabel = null;\n if (this.isWorkflowOutput(outputName)) {\n var workflowOutput = this.getWorkflowOutput(outputName);\n oldLabel = workflowOutput[\"label\"];\n workflowOutput[\"label\"] = label;\n changed = oldLabel != label;\n } else {\n changed = this.addWorkflowOutput(outputName, label);\n }\n if (changed) {\n this.app.workflow.updateOutputLabel(oldLabel, label);\n this.markChanged();\n this.nodeView.redrawWorkflowOutputs();\n }\n return changed;\n },\n connectedOutputTerminals: function() {\n return this._connectedTerminals(this.output_terminals);\n },\n _connectedTerminals: function(terminals) {\n var connectedTerminals = [];\n $.each(terminals, function(_, t) {\n if (t.connectors.length > 0) {\n connectedTerminals.push(t);\n }\n });\n return connectedTerminals;\n },\n hasConnectedOutputTerminals: function() {\n // return this.connectedOutputTerminals().length > 0; <- optimized this\n var outputTerminals = this.output_terminals;\n for (var outputName in outputTerminals) {\n if (outputTerminals[outputName].connectors.length > 0) {\n return true;\n }\n }\n return false;\n },\n connectedMappedInputTerminals: function() {\n return this._connectedMappedTerminals(this.input_terminals);\n },\n hasConnectedMappedInputTerminals: function() {\n // return this.connectedMappedInputTerminals().length > 0; <- optimized this\n var inputTerminals = this.input_terminals;\n for (var inputName in inputTerminals) {\n var inputTerminal = inputTerminals[inputName];\n if (\n inputTerminal.connectors.length > 0 &&\n inputTerminal.isMappedOver()\n ) {\n return true;\n }\n }\n return false;\n },\n _connectedMappedTerminals: function(terminals) {\n var mapped_outputs = [];\n $.each(terminals, function(_, t) {\n var mapOver = t.mapOver();\n if (mapOver.isCollection) {\n if (t.connectors.length > 0) {\n mapped_outputs.push(t);\n }\n }\n });\n return mapped_outputs;\n },\n mappedInputTerminals: function() {\n return this._mappedTerminals(this.input_terminals);\n },\n _mappedTerminals: function(terminals) {\n var mappedTerminals = [];\n $.each(terminals, function(_, t) {\n var mapOver = t.mapOver();\n if (mapOver.isCollection) {\n mappedTerminals.push(t);\n }\n });\n return mappedTerminals;\n },\n hasMappedOverInputTerminals: function() {\n var found = false;\n _.each(this.input_terminals, function(t) {\n var mapOver = t.mapOver();\n if (mapOver.isCollection) {\n found = true;\n }\n });\n return found;\n },\n redraw: function() {\n $.each(this.input_terminals, function(_, t) {\n t.redraw();\n });\n $.each(this.output_terminals, function(_, t) {\n t.redraw();\n });\n },\n destroy: function() {\n $.each(this.input_terminals, function(k, t) {\n t.destroy();\n });\n $.each(this.output_terminals, function(k, t) {\n t.destroy();\n });\n this.app.workflow.remove_node(this);\n $(this.element).remove();\n },\n make_active: function() {\n $(this.element).addClass(\"toolForm-active\");\n },\n make_inactive: function() {\n // Keep inactive nodes stacked from most to least recently active\n // by moving element to the end of parent's node list\n var element = this.element.get(0);\n (function(p) {\n p.removeChild(element);\n p.appendChild(element);\n })(element.parentNode);\n // Remove active class\n $(element).removeClass(\"toolForm-active\");\n },\n init_field_data: function(data) {\n if (data.type) {\n this.type = data.type;\n }\n this.name = data.name;\n this.config_form = data.config_form;\n this.tool_version = this.config_form && this.config_form.version;\n this.tool_state = data.tool_state;\n this.errors = data.errors;\n this.tooltip = data.tooltip ? data.tooltip : \"\";\n this.annotation = data.annotation;\n this.post_job_actions = data.post_job_actions\n ? data.post_job_actions\n : {};\n this.label = data.label;\n this.uuid = data.uuid;\n this.workflow_outputs = data.workflow_outputs\n ? data.workflow_outputs\n : [];\n var node = this;\n var nodeView = new NodeView({\n el: this.element[0],\n node: node\n });\n node.nodeView = nodeView;\n $.each(data.data_inputs, function(i, input) {\n nodeView.addDataInput(input);\n });\n if (data.data_inputs.length > 0 && data.data_outputs.length > 0) {\n nodeView.addRule();\n }\n $.each(data.data_outputs, function(i, output) {\n nodeView.addDataOutput(output);\n });\n nodeView.render();\n this.app.workflow.node_changed(this, true);\n },\n update_field_data: function(data) {\n var node = this;\n var nodeView = node.nodeView;\n // remove unused output views and remove pre-existing output views from data.data_outputs,\n // so that these are not added twice.\n var unused_outputs = [];\n // nodeView.outputViews contains pre-existing outputs,\n // while data.data_output contains what should be displayed.\n // Now we gather the unused outputs\n $.each(nodeView.outputViews, function(i, output_view) {\n var cur_name = output_view.output.name;\n var data_names = data.data_outputs;\n var cur_name_in_data_outputs = false;\n _.each(data_names, function(data_name) {\n if (data_name.name == cur_name) {\n cur_name_in_data_outputs = true;\n }\n });\n if (cur_name_in_data_outputs === false) {\n unused_outputs.push(cur_name);\n }\n });\n\n // Remove the unused outputs\n _.each(unused_outputs, function(unused_output) {\n _.each(\n nodeView.outputViews[unused_output].terminalElement.terminal\n .connectors,\n function(x) {\n if (x) {\n x.destroy(); // Removes the noodle connectors\n }\n }\n );\n nodeView.outputViews[unused_output].remove(); // removes the rendered output\n delete nodeView.outputViews[unused_output]; // removes the reference to the output\n delete node.output_terminals[unused_output]; // removes the output terminal\n });\n $.each(node.workflow_outputs, function(i, wf_output) {\n if (\n wf_output &&\n !node.output_terminals[wf_output.output_name]\n ) {\n node.workflow_outputs.splice(i, 1); // removes output from list of workflow outputs\n }\n });\n $.each(data.data_outputs, function(i, output) {\n if (!nodeView.outputViews[output.name]) {\n nodeView.addDataOutput(output); // add data output if it does not yet exist\n } else {\n // the output already exists, but the output formats may have changed.\n // Therefore we update the datatypes and destroy invalid connections.\n node.output_terminals[output.name].datatypes =\n output.extensions;\n node.output_terminals[\n output.name\n ].destroyInvalidConnections();\n }\n });\n this.tool_state = data.tool_state;\n this.config_form = data.config_form;\n this.tool_version = this.config_form && this.config_form.version;\n this.errors = data.errors;\n this.annotation = data[\"annotation\"];\n this.label = data.label;\n if (\"post_job_actions\" in data) {\n // Won't be present in response for data inputs\n var pja_in = data.post_job_actions;\n this.post_job_actions = pja_in ? pja_in : {};\n }\n node.nodeView.renderToolErrors();\n // Update input rows\n var old_body = nodeView.$(\"div.inputs\");\n var new_body = nodeView.newInputsDiv();\n var newTerminalViews = {};\n _.each(data.data_inputs, function(input) {\n var terminalView = node.nodeView.addDataInput(input, new_body);\n newTerminalViews[input.name] = terminalView;\n });\n // Cleanup any leftover terminals\n _.each(\n _.difference(\n _.values(nodeView.terminalViews),\n _.values(newTerminalViews)\n ),\n function(unusedView) {\n unusedView.el.terminal.destroy();\n }\n );\n nodeView.terminalViews = newTerminalViews;\n node.nodeView.render();\n // In general workflow editor assumes tool outputs don't change in # or\n // type (not really valid right?) but adding special logic here for\n // data collection input parameters that can have their collection\n // change.\n if (\n data.data_outputs.length == 1 &&\n \"collection_type\" in data.data_outputs[0]\n ) {\n nodeView.updateDataOutput(data.data_outputs[0]);\n }\n old_body.replaceWith(new_body);\n if (\"workflow_outputs\" in data) {\n // Won't be present in response for data inputs\n this.workflow_outputs = workflow_outputs\n ? workflow_outputs\n : [];\n }\n // If active, reactivate with new config_form\n this.markChanged();\n this.redraw();\n },\n error: function(text) {\n var b = $(this.element).find(\".toolFormBody\");\n b.find(\"div\").remove();\n var tmp =\n \"\" +\n text +\n \"\";\n this.config_form = tmp;\n b.html(tmp);\n this.app.workflow.node_changed(this);\n },\n markChanged: function() {\n this.app.workflow.node_changed(this);\n }\n });\n return Node;\n});\n"]} \ No newline at end of file diff --git a/static/maps/mvc/workflow/workflow-terminals.js.map b/static/maps/mvc/workflow/workflow-terminals.js.map index d9584b0d34e..ff2baa100f6 100644 --- a/static/maps/mvc/workflow/workflow-terminals.js.map +++ b/static/maps/mvc/workflow/workflow-terminals.js.map @@ -1 +1 @@ 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function(attr) {\n Terminal.prototype.initialize.call(this, attr);\n this.datatypes = attr.datatypes;\n if (attr.collection_type) {\n this.collectionType = new CollectionTypeDescription(\n attr.collection_type\n );\n } else {\n var collectionTypeSource = attr.collection_type_source;\n if (!collectionTypeSource) {\n console.log(\n \"Warning: No collection type or collection type source defined.\"\n );\n }\n this.collectionType = ANY_COLLECTION_TYPE_DESCRIPTION;\n }\n this.isCollection = true;\n },\n update: function(output) {\n var newCollectionType;\n if (output.collection_type) {\n newCollectionType = new CollectionTypeDescription(\n output.collection_type\n );\n } else {\n var collectionTypeSource = output.collection_type_source;\n if (!collectionTypeSource) {\n console.log(\n \"Warning: No collection type or collection type source defined.\"\n );\n }\n newCollectionType = ANY_COLLECTION_TYPE_DESCRIPTION;\n }\n\n if (\n newCollectionType.collectionType !=\n 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[\n \"mvc/workflow/workflow-globals\",\n \"mvc/workflow/workflow-terminals\",\n \"mvc/workflow/workflow-connector\"\n ],\n function(Globals, Terminals, Connector) {\n var TerminalMappingView = Backbone.View.extend({\n tagName: \"div\",\n className: \"fa-icon-button fa fa-folder-o\",\n initialize: function(options) {\n var mapText = \"Run tool in parallel over collection\";\n this.$el.tooltip({ delay: 500, title: mapText });\n this.model.bind(\"change\", _.bind(this.render, this));\n },\n render: function() {\n if (this.model.mapOver.isCollection) {\n this.$el.show();\n } else {\n this.$el.hide();\n }\n }\n });\n\n var InputTerminalMappingView = TerminalMappingView.extend({\n events: {\n click: \"onClick\",\n mouseenter: \"onMouseEnter\",\n mouseleave: \"onMouseLeave\"\n },\n onMouseEnter: function(e) {\n var model = this.model;\n if (!model.terminal.connected() && model.mapOver.isCollection) {\n this.$el.css(\"color\", \"red\");\n }\n },\n onMouseLeave: function(e) {\n this.$el.css(\"color\", \"black\");\n },\n onClick: function(e) {\n var model = this.model;\n if (!model.terminal.connected() && model.mapOver.isCollection) {\n // TODO: Consider prompting...\n model.terminal.resetMapping();\n }\n }\n });\n\n var TerminalView = Backbone.View.extend({\n setupMappingView: function(terminal) {\n var terminalMapping = new this.terminalMappingClass({\n terminal: terminal\n });\n var terminalMappingView = new this.terminalMappingViewClass({\n model: terminalMapping\n });\n terminalMappingView.render();\n terminal.terminalMappingView = terminalMappingView;\n this.terminalMappingView = terminalMappingView;\n },\n terminalElements: function() {\n if (this.terminalMappingView) {\n return [this.terminalMappingView.el, this.el];\n } else {\n return [this.el];\n }\n }\n });\n\n var BaseInputTerminalView = TerminalView.extend({\n className: \"terminal input-terminal\",\n initialize: function(options) {\n var node = options.node;\n var input = options.input;\n var name = input.name;\n var terminal = this.terminalForInput(input);\n if (!terminal.multiple) {\n this.setupMappingView(terminal);\n }\n this.el.terminal = terminal;\n terminal.node = node;\n terminal.name = name;\n node.input_terminals[name] = terminal;\n },\n events: {\n dropinit: \"onDropInit\",\n dropstart: \"onDropStart\",\n dropend: \"onDropEnd\",\n drop: \"onDrop\",\n hover: \"onHover\"\n },\n onDropInit: function(e, d) {\n var terminal = this.el.terminal;\n // Accept a dragable if it is an output terminal and has a\n // compatible type\n return (\n $(d.drag).hasClass(\"output-terminal\") &&\n terminal.canAccept(d.drag.terminal)\n );\n },\n onDropStart: function(e, d) {\n if (d.proxy.terminal) {\n d.proxy.terminal.connectors[0].inner_color = \"#BBFFBB\";\n }\n },\n onDropEnd: function(e, d) {\n if (d.proxy.terminal) {\n d.proxy.terminal.connectors[0].inner_color = \"#FFFFFF\";\n }\n },\n onDrop: function(e, d) {\n var terminal = this.el.terminal;\n new Connector(d.drag.terminal, terminal).redraw();\n },\n onHover: function() {\n var element = this.el;\n var terminal = element.terminal;\n // If connected, create a popup to allow disconnection\n if (terminal.connectors.length > 0) {\n // Create callout\n var t = $(\"\")\n .css({ display: \"none\" })\n .appendTo(\"body\")\n .append(\n $(\"\").append(\n $(\"\")\n .addClass(\"fa-icon-button fa fa-times\")\n .click(function() {\n $.each(terminal.connectors, function(\n _,\n x\n ) {\n if (x) {\n x.destroy();\n }\n });\n t.remove();\n })\n )\n )\n .bind(\"mouseleave\", function() {\n $(this).remove();\n });\n // Position it and show\n t\n .css({\n top: $(element).offset().top - 2,\n left: $(element).offset().left - t.width(),\n \"padding-right\": $(element).width()\n })\n .show();\n }\n }\n });\n\n var InputTerminalView = BaseInputTerminalView.extend({\n terminalMappingClass: Terminals.TerminalMapping,\n terminalMappingViewClass: InputTerminalMappingView,\n terminalForInput: function(input) {\n return new Terminals.InputTerminal({\n element: this.el,\n input: input\n });\n }\n });\n\n var InputCollectionTerminalView = BaseInputTerminalView.extend({\n terminalMappingClass: Terminals.TerminalMapping,\n terminalMappingViewClass: InputTerminalMappingView,\n terminalForInput: function(input) {\n return new Terminals.InputCollectionTerminal({\n element: this.el,\n input: input\n });\n }\n });\n\n var BaseOutputTerminalView = TerminalView.extend({\n className: \"terminal output-terminal\",\n initialize: function(options) {\n var node = options.node;\n var output = options.output;\n var name = output.name;\n var terminal = this.terminalForOutput(output);\n this.setupMappingView(terminal);\n this.el.terminal = terminal;\n terminal.node = node;\n terminal.name = name;\n node.output_terminals[name] = terminal;\n },\n events: {\n drag: \"onDrag\",\n dragstart: \"onDragStart\",\n dragend: \"onDragEnd\"\n },\n onDrag: function(e, d) {\n var onmove = function() {\n var po = $(d.proxy)\n .offsetParent()\n .offset(),\n x = d.offsetX - po.left,\n y = d.offsetY - po.top;\n $(d.proxy).css({ left: x, top: y });\n d.proxy.terminal.redraw();\n // FIXME: global\n Globals.canvas_manager.update_viewport_overlay();\n };\n onmove();\n $(\"#canvas-container\")\n .get(0)\n .scroll_panel.test(e, onmove);\n },\n onDragStart: function(e, d) {\n $(d.available).addClass(\"input-terminal-active\");\n // Save PJAs in the case of change datatype actions.\n Globals.workflow.check_changes_in_active_form();\n // Drag proxy div\n var h = $(\n ''\n )\n .appendTo(\"#canvas-container\")\n .get(0);\n // Terminal and connection to display noodle while dragging\n h.terminal = new Terminals.OutputTerminal({ element: h });\n var c = new Connector();\n c.dragging = true;\n c.connect(this.el.terminal, h.terminal);\n return h;\n },\n onDragEnd: function(e, d) {\n var connector = d.proxy.terminal.connectors[0];\n // check_changes_in_active_form may change the state and cause a\n // the connection to have already been destroyed. There must be better\n // ways to handle this but the following check fixes some serious GUI\n // bugs for now.\n if (connector) {\n connector.destroy();\n }\n $(d.proxy).remove();\n $(d.available).removeClass(\"input-terminal-active\");\n $(\"#canvas-container\")\n .get(0)\n .scroll_panel.stop();\n }\n });\n\n var OutputTerminalView = BaseOutputTerminalView.extend({\n terminalMappingClass: Terminals.TerminalMapping,\n terminalMappingViewClass: TerminalMappingView,\n terminalForOutput: function(output) {\n var type = output.extensions;\n var terminal = new Terminals.OutputTerminal({\n element: this.el,\n datatypes: type\n });\n return terminal;\n }\n });\n\n var OutputCollectionTerminalView = BaseOutputTerminalView.extend({\n terminalMappingClass: Terminals.TerminalMapping,\n terminalMappingViewClass: TerminalMappingView,\n terminalForOutput: function(output) {\n var collection_type = output.collection_type;\n var collection_type_source = output.collection_type_source;\n var terminal = new Terminals.OutputCollectionTerminal({\n element: this.el,\n collection_type: collection_type,\n collection_type_source: collection_type_source,\n datatypes: output.extensions\n });\n return terminal;\n }\n });\n\n return {\n InputTerminalView: InputTerminalView,\n OutputTerminalView: OutputTerminalView,\n InputCollectionTerminalView: InputCollectionTerminalView,\n OutputCollectionTerminalView: OutputCollectionTerminalView\n };\n }\n);\n"]} \ No newline at end of file diff --git a/static/maps/mvc/workflow/workflow-view.js.map b/static/maps/mvc/workflow/workflow-view.js.map index b64be9fd160..055d66ac2bc 100644 --- a/static/maps/mvc/workflow/workflow-view.js.map +++ b/static/maps/mvc/workflow/workflow-view.js.map @@ -1 +1 @@ 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{});\ndefine(\n [\n \"utils/utils\",\n \"mvc/workflow/workflow-globals\",\n \"mvc/workflow/workflow-manager\",\n \"mvc/workflow/workflow-canvas\",\n \"mvc/workflow/workflow-node\",\n \"mvc/workflow/workflow-icons\",\n \"mvc/workflow/workflow-forms\",\n \"mvc/ui/ui-misc\",\n \"utils/async-save-text\",\n \"libs/toastr\",\n \"ui/editable-text\"\n ],\n function(\n Utils,\n Globals,\n Workflow,\n WorkflowCanvas,\n Node,\n WorkflowIcons,\n FormWrappers,\n Ui,\n async_save_text,\n Toastr\n ) {\n // Reset tool search to start state.\n function reset_tool_search(initValue) {\n // Function may be called in top frame or in tool_menu_frame;\n // in either case, get the tool menu frame.\n var tool_menu_frame = $(\"#galaxy_tools\").contents();\n if (tool_menu_frame.length === 0) {\n tool_menu_frame = $(document);\n // Remove classes that indicate searching is active.\n $(this).removeClass(\"search_active\");\n tool_menu_frame.find(\".toolTitle\").removeClass(\"search_match\");\n\n // Reset visibility of tools and labels.\n tool_menu_frame.find(\".toolSectionBody\").hide();\n tool_menu_frame.find(\".toolTitle\").show();\n tool_menu_frame.find(\".toolPanelLabel\").show();\n tool_menu_frame.find(\".toolSectionWrapper\").each(function() {\n if ($(this).attr(\"id\") !== \"recently_used_wrapper\") {\n // Default action.\n $(this).show();\n } else if ($(this).hasClass(\"user_pref_visible\")) {\n $(this).show();\n }\n });\n tool_menu_frame.find(\"#search-no-results\").hide();\n\n // Reset search input.\n tool_menu_frame.find(\"#search-spinner\").hide();\n if (initValue) {\n var search_input = tool_menu_frame.find(\n \"#tool-search-query\"\n );\n search_input.val(\"search tools\");\n }\n }\n }\n\n function add_node_icon($to_el, nodeType) {\n var iconStyle = WorkflowIcons[nodeType];\n if (iconStyle) {\n var $icon = $(' ').addClass(\n iconStyle\n );\n $to_el.before($icon);\n }\n }\n\n // create form view\n return Backbone.View.extend({\n initialize: function(options) {\n var self = (Globals.app = this);\n this.options = options;\n this.urls = (options && options.urls) || {};\n var close_editor = function() {\n self.workflow.check_changes_in_active_form();\n if (workflow && self.workflow.has_changes) {\n var do_close = function() {\n window.onbeforeunload = undefined;\n window.document.location = self.urls.workflow_index;\n };\n window.show_modal(\n \"Close workflow editor\",\n \"There are unsaved changes to your workflow which will be lost.\",\n {\n Cancel: hide_modal,\n \"Save Changes\": function() {\n save_current_workflow(null, do_close);\n }\n },\n {\n \"Don't Save\": do_close\n }\n );\n } else {\n window.document.location = self.urls.workflow_index;\n }\n };\n var save_current_workflow = function(\n eventObj,\n success_callback\n ) {\n show_message(\"Saving workflow\", \"progress\");\n self.workflow.check_changes_in_active_form();\n if (!self.workflow.has_changes) {\n hide_modal();\n if (success_callback) {\n success_callback();\n }\n return;\n }\n self.workflow.rectify_workflow_outputs();\n Utils.request({\n url: Galaxy.root + \"api/workflows/\" + self.options.id,\n type: \"PUT\",\n data: { workflow: self.workflow.to_simple() },\n success: function(data) {\n var body = $(\"\").text(data.message);\n if (data.errors) {\n body.addClass(\"warningmark\");\n var errlist = $(\"
- \" +\n upgrade_message +\n \"
\";\n }\n }\n $(\"#output-fill-area\").html(new_content);\n $(\"#output-fill-area input\").bind(\"click\", function() {\n var node_id = this.name.split(\"|\")[0];\n var workflowNode = this.workflow.nodes[node_id];\n var output_name = this.name.split(\"|\")[1];\n if (this.checked) {\n workflowNode.addWorkflowOutput(output_name);\n } else {\n workflowNode.removeWorkflowOutput(output_name);\n }\n self.workflow.has_changes = true;\n });\n $(\"#workflow-output-area\").show();\n }\n\n function layout_editor() {\n self.workflow.layout();\n self.workflow.fit_canvas_to_nodes();\n self.scroll_to_nodes();\n self.canvas_manager.draw_overview();\n }\n\n // On load, set the size to the pref stored in local storage if it exists\n var overview_size = $.jStorage.get(\"overview-size\");\n if (overview_size !== undefined) {\n $(\"#overview-border\").css({\n width: overview_size,\n height: overview_size\n });\n }\n\n // Show viewport on load unless pref says it's off\n if ($.jStorage.get(\"overview-off\")) {\n hide_overview();\n } else {\n show_overview();\n }\n\n // Stores the size of the overview into local storage when it's resized\n $(\"#overview-border\").bind(\"dragend\", function(e, d) {\n var op = $(this).offsetParent();\n var opo = op.offset();\n var new_size = Math.max(\n op.width() - (d.offsetX - opo.left),\n op.height() - (d.offsetY - opo.top)\n );\n $.jStorage.set(\"overview-size\", new_size + \"px\");\n });\n\n function show_overview() {\n $.jStorage.set(\"overview-off\", false);\n $(\"#overview-border\").css(\"right\", \"0px\");\n $(\"#close-viewport\").css(\"background-position\", \"0px 0px\");\n }\n\n function hide_overview() {\n $.jStorage.set(\"overview-off\", true);\n $(\"#overview-border\").css(\"right\", \"20000px\");\n $(\"#close-viewport\").css(\"background-position\", \"12px 0px\");\n }\n\n // Lets the overview be toggled visible and invisible, adjusting the arrows accordingly\n $(\"#close-viewport\").click(function() {\n if ($(\"#overview-border\").css(\"right\") === \"0px\") {\n hide_overview();\n } else {\n show_overview();\n }\n });\n\n // Unload handler\n window.onbeforeunload = function() {\n if (workflow && self.workflow.has_changes) {\n return \"There are unsaved changes to your workflow which will be lost.\";\n }\n };\n\n this.options.workflows.length > 0 &&\n $(\"#left\")\n .find(\".toolMenu\")\n .append(this._buildToolPanelWorkflows());\n\n // Tool menu\n $(\"div.toolSectionBody\").hide();\n $(\"div.toolSectionTitle > span\").wrap(\"\");\n var last_expanded = null;\n $(\"div.toolSectionTitle\").each(function() {\n var body = $(this).next(\"div.toolSectionBody\");\n $(this).click(function() {\n if (body.is(\":hidden\")) {\n if (last_expanded) last_expanded.slideUp(\"fast\");\n last_expanded = body;\n body.slideDown(\"fast\");\n } else {\n body.slideUp(\"fast\");\n last_expanded = null;\n }\n });\n });\n\n // Rename async.\n async_save_text(\n \"workflow-name\",\n \"workflow-name\",\n self.urls.rename_async,\n \"new_name\"\n );\n\n // Tag async. Simply have the workflow edit element generate a click on the tag element to activate tagging.\n $(\"#workflow-tag\").click(function() {\n $(\".tag-area\").click();\n return false;\n });\n // Annotate async.\n async_save_text(\n \"workflow-annotation\",\n \"workflow-annotation\",\n self.urls.annotate_async,\n \"new_annotation\",\n 25,\n true,\n 4\n );\n },\n\n _buildToolPanelWorkflows: function() {\n var self = this;\n var $section = $(\n 'Step \" +\n node.id +\n \" - \" +\n node.name +\n \"\";\n for (var ot_key in node.output_terminals) {\n var output = node.output_terminals[ot_key];\n if (node.isWorkflowOutput(output.name)) {\n new_content +=\n \"\" +\n output.name +\n \"
\";\n } else {\n new_content +=\n \"\" +\n output.name +\n \"
\";\n }\n }\n new_content += \"' +\n '\"\n );\n add_node_icon($title.find(\".nodeTitle\"), type);\n $f.append($title);\n $f.css(\"left\", $(window).scrollLeft() + 20);\n $f.css(\"top\", $(window).scrollTop() + 20);\n $f.append($(\"\"));\n var node = new Node(this, { element: $f });\n node.type = type;\n node.content_id = content_id;\n var tmp =\n \"' +\n 'Workflows' +\n \"\" +\n '' +\n '\"\n );\n _.each(this.options.workflows, function(workflow) {\n if (workflow.id !== self.options.id) {\n var copy = new Ui.ButtonIcon({\n icon: \"fa fa-copy\",\n cls: \"ui-button-icon-plain\",\n tooltip: \"Copy and insert individual steps\",\n onclick: function() {\n if (workflow.step_count < 2) {\n self.copy_into_workflow(\n workflow.id,\n workflow.name\n );\n } else {\n // don't ruin the workflow by adding 50 steps unprompted.\n Galaxy.modal.show({\n title: \"Warning\",\n body:\n \"This will copy \" +\n workflow.step_count +\n \" new steps into your workflow.\",\n buttons: {\n Cancel: function() {\n Galaxy.modal.hide();\n },\n Copy: function() {\n Galaxy.modal.hide();\n self.copy_into_workflow(\n workflow.id,\n workflow.name\n );\n }\n }\n });\n }\n }\n });\n var $add = $(\"\")\n .attr(\"href\", \"#\")\n .html(workflow.name)\n .on(\"click\", function() {\n self.add_node_for_subworkflow(\n workflow.latest_id,\n workflow.name\n );\n });\n $section.find(\".toolSectionBg\").append(\n $(\"\")\n .addClass(\"toolTitle\")\n .append($add)\n .append(copy.$el)\n );\n }\n });\n return $section;\n },\n\n copy_into_workflow: function(workflowId) {\n // Load workflow definition\n var self = this;\n this._workflowLoadAjax(workflowId, {\n success: function(data) {\n self.workflow.from_simple(data, false);\n // Determine if any parameters were 'upgraded' and provide message\n var upgrade_message = \"\";\n $.each(data.upgrade_messages, function(k, v) {\n upgrade_message +=\n \"' +\n \"\" +\n \"- \" +\n upgrade_message +\n \"
\" +\n element.substring(2, element.length - 1) +\n \"\";\n });\n wf_parm_container.html(new_parameter_content);\n wf_parm_box.show();\n } else {\n wf_parm_container.html(new_parameter_content);\n wf_parm_box.hide();\n }\n },\n\n showAttributes: function() {\n $(\".right-content\").hide();\n $(\"#edit-attributes\").show();\n },\n\n showForm: function(content, node) {\n var self = this;\n var cls = \"right-content\";\n var id = cls + \"-\" + node.id;\n var $container = $(\"#\" + cls);\n if (content && $container.find(\"#\" + id).length == 0) {\n var $el = $('');\n content.node = node;\n content.workflow = this.workflow;\n content.datatypes = this.datatypes;\n content.icon = WorkflowIcons[node.type];\n content.cls = \"ui-portlet-narrow\";\n if (node) {\n var form_type =\n node.type == \"tool\" ? \"Tool\" : \"Default\";\n $el.append(\n new FormWrappers[form_type](content).form.$el\n );\n $container.append($el);\n } else {\n Galaxy.emit.debug(\n \"workflow-view::initialize()\",\n \"Node 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{});\ndefine(\n [\n \"utils/utils\",\n \"mvc/workflow/workflow-globals\",\n \"mvc/workflow/workflow-manager\",\n \"mvc/workflow/workflow-canvas\",\n \"mvc/workflow/workflow-node\",\n \"mvc/workflow/workflow-icons\",\n \"mvc/workflow/workflow-forms\",\n \"mvc/ui/ui-misc\",\n \"utils/async-save-text\",\n \"libs/toastr\",\n \"ui/editable-text\"\n ],\n function(\n Utils,\n Globals,\n Workflow,\n WorkflowCanvas,\n Node,\n WorkflowIcons,\n FormWrappers,\n Ui,\n async_save_text,\n Toastr\n ) {\n // Reset tool search to start state.\n function reset_tool_search(initValue) {\n // Function may be called in top frame or in tool_menu_frame;\n // in either case, get the tool menu frame.\n var tool_menu_frame = $(\"#galaxy_tools\").contents();\n if (tool_menu_frame.length === 0) {\n tool_menu_frame = $(document);\n // Remove classes that indicate searching is active.\n $(this).removeClass(\"search_active\");\n tool_menu_frame.find(\".toolTitle\").removeClass(\"search_match\");\n\n // Reset visibility of tools and labels.\n tool_menu_frame.find(\".toolSectionBody\").hide();\n tool_menu_frame.find(\".toolTitle\").show();\n tool_menu_frame.find(\".toolPanelLabel\").show();\n tool_menu_frame.find(\".toolSectionWrapper\").each(function() {\n if ($(this).attr(\"id\") !== \"recently_used_wrapper\") {\n // Default action.\n $(this).show();\n } else if ($(this).hasClass(\"user_pref_visible\")) {\n $(this).show();\n }\n });\n tool_menu_frame.find(\"#search-no-results\").hide();\n\n // Reset search input.\n tool_menu_frame.find(\"#search-spinner\").hide();\n if (initValue) {\n var search_input = tool_menu_frame.find(\n \"#tool-search-query\"\n );\n search_input.val(\"search tools\");\n }\n }\n }\n\n function add_node_icon($to_el, nodeType) {\n var iconStyle = WorkflowIcons[nodeType];\n if (iconStyle) {\n var $icon = $(' ').addClass(\n iconStyle\n );\n $to_el.before($icon);\n }\n }\n\n // create form view\n return Backbone.View.extend({\n initialize: function(options) {\n var self = (Globals.app = this);\n this.options = options;\n this.urls = (options && options.urls) || {};\n var close_editor = function() {\n self.workflow.check_changes_in_active_form();\n if (workflow && self.workflow.has_changes) {\n var do_close = function() {\n window.onbeforeunload = undefined;\n window.document.location = self.urls.workflow_index;\n };\n window.show_modal(\n \"Close workflow editor\",\n \"There are unsaved changes to your workflow which will be lost.\",\n {\n Cancel: hide_modal,\n \"Save Changes\": function() {\n save_current_workflow(null, do_close);\n }\n },\n {\n \"Don't Save\": do_close\n }\n );\n } else {\n window.document.location = self.urls.workflow_index;\n }\n };\n var save_current_workflow = function(\n eventObj,\n success_callback\n ) {\n show_message(\"Saving workflow\", \"progress\");\n self.workflow.check_changes_in_active_form();\n if (!self.workflow.has_changes) {\n hide_modal();\n if (success_callback) {\n success_callback();\n }\n return;\n }\n self.workflow.rectify_workflow_outputs();\n Utils.request({\n url: Galaxy.root + \"api/workflows/\" + self.options.id,\n type: \"PUT\",\n data: { workflow: self.workflow.to_simple() },\n success: function(data) {\n var body = $(\"\").text(data.message);\n if (data.errors) {\n body.addClass(\"warningmark\");\n var errlist = $(\"![](\" +\n Galaxy.root +\n \"static/images/loading_small_white_bg.gif)
loading tool info...- \" +\n upgrade_message +\n \"
\";\n }\n }\n $(\"#output-fill-area\").html(new_content);\n $(\"#output-fill-area input\").bind(\"click\", function() {\n var node_id = this.name.split(\"|\")[0];\n var workflowNode = this.workflow.nodes[node_id];\n var output_name = this.name.split(\"|\")[1];\n if (this.checked) {\n workflowNode.addWorkflowOutput(output_name);\n } else {\n workflowNode.removeWorkflowOutput(output_name);\n }\n self.workflow.has_changes = true;\n });\n $(\"#workflow-output-area\").show();\n }\n\n function layout_editor() {\n self.workflow.layout();\n self.workflow.fit_canvas_to_nodes();\n self.scroll_to_nodes();\n self.canvas_manager.draw_overview();\n }\n\n // On load, set the size to the pref stored in local storage if it exists\n var overview_size = $.jStorage.get(\"overview-size\");\n if (overview_size !== undefined) {\n $(\"#overview-border\").css({\n width: overview_size,\n height: overview_size\n });\n }\n\n // Show viewport on load unless pref says it's off\n if ($.jStorage.get(\"overview-off\")) {\n hide_overview();\n } else {\n show_overview();\n }\n\n // Stores the size of the overview into local storage when it's resized\n $(\"#overview-border\").bind(\"dragend\", function(e, d) {\n var op = $(this).offsetParent();\n var opo = op.offset();\n var new_size = Math.max(\n op.width() - (d.offsetX - opo.left),\n op.height() - (d.offsetY - opo.top)\n );\n $.jStorage.set(\"overview-size\", new_size + \"px\");\n });\n\n function show_overview() {\n $.jStorage.set(\"overview-off\", false);\n $(\"#overview-border\").css(\"right\", \"0px\");\n $(\"#close-viewport\").css(\"background-position\", \"0px 0px\");\n }\n\n function hide_overview() {\n $.jStorage.set(\"overview-off\", true);\n $(\"#overview-border\").css(\"right\", \"20000px\");\n $(\"#close-viewport\").css(\"background-position\", \"12px 0px\");\n }\n\n // Lets the overview be toggled visible and invisible, adjusting the arrows accordingly\n $(\"#close-viewport\").click(function() {\n if ($(\"#overview-border\").css(\"right\") === \"0px\") {\n hide_overview();\n } else {\n show_overview();\n }\n });\n\n // Unload handler\n window.onbeforeunload = function() {\n if (workflow && self.workflow.has_changes) {\n return \"There are unsaved changes to your workflow which will be lost.\";\n }\n };\n\n this.options.workflows.length > 0 &&\n $(\"#left\")\n .find(\".toolMenu\")\n .append(this._buildToolPanelWorkflows());\n\n // Tool menu\n $(\"div.toolSectionBody\").hide();\n $(\"div.toolSectionTitle > span\").wrap(\"\");\n var last_expanded = null;\n $(\"div.toolSectionTitle\").each(function() {\n var body = $(this).next(\"div.toolSectionBody\");\n $(this).click(function() {\n if (body.is(\":hidden\")) {\n if (last_expanded) last_expanded.slideUp(\"fast\");\n last_expanded = body;\n body.slideDown(\"fast\");\n } else {\n body.slideUp(\"fast\");\n last_expanded = null;\n }\n });\n });\n\n // Rename async.\n async_save_text(\n \"workflow-name\",\n \"workflow-name\",\n self.urls.rename_async,\n \"new_name\"\n );\n\n // Tag async. Simply have the workflow edit element generate a click on the tag element to activate tagging.\n $(\"#workflow-tag\").click(function() {\n $(\".tag-area\").click();\n return false;\n });\n // Annotate async.\n async_save_text(\n \"workflow-annotation\",\n \"workflow-annotation\",\n self.urls.annotate_async,\n \"new_annotation\",\n 25,\n true,\n 4\n );\n },\n\n _buildToolPanelWorkflows: function() {\n var self = this;\n var $section = $(\n 'Step \" +\n node.id +\n \" - \" +\n node.name +\n \"\";\n for (var ot_key in node.output_terminals) {\n var output = node.output_terminals[ot_key];\n if (node.isWorkflowOutput(output.name)) {\n new_content +=\n \"\" +\n output.name +\n \"
\";\n } else {\n new_content +=\n \"\" +\n output.name +\n \"
\";\n }\n }\n new_content += \"' +\n '\"\n );\n add_node_icon($title.find(\".nodeTitle\"), type);\n $f.append($title);\n $f.css(\"left\", $(window).scrollLeft() + 20);\n $f.css(\"top\", $(window).scrollTop() + 20);\n $f.append($(\"\"));\n var node = new Node(this, { element: $f });\n node.type = type;\n node.content_id = content_id;\n var tmp =\n \"' +\n 'Workflows' +\n \"\" +\n '' +\n '\"\n );\n _.each(this.options.workflows, function(workflow) {\n if (workflow.id !== self.options.id) {\n var copy = new Ui.ButtonIcon({\n icon: \"fa fa-copy\",\n cls: \"ui-button-icon-plain\",\n tooltip: \"Copy and insert individual steps\",\n onclick: function() {\n if (workflow.step_count < 2) {\n self.copy_into_workflow(\n workflow.id,\n workflow.name\n );\n } else {\n // don't ruin the workflow by adding 50 steps unprompted.\n Galaxy.modal.show({\n title: \"Warning\",\n body:\n \"This will copy \" +\n workflow.step_count +\n \" new steps into your workflow.\",\n buttons: {\n Cancel: function() {\n Galaxy.modal.hide();\n },\n Copy: function() {\n Galaxy.modal.hide();\n self.copy_into_workflow(\n workflow.id,\n workflow.name\n );\n }\n }\n });\n }\n }\n });\n var $add = $(\"\")\n .attr(\"href\", \"#\")\n .html(workflow.name)\n .on(\"click\", function() {\n self.add_node_for_subworkflow(\n workflow.latest_id,\n workflow.name\n );\n });\n $section.find(\".toolSectionBg\").append(\n $(\"\")\n .addClass(\"toolTitle\")\n .append($add)\n .append(copy.$el)\n );\n }\n });\n return $section;\n },\n\n copy_into_workflow: function(workflowId) {\n // Load workflow definition\n var self = this;\n this._workflowLoadAjax(workflowId, {\n success: function(data) {\n self.workflow.from_simple(data, false);\n // Determine if any parameters were 'upgraded' and provide message\n var upgrade_message = \"\";\n $.each(data.upgrade_messages, function(k, v) {\n upgrade_message +=\n \"' +\n \"\" +\n \"- \" +\n upgrade_message +\n \"
\" +\n element.substring(2, element.length - 1) +\n \"\";\n });\n wf_parm_container.html(new_parameter_content);\n wf_parm_box.show();\n } else {\n wf_parm_container.html(new_parameter_content);\n wf_parm_box.hide();\n }\n },\n\n showAttributes: function() {\n $(\".right-content\").hide();\n $(\"#edit-attributes\").show();\n },\n\n showForm: function(content, node) {\n var self = this;\n var cls = \"right-content\";\n var id = cls + \"-\" + node.id;\n var $container = $(\"#\" + cls);\n if (content && $container.find(\"#\" + id).length == 0) {\n var $el = $('');\n content.node = node;\n content.workflow = this.workflow;\n content.datatypes = this.datatypes;\n content.icon = WorkflowIcons[node.type];\n content.cls = \"ui-portlet-narrow\";\n if (node) {\n var form_type =\n node.type == \"tool\" ? \"Tool\" : \"Default\";\n $el.append(\n new FormWrappers[form_type](content).form.$el\n );\n $container.append($el);\n } else {\n Galaxy.emit.debug(\n \"workflow-view::initialize()\",\n \"Node 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Workflow view */\ndefine(\n [\n \"libs/toastr\",\n \"mvc/tag\",\n \"mvc/workflow/workflow-model\",\n \"utils/query-string-parsing\"\n ],\n function(mod_toastr, TAGS, WORKFLOWS, QueryStringParsing) {\n /** View of the individual workflows */\n var WorkflowItemView = Backbone.View.extend({\n tagName: \"tr\", // name of (orphan) root tag in this.el\n initialize: function() {\n _.bindAll(\n this,\n \"render\",\n \"_rowTemplate\",\n \"renderTagEditor\",\n \"_templateActions\",\n \"removeWorkflow\",\n \"copyWorkflow\"\n ); // every function that uses 'this' as the current object should be in here\n mod_toastr.options.timeOut = 1500;\n },\n\n events: {\n \"click #show-in-tool-panel\": \"showInToolPanel\",\n \"click #delete-workflow\": \"removeWorkflow\",\n \"click #rename-workflow\": \"renameWorkflow\",\n \"click #copy-workflow\": \"copyWorkflow\"\n },\n\n render: function() {\n $(this.el).html(this._rowTemplate());\n return this;\n },\n\n showInToolPanel: function() {\n this.model.set(\n \"show_in_tool_panel\",\n !this.model.get(\"show_in_tool_panel\")\n );\n this.model.save();\n // This reloads the whole page, so that the workflow appears in the tool panel.\n // Ideally we would notify only the tool panel of a change\n window.location = Galaxy.root + \"workflow\";\n },\n\n removeWorkflow: function() {\n var wfName = this.model.get(\"name\");\n if (\n window.confirm(\n \"Are you sure you want to delete workflow '\" +\n wfName +\n \"'?\"\n )\n ) {\n this.model.destroy({\n success: function() {\n mod_toastr.success(\n \"Successfully deleted workflow '\" + wfName + \"'\"\n );\n }\n });\n this.remove();\n }\n },\n\n renameWorkflow: function() {\n var oldName = this.model.get(\"name\");\n var newName = window.prompt(\n \"Enter a new Name for workflow '\" + oldName + \"'\",\n oldName\n );\n if (newName) {\n this.model.save(\n { name: newName },\n {\n success: function() {\n mod_toastr.success(\n \"Successfully renamed workflow '\" +\n oldName +\n \"' to '\" +\n newName +\n \"'\"\n );\n }\n }\n );\n this.render();\n }\n },\n\n copyWorkflow: function() {\n var self = this;\n var oldName = this.model.get(\"name\");\n $.getJSON(\n this.model.urlRoot + \"/\" + this.model.id + \"/download\",\n function(wfJson) {\n var newName = \"Copy of \" + oldName;\n var currentOwner = self.model.get(\"owner\");\n if (currentOwner != Galaxy.user.attributes.username) {\n newName += \" shared by user \" + currentOwner;\n }\n wfJson.name = newName;\n self.collection.create(wfJson, {\n at: 0,\n wait: true,\n success: function() {\n mod_toastr.success(\n \"Successfully copied workflow '\" +\n oldName +\n \"' to '\" +\n newName +\n \"'\"\n );\n },\n error: function(model, resp, options) {\n // signature seems to have changed over the course of backbone dev\n // see https://github.com/jashkenas/backbone/issues/2606#issuecomment-19289483\n mod_toastr.error(options.errorThrown);\n }\n });\n }\n ).error(function(jqXHR, textStatus, errorThrown) {\n mod_toastr.error(jqXHR.responseJSON.err_msg);\n });\n },\n\n _rowTemplate: function() {\n var show = this.model.get(\"show_in_tool_panel\");\n var wfId = this.model.id;\n var checkboxHtml =\n '';\n var trHtml =\n \" loading tool info...\" +\n ' \" +\n \"' +\n '\" +\n this._templateActions() +\n \"\" +\n \"\" +\n '' +\n \" \" +\n \"\" +\n (this.model.get(\"owner\") === Galaxy.user.attributes.username\n ? \"You\"\n : this.model.get(\"owner\")) +\n \" \" +\n \"\" +\n this.model.get(\"number_of_steps\") +\n \" \" +\n \"\" +\n (this.model.get(\"published\") ? \"Yes\" : \"No\") +\n \" \" +\n \"\" +\n checkboxHtml +\n \" \";\n return trHtml;\n },\n\n renderTagEditor: function() {\n var TagEditor = new TAGS.TagsEditor({\n model: this.model,\n el: $.find(\".\" + this.model.id + \".tags-display\"),\n workflow_mode: true\n });\n TagEditor.toggle(true);\n TagEditor.render();\n },\n\n /** Template for user actions for workflows */\n _templateActions: function() {\n if (\n this.model.get(\"owner\") === Galaxy.user.attributes.username\n ) {\n return (\n '\"\n );\n } else {\n return (\n '\"\n );\n }\n }\n });\n\n /** View of the main workflow list page */\n var WorkflowListView = Backbone.View.extend({\n title: \"Workflows\",\n initialize: function() {\n this.setElement(\"\");\n _.bindAll(this, \"adjustActiondropdown\");\n this.collection = new WORKFLOWS.WorkflowCollection();\n this.collection.fetch().done(this.render());\n this.collection.bind(\"add\", this.appendItem);\n this.collection.on(\"sync\", this.render, this);\n },\n\n events: {\n dragleave: \"unhighlightDropZone\",\n drop: \"drop\",\n dragover: function(ev) {\n $(\".hidden_description_layer\").addClass(\"dragover\");\n $(\".menubutton\").addClass(\"background-none\");\n ev.preventDefault();\n }\n },\n\n unhighlightDropZone: function() {\n $(\".hidden_description_layer\").removeClass(\"dragover\");\n $(\".menubutton\").removeClass(\"background-none\");\n },\n\n drop: function(e) {\n // TODO: check that file is valid galaxy workflow\n this.unhighlightDropZone();\n e.preventDefault();\n var files = e.dataTransfer.files;\n var self = this;\n for (var i = 0, f; (f = files[i]); i++) {\n self.readWorkflowFiles(f);\n }\n },\n\n readWorkflowFiles: function(f) {\n var self = this;\n var reader = new FileReader();\n reader.onload = function(theFile) {\n var wf_json;\n try {\n wf_json = JSON.parse(reader.result);\n } catch (e) {\n mod_toastr.error(\n \"Could not read file '\" +\n f.name +\n \"'. Verify it is a valid Galaxy workflow\"\n );\n wf_json = null;\n }\n if (wf_json) {\n self.collection.create(wf_json, {\n at: 0,\n wait: true,\n success: function() {\n mod_toastr.success(\n \"Successfully imported workflow '\" +\n wf_json.name +\n \"'\"\n );\n },\n error: function(model, resp, options) {\n mod_toastr.error(options.errorThrown);\n }\n });\n }\n };\n reader.readAsText(f, \"utf-8\");\n },\n\n _showArgErrors: _.once(function() {\n // Parse args out of params, display if there's a message.\n var msg_text = QueryStringParsing.get(\"message\");\n var msg_status = QueryStringParsing.get(\"status\");\n if (msg_status === \"error\") {\n mod_toastr.error(\n _.escape(\n msg_text ||\n \"Unknown Error, please report this to an administrator.\"\n )\n );\n } else if (msg_text) {\n mod_toastr.info(_.escape(msg_text));\n }\n }),\n\n render: function() {\n // Add workflow header\n var header = this._templateHeader();\n // Add the actions buttons\n var templateActions = this._templateActionButtons();\n var tableTemplate = this._templateWorkflowTable();\n this.$el.html(header + templateActions + tableTemplate);\n var self = this;\n _(this.collection.models).each(function(item) {\n // in case collection is not empty\n self.appendItem(item);\n self.confirmDelete(item);\n }, this);\n var minQueryLength = 3;\n this.searchWorkflow(\n this.$(\".search-wf\"),\n this.$(\".workflow-search tr\"),\n minQueryLength\n );\n this.adjustActiondropdown();\n this._showArgErrors();\n return this;\n },\n\n appendItem: function(item) {\n var workflowItemView = new WorkflowItemView({\n model: item,\n collection: this.collection\n });\n $(\".workflow-search\").append(workflowItemView.render().el);\n workflowItemView.renderTagEditor();\n },\n\n /** Add confirm box before removing/unsharing workflow */\n confirmDelete: function(workflow) {\n var $el_shared_wf_link = this.$(\n \".link-confirm-shared-\" + workflow.id\n );\n $el_shared_wf_link.click(function() {\n return window.confirm(\n \"Are you sure you want to remove the shared workflow '\" +\n workflow.attributes.name +\n \"'?\"\n );\n });\n },\n\n /** Implement client side workflow search/filtering */\n searchWorkflow: function(\n $el_searchinput,\n $el_tabletr,\n min_querylen\n ) {\n $el_searchinput.on(\"keyup\", function() {\n var query = $(this).val();\n // Filter when query is at least 3 characters\n // otherwise show all rows\n if (query.length >= min_querylen) {\n // Ignore the query's case using 'i'\n var regular_expression = new RegExp(query, \"i\");\n $el_tabletr.hide();\n $el_tabletr\n .filter(function() {\n // Apply regular expression on each row's text\n // and show when there is a match\n return regular_expression.test($(this).text());\n })\n .show();\n } else {\n $el_tabletr.show();\n }\n });\n },\n\n /** Ajust the position of dropdown with respect to table */\n adjustActiondropdown: function() {\n $(this.el).on(\"show.bs.dropdown\", function() {\n $(this.el).css(\"overflow\", \"inherit\");\n });\n $(this.el).on(\"hide.bs.dropdown\", function() {\n $(this.el).css(\"overflow\", \"auto\");\n });\n },\n\n /** Template for no workflow */\n _templateNoWorkflow: function() {\n return 'You have no workflows.';\n },\n\n /** Template for actions buttons */\n _templateActionButtons: function() {\n return (\n '- ' +\n \"
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Workflow view */\ndefine(\n [\n \"libs/toastr\",\n \"mvc/tag\",\n \"mvc/workflow/workflow-model\",\n \"utils/query-string-parsing\"\n ],\n function(mod_toastr, TAGS, WORKFLOWS, QueryStringParsing) {\n /** View of the individual workflows */\n var WorkflowItemView = Backbone.View.extend({\n tagName: \"tr\", // name of (orphan) root tag in this.el\n initialize: function() {\n _.bindAll(\n this,\n \"render\",\n \"_rowTemplate\",\n \"renderTagEditor\",\n \"_templateActions\",\n \"removeWorkflow\",\n \"copyWorkflow\"\n ); // every function that uses 'this' as the current object should be in here\n mod_toastr.options.timeOut = 1500;\n },\n\n events: {\n \"click #show-in-tool-panel\": \"showInToolPanel\",\n \"click #delete-workflow\": \"removeWorkflow\",\n \"click #rename-workflow\": \"renameWorkflow\",\n \"click #copy-workflow\": \"copyWorkflow\"\n },\n\n render: function() {\n $(this.el).html(this._rowTemplate());\n return this;\n },\n\n showInToolPanel: function() {\n this.model.set(\n \"show_in_tool_panel\",\n !this.model.get(\"show_in_tool_panel\")\n );\n this.model.save();\n // This reloads the whole page, so that the workflow appears in the tool panel.\n // Ideally we would notify only the tool panel of a change\n window.location = Galaxy.root + \"workflow\";\n },\n\n removeWorkflow: function() {\n var wfName = this.model.get(\"name\");\n if (\n window.confirm(\n \"Are you sure you want to delete workflow '\" +\n wfName +\n \"'?\"\n )\n ) {\n this.model.destroy({\n success: function() {\n mod_toastr.success(\n \"Successfully deleted workflow '\" + wfName + \"'\"\n );\n }\n });\n this.remove();\n }\n },\n\n renameWorkflow: function() {\n var oldName = this.model.get(\"name\");\n var newName = window.prompt(\n \"Enter a new Name for workflow '\" + oldName + \"'\",\n oldName\n );\n if (newName) {\n this.model.save(\n { name: newName },\n {\n success: function() {\n mod_toastr.success(\n \"Successfully renamed workflow '\" +\n oldName +\n \"' to '\" +\n newName +\n \"'\"\n );\n }\n }\n );\n this.render();\n }\n },\n\n copyWorkflow: function() {\n var self = this;\n var oldName = this.model.get(\"name\");\n $.getJSON(\n this.model.urlRoot + \"/\" + this.model.id + \"/download\",\n function(wfJson) {\n var newName = \"Copy of \" + oldName;\n var currentOwner = self.model.get(\"owner\");\n if (currentOwner != Galaxy.user.attributes.username) {\n newName += \" shared by user \" + currentOwner;\n }\n wfJson.name = newName;\n self.collection.create(wfJson, {\n at: 0,\n wait: true,\n success: function() {\n mod_toastr.success(\n \"Successfully copied workflow '\" +\n oldName +\n \"' to '\" +\n newName +\n \"'\"\n );\n },\n error: function(model, resp, options) {\n // signature seems to have changed over the course of backbone dev\n // see https://github.com/jashkenas/backbone/issues/2606#issuecomment-19289483\n mod_toastr.error(options.errorThrown);\n }\n });\n }\n ).error(function(jqXHR, textStatus, errorThrown) {\n mod_toastr.error(jqXHR.responseJSON.err_msg);\n });\n },\n\n _rowTemplate: function() {\n var show = this.model.get(\"show_in_tool_panel\");\n var wfId = this.model.id;\n var checkboxHtml =\n '';\n var trHtml =\n \"Import Galaxy workflow\" +\n \"\" +\n \"\" +\n \"\" +\n \"
\" +\n \"\" +\n \"\" +\n \"\" +\n \"\" +\n \" Visit myExperiment\" +\n \"\" +\n \"\" +\n \"Click the link above to visit myExperiment and browse for Galaxy workflows.\" +\n \"\" +\n \"\" +\n \"\" +\n ' \" +\n \"' +\n '\" +\n this._templateActions() +\n \"\" +\n \"\" +\n '' +\n \" \" +\n \"\" +\n (this.model.get(\"owner\") === Galaxy.user.attributes.username\n ? \"You\"\n : this.model.get(\"owner\")) +\n \" \" +\n \"\" +\n this.model.get(\"number_of_steps\") +\n \" \" +\n \"\" +\n (this.model.get(\"published\") ? \"Yes\" : \"No\") +\n \" \" +\n \"\" +\n checkboxHtml +\n \" \";\n return trHtml;\n },\n\n renderTagEditor: function() {\n var TagEditor = new TAGS.TagsEditor({\n model: this.model,\n el: $.find(\".\" + this.model.id + \".tags-display\"),\n workflow_mode: true\n });\n TagEditor.toggle(true);\n TagEditor.render();\n },\n\n /** Template for user actions for workflows */\n _templateActions: function() {\n if (\n this.model.get(\"owner\") === Galaxy.user.attributes.username\n ) {\n return (\n '\"\n );\n } else {\n return (\n '\"\n );\n }\n }\n });\n\n /** View of the main workflow list page */\n var WorkflowListView = Backbone.View.extend({\n title: \"Workflows\",\n initialize: function() {\n this.setElement(\"\");\n _.bindAll(this, \"adjustActiondropdown\");\n this.collection = new WORKFLOWS.WorkflowCollection();\n this.collection.fetch().done(this.render());\n this.collection.bind(\"add\", this.appendItem);\n this.collection.on(\"sync\", this.render, this);\n },\n\n events: {\n dragleave: \"unhighlightDropZone\",\n drop: \"drop\",\n dragover: function(ev) {\n $(\".hidden_description_layer\").addClass(\"dragover\");\n $(\".menubutton\").addClass(\"background-none\");\n ev.preventDefault();\n }\n },\n\n unhighlightDropZone: function() {\n $(\".hidden_description_layer\").removeClass(\"dragover\");\n $(\".menubutton\").removeClass(\"background-none\");\n },\n\n drop: function(e) {\n // TODO: check that file is valid galaxy workflow\n this.unhighlightDropZone();\n e.preventDefault();\n var files = e.dataTransfer.files;\n var self = this;\n for (var i = 0, f; (f = files[i]); i++) {\n self.readWorkflowFiles(f);\n }\n },\n\n readWorkflowFiles: function(f) {\n var self = this;\n var reader = new FileReader();\n reader.onload = function(theFile) {\n var wf_json;\n try {\n wf_json = JSON.parse(reader.result);\n } catch (e) {\n mod_toastr.error(\n \"Could not read file '\" +\n f.name +\n \"'. Verify it is a valid Galaxy workflow\"\n );\n wf_json = null;\n }\n if (wf_json) {\n self.collection.create(wf_json, {\n at: 0,\n wait: true,\n success: function() {\n mod_toastr.success(\n \"Successfully imported workflow '\" +\n wf_json.name +\n \"'\"\n );\n },\n error: function(model, resp, options) {\n mod_toastr.error(options.errorThrown);\n }\n });\n }\n };\n reader.readAsText(f, \"utf-8\");\n },\n\n _showArgErrors: _.once(function() {\n // Parse args out of params, display if there's a message.\n var msg_text = QueryStringParsing.get(\"message\");\n var msg_status = QueryStringParsing.get(\"status\");\n if (msg_status === \"error\") {\n mod_toastr.error(\n _.escape(\n msg_text ||\n \"Unknown Error, please report this to an administrator.\"\n )\n );\n } else if (msg_text) {\n mod_toastr.info(_.escape(msg_text));\n }\n }),\n\n render: function() {\n // Add workflow header\n var header = this._templateHeader();\n // Add the actions buttons\n var templateActions = this._templateActionButtons();\n var tableTemplate = this._templateWorkflowTable();\n this.$el.html(header + templateActions + tableTemplate);\n var self = this;\n _(this.collection.models).each(function(item) {\n // in case collection is not empty\n self.appendItem(item);\n self.confirmDelete(item);\n }, this);\n var minQueryLength = 3;\n this.searchWorkflow(\n this.$(\".search-wf\"),\n this.$(\".workflow-search tr\"),\n minQueryLength\n );\n this.adjustActiondropdown();\n this._showArgErrors();\n return this;\n },\n\n appendItem: function(item) {\n var workflowItemView = new WorkflowItemView({\n model: item,\n collection: this.collection\n });\n $(\".workflow-search\").append(workflowItemView.render().el);\n workflowItemView.renderTagEditor();\n },\n\n /** Add confirm box before removing/unsharing workflow */\n confirmDelete: function(workflow) {\n var $el_shared_wf_link = this.$(\n \".link-confirm-shared-\" + workflow.id\n );\n $el_shared_wf_link.click(function() {\n return window.confirm(\n \"Are you sure you want to remove the shared workflow '\" +\n workflow.attributes.name +\n \"'?\"\n );\n });\n },\n\n /** Implement client side workflow search/filtering */\n searchWorkflow: function(\n $el_searchinput,\n $el_tabletr,\n min_querylen\n ) {\n $el_searchinput.on(\"keyup\", function() {\n var query = $(this).val();\n // Filter when query is at least 3 characters\n // otherwise show all rows\n if (query.length >= min_querylen) {\n // Ignore the query's case using 'i'\n var regular_expression = new RegExp(query, \"i\");\n $el_tabletr.hide();\n $el_tabletr\n .filter(function() {\n // Apply regular expression on each row's text\n // and show when there is a match\n return regular_expression.test($(this).text());\n })\n .show();\n } else {\n $el_tabletr.show();\n }\n });\n },\n\n /** Ajust the position of dropdown with respect to table */\n adjustActiondropdown: function() {\n $(this.el).on(\"show.bs.dropdown\", function() {\n $(this.el).css(\"overflow\", \"inherit\");\n });\n $(this.el).on(\"hide.bs.dropdown\", function() {\n $(this.el).css(\"overflow\", \"auto\");\n });\n },\n\n /** Template for no workflow */\n _templateNoWorkflow: function() {\n return 'You have no workflows.';\n },\n\n /** Template for actions buttons */\n _templateActionButtons: function() {\n return (\n '- ' +\n \"
' +\n '
' +\n \" \";\n return (\n tableHtml +\n 'Name \" +\n \"Tags \" +\n \"Owner \" +\n \"# of Steps \" +\n \"Published \" +\n \"Show in tools panel \" +\n \"Drop workflow files here to import
' +\n \"' +\n '\"\n );\n }\n });\n\n var ImportWorkflowView = Backbone.View.extend({\n initialize: function() {\n this.setElement(\"\");\n this.render();\n },\n\n /** Open page to import workflow */\n render: function() {\n var self = this;\n $.getJSON(\n Galaxy.root + \"workflow/upload_import_workflow\",\n function(options) {\n self.$el.empty().append(self._mainTemplate(options));\n }\n );\n },\n\n /** Template for the import workflow page */\n _mainTemplate: function(options) {\n return (\n \"' +\n '' +\n \"\" +\n \"Your workflows
\" +\n \"\" +\n \"\"\n );\n }\n });\n\n return {\n View: WorkflowListView,\n ImportWorkflowView: ImportWorkflowView\n };\n }\n);\n"]} \ No newline at end of file diff --git a/static/maps/nls/de/locale.js.map b/static/maps/nls/de/locale.js.map index 69036f306aa..00b5eef8037 100644 --- a/static/maps/nls/de/locale.js.map +++ b/static/maps/nls/de/locale.js.map @@ -1 +1 @@ -{"version":3,"sources":["nls/de/locale.js"],"names":["define","Workflow","Shared Data","Histories","Workflows","Visualizations","Pages","Visualization","Interactive Environments","Admin","Help","Support","Search","Wiki","Videos","User","Login","Register","Preferences","Custom Builds","Saved Histories","Logout","Saved Pages","Account and saved data","Account registration or login","Support, contact, and community","Administer this Galaxy","Visualize datasets","Access published resources","Chain tools into workflows","Analysis home view","History Lists","Histories Shared with Me","Current History","Create New","Copy History","Share or Publish","Show Structure","Extract Workflow","Delete Permanently","Dataset Actions","Copy Datasets","Dataset Security","Resume Paused Jobs","Collapse Expanded Datasets","Unhide Hidden Datasets","Delete Hidden Datasets","Purge Deleted Datasets","Downloads","Export Tool Citations","Other Actions","Import from File","Webhooks","This history is empty","No matching datasets found","An error occurred while getting updates from the server","Please contact a Galaxy administrator if the problem persists","search datasets","You are currently viewing a deleted history!","You are over your disk quota","All","None","For all selected","Edit history tags","Edit history Annotation","Click to rename history","Operations on multiple datasets","Hide datasets","Unhide datasets","Delete datasets","Undelete datasets","Permanently delete datasets","Dataset","Annotation","This history is empty. 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en/main localization hash - for use with requirejs' i18n plugin */\ndefine({\n // ----------------------------------------------------------------------------- masthead\n \"Analyze Data\": \"Daten analysieren\",\n Workflow: \"Arbeitsablauf\",\n \"Shared Data\": \"Gemeinsame Daten\",\n \"Data Libraries\": \"Datenbibliotheken\",\n Histories: \"Geschichten\",\n Workflows: \"Workflows\",\n Visualizations: \"Visualisierungen\",\n Pages: \"Seiten\",\n Visualization: \"Visualisierung\",\n \"New Track Browser\": \"Neuer Track Browser\",\n \"Saved Visualizations\": \"Gespeicherte Visualisierungen\",\n \"Interactive Environments\": \"Interaktive Umgebungen\",\n Admin: \"Administrator\",\n Help: \"Hilfe\",\n Support: \"Unterstützung\",\n Search: \"Suche\",\n \"Mailing Lists\": \"Mailinglisten\",\n Videos: \"Videos\",\n Wiki: \"Wiki\",\n \"How to Cite Galaxy\": \"Wie man Galaxie zitiert\",\n \"Interactive Tours\": \"Interactive Tours\",\n User: \"Benutzer\",\n Login: \"Anmeldung\",\n Register: \"Neu registrieren\",\n \"Login or Register\": \"Einloggen oder Registrieren\",\n \"Logged in as\": \"Angemeldet als\",\n Preferences: \"Präferenzen\",\n \"Custom Builds\": \"Custom Builds\",\n Logout: \"Ausloggen\",\n \"Saved Histories\": \"Gespeicherte Geschichten\",\n \"Saved Datasets\": \"Gespeicherte Datasets\",\n \"Saved Pages\": \"Gespeicherte Seiten\",\n //Tooltip\n \"Account and saved data\": \"Konto und gespeicherte Daten\",\n \"Account registration or login\": \"Konto Registrierung oder Login\",\n \"Support, contact, and community\": \"Unterstützung, Kontakt und Community\",\n \"Administer this Galaxy\": \"Verwalte diese Galaxie\",\n \"Visualize datasets\": \"Visualisieren von Datensätzen\",\n \"Access published resources\": \"Zugriff auf veröffentlichte Ressourcen\",\n \"Chain tools into workflows\": \"Kettenwerkzeuge in Workflows\",\n \"Analysis home view\": \"Analyse home view\",\n // ---------------------------------------------------------------------------- histories\n // ---- history/options-menu\n \"History Lists\": \"History Lists\",\n // Saved histories is defined above.\n // \"Saved Histories\":\n // false,\n \"Histories Shared with Me\": \"Geschichten mit mir geteilt\",\n \"Current History\": \"Aktuelle Geschichte\",\n \"Create New\": \"Erstelle neu\",\n \"Copy History\": \"Geschichte kopieren\",\n \"Share or Publish\": \"Teilen oder veröffentlichen\",\n \"Show Structure\": \"Struktur anzeigen\",\n \"Extract Workflow\": \"Workflow extrahieren\",\n // Delete is defined elsewhere, but is also in this menu.\n // \"Delete\":\n // false,\n \"Delete Permanently\": \"Dauerhaft löschen\",\n \"Dataset Actions\": \"Datensatzaktionen\",\n \"Copy Datasets\": \"Datensätze kopieren\",\n \"Dataset Security\": \"Datensatz Sicherheit\",\n \"Resume Paused Jobs\": \"Fortsetzen pausierte Jobs\",\n \"Collapse Expanded Datasets\": \"Collapse Expanded Datasets\",\n \"Unhide Hidden Datasets\": \"Hidden Datasets verstecken\",\n \"Delete Hidden Datasets\": \"Hidden Datasets löschen\",\n \"Purge Deleted Datasets\": \"Gelöschte Datasets löschen\",\n Downloads: \"Downloads\",\n \"Export Tool Citations\": \"Export Tool Zitate\",\n \"Export History to File\": \"Export History to File\",\n \"Other Actions\": \"Andere Aktionen\",\n \"Import from File\": \"Import aus Datei\",\n Webhooks: \"Webhooks\",\n // ---- history-model\n // ---- history-view\n \"This history is empty\": \"Diese Geschichte ist leer\",\n \"No matching datasets found\": \"Keine passenden Datensätze gefunden\",\n \"An error occurred while getting updates from the server\":\n \"Ein Fehler ist aufgetreten beim Aktualisieren vom Server\",\n \"Please contact a Galaxy administrator if the problem persists\":\n \"Bitte wenden Sie sich an einen Galaxy-Administrator, wenn das Problem weiterhin besteht\",\n //TODO:\n //\"An error was encountered while <% where %>\" :\n //false,\n \"search datasets\": \"Suchdatensätze\",\n \"You are currently viewing a deleted history!\":\n \"Du siehst derzeit einen gelöschten Verlauf!\",\n \"You are over your disk quota\": \"Du bist über dein Festplatten-Kontingent\",\n \"Tool execution is on hold until your disk usage drops below your allocated quota\":\n \"Tool-Ausführung ist in der Warteschleife, bis Ihre Datenträgerverwendung unter Ihrem zugeteilten Kontingent fällt\",\n All: \"Alle\",\n None: \"Keiner\",\n \"For all selected\": \"Für alle ausgewählt\",\n // ---- history-view-edit\n \"Edit history tags\": \"Geschichte bearbeiten\",\n \"Edit history Annotation\": \"Historie bearbeiten\",\n \"Click to rename history\": \"Klicken Sie hier, um den Verlauf umzubenennen\",\n // multi operations\n \"Operations on multiple datasets\": \"Operationen auf mehreren Datensätzen\",\n \"Hide datasets\": \"Datensätze ausblenden\",\n \"Unhide datasets\": \"Datasets einblenden\",\n \"Delete datasets\": \"Datensätze löschen\",\n \"Undelete datasets\": \"Undelete-Datasets\",\n \"Permanently delete datasets\": \"Datensätze dauerhaft löschen\",\n \"This will permanently remove the data in your datasets. Are you sure?\":\n \"Das wird endgültig die Daten in deinen Datasets entfernen. Bist du sicher?\",\n // ---- history-view-annotated\n Dataset: \"Dataset\",\n Annotation: \"Annotation\",\n // ---- history-view-edit-current\n \"This history is empty. Click 'Get Data' on the left tool menu to start\":\n \"Diese Geschichte ist leer. Klicken Sie auf 'Get Data' im linken Tool-Menü, um\",\n \"You must be logged in to create histories\":\n \"Du musst eingeloggt sein, um Geschichten zu schaffen\",\n //TODO:\n //\"You can <% loadYourOwn %> or <% externalSource %>\" :\n //false,\n //\"load your own data\" :\n //false,\n //\"get data from an external source\" :\n //false,\n\n // these aren't in zh/ginga.po and the template doesn't localize\n //\"Include Deleted Datasets\" :\n //false,\n //\"Include Hidden Datasets\" :\n //false,\n\n // ---------------------------------------------------------------------------- datasets\n // ---- hda-model\n \"Unable to purge dataset\": \"Dataset kann nicht gelöscht werden\",\n // ---- hda-base\n // display button\n \"Cannot display datasets removed from disk\":\n \"Datasets können nicht von der Festplatte entfernt werden\",\n \"This dataset must finish uploading before it can be viewed\":\n \"Dieser Datensatz muss das Hochladen beenden, bevor es angezeigt werden kann\",\n \"This dataset is not yet viewable\":\n \"Dieser Datensatz ist noch nicht sichtbar\",\n \"View data\": \"Daten anzeigen\",\n // download button\n Download: \"Herunterladen\",\n \"Download dataset\": \"Dataset herunterladen\",\n \"Additional files\": \"Zusätzliche Dateien\",\n // info/show_params\n \"View details\": \"Details anzeigen\",\n // dataset states\n // state: new\n \"This is a new dataset and not all of its data are available yet\":\n \"Dies ist ein neuer Datensatz und nicht alle seine Daten sind noch verfügbar\",\n // state: noPermission\n \"You do not have permission to view this dataset\":\n \"Sie haben keine Berechtigung, diesen Datensatz anzuzeigen\",\n // state: discarded\n \"The job creating this dataset was cancelled before completion\":\n \"Der Job, der diesen Datensatz erstellt hat, wurde vor der Fertigstellung abgebrochen\",\n // state: queued\n \"This job is waiting to run\": \"Dieser Job wartet darauf, zu rennen\",\n // state: upload\n \"This dataset is currently uploading\": \"Dieser Datensatz lädt derzeit\",\n // state: setting_metadata\n \"Metadata is being auto-detected\": \"Metadaten werden automatisch erkannt\",\n // state: running\n \"This job is currently running\": \"Dieser Job läuft derzeit\",\n // state: paused\n 'This job is paused. Use the \"Resume Paused Jobs\" in the history menu to resume':\n 'Dieser Job wird pausiert. Verwenden Sie die \"Resume Paused Jobs \" im Verlaufsmenü, um',\n // state: error\n \"An error occurred with this dataset\":\n \"Ein Fehler ist mit diesem Datensatz aufgetreten\",\n // state: empty\n \"No data\": \"Keine Daten\",\n // state: failed_metadata\n \"An error occurred setting the metadata for this dataset\":\n \"Ein Fehler ist aufgetreten Einstellung der Metadaten für diese Datenmenge\",\n // ajax error prefix\n \"There was an error getting the data for this dataset\":\n \"Es gab einen Fehler, der die Daten für diesen Datensatz bekam\",\n // purged'd/del'd msg\n \"This dataset has been deleted and removed from disk\":\n \"Dieser Datensatz wurde gelöscht und von der Festplatte entfernt\",\n \"This dataset has been deleted\": \"Dieser Datensatz wurde gelöscht\",\n \"This dataset has been hidden\": \"Dieser Datensatz wurde ausgeblendet\",\n format: \"Format\",\n database: \"Datenbank\",\n // ---- hda-edit\n \"Edit attributes\": \"Attribute bearbeiten\",\n \"Cannot edit attributes of datasets removed from disk\":\n \"Kann keine Attribute von Datasets aus dem Datenträger entfernen\",\n \"Undelete dataset to edit attributes\":\n \"Undelete-Dataset zum Bearbeiten von Attributen\",\n \"This dataset must finish uploading before it can be edited\":\n \"Dieser Datensatz muss das Hochladen beenden, bevor es bearbeitet werden kann\",\n \"This dataset is not yet editable\":\n \"Dieser Datensatz ist noch nicht bearbeitbar\",\n Delete: \"Löschen\",\n \"Dataset is already deleted\": \"Dataset ist bereits gelöscht\",\n \"View or report this error\": \"Diesen Fehler anzeigen oder melden\",\n \"Run this job again\": \"Führen Sie diesen Job wieder\",\n Visualize: \"Visualisieren\",\n \"Visualize in\": \"Visualize in\",\n \"Undelete it\": \"Untelete it\",\n \"Permanently remove it from disk\": \"Permanent aus der Scheibe entfernen\",\n \"Unhide it\": \"Ausblenden\",\n \"You may be able to\": \"Sie können in der Lage sein\",\n \"set it manually or retry auto-detection\":\n \"Manuell einstellen oder Auto-Erkennung wiederholen\",\n \"Edit dataset tags\": \"Dataset-Tags bearbeiten\",\n \"Edit dataset annotation\": \"Datensatz-Annotation bearbeiten\",\n // ---------------------------------------------------------------------------- misc. MVC\n Tags: \"Variablen\",\n \"Edit annotation\": \"Anmerkung bearbeiten\"\n});\n"]} \ No newline at end of file +{"version":3,"sources":["nls/de/locale.js"],"names":["define","Analyze Data","Shared Data","Data Libraries","Workflow","Workflows","Visualizations","Histories","Pages","Visualization","Admin","Help","Support","Search","How to Cite Galaxy","Videos","Wiki","Login","Register","User","Custom Builds","Logout","Preferences","Saved Datasets","Account and saved data","Account registration or login","Support, contact, and community","Administer this Galaxy","Visualize datasets","Access published resources","Chain tools into workflows","Analysis home view","History Lists","Histories Shared with Me","Current History","Create New","Copy History","Share or Publish","Show Structure","Extract Workflow","Delete Permanently","Dataset Actions","Copy Datasets","Dataset Security","Resume Paused Jobs","Collapse Expanded Datasets","Unhide Hidden Datasets","Delete Hidden Datasets","Purge Deleted Datasets","Downloads","Export Tool Citations","Export History to File","Import from File","Webhooks","No matching datasets found","An error occurred while getting updates from the server","Please contact a Galaxy administrator if the problem persists","search datasets","You are currently viewing a deleted history!","You are over your disk quota","Tool execution is on hold until your disk usage drops below your allocated quota","All","None","For all selected","Edit history tags","Edit history Annotation","Click to rename history","Operations on multiple datasets","Hide datasets","Unhide datasets","Delete datasets","Undelete datasets","Permanently delete datasets","This will permanently remove the data in your datasets. 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en/main localization hash - for use with requirejs' i18n plugin */\ndefine({\n // ----------------------------------------------------------------------------- masthead\n \"Analyze Data\": \"Daten analysieren\",\n Workflow: \"Arbeitsablauf\",\n \"Shared Data\": \"Gemeinsame Daten\",\n \"Data Libraries\": \"Datenbibliotheken\",\n Histories: \"Geschichten\",\n Workflows: \"Workflows\",\n Visualizations: \"Visualisierungen\",\n Pages: \"Seiten\",\n Visualization: \"Visualisierung\",\n \"New Track Browser\": \"Neuer Track Browser\",\n \"Saved Visualizations\": \"Gespeicherte Visualisierungen\",\n \"Interactive Environments\": \"Interaktive Umgebungen\",\n Admin: \"Administrator\",\n Help: \"Hilfe\",\n Support: \"Unterstützung\",\n Search: \"Suche\",\n \"Mailing Lists\": \"Mailinglisten\",\n Videos: \"Videos\",\n Wiki: \"Wiki\",\n \"How to Cite Galaxy\": \"Wie man Galaxie zitiert\",\n \"Interactive Tours\": \"Interactive Tours\",\n User: \"Benutzer\",\n Login: \"Anmeldung\",\n Register: \"Neu registrieren\",\n \"Login or Register\": \"Einloggen oder Registrieren\",\n \"Logged in as\": \"Angemeldet als\",\n Preferences: \"Präferenzen\",\n \"Custom Builds\": \"Custom Builds\",\n Logout: \"Ausloggen\",\n \"Saved Histories\": \"Gespeicherte Geschichten\",\n \"Saved Datasets\": \"Gespeicherte Datasets\",\n \"Saved Pages\": \"Gespeicherte Seiten\",\n //Tooltip\n \"Account and saved data\": \"Konto und gespeicherte Daten\",\n \"Account registration or login\": \"Konto Registrierung oder Login\",\n \"Support, contact, and community\": \"Unterstützung, Kontakt und Community\",\n \"Administer this Galaxy\": \"Verwalte diese Galaxie\",\n \"Visualize datasets\": \"Visualisieren von Datensätzen\",\n \"Access published resources\": \"Zugriff auf veröffentlichte Ressourcen\",\n \"Chain tools into workflows\": \"Kettenwerkzeuge in Workflows\",\n \"Analysis home view\": \"Analyse home view\",\n // ---------------------------------------------------------------------------- histories\n // ---- history/options-menu\n \"History Lists\": \"History Lists\",\n // Saved histories is defined above.\n // \"Saved Histories\":\n // false,\n \"Histories Shared with Me\": \"Geschichten mit mir geteilt\",\n \"Current History\": \"Aktuelle Geschichte\",\n \"Create New\": \"Erstelle neu\",\n \"Copy History\": \"Geschichte kopieren\",\n \"Share or Publish\": \"Teilen oder veröffentlichen\",\n \"Show Structure\": \"Struktur anzeigen\",\n \"Extract Workflow\": \"Workflow extrahieren\",\n // Delete is defined elsewhere, but is also in this menu.\n // \"Delete\":\n // false,\n \"Delete Permanently\": \"Dauerhaft löschen\",\n \"Dataset Actions\": \"Datensatzaktionen\",\n \"Copy Datasets\": \"Datensätze kopieren\",\n \"Dataset Security\": \"Datensatz Sicherheit\",\n \"Resume Paused Jobs\": \"Fortsetzen pausierte Jobs\",\n \"Collapse Expanded Datasets\": \"Collapse Expanded Datasets\",\n \"Unhide Hidden Datasets\": \"Hidden Datasets verstecken\",\n \"Delete Hidden Datasets\": \"Hidden Datasets löschen\",\n \"Purge Deleted Datasets\": \"Gelöschte Datasets löschen\",\n Downloads: \"Downloads\",\n \"Export Tool Citations\": \"Export Tool Zitate\",\n \"Export History to File\": \"Export History to File\",\n \"Other Actions\": \"Andere Aktionen\",\n \"Import from File\": \"Import aus Datei\",\n Webhooks: \"Webhooks\",\n // ---- history-model\n // ---- history-view\n \"This history is empty\": \"Diese Geschichte ist leer\",\n \"No matching datasets found\": \"Keine passenden Datensätze gefunden\",\n \"An error occurred while getting updates from the server\":\n \"Ein Fehler ist aufgetreten beim Aktualisieren vom Server\",\n \"Please contact a Galaxy administrator if the problem persists\":\n \"Bitte wenden Sie sich an einen Galaxy-Administrator, wenn das Problem weiterhin besteht\",\n //TODO:\n //\"An error was encountered while <% where %>\" :\n //false,\n \"search datasets\": \"Suchdatensätze\",\n \"You are currently viewing a deleted history!\":\n \"Du siehst derzeit einen gelöschten Verlauf!\",\n \"You are over your disk quota\": \"Du bist über dein Festplatten-Kontingent\",\n \"Tool execution is on hold until your disk usage drops below your allocated quota\":\n \"Tool-Ausführung ist in der Warteschleife, bis Ihre Datenträgerverwendung unter Ihrem zugeteilten Kontingent fällt\",\n All: \"Alle\",\n None: \"Keiner\",\n \"For all selected\": \"Für alle ausgewählt\",\n // ---- history-view-edit\n \"Edit history tags\": \"Geschichte bearbeiten\",\n \"Edit history Annotation\": \"Historie bearbeiten\",\n \"Click to rename history\": \"Klicken Sie hier, um den Verlauf umzubenennen\",\n // multi operations\n \"Operations on multiple datasets\": \"Operationen auf mehreren Datensätzen\",\n \"Hide datasets\": \"Datensätze ausblenden\",\n \"Unhide datasets\": \"Datasets einblenden\",\n \"Delete datasets\": \"Datensätze löschen\",\n \"Undelete datasets\": \"Undelete-Datasets\",\n \"Permanently delete datasets\": \"Datensätze dauerhaft löschen\",\n \"This will permanently remove the data in your datasets. Are you sure?\":\n \"Das wird endgültig die Daten in deinen Datasets entfernen. Bist du sicher?\",\n // ---- history-view-annotated\n Dataset: \"Dataset\",\n Annotation: \"Annotation\",\n // ---- history-view-edit-current\n \"This history is empty. Click 'Get Data' on the left tool menu to start\":\n \"Diese Geschichte ist leer. Klicken Sie auf 'Get Data' im linken Tool-Menü, um\",\n \"You must be logged in to create histories\":\n \"Du musst eingeloggt sein, um Geschichten zu schaffen\",\n //TODO:\n //\"You can <% loadYourOwn %> or <% externalSource %>\" :\n //false,\n //\"load your own data\" :\n //false,\n //\"get data from an external source\" :\n //false,\n\n // these aren't in zh/ginga.po and the template doesn't localize\n //\"Include Deleted Datasets\" :\n //false,\n //\"Include Hidden Datasets\" :\n //false,\n\n // ---------------------------------------------------------------------------- datasets\n // ---- hda-model\n \"Unable to purge dataset\": \"Dataset kann nicht gelöscht werden\",\n // ---- hda-base\n // display button\n \"Cannot display datasets removed from disk\":\n \"Datasets können nicht von der Festplatte entfernt werden\",\n \"This dataset must finish uploading before it can be viewed\":\n \"Dieser Datensatz muss das Hochladen beenden, bevor es angezeigt werden kann\",\n \"This dataset is not yet viewable\":\n \"Dieser Datensatz ist noch nicht sichtbar\",\n \"View data\": \"Daten anzeigen\",\n // download button\n Download: \"Herunterladen\",\n \"Download dataset\": \"Dataset herunterladen\",\n \"Additional files\": \"Zusätzliche Dateien\",\n // info/show_params\n \"View details\": \"Details anzeigen\",\n // dataset states\n // state: new\n \"This is a new dataset and not all of its data are available yet\":\n \"Dies ist ein neuer Datensatz und nicht alle seine Daten sind noch verfügbar\",\n // state: noPermission\n \"You do not have permission to view this dataset\":\n \"Sie haben keine Berechtigung, diesen Datensatz anzuzeigen\",\n // state: discarded\n \"The job creating this dataset was cancelled before completion\":\n \"Der Job, der diesen Datensatz erstellt hat, wurde vor der Fertigstellung abgebrochen\",\n // state: queued\n \"This job is waiting to run\": \"Dieser Job wartet darauf, zu rennen\",\n // state: upload\n \"This dataset is currently uploading\": \"Dieser Datensatz lädt derzeit\",\n // state: setting_metadata\n \"Metadata is being auto-detected\": \"Metadaten werden automatisch erkannt\",\n // state: running\n \"This job is currently running\": \"Dieser Job läuft derzeit\",\n // state: paused\n 'This job is paused. Use the \"Resume Paused Jobs\" in the history menu to resume':\n 'Dieser Job wird pausiert. Verwenden Sie die \"Resume Paused Jobs \" im Verlaufsmenü, um',\n // state: error\n \"An error occurred with this dataset\":\n \"Ein Fehler ist mit diesem Datensatz aufgetreten\",\n // state: empty\n \"No data\": \"Keine Daten\",\n // state: failed_metadata\n \"An error occurred setting the metadata for this dataset\":\n \"Ein Fehler ist aufgetreten Einstellung der Metadaten für diese Datenmenge\",\n // ajax error prefix\n \"There was an error getting the data for this dataset\":\n \"Es gab einen Fehler, der die Daten für diesen Datensatz bekam\",\n // purged'd/del'd msg\n \"This dataset has been deleted and removed from disk\":\n \"Dieser Datensatz wurde gelöscht und von der Festplatte entfernt\",\n \"This dataset has been deleted\": \"Dieser Datensatz wurde gelöscht\",\n \"This dataset has been hidden\": \"Dieser Datensatz wurde ausgeblendet\",\n format: \"Format\",\n database: \"Datenbank\",\n // ---- hda-edit\n \"Edit attributes\": \"Attribute bearbeiten\",\n \"Cannot edit attributes of datasets removed from disk\":\n \"Kann keine Attribute von Datasets aus dem Datenträger entfernen\",\n \"Undelete dataset to edit attributes\":\n \"Undelete-Dataset zum Bearbeiten von Attributen\",\n \"This dataset must finish uploading before it can be edited\":\n \"Dieser Datensatz muss das Hochladen beenden, bevor es bearbeitet werden kann\",\n \"This dataset is not yet editable\":\n \"Dieser Datensatz ist noch nicht bearbeitbar\",\n Delete: \"Löschen\",\n \"Dataset is already deleted\": \"Dataset ist bereits gelöscht\",\n \"View or report this error\": \"Diesen Fehler anzeigen oder melden\",\n \"Run this job again\": \"Führen Sie diesen Job wieder\",\n Visualize: \"Visualisieren\",\n \"Visualize in\": \"Visualize in\",\n \"Undelete it\": \"Untelete it\",\n \"Permanently remove it from disk\": \"Permanent aus der Scheibe entfernen\",\n \"Unhide it\": \"Ausblenden\",\n \"You may be able to\": \"Sie können in der Lage sein\",\n \"set it manually or retry auto-detection\":\n \"Manuell einstellen oder Auto-Erkennung wiederholen\",\n \"Edit dataset tags\": \"Dataset-Tags bearbeiten\",\n \"Edit dataset annotation\": \"Datensatz-Annotation bearbeiten\",\n // ---------------------------------------------------------------------------- misc. MVC\n Tags: \"Variablen\",\n \"Edit annotation\": \"Anmerkung bearbeiten\"\n});\n"]} \ No newline at end of file diff --git a/static/maps/nls/es/locale.js.map b/static/maps/nls/es/locale.js.map index 43651ee3ffb..23a886ef43a 100644 --- a/static/maps/nls/es/locale.js.map +++ b/static/maps/nls/es/locale.js.map @@ -1 +1 @@ -{"version":3,"sources":["nls/es/locale.js"],"names":["define","Workflow","Shared Data","Histories","Workflows","Visualizations","Pages","Visualization","Interactive Environments","Admin","Help","Support","Search","Wiki","Videos","User","Login","Register","Preferences","Custom Builds","Saved Histories","Logout","Saved Pages","Account and saved data","Account registration or login","Support, contact, and community","Administer this Galaxy","Visualize datasets","Access published resources","Chain tools into workflows","Analysis home view","History Lists","Histories Shared with Me","Current History","Create New","Copy History","Share or Publish","Show Structure","Extract Workflow","Delete Permanently","Dataset Actions","Copy Datasets","Dataset Security","Resume Paused Jobs","Collapse Expanded Datasets","Unhide Hidden Datasets","Delete Hidden Datasets","Purge Deleted Datasets","Downloads","Export Tool Citations","Other Actions","Import from File","Webhooks","This history is empty","No matching datasets found","An error occurred while getting updates from the server","Please contact a Galaxy administrator if the problem persists","search datasets","You are currently viewing a deleted history!","All","None","For all selected","Edit history tags","Edit history Annotation","Click to rename history","Operations on multiple datasets","Hide datasets","Unhide datasets","Delete datasets","Dataset","Annotation","This will permanently remove the data in your datasets. 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en/main localization hash - for use with requirejs' i18n plugin */\ndefine({\n // ----------------------------------------------------------------------------- masthead\n \"Analyze Data\": \"Analizar datos\",\n Workflow: \"Flujo de trabajo\",\n \"Shared Data\": \"Datos compartidos\",\n \"Data Libraries\": \"Bibliotecas de datos\",\n Histories: \"Historias\",\n Workflows: \"Flujos de trabajo\",\n Visualizations: \"Visualizaciones\",\n Pages: \"Páginas\",\n Visualization: \"Visualización\",\n \"New Track Browser\": \"Nuevo navegador de pistas\",\n \"Saved Visualizations\": \"Visualizaciones Guardadas\",\n \"Interactive Environments\": \"Entornos Interactivos\",\n Admin: \"Administración\",\n Help: \"Ayuda\",\n Support: \"Apoyo\",\n Search: \"Buscar\",\n \"Mailing Lists\": \"Listas de correo\",\n Videos: \"Videos\",\n Wiki: \"Wiki\",\n \"How to Cite Galaxy\": \"Cómo citar a Galaxy\",\n \"Interactive Tours\": \"recorridos interactivos\",\n User: \"Usuario\",\n Login: \"Iniciar sesión\",\n Register: \"Registro\",\n \"Login or Register\": \"Iniciar sesión o Registrarse\",\n \"Logged in as\": \"Conectado como\",\n Preferences: \"Preferencias\",\n \"Custom Builds\": \"Construcciones personalizadas\",\n Logout: \"Cerrar sesión\",\n \"Saved Histories\": \"Historias Guardadas\",\n \"Saved Datasets\": \"Conjuntos de datos guardados\",\n \"Saved Pages\": \"Páginas guardadas\",\n //Tooltip\n \"Account and saved data\": \"Cuenta y datos guardados\",\n \"Account registration or login\": \"Registro de cuenta o inicio de sesión\",\n \"Support, contact, and community\": \"Apoyo, contacto y comunidad\",\n \"Administer this Galaxy\": \"Administrar esta galaxia\",\n \"Visualize datasets\": \"Visualizar conjuntos de datos\",\n \"Access published resources\": \"Acceso a los recursos publicados\",\n \"Chain tools into workflows\": \"Herramientas de cadena en flujos de trabajo\",\n \"Analysis home view\": \"Vista de inicio del análisis\",\n // ---------------------------------------------------------------------------- histories\n // ---- history/options-menu\n \"History Lists\": \"Listas de historia\",\n // Saved histories is defined above.\n // \"Saved Histories\":\n // false,\n \"Histories Shared with Me\": \"Historias compartidas conmigo\",\n \"Current History\": \"Historia actual\",\n \"Create New\": \"Crear nuevo\",\n \"Copy History\": \"Historial de Copias\",\n \"Share or Publish\": \"Compartir o publicar\",\n \"Show Structure\": \"Mostrar Estructura\",\n \"Extract Workflow\": \"Extraer flujo de trabajo\",\n // Delete is defined elsewhere, but is also in this menu.\n // \"Delete\":\n // false,\n \"Delete Permanently\": \"Borrar permanentemente\",\n \"Dataset Actions\": \"Acciones de conjuntos de datos\",\n \"Copy Datasets\": \"Conjuntos de datos de copia\",\n \"Dataset Security\": \"Seguridad del conjunto de datos\",\n \"Resume Paused Jobs\": \"Reanudar trabajos en pausa\",\n \"Collapse Expanded Datasets\": \"Contraer conjuntos de datos expandidos\",\n \"Unhide Hidden Datasets\": \"Mostrar conjuntos de datos ocultos\",\n \"Delete Hidden Datasets\": \"Eliminar conjuntos de datos ocultos\",\n \"Purge Deleted Datasets\": \"Eliminar los conjuntos de datos eliminados\",\n Downloads: \"Descargas\",\n \"Export Tool Citations\": \"Citas de herramientas de exportación\",\n \"Export History to File\": \"Exportar historial a archivo\",\n \"Other Actions\": \"Otras acciones\",\n \"Import from File\": \"Importar desde archivo\",\n Webhooks: \"WebHooks\",\n // ---- history-model\n // ---- history-view\n \"This history is empty\": \"Esta historia está vacía\",\n \"No matching datasets found\":\n \"No se encontraron conjuntos de datos coincidentes\",\n \"An error occurred while getting updates from the server\":\n \"Se ha producido un error al obtener actualizaciones desde el servidor\",\n \"Please contact a Galaxy administrator if the problem persists\":\n \"Póngase en contacto con un administrador de Galaxy si el problema persiste\",\n //TODO:\n //\"An error was encountered while <% where %>\" :\n //false,\n \"search datasets\": \"Conjuntos de datos de búsqueda\",\n \"You are currently viewing a deleted history!\":\n \"¡Actualmente estás viendo un historial eliminado!\",\n \"You are over your disk quota\": \"Has sobrepasado tu cuota de disco\",\n \"Tool execution is on hold until your disk usage drops below your allocated quota\":\n \"La ejecución de la herramienta está en espera hasta que el uso del disco caiga por debajo de la cuota asignada\",\n All: \"Todas\",\n None: \"Ninguna\",\n \"For all selected\": \"Para todos los seleccionados\",\n // ---- history-view-edit\n \"Edit history tags\": \"Editar etiquetas de historial\",\n \"Edit history Annotation\": \"Editar anotación de la historia\",\n \"Click to rename history\": \"Haga clic para cambiar el nombre del historial\",\n // multi operations\n \"Operations on multiple datasets\":\n \"Operaciones en conjuntos de datos múltiples\",\n \"Hide datasets\": \"Ocultar conjuntos de datos\",\n \"Unhide datasets\": \"Mostrar conjuntos de datos\",\n \"Delete datasets\": \"Borrar conjuntos de datos\",\n \"Undelete datasets\": \"Undelete datasets\",\n \"Permanently delete datasets\":\n \"Eliminar permanentemente conjuntos de datos\",\n \"This will permanently remove the data in your datasets. Are you sure?\":\n \"Esto eliminará permanentemente los datos de sus datasets. ¿Está seguro?\",\n // ---- history-view-annotated\n Dataset: \"Conjunto de datos\",\n Annotation: \"Anotación\",\n // ---- history-view-edit-current\n \"This history is empty. Click 'Get Data' on the left tool menu to start\":\n \"Este historial está vacío. 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Use the \"Resume Paused Jobs\" in the history menu to resume':\n 'Este trabajo está en pausa Utilice la opción \" Reanudar pausado Jobs \" en el menú de historial para reanudar',\n // state: error\n \"An error occurred with this dataset\":\n \"Se ha producido un error con este conjunto de datos\",\n // state: empty\n \"No data\": \"Sin datos\",\n // state: failed_metadata\n \"An error occurred setting the metadata for this dataset\":\n \"Se ha producido un error al establecer los metadatos de este conjunto de datos\",\n // ajax error prefix\n \"There was an error getting the data for this dataset\":\n \"Hubo un error al obtener los datos de este conjunto de datos\",\n // purged'd/del'd msg\n \"This dataset has been deleted and removed from disk\":\n \"Este conjunto de datos ha sido eliminado y eliminado del disco\",\n \"This dataset has been deleted\": \"Este conjunto de datos ha sido eliminado\",\n \"This dataset has been hidden\": \"Este conjunto de datos se ha ocultado\",\n format: \"Formato\",\n database: \"base de datos\",\n // ---- hda-edit\n \"Edit attributes\": \"Editar atributos\",\n \"Cannot edit attributes of datasets removed from disk\":\n \"No se pueden editar los atributos de conjuntos de datos eliminados del disco\",\n \"Undelete dataset to edit attributes\":\n \"Undelete el conjunto de datos para editar atributos\",\n \"This dataset must finish uploading before it can be edited\":\n \"Este conjunto de datos debe terminar de cargar antes de que pueda ser editado\",\n \"This dataset is not yet editable\":\n \"Este conjunto de datos aún no es editable\",\n Delete: \"Borrar\",\n \"Dataset is already deleted\": \"El conjunto de datos ya se ha eliminado\",\n \"View or report this error\": \"Ver o informar de este error\",\n \"Run this job again\": \"Ejecutar este trabajo de nuevo\",\n Visualize: \"Visualizar\",\n \"Visualize in\": \"Visualizar en\",\n \"Undelete it\": \"Undelete it\",\n \"Permanently remove it from disk\": \"Eliminar permanentemente del disco\",\n \"Unhide it\": \"Mostrarlo\",\n \"You may be able to\": \"Usted puede ser capaz de\",\n \"set it manually or retry auto-detection\":\n \"Configurar manualmente o volver a intentar la detección automática\",\n \"Edit dataset tags\": \"Editar etiquetas de dataset\",\n \"Edit dataset annotation\": \"Editar anotación del conjunto de datos\",\n // ---------------------------------------------------------------------------- misc. 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en/main localization hash - for use with requirejs' i18n plugin */\ndefine({\n // ----------------------------------------------------------------------------- masthead\n \"Analyze Data\": \"Analizar datos\",\n Workflow: \"Flujo de trabajo\",\n \"Shared Data\": \"Datos compartidos\",\n \"Data Libraries\": \"Bibliotecas de datos\",\n Histories: \"Historias\",\n Workflows: \"Flujos de trabajo\",\n Visualizations: \"Visualizaciones\",\n Pages: \"Páginas\",\n Visualization: \"Visualización\",\n \"New Track Browser\": \"Nuevo navegador de pistas\",\n \"Saved Visualizations\": \"Visualizaciones Guardadas\",\n \"Interactive Environments\": \"Entornos Interactivos\",\n Admin: \"Administración\",\n Help: \"Ayuda\",\n Support: \"Apoyo\",\n Search: \"Buscar\",\n \"Mailing Lists\": \"Listas de correo\",\n Videos: \"Videos\",\n Wiki: \"Wiki\",\n \"How to Cite Galaxy\": \"Cómo citar a Galaxy\",\n \"Interactive Tours\": \"recorridos interactivos\",\n User: \"Usuario\",\n Login: \"Iniciar sesión\",\n Register: \"Registro\",\n \"Login or Register\": \"Iniciar sesión o Registrarse\",\n \"Logged in as\": \"Conectado como\",\n Preferences: \"Preferencias\",\n \"Custom Builds\": \"Construcciones personalizadas\",\n Logout: \"Cerrar sesión\",\n \"Saved Histories\": \"Historias Guardadas\",\n \"Saved Datasets\": \"Conjuntos de datos guardados\",\n \"Saved Pages\": \"Páginas guardadas\",\n //Tooltip\n \"Account and saved data\": \"Cuenta y datos guardados\",\n \"Account registration or login\": \"Registro de cuenta o inicio de sesión\",\n \"Support, contact, and community\": \"Apoyo, contacto y comunidad\",\n \"Administer this Galaxy\": \"Administrar esta galaxia\",\n \"Visualize datasets\": \"Visualizar conjuntos de datos\",\n \"Access published resources\": \"Acceso a los recursos publicados\",\n \"Chain tools into workflows\": \"Herramientas de cadena en flujos de trabajo\",\n \"Analysis home view\": \"Vista de inicio del análisis\",\n // ---------------------------------------------------------------------------- histories\n // ---- history/options-menu\n \"History Lists\": \"Listas de historia\",\n // Saved histories is defined above.\n // \"Saved Histories\":\n // false,\n \"Histories Shared with Me\": \"Historias compartidas conmigo\",\n \"Current History\": \"Historia actual\",\n \"Create New\": \"Crear nuevo\",\n \"Copy History\": \"Historial de Copias\",\n \"Share or Publish\": \"Compartir o publicar\",\n \"Show Structure\": \"Mostrar Estructura\",\n \"Extract Workflow\": \"Extraer flujo de trabajo\",\n // Delete is defined elsewhere, but is also in this menu.\n // \"Delete\":\n // false,\n \"Delete Permanently\": \"Borrar permanentemente\",\n \"Dataset Actions\": \"Acciones de conjuntos de datos\",\n \"Copy Datasets\": \"Conjuntos de datos de copia\",\n \"Dataset Security\": \"Seguridad del conjunto de datos\",\n \"Resume Paused Jobs\": \"Reanudar trabajos en pausa\",\n \"Collapse Expanded Datasets\": \"Contraer conjuntos de datos expandidos\",\n \"Unhide Hidden Datasets\": \"Mostrar conjuntos de datos ocultos\",\n \"Delete Hidden Datasets\": \"Eliminar conjuntos de datos ocultos\",\n \"Purge Deleted Datasets\": \"Eliminar los conjuntos de datos eliminados\",\n Downloads: \"Descargas\",\n \"Export Tool Citations\": \"Citas de herramientas de exportación\",\n \"Export History to File\": \"Exportar historial a archivo\",\n \"Other Actions\": \"Otras acciones\",\n \"Import from File\": \"Importar desde archivo\",\n Webhooks: \"WebHooks\",\n // ---- history-model\n // ---- history-view\n \"This history is empty\": \"Esta historia está vacía\",\n \"No matching datasets found\":\n \"No se encontraron conjuntos de datos coincidentes\",\n \"An error occurred while getting updates from the server\":\n \"Se ha producido un error al obtener actualizaciones desde el servidor\",\n \"Please contact a Galaxy administrator if the problem persists\":\n \"Póngase en contacto con un administrador de Galaxy si el problema persiste\",\n //TODO:\n //\"An error was encountered while <% where %>\" :\n //false,\n \"search datasets\": \"Conjuntos de datos de búsqueda\",\n \"You are currently viewing a deleted history!\":\n \"¡Actualmente estás viendo un historial eliminado!\",\n \"You are over your disk quota\": \"Has sobrepasado tu cuota de disco\",\n \"Tool execution is on hold until your disk usage drops below your allocated quota\":\n \"La ejecución de la herramienta está en espera hasta que el uso del disco caiga por debajo de la cuota asignada\",\n All: \"Todas\",\n None: \"Ninguna\",\n \"For all selected\": \"Para todos los seleccionados\",\n // ---- history-view-edit\n \"Edit history tags\": \"Editar etiquetas de historial\",\n \"Edit history Annotation\": \"Editar anotación de la historia\",\n \"Click to rename history\": \"Haga clic para cambiar el nombre del historial\",\n // multi operations\n \"Operations on multiple datasets\":\n \"Operaciones en conjuntos de datos múltiples\",\n \"Hide datasets\": \"Ocultar conjuntos de datos\",\n \"Unhide datasets\": \"Mostrar conjuntos de datos\",\n \"Delete datasets\": \"Borrar conjuntos de datos\",\n \"Undelete datasets\": \"Undelete datasets\",\n \"Permanently delete datasets\":\n \"Eliminar permanentemente conjuntos de datos\",\n \"This will permanently remove the data in your datasets. Are you sure?\":\n \"Esto eliminará permanentemente los datos de sus datasets. ¿Está seguro?\",\n // ---- history-view-annotated\n Dataset: \"Conjunto de datos\",\n Annotation: \"Anotación\",\n // ---- history-view-edit-current\n \"This history is empty. Click 'Get Data' on the left tool menu to start\":\n \"Este historial está vacío. Haga clic en 'Obtener datos' en el menú de herramientas de la izquierda para iniciar\",\n \"You must be logged in to create histories\":\n \"Debe haber iniciado sesión para crear historiales\",\n //TODO:\n //\"You can <% loadYourOwn %> or <% externalSource %>\" :\n //false,\n //\"load your own data\" :\n //false,\n //\"get data from an external source\" :\n //false,\n\n // these aren't in zh/ginga.po and the template doesn't localize\n //\"Include Deleted Datasets\" :\n //false,\n //\"Include Hidden Datasets\" :\n //false,\n\n // ---------------------------------------------------------------------------- datasets\n // ---- hda-model\n \"Unable to purge dataset\": \"No se puede purgar el dataset\",\n // ---- hda-base\n // display button\n \"Cannot display datasets removed from disk\":\n \"No se pueden mostrar conjuntos de datos eliminados del disco\",\n \"This dataset must finish uploading before it can be viewed\":\n \"Este conjunto de datos debe terminar de cargar antes de que se pueda ver\",\n \"This dataset is not yet viewable\":\n \"Este conjunto de datos aún no se puede ver\",\n \"View data\": \"Ver datos\",\n // download button\n Download: \"Descargar\",\n \"Download dataset\": \"Descargar dataset\",\n \"Additional files\": \"Archivos adicionales\",\n // info/show_params\n \"View details\": \"Ver detalles\",\n // dataset states\n // state: new\n \"This is a new dataset and not all of its data are available yet\":\n \"Este es un nuevo conjunto de datos y no todos sus datos están disponibles todavía\",\n // state: noPermission\n \"You do not have permission to view this dataset\":\n \"No tiene permiso para ver este conjunto de datos\",\n // state: discarded\n \"The job creating this dataset was cancelled before completion\":\n \"El trabajo que creó este conjunto de datos se canceló antes de completarse\",\n // state: queued\n \"This job is waiting to run\": \"Este trabajo está a la espera de ejecutar\",\n // state: upload\n \"This dataset is currently uploading\":\n \"Este conjunto de datos se está subiendo actualmente\",\n // state: setting_metadata\n \"Metadata is being auto-detected\":\n \"Los metadatos se detectan automáticamente\",\n // state: running\n \"This job is currently running\":\n \"Este trabajo se está ejecutando actualmente\",\n // state: paused\n 'This job is paused. Use the \"Resume Paused Jobs\" in the history menu to resume':\n 'Este trabajo está en pausa Utilice la opción \" Reanudar pausado Jobs \" en el menú de historial para reanudar',\n // state: error\n \"An error occurred with this dataset\":\n \"Se ha producido un error con este conjunto de datos\",\n // state: empty\n \"No data\": \"Sin datos\",\n // state: failed_metadata\n \"An error occurred setting the metadata for this dataset\":\n \"Se ha producido un error al establecer los metadatos de este conjunto de datos\",\n // ajax error prefix\n \"There was an error getting the data for this dataset\":\n \"Hubo un error al obtener los datos de este conjunto de datos\",\n // purged'd/del'd msg\n \"This dataset has been deleted and removed from disk\":\n \"Este conjunto de datos ha sido eliminado y eliminado del disco\",\n \"This dataset has been deleted\": \"Este conjunto de datos ha sido eliminado\",\n \"This dataset has been hidden\": \"Este conjunto de datos se ha ocultado\",\n format: \"Formato\",\n database: \"base de datos\",\n // ---- hda-edit\n \"Edit attributes\": \"Editar atributos\",\n \"Cannot edit attributes of datasets removed from disk\":\n \"No se pueden editar los atributos de conjuntos de datos eliminados del disco\",\n \"Undelete dataset to edit attributes\":\n \"Undelete el conjunto de datos para editar atributos\",\n \"This dataset must finish uploading before it can be edited\":\n \"Este conjunto de datos debe terminar de cargar antes de que pueda ser editado\",\n \"This dataset is not yet editable\":\n \"Este conjunto de datos aún no es editable\",\n Delete: \"Borrar\",\n \"Dataset is already deleted\": \"El conjunto de datos ya se ha eliminado\",\n \"View or report this error\": \"Ver o informar de este error\",\n \"Run this job again\": \"Ejecutar este trabajo de nuevo\",\n Visualize: \"Visualizar\",\n \"Visualize in\": \"Visualizar en\",\n \"Undelete it\": \"Undelete it\",\n \"Permanently remove it from disk\": \"Eliminar permanentemente del disco\",\n \"Unhide it\": \"Mostrarlo\",\n \"You may be able to\": \"Usted puede ser capaz de\",\n \"set it manually or retry auto-detection\":\n \"Configurar manualmente o volver a intentar la detección automática\",\n \"Edit dataset tags\": \"Editar etiquetas de dataset\",\n \"Edit dataset annotation\": \"Editar anotación del conjunto de datos\",\n // ---------------------------------------------------------------------------- misc. MVC\n Tags: \"Tags\",\n \"Edit annotation\": \"Editar anotación\"\n});\n"]} \ No newline at end of file diff --git a/static/maps/nls/fr/locale.js.map b/static/maps/nls/fr/locale.js.map index 84c822fef0b..6364d9e403b 100644 --- a/static/maps/nls/fr/locale.js.map +++ b/static/maps/nls/fr/locale.js.map @@ -1 +1 @@ -{"version":3,"sources":["nls/fr/locale.js"],"names":["define","Workflow","Shared Data","Histories","Workflows","Visualizations","Pages","Visualization","Interactive Environments","Admin","Help","Support","Search","Wiki","Videos","User","Login","Register","Preferences","Custom Builds","Saved Histories","Logout","Saved Pages","Account and saved data","Account registration or login","Support, contact, and community","Administer this Galaxy","Visualize datasets","Access published resources","Chain tools into workflows","Analysis home view","History Lists","Histories Shared with Me","Current History","Create New","Copy History","Share or Publish","Show Structure","Extract Workflow","Delete Permanently","Dataset Actions","Copy Datasets","Dataset Security","Resume Paused Jobs","Collapse Expanded Datasets","Unhide Hidden Datasets","Delete Hidden Datasets","Purge Deleted Datasets","Downloads","Export Tool Citations","Other Actions","Import from File","Webhooks","This history is empty","No matching datasets found","An error occurred while getting updates from the server","Please contact a Galaxy administrator if the problem persists","search datasets","You are currently viewing a deleted history!","All","None","Tool execution is on hold until your disk usage drops below your allocated quota","For all selected","Edit history tags","Edit history Annotation","Click to rename history","Operations on multiple datasets","Hide datasets","Unhide datasets","Delete datasets","Undelete datasets","Permanently delete datasets","Dataset","Annotation","This history is empty. 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fr localization */\ndefine({\n // ----------------------------------------------------------------------------- masthead\n \"Analyze Data\": \"Analyse de données\",\n Workflow: \"Workflow\",\n \"Shared Data\": \"Données partagées\",\n \"Data Libraries\": \"Bibliothèque de données\",\n Histories: \"Historiques\",\n Workflows: \"Workflows\",\n Visualizations: \"Visualisations\",\n Pages: \"Pages\",\n Visualization: \"Visualisation\",\n \"New Track Browser\": \"Nouveau Navigateur de Tracks/Pistes\",\n \"Saved Visualizations\": \"Visualisations sauvegardées\",\n \"Interactive Environments\": \"Environnements interactifs\",\n Admin: \"Admin\",\n Help: \"Aide\",\n Support: \"Assistance\",\n Search: \"Recherche\",\n \"Mailing Lists\": \"Liste de diffusion\",\n Videos: \"Vidéos\",\n Wiki: \"Documentations\",\n \"How to Cite Galaxy\": \"Comment citer Galaxy\",\n \"Interactive Tours\": \"Guides interactifs\",\n User: \"Utilisateur\",\n Login: \"Authentification\",\n Register: \"Enregistrement\",\n \"Login or Register\": \"Authentification et Enregistrement\",\n \"Logged in as\": \"Authentifié en tant que\",\n Preferences: \"Préférences\",\n \"Custom Builds\": \"Mes génomes Builds de référence\",\n Logout: \"Déconnexion\",\n \"Saved Histories\": \"Historiques sauvegardés\",\n \"Saved Datasets\": \"Jeux de données sauvegardés\",\n \"Saved Pages\": \"Pages sauvegardées\",\n //Tooltip\n \"Account and saved data\": \"Compte et données sauvegardées\",\n \"Account registration or login\": \"Enregistrement ou authentification\",\n \"Support, contact, and community\": \"Support,contact et communauté\",\n \"Administer this Galaxy\": \"Outils Admin\",\n \"Visualize datasets\": \"Visualiser les jeux de données\",\n \"Access published resources\": \"Accéder aux données partagées\",\n \"Chain tools into workflows\": \"Relier outils dans un workflow\",\n \"Analysis home view\": \"Accueil analyse de données\",\n // ---------------------------------------------------------------------------- histories\n // ---- history/options-menu\n \"History Lists\": \"Tableaux des historiques\",\n // Saved histories is defined above.\n // \"Saved Histories\":\n // false,\n \"Histories Shared with Me\": \"Historiques partagés avec moi\",\n \"Current History\": \"Cet Historique\",\n \"Create New\": \"Créer un nouveau\",\n \"Copy History\": \"Copier l'Historique\",\n \"Share or Publish\": \"Partager et publier\",\n \"Show Structure\": \"Montrer la structure\",\n \"Extract Workflow\": \"Extraire un Workflow\",\n // Delete is defined elsewhere, but is also in this menu.\n // \"Delete\":\n // false,\n \"Delete Permanently\": \"Supprimer définitivement\",\n \"Dataset Actions\": \"Actions sur les jeux de données\",\n \"Copy Datasets\": \"Copier des jeux de données\",\n \"Dataset Security\": \"Permissions/Sécurité\",\n \"Resume Paused Jobs\": \"Reprendre les processus en pause\",\n \"Collapse Expanded Datasets\": \"Réduire les données étendues\",\n \"Unhide Hidden Datasets\": \"Afficher les données cachées\",\n \"Delete Hidden Datasets\": \"Supprimer les données cachées\",\n \"Purge Deleted Datasets\": \"Purger les données supprimées\",\n Downloads: \"Télécharger\",\n \"Export Tool Citations\": \"Exporter les citations des outils\",\n \"Export History to File\": \"Exporter l'Historique dans un fichier\",\n \"Other Actions\": \"Autres actions\",\n \"Import from File\": \"Importer depuis un fichier\",\n Webhooks: \"Webhooks\",\n\n // ---- history-model\n // ---- history-view\n \"This history is empty\": \"Cet historique est vide\",\n \"No matching datasets found\":\n \"Aucunes données correspondantes n'ont été trouvées\",\n \"An error occurred while getting updates from the server\":\n \"Une erreur s'est produite lors de la réception des données depuis le serveur\",\n \"Please contact a Galaxy administrator if the problem persists\":\n \"Veuillez contacter un administrateur de l'instance Galaxy si ce problème persiste\",\n //TODO:\n //\"An error was encountered while <% where %>\" :\n //false,\n \"search datasets\": \"Rechercher des données\",\n \"You are currently viewing a deleted history!\":\n \"Vous consultez actuellement un historique supprimé!\",\n \"You are over your disk quota\":\n \"Vous avez dépassé votre quota d'espace disque\",\n \"Tool execution is on hold until your disk usage drops below your allocated quota\":\n \"L'exécution de l'outil est en attente tant que votre utilisation d'espace disque dépasse le quota attribué\",\n All: \"Tout\",\n None: \"Aucun\",\n \"For all selected\": \"Pour toute la sélection\",\n\n // // ---- history-view-edit\n \"Edit history tags\": \"Editer les mots-clés de l'historique\",\n \"Edit history Annotation\": \"Editer l'annotation de l'historique\",\n \"Click to rename history\": \"Cliquer pour renommer l'historique\",\n // multi operations\n \"Operations on multiple datasets\":\n \"Opérer sur plusieurs jeux de données en même temps\",\n \"Hide datasets\": \"Cacher les jeux de données\",\n \"Unhide datasets\": \"Afficher les jeux de données cachés\",\n \"Delete datasets\": \"Supprimer les jeux de données\",\n \"Undelete datasets\": \"Restaurer les jeux de données supprimés\",\n \"Permanently delete datasets\":\n \"Supprimer définitivement les jeux de données\",\n \"This will permanently remove the data in your datasets. Are you sure?\":\n \"Cela supprimera de manière permanente les données de votre historique. Êtes-vous certain?\",\n\n // menu operations\n\n // // ---- history-view-annotated\n Dataset: \"Jeu de données\",\n Annotation: \"Annotation\",\n\n // ---- history-view-edit-current\n \"This history is empty. Click 'Get Data' on the left tool menu to start\":\n \"Cet historique est vide. Cliquer sur 'Get Data' au niveau du menu d'outils à gauche pour démarrer\",\n \"You must be logged in to create histories\":\n \"Vous devez être connecté pour créer un historique\",\n //TODO:\n //\"You can <% loadYourOwn %> or <% externalSource %>\" :\n //\"Vous pouvez <% loadYourOwn %> ou <% externalSource %>\",\n \"load your own data\": \"Charger vos propres données\",\n \"get data from an external source\":\n \"Charger des données depuis une source externe\",\n\n // these aren't in zh/ginga.po and the template doesn't localize\n \"Include Deleted Datasets\": \"Inclure les jeux de données supprimés\",\n \"Include Hidden Datasets\": \"Inclure les jeux de données cachés\",\n\n // ---------------------------------------------------------------------------- datasets\n // ---- hda-model\n \"Unable to purge dataset\": \"Impossible de purger le jeu de données\",\n\n // ---- hda-base\n // display button\n \"Cannot display datasets removed from disk\":\n \"Impossible de visualiser les jeux de données supprimés du disque\",\n \"This dataset must finish uploading before it can be viewed\":\n \"Le jeu de données doit être totalement téléversé avant de pouvoir être visualiser\",\n \"This dataset is not yet viewable\":\n \"Ce jeu de données n'est pas visualisable\",\n \"View data\": \"Voir les données\",\n // download button\n Download: \"Télécharger\",\n \"Download dataset\": \"Télécharger le jeu de données\",\n \"Additional files\": \"Fichiers additionnels\",\n // info/show_params\n \"View details\": \"Voir les détails\",\n\n // dataset states\n // state: new\n \"This is a new dataset and not all of its data are available yet\":\n \"Il s'agit d'un nouveau jeu de données et seule une partie des données est accessible pour le moment\",\n // state: noPermission\n \"You do not have permission to view this dataset\":\n \"Vous n'avez pas la permission de voir ce jeu de données\",\n // state: discarded\n \"The job creating this dataset was cancelled before completion\":\n \"Le processus à l'origine de ce jeu de données a été annulé prématurément\",\n // state: queued\n \"This job is waiting to run\": \"Ce calcul est en attente de traitement\",\n // state: upload\n \"This dataset is currently uploading\":\n \"Ce jeu de données est en cours de téléversement\",\n // state: setting_metadata\n \"Metadata is being auto-detected\": \"Les métadonnées sont auto-détectées\",\n // state: running\n \"This job is currently running\": \"Le traitement est en cours\",\n // state: paused\n 'This job is paused. Use the \"Resume Paused Jobs\" in the history menu to resume':\n 'Ce traitement est en pause. Utilisez le \"Relancer les traitements en pause\" dans le menu d\\'historique pour le relancer',\n // state: error\n \"An error occurred with this dataset\":\n \"Une erreur est survenue avec ce jeu de données\",\n // state: empty\n \"No data\": \"Aucune donnée\",\n // state: failed_metadata\n \"An error occurred setting the metadata for this dataset\":\n \"Une erreur est survenue pendant la récupération des métadonnées de ce jeu de données\",\n\n // ajax error prefix\n \"There was an error getting the data for this dataset\":\n \"Il est survenu une erreur durant la récupération du contenu de ce jeu de données\",\n\n // purged'd/del'd msg\n \"This dataset has been deleted and removed from disk\":\n \"Ce jeu de données a été supprimé et effacé du disque\",\n \"This dataset has been deleted\": \"Ce jeu de données a été supprimé\",\n \"This dataset has been hidden\": \"Ce jeu de données a été caché\",\n\n format: \"format\",\n database: \"génome de référence\",\n\n // ---- hda-edit\n \"Edit attributes\": \"Editer les attributs\",\n \"Cannot edit attributes of datasets removed from disk\":\n \"Impossible d'éditer les attributs de jeux de données effacés du disque\",\n \"Undelete dataset to edit attributes\":\n \"Restaurer le jeu de données pour en éditer les attributs\",\n \"This dataset must finish uploading before it can be edited\":\n \"Ce jeu de données doit être entièrement téléversé avant toute modification\",\n \"This dataset is not yet editable\":\n \"Ce jeu de données n'est pas encore éditable\",\n\n Delete: \"Supprimer\",\n \"Dataset is already deleted\": \"Le jeu de données est déjà supprimé\",\n\n \"View or report this error\": \"Voir ou remonter cette erreur\",\n\n \"Run this job again\": \"Exécuter ce traitement à nouveau\",\n\n Visualize: \"Visualiser\",\n \"Visualize in\": \"Visualiser via\",\n\n \"Undelete it\": \"Restaurer\",\n \"Permanently remove it from disk\": \"Supprimer définitivement du disque\",\n \"Unhide it\": \"Rendre visible\",\n\n \"You may be able to\": \"Vous devriez être en mesure de\",\n \"set it manually or retry auto-detection\":\n \"Traitez le manuellement ou retenter la détection automatique\",\n\n \"Edit dataset tags\": \"Editer les mots-clés du jeu de données\",\n \"Edit dataset annotation\": \"Editer les annotations du jeu de données\",\n\n // ---------------------------------------------------------------------------- misc. MVC\n Tags: \"Mots-clés\",\n \"Edit annotation\": \"Editer les annotations\"\n});\n"]} \ No newline at end of file +{"version":3,"sources":["nls/fr/locale.js"],"names":["define","Analyze Data","Shared Data","Data Libraries","Workflow","Workflows","Visualizations","Histories","Pages","Visualization","Admin","Help","Support","Search","How to Cite Galaxy","Videos","Wiki","Login","Register","User","Custom Builds","Logout","Preferences","Saved Datasets","Account and saved data","Account registration or login","Support, contact, and community","Administer this Galaxy","Visualize datasets","Access published resources","Chain tools into workflows","Analysis home view","History Lists","Histories Shared with Me","Current History","Create New","Copy History","Share or Publish","Show Structure","Extract Workflow","Delete Permanently","Dataset Actions","Copy Datasets","Dataset Security","Resume Paused Jobs","Collapse Expanded Datasets","Unhide Hidden Datasets","Delete Hidden Datasets","Purge Deleted Datasets","Downloads","Export Tool Citations","Export History to File","Import from File","Webhooks","This history is empty","No matching datasets found","An error occurred while getting updates from the server","Please contact a Galaxy administrator if the problem persists","search datasets","You are currently viewing a deleted history!","You are over your disk quota","All","None","For all selected","Edit history tags","Edit history Annotation","Click to rename history","Operations on multiple datasets","Hide datasets","Unhide datasets","Delete datasets","Undelete datasets","Permanently delete datasets","Dataset","Annotation","This history is empty. 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fr localization */\ndefine({\n // ----------------------------------------------------------------------------- masthead\n \"Analyze Data\": \"Analyse de données\",\n Workflow: \"Workflow\",\n \"Shared Data\": \"Données partagées\",\n \"Data Libraries\": \"Bibliothèque de données\",\n Histories: \"Historiques\",\n Workflows: \"Workflows\",\n Visualizations: \"Visualisations\",\n Pages: \"Pages\",\n Visualization: \"Visualisation\",\n \"New Track Browser\": \"Nouveau Navigateur de Tracks/Pistes\",\n \"Saved Visualizations\": \"Visualisations sauvegardées\",\n \"Interactive Environments\": \"Environnements interactifs\",\n Admin: \"Admin\",\n Help: \"Aide\",\n Support: \"Assistance\",\n Search: \"Recherche\",\n \"Mailing Lists\": \"Liste de diffusion\",\n Videos: \"Vidéos\",\n Wiki: \"Documentations\",\n \"How to Cite Galaxy\": \"Comment citer Galaxy\",\n \"Interactive Tours\": \"Guides interactifs\",\n User: \"Utilisateur\",\n Login: \"Authentification\",\n Register: \"Enregistrement\",\n \"Login or Register\": \"Authentification et Enregistrement\",\n \"Logged in as\": \"Authentifié en tant que\",\n Preferences: \"Préférences\",\n \"Custom Builds\": \"Mes génomes Builds de référence\",\n Logout: \"Déconnexion\",\n \"Saved Histories\": \"Historiques sauvegardés\",\n \"Saved Datasets\": \"Jeux de données sauvegardés\",\n \"Saved Pages\": \"Pages sauvegardées\",\n //Tooltip\n \"Account and saved data\": \"Compte et données sauvegardées\",\n \"Account registration or login\": \"Enregistrement ou authentification\",\n \"Support, contact, and community\": \"Support,contact et communauté\",\n \"Administer this Galaxy\": \"Outils Admin\",\n \"Visualize datasets\": \"Visualiser les jeux de données\",\n \"Access published resources\": \"Accéder aux données partagées\",\n \"Chain tools into workflows\": \"Relier outils dans un workflow\",\n \"Analysis home view\": \"Accueil analyse de données\",\n // ---------------------------------------------------------------------------- histories\n // ---- history/options-menu\n \"History Lists\": \"Tableaux des historiques\",\n // Saved histories is defined above.\n // \"Saved Histories\":\n // false,\n \"Histories Shared with Me\": \"Historiques partagés avec moi\",\n \"Current History\": \"Cet Historique\",\n \"Create New\": \"Créer un nouveau\",\n \"Copy History\": \"Copier l'Historique\",\n \"Share or Publish\": \"Partager et publier\",\n \"Show Structure\": \"Montrer la structure\",\n \"Extract Workflow\": \"Extraire un Workflow\",\n // Delete is defined elsewhere, but is also in this menu.\n // \"Delete\":\n // false,\n \"Delete Permanently\": \"Supprimer définitivement\",\n \"Dataset Actions\": \"Actions sur les jeux de données\",\n \"Copy Datasets\": \"Copier des jeux de données\",\n \"Dataset Security\": \"Permissions/Sécurité\",\n \"Resume Paused Jobs\": \"Reprendre les processus en pause\",\n \"Collapse Expanded Datasets\": \"Réduire les données étendues\",\n \"Unhide Hidden Datasets\": \"Afficher les données cachées\",\n \"Delete Hidden Datasets\": \"Supprimer les données cachées\",\n \"Purge Deleted Datasets\": \"Purger les données supprimées\",\n Downloads: \"Télécharger\",\n \"Export Tool Citations\": \"Exporter les citations des outils\",\n \"Export History to File\": \"Exporter l'Historique dans un fichier\",\n \"Other Actions\": \"Autres actions\",\n \"Import from File\": \"Importer depuis un fichier\",\n Webhooks: \"Webhooks\",\n\n // ---- history-model\n // ---- history-view\n \"This history is empty\": \"Cet historique est vide\",\n \"No matching datasets found\":\n \"Aucunes données correspondantes n'ont été trouvées\",\n \"An error occurred while getting updates from the server\":\n \"Une erreur s'est produite lors de la réception des données depuis le serveur\",\n \"Please contact a Galaxy administrator if the problem persists\":\n \"Veuillez contacter un administrateur de l'instance Galaxy si ce problème persiste\",\n //TODO:\n //\"An error was encountered while <% where %>\" :\n //false,\n \"search datasets\": \"Rechercher des données\",\n \"You are currently viewing a deleted history!\":\n \"Vous consultez actuellement un historique supprimé!\",\n \"You are over your disk quota\":\n \"Vous avez dépassé votre quota d'espace disque\",\n \"Tool execution is on hold until your disk usage drops below your allocated quota\":\n \"L'exécution de l'outil est en attente tant que votre utilisation d'espace disque dépasse le quota attribué\",\n All: \"Tout\",\n None: \"Aucun\",\n \"For all selected\": \"Pour toute la sélection\",\n\n // // ---- history-view-edit\n \"Edit history tags\": \"Editer les mots-clés de l'historique\",\n \"Edit history Annotation\": \"Editer l'annotation de l'historique\",\n \"Click to rename history\": \"Cliquer pour renommer l'historique\",\n // multi operations\n \"Operations on multiple datasets\":\n \"Opérer sur plusieurs jeux de données en même temps\",\n \"Hide datasets\": \"Cacher les jeux de données\",\n \"Unhide datasets\": \"Afficher les jeux de données cachés\",\n \"Delete datasets\": \"Supprimer les jeux de données\",\n \"Undelete datasets\": \"Restaurer les jeux de données supprimés\",\n \"Permanently delete datasets\":\n \"Supprimer définitivement les jeux de données\",\n \"This will permanently remove the data in your datasets. Are you sure?\":\n \"Cela supprimera de manière permanente les données de votre historique. Êtes-vous certain?\",\n\n // menu operations\n\n // // ---- history-view-annotated\n Dataset: \"Jeu de données\",\n Annotation: \"Annotation\",\n\n // ---- history-view-edit-current\n \"This history is empty. Click 'Get Data' on the left tool menu to start\":\n \"Cet historique est vide. Cliquer sur 'Get Data' au niveau du menu d'outils à gauche pour démarrer\",\n \"You must be logged in to create histories\":\n \"Vous devez être connecté pour créer un historique\",\n //TODO:\n //\"You can <% loadYourOwn %> or <% externalSource %>\" :\n //\"Vous pouvez <% loadYourOwn %> ou <% externalSource %>\",\n \"load your own data\": \"Charger vos propres données\",\n \"get data from an external source\":\n \"Charger des données depuis une source externe\",\n\n // these aren't in zh/ginga.po and the template doesn't localize\n \"Include Deleted Datasets\": \"Inclure les jeux de données supprimés\",\n \"Include Hidden Datasets\": \"Inclure les jeux de données cachés\",\n\n // ---------------------------------------------------------------------------- datasets\n // ---- hda-model\n \"Unable to purge dataset\": \"Impossible de purger le jeu de données\",\n\n // ---- hda-base\n // display button\n \"Cannot display datasets removed from disk\":\n \"Impossible de visualiser les jeux de données supprimés du disque\",\n \"This dataset must finish uploading before it can be viewed\":\n \"Le jeu de données doit être totalement téléversé avant de pouvoir être visualiser\",\n \"This dataset is not yet viewable\":\n \"Ce jeu de données n'est pas visualisable\",\n \"View data\": \"Voir les données\",\n // download button\n Download: \"Télécharger\",\n \"Download dataset\": \"Télécharger le jeu de données\",\n \"Additional files\": \"Fichiers additionnels\",\n // info/show_params\n \"View details\": \"Voir les détails\",\n\n // dataset states\n // state: new\n \"This is a new dataset and not all of its data are available yet\":\n \"Il s'agit d'un nouveau jeu de données et seule une partie des données est accessible pour le moment\",\n // state: noPermission\n \"You do not have permission to view this dataset\":\n \"Vous n'avez pas la permission de voir ce jeu de données\",\n // state: discarded\n \"The job creating this dataset was cancelled before completion\":\n \"Le processus à l'origine de ce jeu de données a été annulé prématurément\",\n // state: queued\n \"This job is waiting to run\": \"Ce calcul est en attente de traitement\",\n // state: upload\n \"This dataset is currently uploading\":\n \"Ce jeu de données est en cours de téléversement\",\n // state: setting_metadata\n \"Metadata is being auto-detected\": \"Les métadonnées sont auto-détectées\",\n // state: running\n \"This job is currently running\": \"Le traitement est en cours\",\n // state: paused\n 'This job is paused. Use the \"Resume Paused Jobs\" in the history menu to resume':\n 'Ce traitement est en pause. Utilisez le \"Relancer les traitements en pause\" dans le menu d\\'historique pour le relancer',\n // state: error\n \"An error occurred with this dataset\":\n \"Une erreur est survenue avec ce jeu de données\",\n // state: empty\n \"No data\": \"Aucune donnée\",\n // state: failed_metadata\n \"An error occurred setting the metadata for this dataset\":\n \"Une erreur est survenue pendant la récupération des métadonnées de ce jeu de données\",\n\n // ajax error prefix\n \"There was an error getting the data for this dataset\":\n \"Il est survenu une erreur durant la récupération du contenu de ce jeu de données\",\n\n // purged'd/del'd msg\n \"This dataset has been deleted and removed from disk\":\n \"Ce jeu de données a été supprimé et effacé du disque\",\n \"This dataset has been deleted\": \"Ce jeu de données a été supprimé\",\n \"This dataset has been hidden\": \"Ce jeu de données a été caché\",\n\n format: \"format\",\n database: \"génome de référence\",\n\n // ---- hda-edit\n \"Edit attributes\": \"Editer les attributs\",\n \"Cannot edit attributes of datasets removed from disk\":\n \"Impossible d'éditer les attributs de jeux de données effacés du disque\",\n \"Undelete dataset to edit attributes\":\n \"Restaurer le jeu de données pour en éditer les attributs\",\n \"This dataset must finish uploading before it can be edited\":\n \"Ce jeu de données doit être entièrement téléversé avant toute modification\",\n \"This dataset is not yet editable\":\n \"Ce jeu de données n'est pas encore éditable\",\n\n Delete: \"Supprimer\",\n \"Dataset is already deleted\": \"Le jeu de données est déjà supprimé\",\n\n \"View or report this error\": \"Voir ou remonter cette erreur\",\n\n \"Run this job again\": \"Exécuter ce traitement à nouveau\",\n\n Visualize: \"Visualiser\",\n \"Visualize in\": \"Visualiser via\",\n\n \"Undelete it\": \"Restaurer\",\n \"Permanently remove it from disk\": \"Supprimer définitivement du disque\",\n \"Unhide it\": \"Rendre visible\",\n\n \"You may be able to\": \"Vous devriez être en mesure de\",\n \"set it manually or retry auto-detection\":\n \"Traitez le manuellement ou retenter la détection automatique\",\n\n \"Edit dataset tags\": \"Editer les mots-clés du jeu de données\",\n \"Edit dataset annotation\": \"Editer les annotations du jeu de données\",\n\n // ---------------------------------------------------------------------------- misc. 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ja localization */\ndefine({\n // ----------------------------------------------------------------------------- masthead\n \"Analyze Data\": \"データ解析\",\n Workflow: \"ワークフロー\",\n \"Shared Data\": \"共有データ\",\n \"Data Libraries\": \"データライブラリ\",\n Histories: \"ヒストリー\",\n Workflows: \"ワークフロー\",\n Visualizations: \"可視化\",\n Pages: \"ページ\",\n Visualization: \"可視化\",\n \"New Track Browser\": \"新しい Track Browser\",\n \"Saved Visualizations\": \"保存された可視化\",\n \"Interactive Environments\": \"インタラクティブ環境\",\n Admin: \"管理者\",\n Help: \"ヘルプ\",\n Support: \"サポート\",\n Search: \"検索\",\n Support: \"サポート\",\n Search: \"検索\",\n \"Mailing Lists\": \"メーリングリスト\",\n Videos: \"動画\",\n //\"Wiki\":\n // \"ドキュメント\",\n \"How to Cite Galaxy\": \"Galaxy を引用する方法\",\n \"Interactive Tours\": \"インタラクティブツアー\",\n User: \"ユーザー\",\n Login: \"ログイン\",\n Register: \"登録\",\n \"Login or Register\": \"ログイン/登録\",\n //\"Logged in as\":\n // \"\",\n Preferences: \"設定\",\n \"Custom Builds\": \"カスタムビルド\",\n Logout: \"ログアウト\",\n \"Saved Histories\": \"保存されたヒストリー\",\n \"Saved Datasets\": \"保存されたデータセット\",\n \"Saved Pages\": \"保存されたページ\",\n //Tooltip\n \"Account and saved data\": \"アカウントと保存されたデータ\",\n \"Account registration or login\": \"アカウントの登録またはログイン\",\n \"Support, contact, and community\": \"サポート、コンタクト、コミュニティ\",\n \"Administer this Galaxy\": \"この Galaxy の管理者\",\n \"Visualize datasets\": \"データセットの可視化\",\n \"Access published resources\": \"パブリッシュされたリソースへアクセス\",\n \"Chain tools into workflows\": \"ツールとワークフローの連携\",\n \"Analysis home view\": \"解析ホーム\",\n\n // ---------------------------------------------------------------------------- histories\n \"History Lists\": \"ヒストリーリスト\",\n // Saved histories is defined above.\n // \"Saved Histories\":\n // false,\n \"Histories Shared with Me\": \"私と共有されているヒストリー\",\n \"Current History\": \"現在のヒストリー\",\n \"Create New\": \"新しく作成\",\n \"Copy History\": \"ヒストリーをコピーする\",\n \"Share or Publish\": \"共有またはパブリッシュ\",\n \"Show Structure\": \"構造を見る\",\n \"Extract Workflow\": \"ワークフローを抽出\",\n // Delete is defined elsewhere, but is also in this menu.\n // \"Delete\":\n // false,\n \"Delete Permanently\": \"永久に削除\",\n \"Dataset Actions\": \"データセットの操作\",\n \"Copy Datasets\": \"データセットをコピー\",\n \"Dataset Security\": \"データセットのセキュリティ\",\n \"Resume Paused Jobs\": \"一時停止したジョブの再開\",\n \"Collapse Expanded Datasets\": \"展開されたデータセットを畳む\",\n \"Unhide Hidden Datasets\": \"隠されたデータセットを表示する\",\n \"Delete Hidden Datasets\": \"隠されたデータセットを削除する\",\n \"Purge Deleted Datasets\": \"削除されたデータセットを永久に削除\",\n Downloads: \"ダウンロード\",\n \"Export Tool Citations\": \"ツールの引用をエクスポート\",\n \"Export History to File\": \"ヒストリーをファイルへエクスポート\",\n \"Other Actions\": \"その他のアクション\",\n \"Import from File\": \"ファイルからインポート\",\n Webhooks: \"Webhooks\",\n // ---- history-model\n // ---- history-view\n \"This history is empty\": \"ヒストリーは空です\",\n \"No matching datasets found\": \"一致するデータセットが見つかりませんでした\",\n //\"An error occurred while getting updates from the server\" :\n //false,\n //\"Please contact a Galaxy administrator if the problem persists\" :\n //false,\n //TODO:\n //\"An error was encountered while <% where %>\" :\n //false,\n \"Search datasets\": \"データセットを検索する\",\n \"You are currently viewing a deleted history!\": \"消去したヒストリーをみています。\",\n \"You are over your disk quota\": \"あなたはディスククォータを超えている\",\n //\"Tool execution is on hold until your disk usage drops below your allocated quota\" :\n //false,\n All: \"一式\",\n None: \"なし\",\n \"For all selected\": \"各項目を\",\n\n // ---- history-view-edit\n \"Edit history tags\": \"ヒストリーのタグを編集\",\n \"Edit history annotation\": \"ヒストリーのアノテーションを編集\",\n \"Click to rename history\": \"ヒストリーの名前を変更するにはクリック\",\n // multi operations\n \"Operations on multiple datasets\": \"複数のデータセットに対する操作\",\n //\"Hide datasets\" :\n //false,\n //\"Unhide datasets\" :\n //false,\n //\"Delete datasets\" :\n //false,\n //\"Undelete datasets\" :\n //false,\n \"Permanently delete datasets\": \"永久にデータセットを削除\",\n \"This will permanently remove the data in your datasets. Are you sure?\":\n \"これは永久にあなたのデータセット内のデータを削除します。本当に？\",\n\n // ---- history-view-annotated\n Dataset: \"データセット\",\n //\"Annotation\" :\n //false,\n\n // ---- history-view-edit-current\n \"This history is empty. Click 'Get Data' on the left tool menu to start\":\n \"ヒストリーは空です。解析をはじめるには、左パネルの 'データ取得' をクリック\",\n \"You must be logged in to create histories\": \"ヒストリーを作成するためにはログインする必要があります\",\n //TODO:\n //\"You can <% loadYourOwn %> or <% externalSource %>\" :\n //false,\n //\"load your own data\" :\n //false,\n //\"get data from an external source\" :\n //false,\n\n // these aren't in zh/ginga.po and the template doesn't localize\n //\"Include Deleted Datasets\" :\n //false,\n //\"Include Hidden Datasets\" :\n //false,\n\n // ---------------------------------------------------------------------------- datasets\n // ---- hda-model\n //\"Unable to purge dataset\" :\n //false,\n\n // ---- hda-base\n // display button\n //\"Cannot display datasets removed from disk\" :\n //false,\n //\"This dataset must finish uploading before it can be viewed\" :\n //false,\n //\"This dataset is not yet viewable\" :\n //false,\n \"View data\": \"データを表示\",\n // download button\n Download: \"ダウンロード\",\n \"Download dataset\": \"データセットをダウンロード\",\n //\"Additional files\" :\n //false,\n // info/show_params\n \"View details\": \"細部を表示\",\n\n // dataset states\n // state: new\n //\"This is a new dataset and not all of its data are available yet\" :\n //false,\n // state: noPermission\n //\"You do not have permission to view this dataset\" :\n //false,\n // state: discarded\n //\"The job creating this dataset was cancelled before completion\" :\n //false,\n // state: queued\n \"This job is waiting to run\": \"ジョブは実行待ちです\",\n // state: upload\n //\"This dataset is currently uploading\" :\n //false,\n // state: setting_metadata\n //\"Metadata is being auto-detected\" :\n //false,\n // state: running\n \"This job is currently running\": \"ジョブは実行中です\",\n // state: paused\n //\"This job is paused. Use the \\\"Resume Paused Jobs\\\" in the history menu to resume\" :\n //false,\n // state: error\n \"An error occurred with this dataset\": \"このジョブの実行中に発生したエラー\",\n // state: empty\n \"No data\": \"データ無し\",\n // state: failed_metadata\n //\"An error occurred setting the metadata for this dataset\" :\n //false,\n\n // ajax error prefix\n //\"There was an error getting the data for this dataset\" :\n //false,\n\n // purged'd/del'd msg\n \"This dataset has been deleted and removed from disk\":\n \"このデータセットは、永続的にディスクから削除されました\",\n \"This dataset has been deleted\": \"このデータセットは削除されました\",\n \"This dataset has been hidden\": \"このデータセットは、非表示にされた\",\n\n format: \"フォーマット\",\n database: \"データベース\",\n\n // ---- hda-edit\n \"Edit attributes\": \"変数を編集する\",\n //\"Cannot edit attributes of datasets removed from disk\" :\n //false,\n //\"Undelete dataset to edit attributes\" :\n //false,\n //\"This dataset must finish uploading before it can be edited\" :\n //false,\n //\"This dataset is not yet editable\" :\n //false,\n\n Delete: \"削除する\",\n //\"Dataset is already deleted\" :\n //false,\n\n \"View or report this error\": \"このエラーを届け出る\",\n\n \"Run this job again\": \"もう一度このジョブを実行する\",\n\n Visualize: \"可視化する\",\n //\"Visualize in\" :\n //false,\n\n \"Undelete it\": \"復元する\",\n \"Permanently remove it from disk\": \"永久にディスクから削除\",\n \"Unhide it\": \"非表示解除する\",\n \"Saved Histories\": \"保存されたヒストリ\",\n \"Import from File\": \"ファイルからの読み込み\",\n\n //\"You may be able to\" :\n //false,\n //\"set it manually or retry auto-detection\" :\n //false,\n\n //\"Edit dataset tags\" :\n //false,\n //\"Edit dataset annotation\" :\n //false,\n\n // ---------------------------------------------------------------------------- admin\n \"Search Tool Shed\": \"Tool Shed で探す\",\n \"Search Tool Shed (Beta)\": \"Tool Shed (Beta) で探す\",\n \"Monitor installing repositories\": \"インストールレポジトリのモニタ\",\n \"Manage installed tools\": \"インストールしたツールの管理\",\n \"Reset metadata\": \"メタデータのリセット\",\n \"Download local tool\": \"ローカルツールのダウンロード\",\n \"Tool lineage\": \"ツール系統\",\n \"Reload a tool's configuration\": \"ツールのコンフィグのリロード\",\n \"Review tool migration stages\": \"ツール移行ステージのレビュー\",\n \"View Tool Error Logs\": \"ツールのエラーログ\",\n \"Manage Display Whitelist\": \"表示ホワイトリストの管理\",\n \"Manage Tool Dependencies\": \"ツール依存関係の管理\",\n Users: \"ユーザー\",\n Groups: \"グループ\",\n \"API keys\": \"API キー\",\n \"Impersonate a user\": \"ユーザー偽装\",\n Data: \"データ\",\n Quotas: \"クォータ\",\n Roles: \"ロール\",\n \"Local data\": \"ローカルデータ\",\n \"Form definitions\": \"フォーム定義\",\n Administration: \"管理\",\n Server: \"サーバー\",\n \"Tools and Tool Shed\": \"ツールと Tool Shed\",\n \"User Management\": \"ユーザ管理\",\n Data: \"データ\",\n \"Form Definitions\": \"フォーム定義\"\n // ---------------------------------------------------------------------------- misc. MVC\n //\"Tags\" :\n //false,\n //\"Annotation\" :\n //false,\n //\"Edit annotation\" :\n //false,\n});\n"]} \ No newline at end of file +{"version":3,"sources":["nls/ja/locale.js"],"names":["define","Analyze Data","Workflow","Shared Data","Data Libraries","Histories","Workflows","Visualizations","Pages","Visualization","New Track Browser","Saved Visualizations","Interactive 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ja localization */\ndefine({\n // ----------------------------------------------------------------------------- masthead\n \"Analyze Data\": \"データ解析\",\n Workflow: \"ワークフロー\",\n \"Shared Data\": \"共有データ\",\n \"Data Libraries\": \"データライブラリ\",\n Histories: \"ヒストリー\",\n Workflows: \"ワークフロー\",\n Visualizations: \"可視化\",\n Pages: \"ページ\",\n Visualization: \"可視化\",\n \"New Track Browser\": \"新しい Track Browser\",\n \"Saved Visualizations\": \"保存された可視化\",\n \"Interactive Environments\": \"インタラクティブ環境\",\n Admin: \"管理者\",\n Help: \"ヘルプ\",\n Support: \"サポート\",\n Search: \"検索\",\n Support: \"サポート\",\n Search: \"検索\",\n \"Mailing Lists\": \"メーリングリスト\",\n Videos: \"動画\",\n //\"Wiki\":\n // \"ドキュメント\",\n \"How to Cite Galaxy\": \"Galaxy を引用する方法\",\n \"Interactive Tours\": \"インタラクティブツアー\",\n User: \"ユーザー\",\n Login: \"ログイン\",\n Register: \"登録\",\n \"Login or Register\": \"ログイン/登録\",\n //\"Logged in as\":\n // \"\",\n Preferences: \"設定\",\n \"Custom Builds\": \"カスタムビルド\",\n Logout: \"ログアウト\",\n \"Saved Histories\": \"保存されたヒストリー\",\n \"Saved Datasets\": \"保存されたデータセット\",\n \"Saved Pages\": \"保存されたページ\",\n //Tooltip\n \"Account and saved data\": \"アカウントと保存されたデータ\",\n \"Account registration or login\": \"アカウントの登録またはログイン\",\n \"Support, contact, and community\": \"サポート、コンタクト、コミュニティ\",\n \"Administer this Galaxy\": \"この Galaxy の管理者\",\n \"Visualize datasets\": \"データセットの可視化\",\n \"Access published resources\": \"パブリッシュされたリソースへアクセス\",\n \"Chain tools into workflows\": \"ツールとワークフローの連携\",\n \"Analysis home view\": \"解析ホーム\",\n\n // ---------------------------------------------------------------------------- histories\n \"History Lists\": \"ヒストリーリスト\",\n // Saved histories is defined above.\n // \"Saved Histories\":\n // false,\n \"Histories Shared with Me\": \"私と共有されているヒストリー\",\n \"Current History\": \"現在のヒストリー\",\n \"Create New\": \"新しく作成\",\n \"Copy History\": \"ヒストリーをコピーする\",\n \"Share or Publish\": \"共有またはパブリッシュ\",\n \"Show Structure\": \"構造を見る\",\n \"Extract Workflow\": \"ワークフローを抽出\",\n // Delete is defined elsewhere, but is also in this menu.\n // \"Delete\":\n // false,\n \"Delete Permanently\": \"永久に削除\",\n \"Dataset Actions\": \"データセットの操作\",\n \"Copy Datasets\": \"データセットをコピー\",\n \"Dataset Security\": \"データセットのセキュリティ\",\n \"Resume Paused Jobs\": \"一時停止したジョブの再開\",\n \"Collapse Expanded Datasets\": \"展開されたデータセットを畳む\",\n \"Unhide Hidden Datasets\": \"隠されたデータセットを表示する\",\n \"Delete Hidden Datasets\": \"隠されたデータセットを削除する\",\n \"Purge Deleted Datasets\": \"削除されたデータセットを永久に削除\",\n Downloads: \"ダウンロード\",\n \"Export Tool Citations\": \"ツールの引用をエクスポート\",\n \"Export History to File\": \"ヒストリーをファイルへエクスポート\",\n \"Other Actions\": \"その他のアクション\",\n \"Import from File\": \"ファイルからインポート\",\n Webhooks: \"Webhooks\",\n // ---- history-model\n // ---- history-view\n \"This history is empty\": \"ヒストリーは空です\",\n \"No matching datasets found\": \"一致するデータセットが見つかりませんでした\",\n //\"An error occurred while getting updates from the server\" :\n //false,\n //\"Please contact a Galaxy administrator if the problem persists\" :\n //false,\n //TODO:\n //\"An error was encountered while <% where %>\" :\n //false,\n \"Search datasets\": \"データセットを検索する\",\n \"You are currently viewing a deleted history!\": \"消去したヒストリーをみています。\",\n \"You are over your disk quota\": \"あなたはディスククォータを超えている\",\n //\"Tool execution is on hold until your disk usage drops below your allocated quota\" :\n //false,\n All: \"一式\",\n None: \"なし\",\n \"For all selected\": \"各項目を\",\n\n // ---- history-view-edit\n \"Edit history tags\": \"ヒストリーのタグを編集\",\n \"Edit history annotation\": \"ヒストリーのアノテーションを編集\",\n \"Click to rename history\": \"ヒストリーの名前を変更するにはクリック\",\n // multi operations\n \"Operations on multiple datasets\": \"複数のデータセットに対する操作\",\n //\"Hide datasets\" :\n //false,\n //\"Unhide datasets\" :\n //false,\n //\"Delete datasets\" :\n //false,\n //\"Undelete datasets\" :\n //false,\n \"Permanently delete datasets\": \"永久にデータセットを削除\",\n \"This will permanently remove the data in your datasets. Are you sure?\":\n \"これは永久にあなたのデータセット内のデータを削除します。本当に？\",\n\n // ---- history-view-annotated\n Dataset: \"データセット\",\n //\"Annotation\" :\n //false,\n\n // ---- history-view-edit-current\n \"This history is empty. Click 'Get Data' on the left tool menu to start\":\n \"ヒストリーは空です。解析をはじめるには、左パネルの 'データ取得' をクリック\",\n \"You must be logged in to create histories\": \"ヒストリーを作成するためにはログインする必要があります\",\n //TODO:\n //\"You can <% loadYourOwn %> or <% externalSource %>\" :\n //false,\n //\"load your own data\" :\n //false,\n //\"get data from an external source\" :\n //false,\n\n // these aren't in zh/ginga.po and the template doesn't localize\n //\"Include Deleted Datasets\" :\n //false,\n //\"Include Hidden Datasets\" :\n //false,\n\n // ---------------------------------------------------------------------------- datasets\n // ---- hda-model\n //\"Unable to purge dataset\" :\n //false,\n\n // ---- hda-base\n // display button\n //\"Cannot display datasets removed from disk\" :\n //false,\n //\"This dataset must finish uploading before it can be viewed\" :\n //false,\n //\"This dataset is not yet viewable\" :\n //false,\n \"View data\": \"データを表示\",\n // download button\n Download: \"ダウンロード\",\n \"Download dataset\": \"データセットをダウンロード\",\n //\"Additional files\" :\n //false,\n // info/show_params\n \"View details\": \"細部を表示\",\n\n // dataset states\n // state: new\n //\"This is a new dataset and not all of its data are available yet\" :\n //false,\n // state: noPermission\n //\"You do not have permission to view this dataset\" :\n //false,\n // state: discarded\n //\"The job creating this dataset was cancelled before completion\" :\n //false,\n // state: queued\n \"This job is waiting to run\": \"ジョブは実行待ちです\",\n // state: upload\n //\"This dataset is currently uploading\" :\n //false,\n // state: setting_metadata\n //\"Metadata is being auto-detected\" :\n //false,\n // state: running\n \"This job is currently running\": \"ジョブは実行中です\",\n // state: paused\n //\"This job is paused. Use the \\\"Resume Paused Jobs\\\" in the history menu to resume\" :\n //false,\n // state: error\n \"An error occurred with this dataset\": \"このジョブの実行中に発生したエラー\",\n // state: empty\n \"No data\": \"データ無し\",\n // state: failed_metadata\n //\"An error occurred setting the metadata for this dataset\" :\n //false,\n\n // ajax error prefix\n //\"There was an error getting the data for this dataset\" :\n //false,\n\n // purged'd/del'd msg\n \"This dataset has been deleted and removed from disk\":\n \"このデータセットは、永続的にディスクから削除されました\",\n \"This dataset has been deleted\": \"このデータセットは削除されました\",\n \"This dataset has been hidden\": \"このデータセットは、非表示にされた\",\n\n format: \"フォーマット\",\n database: \"データベース\",\n\n // ---- hda-edit\n \"Edit attributes\": \"変数を編集する\",\n //\"Cannot edit attributes of datasets removed from disk\" :\n //false,\n //\"Undelete dataset to edit attributes\" :\n //false,\n //\"This dataset must finish uploading before it can be edited\" :\n //false,\n //\"This dataset is not yet editable\" :\n //false,\n\n Delete: \"削除する\",\n //\"Dataset is already deleted\" :\n //false,\n\n \"View or report this error\": \"このエラーを届け出る\",\n\n \"Run this job again\": \"もう一度このジョブを実行する\",\n\n Visualize: \"可視化する\",\n //\"Visualize in\" :\n //false,\n\n \"Undelete it\": \"復元する\",\n \"Permanently remove it from disk\": \"永久にディスクから削除\",\n \"Unhide it\": \"非表示解除する\",\n \"Saved Histories\": \"保存されたヒストリ\",\n \"Import from File\": \"ファイルからの読み込み\",\n\n //\"You may be able to\" :\n //false,\n //\"set it manually or retry auto-detection\" :\n //false,\n\n //\"Edit dataset tags\" :\n //false,\n //\"Edit dataset annotation\" :\n //false,\n\n // ---------------------------------------------------------------------------- admin\n \"Search Tool Shed\": \"Tool Shed で探す\",\n \"Search Tool Shed (Beta)\": \"Tool Shed (Beta) で探す\",\n \"Monitor installing repositories\": \"インストールレポジトリのモニタ\",\n \"Manage installed tools\": \"インストールしたツールの管理\",\n \"Reset metadata\": \"メタデータのリセット\",\n \"Download local tool\": \"ローカルツールのダウンロード\",\n \"Tool lineage\": \"ツール系統\",\n \"Reload a tool's configuration\": \"ツールのコンフィグのリロード\",\n \"Review tool migration stages\": \"ツール移行ステージのレビュー\",\n \"View Tool Error Logs\": \"ツールのエラーログ\",\n \"Manage Display Whitelist\": \"表示ホワイトリストの管理\",\n \"Manage Tool Dependencies\": \"ツール依存関係の管理\",\n Users: \"ユーザー\",\n Groups: \"グループ\",\n \"API keys\": \"API キー\",\n \"Impersonate a user\": \"ユーザー偽装\",\n Data: \"データ\",\n Quotas: \"クォータ\",\n Roles: \"ロール\",\n \"Local data\": \"ローカルデータ\",\n \"Form definitions\": \"フォーム定義\",\n Administration: \"管理\",\n Server: \"サーバー\",\n \"Tools and Tool Shed\": \"ツールと Tool Shed\",\n \"User Management\": \"ユーザ管理\",\n Data: \"データ\",\n \"Form Definitions\": \"フォーム定義\"\n // ---------------------------------------------------------------------------- misc. MVC\n //\"Tags\" :\n //false,\n //\"Annotation\" :\n //false,\n //\"Edit annotation\" :\n //false,\n});\n"]} \ No newline at end of file diff --git a/static/maps/nls/locale.js.map b/static/maps/nls/locale.js.map index 2c7e1cd37d2..3808ab9f11f 100644 --- a/static/maps/nls/locale.js.map +++ b/static/maps/nls/locale.js.map @@ -1 +1 @@ -{"version":3,"sources":["nls/locale.js"],"names":["define","root","Workflow","Shared Data","Histories","Workflows","Visualizations","Pages","Visualization","Interactive Environments","Admin","Help","Support","Search","Wiki","Videos","User","Login","Register","Preferences","Custom Builds","Saved Histories","Logout","Saved Pages","Account and saved data","Account registration or login","Support, contact, and community","Administer this Galaxy","Visualize datasets","Access published resources","Chain tools into workflows","Analysis home view","History Lists","Histories Shared with Me","Current History","Create New","Copy History","Share or Publish","Show Structure","Extract Workflow","Delete Permanently","Dataset Actions","Copy Datasets","Dataset Security","Resume Paused Jobs","Collapse Expanded Datasets","Unhide Hidden Datasets","Delete Hidden Datasets","Purge Deleted Datasets","Downloads","Export Tool Citations","Other Actions","Import from File","Webhooks","This history is empty","No matching datasets found","An error occurred while getting updates from the server","Please contact a Galaxy administrator if the problem persists","search datasets","You are currently viewing a deleted history!","You are over your disk quota","Tool execution is on hold until your disk usage drops below your allocated quota","All","None","Edit history tags","Edit history Annotation","Click to rename history","Operations on multiple datasets","Hide datasets","Unhide datasets","Delete datasets","Undelete datasets","Permanently delete datasets","This will permanently remove the data in your datasets. 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for use with requirejs' i18n plugin */\ndefine({\n root: {\n // ----------------------------------------------------------------------------- masthead\n \"Analyze Data\": false,\n Workflow: false,\n \"Shared Data\": false,\n \"Data Libraries\": false,\n Histories: false,\n Workflows: false,\n Visualizations: false,\n Pages: false,\n Visualization: false,\n \"New Track Browser\": false,\n \"Saved Visualizations\": false,\n \"Interactive Environments\": false,\n Admin: false,\n Help: false,\n Support: false,\n Search: false,\n \"Mailing Lists\": false,\n Videos: false,\n Wiki: false,\n \"How to Cite Galaxy\": false,\n \"Interactive Tours\": false,\n User: false,\n Login: false,\n Register: false,\n \"Login or Register\": false,\n \"Logged in as\": false,\n Preferences: false,\n \"Custom Builds\": false,\n Logout: false,\n \"Saved Histories\": false,\n \"Saved Datasets\": false,\n \"Saved Pages\": false,\n\n //Tooltip\n \"Account and saved data\": false,\n \"Account registration or login\": false,\n \"Support, contact, and community\": false,\n \"Administer this Galaxy\": false,\n \"Visualize datasets\": false,\n \"Access published resources\": false,\n \"Chain tools into workflows\": false,\n \"Analysis home view\": false,\n\n // ---------------------------------------------------------------------------- histories\n // ---- history/options-menu\n \"History Lists\": false,\n // Saved histories is defined above.\n // \"Saved Histories\":\n // false,\n \"Histories Shared with Me\": false,\n \"Current History\": false,\n \"Create New\": false,\n \"Copy History\": false,\n \"Share or Publish\": false,\n \"Show Structure\": false,\n \"Extract Workflow\": false,\n // Delete is defined elsewhere, but is also in this menu.\n // \"Delete\":\n // false,\n \"Delete Permanently\": false,\n \"Dataset Actions\": false,\n \"Copy Datasets\": false,\n \"Dataset Security\": false,\n \"Resume Paused Jobs\": false,\n \"Collapse Expanded Datasets\": false,\n \"Unhide Hidden Datasets\": false,\n \"Delete Hidden Datasets\": false,\n \"Purge Deleted Datasets\": false,\n Downloads: false,\n \"Export Tool Citations\": false,\n \"Export History to File\": false,\n \"Other Actions\": false,\n \"Import from File\": false,\n Webhooks: false,\n\n // ---- history-model\n // ---- history-view\n \"This history is empty\": false,\n \"No matching datasets found\": false,\n \"An error occurred while getting updates from the server\": false,\n \"Please contact a Galaxy administrator if the problem persists\": false,\n //TODO:\n //\"An error was encountered while <% where %>\" :\n //false,\n \"search datasets\": false,\n \"You are currently viewing a deleted history!\": false,\n \"You are over your disk quota\": false,\n \"Tool execution is on hold until your disk usage drops below your allocated quota\": false,\n All: false,\n None: false,\n \"For all selected\": false,\n\n // ---- history-view-edit\n \"Edit history tags\": false,\n \"Edit history Annotation\": false,\n \"Click to rename history\": false,\n // multi operations\n \"Operations on multiple datasets\": false,\n \"Hide datasets\": false,\n \"Unhide datasets\": false,\n \"Delete datasets\": false,\n \"Undelete datasets\": false,\n \"Permanently delete datasets\": false,\n \"This will permanently remove the data in your datasets. Are you sure?\": false,\n\n // ---- history-view-annotated\n Dataset: false,\n Annotation: false,\n\n // ---- history-view-edit-current\n \"This history is empty. Click 'Get Data' on the left tool menu to start\": false,\n \"You must be logged in to create histories\": false,\n //TODO:\n //\"You can <% loadYourOwn %> or <% externalSource %>\" :\n //false,\n //\"load your own data\" :\n //false,\n //\"get data from an external source\" :\n //false,\n\n // these aren't in zh/ginga.po and the template doesn't localize\n //\"Include Deleted Datasets\" :\n //false,\n //\"Include Hidden Datasets\" :\n //false,\n\n // ---------------------------------------------------------------------------- datasets\n // ---- hda-model\n \"Unable to purge dataset\": false,\n\n // ---- hda-base\n // display button\n \"Cannot display datasets removed from disk\": false,\n \"This dataset must finish uploading before it can be viewed\": false,\n \"This dataset is not yet viewable\": false,\n \"View data\": false,\n // download button\n Download: false,\n \"Download dataset\": false,\n \"Additional files\": false,\n // info/show_params\n \"View details\": false,\n\n // dataset states\n // state: new\n \"This is a new dataset and not all of its data are available yet\": false,\n // state: noPermission\n \"You do not have permission to view this dataset\": false,\n // state: discarded\n \"The job creating this dataset was cancelled before completion\": false,\n // state: queued\n \"This job is waiting to run\": false,\n // state: upload\n \"This dataset is currently uploading\": false,\n // state: setting_metadata\n \"Metadata is being auto-detected\": false,\n // state: running\n \"This job is currently running\": false,\n // state: paused\n 'This job is paused. Use the \"Resume Paused Jobs\" in the history menu to resume': false,\n // state: error\n \"An error occurred with this dataset\": false,\n // state: empty\n \"No data\": false,\n // state: failed_metadata\n \"An error occurred setting the metadata for this dataset\": false,\n\n // ajax error prefix\n \"There was an error getting the data for this dataset\": false,\n\n // purged'd/del'd msg\n \"This dataset has been deleted and removed from disk\": false,\n \"This dataset has been deleted\": false,\n \"This dataset has been hidden\": false,\n\n format: false,\n database: false,\n\n // ---- hda-edit\n \"Edit attributes\": false,\n \"Cannot edit attributes of datasets removed from disk\": false,\n \"Undelete dataset to edit attributes\": false,\n \"This dataset must finish uploading before it can be edited\": false,\n \"This dataset is not yet editable\": false,\n\n Delete: false,\n \"Dataset is already deleted\": false,\n\n \"View or report this error\": false,\n\n \"Run this job again\": false,\n\n Visualize: false,\n \"Visualize in\": false,\n\n \"Undelete it\": false,\n \"Permanently remove it from disk\": false,\n \"Unhide it\": false,\n\n \"You may be able to\": false,\n \"set it manually or retry auto-detection\": false,\n\n \"Edit dataset tags\": false,\n \"Edit dataset annotation\": false,\n\n \"Tool Help\": false,\n\n // ---------------------------------------------------------------------------- admin\n \"Search Tool Shed\": false,\n \"Monitor installing repositories\": false,\n \"Manage installed tools\": false,\n \"Reset metadata\": false,\n \"Download local tool\": false,\n \"Tool lineage\": false,\n \"Reload a tool's configuration\": false,\n \"Review tool migration stages\": false,\n \"View Tool Error Logs\": false,\n \"Manage Display Whitelist\": false,\n \"Manage Tool Dependencies\": false,\n Users: false,\n Groups: false,\n \"API keys\": false,\n \"Impersonate a user\": false,\n Data: false,\n Quotas: false,\n Roles: false,\n \"Local data\": false,\n \"Form Definitions\": false,\n\n // ---------------------------------------------------------------------------- Scratchbook\n \"Enable/Disable Scratchbook\": false,\n \"Show/Hide Scratchbook\": false,\n\n // ---------------------------------------------------------------------------- misc. MVC\n Tags: false,\n \"Edit annotation\": false\n\n // ----------------------------------------------------------------------------\n },\n ja: true,\n fr: true,\n zh: true\n});\n"]} \ No newline at end of file +{"version":3,"sources":["nls/locale.js"],"names":["define","root","Shared Data","Data Libraries","Workflow","Workflows","Visualizations","Histories","Pages","Visualization","Admin","Help","Support","Search","How to Cite Galaxy","Videos","Wiki","Login","Register","User","Custom Builds","Logout","Preferences","Saved Datasets","Account and saved data","Account registration or login","Support, contact, and community","Administer this Galaxy","Visualize datasets","Access published resources","Chain tools into workflows","Analysis home view","History Lists","Histories Shared with Me","Current History","Create New","Copy History","Share or Publish","Show Structure","Extract Workflow","Delete Permanently","Dataset Actions","Copy Datasets","Dataset Security","Resume Paused Jobs","Collapse Expanded Datasets","Unhide Hidden Datasets","Delete Hidden Datasets","Purge Deleted Datasets","Downloads","Export Tool Citations","Export History to File","Import from File","Webhooks","This history is empty","No matching datasets found","An error occurred while getting updates from the server","Please contact a Galaxy administrator if the problem persists","search datasets","You are currently viewing a deleted history!","You are over your disk quota","Tool execution is on hold until your disk usage drops below your allocated quota","All","None","For all selected","Edit history tags","Edit history Annotation","Click to rename history","Operations on multiple datasets","Hide datasets","Unhide datasets","Delete datasets","Undelete datasets","Permanently delete datasets","This will permanently remove the data in your datasets. 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for use with requirejs' i18n plugin */\ndefine({\n root: {\n // ----------------------------------------------------------------------------- masthead\n \"Analyze Data\": false,\n Workflow: false,\n \"Shared Data\": false,\n \"Data Libraries\": false,\n Histories: false,\n Workflows: false,\n Visualizations: false,\n Pages: false,\n Visualization: false,\n \"New Track Browser\": false,\n \"Saved Visualizations\": false,\n \"Interactive Environments\": false,\n Admin: false,\n Help: false,\n Support: false,\n Search: false,\n \"Mailing Lists\": false,\n Videos: false,\n Wiki: false,\n \"How to Cite Galaxy\": false,\n \"Interactive Tours\": false,\n User: false,\n Login: false,\n Register: false,\n \"Login or Register\": false,\n \"Logged in as\": false,\n Preferences: false,\n \"Custom Builds\": false,\n Logout: false,\n \"Saved Histories\": false,\n \"Saved Datasets\": false,\n \"Saved Pages\": false,\n\n //Tooltip\n \"Account and saved data\": false,\n \"Account registration or login\": false,\n \"Support, contact, and community\": false,\n \"Administer this Galaxy\": false,\n \"Visualize datasets\": false,\n \"Access published resources\": false,\n \"Chain tools into workflows\": false,\n \"Analysis home view\": false,\n\n // ---------------------------------------------------------------------------- histories\n // ---- history/options-menu\n \"History Lists\": false,\n // Saved histories is defined above.\n // \"Saved Histories\":\n // false,\n \"Histories Shared with Me\": false,\n \"Current History\": false,\n \"Create New\": false,\n \"Copy History\": false,\n \"Share or Publish\": false,\n \"Show Structure\": false,\n \"Extract Workflow\": false,\n // Delete is defined elsewhere, but is also in this menu.\n // \"Delete\":\n // false,\n \"Delete Permanently\": false,\n \"Dataset Actions\": false,\n \"Copy Datasets\": false,\n \"Dataset Security\": false,\n \"Resume Paused Jobs\": false,\n \"Collapse Expanded Datasets\": false,\n \"Unhide Hidden Datasets\": false,\n \"Delete Hidden Datasets\": false,\n \"Purge Deleted Datasets\": false,\n Downloads: false,\n \"Export Tool Citations\": false,\n \"Export History to File\": false,\n \"Other Actions\": false,\n \"Import from File\": false,\n Webhooks: false,\n\n // ---- history-model\n // ---- history-view\n \"This history is empty\": false,\n \"No matching datasets found\": false,\n \"An error occurred while getting updates from the server\": false,\n \"Please contact a Galaxy administrator if the problem persists\": false,\n //TODO:\n //\"An error was encountered while <% where %>\" :\n //false,\n \"search datasets\": false,\n \"You are currently viewing a deleted history!\": false,\n \"You are over your disk quota\": false,\n \"Tool execution is on hold until your disk usage drops below your allocated quota\": false,\n All: false,\n None: false,\n \"For all selected\": false,\n\n // ---- history-view-edit\n \"Edit history tags\": false,\n \"Edit history Annotation\": false,\n \"Click to rename history\": false,\n // multi operations\n \"Operations on multiple datasets\": false,\n \"Hide datasets\": false,\n \"Unhide datasets\": false,\n \"Delete datasets\": false,\n \"Undelete datasets\": false,\n \"Permanently delete datasets\": false,\n \"This will permanently remove the data in your datasets. Are you sure?\": false,\n\n // ---- history-view-annotated\n Dataset: false,\n Annotation: false,\n\n // ---- history-view-edit-current\n \"This history is empty. Click 'Get Data' on the left tool menu to start\": false,\n \"You must be logged in to create histories\": false,\n //TODO:\n //\"You can <% loadYourOwn %> or <% externalSource %>\" :\n //false,\n //\"load your own data\" :\n //false,\n //\"get data from an external source\" :\n //false,\n\n // these aren't in zh/ginga.po and the template doesn't localize\n //\"Include Deleted Datasets\" :\n //false,\n //\"Include Hidden Datasets\" :\n //false,\n\n // ---------------------------------------------------------------------------- datasets\n // ---- hda-model\n \"Unable to purge dataset\": false,\n\n // ---- hda-base\n // display button\n \"Cannot display datasets removed from disk\": false,\n \"This dataset must finish uploading before it can be viewed\": false,\n \"This dataset is not yet viewable\": false,\n \"View data\": false,\n // download button\n Download: false,\n \"Download dataset\": false,\n \"Additional files\": false,\n // info/show_params\n \"View details\": false,\n\n // dataset states\n // state: new\n \"This is a new dataset and not all of its data are available yet\": false,\n // state: noPermission\n \"You do not have permission to view this dataset\": false,\n // state: discarded\n \"The job creating this dataset was cancelled before completion\": false,\n // state: queued\n \"This job is waiting to run\": false,\n // state: upload\n \"This dataset is currently uploading\": false,\n // state: setting_metadata\n \"Metadata is being auto-detected\": false,\n // state: running\n \"This job is currently running\": false,\n // state: paused\n 'This job is paused. Use the \"Resume Paused Jobs\" in the history menu to resume': false,\n // state: error\n \"An error occurred with this dataset\": false,\n // state: empty\n \"No data\": false,\n // state: failed_metadata\n \"An error occurred setting the metadata for this dataset\": false,\n\n // ajax error prefix\n \"There was an error getting the data for this dataset\": false,\n\n // purged'd/del'd msg\n \"This dataset has been deleted and removed from disk\": false,\n \"This dataset has been deleted\": false,\n \"This dataset has been hidden\": false,\n\n format: false,\n database: false,\n\n // ---- hda-edit\n \"Edit attributes\": false,\n \"Cannot edit attributes of datasets removed from disk\": false,\n \"Undelete dataset to edit attributes\": false,\n \"This dataset must finish uploading before it can be edited\": false,\n \"This dataset is not yet editable\": false,\n\n Delete: false,\n \"Dataset is already deleted\": false,\n\n \"View or report this error\": false,\n\n \"Run this job again\": false,\n\n Visualize: false,\n \"Visualize in\": false,\n\n \"Undelete it\": false,\n \"Permanently remove it from disk\": false,\n \"Unhide it\": false,\n\n \"You may be able to\": false,\n \"set it manually or retry auto-detection\": false,\n\n \"Edit dataset tags\": false,\n \"Edit dataset annotation\": false,\n\n \"Tool Help\": false,\n\n // ---------------------------------------------------------------------------- admin\n \"Search Tool Shed\": false,\n \"Monitor installing repositories\": false,\n \"Manage installed tools\": false,\n \"Reset metadata\": false,\n \"Download local tool\": false,\n \"Tool lineage\": false,\n \"Reload a tool's configuration\": false,\n \"Review tool migration stages\": false,\n \"View Tool Error Logs\": false,\n \"Manage Display Whitelist\": false,\n \"Manage Tool Dependencies\": false,\n Users: false,\n Groups: false,\n \"API keys\": false,\n \"Impersonate a user\": false,\n Data: false,\n Quotas: false,\n Roles: false,\n \"Local data\": false,\n \"Form Definitions\": false,\n\n // ---------------------------------------------------------------------------- Scratchbook\n \"Enable/Disable Scratchbook\": false,\n \"Show/Hide Scratchbook\": false,\n\n // ---------------------------------------------------------------------------- misc. MVC\n Tags: false,\n \"Edit annotation\": false\n\n // ----------------------------------------------------------------------------\n },\n ja: true,\n fr: true,\n zh: true\n});\n"]} \ No newline at end of file diff --git a/static/maps/nls/zh/locale.js.map b/static/maps/nls/zh/locale.js.map index 75d1e018736..3f6c58501a3 100644 --- a/static/maps/nls/zh/locale.js.map +++ b/static/maps/nls/zh/locale.js.map @@ -1 +1 @@ -{"version":3,"sources":["nls/zh/locale.js"],"names":["define","This history is empty","No matching datasets found","Search datasets","You are currently viewing a deleted history!","You are over your disk quota","All","None","Click to rename history","Operations on multiple datasets","Permanently delete datasets","This will permanently remove the data in your datasets. Are you sure?","Dataset","This history is empty. Click 'Get Data' on the left tool menu to start","You must be logged in to create histories","View data","Download","Download dataset","View details","This job is waiting to run","This job is currently running","An error occurred with this dataset","No data","This dataset has been deleted","This dataset has been hidden","format","database","Edit attributes","Delete","View or report this error","Run this job again","Visualize","Undelete it","Permanently remove it from disk","Unhide it"],"mappings":"aACAA,QAEIC,wBAAA,OACAC,6BAAA,YAQAC,kBAAA,QACAC,+CAAA,aACAC,+BAbG,WAgBHC,IAAA,IACAC,KAAA,QACAD,mBAlBG,QAyBHE,0BAAA,YAEAC,kCAA2B,UAS3BC,8BAAA,UACAC,wEACA,sBAIAC,QAAA,MAKAC,yEACA,sBAEAC,4CAA6C,eAsB7CC,YAAa,KAEbC,SAAU,KACVC,mBAAoB,QAIpBC,eAAgB,OAahBC,6BAA8B,UAQ9BC,gCAAiC,UAKjCC,sCAAuC,UAEvCC,UAAW,OAYXC,gCAAiC,WACjCC,+BAAgC,UAEhCC,OAAQ,KACRC,SAAU,MAGVC,kBAAmB,OAUnBC,OAAQ,KAIRC,4BAA6B,OAE7BC,qBAAsB,OAEtBC,UAAW,KAIXC,cAAe,MACfC,kCAAmC,WACnCC,YAAa","file":"../../../scripts/nls/zh/locale.js","sourcesContent":["/** zh localization */\ndefine({\n // ---------------------------------------------------------------------------- histories\n // ---- history-model\n // ---- history-view\n \"This history is empty\": \"历史已空\",\n \"No matching datasets found\": \"未找到匹配的数据集\",\n //\"An error occurred while getting updates from the server\" :\n //false,\n //\"Please contact a Galaxy administrator if the problem persists\" :\n //false,\n //TODO:\n //\"An error was encountered while <% where %>\" :\n //false,\n \"Search datasets\": \"搜索数据集\",\n \"You are currently viewing a deleted history!\": \"正在查看已删除的历史\",\n \"You are over your disk quota\": \"您已超过磁盘配额\",\n //\"Tool execution is on hold until your disk usage drops below your allocated quota\" :\n //false,\n All: \"皆\",\n None: \"一个也没有\",\n \"For all selected\": \"为每个选定\",\n\n // ---- history-view-edit\n //\"Edit history tags\" :\n //false,\n //\"Edit history Annotation\" :\n //false,\n \"Click to rename history\": \"单击要重命名的历史\",\n // multi operations\n \"Operations on multiple datasets\": \"编辑多个数据集\",\n //\"Hide datasets\" :\n //false,\n //\"Unhide datasets\" :\n //false,\n //\"Delete datasets\" :\n //false,\n //\"Undelete datasets\" :\n //false,\n \"Permanently delete datasets\": \"永久删除数据集\",\n \"This will permanently remove the data in your datasets. Are you sure?\":\n \"这将永久在你的数据集删除数据。你确定？\",\n\n // ---- history-view-annotated\n Dataset: \"数据集\",\n //\"Annotation\" :\n //false,\n\n // ---- history-view-edit-current\n \"This history is empty. Click 'Get Data' on the left tool menu to start\":\n \"历史已空，请单击左边窗格中‘获取数据’\",\n \"You must be logged in to create histories\": \"你必须登录后才能创建历史\",\n //TODO:\n //\"You can <% loadYourOwn %> or <% externalSource %>\" :\n //false,\n //\"load your own data\" :\n //false,\n //\"get data from an external source\" :\n //false,\n\n // ---------------------------------------------------------------------------- datasets\n // ---- hda-model\n //\"Unable to purge dataset\" :\n //false,\n\n // ---- hda-base\n // display button\n //\"Cannot display datasets removed from disk\" :\n //false,\n //\"This dataset must finish uploading before it can be viewed\" :\n //false,\n //\"This dataset is not yet viewable\" :\n //false,\n \"View data\": \"数据\",\n // download button\n Download: \"下载\",\n \"Download dataset\": \"下载数据集\",\n //\"Additional files\" :\n //false,\n // info/show_params\n \"View details\": \"查看详情\",\n\n // dataset states\n // state: new\n //\"This is a new dataset and not all of its data are available yet\" :\n //false,\n // state: noPermission\n //\"You do not have permission to view this dataset\" :\n //false,\n // state: discarded\n //\"The job creating this dataset was cancelled before completion\" :\n //false,\n // state: queued\n \"This job is waiting to run\": \"等待运行的进程\",\n // state: upload\n //\"This dataset is currently uploading\" :\n //false,\n // state: setting_metadata\n //\"Metadata is being auto-detected\" :\n //false,\n // state: running\n \"This job is currently running\": \"正在运行的进程\",\n // state: paused\n //\"This job is paused. Use the \\\"Resume Paused Jobs\\\" in the history menu to resume\" :\n //false,\n // state: error\n \"An error occurred with this dataset\": \"进程运行时出错\",\n // state: empty\n \"No data\": \"没有数据\",\n // state: failed_metadata\n //\"An error occurred setting the metadata for this dataset\" :\n //false,\n\n // ajax error prefix\n //\"There was an error getting the data for this dataset\" :\n //false,\n\n // purged'd/del'd msg\n //\"This dataset has been deleted and removed from disk\" :\n //false,\n \"This dataset has been deleted\": \"此数据集已被删除\",\n \"This dataset has been hidden\": \"此数据集已隐藏\",\n\n format: \"格式\",\n database: \"数据库\",\n\n // ---- hda-edit\n \"Edit attributes\": \"编辑属性\",\n //\"Cannot edit attributes of datasets removed from disk\" :\n //false,\n //\"Undelete dataset to edit attributes\" :\n //false,\n //\"This dataset must finish uploading before it can be edited\" :\n //false,\n //\"This dataset is not yet editable\" :\n //false,\n\n Delete: \"删除\",\n //\"Dataset is already deleted\" :\n //false,\n\n \"View or report this error\": \"报告错误\",\n\n \"Run this job again\": \"重新运行\",\n\n Visualize: \"图形\",\n //\"Visualize in\" :\n //false,\n\n \"Undelete it\": \"反删除\",\n \"Permanently remove it from disk\": \"从磁盘中永久删除\",\n \"Unhide it\": \"取消隐藏\"\n\n //\"You may be able to\" :\n //false,\n //\"set it manually or retry auto-detection\" :\n //false,\n\n //\"Edit dataset tags\" :\n //false,\n //\"Edit dataset annotation\" :\n //false,\n\n // ---------------------------------------------------------------------------- misc. MVC\n //\"Tags\" :\n //false,\n //\"Annotation\" :\n //false,\n //\"Edit annotation\" :\n //false,\n});\n"]} \ No newline at end of file +{"version":3,"sources":["nls/zh/locale.js"],"names":["define","This history is empty","No matching datasets found","Search datasets","You are currently viewing a deleted history!","You are over your disk quota","All","None","For all selected","Click to rename history","Operations on multiple datasets","Permanently delete datasets","This will permanently remove the data in your datasets. Are you sure?","Dataset","This history is empty. Click 'Get Data' on the left tool menu to start","You must be logged in to create histories","View data","Download","View details","This job is waiting to run","This job is currently running","An error occurred with this dataset","No data","This dataset has been deleted","This dataset has been hidden","format","Edit attributes","Delete","View or report this error","Run this job again","Visualize","Undelete it","Permanently remove it from disk","Unhide it"],"mappings":"kCACAA,QACIC,wBAAA,OACAC,6BAAA,YAQAC,kBAAA,QACAC,+CAAA,aACAC,+BAAA,WAGAC,IAAA,IACAC,KAAA,QACAC,mBAAA,QAOAC,0BAAA,YAEAC,kCAAA,UASAC,8BAAA,UACAC,wEACA,sBAMAC,QAAS,MAKTC,yEADA,sBACAC,4CAAA,eAuBAC,YAAA,KAEAC,SAAA,KACAA,mBA1EG,QA8EHC,eAAA,OAaAC,6BAAA,UAQAC,gCAAA,UAKAC,sCAAA,UAEAC,UAAA,OAYAC,gCAAA,WACAC,+BAAA,UAGAC,OAAQ,KAARA,SAAAA,MAGAC,kBAAA,OAWAC,OAAQ,KAIRC,4BAA6B,OAE7BC,qBAAsB,OAEtBC,UAAW,KAIXC,cAAe,MAAfC,kCApJG,WAqJHC,YAAA","file":"../../../scripts/nls/zh/locale.js","sourcesContent":["/** zh localization */\ndefine({\n // ---------------------------------------------------------------------------- histories\n // ---- history-model\n // ---- history-view\n \"This history is empty\": \"历史已空\",\n \"No matching datasets found\": \"未找到匹配的数据集\",\n //\"An error occurred while getting updates from the server\" :\n //false,\n //\"Please contact a Galaxy administrator if the problem persists\" :\n //false,\n //TODO:\n //\"An error was encountered while <% where %>\" :\n //false,\n \"Search datasets\": \"搜索数据集\",\n \"You are currently viewing a deleted history!\": \"正在查看已删除的历史\",\n \"You are over your disk quota\": \"您已超过磁盘配额\",\n //\"Tool execution is on hold until your disk usage drops below your allocated quota\" :\n //false,\n All: \"皆\",\n None: \"一个也没有\",\n \"For all selected\": \"为每个选定\",\n\n // ---- history-view-edit\n //\"Edit history tags\" :\n //false,\n //\"Edit history Annotation\" :\n //false,\n \"Click to rename history\": \"单击要重命名的历史\",\n // multi operations\n \"Operations on multiple datasets\": \"编辑多个数据集\",\n //\"Hide datasets\" :\n //false,\n //\"Unhide datasets\" :\n //false,\n //\"Delete datasets\" :\n //false,\n //\"Undelete datasets\" :\n //false,\n \"Permanently delete datasets\": \"永久删除数据集\",\n \"This will permanently remove the data in your datasets. Are you sure?\":\n \"这将永久在你的数据集删除数据。你确定？\",\n\n // ---- history-view-annotated\n Dataset: \"数据集\",\n //\"Annotation\" :\n //false,\n\n // ---- history-view-edit-current\n \"This history is empty. Click 'Get Data' on the left tool menu to start\":\n \"历史已空，请单击左边窗格中‘获取数据’\",\n \"You must be logged in to create histories\": \"你必须登录后才能创建历史\",\n //TODO:\n //\"You can <% loadYourOwn %> or <% externalSource %>\" :\n //false,\n //\"load your own data\" :\n //false,\n //\"get data from an external source\" :\n //false,\n\n // ---------------------------------------------------------------------------- datasets\n // ---- hda-model\n //\"Unable to purge dataset\" :\n //false,\n\n // ---- hda-base\n // display button\n //\"Cannot display datasets removed from disk\" :\n //false,\n //\"This dataset must finish uploading before it can be viewed\" :\n //false,\n //\"This dataset is not yet viewable\" :\n //false,\n \"View data\": \"数据\",\n // download button\n Download: \"下载\",\n \"Download dataset\": \"下载数据集\",\n //\"Additional files\" :\n //false,\n // info/show_params\n \"View details\": \"查看详情\",\n\n // dataset states\n // state: new\n //\"This is a new dataset and not all of its data are available yet\" :\n //false,\n // state: noPermission\n //\"You do not have permission to view this dataset\" :\n //false,\n // state: discarded\n //\"The job creating this dataset was cancelled before completion\" :\n //false,\n // state: queued\n \"This job is waiting to run\": \"等待运行的进程\",\n // state: upload\n //\"This dataset is currently uploading\" :\n //false,\n // state: setting_metadata\n //\"Metadata is being auto-detected\" :\n //false,\n // state: running\n \"This job is currently running\": \"正在运行的进程\",\n // state: paused\n //\"This job is paused. Use the \\\"Resume Paused Jobs\\\" in the history menu to resume\" :\n //false,\n // state: error\n \"An error occurred with this dataset\": \"进程运行时出错\",\n // state: empty\n \"No data\": \"没有数据\",\n // state: failed_metadata\n //\"An error occurred setting the metadata for this dataset\" :\n //false,\n\n // ajax error prefix\n //\"There was an error getting the data for this dataset\" :\n //false,\n\n // purged'd/del'd msg\n //\"This dataset has been deleted and removed from disk\" :\n //false,\n \"This dataset has been deleted\": \"此数据集已被删除\",\n \"This dataset has been hidden\": \"此数据集已隐藏\",\n\n format: \"格式\",\n database: \"数据库\",\n\n // ---- hda-edit\n \"Edit attributes\": \"编辑属性\",\n //\"Cannot edit attributes of datasets removed from disk\" :\n //false,\n //\"Undelete dataset to edit attributes\" :\n //false,\n //\"This dataset must finish uploading before it can be edited\" :\n //false,\n //\"This dataset is not yet editable\" :\n //false,\n\n Delete: \"删除\",\n //\"Dataset is already deleted\" :\n //false,\n\n \"View or report this error\": \"报告错误\",\n\n \"Run this job again\": \"重新运行\",\n\n Visualize: \"图形\",\n //\"Visualize in\" :\n //false,\n\n \"Undelete it\": \"反删除\",\n \"Permanently remove it from disk\": \"从磁盘中永久删除\",\n \"Unhide it\": \"取消隐藏\"\n\n //\"You may be able to\" :\n //false,\n //\"set it manually or retry auto-detection\" :\n //false,\n\n //\"Edit dataset tags\" :\n //false,\n //\"Edit dataset annotation\" :\n //false,\n\n // ---------------------------------------------------------------------------- misc. 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Perform feature inference and redirect if below some minimum (must have canvas, etc.)\n and polyfill for non-standard features.\n */\n\n(function() {\n /* TODO: move to modernizr or something besides us doing this...\n * These are across all of our apps (reports, tool shed), but:\n * these should be configurable via options because they all need different things.\n * So, analysis-polyfills.js, reports-polyfills.js (or analysis/polyfills)\n */\n \"use strict\";\n /*globals window, clearTimeout */\n\n // ------------------------------------------------------------------ polyfills\n // console protection needed in some versions of IE (at this point (IE>=9), shouldn't be needed)\n window.console = window.console || {\n log: function() {},\n debug: function() {},\n info: function() {},\n warn: function() {},\n error: function() {},\n assert: function() {}\n };\n\n // phantomjs: does not have the native extend fn assign\n Object.assign = Object.assign || _.extend;\n\n // requestAnimationFrame polyfill\n var lastTime = 0;\n var vendors = [\"ms\", \"moz\", \"webkit\", \"o\"];\n for (var x = 0; x < vendors.length && !window.requestAnimationFrame; ++x) {\n window.requestAnimationFrame =\n window[vendors[x] + \"RequestAnimationFrame\"];\n window.cancelRequestAnimationFrame =\n window[vendors[x] + \"CancelRequestAnimationFrame\"];\n }\n\n if (!window.requestAnimationFrame)\n window.requestAnimationFrame = function(callback, element) {\n var currTime = new Date().getTime();\n var timeToCall = Math.max(0, 16 - (currTime - lastTime));\n var id = window.setTimeout(function() {\n callback(currTime + timeToCall);\n }, timeToCall);\n lastTime = currTime + timeToCall;\n return id;\n };\n\n if (!window.cancelAnimationFrame)\n window.cancelAnimationFrame = function(id) {\n clearTimeout(id);\n };\n\n // ------------------------------------------------------------------ can't/won't polyfill\n var features = [\n {\n name: \"canvas\",\n compatible: function() {\n return window.CanvasRenderingContext2D;\n }\n },\n {\n name: \"sessionStorage\",\n compatible: function() {\n try {\n return window.sessionStorage.length >= 0;\n } catch (err) {}\n return false;\n }\n }\n ];\n // build a list of feature names for features that were not found\n var incompatibilities = features\n .filter(function(feature) {\n return !feature.compatible();\n })\n .map(function(feature) {\n return feature.name;\n });\n\n // if there are needed features missing, follow the index link to the static incompat warning\n if (!!incompatibilities.length) {\n var root = document.querySelectorAll('link[rel=\"index\"]').item(0);\n if (root) {\n window.location = root.href + \"static/incompatible-browser.html\";\n }\n console.log(\"incompatible browser:\\n\" + incompatibilities.join(\"\\n\"));\n }\n})();\n"]} \ No newline at end of file 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Perform feature inference and redirect if below some minimum (must have canvas, etc.)\n and polyfill for non-standard features.\n */\n\n(function() {\n /* TODO: move to modernizr or something besides us doing this...\n * These are across all of our apps (reports, tool shed), but:\n * these should be configurable via options because they all need different things.\n * So, analysis-polyfills.js, reports-polyfills.js (or analysis/polyfills)\n */\n \"use strict\";\n /*globals window, clearTimeout */\n\n // ------------------------------------------------------------------ polyfills\n // console protection needed in some versions of IE (at this point (IE>=9), shouldn't be needed)\n window.console = window.console || {\n log: function() {},\n debug: function() {},\n info: function() {},\n warn: function() {},\n error: function() {},\n assert: function() {}\n };\n\n // phantomjs: does not have the native extend fn assign\n Object.assign = Object.assign || _.extend;\n\n // requestAnimationFrame polyfill\n var lastTime = 0;\n var vendors = [\"ms\", \"moz\", \"webkit\", \"o\"];\n for (var x = 0; x < vendors.length && !window.requestAnimationFrame; ++x) {\n window.requestAnimationFrame =\n window[vendors[x] + \"RequestAnimationFrame\"];\n window.cancelRequestAnimationFrame =\n window[vendors[x] + \"CancelRequestAnimationFrame\"];\n }\n\n if (!window.requestAnimationFrame)\n window.requestAnimationFrame = function(callback, element) {\n var currTime = new Date().getTime();\n var timeToCall = Math.max(0, 16 - (currTime - lastTime));\n var id = window.setTimeout(function() {\n callback(currTime + timeToCall);\n }, timeToCall);\n lastTime = currTime + timeToCall;\n return id;\n };\n\n if (!window.cancelAnimationFrame)\n window.cancelAnimationFrame = function(id) {\n clearTimeout(id);\n };\n\n // ------------------------------------------------------------------ can't/won't polyfill\n var features = [\n {\n name: \"canvas\",\n compatible: function() {\n return 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a/static/maps/reports_webapp/run_stats.js.map +++ b/static/maps/reports_webapp/run_stats.js.map @@ -1 +1 @@ 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days_in_month(month, year) {\n return new Date(year, month, 0).getDate();\n}\n\nfunction date_by_subtracting_days(date, days) {\n return new Date(\n date.getFullYear(),\n date.getMonth(),\n date.getDate() - days,\n date.getHours(),\n date.getMinutes(),\n date.getSeconds(),\n date.getMilliseconds()\n );\n}\n\nfunction date_by_subtracting_hours(date, hours) {\n return new Date(\n date.getFullYear(),\n date.getMonth(),\n date.getDate(),\n date.getHours() - hours,\n date.getMinutes(),\n date.getSeconds(),\n date.getMilliseconds()\n );\n}\n\n// Gets the utc time without minutes and seconds\nfunction get_utc_time_hours() {\n var date = new Date();\n return new Date(\n date.getUTCFullYear(),\n date.getUTCMonth(),\n date.getUTCDate(),\n date.getUTCHours(),\n 0,\n 0\n );\n}\n\n// Refreshes the page for more up to date information\nfunction refresh() {\n window.location.reload(true);\n}\n\n// This is commented out until we make Reports more responsive.\n// setTimeout(refresh, 60000); //1 minute = 60000 ms\n\nfunction create_chart(inp_data, name, time, title) {\n // Initialize starting variables\n var data = inp_data;\n\n var hours_array = [];\n var now = get_utc_time_hours();\n for (var i = 0; i < 24; i++) {\n hours_array.push(date_by_subtracting_hours(now, i));\n }\n\n var days_array = [];\n var now = get_utc_time_hours();\n for (var i = 0; i < 30; i++) {\n days_array.push(date_by_subtracting_days(now, i));\n }\n\n var margin = { top: 60, right: 30, bottom: 50, left: 60 };\n var width = 300;\n var barWidth = 0;\n if (time == \"hours\") {\n barWidth = width / 24;\n } else if (time == \"days\") {\n barWidth = width / 30;\n }\n var chart_width = width + margin.left + margin.right;\n\n var chart_zoom = 1.75;\n var height = 150;\n if (d3.max(data) != 0) {\n var zoom = height / d3.max(data);\n } else {\n var zoom = 1.0;\n }\n var chart_height = height + margin.top + margin.bottom;\n\n // Function for zooming in and out of charts\n function click() {\n var classes = d3.select(this).attr(\"class\");\n classes = classes.split(\" \");\n d3\n .selectAll(\".\" + classes[0])\n .filter(\".\" + classes[1])\n .style(\"cursor\", \"zoom-in\")\n .transition()\n .duration(750)\n .attr(\"height\", chart_height)\n .attr(\"width\", chart_width);\n\n d3\n .select(this)\n .style(\"cursor\", \"default\")\n .transition()\n .duration(750)\n .attr(\"height\", chart_height * chart_zoom)\n .attr(\"width\", chart_width * chart_zoom);\n }\n\n // Initialize all chart containers to have the correct height\n $(\".charts\").css(\"height\", chart_height * chart_zoom);\n\n // Create the chart object\n var chart = d3\n .select(\"#\" + name)\n .attr(\"width\", chart_width)\n .attr(\"height\", chart_height)\n .attr(\"preserveAspectRatio\", \"xMidYMin\")\n .attr(\"viewBox\", \"0 0 \" + chart_width + \" \" + chart_height)\n .on(\"click\", click);\n\n // Create bars on the chart and assosciate data with it\n var bar = chart\n .selectAll(\"g\")\n .data(data)\n .enter()\n .append(\"g\")\n .attr(\"transform\", function(d, i) {\n // Place the bar in the correct place\n var curr_margin = +margin.left;\n curr_margin += +(i * barWidth);\n return \"translate(\" + curr_margin + \",\" + margin.top + \")\";\n })\n .on(\"mouseenter\", function(d) {\n // Show tool tip\n var i = 1;\n var size = d;\n\n while (size >= 10) {\n size = size / 10;\n i++;\n }\n\n var wdth = i * 4 + 10;\n d3\n .select(d3.event.path[1])\n .select(\".tool_tip\")\n .select(\"text\")\n .attr(\n \"transform\",\n \"translate( \" +\n (margin.left - 5) +\n \", \" +\n (height - d * zoom + +margin.top + 10) +\n \" )\"\n )\n .attr(\"visibility\", \"visible\")\n .text(d);\n\n d3\n .select(d3.event.path[1])\n .select(\".tool_tip\")\n .attr(\"width\", wdth + \"px\")\n .attr(\"height\", \"15px\")\n .select(\"rect\")\n .attr(\n \"transform\",\n \"translate( \" +\n (+margin.left - wdth) +\n \", \" +\n (height - d * zoom + +margin.top) +\n \" )\"\n )\n .attr(\"width\", wdth + \"px\")\n .attr(\"height\", \"15px\")\n .attr(\"fill\", \"#ebd9b2\");\n })\n .on(\"mouseleave\", function(d) {\n // Remove tool tip\n d3\n .select(d3.event.path[1])\n .select(\".tool_tip\")\n .select(\"text\")\n .attr(\"visibility\", \"hidden\");\n\n d3\n .select(d3.event.path[1])\n .select(\".tool_tip\")\n .select(\"rect\")\n .attr(\"width\", \"0\")\n .attr(\"height\", \"0\")\n .attr(\"fill\", \"\")\n .text(d);\n });\n\n // Add a title to the chart\n chart\n .append(\"g\")\n .append(\"text\")\n .attr(\"class\", \"title\")\n .attr(\"text-anchor\", \"end\")\n .attr(\"transform\", function(e) {\n return \"translate( \" + width + \",15 )\";\n })\n .text(title);\n\n // Add an x axis line to the chart\n chart\n .append(\"g\")\n .attr(\"class\", \"axis\")\n .append(\"path\")\n .attr(\"class\", \"x\")\n .attr(\"d\", function(d) {\n var m_x = margin.left;\n var m_y = +margin.top + height;\n var l_x = m_x + width;\n var l_y = m_y;\n\n return \"M\" + m_x + \" \" + m_y + \" L \" + l_x + \" \" + l_y;\n });\n\n // Declare how high the y axis goes\n var y = d3.scale.linear().range([height, 0]);\n\n // Create a yAxis object\n var yAxis = d3.svg\n .axis()\n .scale(y)\n .orient(\"left\")\n .tickFormat(function(d) {\n return d3.round(d * d3.max(data), 0);\n });\n\n // Put the y axis on the chart\n chart\n .append(\"g\")\n .attr(\"class\", \"y axis\")\n .attr(\"id\", \"y_\" + name)\n .attr(\"text-anchor\", \"end\")\n .attr(\"transform\", \"translate( \" + margin.left + \",\" + margin.top + \")\")\n .call(yAxis)\n .select(\".domain\");\n\n // Put a title for y axis on chart\n chart\n .append(\"g\")\n .append(\"text\")\n .attr(\"class\", \"ax_title\")\n .attr(\"transform\", function(e) {\n var axis = d3.select(\"#y_\" + name).node();\n var left_pad =\n +margin.left - axis.getBoundingClientRect().width - 5;\n var top_pad =\n +margin.top + axis.getBoundingClientRect().height / 2 - 30;\n var trans =\n \"translate(\" + left_pad + \",\" + top_pad + \")rotate(-90)\";\n\n return trans;\n })\n .text(\"Number of Jobs\");\n\n // Add color to the chart's bars\n bar\n .append(\"rect\")\n .attr(\"y\", function(d) {\n return height - d * zoom;\n })\n .attr(\"height\", function(d) {\n return d * zoom;\n })\n .attr(\"width\", barWidth - 1);\n\n // Append x axis\n if (time == \"hours\") {\n // Append hour lines\n bar\n .append(\"line\")\n .attr(\"x1\", 0)\n .attr(\"y1\", 0)\n .attr(\"x2\", 0)\n .attr(\"y2\", 3)\n .attr(\"stroke\", \"black\")\n .attr(\"stroke-width\", 1)\n .attr(\"pointer-events\", \"none\")\n .attr(\"transform\", function(d, i) {\n return \"translate( \" + barWidth / 2 + \", \" + height + \")\";\n });\n\n // Append hour numbers\n bar\n .append(\"text\")\n .attr(\"fill\", \"rgb(0,0,0)\")\n .attr(\"transform\", \"translate( 10, \" + (height + 10) + \" )\")\n .text(function(d, i) {\n var time = \"0000\";\n\n if (hours_array[i].getHours() < 10) {\n time = \"0\" + String(hours_array[i].getHours());\n } else {\n time = hours_array[i].getHours();\n }\n\n return time;\n });\n\n // Append day lines\n var curr_day = \"\";\n var first = false;\n bar\n .append(\"line\")\n .attr(\"x1\", 0)\n .attr(\"y1\", 0)\n .attr(\"x2\", 0)\n .attr(\"y2\", function(d, i) {\n var _y2 = 0;\n\n if (hours_array[i].getDate() != curr_day) {\n if (!first) {\n _y2 = 27;\n first = true;\n } else {\n _y2 = 20;\n }\n\n curr_day = hours_array[i].getDate();\n }\n\n return _y2;\n })\n .attr(\"stroke\", \"black\")\n .attr(\"stroke-width\", 1)\n .attr(\"pointer-events\", \"none\")\n .attr(\"transform\", function(d, i) {\n return \"translate( 0, \" + height + \")\";\n });\n\n // Append day numbers\n curr_day = \"\";\n curr_day_text = \"\";\n first = false;\n bar\n .append(\"text\")\n .attr(\"fill\", \"rgb(0,0,0)\")\n .attr(\"pointer-events\", \"none\")\n .text(function(d, i) {\n var time = \"\";\n var locale = \"en-us\";\n\n if (hours_array[i].getDate() != curr_day_text) {\n time = String(\n hours_array[i].toLocaleString(locale, { month: \"long\" })\n );\n time += \" \" + String(hours_array[i].getDate());\n\n curr_day_text = hours_array[i].getDate();\n }\n\n return time;\n })\n .attr(\"transform\", function(d, i) {\n var text_height = height;\n var this_width = d3\n .select(this)\n .node()\n .getBBox().width;\n\n if (hours_array[i].getDate() != curr_day) {\n if (!first) {\n text_height += 26;\n first = true;\n } else {\n text_height += 18;\n }\n\n curr_day = hours_array[i].getDate();\n }\n\n return (\n \"translate( \" + (this_width + 2) + \", \" + text_height + \" )\"\n );\n });\n } else if (time == \"days\") {\n // Append day lines\n bar\n .append(\"line\")\n .attr(\"x1\", 0)\n .attr(\"y1\", 0)\n .attr(\"x2\", 0)\n .attr(\"y2\", 3)\n .attr(\"stroke\", \"black\")\n .attr(\"stroke-width\", 1)\n .attr(\"pointer-events\", \"none\")\n .attr(\"transform\", function(d, i) {\n return \"translate( \" + barWidth / 2 + \", \" + height + \")\";\n });\n\n // Append day numbers\n bar\n .append(\"text\")\n .attr(\"fill\", \"rgb(0,0,0)\")\n .attr(\"transform\", \"translate( 9, \" + (height + 10) + \" )\")\n .text(function(d, i) {\n var time = \"0000\";\n\n if (days_array[i].getDate() < 10) {\n time = \"0\" + String(days_array[i].getDate());\n } else {\n time = days_array[i].getDate();\n }\n\n return time;\n });\n\n // Append month lines\n var curr_month = \"\";\n var first = false;\n bar\n .append(\"line\")\n .attr(\"x1\", 0)\n .attr(\"y1\", 0)\n .attr(\"x2\", 0)\n .attr(\"y2\", function(d, i) {\n var _y2 = 0;\n\n if (days_array[i].getMonth() != curr_month) {\n if (!first) {\n _y2 = 27;\n first = true;\n } else {\n _y2 = 20;\n }\n\n curr_month = days_array[i].getMonth();\n }\n\n return _y2;\n })\n .attr(\"stroke\", \"black\")\n .attr(\"stroke-width\", 1)\n .attr(\"pointer-events\", \"none\")\n .attr(\"transform\", function(d, i) {\n return \"translate( 0, \" + height + \")\";\n });\n\n // Append month numbers\n curr_month = \"\";\n curr_month_text = \"\";\n first = false;\n bar\n .append(\"text\")\n .attr(\"fill\", \"rgb(0,100,0)\")\n .attr(\"pointer-events\", \"none\")\n .text(function(d, i) {\n var time = \"\";\n var locale = \"en-us\";\n\n if (days_array[i].getMonth() != curr_month_text) {\n time = String(\n days_array[i].toLocaleString(locale, { month: \"long\" })\n );\n time += \" \" + String(days_array[i].getFullYear());\n\n curr_month_text = days_array[i].getMonth();\n }\n\n return time;\n })\n .attr(\"transform\", function(d, i) {\n var text_height = height;\n var this_width = d3\n .select(this)\n .node()\n .getBBox().width;\n\n if (days_array[i].getMonth() != curr_month) {\n if (!first) {\n text_height += 26;\n first = true;\n } else {\n text_height += 18;\n }\n\n curr_month = days_array[i].getMonth();\n }\n\n return (\n \"translate( \" + (this_width + 2) + \", \" + text_height + \" )\"\n );\n });\n }\n\n // Put an invisible tool tip on the chart\n chart\n .append(\"g\")\n .attr(\"class\", \"tool_tip\")\n .append(\"rect\");\n chart.select(\".tool_tip\").append(\"text\");\n\n // Initialize initial zoomed charts\n if (name == \"jc_dy_chart\" || name == \"jc_hr_chart\") {\n d3\n .select(\"#\" + name)\n .attr(\"height\", chart_height * chart_zoom)\n .attr(\"width\", chart_width * chart_zoom)\n .style(\"cursor\", \"default\");\n }\n}\n\n//============================================================================================================\n\nfunction create_histogram(inp_data, name, title) {\n // Initialize initial variables\n // inp_data is an array of numbers that are the amount of minutes per run\n var data = inp_data;\n\n var chart_zoom = 1.75;\n var margin = { top: 60, right: 30, bottom: 50, left: 60 };\n\n var height = 150;\n var chart_height = height + margin.top + margin.bottom;\n\n var width = 300;\n var chart_width = width + margin.left + margin.right;\n\n // Cereate x axis metadata\n // Used for x axis, histogram creation, and bar initialization\n var x = d3.scale\n .linear()\n .domain([0, d3.max(data)])\n .range([0, width]);\n\n // Generate a histogram using twenty uniformly-spaced bins.\n var data = d3.layout.histogram().bins(x.ticks(20))(data);\n\n // Create an array of the sizes of the bars\n var lengths = [];\n for (var i = 0; i < data.length; i++) {\n lengths.push(data[i].length);\n }\n\n // Find the amount needed to magnify the bars\n if (d3.max(data) != 0) {\n var zoom = height / d3.max(lengths);\n } else {\n var zoom = 1.0;\n }\n\n // Create y axis metadata\n // Used for y axis and bar initialization\n var y = d3.scale\n .linear()\n .domain([\n 0,\n d3.max(data, function(d) {\n return d.y;\n })\n ])\n .range([height, 0]);\n\n // Function for zooming in and out of charts\n function click() {\n var classes = d3.select(this).attr(\"class\");\n classes = classes.split(\" \");\n d3\n .selectAll(\".\" + classes[0])\n .filter(\".\" + classes[1])\n .style(\"cursor\", \"zoom-in\")\n .transition()\n .duration(750)\n .attr(\"height\", chart_height)\n .attr(\"width\", chart_width);\n\n d3\n .select(this)\n .style(\"cursor\", \"default\")\n .transition()\n .duration(750)\n .attr(\"height\", chart_height * chart_zoom)\n .attr(\"width\", chart_width * chart_zoom);\n }\n\n // Formatter for x axis times (converting minutes to HH:MM).\n var formatMinutes = function(d) {\n var hours = Math.floor(d / 60),\n minutes = Math.floor(d - hours * 60);\n\n if (hours < 10) {\n hours = \"0\" + hours;\n }\n if (minutes < 10) {\n minutes = \"0\" + minutes;\n }\n\n return hours + \":\" + minutes;\n };\n\n // Create a chart object\n var chart = d3\n .select(\"#\" + name)\n .attr(\"viewBox\", \"0 0 \" + chart_width + \" \" + chart_height)\n .attr(\"width\", chart_width)\n .attr(\"height\", chart_height)\n .attr(\"preserveAspectRatio\", \"xMidYMin\")\n .on(\"click\", click);\n\n // Put title on chart\n chart\n .append(\"g\")\n .append(\"text\")\n .attr(\"class\", \"title\")\n .attr(\"transform\", function(e) {\n return \"translate( \" + width + \",15 )\";\n })\n .text(title);\n\n // Put bars on chart\n var bar = chart\n .selectAll(\".bar\")\n .data(data)\n .enter()\n .append(\"g\")\n .attr(\"class\", \"bar\")\n .attr(\"transform\", function(d) {\n return (\n \"translate(\" +\n (+x(d.x) + +margin.left) +\n \",\" +\n (+y(d.y) + +margin.top) +\n \")\"\n );\n })\n .on(\"mouseenter\", function(d) {\n // Show tool tip\n var i = 0,\n size = d.length;\n\n while (size >= 1) {\n size = size / 10;\n i++;\n }\n var wdth = i * 4 + 10;\n d3\n .select(d3.event.path[1])\n .select(\".tool_tip\")\n .select(\"text\")\n .attr(\n \"transform\",\n \"translate( \" +\n (margin.left - 5) +\n \", \" +\n (height - d.length * zoom + +margin.top + 10) +\n \" )\"\n )\n .attr(\"visibility\", \"visible\")\n .text(d.length);\n\n d3\n .select(d3.event.path[1])\n .select(\".tool_tip\")\n .attr(\"width\", wdth + \"px\")\n .attr(\"height\", \"15px\")\n .select(\"rect\")\n .attr(\n \"transform\",\n \"translate( \" +\n (+margin.left - wdth) +\n \", \" +\n (height - d.length * zoom + +margin.top) +\n \" )\"\n )\n .attr(\"width\", wdth + \"px\")\n .attr(\"height\", \"15px\")\n .attr(\"fill\", \"#ebd9b2\");\n })\n .on(\"mouseleave\", function(d) {\n // Remove tool tip\n d3\n .select(d3.event.path[1])\n .select(\".tool_tip\")\n .select(\"text\")\n .attr(\"visibility\", \"hidden\");\n\n d3\n .select(d3.event.path[1])\n .select(\".tool_tip\")\n .select(\"rect\")\n .attr(\"width\", \"0\")\n .attr(\"height\", \"0\")\n .attr(\"fill\", \"\");\n });\n\n // Create bar width\n var bar_x;\n if (data[0] == undefined) {\n bar_x = 1;\n } else {\n bar_x = x(data[0].dx);\n }\n\n // Add color to bar\n bar\n .append(\"rect\")\n .attr(\"x\", 1)\n .attr(\"width\", bar_x - 1)\n .attr(\"height\", function(d) {\n return height - y(d.y);\n });\n\n // Create x axis\n var xAxis = d3.svg\n .axis()\n .scale(x)\n .orient(\"bottom\")\n .tickFormat(formatMinutes);\n\n // Add x axis to chart\n chart\n .append(\"g\")\n .attr(\"class\", \"x axis\")\n .attr(\"id\", \"x_\" + name)\n .attr(\n \"transform\",\n \"translate( \" + margin.left + \",\" + (+height + +margin.top) + \")\"\n )\n .call(xAxis);\n\n // Add a title to the x axis\n chart\n .append(\"g\")\n .append(\"text\")\n .attr(\"class\", \"ax_title\")\n .attr(\"transform\", function(e) {\n var axis = d3.select(\"#x_\" + name).node();\n var left_pad =\n +margin.left + axis.getBoundingClientRect().width / 2 + 30;\n var top_pad =\n +margin.top + height + axis.getBoundingClientRect().height + 10;\n var trans = \"translate(\" + left_pad + \",\" + top_pad + \")\";\n\n return trans;\n })\n .text(\"ETA - hrs:mins\");\n\n // Create y axis\n var yAxis = d3.svg\n .axis()\n .scale(y)\n .orient(\"left\");\n\n // Add y axis to chart\n chart\n .append(\"g\")\n .attr(\"class\", \"y axis\")\n .attr(\"id\", \"y_\" + name)\n .attr(\"transform\", \"translate( \" + margin.left + \",\" + margin.top + \")\")\n .call(yAxis);\n\n // Add a title to the y axis\n chart\n .append(\"g\")\n .append(\"text\")\n .attr(\"class\", \"ax_title\")\n .attr(\"transform\", function(e) {\n var axis = d3.select(\"#y_\" + name).node();\n var left_pad =\n +margin.left - axis.getBoundingClientRect().width - 5;\n var top_pad =\n +margin.top + axis.getBoundingClientRect().height / 2 - 30;\n var trans =\n \"translate(\" + left_pad + \",\" + top_pad + \")rotate(-90)\";\n\n return trans;\n })\n .text(\"Number of Jobs\");\n\n // Put an invisible tool tip on the chart\n chart\n .append(\"g\")\n .attr(\"class\", \"tool_tip\")\n .append(\"rect\");\n chart.select(\".tool_tip\").append(\"text\");\n}\n"]} \ No newline at end of file +{"version":3,"sources":[],"names":[],"mappings":"","file":"../../scripts/reports_webapp/run_stats.js","sourcesContent":[]} \ No newline at end of file diff --git a/static/maps/ui/autocom_tagging.js.map b/static/maps/ui/autocom_tagging.js.map index 1a07221cd89..51fa51ae70e 100644 --- a/static/maps/ui/autocom_tagging.js.map +++ b/static/maps/ui/autocom_tagging.js.map @@ -1 +1 @@ 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from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js\n// Uses AMD or browser globals to create a jQuery plugin.\n(function(factory) {\n if (typeof define === \"function\" && define.amd) {\n //TODO: So...this turns out to be an all or nothing thing. If I load jQuery in the define below, it will\n // (of course) wipe the old jquery *and all the plugins loaded into it*. So the define below *is still\n // relying on jquery being loaded globally* in order to preserve plugins.\n define([\"jquery\"], factory);\n } else {\n // Browser globals\n factory(jQuery);\n }\n})(function(jQuery) {\n \"use_strict\";\n\n var $ = jQuery;\n\n // ============================================================================\n /**\n* JQuery extension for tagging with autocomplete.\n* @author: Jeremy Goecks\n* @require: jquery.autocomplete plugin\n*/\n //\n // Initialize \"tag click functions\" for tags.\n //\n function init_tag_click_function(tag_elt, click_func) {\n $(tag_elt)\n .find(\".tag-name\")\n .each(function() {\n $(this).click(function() {\n var tag_str = $(this).text();\n var tag_name_and_value = tag_str.split(\":\");\n click_func(tag_name_and_value[0], tag_name_and_value[1]);\n return true;\n });\n });\n }\n\n jQuery.fn.autocomplete_tagging = function(options) {\n var defaults = {\n get_toggle_link_text_fn: function(tags) {\n var text = \"\";\n var num_tags = _.size(tags);\n if (num_tags > 0) {\n text = num_tags + (num_tags > 1 ? \" Tags\" : \" Tag\");\n } else {\n text = \"Add tags\";\n }\n return text;\n },\n tag_click_fn: function(name, value) {},\n editable: true,\n input_size: 20,\n in_form: false,\n tags: {},\n use_toggle_link: true,\n item_id: \"\",\n add_tag_img: \"\",\n add_tag_img_rollover: \"\",\n delete_tag_img: \"\",\n ajax_autocomplete_tag_url: \"\",\n ajax_retag_url: \"\",\n ajax_delete_tag_url: \"\",\n ajax_add_tag_url: \"\"\n };\n\n var settings = jQuery.extend(defaults, options);\n\n //\n // Initalize object's elements.\n //\n\n // Get elements for this object. 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Roll back changes and show alert.\n new_tag_button.remove();\n delete settings.tags[tag_name_and_value[0]];\n var new_text = settings.get_toggle_link_text_fn(\n settings.tags\n );\n toggle_link.text(new_text);\n alert(\"Add tag failed\");\n },\n success: function() {\n // Flush autocomplete cache because it's not out of date.\n // TODO: in the future, we could remove the particular item\n // that was chosen from the cache rather than flush it.\n zz.data(\"autocompleter\").cacheFlush();\n }\n });\n\n return false;\n }\n });\n\n // Add autocomplete to input.\n var format_item_func = function(\n key,\n row_position,\n num_rows,\n value,\n search_term\n ) {\n var tag_name_and_value = value.split(\":\");\n return tag_name_and_value.length === 1\n ? tag_name_and_value[0]\n : tag_name_and_value[1];\n };\n var autocomplete_options = {\n selectFirst: false,\n formatItem: format_item_func,\n autoFill: false,\n highlight: false\n };\n tag_input_field.autocomplete_verheul(\n settings.ajax_autocomplete_tag_url,\n autocomplete_options\n );\n\n // Initialize delete tag images for current tags.\n this_obj.find(\".delete-tag-img\").each(function() {\n init_delete_tag_image($(this));\n });\n\n // Initialize tag click function.\n init_tag_click_function($(this), settings.tag_click_fn);\n\n // Initialize \"add tag\" button.\n add_tag_button.click(function() {\n $(this).hide();\n\n // Clicking on button is the same as clicking on the tag area.\n tag_area.click();\n return false;\n });\n\n //\n // Set up tag area interactions; these are needed only if tags are editable.\n //\n if (settings.editable) {\n // When the tag area blurs, go to \"view tag\" mode.\n tag_area.bind(\"blur\", function(e) {\n if (_.size(settings.tags) > 0) {\n add_tag_button.show();\n tag_input_field.hide();\n tag_area.removeClass(\"active-tag-area\");\n // tag_area.addClass(\"tooltip\");\n } else {\n // No tags, so do nothing to ensure that input is still visible.\n }\n });\n\n // On click, enable user to add tags.\n tag_area.click(function(e) {\n var is_active = $(this).hasClass(\"active-tag-area\");\n\n // If a \"delete image\" object was pressed and area is inactive, do nothing.\n if ($(e.target).hasClass(\"delete-tag-img\") && !is_active) {\n return false;\n }\n\n // If a \"tag name\" object was pressed and area is inactive, do nothing.\n if ($(e.target).hasClass(\"tag-name\") && !is_active) {\n return false;\n }\n\n // Remove tooltip.\n // $(this).removeClass(\"tooltip\");\n\n // Hide add tag button, show tag_input field. Change background to show\n // area is active.\n $(this).addClass(\"active-tag-area\");\n add_tag_button.hide();\n tag_input_field.show();\n tag_input_field.focus();\n\n // Add handler to document that will call blur when the tag area is blurred;\n // a tag area is blurred when a user clicks on an element outside the area.\n var handle_document_click = function(e) {\n var check_click = function(tag_area, target) {\n var tag_area_id = tag_area.attr(\"id\");\n // Blur the tag area if the element clicked on is not in the tag area.\n if (target !== tag_area) {\n tag_area.blur();\n $(window).unbind(\"click.tagging_blur\");\n $(this).addClass(\"tooltip\");\n }\n };\n check_click(tag_area, $(e.target));\n };\n // TODO: we should attach the click handler to all frames in order to capture\n // clicks outside the frame that this element is in.\n //window.parent.document.onclick = handle_document_click;\n //var temp = $(window.parent.document.body).contents().find(\"iframe\").html();\n //alert(temp);\n //$(document).parent().click(handle_document_click);\n $(window).bind(\"click.tagging_blur\", handle_document_click);\n\n return false;\n });\n }\n\n // If using toggle link, hide the tag area. Otherwise, show the tag area.\n if (settings.use_toggle_link) {\n tag_area.hide();\n }\n\n //\n // Helper functions.\n //\n\n //\n // Collapse tag name + value into a single string.\n //\n function build_tag_str(tag_name, tag_value) {\n return tag_name + (tag_value ? \":\" + tag_value : \"\");\n }\n\n // Initialize a \"delete tag image\": when click, delete tag from UI and send delete request to server.\n function init_delete_tag_image(delete_img) {\n $(delete_img).mouseenter(function() {\n $(this).attr(\"src\", settings.delete_tag_img_rollover);\n });\n $(delete_img).mouseleave(function() {\n $(this).attr(\"src\", settings.delete_tag_img);\n });\n $(delete_img).click(function() {\n // Tag button is image's parent.\n var tag_button = $(this).parent();\n\n // Get tag name, value.\n var tag_name_elt = tag_button.find(\".tag-name\").eq(0);\n var tag_str = tag_name_elt.text();\n var tag_name_and_value = tag_str.split(\":\");\n var tag_name = tag_name_and_value[0];\n var tag_value = tag_name_and_value[1];\n\n var prev_button = tag_button.prev();\n tag_button.remove();\n\n // Remove tag from local list for consistency.\n delete settings.tags[tag_name];\n\n // Update toggle link text.\n var new_text = settings.get_toggle_link_text_fn(settings.tags);\n toggle_link.text(new_text);\n\n // Delete tag.\n $.ajax({\n url: settings.ajax_delete_tag_url,\n data: { tag_name: tag_name },\n error: function() {\n // Failed. Roll back changes and show alert.\n settings.tags[tag_name] = tag_value;\n if (prev_button.hasClass(\"tag-button\")) {\n prev_button.after(tag_button);\n } else {\n tag_area.prepend(tag_button);\n }\n alert(\"Remove tag failed\");\n\n toggle_link.text(\n settings.get_toggle_link_text_fn(settings.tags)\n );\n\n // TODO: no idea why it's necessary to set this up again.\n delete_img.mouseenter(function() {\n $(this).attr(\n \"src\",\n settings.delete_tag_img_rollover\n );\n });\n delete_img.mouseleave(function() {\n $(this).attr(\"src\", settings.delete_tag_img);\n });\n },\n success: function() {}\n });\n\n return true;\n });\n }\n\n //\n // Function that builds a tag button.\n //\n function build_tag_button(tag_str) {\n // Build \"delete tag\" image.\n var delete_img = $(\"Import Galaxy workflow\" +\n \"\" +\n \"\" +\n \"\" +\n \"
\" +\n \"\" +\n \"\" +\n \"\" +\n \"\" +\n \" Visit myExperiment\" +\n \"\" +\n \"\" +\n \"Click the link above to visit myExperiment and browse for Galaxy workflows.\" +\n \"\" +\n \"\" +\n \"\")\n .attr(\"src\", settings.delete_tag_img)\n .addClass(\"delete-tag-img\");\n init_delete_tag_image(delete_img);\n\n // Build tag button.\n var tag_name_elt = $(\"\")\n .text(tag_str)\n .addClass(\"tag-name\");\n tag_name_elt.click(function() {\n var tag_name_and_value = tag_str.split(\":\");\n settings.tag_click_fn(\n tag_name_and_value[0],\n tag_name_and_value[1]\n );\n return true;\n });\n\n var tag_button = $(\"\").addClass(\"tag-button\");\n tag_button.append(tag_name_elt);\n // Allow delete only if element is editable.\n if (settings.editable) {\n tag_button.append(delete_img);\n }\n\n return tag_button;\n }\n };\n\n // ============================================================================\n return init_tag_click_function;\n});\n"]} \ No newline at end of file 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from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js\n// Uses AMD or browser globals to create a jQuery plugin.\n(function(factory) {\n if (typeof define === \"function\" && define.amd) {\n //TODO: So...this turns out to be an all or nothing thing. If I load jQuery in the define below, it will\n // (of course) wipe the old jquery *and all the plugins loaded into it*. So the define below *is still\n // relying on jquery being loaded globally* in order to preserve plugins.\n define([\"jquery\"], factory);\n } else {\n // Browser globals\n factory(jQuery);\n }\n})(function(jQuery) {\n \"use_strict\";\n\n var $ = jQuery;\n\n // ============================================================================\n /**\n* JQuery extension for tagging with autocomplete.\n* @author: Jeremy Goecks\n* @require: jquery.autocomplete plugin\n*/\n //\n // Initialize \"tag click functions\" for tags.\n //\n function init_tag_click_function(tag_elt, click_func) {\n $(tag_elt)\n .find(\".tag-name\")\n .each(function() {\n $(this).click(function() {\n var tag_str = $(this).text();\n var tag_name_and_value = tag_str.split(\":\");\n click_func(tag_name_and_value[0], tag_name_and_value[1]);\n return true;\n });\n });\n }\n\n jQuery.fn.autocomplete_tagging = function(options) {\n var defaults = {\n get_toggle_link_text_fn: function(tags) {\n var text = \"\";\n var num_tags = _.size(tags);\n if (num_tags > 0) {\n text = num_tags + (num_tags > 1 ? \" Tags\" : \" Tag\");\n } else {\n text = \"Add tags\";\n }\n return text;\n },\n tag_click_fn: function(name, value) {},\n editable: true,\n input_size: 20,\n in_form: false,\n tags: {},\n use_toggle_link: true,\n item_id: \"\",\n add_tag_img: \"\",\n add_tag_img_rollover: \"\",\n delete_tag_img: \"\",\n ajax_autocomplete_tag_url: \"\",\n ajax_retag_url: \"\",\n ajax_delete_tag_url: \"\",\n ajax_add_tag_url: \"\"\n };\n\n var settings = jQuery.extend(defaults, options);\n\n //\n // Initalize object's elements.\n //\n\n // Get elements for this object. For this_obj, assume the last element with the id is the \"this\"; this is somewhat of a hack to address the problem\n // that there may be two tagging elements for a single item if there are both community and individual tags for an element.\n var this_obj = $(this);\n var tag_area = this_obj.find(\".tag-area\");\n var toggle_link = this_obj.find(\".toggle-link\");\n var tag_input_field = this_obj.find(\".tag-input\");\n var add_tag_button = this_obj.find(\".add-tag-button\");\n\n // Initialize toggle link.\n toggle_link.click(function() {\n // Take special actions depending on whether toggle is showing or hiding link.\n var after_toggle_fn;\n if (tag_area.is(\":hidden\")) {\n after_toggle_fn = function() {\n // If there are no tags, go right to editing mode by generating a click on the area.\n var num_tags = $(this).find(\".tag-button\").length;\n if (num_tags === 0) {\n tag_area.click();\n }\n };\n } else {\n after_toggle_fn = function() {\n tag_area.blur();\n };\n }\n tag_area.slideToggle(\"fast\", after_toggle_fn);\n return $(this);\n });\n\n // Initialize tag input field.\n if (settings.editable) {\n tag_input_field.hide();\n }\n tag_input_field.keyup(function(e) {\n if (e.keyCode === 27) {\n // Escape key\n $(this).trigger(\"blur\");\n } else if (\n e.keyCode === 13 || // Return Key\n e.keyCode === 188 || // Comma\n e.keyCode === 32 // Space\n ) {\n //\n // Check input.\n //\n\n var new_value = this.value;\n\n // Suppress space after a \":\"\n if (new_value.indexOf(\": \", new_value.length - 2) !== -1) {\n this.value = new_value.substring(0, new_value.length - 1);\n return false;\n }\n\n // Remove trigger keys from input.\n if (e.keyCode === 188 || e.keyCode === 32) {\n new_value = new_value.substring(0, new_value.length - 1);\n }\n\n // Trim whitespace.\n new_value = $.trim(new_value);\n\n // Too short?\n if (new_value.length < 2) {\n return false;\n }\n\n //\n // New tag OK - apply it.\n //\n\n this.value = \"\"; // Reset text field now that tag is being added\n\n // Add button for tag after all other tag buttons.\n var new_tag_button = build_tag_button(new_value);\n var tag_buttons = tag_area.children(\".tag-button\");\n if (tag_buttons.length !== 0) {\n var last_tag_button = tag_buttons.slice(\n tag_buttons.length - 1\n );\n last_tag_button.after(new_tag_button);\n } else {\n tag_area.prepend(new_tag_button);\n }\n\n // Add tag to internal list.\n var tag_name_and_value = new_value.split(\":\");\n settings.tags[tag_name_and_value[0]] = tag_name_and_value[1];\n\n // Update toggle link text.\n var new_text = settings.get_toggle_link_text_fn(settings.tags);\n toggle_link.text(new_text);\n\n // Commit tag to server.\n var zz = $(this);\n $.ajax({\n url: settings.ajax_add_tag_url,\n data: { new_tag: new_value },\n error: function() {\n // Failed. Roll back changes and show alert.\n new_tag_button.remove();\n delete settings.tags[tag_name_and_value[0]];\n var new_text = settings.get_toggle_link_text_fn(\n settings.tags\n );\n toggle_link.text(new_text);\n alert(\"Add tag failed\");\n },\n success: function() {\n // Flush autocomplete cache because it's not out of date.\n // TODO: in the future, we could remove the particular item\n // that was chosen from the cache rather than flush it.\n zz.data(\"autocompleter\").cacheFlush();\n }\n });\n\n return false;\n }\n });\n\n // Add autocomplete to input.\n var format_item_func = function(\n key,\n row_position,\n num_rows,\n value,\n search_term\n ) {\n var tag_name_and_value = value.split(\":\");\n return tag_name_and_value.length === 1\n ? tag_name_and_value[0]\n : tag_name_and_value[1];\n };\n var autocomplete_options = {\n selectFirst: false,\n formatItem: format_item_func,\n autoFill: false,\n highlight: false\n };\n tag_input_field.autocomplete_verheul(\n settings.ajax_autocomplete_tag_url,\n autocomplete_options\n );\n\n // Initialize delete tag images for current tags.\n this_obj.find(\".delete-tag-img\").each(function() {\n init_delete_tag_image($(this));\n });\n\n // Initialize tag click function.\n init_tag_click_function($(this), settings.tag_click_fn);\n\n // Initialize \"add tag\" button.\n add_tag_button.click(function() {\n $(this).hide();\n\n // Clicking on button is the same as clicking on the tag area.\n tag_area.click();\n return false;\n });\n\n //\n // Set up tag area interactions; these are needed only if tags are editable.\n //\n if (settings.editable) {\n // When the tag area blurs, go to \"view tag\" mode.\n tag_area.bind(\"blur\", function(e) {\n if (_.size(settings.tags) > 0) {\n add_tag_button.show();\n tag_input_field.hide();\n tag_area.removeClass(\"active-tag-area\");\n // tag_area.addClass(\"tooltip\");\n } else {\n // No tags, so do nothing to ensure that input is still visible.\n }\n });\n\n // On click, enable user to add tags.\n tag_area.click(function(e) {\n var is_active = $(this).hasClass(\"active-tag-area\");\n\n // If a \"delete image\" object was pressed and area is inactive, do nothing.\n if ($(e.target).hasClass(\"delete-tag-img\") && !is_active) {\n return false;\n }\n\n // If a \"tag name\" object was pressed and area is inactive, do nothing.\n if ($(e.target).hasClass(\"tag-name\") && !is_active) {\n return false;\n }\n\n // Remove tooltip.\n // $(this).removeClass(\"tooltip\");\n\n // Hide add tag button, show tag_input field. Change background to show\n // area is active.\n $(this).addClass(\"active-tag-area\");\n add_tag_button.hide();\n tag_input_field.show();\n tag_input_field.focus();\n\n // Add handler to document that will call blur when the tag area is blurred;\n // a tag area is blurred when a user clicks on an element outside the area.\n var handle_document_click = function(e) {\n var check_click = function(tag_area, target) {\n var tag_area_id = tag_area.attr(\"id\");\n // Blur the tag area if the element clicked on is not in the tag area.\n if (target !== tag_area) {\n tag_area.blur();\n $(window).unbind(\"click.tagging_blur\");\n $(this).addClass(\"tooltip\");\n }\n };\n check_click(tag_area, $(e.target));\n };\n // TODO: we should attach the click handler to all frames in order to capture\n // clicks outside the frame that this element is in.\n //window.parent.document.onclick = handle_document_click;\n //var temp = $(window.parent.document.body).contents().find(\"iframe\").html();\n //alert(temp);\n //$(document).parent().click(handle_document_click);\n $(window).bind(\"click.tagging_blur\", handle_document_click);\n\n return false;\n });\n }\n\n // If using toggle link, hide the tag area. 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Register as an anonymous module.\n define([\"jquery\"], factory);\n } else {\n // Browser globals\n factory(jQuery);\n }\n})(function($) {\n //==============================================================================\n /**\n\t * Template function that produces a bootstrap dropdown to replace the\n\t * vanilla HTML select input. Pass in an array of options and an initial selection:\n\t * $( '.my-div' ).append( dropDownSelect( [ 'option1', 'option2' ], 'option2' );\n\t *\n\t * When the user changes the selected option a 'change.dropdown-select' event will\n\t * fire with both the jq event and the new selection text as arguments.\n\t *\n\t * Get the currently selected choice using:\n\t * var userChoice = $( '.my-div .dropdown-select .dropdown-select-selected' ).text();\n\t *\n\t */\n function dropDownSelect(options, selected) {\n // replacement for vanilla select element using bootstrap dropdowns instead\n selected = selected || (!_.isEmpty(options) ? options[0] : \"\");\n var $select = $(\n [\n '',\n '\",\n \"\"\n ].join(\"\\n\")\n );\n\n // if there's only one option, do not style/create as buttons, dropdown - use simple span\n // otherwise, a dropdown displaying the current selection\n if (options && options.length > 1) {\n $select\n .find(\"button\")\n .addClass(\"dropdown-toggle\")\n .attr(\"data-toggle\", \"dropdown\")\n .append(' ');\n $select.append(\n [\n '\"\n ].join(\"\\n\")\n );\n }\n\n // trigger 'change.dropdown-select' when a new selection is made using the dropdown\n function selectThis(event) {\n var $this = $(this),\n $select = $this.parents(\".dropdown-select\"),\n newSelection = $this.text();\n $select.find(\".dropdown-select-selected\").text(newSelection);\n $select.trigger(\"change.dropdown-select\", newSelection);\n }\n\n $select.find(\"a\").click(selectThis);\n return $select;\n }\n\n //==============================================================================\n /**\n * Creates a three part bootstrap button group (key, op, value) meant to\n * allow the user control of filters (e.g. { key: 'name', op: 'contains', value: 'my_history' })\n *\n * Each field uses a dropDownSelect (from ui.js) to allow selection\n * (with the 'value' field appearing as an input when set to do so).\n *\n * Any change or update in any of the fields will trigger a 'change.filter-control'\n 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\"filter-control\";\n\n /** parses options, sets up instance vars, and does initial render */\n FilterControl.prototype.init = function _init(element, options) {\n options = options || { filters: [] };\n this.$element = $(element).addClass(\"filter-control btn-group\");\n this.options = jQuery.extend(true, {}, this.defaults, options);\n\n this.currFilter = this.options.filters[0];\n return this.render();\n };\n\n /** render (or re-render) the controls on the element */\n FilterControl.prototype.render = function _render() {\n this.$element\n .empty()\n .append([\n this._renderKeySelect(),\n this._renderOpSelect(),\n this._renderValueInput()\n ]);\n return this;\n };\n\n /** render the key dropDownSelect, bind a change event to it, and return it */\n FilterControl.prototype._renderKeySelect = function __renderKeySelect() {\n var filterControl = this;\n var keys = this.options.filters.map(function(filter) {\n return filter.key;\n });\n this.$keySelect = dropDownSelect(keys, this.currFilter.key)\n .addClass(\"filter-control-key\")\n .on(\"change.dropdown-select\", function(event, selection) {\n filterControl.currFilter = _.findWhere(\n filterControl.options.filters,\n { key: selection }\n );\n // when the filter/key changes, re-render the control entirely\n filterControl.render()._triggerChange();\n });\n return this.$keySelect;\n };\n\n /** render the op dropDownSelect, bind a change event to it, and return it */\n FilterControl.prototype._renderOpSelect = function __renderOpSelect() {\n var filterControl = this,\n ops = this.currFilter.ops;\n //TODO: search for currOp in avail. ops: use that for selected if there; otherwise: first op\n this.$opSelect = dropDownSelect(ops, ops[0])\n .addClass(\"filter-control-op\")\n .on(\"change.dropdown-select\", function(event, selection) {\n filterControl._triggerChange();\n });\n return this.$opSelect;\n };\n\n /** render the value control, bind a change event to it, and return it */\n 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Register as an anonymous module.\n define([\"jquery\"], factory);\n } else {\n // Browser globals\n factory(jQuery);\n }\n})(function($) {\n //==============================================================================\n /**\n\t * Template function that produces a bootstrap dropdown to replace the\n\t * vanilla HTML select input. 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the given index and set button html */\n ModeButton.prototype._setModeByIndex = function _setModeByIndex(index) {\n var newMode = this.options.modes[index];\n if (!newMode) {\n throw new Error(\"mode index not found: \" + index);\n }\n this.currModeIndex = index;\n if (newMode.html) {\n this.$element.html(newMode.html);\n }\n return this;\n };\n\n // ---- public interface\n /** get the current mode object (not just the mode name) */\n ModeButton.prototype.currentMode = function currentMode() {\n return this.options.modes[this.currModeIndex];\n };\n /** return the mode key of the current mode */\n ModeButton.prototype.current = function current() {\n // sugar for returning mode name\n return this.currentMode().mode;\n };\n /** get the mode with the given modeKey or the current mode if modeKey is undefined */\n ModeButton.prototype.getMode = function getMode(modeKey) {\n if (!modeKey) {\n return this.currentMode();\n }\n return this.options.modes[this._getModeIndex(modeKey)];\n };\n /** T/F if the button has the given mode */\n ModeButton.prototype.hasMode = function hasMode(modeKey) {\n try {\n return !!this.getMode(modeKey);\n } catch (err) {}\n return false;\n };\n /** set the current mode to the mode with the given name */\n ModeButton.prototype.setMode = function setMode(modeKey) {\n return this._setModeByIndex(this._getModeIndex(modeKey));\n };\n /** reset to the initial mode */\n ModeButton.prototype.reset = function reset() {\n this.currModeIndex = 0;\n if (this.options.initialMode) {\n this.currModeIndex = this._getModeIndex(this.options.initialMode);\n }\n return this._setModeByIndex(this.currModeIndex);\n };\n /** manually call the click handler of the given mode */\n ModeButton.prototype.callModeFn = function callModeFn(modeKey) {\n var modeFn = this.getMode(modeKey).onclick;\n if (modeFn && $.type(modeFn === \"function\")) {\n // call with the element as context (std jquery pattern)\n return modeFn.call(this.$element.get(0));\n }\n return undefined;\n 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from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js\n// Uses AMD or browser globals to create a jQuery plugin.\n(function(factory) {\n if (typeof define === \"function\" && define.amd) {\n //TODO: So...this turns out to be an all or nothing thing. If I load jQuery in the define below, it will\n // (of course) wipe the old jquery *and all the plugins loaded into it*. So the define below *is still\n // relying on jquery being loaded globally* in order to preserve plugins.\n define([], factory);\n } else {\n // Browser globals\n factory(jQuery);\n }\n})(function() {\n /** Multi 'mode' button (or any element really) that changes the html\n * contents of itself when clicked. Pass in an ordered list of\n * objects with 'html' and (optional) onclick functions.\n *\n * When clicked in a particular node, the onclick function will\n * be called (with the element as this) and the element will\n * switch to the next mode, replacing its html content with\n * that mode's html.\n *\n * If there is no next mode, the element will switch back to\n * the first mode.\n * @example:\n * $( '.myElement' ).modeButton({\n * modes : [\n * {\n * mode: 'bler',\n * html: 'Bler
',\n * onclick : function(){\n * $( 'body' ).css( 'background-color', 'red' );\n * }\n * },\n * {\n * mode: 'bloo',\n * html: 'Bloo
',\n * onclick : function(){\n * $( 'body' ).css( 'background-color', 'blue' );\n * }\n * },\n * {\n * mode: 'blah',\n * html: 'Blah
',\n * onclick : function(){\n * $( 'body' ).css( 'background-color', 'grey' );\n * }\n * },\n * ]\n * });\n * $( '.myElement' ).modeButton( 'callModeFn', 'bler' );\n */\n /** constructor */\n function ModeButton(element, options) {\n this.currModeIndex = 0;\n return this._init(element, options);\n }\n\n /** html5 data key to store this object inside an element */\n ModeButton.prototype.DATA_KEY = \"mode-button\";\n /** default options */\n ModeButton.prototype.defaults = {\n switchModesOnClick: true\n };\n\n // ---- private interface\n /** set up options, intial mode, and the click handler */\n ModeButton.prototype._init = function _init(element, options) {\n //console.debug( 'ModeButton._init:', element, options );\n options = options || {};\n this.$element = $(element);\n this.options = $.extend(true, {}, this.defaults, options);\n if (!options.modes) {\n throw new Error('ModeButton requires a \"modes\" array');\n }\n\n var modeButton = this;\n this.$element.click(function _ModeButtonClick(event) {\n // call the curr mode fn\n modeButton.callModeFn();\n // inc the curr mode index\n if (modeButton.options.switchModesOnClick) {\n modeButton._incModeIndex();\n }\n // set the element html\n $(this).html(\n modeButton.options.modes[modeButton.currModeIndex].html\n );\n });\n return this.reset();\n };\n /** increment the mode index to the next in the array, looping back to zero if at the last */\n ModeButton.prototype._incModeIndex = function _incModeIndex() {\n this.currModeIndex += 1;\n if (this.currModeIndex >= this.options.modes.length) {\n this.currModeIndex = 0;\n }\n return this;\n };\n /** get the mode index in the modes array for the given key (mode name) */\n ModeButton.prototype._getModeIndex = function _getModeIndex(modeKey) {\n for (var i = 0; i < this.options.modes.length; i += 1) {\n if (this.options.modes[i].mode === modeKey) {\n return i;\n }\n }\n throw new Error(\"mode not found: \" + modeKey);\n };\n /** set the current mode to the one with the given index and set button html */\n ModeButton.prototype._setModeByIndex = function _setModeByIndex(index) {\n var newMode = this.options.modes[index];\n if (!newMode) {\n throw new Error(\"mode index not found: \" + index);\n }\n this.currModeIndex = index;\n if (newMode.html) {\n this.$element.html(newMode.html);\n }\n return this;\n };\n\n // ---- public interface\n /** get the current mode object (not just the mode name) */\n ModeButton.prototype.currentMode = function currentMode() {\n return this.options.modes[this.currModeIndex];\n };\n /** return the mode key of the current mode */\n ModeButton.prototype.current = function current() {\n // sugar for returning mode name\n return this.currentMode().mode;\n };\n /** get the mode with the given modeKey or the current mode if modeKey is undefined */\n ModeButton.prototype.getMode = function getMode(modeKey) {\n if (!modeKey) {\n return this.currentMode();\n }\n return this.options.modes[this._getModeIndex(modeKey)];\n };\n /** T/F if the button has the given mode */\n ModeButton.prototype.hasMode = function hasMode(modeKey) {\n try {\n return !!this.getMode(modeKey);\n } catch (err) {}\n return false;\n };\n /** set the current mode to the mode with the given name */\n ModeButton.prototype.setMode = function setMode(modeKey) {\n return this._setModeByIndex(this._getModeIndex(modeKey));\n };\n /** reset to the initial mode */\n ModeButton.prototype.reset = function reset() {\n this.currModeIndex = 0;\n if (this.options.initialMode) {\n this.currModeIndex = this._getModeIndex(this.options.initialMode);\n }\n return this._setModeByIndex(this.currModeIndex);\n };\n /** manually call the click handler of the given mode */\n ModeButton.prototype.callModeFn = function callModeFn(modeKey) {\n var modeFn = this.getMode(modeKey).onclick;\n if (modeFn && $.type(modeFn === \"function\")) {\n // call with the element as context (std jquery pattern)\n return modeFn.call(this.$element.get(0));\n }\n return undefined;\n };\n\n // as jq plugin\n $.fn.modeButton = function $modeButton(options) {\n if (!this.length) {\n return this;\n }\n\n //TODO: does map still work with jq multi selection (i.e. $( '.class-for-many-btns' ).modeButton)?\n if ($.type(options) === \"object\") {\n return this.map(function() {\n var $this = $(this);\n $this.data(\"mode-button\", new ModeButton($this, options));\n return this;\n });\n }\n\n var $first = $(this[0]),\n button = $first.data(\"mode-button\");\n\n if (!button) {\n throw new Error(\n \"modeButton needs an options object or string name of a function\"\n );\n }\n\n if (button && $.type(options) === \"string\") {\n var fnName = options;\n if (button && $.type(button[fnName]) === \"function\") {\n return button[fnName].apply(\n button,\n $.makeArray(arguments).slice(1)\n );\n }\n }\n return button;\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/ui/pagination.js.map b/static/maps/ui/pagination.js.map index d4976144bc3..1b962f41459 100644 --- 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from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js\n// Uses AMD or browser globals to create a jQuery plugin.\n(function(factory) {\n if (typeof define === \"function\" && define.amd) {\n // AMD. 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setSelectedText($cell, control, columnIndex);\n\n // fire the event from the table itself, passing the id and index of selected\n var eventData = {},\n key = $cell.parent().attr(\"id\"),\n val = $cell.data(COLUMN_INDEX_DATA_KEY);\n eventData[key] = val;\n $cell.parents(\".peek\").trigger(CHANGE_EVENT, eventData);\n }\n });\n }\n return $cell;\n }\n\n /** build a cell for a row that allows multiple selections */\n function buildMultiSelectCell(control, columnIndex) {\n var $cell = buildControlCell(control, columnIndex);\n // multiple selection - selected is an array\n if (control.selected && control.selected.indexOf(columnIndex) !== -1) {\n $cell.addClass(SELECTED_CLASS);\n }\n setSelectedText($cell, control, columnIndex);\n\n // only add the handler to non-disabled controls\n if (!$cell.hasClass(DISABLED_CLASS)) {\n $cell.click(function multiselectClick(ev) {\n var $cell = $(this);\n // can be more than one selected - toggle selected on this cell\n $cell.toggleClass(SELECTED_CLASS);\n 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.children(\"th:not(.top-left)\")\n .map(function() {\n return $(this).data(COLUMN_NAME_DATA_KEY);\n })\n );\n $this\n .parents(\".peek\")\n .trigger(RENAME_EVENT, columnNames);\n }\n });\n }\n\n // build a row for each control\n options.controls.forEach(function(control, i) {\n validateControl(control);\n var $controlRow = buildControlRow(\n columnCount,\n control,\n options.includePrompts\n );\n $peektable.find(\"tbody\").append($controlRow);\n });\n return this;\n }\n\n // ........................................................................\n // as jq plugin\n jQuery.fn.extend({\n peekColumnSelector: function $peekColumnSelector(options) {\n return this.map(function() {\n return peekColumnSelector.call(this, options);\n });\n }\n });\n});\n"]} \ No newline at end of file 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from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js\n// Uses AMD or browser globals to create a jQuery plugin.\n(function(factory) {\n if (typeof define === \"function\" && define.amd) {\n // AMD. Register as an anonymous module.\n define([\"jquery\"], factory);\n } else {\n // Browser globals\n factory(jQuery);\n }\n})(function($) {\n //==============================================================================\n /** Column selection using the peek display as the control.\n * Adds rows to the bottom of the peek with clickable areas in each cell\n * to allow the user to select columns.\n * Column selection can be limited to a single column or multiple.\n * (Optionally) adds a left hand column of column selection prompts.\n * (Optionally) allows the column headers to be clicked/renamed\n * and set to some initial value.\n * (Optionally) hides comment rows.\n * (Optionally) allows pre-selecting and disabling certain columns for\n * each row control.\n *\n * Construct by selecting a peek table to be used with jQuery and\n * calling 'peekColumnSelector' with options.\n * Options must include a 'controls' array and can include other options\n * listed below.\n * @example:\n * $( 'pre.peek' ).peekColumnSelector({\n * columnNames : [\"Chromosome\", \"Start\", \"Base\", \"\", \"\", \"Qual\" ],\n * controls : [\n * { label: 'X Column', id: 'xColumn' },\n * { label: 'Y Column', id: 'yColumn', selected: 2 },\n * { label: 'ID Column', id: 'idColumn', selected: 4, disabled: [ 1, 5 ] },\n * { label: 'Heatmap', id: 'heatmap', selected: [ 2, 4 ], disabled: [ 0, 1 ], multiselect: true,\n * selectedText: 'Included', unselectedText: 'Excluded' }\n * ],\n * renameColumns : true,\n * hideCommentRows : true,\n * includePrompts : true,\n * topLeftContent : 'Data sample:'\n * }).on( 'peek-column-selector.change', function( ev, selection ){\n * console.info( 'new selection:', selection );\n * //{ yColumn: 2 }\n * }).on( 'peek-column-selector.rename', function( ev, names ){\n * console.info( 'column names', names );\n * //[ 'Bler', 'Start', 'Base', '', '', 'Qual' ]\n * });\n *\n * An event is fired when column selection is changed and the event\n * is passed an object in the form: { the row id : the new selection value }.\n * An event is also fired when the table headers are re-named and\n * is passed the new array of column names.\n */\n\n /** option defaults */\n var defaults = {\n /** does this control allow renaming headers? */\n renameColumns: false,\n /** does this control allow renaming headers? */\n columnNames: [],\n /** the comment character used by the peek's datatype */\n commentChar: \"#\",\n /** should comment rows be shown or hidden in the peek */\n hideCommentRows: false,\n /** should a column of row control prompts be used */\n includePrompts: true,\n /** what is the content of the top left cell (often a title) */\n topLeftContent: \"Columns:\"\n },\n /** class added to the pre.peek element (to allow css on just the control) */\n PEEKCONTROL_CLASS = \"peek-column-selector\",\n /** the string of the event fired when a control row changes */\n CHANGE_EVENT = \"peek-column-selector.change\",\n /** the string of the event fired when a column is renamed */\n RENAME_EVENT = \"peek-column-selector.rename\",\n /** class added to the control rows */\n ROW_CLASS = \"control\",\n /** class added to the left-hand cells that serve as row prompts */\n PROMPT_CLASS = \"control-prompt\",\n /** class added to selected _cells_/tds */\n SELECTED_CLASS = \"selected\",\n /** class added to disabled/un-clickable cells/tds */\n DISABLED_CLASS = \"disabled\",\n /** class added to the clickable surface within a cell to select it */\n BUTTON_CLASS = \"button\",\n /** class added to peek table header (th) cells to indicate they can be clicked and are renamable */\n RENAMABLE_HEADER_CLASS = \"renamable-header\",\n /** the data key used for each cell to store the column index ('data-...') */\n COLUMN_INDEX_DATA_KEY = \"column-index\",\n /** renamable header data key used to store the column name (w/o the number and dot: '1.Bler') */\n COLUMN_NAME_DATA_KEY = \"column-name\";\n\n //TODO: not happy with pure functional here - rows should polymorph (multi, single, etc.)\n //TODO: needs clean up, move handlers to outer scope\n\n // ........................................................................\n /** validate the control data sent in for each row */\n function validateControl(control) {\n if (control.disabled && jQuery.type(control.disabled) !== \"array\") {\n throw new Error(\n '\"disabled\" must be defined as an array of indeces: ' +\n JSON.stringify(control)\n );\n }\n if (\n control.multiselect &&\n control.selected &&\n jQuery.type(control.selected) !== \"array\"\n ) {\n throw new Error(\n 'Mulitselect rows need an array for \"selected\": ' +\n JSON.stringify(control)\n );\n }\n if (!control.label || !control.id) {\n throw new Error(\n \"Peek controls need a label and id for each control row: \" +\n JSON.stringify(control)\n );\n }\n if (\n control.disabled &&\n control.disabled.indexOf(control.selected) !== -1\n ) {\n throw new Error(\n \"Selected column is in the list of disabled columns: \" +\n JSON.stringify(control)\n );\n }\n return control;\n }\n\n /** build the inner control surface (i.e. button-like) */\n function buildButton(control, columnIndex) {\n return $(\"\")\n .addClass(BUTTON_CLASS)\n .text(control.label);\n }\n\n /** build the basic (shared) cell structure */\n function buildControlCell(control, columnIndex) {\n var $td = $(\" \")\n .html(buildButton(control, columnIndex))\n .attr(\"data-\" + COLUMN_INDEX_DATA_KEY, columnIndex);\n\n // disable if index in disabled array\n if (control.disabled && control.disabled.indexOf(columnIndex) !== -1) {\n $td.addClass(DISABLED_CLASS);\n }\n return $td;\n }\n\n /** set the text of the control based on selected/un */\n function setSelectedText($cell, control, columnIndex) {\n var $button = $cell.children(\".\" + BUTTON_CLASS);\n if ($cell.hasClass(SELECTED_CLASS)) {\n $button.html(\n control.selectedText !== undefined\n ? control.selectedText\n : control.label\n );\n } else {\n $button.html(\n control.unselectedText !== undefined\n ? control.unselectedText\n : control.label\n );\n }\n }\n\n /** build a cell for a row that only allows one selection */\n function buildSingleSelectCell(control, columnIndex) {\n // only one selection - selected is single index\n var $cell = buildControlCell(control, columnIndex);\n if (control.selected === columnIndex) {\n $cell.addClass(SELECTED_CLASS);\n }\n setSelectedText($cell, control, columnIndex);\n\n // only add the handler to non-disabled controls\n if (!$cell.hasClass(DISABLED_CLASS)) {\n $cell.click(function selectClick(ev) {\n var $cell = $(this);\n // don't re-select or fire event if already selected\n if (!$cell.hasClass(SELECTED_CLASS)) {\n // only one can be selected - remove selected on all others, add it here\n var $otherSelected = $cell\n .parent()\n .children(\".\" + SELECTED_CLASS)\n .removeClass(SELECTED_CLASS);\n $otherSelected.each(function() {\n setSelectedText($(this), control, columnIndex);\n });\n\n $cell.addClass(SELECTED_CLASS);\n setSelectedText($cell, control, columnIndex);\n\n // fire the event from the table itself, passing the id and index of selected\n var eventData = {},\n key = $cell.parent().attr(\"id\"),\n val = $cell.data(COLUMN_INDEX_DATA_KEY);\n eventData[key] = val;\n $cell.parents(\".peek\").trigger(CHANGE_EVENT, eventData);\n }\n });\n }\n return $cell;\n }\n\n /** build a cell for a row that allows multiple selections */\n function buildMultiSelectCell(control, columnIndex) {\n var $cell = buildControlCell(control, columnIndex);\n // multiple selection - selected is an array\n if (control.selected && control.selected.indexOf(columnIndex) !== -1) {\n $cell.addClass(SELECTED_CLASS);\n }\n setSelectedText($cell, control, columnIndex);\n\n // only add the handler to non-disabled controls\n if (!$cell.hasClass(DISABLED_CLASS)) {\n $cell.click(function multiselectClick(ev) {\n var $cell = $(this);\n // can be more than one selected - toggle selected on this cell\n $cell.toggleClass(SELECTED_CLASS);\n setSelectedText($cell, control, columnIndex);\n var selectedColumnIndeces = $cell\n .parent()\n .find(\".\" + SELECTED_CLASS)\n .map(function(i, e) {\n return $(e).data(COLUMN_INDEX_DATA_KEY);\n });\n // fire the event from the table itself, passing the id and index of selected\n var eventData = {},\n key = $cell.parent().attr(\"id\"),\n val = jQuery.makeArray(selectedColumnIndeces);\n eventData[key] = val;\n $cell.parents(\".peek\").trigger(CHANGE_EVENT, eventData);\n });\n }\n return $cell;\n }\n\n /** iterate over columns in peek and create a control for each */\n function buildControlCells(count, control) {\n var $cells = [];\n // build a control for each column - using a build fn based on control\n for (var columnIndex = 0; columnIndex < count; columnIndex += 1) {\n $cells.push(\n control.multiselect\n ? buildMultiSelectCell(control, columnIndex)\n : buildSingleSelectCell(control, columnIndex)\n );\n }\n return $cells;\n }\n\n /** build a row of controls for the peek */\n function buildControlRow(cellCount, control, includePrompts) {\n var $controlRow = $(\" \")\n .attr(\"id\", control.id)\n .addClass(ROW_CLASS);\n if (includePrompts) {\n var $promptCell = $(\" \")\n .addClass(PROMPT_CLASS)\n .text(control.label + \":\");\n $controlRow.append($promptCell);\n }\n $controlRow.append(buildControlCells(cellCount, control));\n return $controlRow;\n }\n\n // ........................................................................\n /** add to the peek, using options for configuration, return the peek */\n function peekColumnSelector(options) {\n options = jQuery.extend(true, {}, defaults, options);\n\n var $peek = $(this).addClass(PEEKCONTROL_CLASS),\n $peektable = $peek.find(\"table\"),\n // get the size of the tables - width and height, number of comment rows\n columnCount = $peektable.find(\"th\").length,\n rowCount = $peektable.find(\"tr\").length,\n // get the rows containing text starting with the comment char (also make them grey)\n $commentRows = $peektable.find(\"td[colspan]\").map(function(e, i) {\n var $this = $(this);\n if (\n $this.text() &&\n $this.text().match(new RegExp(\"^\" + options.commentChar))\n ) {\n return $(this)\n .css(\"color\", \"grey\")\n .parent()\n .get(0);\n }\n return null;\n });\n\n // should comment rows in the peek be hidden?\n if (options.hideCommentRows) {\n $commentRows.hide();\n rowCount -= $commentRows.length;\n }\n //console.debug( 'rowCount:', rowCount, 'columnCount:', columnCount, '$commentRows:', $commentRows );\n\n // should a first column of control prompts be added?\n if (options.includePrompts) {\n var $topLeft = $(\" \")\n .addClass(\"top-left\")\n .text(options.topLeftContent)\n .attr(\"rowspan\", rowCount);\n $peektable\n .find(\"tr\")\n .first()\n .prepend($topLeft);\n }\n\n // save either the options column name or the parsed text of each column header in html5 data attr and text\n var $headers = $peektable\n .find(\"th:not(.top-left)\")\n .each(function(i, e) {\n var $this = $(this),\n // can be '1.name' or '1'\n text = $this.text().replace(/^\\d+\\.*/, \"\"),\n name = options.columnNames[i] || text;\n $this\n .attr(\"data-\" + COLUMN_NAME_DATA_KEY, name)\n .text(i + 1 + (name ? \".\" + name : \"\"));\n });\n\n // allow renaming of columns when the header is clicked\n if (options.renameColumns) {\n $headers\n .addClass(RENAMABLE_HEADER_CLASS)\n .click(function renameColumn() {\n // prompt for new name\n var $this = $(this),\n index =\n $this.index() + (options.includePrompts ? 0 : 1),\n prevName = $this.data(COLUMN_NAME_DATA_KEY),\n newColumnName = prompt(\"New column name:\", prevName);\n if (newColumnName !== null && newColumnName !== prevName) {\n // set the new text and data\n $this\n .text(\n index +\n (newColumnName ? \".\" + newColumnName : \"\")\n )\n .data(COLUMN_NAME_DATA_KEY, newColumnName)\n .attr(\"data-\", COLUMN_NAME_DATA_KEY, newColumnName);\n // fire event for new column names\n var columnNames = jQuery.makeArray(\n $this\n .parent()\n .children(\"th:not(.top-left)\")\n .map(function() {\n return $(this).data(COLUMN_NAME_DATA_KEY);\n })\n );\n $this\n .parents(\".peek\")\n .trigger(RENAME_EVENT, columnNames);\n }\n });\n }\n\n // build a row for each control\n options.controls.forEach(function(control, i) {\n validateControl(control);\n var $controlRow = buildControlRow(\n columnCount,\n control,\n options.includePrompts\n );\n $peektable.find(\"tbody\").append($controlRow);\n });\n return this;\n }\n\n // ........................................................................\n // as jq plugin\n jQuery.fn.extend({\n peekColumnSelector: function $peekColumnSelector(options) {\n return this.map(function() {\n return peekColumnSelector.call(this, options);\n });\n }\n });\n});\n"]} \ No newline at end of file diff --git a/static/maps/ui/popupmenu.js.map b/static/maps/ui/popupmenu.js.map index 3fe9e05aa11..6991a78b52e 100644 --- a/static/maps/ui/popupmenu.js.map +++ b/static/maps/ui/popupmenu.js.map @@ -1 +1 @@ -{"version":3,"sources":["ui/popupmenu.js"],"names":["define","jQuery","make_popupmenu","button_element","initial_options","element_menu_exists","data","bind","e","remove","setTimeout","$","menu_element","attr","options","appendTo","_","size","each","k","v","action","append","url","html","wrapper","width","css","pageY","x","pageX","Math","min","close_popup","window","frame_id","frame","max","document","scrollLeft","top","left","el","unbind","make_popup_menus","parent","frames","length","find","menu","this","event","link_dom","link","get","confirmtext","getAttribute","href","target","text","stopPropagation","confirm","open","click","preventDefault","box","addClass"],"mappings":"aAAAA,QAAQ,UAAW,SAASC,GACxB,aAYA,SAASC,EAAeC,EAAgBC,GAIpC,IAAIC,EAAsBF,EAAeG,KAAK,gBAC9CH,EAAeG,KAAK,eAAgBF,GAGhCC,GAEHF,EAAAI,KAAA,mBAAA,SAAAC,GAuGO,OArGRL,EAAAA,oBAAoBM,SAKhBC,WAAW,WAAXA,IAAAA,EAAsBC,EAClB,iCACIC,EACAC,KAAA,MAIAC,gBAEAH,EAAER,EAAFG,KAA0BS,gBAC7BC,EAAAC,KAAAH,IAAA,GACCI,EAAF,wBAAgBH,SAAeH,GAEvBD,EAAAO,KAAAJ,EAAA,SAAAK,EAAAC,GACA,GAAAA,EAAA,CAFJ,IAWOC,EAAAD,EAAAC,QAAAD,EACHR,EAAaU,OAKhBX,EAAA,aAAAW,OAlBLX,EAAA,OAqBIE,KAAA,OAAAO,EAAAG,KAbiBC,KAAKL,GAkBRM,MAAQC,UAUlBC,EAAIL,OACDM,EAAAA,aACDC,SAAAA,QAFVP,OAAAX,EAAA,oBAAAa,KAAAL,OAOA,IAAAM,EAAAd,EACA,uFAEIA,OAAMJ,GACFI,SAAE,QAELkB,EAHDrB,EAAAsB,MAAAL,EAAAC,QAAA,EAIHG,EALDE,KAAAC,IAMAC,EACAA,EAAAA,UAAcC,aACTvB,EAAIwB,QAAAA,QACLxB,EAAAc,GAAAC,QACIU,GAEPP,EAAAE,KAAAM,IAAAR,EAAAlB,EAAA2B,UAAAC,aAAA,GArBDd,EAAQE,KAwBLa,IAAPhC,EAAAoB,MA5EJa,KAAAZ,KAwDO,IAEHnB,WAAW,WAGP,IAAIuB,EAAc,SAASS,GACvB/B,EAAE+B,GAAInC,KAAK,oBAAqB,WAC5BI,EAAE,oBAAoBF,SACtBiC,EAAGC,OAAO,wBAGlBV,EAAYtB,EAAEuB,OAAOI,WAwBxBM,EAAAA,EAAiBC,OAA1BL,IAAkCF,WAC9B,IAAA,IAAAH,EAAAD,OAAAM,IAAAM,OAAAC,OAAAZ,KAIKa,EAFcV,EAAAA,OAAnBE,IAAAM,OAAAX,GAAAG,YAKQ,KAEA,IA7HZ,IAAA3B,EAAAV,EAgLA,OACIC,eAAgBA,EAChB0C,iBAtCwB,SAAAC,GAGIA,EAAAA,GAAAP,SACA3B,EAAAkC,GACIX,KAAAA,kBACAhB,KAAA,WACH,IAAAJ,KACGmC,EAAAtC,EAAAuC,MAGPD,EAAAD,KAAA,KAVD9B,KAUO,WACHiC,IAAAA,EAAAA,EAAAA,MACHC,EAAAC,EAAAC,IAAA,GACJC,EAAAH,EAAAI,aAAA,WAjBLC,EAAAL,EAAAI,aAAA,QAmBHE,EAAAN,EAAAI,aAAA,UAML1C,EAAAuC,EAAAM,QAHYd,GAIEtC,IAAKkD,EACbG,OADkC,SACfT,GADzB,IAAAI,GAAAM,QAAAN,GAAA,CAMoBzC,GAApB4C,EAEA,OADAxB,OAAA4B,KAAAL,EAAAC,IACA,EAtBwBL,EAAKU,aA4BrB7D,EADb8D,mBAzCoC,OAwB/B,IAAIC,EAAMtD,EAAEkC,GAAQG,KAAK,IAAMC,EAAKpC,KAAK,cAIzCoD,EAAIjB,KAAK,KAAKzC,KAAK,QAAS,SAASC,GAEjC,OADAA,EAAEoD,mBACK,IAIX1D,EAAe+D,EAAKnD,GACpBmD,EAAIC,SAAS,SACbjB,EAAKxC","file":"../../scripts/ui/popupmenu.js","sourcesContent":["define([\"jquery\"], function(jQuery) {\n \"use_strict\";\n\n var $ = jQuery;\n\n // ============================================================================\n // TODO: unify popup menus and/or eliminate this\n /**\n * Sets up popupmenu rendering and binds options functions to the appropriate links.\n * initial_options is a dict with text describing the option pointing to either (a) a\n * function to perform; or (b) another dict with two required keys, 'url' and 'action' (the\n * function to perform. (b) is useful for exposing the underlying URL of the option.\n */\n function make_popupmenu(button_element, initial_options) {\n /* Use the $.data feature to store options with the link element.\n This allows options to be changed at a later time\n */\n var element_menu_exists = button_element.data(\"menu_options\");\n button_element.data(\"menu_options\", initial_options);\n\n // If element already has menu, nothing else to do since HTML and actions are already set.\n if (element_menu_exists) {\n return;\n }\n\n button_element.bind(\"click.show_popup\", function(e) {\n // Close existing visible menus\n $(\".popmenu-wrapper\").remove();\n\n // Need setTimeouts so clicks don't interfere with each other\n setTimeout(function() {\n // Dynamically generate the wrapper holding all the selectable options of the menu.\n var menu_element = $(\n \"\"\n );\n var options = button_element.data(\"menu_options\");\n if (_.size(options) <= 0) {\n $(\"
\" : \"\") +\n \"Dist: \" +\n d.dist +\n \"
Annotation1: \" +\n annotation +\n (d.bootstrap\n ? \"
Confidence level: \" +\n Math.round(100 * d.bootstrap)\n : \"\")\n : \"\";\n })\n .tooltip({ placement: \"top\", trigger: \"hover\" });\n }\n });\n\n /**\n * Linea layout class of Phyloviz, is responsible for rendering the nodes\n * calls PhyloTreeLayout to determine the positions of the nodes\n */\n var PhylovizLinearView = PhylovizLayoutBase.extend({\n initialize: function(options) {\n // Default values of linear layout\n var self = this;\n self.margins = options.margins;\n self.layoutMode = \"Linear\";\n\n self.stdInit(options);\n\n self.layout();\n self.updateAndRender(self.model.root);\n },\n\n /**\n * Creates the basic layout of a linear tree by precalculating fixed values.\n * One of calculations are also made here\n */\n layout: function() {\n var self = this;\n self.tree = new PhyloTreeLayout().layoutMode(\"Linear\");\n self.diagonal = d3.svg.diagonal().projection(function(d) {\n return [d.y, d.x];\n });\n },\n\n /**\n * Renders the nodes base on Linear layout.\n */\n renderNodes: function(source) {\n var self = this,\n fontSize = self.model.get(\"fontSize\") + \"px\";\n\n // assigning properties from models\n self.tree\n .separation(self.model.get(\"separation\"))\n .leafHeight(self.model.get(\"leafHeight\"));\n\n var duration = 500,\n nodes = self.tree\n .separation(self.model.get(\"separation\"))\n .nodes(self.model.root);\n\n var node = self.vis\n .selectAll(\"g.node\")\n .data(nodes, function(d) {\n return d.name + d.id || (d.id = ++self.i);\n });\n\n // These variables has to be passed into update links which are in the base methods\n self.nodes = nodes;\n self.duration = duration;\n\n // ------- D3 ENTRY --------\n // Enter any new nodes at the parent's previous position.\n var nodeEnter = node\n .enter()\n .append(\"svg:g\")\n .attr(\"class\", \"node\")\n .on(\"dblclick\", function() {\n d3.event.stopPropagation();\n })\n .on(\"click\", function(d) {\n if (d3.event.altKey) {\n self.selectNode(d); // display info if alt is pressed\n } else {\n if (d.children && d.children.length === 0) {\n return;\n } // there is no need to toggle leaves\n self.model.toggle(d); // contract/expand nodes at data level\n self.updateAndRender(d); // re-render the tree\n }\n });\n //TODO: newick and phyloxml return arrays. where should this go (client (here, else), server)?\n if (toString.call(source) === \"[object Array]\") {\n // if d is an array, replate with the first object (newick, phyloxml)\n source = source[0];\n }\n nodeEnter.attr(\"transform\", function(d) {\n return \"translate(\" + source.y0 + \",\" + source.x0 + \")\";\n });\n\n nodeEnter\n .append(\"svg:circle\")\n .attr(\"r\", 1e-6)\n .style(\"fill\", function(d) {\n return d._children ? \"lightsteelblue\" : \"#fff\";\n });\n\n nodeEnter\n .append(\"svg:text\")\n .attr(\"class\", \"nodeLabel\")\n .attr(\"x\", function(d) {\n return d.children || d._children ? -10 : 10;\n })\n .attr(\"dy\", \".35em\")\n .attr(\"text-anchor\", function(d) {\n return d.children || d._children ? \"end\" : \"start\";\n })\n .style(\"fill-opacity\", 1e-6);\n\n // ------- D3 TRANSITION --------\n // Transition nodes to their new position.\n var nodeUpdate = node.transition().duration(duration);\n\n nodeUpdate.attr(\"transform\", function(d) {\n return \"translate(\" + d.y + \",\" + d.x + \")\";\n });\n\n nodeUpdate\n .select(\"circle\")\n .attr(\"r\", self.defaults.nodeRadius)\n .style(\"fill\", function(d) {\n return d._children ? \"lightsteelblue\" : \"#fff\";\n });\n\n nodeUpdate\n .select(\"text\")\n .style(\"fill-opacity\", 1)\n .style(\"font-size\", fontSize)\n .text(function(d) {\n return d.name && d.name !== \"\"\n ? d.name\n : d.bootstrap ? Math.round(100 * d.bootstrap) : \"\";\n });\n\n // ------- D3 EXIT --------\n // Transition exiting nodes to the parent's new position.\n var nodeExit = node\n .exit()\n .transition()\n .duration(duration)\n .remove();\n\n nodeExit.select(\"circle\").attr(\"r\", 1e-6);\n\n nodeExit.select(\"text\").style(\"fill-opacity\", 1e-6);\n\n // Stash the old positions for transition.\n nodes.forEach(function(d) {\n d.x0 = d.x; // we need the x0, y0 for parents with children\n d.y0 = d.y;\n });\n }\n });\n\n var PhylovizView = Backbone.View.extend({\n className: \"phyloviz\",\n\n initialize: function(options) {\n var self = this;\n // -- Default values of the vis\n self.MIN_SCALE = 0.05; //for zooming\n self.MAX_SCALE = 5;\n self.MAX_DISPLACEMENT = 500;\n self.margins = [10, 60, 10, 80];\n\n self.width = $(\"#PhyloViz\").width();\n self.height = $(\"#PhyloViz\").height();\n self.radius = self.width;\n self.data = options.data;\n\n // -- Events Phyloviz view responses to\n $(window).resize(function() {\n self.width = $(\"#PhyloViz\").width();\n self.height = $(\"#PhyloViz\").height();\n self.render();\n });\n\n // -- Create phyloTree model\n self.phyloTree = new PhyloTree(options.config);\n self.phyloTree.root = self.data;\n\n // -- Set up UI functions of main view\n self.zoomFunc = d3.behavior\n .zoom()\n .scaleExtent([self.MIN_SCALE, self.MAX_SCALE]);\n self.zoomFunc.translate(self.phyloTree.get(\"translate\"));\n self.zoomFunc.scale(self.phyloTree.get(\"scaleFactor\"));\n\n // -- set up header buttons, search and settings menu\n self.navMenu = new HeaderButtons(self);\n self.settingsMenu = new SettingsMenu({\n phyloTree: self.phyloTree\n });\n self.nodeSelectionView = new NodeSelectionView({\n phyloTree: self.phyloTree\n });\n self.search = new PhyloVizSearch();\n\n // using settimeout to call the zoomAndPan function according to the stored attributes in viz_config\n setTimeout(function() {\n self.zoomAndPan();\n }, 1000);\n },\n\n render: function() {\n // -- Creating helper function for vis. --\n var self = this;\n $(\"#PhyloViz\").empty();\n\n // -- Layout viz. --\n self.mainSVG = d3\n .select(\"#PhyloViz\")\n .append(\"svg:svg\")\n .attr(\"width\", self.width)\n .attr(\"height\", self.height)\n .attr(\"pointer-events\", \"all\")\n .call(\n self.zoomFunc.on(\"zoom\", function() {\n self.zoomAndPan();\n })\n );\n\n self.boundingRect = self.mainSVG\n .append(\"svg:rect\")\n .attr(\"class\", \"boundingRect\")\n .attr(\"width\", self.width)\n .attr(\"height\", self.height)\n .attr(\"stroke\", \"black\")\n .attr(\"fill\", \"white\");\n\n self.vis = self.mainSVG.append(\"svg:g\").attr(\"class\", \"vis\");\n\n self.layoutOptions = {\n model: self.phyloTree,\n width: self.width,\n height: self.height,\n vis: self.vis,\n margins: self.margins\n };\n\n // -- Creating Title\n $(\"#title\").text(\n \"Phylogenetic Tree from \" +\n self.phyloTree.get(\"title\") +\n \":\"\n );\n\n // -- Create Linear view instance --\n var linearView = new PhylovizLinearView(self.layoutOptions);\n },\n\n /**\n * Function to zoom and pan the svg element which the entire tree is contained within\n * Uses d3.zoom events, and extend them to allow manual updates and keeping states in model\n */\n zoomAndPan: function(event) {\n var zoomParams, translateParams;\n if (typeof event !== \"undefined\") {\n zoomParams = event.zoom;\n translateParams = event.translate;\n }\n\n var self = this,\n scaleFactor = self.zoomFunc.scale(),\n translationCoor = self.zoomFunc.translate(),\n zoomStatement = \"\",\n translateStatement = \"\";\n\n // Do manual scaling.\n switch (zoomParams) {\n case \"reset\":\n scaleFactor = 1.0;\n translationCoor = [0, 0];\n break;\n case \"+\":\n scaleFactor *= 1.1;\n break;\n case \"-\":\n scaleFactor *= 0.9;\n break;\n default:\n if (typeof zoomParams === \"number\") {\n scaleFactor = zoomParams;\n } else if (d3.event !== null) {\n scaleFactor = d3.event.scale;\n }\n }\n if (\n scaleFactor < self.MIN_SCALE ||\n scaleFactor > self.MAX_SCALE\n ) {\n return;\n }\n self.zoomFunc.scale(scaleFactor); //update scale Factor\n zoomStatement =\n \"translate(\" +\n self.margins[3] +\n \",\" +\n self.margins[0] +\n \")\" +\n \" scale(\" +\n scaleFactor +\n \")\";\n\n // Do manual translation.\n if (d3.event !== null) {\n translateStatement =\n \"translate(\" + d3.event.translate + \")\";\n } else {\n if (typeof translateParams !== \"undefined\") {\n var x = translateParams.split(\",\")[0];\n var y = translateParams.split(\",\")[1];\n if (!isNaN(x) && !isNaN(y)) {\n translationCoor = [\n translationCoor[0] + parseFloat(x),\n translationCoor[1] + parseFloat(y)\n ];\n }\n }\n self.zoomFunc.translate(translationCoor); // update zoomFunc\n translateStatement = \"translate(\" + translationCoor + \")\";\n }\n\n self.phyloTree.set(\"scaleFactor\", scaleFactor);\n self.phyloTree.set(\"translate\", translationCoor);\n //refers to the view that we are actually zooming\n self.vis.attr(\"transform\", translateStatement + zoomStatement);\n },\n\n /**\n * Primes the Ajax URL to load another Nexus tree\n */\n reloadViz: function() {\n var self = this,\n treeIndex = $(\"#phylovizNexSelector :selected\").val();\n $.getJSON(\n self.phyloTree.get(\"dataset\").url(),\n {\n tree_index: treeIndex,\n data_type: \"raw_data\"\n },\n function(packedJson) {\n self.data = packedJson.data;\n self.config = packedJson;\n self.render();\n }\n );\n }\n });\n\n var HeaderButtons = Backbone.View.extend({\n initialize: function(phylovizView) {\n var self = this;\n self.phylovizView = phylovizView;\n\n // Clean up code - if the class initialized more than once\n $(\"#panelHeaderRightBtns\").empty();\n $(\"#phyloVizNavBtns\").empty();\n $(\"#phylovizNexSelector\").off();\n\n self.initNavBtns();\n self.initRightHeaderBtns();\n\n // Initial a tree selector in the case of nexus\n $(\"#phylovizNexSelector\")\n .off()\n .on(\"change\", function() {\n self.phylovizView.reloadViz();\n });\n },\n\n initRightHeaderBtns: function() {\n var self = this;\n\n var rightMenu = mod_icon_btn.create_icon_buttons_menu(\n [\n {\n icon_class: \"gear\",\n title: \"PhyloViz Settings\",\n on_click: function() {\n $(\"#SettingsMenu\").show();\n self.settingsMenu.updateUI();\n }\n },\n {\n icon_class: \"disk\",\n title: \"Save visualization\",\n on_click: function() {\n var nexSelected = $(\n \"#phylovizNexSelector option:selected\"\n ).text();\n if (nexSelected) {\n self.phylovizView.phyloTree.set(\n \"title\",\n nexSelected\n );\n }\n self.phylovizView.phyloTree.save();\n }\n },\n {\n icon_class: \"chevron-expand\",\n title: \"Search / Edit Nodes\",\n on_click: function() {\n $(\"#nodeSelectionView\").show();\n }\n },\n {\n icon_class: \"information\",\n title: \"Phyloviz Help\",\n on_click: function() {\n window.open(\n \"https://galaxyproject.org/learn/visualization/phylogenetic-tree/\"\n );\n // https://docs.google.com/document/d/1AXFoJgEpxr21H3LICRs3EyMe1B1X_KFPouzIgrCz3zk/edit\n }\n }\n ],\n {\n tooltip_config: { placement: \"bottom\" }\n }\n );\n $(\"#panelHeaderRightBtns\").append(rightMenu.$el);\n },\n\n initNavBtns: function() {\n var self = this,\n navMenu = mod_icon_btn.create_icon_buttons_menu(\n [\n {\n icon_class: \"zoom-in\",\n title: \"Zoom in\",\n on_click: function() {\n self.phylovizView.zoomAndPan({ zoom: \"+\" });\n }\n },\n {\n icon_class: \"zoom-out\",\n title: \"Zoom out\",\n on_click: function() {\n self.phylovizView.zoomAndPan({ zoom: \"-\" });\n }\n },\n {\n icon_class: \"arrow-circle\",\n title: \"Reset Zoom/Pan\",\n on_click: function() {\n self.phylovizView.zoomAndPan({\n zoom: \"reset\"\n });\n }\n }\n ],\n {\n tooltip_config: { placement: \"bottom\" }\n }\n );\n $(\"#phyloVizNavBtns\").append(navMenu.$el);\n }\n });\n\n var SettingsMenu = UserMenuBase.extend({\n className: \"Settings\",\n\n initialize: function(options) {\n // settings needs to directly interact with the phyloviz model so it will get access to it.\n var self = this;\n self.phyloTree = options.phyloTree;\n self.el = $(\"#SettingsMenu\");\n self.inputs = {\n separation: $(\"#phyloVizTreeSeparation\"),\n leafHeight: $(\"#phyloVizTreeLeafHeight\"),\n fontSize: $(\"#phyloVizTreeFontSize\")\n };\n\n //init all buttons of settings\n $(\"#settingsCloseBtn\")\n .off()\n .on(\"click\", function() {\n self.el.hide();\n });\n $(\"#phylovizResetSettingsBtn\")\n .off()\n .on(\"click\", function() {\n self.resetToDefaults();\n });\n $(\"#phylovizApplySettingsBtn\")\n .off()\n .on(\"click\", function() {\n self.apply();\n });\n },\n\n /**\n * Applying user values to phylotree model.\n */\n apply: function() {\n var self = this;\n if (\n !self.isAcceptableValue(self.inputs.separation, 50, 2500) ||\n !self.isAcceptableValue(self.inputs.leafHeight, 5, 30) ||\n !self.isAcceptableValue(self.inputs.fontSize, 5, 20)\n ) {\n return;\n }\n $.each(self.inputs, function(key, $input) {\n self.phyloTree.set(key, $input.val());\n });\n },\n /**\n * Called to update the values input to that stored in the model\n */\n updateUI: function() {\n var self = this;\n $.each(self.inputs, function(key, $input) {\n $input.val(self.phyloTree.get(key));\n });\n },\n /**\n * Resets the value of the phyloTree model to its default\n */\n resetToDefaults: function() {\n $(\".tooltip\").remove(); // just in case the tool tip was not removed\n var self = this;\n $.each(self.phyloTree.defaults, function(key, value) {\n self.phyloTree.set(key, value);\n });\n self.updateUI();\n },\n\n render: function() {}\n });\n\n /**\n * View for inspecting node properties and editing them\n */\n var NodeSelectionView = UserMenuBase.extend({\n className: \"Settings\",\n\n initialize: function(options) {\n var self = this;\n self.el = $(\"#nodeSelectionView\");\n self.phyloTree = options.phyloTree;\n\n self.UI = {\n enableEdit: $(\"#phylovizEditNodesCheck\"),\n saveChanges: $(\"#phylovizNodeSaveChanges\"),\n cancelChanges: $(\"#phylovizNodeCancelChanges\"),\n name: $(\"#phyloVizSelectedNodeName\"),\n dist: $(\"#phyloVizSelectedNodeDist\"),\n annotation: $(\"#phyloVizSelectedNodeAnnotation\")\n };\n\n // temporarily stores the values in case user change their mind\n self.valuesOfConcern = {\n name: null,\n dist: null,\n annotation: null\n };\n\n //init UI buttons\n $(\"#nodeSelCloseBtn\")\n .off()\n .on(\"click\", function() {\n self.el.hide();\n });\n self.UI.saveChanges.off().on(\"click\", function() {\n self.updateNodes();\n });\n self.UI.cancelChanges.off().on(\"click\", function() {\n self.cancelChanges();\n });\n\n (function($) {\n // extending jquery fxn for enabling and disabling nodes.\n $.fn.enable = function(isEnabled) {\n return $(this).each(function() {\n if (isEnabled) {\n $(this).removeAttr(\"disabled\");\n } else {\n $(this).attr(\"disabled\", \"disabled\");\n }\n });\n };\n })(jQuery);\n\n self.UI.enableEdit.off().on(\"click\", function() {\n self.toggleUI();\n });\n },\n\n /**\n * For turning on and off the child elements\n */\n toggleUI: function() {\n var self = this,\n checked = self.UI.enableEdit.is(\":checked\");\n\n if (!checked) {\n self.cancelChanges();\n }\n\n $.each(self.valuesOfConcern, function(key, value) {\n self.UI[key].enable(checked);\n });\n if (checked) {\n self.UI.saveChanges.show();\n self.UI.cancelChanges.show();\n } else {\n self.UI.saveChanges.hide();\n self.UI.cancelChanges.hide();\n }\n },\n\n /**\n * Reverting to previous values in case user change their minds\n */\n cancelChanges: function() {\n var self = this,\n node = self.phyloTree.get(\"selectedNode\");\n if (node) {\n $.each(self.valuesOfConcern, function(key, value) {\n self.UI[key].val(node[key]);\n });\n }\n },\n\n /**\n * Changing the data in the underlying tree with user-specified values\n */\n updateNodes: function() {\n var self = this,\n node = self.phyloTree.get(\"selectedNode\");\n if (node) {\n if (\n !self.isAcceptableValue(self.UI.dist, 0, 1) ||\n self.hasIllegalJsonCharacters(self.UI.name) ||\n self.hasIllegalJsonCharacters(self.UI.annotation)\n ) 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[\"libs/d3\", \"viz/visualization\", \"mvc/dataset/data\", \"mvc/ui/icon-button\"],\n function(d3, visualization_mod, data_mod, mod_icon_btn) {\n /**\n * Base class of any menus that takes in user interaction. Contains checking methods.\n */\n var UserMenuBase = Backbone.View.extend({\n className: \"UserMenuBase\",\n\n /**\n * Check if an input value is a number and falls within max min.\n */\n isAcceptableValue: function($inputKey, min, max) {\n //TODO: use better feedback than alert\n var value = $inputKey.val(),\n fieldName =\n $inputKey.attr(\"displayLabel\") ||\n $inputKey.attr(\"id\").replace(\"phyloViz\", \"\");\n\n function isNumeric(n) {\n return !isNaN(parseFloat(n)) && isFinite(n);\n }\n\n if (!isNumeric(value)) {\n alert(fieldName + \" is not a number!\");\n return false;\n }\n\n if (value > max) {\n alert(fieldName + \" is too large.\");\n return false;\n } else if (value < min) {\n alert(fieldName + \" is too small.\");\n return false;\n }\n return true;\n },\n\n /**\n * Check if any user string inputs has illegal characters that json cannot accept\n */\n hasIllegalJsonCharacters: function($inputKey) {\n if ($inputKey.val().search(/\"|'|\\\\/) !== -1) {\n alert(\n \"Named fields cannot contain these illegal characters: \" +\n \"double quote(\\\"), single guote('), or back slash(\\\\). \"\n );\n return true;\n }\n return false;\n }\n });\n\n /**\n * -- Custom Layout call for phyloViz to suit the needs of a phylogenetic tree.\n * -- Specifically: 1) Nodes have a display display of (= evo dist X depth separation) from their parent\n * 2) Nodes must appear in other after they have expand and contracted\n */\n function PhyloTreeLayout() {\n var self = this,\n hierarchy = d3.layout\n .hierarchy()\n .sort(null)\n .value(null),\n height = 360, // ! represents both the layout angle and the height of the layout, in px\n layoutMode = \"Linear\",\n leafHeight = 18, // height of each individual leaf node\n depthSeparation = 200, // separation between nodes of different depth, in px\n leafIndex = 0, // change to recurssive call\n defaultDist = 0.5, // tree defaults to 0.5 dist if no dist is specified\n maxTextWidth = 50; // maximum length of the text labels\n\n self.leafHeight = function(inputLeafHeight) {\n if (typeof inputLeafHeight === \"undefined\") {\n return leafHeight;\n } else {\n leafHeight = inputLeafHeight;\n return self;\n }\n };\n\n self.layoutMode = function(mode) {\n if (typeof mode === \"undefined\") {\n return layoutMode;\n } else {\n layoutMode = mode;\n return self;\n }\n };\n\n // changes the layout angle of the display, which is really changing the height\n self.layoutAngle = function(angle) {\n if (typeof angle === \"undefined\") {\n return height;\n }\n // to use default if the user puts in strange values\n if (isNaN(angle) || angle < 0 || angle > 360) {\n return self;\n } else {\n height = angle;\n return self;\n }\n };\n\n self.separation = function(dist) {\n // changes the dist between the nodes of different depth\n if (typeof dist === \"undefined\") {\n return depthSeparation;\n } else {\n depthSeparation = dist;\n return self;\n }\n };\n\n self.links = function(nodes) {\n // uses d3 native method to generate links. Done.\n return d3.layout.tree().links(nodes);\n };\n\n // -- Custom method for laying out phylogeny tree in a linear fashion\n self.nodes = function(d, i) {\n //TODO: newick and phyloxml return arrays. where should this go (client (here, else), server)?\n if (toString.call(d) === \"[object Array]\") {\n // if d is an array, replate with the first object (newick, phyloxml)\n d = d[0];\n }\n // self is to find the depth of all the nodes, assumes root is passed in\n var _nodes = hierarchy.call(self, d, i),\n nodes = [],\n maxDepth = 0,\n numLeaves = 0;\n //console.debug( JSON.stringify( _nodes, null, 2 ) )\n window._d = d;\n window._nodes = _nodes;\n\n //TODO: remove dbl-touch loop\n // changing from hierarchy's custom format for data to usable format\n _nodes.forEach(function(node) {\n maxDepth = node.depth > maxDepth ? node.depth : maxDepth; //finding max depth of tree\n nodes.push(node);\n });\n // counting the number of leaf nodes and assigning max depth\n // to nodes that do not have children to flush all the leave nodes\n nodes.forEach(function(node) {\n if (!node.children) {\n //&& !node._children\n numLeaves += 1;\n node.depth = maxDepth; // if a leaf has no child it would be assigned max depth\n }\n });\n\n leafHeight =\n layoutMode === \"Circular\" ? height / numLeaves : leafHeight;\n leafIndex = 0;\n layout(nodes[0], maxDepth, leafHeight, null);\n\n return nodes;\n };\n\n /**\n * -- Function with side effect of adding x0, y0 to all child; take in the root as starting point\n * assuming that the leave nodes would be sorted in presented order\n * horizontal(y0) is calculated according to (= evo dist X depth separation) from their parent\n * vertical (x0) - if leave node: find its order in all of the leave node === node.id,\n * then multiply by verticalSeparation\n * - if parent node: is place in the mid point all of its children nodes\n * -- The layout will first calculate the y0 field going towards the leaves, and x0 when returning\n */\n function layout(node, maxDepth, vertSeparation, parent) {\n var children = node.children,\n sumChildVertSeparation = 0;\n\n // calculation of node's dist from parents, going down.\n var dist = node.dist || defaultDist;\n dist = dist > 1 ? 1 : dist; // We constrain all dist to be less than one\n node.dist = dist;\n if (parent !== null) {\n node.y0 = parent.y0 + dist * depthSeparation;\n } else {\n //root node\n node.y0 = maxTextWidth;\n }\n\n // if a node have no children, we will treat it as a leaf and start laying it out first\n if (!children) {\n node.x0 = leafIndex * vertSeparation;\n leafIndex += 1;\n } else {\n // if it has children, we will visit all its children and calculate its position from its children\n children.forEach(function(child) {\n child.parent = node;\n sumChildVertSeparation += layout(\n child,\n maxDepth,\n vertSeparation,\n node\n );\n });\n node.x0 = sumChildVertSeparation / children.length;\n }\n\n // adding properties to the newly created node\n node.x = node.x0;\n node.y = node.y0;\n return node.x0;\n }\n return self;\n }\n\n /**\n * -- PhyloTree Model --\n */\n var PhyloTree = visualization_mod.Visualization.extend({\n defaults: {\n layout: \"Linear\",\n separation: 250, // px dist between nodes of different depth to represent 1 evolutionary until\n leafHeight: 18,\n type: \"phyloviz\", // visualization type\n title: \"Title\",\n scaleFactor: 1,\n translate: [0, 0],\n fontSize: 12, //fontSize of node label\n selectedNode: null,\n nodeAttrChangedTime: 0\n },\n\n initialize: function(options) {\n this.set(\n \"dataset\",\n new data_mod.Dataset({\n id: options.dataset_id\n })\n );\n },\n\n root: {}, // Root has to be its own independent object because it is not part of the viz_config\n\n /**\n * Mechanism to expand or contract a single node. Expanded nodes have a children list, while for\n * contracted nodes the list is stored in _children. Nodes with their children data stored in _children will not\n * have their children rendered.\n */\n toggle: function(d) {\n if (typeof d === \"undefined\") {\n return;\n }\n if (d.children) {\n d._children = d.children;\n d.children = null;\n } else {\n d.children = d._children;\n d._children = null;\n }\n },\n\n /**\n * Contracts the phylotree to a single node by repeatedly calling itself to place all the list\n * of children under _children.\n */\n toggleAll: function(d) {\n if (d.children && d.children.length !== 0) {\n d.children.forEach(this.toggleAll);\n toggle(d);\n }\n },\n\n /**\n * Return the data of the tree. Used for preserving state.\n */\n getData: function() {\n return this.root;\n },\n\n /**\n * Overriding the default save mechanism to do some clean of circular reference of the\n * phyloTree and to include phyloTree in the saved json\n */\n save: function() {\n var root = this.root;\n cleanTree(root);\n //this.set(\"root\", root);\n\n function cleanTree(node) {\n // we need to remove parent to delete circular reference\n delete node.parent;\n\n // removing unnecessary attributes\n if (node._selected) {\n delete node._selected;\n }\n\n if (node.children) {\n node.children.forEach(cleanTree);\n }\n if (node._children) {\n node._children.forEach(cleanTree);\n }\n }\n\n var config = jQuery.extend(true, {}, this.attributes);\n config.selectedNode = null;\n\n show_message(\"Saving to Galaxy\", \"progress\");\n\n return $.ajax({\n url: this.url(),\n type: \"POST\",\n dataType: \"json\",\n data: {\n config: JSON.stringify(config),\n type: \"phyloviz\"\n },\n success: function(res) {\n hide_modal();\n }\n });\n }\n });\n\n // -- Views --\n /**\n * Stores the default variable for setting up the visualization\n */\n var PhylovizLayoutBase = Backbone.View.extend({\n defaults: {\n nodeRadius: 4.5 // radius of each node in the diagram\n },\n\n /**\n * Common initialization in layouts\n */\n stdInit: function(options) {\n var self = this;\n self.model.on(\n \"change:separation change:leafHeight change:fontSize change:nodeAttrChangedTime\",\n self.updateAndRender,\n self\n );\n\n self.vis = options.vis;\n self.i = 0;\n self.maxDepth = -1; // stores the max depth of the tree\n\n self.width = options.width;\n self.height = options.height;\n },\n\n /**\n * Updates the visualization whenever there are changes in the expansion and contraction of nodes\n * AND possibly when the tree is edited.\n */\n updateAndRender: function(source) {\n var vis = d3.select(\".vis\"),\n self = this;\n source = source || self.model.root;\n\n self.renderNodes(source);\n self.renderLinks(source);\n self.addTooltips();\n },\n\n /**\n * Renders the links for the visualization.\n */\n renderLinks: function(source) {\n var self = this;\n var diagonal = self.diagonal;\n var duration = self.duration;\n var layoutMode = self.layoutMode;\n var link = self.vis\n .selectAll(\"g.completeLink\")\n .data(self.tree.links(self.nodes), function(d) {\n return d.target.id;\n });\n\n var calcalateLinePos = function(d) {\n // position of the source node <=> starting location of the line drawn\n d.pos0 = d.source.y0 + \" \" + d.source.x0;\n // position where the line makes a right angle bend\n d.pos1 = d.source.y0 + \" \" + d.target.x0;\n // point where the horizontal line becomes a dotted line\n d.pos2 = d.target.y0 + \" \" + d.target.x0;\n };\n\n var linkEnter = link\n .enter()\n .insert(\"svg:g\", \"g.node\")\n .attr(\"class\", \"completeLink\");\n\n linkEnter\n .append(\"svg:path\")\n .attr(\"class\", \"link\")\n .attr(\"d\", function(d) {\n calcalateLinePos(d);\n return \"M \" + d.pos0 + \" L \" + d.pos1;\n });\n\n var linkUpdate = link.transition().duration(500);\n\n linkUpdate.select(\"path.link\").attr(\"d\", function(d) {\n calcalateLinePos(d);\n return \"M \" + d.pos0 + \" L \" + d.pos1 + \" L \" + d.pos2;\n });\n\n var linkExit = link.exit().remove();\n },\n\n // User Interaction methods below\n\n /**\n * Displays the information for editing\n */\n selectNode: function(node) {\n var self = this;\n d3\n .selectAll(\"g.node\")\n .classed(\"selectedHighlight\", function(d) {\n if (node.id === d.id) {\n if (node._selected) {\n // for de=selecting node.\n delete node._selected;\n return false;\n } else {\n node._selected = true;\n return true;\n }\n }\n return false;\n });\n\n self.model.set(\"selectedNode\", node);\n $(\"#phyloVizSelectedNodeName\").val(node.name);\n $(\"#phyloVizSelectedNodeDist\").val(node.dist);\n $(\"#phyloVizSelectedNodeAnnotation\").val(node.annotation || \"\");\n },\n\n /**\n * Creates bootstrap tooltip for the visualization. Has to be called repeatedly due to newly generated\n * enterNodes\n */\n addTooltips: function() {\n $(\".tooltip\").remove(); //clean up tooltip, just in case its listeners are removed by d3\n $(\".node\")\n .attr(\"data-original-title\", function() {\n var d = this.__data__,\n annotation = d.annotation || \"None\";\n return d\n ? (d.name ? d.name + \"
\" : \"\") +\n \"Dist: \" +\n d.dist +\n \"
Annotation1: \" +\n annotation +\n (d.bootstrap\n ? \"
Confidence level: \" +\n Math.round(100 * d.bootstrap)\n : \"\")\n : \"\";\n })\n .tooltip({ placement: \"top\", trigger: \"hover\" });\n }\n });\n\n /**\n * Linea layout class of Phyloviz, is responsible for rendering the nodes\n * calls PhyloTreeLayout to determine the positions of the nodes\n */\n var PhylovizLinearView = PhylovizLayoutBase.extend({\n initialize: function(options) {\n // Default values of linear layout\n var self = this;\n self.margins = options.margins;\n self.layoutMode = \"Linear\";\n\n self.stdInit(options);\n\n self.layout();\n self.updateAndRender(self.model.root);\n },\n\n /**\n * Creates the basic layout of a linear tree by precalculating fixed values.\n * One of calculations are also made here\n */\n layout: function() {\n var self = this;\n self.tree = new PhyloTreeLayout().layoutMode(\"Linear\");\n self.diagonal = d3.svg.diagonal().projection(function(d) {\n return [d.y, d.x];\n });\n },\n\n /**\n * Renders the nodes base on Linear layout.\n */\n renderNodes: function(source) {\n var self = this,\n fontSize = self.model.get(\"fontSize\") + \"px\";\n\n // assigning properties from models\n self.tree\n .separation(self.model.get(\"separation\"))\n .leafHeight(self.model.get(\"leafHeight\"));\n\n var duration = 500,\n nodes = self.tree\n .separation(self.model.get(\"separation\"))\n .nodes(self.model.root);\n\n var node = self.vis\n .selectAll(\"g.node\")\n .data(nodes, function(d) {\n return d.name + d.id || (d.id = ++self.i);\n });\n\n // These variables has to be passed into update links which are in the base methods\n self.nodes = nodes;\n self.duration = duration;\n\n // ------- D3 ENTRY --------\n // Enter any new nodes at the parent's previous position.\n var nodeEnter = node\n .enter()\n .append(\"svg:g\")\n .attr(\"class\", \"node\")\n .on(\"dblclick\", function() {\n d3.event.stopPropagation();\n })\n .on(\"click\", function(d) {\n if (d3.event.altKey) {\n self.selectNode(d); // display info if alt is pressed\n } else {\n if (d.children && d.children.length === 0) {\n return;\n } // there is no need to toggle leaves\n self.model.toggle(d); // contract/expand nodes at data level\n self.updateAndRender(d); // re-render the tree\n }\n });\n //TODO: newick and phyloxml return arrays. where should this go (client (here, else), server)?\n if (toString.call(source) === \"[object Array]\") {\n // if d is an array, replate with the first object (newick, phyloxml)\n source = source[0];\n }\n nodeEnter.attr(\"transform\", function(d) {\n return \"translate(\" + source.y0 + \",\" + source.x0 + \")\";\n });\n\n nodeEnter\n .append(\"svg:circle\")\n .attr(\"r\", 1e-6)\n .style(\"fill\", function(d) {\n return d._children ? \"lightsteelblue\" : \"#fff\";\n });\n\n nodeEnter\n .append(\"svg:text\")\n .attr(\"class\", \"nodeLabel\")\n .attr(\"x\", function(d) {\n return d.children || d._children ? -10 : 10;\n })\n .attr(\"dy\", \".35em\")\n .attr(\"text-anchor\", function(d) {\n return d.children || d._children ? \"end\" : \"start\";\n })\n .style(\"fill-opacity\", 1e-6);\n\n // ------- D3 TRANSITION --------\n // Transition nodes to their new position.\n var nodeUpdate = node.transition().duration(duration);\n\n nodeUpdate.attr(\"transform\", function(d) {\n return \"translate(\" + d.y + \",\" + d.x + \")\";\n });\n\n nodeUpdate\n .select(\"circle\")\n .attr(\"r\", self.defaults.nodeRadius)\n .style(\"fill\", function(d) {\n return d._children ? \"lightsteelblue\" : \"#fff\";\n });\n\n nodeUpdate\n .select(\"text\")\n .style(\"fill-opacity\", 1)\n .style(\"font-size\", fontSize)\n .text(function(d) {\n return d.name && d.name !== \"\"\n ? d.name\n : d.bootstrap ? Math.round(100 * d.bootstrap) : \"\";\n });\n\n // ------- D3 EXIT --------\n // Transition exiting nodes to the parent's new position.\n var nodeExit = node\n .exit()\n .transition()\n .duration(duration)\n .remove();\n\n nodeExit.select(\"circle\").attr(\"r\", 1e-6);\n\n nodeExit.select(\"text\").style(\"fill-opacity\", 1e-6);\n\n // Stash the old positions for transition.\n nodes.forEach(function(d) {\n d.x0 = d.x; // we need the x0, y0 for parents with children\n d.y0 = d.y;\n });\n }\n });\n\n var PhylovizView = Backbone.View.extend({\n className: \"phyloviz\",\n\n initialize: function(options) {\n var self = this;\n // -- Default values of the vis\n self.MIN_SCALE = 0.05; //for zooming\n self.MAX_SCALE = 5;\n self.MAX_DISPLACEMENT = 500;\n self.margins = [10, 60, 10, 80];\n\n self.width = $(\"#PhyloViz\").width();\n self.height = $(\"#PhyloViz\").height();\n self.radius = self.width;\n self.data = options.data;\n\n // -- Events Phyloviz view responses to\n $(window).resize(function() {\n self.width = $(\"#PhyloViz\").width();\n self.height = $(\"#PhyloViz\").height();\n self.render();\n });\n\n // -- Create phyloTree model\n self.phyloTree = new PhyloTree(options.config);\n self.phyloTree.root = self.data;\n\n // -- Set up UI functions of main view\n self.zoomFunc = d3.behavior\n .zoom()\n .scaleExtent([self.MIN_SCALE, self.MAX_SCALE]);\n self.zoomFunc.translate(self.phyloTree.get(\"translate\"));\n self.zoomFunc.scale(self.phyloTree.get(\"scaleFactor\"));\n\n // -- set up header buttons, search and settings menu\n self.navMenu = new HeaderButtons(self);\n self.settingsMenu = new SettingsMenu({\n phyloTree: self.phyloTree\n });\n self.nodeSelectionView = new NodeSelectionView({\n phyloTree: self.phyloTree\n });\n self.search = new PhyloVizSearch();\n\n // using settimeout to call the zoomAndPan function according to the stored attributes in viz_config\n setTimeout(function() {\n self.zoomAndPan();\n }, 1000);\n },\n\n render: function() {\n // -- Creating helper function for vis. --\n var self = this;\n $(\"#PhyloViz\").empty();\n\n // -- Layout viz. --\n self.mainSVG = d3\n .select(\"#PhyloViz\")\n .append(\"svg:svg\")\n .attr(\"width\", self.width)\n .attr(\"height\", self.height)\n .attr(\"pointer-events\", \"all\")\n .call(\n self.zoomFunc.on(\"zoom\", function() {\n self.zoomAndPan();\n })\n );\n\n self.boundingRect = self.mainSVG\n .append(\"svg:rect\")\n .attr(\"class\", \"boundingRect\")\n .attr(\"width\", self.width)\n .attr(\"height\", self.height)\n .attr(\"stroke\", \"black\")\n .attr(\"fill\", \"white\");\n\n self.vis = self.mainSVG.append(\"svg:g\").attr(\"class\", \"vis\");\n\n self.layoutOptions = {\n model: self.phyloTree,\n width: self.width,\n height: self.height,\n vis: self.vis,\n margins: self.margins\n };\n\n // -- Creating Title\n $(\"#title\").text(\n \"Phylogenetic Tree from \" +\n self.phyloTree.get(\"title\") +\n \":\"\n );\n\n // -- Create Linear view instance --\n var linearView = new PhylovizLinearView(self.layoutOptions);\n },\n\n /**\n * Function to zoom and pan the svg element which the entire tree is contained within\n * Uses d3.zoom events, and extend them to allow manual updates and keeping states in model\n */\n zoomAndPan: function(event) {\n var zoomParams, translateParams;\n if (typeof event !== \"undefined\") {\n zoomParams = event.zoom;\n translateParams = event.translate;\n }\n\n var self = this,\n scaleFactor = self.zoomFunc.scale(),\n translationCoor = self.zoomFunc.translate(),\n zoomStatement = \"\",\n translateStatement = \"\";\n\n // Do manual scaling.\n switch (zoomParams) {\n case \"reset\":\n scaleFactor = 1.0;\n translationCoor = [0, 0];\n break;\n case \"+\":\n scaleFactor *= 1.1;\n break;\n case \"-\":\n scaleFactor *= 0.9;\n break;\n default:\n if (typeof zoomParams === \"number\") {\n scaleFactor = zoomParams;\n } else if (d3.event !== null) {\n scaleFactor = d3.event.scale;\n }\n }\n if (\n scaleFactor < self.MIN_SCALE ||\n scaleFactor > self.MAX_SCALE\n ) {\n return;\n }\n self.zoomFunc.scale(scaleFactor); //update scale Factor\n zoomStatement =\n \"translate(\" +\n self.margins[3] +\n \",\" +\n self.margins[0] +\n \")\" +\n \" scale(\" +\n scaleFactor +\n \")\";\n\n // Do manual translation.\n if (d3.event !== null) {\n translateStatement =\n \"translate(\" + d3.event.translate + \")\";\n } else {\n if (typeof translateParams !== \"undefined\") {\n var x = translateParams.split(\",\")[0];\n var y = translateParams.split(\",\")[1];\n if (!isNaN(x) && !isNaN(y)) {\n translationCoor = [\n translationCoor[0] + parseFloat(x),\n translationCoor[1] + parseFloat(y)\n ];\n }\n }\n self.zoomFunc.translate(translationCoor); // update zoomFunc\n translateStatement = \"translate(\" + translationCoor + \")\";\n }\n\n self.phyloTree.set(\"scaleFactor\", scaleFactor);\n self.phyloTree.set(\"translate\", translationCoor);\n //refers to the view that we are actually zooming\n self.vis.attr(\"transform\", translateStatement + zoomStatement);\n },\n\n /**\n * Primes the Ajax URL to load another Nexus tree\n */\n reloadViz: function() {\n var self = this,\n treeIndex = $(\"#phylovizNexSelector :selected\").val();\n $.getJSON(\n self.phyloTree.get(\"dataset\").url(),\n {\n tree_index: treeIndex,\n data_type: \"raw_data\"\n },\n function(packedJson) {\n self.data = packedJson.data;\n self.config = packedJson;\n self.render();\n }\n );\n }\n });\n\n var HeaderButtons = Backbone.View.extend({\n initialize: function(phylovizView) {\n var self = this;\n self.phylovizView = phylovizView;\n\n // Clean up code - if the class initialized more than once\n $(\"#panelHeaderRightBtns\").empty();\n $(\"#phyloVizNavBtns\").empty();\n $(\"#phylovizNexSelector\").off();\n\n self.initNavBtns();\n self.initRightHeaderBtns();\n\n // Initial a tree selector in the case of nexus\n $(\"#phylovizNexSelector\")\n .off()\n .on(\"change\", function() {\n self.phylovizView.reloadViz();\n });\n },\n\n initRightHeaderBtns: function() {\n var self = this;\n\n var rightMenu = mod_icon_btn.create_icon_buttons_menu(\n [\n {\n icon_class: \"gear\",\n title: \"PhyloViz Settings\",\n on_click: function() {\n $(\"#SettingsMenu\").show();\n self.settingsMenu.updateUI();\n }\n },\n {\n icon_class: \"disk\",\n title: \"Save visualization\",\n on_click: function() {\n var nexSelected = $(\n \"#phylovizNexSelector option:selected\"\n ).text();\n if (nexSelected) {\n self.phylovizView.phyloTree.set(\n \"title\",\n nexSelected\n );\n }\n self.phylovizView.phyloTree.save();\n }\n },\n {\n icon_class: \"chevron-expand\",\n title: \"Search / Edit Nodes\",\n on_click: function() {\n $(\"#nodeSelectionView\").show();\n }\n },\n {\n icon_class: \"information\",\n title: \"Phyloviz Help\",\n on_click: function() {\n window.open(\n \"https://galaxyproject.org/learn/visualization/phylogenetic-tree/\"\n );\n // https://docs.google.com/document/d/1AXFoJgEpxr21H3LICRs3EyMe1B1X_KFPouzIgrCz3zk/edit\n }\n }\n ],\n {\n tooltip_config: { placement: \"bottom\" }\n }\n );\n $(\"#panelHeaderRightBtns\").append(rightMenu.$el);\n },\n\n initNavBtns: function() {\n var self = this,\n navMenu = mod_icon_btn.create_icon_buttons_menu(\n [\n {\n icon_class: \"zoom-in\",\n title: \"Zoom in\",\n on_click: function() {\n self.phylovizView.zoomAndPan({ zoom: \"+\" });\n }\n },\n {\n icon_class: \"zoom-out\",\n title: \"Zoom out\",\n on_click: function() {\n self.phylovizView.zoomAndPan({ zoom: \"-\" });\n }\n },\n {\n icon_class: \"arrow-circle\",\n title: \"Reset Zoom/Pan\",\n on_click: function() {\n self.phylovizView.zoomAndPan({\n zoom: \"reset\"\n });\n }\n }\n ],\n {\n tooltip_config: { placement: \"bottom\" }\n }\n );\n $(\"#phyloVizNavBtns\").append(navMenu.$el);\n }\n });\n\n var SettingsMenu = UserMenuBase.extend({\n className: \"Settings\",\n\n initialize: function(options) {\n // settings needs to directly interact with the phyloviz model so it will get access to it.\n var self = this;\n self.phyloTree = options.phyloTree;\n self.el = $(\"#SettingsMenu\");\n self.inputs = {\n separation: $(\"#phyloVizTreeSeparation\"),\n leafHeight: $(\"#phyloVizTreeLeafHeight\"),\n fontSize: $(\"#phyloVizTreeFontSize\")\n };\n\n //init all buttons of settings\n $(\"#settingsCloseBtn\")\n .off()\n .on(\"click\", function() {\n self.el.hide();\n });\n $(\"#phylovizResetSettingsBtn\")\n .off()\n .on(\"click\", function() {\n self.resetToDefaults();\n });\n $(\"#phylovizApplySettingsBtn\")\n .off()\n .on(\"click\", function() {\n self.apply();\n });\n },\n\n /**\n * Applying user values to phylotree model.\n */\n apply: function() {\n var self = this;\n if (\n !self.isAcceptableValue(self.inputs.separation, 50, 2500) ||\n !self.isAcceptableValue(self.inputs.leafHeight, 5, 30) ||\n !self.isAcceptableValue(self.inputs.fontSize, 5, 20)\n ) {\n return;\n }\n $.each(self.inputs, function(key, $input) {\n self.phyloTree.set(key, $input.val());\n });\n },\n /**\n * Called to update the values input to that stored in the model\n */\n updateUI: function() {\n var self = this;\n $.each(self.inputs, function(key, $input) {\n $input.val(self.phyloTree.get(key));\n });\n },\n /**\n * Resets the value of the phyloTree model to its default\n */\n resetToDefaults: function() {\n $(\".tooltip\").remove(); // just in case the tool tip was not removed\n var self = this;\n $.each(self.phyloTree.defaults, function(key, value) {\n self.phyloTree.set(key, value);\n });\n self.updateUI();\n },\n\n render: function() {}\n });\n\n /**\n * View for inspecting node properties and editing them\n */\n var NodeSelectionView = UserMenuBase.extend({\n className: \"Settings\",\n\n initialize: function(options) {\n var self = this;\n self.el = $(\"#nodeSelectionView\");\n self.phyloTree = options.phyloTree;\n\n self.UI = {\n enableEdit: $(\"#phylovizEditNodesCheck\"),\n saveChanges: $(\"#phylovizNodeSaveChanges\"),\n cancelChanges: $(\"#phylovizNodeCancelChanges\"),\n name: $(\"#phyloVizSelectedNodeName\"),\n dist: $(\"#phyloVizSelectedNodeDist\"),\n annotation: $(\"#phyloVizSelectedNodeAnnotation\")\n };\n\n // temporarily stores the values in case user change their mind\n self.valuesOfConcern = {\n name: null,\n dist: null,\n annotation: null\n };\n\n //init UI buttons\n $(\"#nodeSelCloseBtn\")\n .off()\n .on(\"click\", function() {\n self.el.hide();\n });\n self.UI.saveChanges.off().on(\"click\", function() {\n self.updateNodes();\n });\n self.UI.cancelChanges.off().on(\"click\", function() {\n self.cancelChanges();\n });\n\n (function($) {\n // extending jquery fxn for enabling and disabling nodes.\n $.fn.enable = function(isEnabled) {\n return $(this).each(function() {\n if (isEnabled) {\n $(this).removeAttr(\"disabled\");\n } else {\n $(this).attr(\"disabled\", \"disabled\");\n }\n });\n };\n })(jQuery);\n\n self.UI.enableEdit.off().on(\"click\", function() {\n self.toggleUI();\n });\n },\n\n /**\n * For turning on and off the child elements\n */\n toggleUI: function() {\n var self = this,\n checked = self.UI.enableEdit.is(\":checked\");\n\n if (!checked) {\n self.cancelChanges();\n }\n\n $.each(self.valuesOfConcern, function(key, value) {\n self.UI[key].enable(checked);\n });\n if (checked) {\n self.UI.saveChanges.show();\n self.UI.cancelChanges.show();\n } else {\n self.UI.saveChanges.hide();\n self.UI.cancelChanges.hide();\n }\n },\n\n /**\n * Reverting to previous values in case user change their minds\n */\n cancelChanges: function() {\n var self = this,\n node = self.phyloTree.get(\"selectedNode\");\n if (node) {\n $.each(self.valuesOfConcern, function(key, value) {\n self.UI[key].val(node[key]);\n });\n }\n },\n\n /**\n * Changing the data in the underlying tree with user-specified values\n */\n updateNodes: function() {\n var self = this,\n node = self.phyloTree.get(\"selectedNode\");\n if (node) {\n if (\n !self.isAcceptableValue(self.UI.dist, 0, 1) ||\n self.hasIllegalJsonCharacters(self.UI.name) ||\n self.hasIllegalJsonCharacters(self.UI.annotation)\n ) {\n return;\n }\n $.each(self.valuesOfConcern, function(key, value) {\n node[key] = self.UI[key].val();\n });\n self.phyloTree.set(\"nodeAttrChangedTime\", new Date());\n } else {\n alert(\"No node selected\");\n }\n }\n });\n\n /**\n * Initializes the search panel on phyloviz and handles its user interaction\n * It allows user to search the entire free based on some qualifer, like dist <= val.\n */\n var PhyloVizSearch = UserMenuBase.extend({\n initialize: function() {\n var self = this;\n\n $(\"#phyloVizSearchBtn\").on(\"click\", function() {\n var searchTerm = $(\"#phyloVizSearchTerm\"),\n searchConditionVal = $(\"#phyloVizSearchCondition\")\n .val()\n .split(\"-\"),\n attr = searchConditionVal[0],\n condition = searchConditionVal[1];\n self.hasIllegalJsonCharacters(searchTerm);\n\n if (attr === \"dist\") {\n self.isAcceptableValue(searchTerm, 0, 1);\n }\n self.searchTree(attr, condition, searchTerm.val());\n });\n },\n\n /**\n * Searches the entire tree and will highlight the nodes that match the condition in green\n */\n searchTree: function(attr, condition, val) {\n d3.selectAll(\"g.node\").classed(\"searchHighlight\", function(d) {\n var attrVal = d[attr];\n if (typeof attrVal !== \"undefined\" && attrVal !== null) {\n if (attr === \"dist\") {\n switch (condition) {\n case \"greaterEqual\":\n return attrVal >= +val;\n case \"lesserEqual\":\n return attrVal <= +val;\n default:\n return;\n }\n } else if (attr === \"name\" || attr === \"annotation\") {\n return (\n attrVal\n .toLowerCase()\n .indexOf(val.toLowerCase()) !== -1\n );\n }\n }\n });\n }\n });\n\n return {\n PhylovizView: PhylovizView\n };\n }\n);\n"]} \ No newline at end of file diff --git a/static/maps/viz/sweepster.js.map b/static/maps/viz/sweepster.js.map index fe9fb9c2e18..0d86fcab779 100644 --- a/static/maps/viz/sweepster.js.map +++ b/static/maps/viz/sweepster.js.map @@ -1 +1 @@ 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* Visualization and components for Sweepster, a visualization for exploring a tool's parameter space via\n * genomic visualization.\n */\n\ndefine(\n [\n \"libs/underscore\",\n \"libs/d3\",\n \"viz/trackster/util\",\n \"viz/visualization\",\n \"viz/trackster/tracks\",\n \"mvc/tool/tools\",\n \"mvc/dataset/data\",\n \"utils/config\",\n \"mvc/ui/icon-button\"\n ],\n function(\n _,\n d3,\n util,\n visualization,\n tracks,\n tools,\n data,\n config,\n mod_icon_btn\n ) {\n /**\n * A collection of tool input settings. Object is useful for keeping a list of settings\n * for future use without changing the input's value and for preserving inputs order.\n */\n var ToolInputsSettings = Backbone.Model.extend({\n defaults: {\n inputs: null,\n values: null\n }\n });\n\n /**\n * Tree for a tool's parameters.\n */\n var ToolParameterTree = Backbone.Model.extend({\n defaults: {\n tool: null,\n tree_data: null\n },\n\n initialize: function(options) {\n // Set up tool parameters to work with tree.\n var self = this;\n this.get(\"tool\")\n .get(\"inputs\")\n .each(function(input) {\n // Listen for changes to input's attributes.\n input.on(\n \"change:min change:max change:num_samples\",\n function(input) {\n if (input.get(\"in_ptree\")) {\n self.set_tree_data();\n }\n },\n self\n );\n input.on(\n \"change:in_ptree\",\n function(input) {\n if (input.get(\"in_ptree\")) {\n self.add_param(input);\n } else {\n self.remove_param(input);\n }\n self.set_tree_data();\n },\n self\n );\n });\n\n // If there is a config, use it.\n if (options.config) {\n _.each(options.config, function(input_config) {\n var input = self\n .get(\"tool\")\n .get(\"inputs\")\n .find(function(input) {\n return input.get(\"name\") === input_config.name;\n });\n self.add_param(input);\n input.set(input_config);\n });\n }\n },\n\n add_param: function(param) {\n // If parameter already present, do not add it.\n if (param.get(\"ptree_index\")) {\n return;\n }\n\n param.set(\"in_ptree\", true);\n param.set(\"ptree_index\", this.get_tree_params().length);\n },\n\n remove_param: function(param) {\n // Remove param from tree.\n param.set(\"in_ptree\", false);\n param.set(\"ptree_index\", null);\n\n // Update ptree indices for remaining params.\n _(this.get_tree_params()).each(function(input, index) {\n // +1 to use 1-based indexing.\n input.set(\"ptree_index\", index + 1);\n });\n },\n\n /**\n * Sets tree data using tool's inputs.\n */\n set_tree_data: function() {\n // Get samples for each parameter.\n var params_samples = _.map(this.get_tree_params(), function(\n param\n ) {\n return {\n param: param,\n samples: param.get_samples()\n };\n });\n var node_id = 0,\n // Creates tree data recursively.\n create_tree_data = function(params_samples, index) {\n var param_samples = params_samples[index],\n param = param_samples.param,\n param_label = param.get(\"label\"),\n settings = param_samples.samples;\n\n // Create leaves when last parameter setting is reached.\n if (params_samples.length - 1 === index) {\n return _.map(settings, function(setting) {\n return {\n id: node_id++,\n name: setting,\n param: param,\n value: setting\n };\n });\n }\n\n // Recurse to handle other parameters.\n return _.map(settings, function(setting) {\n return {\n id: node_id++,\n name: setting,\n param: param,\n value: setting,\n children: create_tree_data(\n params_samples,\n index + 1\n )\n };\n });\n };\n\n this.set(\"tree_data\", {\n name: \"Root\",\n id: node_id++,\n children:\n params_samples.length !== 0\n ? create_tree_data(params_samples, 0)\n : null\n });\n },\n\n get_tree_params: function() {\n // Filter and sort parameters to get list in tree.\n return _(\n this.get(\"tool\")\n .get(\"inputs\")\n .where({ in_ptree: true })\n ).sortBy(function(input) {\n return input.get(\"ptree_index\");\n });\n },\n\n /**\n * Returns number of leaves in tree.\n */\n get_num_leaves: function() {\n return this.get_tree_params().reduce(function(memo, param) {\n return memo * param.get_samples().length;\n }, 1);\n },\n\n /**\n * Returns array of ToolInputsSettings objects based on a node and its subtree.\n */\n get_node_settings: function(target_node) {\n // -- Get fixed settings from tool and parent nodes.\n\n // Start with tool's settings.\n var fixed_settings = this.get(\"tool\").get_inputs_dict();\n\n // Get fixed settings using node's parents.\n var cur_node = target_node.parent;\n if (cur_node) {\n while (cur_node.depth !== 0) {\n fixed_settings[cur_node.param.get(\"name\")] =\n cur_node.value;\n cur_node = cur_node.parent;\n }\n }\n\n // Walk subtree starting at clicked node to get full list of settings.\n var self = this,\n get_settings = function(node, settings) {\n // Add setting for this node. Root node does not have a param,\n // however.\n if (node.param) {\n settings[node.param.get(\"name\")] = node.value;\n }\n\n if (!node.children) {\n // At leaf node, so return settings.\n return new ToolInputsSettings({\n inputs: self.get(\"tool\").get(\"inputs\"),\n values: settings\n });\n } else {\n // At interior node: return list of subtree settings.\n return _.flatten(\n _.map(node.children, function(c) {\n return get_settings(c, _.clone(settings));\n })\n );\n }\n },\n all_settings = get_settings(target_node, fixed_settings);\n\n // If user clicked on leaf, settings is a single dict. Convert to array for simplicity.\n if (!_.isArray(all_settings)) {\n all_settings = [all_settings];\n }\n\n return all_settings;\n },\n\n /**\n * Returns all nodes connected a particular node; this includes parents and children of the node.\n */\n get_connected_nodes: function(node) {\n var get_subtree_nodes = function(a_node) {\n if (!a_node.children) {\n return a_node;\n } else {\n // At interior node: return subtree nodes.\n return _.flatten([\n a_node,\n _.map(a_node.children, function(c) {\n return get_subtree_nodes(c);\n })\n ]);\n }\n };\n\n // Get node's parents.\n var parents = [],\n cur_parent = node.parent;\n while (cur_parent) {\n parents.push(cur_parent);\n cur_parent = cur_parent.parent;\n }\n\n return _.flatten([parents, get_subtree_nodes(node)]);\n },\n\n /**\n * Returns the leaf that corresponds to a settings collection.\n */\n get_leaf: function(settings) {\n var cur_node = this.get(\"tree_data\"),\n find_child = function(children) {\n return _.find(children, function(child) {\n return (\n settings[child.param.get(\"name\")] ===\n child.value\n );\n });\n };\n\n while (cur_node.children) {\n cur_node = find_child(cur_node.children);\n }\n return cur_node;\n },\n\n /**\n * Returns a list of parameters used in tree.\n */\n toJSON: function() {\n // FIXME: returning and jsonifying complete param causes trouble on the server side,\n // so just use essential attributes for now.\n return this.get_tree_params().map(function(param) {\n return {\n name: param.get(\"name\"),\n min: param.get(\"min\"),\n max: param.get(\"max\"),\n num_samples: param.get(\"num_samples\")\n };\n });\n }\n });\n\n var SweepsterTrack = Backbone.Model.extend({\n defaults: {\n track: null,\n mode: \"Pack\",\n settings: null,\n regions: null\n },\n\n initialize: function(options) {\n this.set(\"regions\", options.regions);\n if (options.track) {\n // FIXME: find a better way to deal with needed URLs:\n var track_config = _.extend(\n {\n data_url: Galaxy.root + \"dummy1\",\n converted_datasets_state_url: Galaxy.root + \"dummy2\"\n },\n options.track\n );\n this.set(\n \"track\",\n tracks.object_from_template(track_config, {}, null)\n );\n }\n },\n\n same_settings: function(a_track) {\n var this_settings = this.get(\"settings\"),\n other_settings = a_track.get(\"settings\");\n for (var prop in this_settings) {\n if (\n !other_settings[prop] ||\n this_settings[prop] !== other_settings[prop]\n ) {\n return false;\n }\n }\n return true;\n },\n\n toJSON: function() {\n return {\n track: this.get(\"track\").to_dict(),\n settings: this.get(\"settings\"),\n regions: this.get(\"regions\")\n };\n }\n });\n\n var TrackCollection = Backbone.Collection.extend({\n model: SweepsterTrack\n });\n\n /**\n * Sweepster visualization model.\n */\n var SweepsterVisualization = visualization.Visualization.extend({\n defaults: _.extend(\n {},\n visualization.Visualization.prototype.defaults,\n {\n dataset: null,\n tool: null,\n parameter_tree: null,\n regions: null,\n tracks: null,\n default_mode: \"Pack\"\n }\n ),\n\n initialize: function(options) {\n this.set(\"dataset\", new data.Dataset(options.dataset));\n this.set(\"tool\", new tools.Tool(options.tool));\n this.set(\n \"regions\",\n new visualization.GenomeRegionCollection(options.regions)\n );\n this.set(\"tracks\", new TrackCollection(options.tracks));\n\n var tool_with_samplable_inputs = this.get(\"tool\");\n this.set(\n \"tool_with_samplable_inputs\",\n tool_with_samplable_inputs\n );\n // Remove complex parameters for now.\n tool_with_samplable_inputs.remove_inputs([\n \"data\",\n \"hidden_data\",\n \"conditional\",\n \"text\"\n ]);\n\n this.set(\n \"parameter_tree\",\n new ToolParameterTree({\n tool: tool_with_samplable_inputs,\n config: options.tree_config\n })\n );\n },\n\n add_track: function(track) {\n this.get(\"tracks\").add(track);\n },\n\n toJSON: function() {\n return {\n id: this.get(\"id\"),\n title:\n \"Parameter exploration for dataset '\" +\n this.get(\"dataset\").get(\"name\") +\n \"'\",\n type: \"sweepster\",\n dataset_id: this.get(\"dataset\").id,\n tool_id: this.get(\"tool\").id,\n regions: this.get(\"regions\").toJSON(),\n tree_config: this.get(\"parameter_tree\").toJSON(),\n tracks: this.get(\"tracks\").toJSON()\n };\n }\n });\n\n /**\n * --- Views ---\n */\n\n /**\n * Sweepster track view.\n */\n var SweepsterTrackView = Backbone.View.extend({\n tagName: \"tr\",\n\n TILE_LEN: 250,\n\n initialize: function(options) {\n this.canvas_manager = options.canvas_manager;\n this.render();\n this.model.on(\n \"change:track change:mode\",\n this.draw_tiles,\n this\n );\n },\n\n render: function() {\n // Render settings icon and popup.\n // TODO: use template.\n var settings = this.model.get(\"settings\"),\n values = settings.get(\"values\"),\n settings_td = $(\"\")\n .addClass(\"settings\")\n .appendTo(this.$el),\n settings_div = $(\"\")\n .addClass(\"track-info\")\n .hide()\n .appendTo(settings_td);\n settings_div.append(\n $(\"\")\n .css(\"font-weight\", \"bold\")\n .text(\"Track Settings\")\n );\n settings.get(\"inputs\").each(function(input) {\n settings_div.append(\n input.get(\"label\") +\n \": \" +\n values[input.get(\"name\")] +\n \"
\"\n );\n });\n var self = this,\n run_on_dataset_button = $(\"\")\n .appendTo(settings_div)\n .text(\"Run on complete dataset\")\n .click(function() {\n settings_div.toggle();\n self.trigger(\"run_on_dataset\", settings);\n });\n var icon_menu = mod_icon_btn.create_icon_buttons_menu([\n {\n title: \"Settings\",\n icon_class: \"gear track-settings\",\n on_click: function() {\n settings_div.toggle();\n }\n },\n {\n title: \"Remove\",\n icon_class: \"cross-circle\",\n on_click: function() {\n self.$el.remove();\n $(\".tooltip\").remove();\n // TODO: remove track from viz collection.\n }\n }\n ]);\n settings_td.prepend(icon_menu.$el);\n\n // Render tile placeholders.\n this.model.get(\"regions\").each(function() {\n self.$el.append(\n $(\"\")\n .addClass(\"tile\")\n .html(\n $(\" \").attr(\n \"src\",\n Galaxy.root +\n \"images/loading_large_white_bg.gif\"\n )\n )\n );\n });\n\n if (this.model.get(\"track\")) {\n this.draw_tiles();\n }\n },\n\n /**\n * Draw tiles for regions.\n */\n draw_tiles: function() {\n var self = this,\n track = this.model.get(\"track\"),\n regions = this.model.get(\"regions\"),\n tile_containers = this.$el.find(\"td.tile\");\n\n // Do nothing if track is not defined.\n if (!track) {\n return;\n }\n\n // When data is ready, draw tiles.\n $.when(track.data_manager.data_is_ready()).then(function(\n data_ok\n ) {\n // Draw tile for each region.\n regions.each(function(region, index) {\n var resolution = region.length() / self.TILE_LEN,\n w_scale = 1 / resolution,\n mode = self.model.get(\"mode\");\n $.when(\n track.data_manager.get_data(\n region,\n mode,\n resolution,\n {}\n )\n ).then(function(tile_data) {\n var canvas = self.canvas_manager.new_canvas();\n canvas.width = self.TILE_LEN;\n canvas.height = track.get_canvas_height(\n tile_data,\n mode,\n w_scale,\n canvas.width\n );\n track.draw_tile(\n tile_data,\n canvas.getContext(\"2d\"),\n mode,\n region,\n w_scale\n );\n $(tile_containers[index])\n .empty()\n .append(canvas);\n });\n });\n });\n }\n });\n\n /**\n * Tool input (parameter) that enables both value and sweeping inputs. View is unusual as\n * it augments an existing input form row rather than creates a completely new HTML element.\n */\n var ToolInputValOrSweepView = Backbone.View.extend({\n // Template for rendering sweep inputs:\n number_input_template:\n '
' +\n '\"> - ' +\n '\">' +\n ' samples: \">' +\n \"\",\n\n select_input_template:\n '<%= options %>',\n\n initialize: function(options) {\n this.$el = options.tool_row;\n this.render();\n },\n\n render: function() {\n var input = this.model,\n type = input.get(\"type\"),\n single_input_row = this.$el.find(\".form-row-input\"),\n sweep_inputs_row = null;\n\n // Update tool inputs as single input changes.\n single_input_row.find(\":input\").change(function() {\n input.set(\"value\", $(this).val());\n });\n\n // Add row for parameter sweep inputs.\n if (input instanceof tools.IntegerToolParameter) {\n sweep_inputs_row = $(\n _.template(this.number_input_template)(\n this.model.toJSON()\n )\n );\n } else if (input instanceof tools.SelectToolParameter) {\n var options = _.map(\n this.$el.find(\"select option\"),\n function(option) {\n return $(option).val();\n }\n ),\n options_text = options.join(\", \");\n sweep_inputs_row = $(\n _.template(this.select_input_template)({\n options: options_text\n })\n );\n }\n sweep_inputs_row.insertAfter(single_input_row);\n\n // Add buttons for adding/removing parameter.\n var self = this,\n menu = mod_icon_btn.create_icon_buttons_menu(\n [\n {\n title: \"Add parameter to tree\",\n icon_class: \"plus-button\",\n on_click: function() {\n input.set(\"in_ptree\", true);\n single_input_row.hide();\n sweep_inputs_row.show();\n $(this).hide();\n self.$el.find(\".icon-button.toggle\").show();\n }\n },\n {\n title: \"Remove parameter from tree\",\n icon_class: \"toggle\",\n on_click: function() {\n // Remove parameter from tree params where name matches clicked paramter.\n input.set(\"in_ptree\", false);\n sweep_inputs_row.hide();\n single_input_row.show();\n $(this).hide();\n self.$el\n .find(\".icon-button.plus-button\")\n .show();\n }\n }\n ],\n {}\n );\n this.$el.prepend(menu.$el);\n\n // Show/hide input rows and icons depending on whether parameter is in the tree.\n if (input.get(\"in_ptree\")) {\n single_input_row.hide();\n self.$el.find(\".icon-button.plus-button\").hide();\n } else {\n self.$el.find(\".icon-button.toggle\").hide();\n sweep_inputs_row.hide();\n }\n\n // Update input's min, max, number of samples as values change.\n _.each([\"min\", \"max\", \"num_samples\"], function(attr) {\n sweep_inputs_row.find(\".\" + attr).change(function() {\n input.set(attr, parseFloat($(this).val()));\n });\n });\n }\n });\n\n var ToolParameterTreeDesignView = Backbone.View.extend({\n className: \"tree-design\",\n\n initialize: function(options) {\n this.render();\n },\n\n render: function() {\n // Start with tool form view.\n var tool_form_view = new tools.ToolFormView({\n model: this.model.get(\"tool\")\n });\n tool_form_view.render();\n this.$el.append(tool_form_view.$el);\n\n // Set up views for each tool input.\n var self = this,\n inputs = self.model.get(\"tool\").get(\"inputs\");\n this.$el\n .find(\".form-row\")\n .not(\".form-actions\")\n .each(function(i) {\n var input_view = new ToolInputValOrSweepView({\n model: inputs.at(i),\n tool_row: $(this)\n });\n });\n }\n });\n\n /**\n * Displays and updates parameter tree.\n */\n var ToolParameterTreeView = Backbone.View.extend({\n className: \"tool-parameter-tree\",\n\n initialize: function(options) {\n // When tree data changes, re-render.\n this.model.on(\"change:tree_data\", this.render, this);\n },\n\n render: function() {\n // Start fresh.\n this.$el.children().remove();\n\n var tree_params = this.model.get_tree_params();\n if (!tree_params.length) {\n return;\n }\n\n // Set width, height based on params and samples.\n this.width = 100 * (2 + tree_params.length);\n this.height = 15 * this.model.get_num_leaves();\n\n var self = this;\n\n // Layout tree.\n var cluster = d3.layout\n .cluster()\n .size([this.height, this.width - 160]);\n\n var diagonal = d3.svg.diagonal().projection(function(d) {\n return [d.y, d.x];\n });\n\n // Layout nodes.\n var nodes = cluster.nodes(this.model.get(\"tree_data\"));\n\n // Setup and add labels for tree levels.\n var param_depths = _.uniq(_.pluck(nodes, \"y\"));\n _.each(tree_params, function(param, index) {\n var x = param_depths[index + 1],\n center_left = $(\"#center\").position().left;\n self.$el.append(\n $(\"\")\n .addClass(\"label\")\n .text(param.get(\"label\"))\n .css(\"left\", x + center_left)\n );\n });\n\n // Set up vis element.\n var vis = d3\n .select(this.$el[0])\n .append(\"svg\")\n .attr(\"width\", this.width)\n .attr(\"height\", this.height + 30)\n .append(\"g\")\n .attr(\"transform\", \"translate(40, 20)\");\n\n // Draw links.\n var link = vis\n .selectAll(\"path.link\")\n .data(cluster.links(nodes))\n .enter()\n .append(\"path\")\n .attr(\"class\", \"link\")\n .attr(\"d\", diagonal);\n\n // Draw nodes.\n var node = vis\n .selectAll(\"g.node\")\n .data(nodes)\n .enter()\n .append(\"g\")\n .attr(\"class\", \"node\")\n .attr(\"transform\", function(d) {\n return \"translate(\" + d.y + \",\" + d.x + \")\";\n })\n .on(\"mouseover\", function(a_node) {\n var connected_node_ids = _.pluck(\n self.model.get_connected_nodes(a_node),\n \"id\"\n );\n // TODO: probably can use enter() to do this more easily.\n node\n .filter(function(d) {\n return (\n _.find(connected_node_ids, function(id) {\n return id === d.id;\n }) !== undefined\n );\n })\n .style(\"fill\", \"#f00\");\n })\n .on(\"mouseout\", function() {\n node.style(\"fill\", \"#000\");\n });\n\n node.append(\"circle\").attr(\"r\", 9);\n\n node\n .append(\"text\")\n .attr(\"dx\", function(d) {\n return d.children ? -12 : 12;\n })\n .attr(\"dy\", 3)\n .attr(\"text-anchor\", function(d) {\n return d.children ? \"end\" : \"start\";\n })\n .text(function(d) {\n return d.name;\n });\n }\n });\n\n /**\n * Sweepster visualization view. View requires rendering in 3-panel setup for now.\n */\n var SweepsterVisualizationView = Backbone.View.extend({\n className: \"Sweepster\",\n\n helpText:\n \"\",\n\n initialize: function(options) {\n this.canvas_manager = new visualization.CanvasManager(\n this.$el.parents(\"body\")\n );\n this.tool_param_tree_view = new ToolParameterTreeView({\n model: this.model.get(\"parameter_tree\")\n });\n this.track_collection_container = $(\"Getting Started
\" +\n \"\").addClass(\n \"tracks\"\n );\n\n // Handle node clicks for tree data.\n this.model\n .get(\"parameter_tree\")\n .on(\"change:tree_data\", this.handle_node_clicks, this);\n\n // Each track must have a view so it has a canvas manager.\n var self = this;\n this.model.get(\"tracks\").each(function(track) {\n track.get(\"track\").view = self;\n });\n\n // Set block, reverse strand block colors; these colors will be used for all tracks.\n this.config = config.ConfigSettingCollection.from_models_and_saved_values(\n [\n {\n key: \"name\",\n label: \"Name\",\n type: \"text\",\n default_value: \"\"\n },\n {\n key: \"a_color\",\n label: \"A Color\",\n type: \"color\",\n default_value: \"#FF0000\"\n },\n {\n key: \"c_color\",\n label: \"C Color\",\n type: \"color\",\n default_value: \"#00FF00\"\n },\n {\n key: \"g_color\",\n label: \"G Color\",\n type: \"color\",\n default_value: \"#0000FF\"\n },\n {\n key: \"t_color\",\n label: \"T Color\",\n type: \"color\",\n default_value: \"#FF00FF\"\n },\n {\n key: \"n_color\",\n label: \"N Color\",\n type: \"color\",\n default_value: \"#AAAAAA\"\n },\n {\n key: \"block_color\",\n label: \"Block color\",\n type: \"color\"\n },\n {\n key: \"reverse_strand_color\",\n label: \"Antisense strand color\",\n type: \"color\"\n }\n ],\n {}\n );\n },\n\n render: function() {\n // Render tree design view in left panel.\n var tree_design_view = new ToolParameterTreeDesignView({\n model: this.model.get(\"parameter_tree\")\n });\n\n $(\"#left\").append(tree_design_view.$el);\n\n // Render track collection container/view in right panel.\n var self = this,\n regions = self.model.get(\"regions\"),\n tr = $(\"
\").appendTo(this.track_collection_container);\n\n regions.each(function(region) {\n tr.append($(\" \").text(region.toString()));\n });\n tr\n .children()\n .first()\n .attr(\"colspan\", 2);\n\n var tracks_div = $(\" \").addClass(\"tiles\");\n $(\"#right\").append(\n tracks_div.append(this.track_collection_container)\n );\n\n self.model.get(\"tracks\").each(function(track) {\n self.add_track(track);\n });\n\n // -- Render help and tool parameter tree in center panel. --\n\n // Help includes text and a close button.\n var help_div = $(this.helpText).addClass(\"help\"),\n close_button = mod_icon_btn.create_icon_buttons_menu([\n {\n title: \"Close\",\n icon_class: \"cross-circle\",\n on_click: function() {\n $(\".tooltip\").remove();\n help_div.remove();\n }\n }\n ]);\n\n help_div.prepend(close_button.$el.css(\"float\", \"right\"));\n $(\"#center\").append(help_div);\n\n // Parameter tree:\n this.tool_param_tree_view.render();\n $(\"#center\").append(this.tool_param_tree_view.$el);\n\n // Set up handler for tree node clicks.\n this.handle_node_clicks();\n\n // Set up visualization menu.\n var menu = mod_icon_btn.create_icon_buttons_menu(\n [\n // Save.\n /*\n { icon_class: 'disk--arrow', title: 'Save', on_click: function() {\n // Show saving dialog box\n show_modal(\"Saving...\", \"progress\");\n\n viz.save().success(function(vis_info) {\n hide_modal();\n viz.set({\n 'id': vis_info.vis_id,\n 'has_changes': false\n });\n })\n .error(function() {\n show_modal( \"Could Not Save\", \"Could not save visualization. Please try again later.\",\n { \"Close\" : hide_modal } );\n });\n } },\n */\n // Change track modes.\n {\n icon_class: \"chevron-expand\",\n title: \"Set display mode\"\n },\n // Close viz.\n {\n icon_class: \"cross-circle\",\n title: \"Close\",\n on_click: function() {\n window.location =\n \"${h.url_for( controller='visualization', action='list' )}\";\n }\n }\n ],\n {\n tooltip_config: { placement: \"bottom\" }\n }\n );\n\n // Create mode selection popup. Mode selection changes default mode and mode for all tracks.\n var modes = [\"Squish\", \"Pack\"],\n mode_mapping = {};\n _.each(modes, function(mode) {\n mode_mapping[mode] = function() {\n self.model.set(\"default_mode\", mode);\n self.model.get(\"tracks\").each(function(track) {\n track.set(\"mode\", mode);\n });\n };\n });\n\n make_popupmenu(menu.$el.find(\".chevron-expand\"), mode_mapping);\n\n menu.$el.attr(\"style\", \"float: right\");\n $(\"#right .unified-panel-header-inner\").append(menu.$el);\n },\n\n get_base_color: function(base) {\n return (\n this.config.get_value(base.toLowerCase() + \"_color\") ||\n this.config.get_value(\"n_color\")\n );\n },\n\n run_tool_on_dataset: function(settings) {\n var tool = this.model.get(\"tool\"),\n tool_name = tool.get(\"name\"),\n dataset = this.model.get(\"dataset\");\n tool.set_input_values(settings.get(\"values\"));\n $.when(tool.rerun(dataset)).then(function(outputs) {\n // TODO.\n });\n\n show_modal(\n \"Running \" + tool_name + \" on complete dataset\",\n tool_name +\n \" is running on dataset '\" +\n dataset.get(\"name\") +\n \"'. Outputs are in the dataset's history.\",\n {\n Ok: function() {\n hide_modal();\n }\n }\n );\n },\n\n /**\n * Add track to model and view.\n */\n add_track: function(pm_track) {\n var self = this,\n param_tree = this.model.get(\"parameter_tree\");\n\n // Add track to model.\n self.model.add_track(pm_track);\n\n var track_view = new SweepsterTrackView({\n model: pm_track,\n canvas_manager: self.canvas_manager\n });\n track_view.on(\"run_on_dataset\", self.run_tool_on_dataset, self);\n self.track_collection_container.append(track_view.$el);\n track_view.$el.hover(\n function() {\n var settings_leaf = param_tree.get_leaf(\n pm_track.get(\"settings\").get(\"values\")\n );\n var connected_node_ids = _.pluck(\n param_tree.get_connected_nodes(settings_leaf),\n \"id\"\n );\n\n // TODO: can do faster with enter?\n d3\n .select(self.tool_param_tree_view.$el[0])\n .selectAll(\"g.node\")\n .filter(function(d) {\n return (\n _.find(connected_node_ids, function(id) {\n return id === d.id;\n }) !== undefined\n );\n })\n .style(\"fill\", \"#f00\");\n },\n function() {\n d3\n .select(self.tool_param_tree_view.$el[0])\n .selectAll(\"g.node\")\n .style(\"fill\", \"#000\");\n }\n );\n return pm_track;\n },\n\n /**\n * Sets up handling when tree nodes are clicked. When a node is clicked, the tool is run for each of\n * the settings defined by the node's subtree and tracks are added for each run.\n */\n handle_node_clicks: function() {\n // When node clicked in tree, run tool and add tracks to model.\n var self = this,\n param_tree = this.model.get(\"parameter_tree\"),\n regions = this.model.get(\"regions\"),\n node = d3\n .select(this.tool_param_tree_view.$el[0])\n .selectAll(\"g.node\");\n node.on(\"click\", function(d, i) {\n // Get all settings corresponding to node.\n var tool = self.model.get(\"tool\"),\n dataset = self.model.get(\"dataset\"),\n all_settings = param_tree.get_node_settings(d),\n run_jobs_deferred = $.Deferred();\n\n // Do not allow 10+ jobs to be run.\n if (all_settings.length >= 10) {\n show_modal(\n \"Whoa there cowboy!\",\n \"You clicked on a node to try \" +\n self.model.get(\"tool\").get(\"name\") +\n \" with \" +\n all_settings.length +\n \" different combinations of settings. You can only run 10 jobs at a time.\",\n {\n Ok: function() {\n hide_modal();\n run_jobs_deferred.resolve(false);\n }\n }\n );\n } else {\n run_jobs_deferred.resolve(true);\n }\n\n // Take action when deferred resolves.\n $.when(run_jobs_deferred).then(function(run_jobs) {\n if (!run_jobs) {\n return;\n }\n\n // Create and add tracks for each settings group.\n var new_tracks = _.map(all_settings, function(\n settings\n ) {\n var pm_track = new SweepsterTrack({\n settings: settings,\n regions: regions,\n mode: self.model.get(\"default_mode\")\n });\n self.add_track(pm_track);\n return pm_track;\n });\n\n // For each track, run tool using track's settings and update track.\n _.each(new_tracks, function(pm_track, index) {\n setTimeout(function() {\n // Set inputs and run tool.\n tool.set_input_values(\n pm_track.get(\"settings\").get(\"values\")\n );\n $.when(\n tool.rerun(dataset, regions)\n ).then(function(output) {\n // HACKish: output is an HDA with track config attribute. To create a track\n // that works correctly with Backbone relational, it is necessary to\n // use a modified version of the track config.\n var dataset = output.first(),\n track_config = dataset.get(\n \"track_config\"\n );\n // Set dataset to be the tool's output.\n track_config.dataset = dataset;\n // Set tool to null so that it is not unpacked; unpacking it messes with\n // the tool parameters and parameter tree.\n track_config.tool = null;\n\n track_config.prefs = self.config.to_key_value_dict();\n\n // Create and add track for output dataset.\n var track_obj = tracks.object_from_template(\n track_config,\n self,\n null\n );\n track_obj.init_for_tool_data();\n\n pm_track.set(\"track\", track_obj);\n });\n }, index * 10000);\n });\n });\n });\n }\n });\n\n return {\n SweepsterVisualization: SweepsterVisualization,\n SweepsterVisualizationView: SweepsterVisualizationView\n };\n }\n);\n"]} \ No newline at end of file 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* Visualization and components for Sweepster, a visualization for exploring a tool's parameter space via\n * genomic visualization.\n */\n\ndefine(\n [\n \"libs/underscore\",\n \"libs/d3\",\n \"viz/trackster/util\",\n \"viz/visualization\",\n \"viz/trackster/tracks\",\n \"mvc/tool/tools\",\n \"mvc/dataset/data\",\n \"utils/config\",\n \"mvc/ui/icon-button\"\n ],\n function(\n _,\n d3,\n util,\n visualization,\n tracks,\n tools,\n data,\n config,\n mod_icon_btn\n ) {\n /**\n * A collection of tool input settings. Object is useful for keeping a list of settings\n * for future use without changing the input's value and for preserving inputs order.\n */\n var ToolInputsSettings = Backbone.Model.extend({\n defaults: {\n inputs: null,\n values: null\n }\n });\n\n /**\n * Tree for a tool's parameters.\n */\n var ToolParameterTree = Backbone.Model.extend({\n defaults: {\n tool: null,\n tree_data: null\n },\n\n initialize: function(options) {\n // Set up tool parameters to work with tree.\n var self = this;\n this.get(\"tool\")\n .get(\"inputs\")\n .each(function(input) {\n // Listen for changes to input's attributes.\n input.on(\n \"change:min change:max change:num_samples\",\n function(input) {\n if (input.get(\"in_ptree\")) {\n self.set_tree_data();\n }\n },\n self\n );\n input.on(\n \"change:in_ptree\",\n function(input) {\n if (input.get(\"in_ptree\")) {\n self.add_param(input);\n } else {\n self.remove_param(input);\n }\n self.set_tree_data();\n },\n self\n );\n });\n\n // If there is a config, use it.\n if (options.config) {\n _.each(options.config, function(input_config) {\n var input = self\n .get(\"tool\")\n .get(\"inputs\")\n .find(function(input) {\n return input.get(\"name\") === input_config.name;\n });\n self.add_param(input);\n input.set(input_config);\n });\n }\n },\n\n add_param: function(param) {\n // If parameter already present, do not add it.\n if (param.get(\"ptree_index\")) {\n return;\n }\n\n param.set(\"in_ptree\", true);\n param.set(\"ptree_index\", this.get_tree_params().length);\n },\n\n remove_param: function(param) {\n // Remove param from tree.\n param.set(\"in_ptree\", false);\n param.set(\"ptree_index\", null);\n\n // Update ptree indices for remaining params.\n _(this.get_tree_params()).each(function(input, index) {\n // +1 to use 1-based indexing.\n input.set(\"ptree_index\", index + 1);\n });\n },\n\n /**\n * Sets tree data using tool's inputs.\n */\n set_tree_data: function() {\n // Get samples for each parameter.\n var params_samples = _.map(this.get_tree_params(), function(\n param\n ) {\n return {\n param: param,\n samples: param.get_samples()\n };\n });\n var node_id = 0,\n // Creates tree data recursively.\n create_tree_data = function(params_samples, index) {\n var param_samples = params_samples[index],\n param = param_samples.param,\n param_label = param.get(\"label\"),\n settings = param_samples.samples;\n\n // Create leaves when last parameter setting is reached.\n if (params_samples.length - 1 === index) {\n return _.map(settings, function(setting) {\n return {\n id: node_id++,\n name: setting,\n param: param,\n value: setting\n };\n });\n }\n\n // Recurse to handle other parameters.\n return _.map(settings, function(setting) {\n return {\n id: node_id++,\n name: setting,\n param: param,\n value: setting,\n children: create_tree_data(\n params_samples,\n index + 1\n )\n };\n });\n };\n\n this.set(\"tree_data\", {\n name: \"Root\",\n id: node_id++,\n children:\n params_samples.length !== 0\n ? create_tree_data(params_samples, 0)\n : null\n });\n },\n\n get_tree_params: function() {\n // Filter and sort parameters to get list in tree.\n return _(\n this.get(\"tool\")\n .get(\"inputs\")\n .where({ in_ptree: true })\n ).sortBy(function(input) {\n return input.get(\"ptree_index\");\n });\n },\n\n /**\n * Returns number of leaves in tree.\n */\n get_num_leaves: function() {\n return this.get_tree_params().reduce(function(memo, param) {\n return memo * param.get_samples().length;\n }, 1);\n },\n\n /**\n * Returns array of ToolInputsSettings objects based on a node and its subtree.\n */\n get_node_settings: function(target_node) {\n // -- Get fixed settings from tool and parent nodes.\n\n // Start with tool's settings.\n var fixed_settings = this.get(\"tool\").get_inputs_dict();\n\n // Get fixed settings using node's parents.\n var cur_node = target_node.parent;\n if (cur_node) {\n while (cur_node.depth !== 0) {\n fixed_settings[cur_node.param.get(\"name\")] =\n cur_node.value;\n cur_node = cur_node.parent;\n }\n }\n\n // Walk subtree starting at clicked node to get full list of settings.\n var self = this,\n get_settings = function(node, settings) {\n // Add setting for this node. Root node does not have a param,\n // however.\n if (node.param) {\n settings[node.param.get(\"name\")] = node.value;\n }\n\n if (!node.children) {\n // At leaf node, so return settings.\n return new ToolInputsSettings({\n inputs: self.get(\"tool\").get(\"inputs\"),\n values: settings\n });\n } else {\n // At interior node: return list of subtree settings.\n return _.flatten(\n _.map(node.children, function(c) {\n return get_settings(c, _.clone(settings));\n })\n );\n }\n },\n all_settings = get_settings(target_node, fixed_settings);\n\n // If user clicked on leaf, settings is a single dict. Convert to array for simplicity.\n if (!_.isArray(all_settings)) {\n all_settings = [all_settings];\n }\n\n return all_settings;\n },\n\n /**\n * Returns all nodes connected a particular node; this includes parents and children of the node.\n */\n get_connected_nodes: function(node) {\n var get_subtree_nodes = function(a_node) {\n if (!a_node.children) {\n return a_node;\n } else {\n // At interior node: return subtree nodes.\n return _.flatten([\n a_node,\n _.map(a_node.children, function(c) {\n return get_subtree_nodes(c);\n })\n ]);\n }\n };\n\n // Get node's parents.\n var parents = [],\n cur_parent = node.parent;\n while (cur_parent) {\n parents.push(cur_parent);\n cur_parent = cur_parent.parent;\n }\n\n return _.flatten([parents, get_subtree_nodes(node)]);\n },\n\n /**\n * Returns the leaf that corresponds to a settings collection.\n */\n get_leaf: function(settings) {\n var cur_node = this.get(\"tree_data\"),\n find_child = function(children) {\n return _.find(children, function(child) {\n return (\n settings[child.param.get(\"name\")] ===\n child.value\n );\n });\n };\n\n while (cur_node.children) {\n cur_node = find_child(cur_node.children);\n }\n return cur_node;\n },\n\n /**\n * Returns a list of parameters used in tree.\n */\n toJSON: function() {\n // FIXME: returning and jsonifying complete param causes trouble on the server side,\n // so just use essential attributes for now.\n return this.get_tree_params().map(function(param) {\n return {\n name: param.get(\"name\"),\n min: param.get(\"min\"),\n max: param.get(\"max\"),\n num_samples: param.get(\"num_samples\")\n };\n });\n }\n });\n\n var SweepsterTrack = Backbone.Model.extend({\n defaults: {\n track: null,\n mode: \"Pack\",\n settings: null,\n regions: null\n },\n\n initialize: function(options) {\n this.set(\"regions\", options.regions);\n if (options.track) {\n // FIXME: find a better way to deal with needed URLs:\n var track_config = _.extend(\n {\n data_url: Galaxy.root + \"dummy1\",\n converted_datasets_state_url: Galaxy.root + \"dummy2\"\n },\n options.track\n );\n this.set(\n \"track\",\n tracks.object_from_template(track_config, {}, null)\n );\n }\n },\n\n same_settings: function(a_track) {\n var this_settings = this.get(\"settings\"),\n other_settings = a_track.get(\"settings\");\n for (var prop in this_settings) {\n if (\n !other_settings[prop] ||\n this_settings[prop] !== other_settings[prop]\n ) {\n return false;\n }\n }\n return true;\n },\n\n toJSON: function() {\n return {\n track: this.get(\"track\").to_dict(),\n settings: this.get(\"settings\"),\n regions: this.get(\"regions\")\n };\n }\n });\n\n var TrackCollection = Backbone.Collection.extend({\n model: SweepsterTrack\n });\n\n /**\n * Sweepster visualization model.\n */\n var SweepsterVisualization = visualization.Visualization.extend({\n defaults: _.extend(\n {},\n visualization.Visualization.prototype.defaults,\n {\n dataset: null,\n tool: null,\n parameter_tree: null,\n regions: null,\n tracks: null,\n default_mode: \"Pack\"\n }\n ),\n\n initialize: function(options) {\n this.set(\"dataset\", new data.Dataset(options.dataset));\n this.set(\"tool\", new tools.Tool(options.tool));\n this.set(\n \"regions\",\n new visualization.GenomeRegionCollection(options.regions)\n );\n this.set(\"tracks\", new TrackCollection(options.tracks));\n\n var tool_with_samplable_inputs = this.get(\"tool\");\n this.set(\n \"tool_with_samplable_inputs\",\n tool_with_samplable_inputs\n );\n // Remove complex parameters for now.\n tool_with_samplable_inputs.remove_inputs([\n \"data\",\n \"hidden_data\",\n \"conditional\",\n \"text\"\n ]);\n\n this.set(\n \"parameter_tree\",\n new ToolParameterTree({\n tool: tool_with_samplable_inputs,\n config: options.tree_config\n })\n );\n },\n\n add_track: function(track) {\n this.get(\"tracks\").add(track);\n },\n\n toJSON: function() {\n return {\n id: this.get(\"id\"),\n title:\n \"Parameter exploration for dataset '\" +\n this.get(\"dataset\").get(\"name\") +\n \"'\",\n type: \"sweepster\",\n dataset_id: this.get(\"dataset\").id,\n tool_id: this.get(\"tool\").id,\n regions: this.get(\"regions\").toJSON(),\n tree_config: this.get(\"parameter_tree\").toJSON(),\n tracks: this.get(\"tracks\").toJSON()\n };\n }\n });\n\n /**\n * --- Views ---\n */\n\n /**\n * Sweepster track view.\n */\n var SweepsterTrackView = Backbone.View.extend({\n tagName: \"tr\",\n\n TILE_LEN: 250,\n\n initialize: function(options) {\n this.canvas_manager = options.canvas_manager;\n this.render();\n this.model.on(\n \"change:track change:mode\",\n this.draw_tiles,\n this\n );\n },\n\n render: function() {\n // Render settings icon and popup.\n // TODO: use template.\n var settings = this.model.get(\"settings\"),\n values = settings.get(\"values\"),\n settings_td = $(\"\")\n .addClass(\"settings\")\n .appendTo(this.$el),\n settings_div = $(\"\")\n .addClass(\"track-info\")\n .hide()\n .appendTo(settings_td);\n settings_div.append(\n $(\"\")\n .css(\"font-weight\", \"bold\")\n .text(\"Track Settings\")\n );\n settings.get(\"inputs\").each(function(input) {\n settings_div.append(\n input.get(\"label\") +\n \": \" +\n values[input.get(\"name\")] +\n \"
\"\n );\n });\n var self = this,\n run_on_dataset_button = $(\"\")\n .appendTo(settings_div)\n .text(\"Run on complete dataset\")\n .click(function() {\n settings_div.toggle();\n self.trigger(\"run_on_dataset\", settings);\n });\n var icon_menu = mod_icon_btn.create_icon_buttons_menu([\n {\n title: \"Settings\",\n icon_class: \"gear track-settings\",\n on_click: function() {\n settings_div.toggle();\n }\n },\n {\n title: \"Remove\",\n icon_class: \"cross-circle\",\n on_click: function() {\n self.$el.remove();\n $(\".tooltip\").remove();\n // TODO: remove track from viz collection.\n }\n }\n ]);\n settings_td.prepend(icon_menu.$el);\n\n // Render tile placeholders.\n this.model.get(\"regions\").each(function() {\n self.$el.append(\n $(\"\")\n .addClass(\"tile\")\n .html(\n $(\" \").attr(\n \"src\",\n Galaxy.root +\n \"images/loading_large_white_bg.gif\"\n )\n )\n );\n });\n\n if (this.model.get(\"track\")) {\n this.draw_tiles();\n }\n },\n\n /**\n * Draw tiles for regions.\n */\n draw_tiles: function() {\n var self = this,\n track = this.model.get(\"track\"),\n regions = this.model.get(\"regions\"),\n tile_containers = this.$el.find(\"td.tile\");\n\n // Do nothing if track is not defined.\n if (!track) {\n return;\n }\n\n // When data is ready, draw tiles.\n $.when(track.data_manager.data_is_ready()).then(function(\n data_ok\n ) {\n // Draw tile for each region.\n regions.each(function(region, index) {\n var resolution = region.length() / self.TILE_LEN,\n w_scale = 1 / resolution,\n mode = self.model.get(\"mode\");\n $.when(\n track.data_manager.get_data(\n region,\n mode,\n resolution,\n {}\n )\n ).then(function(tile_data) {\n var canvas = self.canvas_manager.new_canvas();\n canvas.width = self.TILE_LEN;\n canvas.height = track.get_canvas_height(\n tile_data,\n mode,\n w_scale,\n canvas.width\n );\n track.draw_tile(\n tile_data,\n canvas.getContext(\"2d\"),\n mode,\n region,\n w_scale\n );\n $(tile_containers[index])\n .empty()\n .append(canvas);\n });\n });\n });\n }\n });\n\n /**\n * Tool input (parameter) that enables both value and sweeping inputs. View is unusual as\n * it augments an existing input form row rather than creates a completely new HTML element.\n */\n var ToolInputValOrSweepView = Backbone.View.extend({\n // Template for rendering sweep inputs:\n number_input_template:\n '
' +\n '\"> - ' +\n '\">' +\n ' samples: \">' +\n \"\",\n\n select_input_template:\n '<%= options %>',\n\n initialize: function(options) {\n this.$el = options.tool_row;\n this.render();\n },\n\n render: function() {\n var input = this.model,\n type = input.get(\"type\"),\n single_input_row = this.$el.find(\".form-row-input\"),\n sweep_inputs_row = null;\n\n // Update tool inputs as single input changes.\n single_input_row.find(\":input\").change(function() {\n input.set(\"value\", $(this).val());\n });\n\n // Add row for parameter sweep inputs.\n if (input instanceof tools.IntegerToolParameter) {\n sweep_inputs_row = $(\n _.template(this.number_input_template)(\n this.model.toJSON()\n )\n );\n } else if (input instanceof tools.SelectToolParameter) {\n var options = _.map(\n this.$el.find(\"select option\"),\n function(option) {\n return $(option).val();\n }\n ),\n options_text = options.join(\", \");\n sweep_inputs_row = $(\n _.template(this.select_input_template)({\n options: options_text\n })\n );\n }\n sweep_inputs_row.insertAfter(single_input_row);\n\n // Add buttons for adding/removing parameter.\n var self = this,\n menu = mod_icon_btn.create_icon_buttons_menu(\n [\n {\n title: \"Add parameter to tree\",\n icon_class: \"plus-button\",\n on_click: function() {\n input.set(\"in_ptree\", true);\n single_input_row.hide();\n sweep_inputs_row.show();\n $(this).hide();\n self.$el.find(\".icon-button.toggle\").show();\n }\n },\n {\n title: \"Remove parameter from tree\",\n icon_class: \"toggle\",\n on_click: function() {\n // Remove parameter from tree params where name matches clicked paramter.\n input.set(\"in_ptree\", false);\n sweep_inputs_row.hide();\n single_input_row.show();\n $(this).hide();\n self.$el\n .find(\".icon-button.plus-button\")\n .show();\n }\n }\n ],\n {}\n );\n this.$el.prepend(menu.$el);\n\n // Show/hide input rows and icons depending on whether parameter is in the tree.\n if (input.get(\"in_ptree\")) {\n single_input_row.hide();\n self.$el.find(\".icon-button.plus-button\").hide();\n } else {\n self.$el.find(\".icon-button.toggle\").hide();\n sweep_inputs_row.hide();\n }\n\n // Update input's min, max, number of samples as values change.\n _.each([\"min\", \"max\", \"num_samples\"], function(attr) {\n sweep_inputs_row.find(\".\" + attr).change(function() {\n input.set(attr, parseFloat($(this).val()));\n });\n });\n }\n });\n\n var ToolParameterTreeDesignView = Backbone.View.extend({\n className: \"tree-design\",\n\n initialize: function(options) {\n this.render();\n },\n\n render: function() {\n // Start with tool form view.\n var tool_form_view = new tools.ToolFormView({\n model: this.model.get(\"tool\")\n });\n tool_form_view.render();\n this.$el.append(tool_form_view.$el);\n\n // Set up views for each tool input.\n var self = this,\n inputs = self.model.get(\"tool\").get(\"inputs\");\n this.$el\n .find(\".form-row\")\n .not(\".form-actions\")\n .each(function(i) {\n var input_view = new ToolInputValOrSweepView({\n model: inputs.at(i),\n tool_row: $(this)\n });\n });\n }\n });\n\n /**\n * Displays and updates parameter tree.\n */\n var ToolParameterTreeView = Backbone.View.extend({\n className: \"tool-parameter-tree\",\n\n initialize: function(options) {\n // When tree data changes, re-render.\n this.model.on(\"change:tree_data\", this.render, this);\n },\n\n render: function() {\n // Start fresh.\n this.$el.children().remove();\n\n var tree_params = this.model.get_tree_params();\n if (!tree_params.length) {\n return;\n }\n\n // Set width, height based on params and samples.\n this.width = 100 * (2 + tree_params.length);\n this.height = 15 * this.model.get_num_leaves();\n\n var self = this;\n\n // Layout tree.\n var cluster = d3.layout\n .cluster()\n .size([this.height, this.width - 160]);\n\n var diagonal = d3.svg.diagonal().projection(function(d) {\n return [d.y, d.x];\n });\n\n // Layout nodes.\n var nodes = cluster.nodes(this.model.get(\"tree_data\"));\n\n // Setup and add labels for tree levels.\n var param_depths = _.uniq(_.pluck(nodes, \"y\"));\n _.each(tree_params, function(param, index) {\n var x = param_depths[index + 1],\n center_left = $(\"#center\").position().left;\n self.$el.append(\n $(\"\")\n .addClass(\"label\")\n .text(param.get(\"label\"))\n .css(\"left\", x + center_left)\n );\n });\n\n // Set up vis element.\n var vis = d3\n .select(this.$el[0])\n .append(\"svg\")\n .attr(\"width\", this.width)\n .attr(\"height\", this.height + 30)\n .append(\"g\")\n .attr(\"transform\", \"translate(40, 20)\");\n\n // Draw links.\n var link = vis\n .selectAll(\"path.link\")\n .data(cluster.links(nodes))\n .enter()\n .append(\"path\")\n .attr(\"class\", \"link\")\n .attr(\"d\", diagonal);\n\n // Draw nodes.\n var node = vis\n .selectAll(\"g.node\")\n .data(nodes)\n .enter()\n .append(\"g\")\n .attr(\"class\", \"node\")\n .attr(\"transform\", function(d) {\n return \"translate(\" + d.y + \",\" + d.x + \")\";\n })\n .on(\"mouseover\", function(a_node) {\n var connected_node_ids = _.pluck(\n self.model.get_connected_nodes(a_node),\n \"id\"\n );\n // TODO: probably can use enter() to do this more easily.\n node\n .filter(function(d) {\n return (\n _.find(connected_node_ids, function(id) {\n return id === d.id;\n }) !== undefined\n );\n })\n .style(\"fill\", \"#f00\");\n })\n .on(\"mouseout\", function() {\n node.style(\"fill\", \"#000\");\n });\n\n node.append(\"circle\").attr(\"r\", 9);\n\n node\n .append(\"text\")\n .attr(\"dx\", function(d) {\n return d.children ? -12 : 12;\n })\n .attr(\"dy\", 3)\n .attr(\"text-anchor\", function(d) {\n return d.children ? \"end\" : \"start\";\n })\n .text(function(d) {\n return d.name;\n });\n }\n });\n\n /**\n * Sweepster visualization view. View requires rendering in 3-panel setup for now.\n */\n var SweepsterVisualizationView = Backbone.View.extend({\n className: \"Sweepster\",\n\n helpText:\n \"\",\n\n initialize: function(options) {\n this.canvas_manager = new visualization.CanvasManager(\n this.$el.parents(\"body\")\n );\n this.tool_param_tree_view = new ToolParameterTreeView({\n model: this.model.get(\"parameter_tree\")\n });\n this.track_collection_container = $(\"Getting Started
\" +\n \"\").addClass(\n \"tracks\"\n );\n\n // Handle node clicks for tree data.\n this.model\n .get(\"parameter_tree\")\n .on(\"change:tree_data\", this.handle_node_clicks, this);\n\n // Each track must have a view so it has a canvas manager.\n var self = this;\n this.model.get(\"tracks\").each(function(track) {\n track.get(\"track\").view = self;\n });\n\n // Set block, reverse strand block colors; these colors will be used for all tracks.\n this.config = config.ConfigSettingCollection.from_models_and_saved_values(\n [\n {\n key: \"name\",\n label: \"Name\",\n type: \"text\",\n default_value: \"\"\n },\n {\n key: \"a_color\",\n label: \"A Color\",\n type: \"color\",\n default_value: \"#FF0000\"\n },\n {\n key: \"c_color\",\n label: \"C Color\",\n type: \"color\",\n default_value: \"#00FF00\"\n },\n {\n key: \"g_color\",\n label: \"G Color\",\n type: \"color\",\n default_value: \"#0000FF\"\n },\n {\n key: \"t_color\",\n label: \"T Color\",\n type: \"color\",\n default_value: \"#FF00FF\"\n },\n {\n key: \"n_color\",\n label: \"N Color\",\n type: \"color\",\n default_value: \"#AAAAAA\"\n },\n {\n key: \"block_color\",\n label: \"Block color\",\n type: \"color\"\n },\n {\n key: \"reverse_strand_color\",\n label: \"Antisense strand color\",\n type: \"color\"\n }\n ],\n {}\n );\n },\n\n render: function() {\n // Render tree design view in left panel.\n var tree_design_view = new ToolParameterTreeDesignView({\n model: this.model.get(\"parameter_tree\")\n });\n\n $(\"#left\").append(tree_design_view.$el);\n\n // Render track collection container/view in right panel.\n var self = this,\n regions = self.model.get(\"regions\"),\n tr = $(\"
\").appendTo(this.track_collection_container);\n\n regions.each(function(region) {\n tr.append($(\" \").text(region.toString()));\n });\n tr\n .children()\n .first()\n .attr(\"colspan\", 2);\n\n var tracks_div = $(\" \").addClass(\"tiles\");\n $(\"#right\").append(\n tracks_div.append(this.track_collection_container)\n );\n\n self.model.get(\"tracks\").each(function(track) {\n self.add_track(track);\n });\n\n // -- Render help and tool parameter tree in center panel. --\n\n // Help includes text and a close button.\n var help_div = $(this.helpText).addClass(\"help\"),\n close_button = mod_icon_btn.create_icon_buttons_menu([\n {\n title: \"Close\",\n icon_class: \"cross-circle\",\n on_click: function() {\n $(\".tooltip\").remove();\n help_div.remove();\n }\n }\n ]);\n\n help_div.prepend(close_button.$el.css(\"float\", \"right\"));\n $(\"#center\").append(help_div);\n\n // Parameter tree:\n this.tool_param_tree_view.render();\n $(\"#center\").append(this.tool_param_tree_view.$el);\n\n // Set up handler for tree node clicks.\n this.handle_node_clicks();\n\n // Set up visualization menu.\n var menu = mod_icon_btn.create_icon_buttons_menu(\n [\n // Save.\n /*\n { icon_class: 'disk--arrow', title: 'Save', on_click: function() {\n // Show saving dialog box\n show_modal(\"Saving...\", \"progress\");\n\n viz.save().success(function(vis_info) {\n hide_modal();\n viz.set({\n 'id': vis_info.vis_id,\n 'has_changes': false\n });\n })\n .error(function() {\n show_modal( \"Could Not Save\", \"Could not save visualization. Please try again later.\",\n { \"Close\" : hide_modal } );\n });\n } },\n */\n // Change track modes.\n {\n icon_class: \"chevron-expand\",\n title: \"Set display mode\"\n },\n // Close viz.\n {\n icon_class: \"cross-circle\",\n title: \"Close\",\n on_click: function() {\n window.location =\n \"${h.url_for( controller='visualization', action='list' )}\";\n }\n }\n ],\n {\n tooltip_config: { placement: \"bottom\" }\n }\n );\n\n // Create mode selection popup. Mode selection changes default mode and mode for all tracks.\n var modes = [\"Squish\", \"Pack\"],\n mode_mapping = {};\n _.each(modes, function(mode) {\n mode_mapping[mode] = function() {\n self.model.set(\"default_mode\", mode);\n self.model.get(\"tracks\").each(function(track) {\n track.set(\"mode\", mode);\n });\n };\n });\n\n make_popupmenu(menu.$el.find(\".chevron-expand\"), mode_mapping);\n\n menu.$el.attr(\"style\", \"float: right\");\n $(\"#right .unified-panel-header-inner\").append(menu.$el);\n },\n\n get_base_color: function(base) {\n return (\n this.config.get_value(base.toLowerCase() + \"_color\") ||\n this.config.get_value(\"n_color\")\n );\n },\n\n run_tool_on_dataset: function(settings) {\n var tool = this.model.get(\"tool\"),\n tool_name = tool.get(\"name\"),\n dataset = this.model.get(\"dataset\");\n tool.set_input_values(settings.get(\"values\"));\n $.when(tool.rerun(dataset)).then(function(outputs) {\n // TODO.\n });\n\n show_modal(\n \"Running \" + tool_name + \" on complete dataset\",\n tool_name +\n \" is running on dataset '\" +\n dataset.get(\"name\") +\n \"'. Outputs are in the dataset's history.\",\n {\n Ok: function() {\n hide_modal();\n }\n }\n );\n },\n\n /**\n * Add track to model and view.\n */\n add_track: function(pm_track) {\n var self = this,\n param_tree = this.model.get(\"parameter_tree\");\n\n // Add track to model.\n self.model.add_track(pm_track);\n\n var track_view = new SweepsterTrackView({\n model: pm_track,\n canvas_manager: self.canvas_manager\n });\n track_view.on(\"run_on_dataset\", self.run_tool_on_dataset, self);\n self.track_collection_container.append(track_view.$el);\n track_view.$el.hover(\n function() {\n var settings_leaf = param_tree.get_leaf(\n pm_track.get(\"settings\").get(\"values\")\n );\n var connected_node_ids = _.pluck(\n param_tree.get_connected_nodes(settings_leaf),\n \"id\"\n );\n\n // TODO: can do faster with enter?\n d3\n .select(self.tool_param_tree_view.$el[0])\n .selectAll(\"g.node\")\n .filter(function(d) {\n return (\n _.find(connected_node_ids, function(id) {\n return id === d.id;\n }) !== undefined\n );\n })\n .style(\"fill\", \"#f00\");\n },\n function() {\n d3\n .select(self.tool_param_tree_view.$el[0])\n .selectAll(\"g.node\")\n .style(\"fill\", \"#000\");\n }\n );\n return pm_track;\n },\n\n /**\n * Sets up handling when tree nodes are clicked. When a node is clicked, the tool is run for each of\n * the settings defined by the node's subtree and tracks are added for each run.\n */\n handle_node_clicks: function() {\n // When node clicked in tree, run tool and add tracks to model.\n var self = this,\n param_tree = this.model.get(\"parameter_tree\"),\n regions = this.model.get(\"regions\"),\n node = d3\n .select(this.tool_param_tree_view.$el[0])\n .selectAll(\"g.node\");\n node.on(\"click\", function(d, i) {\n // Get all settings corresponding to node.\n var tool = self.model.get(\"tool\"),\n dataset = self.model.get(\"dataset\"),\n all_settings = param_tree.get_node_settings(d),\n run_jobs_deferred = $.Deferred();\n\n // Do not allow 10+ jobs to be run.\n if (all_settings.length >= 10) {\n show_modal(\n \"Whoa there cowboy!\",\n \"You clicked on a node to try \" +\n self.model.get(\"tool\").get(\"name\") +\n \" with \" +\n all_settings.length +\n \" different combinations of settings. You can only run 10 jobs at a time.\",\n {\n Ok: function() {\n hide_modal();\n run_jobs_deferred.resolve(false);\n }\n }\n );\n } else {\n run_jobs_deferred.resolve(true);\n }\n\n // Take action when deferred resolves.\n $.when(run_jobs_deferred).then(function(run_jobs) {\n if (!run_jobs) {\n return;\n }\n\n // Create and add tracks for each settings group.\n var new_tracks = _.map(all_settings, function(\n settings\n ) {\n var pm_track = new SweepsterTrack({\n settings: settings,\n regions: regions,\n mode: self.model.get(\"default_mode\")\n });\n self.add_track(pm_track);\n return pm_track;\n });\n\n // For each track, run tool using track's settings and update track.\n _.each(new_tracks, function(pm_track, index) {\n setTimeout(function() {\n // Set inputs and run tool.\n tool.set_input_values(\n pm_track.get(\"settings\").get(\"values\")\n );\n $.when(\n tool.rerun(dataset, regions)\n ).then(function(output) {\n // HACKish: output is an HDA with track config attribute. To create a track\n // that works correctly with Backbone relational, it is necessary to\n // use a modified version of the track config.\n var dataset = output.first(),\n track_config = dataset.get(\n \"track_config\"\n );\n // Set dataset to be the tool's output.\n track_config.dataset = dataset;\n // Set tool to null so that it is not unpacked; unpacking it messes with\n // the tool parameters and parameter tree.\n track_config.tool = null;\n\n track_config.prefs = self.config.to_key_value_dict();\n\n // Create and add track for output dataset.\n var track_obj = tracks.object_from_template(\n track_config,\n self,\n null\n );\n track_obj.init_for_tool_data();\n\n pm_track.set(\"track\", track_obj);\n });\n }, index * 10000);\n });\n });\n });\n }\n });\n\n return {\n SweepsterVisualization: SweepsterVisualization,\n SweepsterVisualizationView: SweepsterVisualizationView\n };\n }\n);\n"]} \ No newline at end of file diff --git a/static/maps/viz/trackster.js.map b/static/maps/viz/trackster.js.map index 35df40cb5ba..e0f6372cd9c 100644 --- a/static/maps/viz/trackster.js.map +++ b/static/maps/viz/trackster.js.map @@ -1 +1 @@ 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* Top-level trackster code, used for creating/loading visualizations and user interface elements.\n */\n\n// global variables\nvar ui = null;\nvar view = null;\nvar browser_router = null;\n\n// load required libraries\nrequire([\n \"utils/utils\",\n \"libs/jquery/jquery.event.drag\",\n \"libs/jquery/jquery.event.hover\",\n \"libs/jquery/jquery.mousewheel\",\n \"libs/jquery/jquery-ui\",\n \"libs/jquery/select2\",\n \"libs/farbtastic\",\n \"libs/jquery/jquery.form\",\n \"libs/jquery/jquery.rating\",\n \"ui/editable-text\"\n], function(mod_utils) {\n mod_utils.cssLoadFile(\"static/style/jquery.rating.css\");\n mod_utils.cssLoadFile(\"static/style/autocomplete_tagging.css\");\n mod_utils.cssLoadFile(\"static/style/jquery-ui/smoothness/jquery-ui.css\");\n mod_utils.cssLoadFile(\"static/style/library.css\");\n mod_utils.cssLoadFile(\"static/style/trackster.css\");\n});\n\n// trackster viewer\ndefine(\n [\n \"libs/underscore\",\n \"viz/trackster/tracks\",\n \"viz/visualization\",\n \"mvc/ui/icon-button\",\n \"utils/query-string-parsing\",\n \"mvc/grid/grid-view\"\n ],\n function(_, tracks, visualization, mod_icon_btn, query_string, GridView) {\n /**\n * Base Object/Model for inhertiance.\n */\n var Base = function() {\n if (this.initialize) {\n this.initialize.apply(this, arguments);\n }\n };\n Base.extend = Backbone.Model.extend;\n\n /**\n * User interface controls for trackster\n */\n var TracksterUI = Base.extend({\n initialize: function(baseURL) {\n this.baseURL = baseURL;\n },\n\n /**\n * Save visualization, returning a Deferred object for the remote call to save.\n */\n save_viz: function() {\n // show dialog\n Galaxy.modal.show({ title: \"Saving...\", body: \"progress\" });\n\n // Save bookmarks.\n var bookmarks = [];\n $(\".bookmark\").each(function() {\n bookmarks.push({\n position: $(this)\n .children(\".position\")\n .text(),\n annotation: $(this)\n .children(\".annotation\")\n .text()\n });\n });\n\n // FIXME: give unique IDs to Drawables and save overview as ID.\n var overview_track_name = view.overview_drawable\n ? view.overview_drawable.config.get_value(\"name\")\n : null,\n viz_config = {\n view: view.to_dict(),\n viewport: {\n chrom: view.chrom,\n start: view.low,\n end: view.high,\n overview: overview_track_name\n },\n bookmarks: bookmarks\n };\n\n // Make call to save visualization.\n return $.ajax({\n url: Galaxy.root + \"visualization/save\",\n type: \"POST\",\n dataType: \"json\",\n data: {\n id: view.vis_id,\n title: view.config.get_value(\"name\"),\n dbkey: view.dbkey,\n type: \"trackster\",\n vis_json: JSON.stringify(viz_config)\n }\n })\n .success(function(vis_info) {\n Galaxy.modal.hide();\n view.vis_id = vis_info.vis_id;\n view.has_changes = false;\n\n // Needed to set URL when first saving a visualization.\n window.history.pushState(\n {},\n \"\",\n vis_info.url + window.location.hash\n );\n })\n .error(function() {\n // show dialog\n Galaxy.modal.show({\n title: \"Could Not Save\",\n body:\n \"Could not save visualization. Please try again later.\",\n buttons: {\n Cancel: function() {\n Galaxy.modal.hide();\n }\n }\n });\n });\n },\n\n /**\n * Create button menu\n */\n createButtonMenu: function() {\n var self = this,\n menu = mod_icon_btn.create_icon_buttons_menu(\n [\n {\n icon_class: \"plus-button\",\n title: \"Add tracks\",\n on_click: function() {\n visualization.select_datasets(\n { dbkey: view.dbkey },\n function(new_tracks) {\n _.each(new_tracks, function(track) {\n view.add_drawable(\n tracks.object_from_template(\n track,\n view,\n view\n )\n );\n });\n }\n );\n }\n },\n {\n icon_class: \"block--plus\",\n title: \"Add group\",\n on_click: function() {\n view.add_drawable(\n new tracks.DrawableGroup(view, view, {\n name: \"New Group\"\n })\n );\n }\n },\n {\n icon_class: \"bookmarks\",\n title: \"Bookmarks\",\n on_click: function() {\n // HACK -- use style to determine if panel is hidden and hide/show accordingly.\n force_right_panel(\n $(\"div#right\").css(\"right\") == \"0px\"\n ? \"hide\"\n : \"show\"\n );\n }\n },\n {\n icon_class: \"globe\",\n title: \"Circster\",\n on_click: function() {\n window.location =\n self.baseURL +\n \"visualization/circster?id=\" +\n view.vis_id;\n }\n },\n {\n icon_class: \"disk--arrow\",\n title: \"Save\",\n on_click: function() {\n self.save_viz();\n }\n },\n {\n icon_class: \"cross-circle\",\n title: \"Close\",\n on_click: function() {\n self.handle_unsaved_changes(view);\n }\n }\n ],\n {\n tooltip_config: { placement: \"bottom\" }\n }\n );\n this.buttonMenu = menu;\n return menu;\n },\n\n /**\n * Add bookmark.\n */\n add_bookmark: function(position, annotation, editable) {\n // Create HTML.\n var bookmarks_container = $(\"#right .unified-panel-body\"),\n new_bookmark = $(\"\")\n .addClass(\"bookmark\")\n .appendTo(bookmarks_container);\n\n var position_div = $(\"\")\n .addClass(\"position\")\n .appendTo(new_bookmark),\n position_link = $(\"\")\n .text(position)\n .appendTo(position_div)\n .click(function() {\n view.go_to(position);\n return false;\n }),\n annotation_div = $(\"\")\n .text(annotation)\n .appendTo(new_bookmark);\n\n // If editable, enable bookmark deletion and annotation editing.\n if (editable) {\n var delete_icon_container = $(\"\")\n .addClass(\"delete-icon-container\")\n .prependTo(new_bookmark)\n .click(function() {\n // Remove bookmark.\n new_bookmark.slideUp(\"fast\");\n new_bookmark.remove();\n view.has_changes = true;\n return false;\n }),\n delete_icon = $(\"\")\n .addClass(\"icon-button delete\")\n .appendTo(delete_icon_container);\n annotation_div\n .make_text_editable({\n num_rows: 3,\n use_textarea: true,\n help_text: \"Edit bookmark note\"\n })\n .addClass(\"annotation\");\n }\n\n view.has_changes = true;\n return new_bookmark;\n },\n\n /**\n * Create a complete Trackster visualization. Returns view.\n */\n create_visualization: function(\n view_config,\n viewport_config,\n drawables_config,\n bookmarks_config,\n editable\n ) {\n // Create view.\n var self = this,\n view = new tracks.TracksterView(\n _.extend(view_config, { header: false })\n );\n view.editor = true;\n $.when(view.load_chroms_deferred).then(function(chrom_info) {\n // Viewport config.\n if (viewport_config) {\n var chrom = viewport_config.chrom,\n start = viewport_config.start,\n end = viewport_config.end,\n overview_drawable_name = viewport_config.overview;\n\n if (chrom && start !== undefined && end) {\n view.change_chrom(chrom, start, end);\n } else {\n // No valid viewport, so use first chromosome.\n view.change_chrom(chrom_info[0].chrom);\n }\n } else {\n // No viewport, so use first chromosome.\n view.change_chrom(chrom_info[0].chrom);\n }\n\n // Add drawables to view.\n if (drawables_config) {\n // FIXME: can from_dict() be used to create view and add drawables?\n var drawable_config, drawable_type, drawable;\n for (var i = 0; i < drawables_config.length; i++) {\n view.add_drawable(\n tracks.object_from_template(\n drawables_config[i],\n view,\n view\n )\n );\n }\n }\n\n // Set overview.\n var overview_drawable;\n for (var i = 0; i < view.drawables.length; i++) {\n if (\n view.drawables[i].config.get_value(\"name\") ===\n overview_drawable_name\n ) {\n view.set_overview(view.drawables[i]);\n break;\n }\n }\n\n // Load bookmarks.\n if (bookmarks_config) {\n var bookmark;\n for (var i = 0; i < bookmarks_config.length; i++) {\n bookmark = bookmarks_config[i];\n self.add_bookmark(\n bookmark[\"position\"],\n bookmark[\"annotation\"],\n editable\n );\n }\n }\n\n // View has no changes as of yet.\n view.has_changes = false;\n });\n\n // Final initialization.\n this.set_up_router({ view: view });\n\n return view;\n },\n\n /**\n * Set up location router to use hashes as track browser locations.\n */\n set_up_router: function(options) {\n new visualization.TrackBrowserRouter(options);\n Backbone.history.start();\n },\n\n /**\n * Set up keyboard navigation for a visualization.\n */\n init_keyboard_nav: function(view) {\n // Keyboard navigation. Scroll ~7% of height when scrolling up/down.\n $(document).keyup(function(e) {\n // Do not navigate if arrow keys used in input element.\n if ($(e.srcElement).is(\":input\")) {\n return;\n }\n\n // Key codes: left == 37, up == 38, right == 39, down == 40\n switch (e.which) {\n case 37:\n view.move_fraction(0.25);\n break;\n case 38:\n var change = Math.round(\n view.viewport_container.height() / 15.0\n );\n view.viewport_container.scrollTop(\n view.viewport_container.scrollTop() - 20\n );\n break;\n case 39:\n view.move_fraction(-0.25);\n break;\n case 40:\n var change = Math.round(\n view.viewport_container.height() / 15.0\n );\n view.viewport_container.scrollTop(\n view.viewport_container.scrollTop() + 20\n );\n break;\n }\n });\n },\n\n /**\n * Handle unsaved changes in visualization.\n */\n handle_unsaved_changes: function(view) {\n if (view.has_changes) {\n var self = this;\n Galaxy.modal.show({\n title: \"Close visualization\",\n body:\n \"There are unsaved changes to your visualization which will be lost if you do not save them.\",\n buttons: {\n Cancel: function() {\n Galaxy.modal.hide();\n },\n \"Leave without Saving\": function() {\n $(window).off(\"beforeunload\");\n window.location = Galaxy.root + \"visualization\";\n },\n Save: function() {\n $.when(self.save_viz()).then(function() {\n window.location =\n Galaxy.root + \"visualization\";\n });\n }\n }\n });\n } else {\n window.location = Galaxy.root + \"visualization\";\n }\n }\n });\n\n var TracksterView = Backbone.View.extend({\n // initalize trackster\n initialize: function() {\n // load ui\n ui = new TracksterUI(Galaxy.root);\n\n // create button menu\n ui.createButtonMenu();\n\n // attach the button menu to the panel header and float it left\n ui.buttonMenu.$el.attr(\"style\", \"float: right\");\n\n // add to center panel\n $(\"#center .unified-panel-header-inner\").append(\n ui.buttonMenu.$el\n );\n\n // configure right panel\n $(\"#right .unified-panel-title\").append(\"Bookmarks\");\n $(\"#right .unified-panel-icons\").append(\n \"\"\n );\n\n // resize view when showing/hiding right panel (bookmarks for now).\n $(\"#right-border\").click(function() {\n view.resize_window();\n });\n\n // hide right panel\n force_right_panel(\"hide\");\n\n // check if id is available\n if (galaxy_config.app.id) {\n this.view_existing();\n } else if (query_string.get(\"dataset_id\")) {\n this.choose_existing_or_new();\n } else {\n this.view_new();\n }\n },\n\n choose_existing_or_new: function() {\n var self = this;\n var dbkey = query_string.get(\"dbkey\"),\n listTracksParams = {},\n dataset_params = {\n dbkey: dbkey,\n dataset_id: query_string.get(\"dataset_id\"),\n hda_ldda: query_string.get(\"hda_ldda\"),\n gene_region: query_string.get(\"gene_region\")\n };\n if (dbkey) {\n listTracksParams[\"f-dbkey\"] = dbkey;\n }\n\n Galaxy.modal.show({\n title: \"View Data in a New or Saved Visualization?\",\n // either have text in here or have to remove body and the header/footer margins\n body:\n \"- You can add this dataset as:\" +\n \"
- You can add this dataset as:\" +\n \"
\n var x_center = s_start - (s_end - s_start) / 2;\n if (\n (mode === \"Pack\" || this.mode === \"Auto\") &&\n read_seq !== undefined &&\n w_scale > char_width_px\n ) {\n // Draw sequence container.\n ctx.fillStyle = \"yellow\";\n ctx.fillRect(\n x_center - gap,\n y_start - 9,\n s_end - s_start,\n 9\n );\n draw_last[draw_last.length] = {\n type: \"triangle\",\n data: [insert_x_coord, y_start + 4, 5]\n };\n ctx.fillStyle = CONNECTOR_COLOR;\n // Based on overlap b/t sequence and tile, get sequence to be drawn.\n switch (compute_overlap(\n [seq_start, seq_start + cig_len],\n tile_region\n )) {\n case OVERLAP_START:\n seq = seq.slice(\n tile_low - seq_start\n );\n break;\n case OVERLAP_END:\n seq = seq.slice(\n 0,\n seq_start - tile_high\n );\n break;\n case CONTAINED_BY:\n // All of sequence drawn.\n break;\n case CONTAINS:\n seq = seq.slice(\n tile_low - seq_start,\n seq_start - tile_high\n );\n break;\n }\n // Draw sequence.\n for (\n var c = 0, str_len = seq.length;\n c < str_len;\n c++\n ) {\n var c_start = Math.floor(\n Math.max(\n 0,\n (seq_start + c - tile_low) *\n w_scale\n )\n );\n ctx.fillText(\n seq[c],\n c_start - (s_end - s_start) / 2,\n y_start\n );\n }\n } else {\n // Draw block.\n ctx.fillStyle = \"yellow\";\n // TODO: This is a pretty hack-ish way to fill rectangle based on mode.\n ctx.fillRect(\n x_center,\n y_start +\n (this.mode !== \"Dense\" ? 2 : 5),\n s_end - s_start,\n mode !== \"Dense\"\n ? SQUISH_FEATURE_HEIGHT\n : DENSE_FEATURE_HEIGHT\n );\n }\n } else {\n if (\n (mode === \"Pack\" || this.mode === \"Auto\") &&\n read_seq !== undefined &&\n w_scale > char_width_px\n ) {\n // Show insertions with a single number at the insertion point.\n draw_last.push({\n type: \"text\",\n data: [\n seq.length,\n insert_x_coord,\n y_start + 9\n ]\n });\n } else {\n // TODO: probably can merge this case with code above.\n }\n }\n }\n seq_offset += cig_len;\n // No change to base offset because insertions are drawn above sequence/read.\n break;\n }\n }\n\n //\n // Draw last items.\n //\n ctx.fillStyle = \"yellow\";\n var item, type, data;\n for (var i = 0; i < draw_last.length; i++) {\n item = draw_last[i];\n type = item.type;\n data = item.data;\n if (type === \"text\") {\n ctx.save();\n ctx.font = \"bold \" + ctx.font;\n ctx.fillText(data[0], data[1], data[2]);\n ctx.restore();\n } else if (type === \"triangle\") {\n drawDownwardEquilateralTriangle(\n ctx,\n data[0],\n data[1],\n data[2]\n );\n }\n }\n },\n\n /**\n * Draw a complete read pair\n */\n draw_element: function(\n ctx,\n mode,\n feature,\n slot,\n tile_low,\n tile_high,\n w_scale,\n y_scale,\n width\n ) {\n // All features need a start, end, and vertical center.\n var feature_uid = feature[0],\n feature_start = feature[1],\n feature_end = feature[2],\n feature_name = feature[3],\n // -0.5 to put element between bases.\n f_start = Math.floor(\n Math.max(\n -0.5 * w_scale,\n (feature_start - tile_low - 0.5) * w_scale\n )\n ),\n f_end = Math.ceil(\n Math.min(\n width,\n Math.max(0, (feature_end - tile_low - 0.5) * w_scale)\n )\n ),\n y_start = (mode === \"Dense\" ? 0 : 0 + slot) * y_scale,\n draw_height =\n mode === \"Pack\"\n ? PACK_FEATURE_HEIGHT\n : SQUISH_FEATURE_HEIGHT,\n label_color = this.prefs.label_color;\n\n // Draw read.\n if (feature[5] instanceof Array) {\n // Read is paired.\n var connector = true;\n\n // Draw left/forward read.\n if (\n feature[4][1] >= tile_low &&\n feature[4][0] <= tile_high &&\n feature[4][2]\n ) {\n this.draw_read(\n ctx,\n mode,\n w_scale,\n y_start,\n tile_low,\n tile_high,\n feature[4][0],\n feature[4][2],\n feature[4][3],\n feature[4][4]\n );\n } else {\n connector = false;\n }\n\n // Draw right/reverse read.\n if (\n feature[5][1] >= tile_low &&\n feature[5][0] <= tile_high &&\n feature[5][2]\n ) {\n this.draw_read(\n ctx,\n mode,\n w_scale,\n y_start,\n tile_low,\n tile_high,\n feature[5][0],\n feature[5][2],\n feature[5][3],\n feature[5][4]\n );\n } else {\n connector = false;\n }\n\n // Draw connector if both reads were drawn.\n // TODO: currently, there is no way to connect reads drawn on different tiles; to connect reads on different tiles, data manager\n // code is needed to join mate pairs from different regions. Alternatively, requesting multiple regions of data at once would\n // make it possible to put together more easily.\n // -0.5 to position connector correctly between reads.\n var b1_end = Math.ceil(\n Math.min(\n width,\n Math.max(\n -0.5 * w_scale,\n (feature[4][1] - tile_low - 0.5) * w_scale\n )\n )\n ),\n b2_start = Math.floor(\n Math.max(\n -0.5 * w_scale,\n (feature[5][0] - tile_low - 0.5) * w_scale\n )\n );\n if (connector && b2_start > b1_end) {\n ctx.fillStyle = CONNECTOR_COLOR;\n var line_height = y_start + 1 + (draw_height - 1) / 2;\n dashedLine(ctx, b1_end, line_height, b2_start, line_height);\n }\n } else {\n // Read is single.\n this.draw_read(\n ctx,\n mode,\n w_scale,\n y_start,\n tile_low,\n tile_high,\n feature_start,\n feature[4],\n feature[5],\n feature[6]\n );\n }\n if (\n mode === \"Pack\" &&\n feature_start >= tile_low &&\n feature_name !== \".\"\n ) {\n // Draw label.\n ctx.fillStyle = this.prefs.label_color;\n if (\n tile_low === 0 &&\n f_start - ctx.measureText(feature_name).width < 0\n ) {\n ctx.textAlign = \"left\";\n ctx.fillText(\n feature_name,\n f_end + LABEL_SPACING,\n y_start + 9,\n this.max_label_length\n );\n } else {\n ctx.textAlign = \"right\";\n ctx.fillText(\n feature_name,\n f_start - LABEL_SPACING,\n y_start + 9,\n this.max_label_length\n );\n }\n }\n\n // FIXME: provide actual coordinates for drawn read.\n return [0, 0];\n }\n });\n\n var ArcLinkedFeaturePainter = function(\n data,\n view_start,\n view_end,\n prefs,\n mode,\n alpha_scaler,\n height_scaler\n ) {\n LinkedFeaturePainter.call(\n this,\n data,\n view_start,\n view_end,\n prefs,\n mode,\n alpha_scaler,\n height_scaler\n );\n // Need to know the longest feature length for adding spacing\n this.longest_feature_length = this.calculate_longest_feature_length();\n this.draw_background_connector = false;\n this.draw_individual_connectors = true;\n };\n\n _.extend(\n ArcLinkedFeaturePainter.prototype,\n FeaturePainter.prototype,\n LinkedFeaturePainter.prototype,\n {\n calculate_longest_feature_length: function() {\n var longest_feature_length = 0;\n for (var i = 0, len = this.data.length; i < len; i++) {\n var feature = this.data[i],\n feature_start = feature[1],\n feature_end = feature[2];\n longest_feature_length = Math.max(\n longest_feature_length,\n feature_end - feature_start\n );\n }\n return longest_feature_length;\n },\n\n get_top_padding: function(width) {\n var view_range = this.view_end - this.view_start,\n w_scale = width / view_range;\n return Math.min(\n 128,\n Math.ceil(this.longest_feature_length / 2 * w_scale)\n );\n },\n\n draw_connector: function(\n ctx,\n block1_start,\n block1_end,\n block2_start,\n block2_end,\n y_start\n ) {\n // Arc drawing -- from closest endpoints\n var x_center = (block1_end + block2_start) / 2,\n radius = block2_start - x_center;\n // For full half circles\n var angle1 = Math.PI,\n angle2 = 0;\n if (radius > 0) {\n ctx.beginPath();\n ctx.arc(\n x_center,\n y_start,\n block2_start - x_center,\n Math.PI,\n 0\n );\n ctx.stroke();\n }\n }\n }\n );\n\n // Color stuff from less.js\n\n var Color = function(rgb, a) {\n /**\n * The end goal here, is to parse the arguments\n * into an integer triplet, such as `128, 255, 0`\n *\n * This facilitates operations and conversions.\n */\n if (Array.isArray(rgb)) {\n this.rgb = rgb;\n } else if (rgb.length == 6) {\n this.rgb = rgb.match(/.{2}/g).map(function(c) {\n return parseInt(c, 16);\n });\n } else if (rgb.length == 7) {\n this.rgb = rgb\n .substring(1, 7)\n .match(/.{2}/g)\n .map(function(c) {\n return parseInt(c, 16);\n });\n } else {\n this.rgb = rgb.split(\"\").map(function(c) {\n return parseInt(c + c, 16);\n });\n }\n this.alpha = typeof a === \"number\" ? a : 1;\n };\n Color.prototype = {\n eval: function() {\n return this;\n },\n\n //\n // If we have some transparency, the only way to represent it\n // is via `rgba`. Otherwise, we use the hex representation,\n // which has better compatibility with older browsers.\n // Values are capped between `0` and `255`, rounded and zero-padded.\n //\n toCSS: function() {\n if (this.alpha < 1.0) {\n return (\n \"rgba(\" +\n this.rgb\n .map(function(c) {\n return Math.round(c);\n })\n .concat(this.alpha)\n .join(\", \") +\n \")\"\n );\n } else {\n return (\n \"#\" +\n this.rgb\n .map(function(i) {\n i = Math.round(i);\n i = (i > 255 ? 255 : i < 0 ? 0 : i).toString(16);\n return i.length === 1 ? \"0\" + i : i;\n })\n .join(\"\")\n );\n }\n },\n\n toHSL: function() {\n var r = this.rgb[0] / 255,\n g = this.rgb[1] / 255,\n b = this.rgb[2] / 255,\n a = this.alpha;\n\n var max = Math.max(r, g, b),\n min = Math.min(r, g, b);\n var h,\n s,\n l = (max + min) / 2,\n d = max - min;\n\n if (max === min) {\n h = s = 0;\n } else {\n s = l > 0.5 ? d / (2 - max - min) : d / (max + min);\n\n switch (max) {\n case r:\n h = (g - b) / d + (g < b ? 6 : 0);\n break;\n case g:\n h = (b - r) / d + 2;\n break;\n case b:\n h = (r - g) / d + 4;\n break;\n }\n h /= 6;\n }\n return { h: h * 360, s: s, l: l, a: a };\n },\n\n toARGB: function() {\n var argb = [Math.round(this.alpha * 255)].concat(this.rgb);\n return (\n \"#\" +\n argb\n .map(function(i) {\n i = Math.round(i);\n i = (i > 255 ? 255 : i < 0 ? 0 : i).toString(16);\n return i.length === 1 ? \"0\" + i : i;\n })\n .join(\"\")\n );\n },\n\n mix: function(color2, weight) {\n var color1 = this;\n\n var p = weight; // .value / 100.0;\n var w = p * 2 - 1;\n var a = color1.toHSL().a - color2.toHSL().a;\n\n var w1 = ((w * a == -1 ? w : (w + a) / (1 + w * a)) + 1) / 2.0;\n var w2 = 1 - w1;\n\n var rgb = [\n color1.rgb[0] * w1 + color2.rgb[0] * w2,\n color1.rgb[1] * w1 + color2.rgb[1] * w2,\n color1.rgb[2] * w1 + color2.rgb[2] * w2\n ];\n\n var alpha = color1.alpha * p + color2.alpha * (1 - p);\n\n return new Color(rgb, alpha);\n }\n };\n\n // End colors from less.js\n\n var LinearRamp = function(start_color, end_color, start_value, end_value) {\n /**\n * Simple linear gradient\n */\n this.start_color = new Color(start_color);\n this.end_color = new Color(end_color);\n this.start_value = start_value;\n this.end_value = end_value;\n this.value_range = end_value - start_value;\n };\n\n LinearRamp.prototype.map_value = function(value) {\n value = Math.max(value, this.start_value);\n value = Math.min(value, this.end_value);\n value = (value - this.start_value) / this.value_range;\n // HACK: just red for now\n // return \"hsl(0,100%,\" + (value * 100) + \"%)\"\n return this.start_color.mix(this.end_color, 1 - value).toCSS();\n };\n\n var SplitRamp = function(\n start_color,\n middle_color,\n end_color,\n start_value,\n end_value\n ) {\n /**\n * Two gradients split away from 0\n */\n this.positive_ramp = new LinearRamp(\n middle_color,\n end_color,\n 0,\n end_value\n );\n this.negative_ramp = new LinearRamp(\n middle_color,\n start_color,\n 0,\n -start_value\n );\n this.start_value = start_value;\n this.end_value = end_value;\n };\n\n SplitRamp.prototype.map_value = function(value) {\n value = Math.max(value, this.start_value);\n value = Math.min(value, this.end_value);\n if (value >= 0) {\n return this.positive_ramp.map_value(value);\n } else {\n return this.negative_ramp.map_value(-value);\n }\n };\n\n var DiagonalHeatmapPainter = function(\n data,\n view_start,\n view_end,\n prefs,\n mode\n ) {\n Painter.call(this, data, view_start, view_end, prefs, mode);\n var i, len;\n\n if (this.prefs.min_value === undefined) {\n var min_value = Infinity;\n for (i = 0, len = this.data.length; i < len; i++) {\n min_value = Math.min(min_value, this.data[i][6]);\n }\n this.prefs.min_value = min_value;\n }\n if (this.prefs.max_value === undefined) {\n var max_value = -Infinity;\n for (i = 0, len = this.data.length; i < len; i++) {\n max_value = Math.max(max_value, this.data[i][6]);\n }\n this.prefs.max_value = max_value;\n }\n };\n\n DiagonalHeatmapPainter.prototype.default_prefs = {\n min_value: undefined,\n max_value: undefined,\n mode: \"Heatmap\",\n pos_color: \"#FF8C00\",\n neg_color: \"#4169E1\"\n };\n\n DiagonalHeatmapPainter.prototype.draw = function(\n ctx,\n width,\n height,\n w_scale\n ) {\n var min_value = this.prefs.min_value,\n max_value = this.prefs.max_value,\n value_range = max_value - min_value,\n height_px = height,\n view_start = this.view_start,\n mode = this.mode,\n data = this.data,\n invsqrt2 = 1 / Math.sqrt(2);\n\n var ramp = new SplitRamp(\n this.prefs.neg_color,\n \"#FFFFFF\",\n this.prefs.pos_color,\n min_value,\n max_value\n );\n\n var d, s1, e1, s2, e2, value;\n\n var scale = function(p) {\n return (p - view_start) * w_scale;\n };\n\n ctx.save();\n\n // Draw into triangle, then rotate and scale\n ctx.rotate(-45 * Math.PI / 180);\n ctx.scale(invsqrt2, invsqrt2);\n\n // Paint track.\n for (var i = 0, len = data.length; i < len; i++) {\n d = data[i];\n\n s1 = scale(d[1]);\n e1 = scale(d[2]);\n s2 = scale(d[4]);\n e2 = scale(d[5]);\n value = d[6];\n\n ctx.fillStyle = ramp.map_value(value);\n ctx.fillRect(s1, s2, e1 - s1, e2 - s2);\n }\n\n ctx.restore();\n };\n\n /**\n * Utilities for painting reads.\n */\n var ReadPainterUtils = function(ctx, row_height, px_per_base, mode) {\n this.ctx = ctx;\n this.row_height = row_height;\n this.px_per_base = px_per_base;\n this.draw_details =\n (mode === \"Pack\" || mode === \"Auto\") &&\n px_per_base >= ctx.canvas.manager.char_width_px;\n this.delete_details_thickness = 0.2;\n };\n\n _.extend(ReadPainterUtils.prototype, {\n /**\n * Draw deletion of base(s).\n * @param draw_detail if true, drawing in detail and deletion is drawn more subtly\n */\n draw_deletion: function(x, y, len) {\n this.ctx.fillStyle = \"black\";\n var thickness =\n (this.draw_details ? this.delete_details_thickness : 1) *\n this.row_height;\n y += 0.5 * (this.row_height - thickness);\n this.ctx.fillRect(x, y, len * this.px_per_base, thickness);\n }\n });\n\n /**\n * Paints variant data onto canvas.\n */\n var VariantPainter = function(\n data,\n view_start,\n view_end,\n prefs,\n mode,\n base_color_fn\n ) {\n Painter.call(this, data, view_start, view_end, prefs, mode);\n this.base_color_fn = base_color_fn;\n this.divider_height = 1;\n };\n\n _.extend(VariantPainter.prototype, Painter.prototype, {\n /**\n * Height of a single row, depends on mode\n */\n get_row_height: function() {\n var mode = this.mode,\n height;\n if (mode === \"Dense\") {\n height = DENSE_TRACK_HEIGHT;\n } else if (mode === \"Squish\") {\n height = SQUISH_TRACK_HEIGHT;\n } else {\n // mode === \"Pack\"\n height = PACK_TRACK_HEIGHT;\n }\n return height;\n },\n\n /**\n * Returns required height to draw a particular number of samples in a given mode.\n */\n get_required_height: function(num_samples) {\n // FIXME: for single-sample data, height should be summary_height when zoomed out and\n // row_height when zoomed in.\n var height = this.prefs.summary_height;\n\n // If showing sample data, height is summary + divider + samples.\n if (num_samples > 1 && this.prefs.show_sample_data) {\n height +=\n this.divider_height + num_samples * this.get_row_height();\n }\n return height;\n },\n\n /**\n * Draw on the context using a rectangle of width x height with scale w_scale.\n */\n draw: function(ctx, width, height, w_scale) {\n ctx.save();\n\n var /**\n * Returns dictionary of information about an indel; returns empty if there no indel. Assumes indel is left-aligned.\n * Dict attributes:\n * -type: 'insertion' or 'deletion'\n * -start: where the deletion starts relative to reference start\n * -len: how long the deletion is\n */\n get_indel_info = function(ref, alt) {\n var ref_len = ref.length,\n alt_len = alt.length,\n start = 0,\n len = 1,\n type = null;\n if (alt === \"-\") {\n type = \"deletion\";\n len = ref.length;\n } else if (ref.indexOf(alt) === 0 && ref_len > alt_len) {\n type = \"deletion\";\n len = ref_len - alt_len;\n start = alt_len;\n } else if (alt.indexOf(ref) === 0 && ref_len < alt_len) {\n // Insertion.\n type = \"insertion\";\n len = alt_len - ref_len;\n start = alt_len;\n }\n\n return type !== null\n ? { type: type, start: start, len: len }\n : {};\n };\n\n // Draw.\n var locus_data,\n pos,\n id,\n ref,\n alt,\n qual,\n filter,\n sample_gts,\n allele_counts,\n variant,\n draw_x_start,\n draw_y_start,\n genotype,\n // Always draw variants at least 1 pixel wide.\n base_px = Math.max(1, Math.floor(w_scale)),\n // Determine number of samples.\n num_samples = this.data.length\n ? this.data[0][7].split(\",\").length\n : 0,\n row_height =\n this.mode === \"Squish\"\n ? SQUISH_TRACK_HEIGHT\n : PACK_TRACK_HEIGHT,\n // If zoomed out, fill the whole row with feature to make it easier to read;\n // when zoomed in, use feature height so that there are gaps in sample rows.\n feature_height =\n w_scale < 0.1\n ? row_height\n : this.mode === \"Squish\"\n ? SQUISH_FEATURE_HEIGHT\n : PACK_FEATURE_HEIGHT,\n draw_summary = true,\n paint_utils = new ReadPainterUtils(\n ctx,\n row_height,\n w_scale,\n this.mode\n ),\n j;\n\n // If there's a single sample, update drawing variables.\n if (num_samples === 1) {\n row_height = feature_height =\n w_scale < ctx.canvas.manager.char_width_px\n ? this.prefs.summary_height\n : row_height;\n paint_utils.row_height = row_height;\n // No summary when there's a single sample.\n draw_summary = false;\n }\n\n // Draw divider between summary and samples.\n if (this.prefs.show_sample_data && draw_summary) {\n ctx.fillStyle = \"#F3F3F3\";\n ctx.globalAlpha = 1;\n ctx.fillRect(\n 0,\n this.prefs.summary_height - this.divider_height,\n width,\n this.divider_height\n );\n }\n\n // Draw variants.\n ctx.textAlign = \"center\";\n for (var i = 0; i < this.data.length; i++) {\n // Get locus data.\n locus_data = this.data[i];\n pos = locus_data[1];\n ref = locus_data[3];\n alt = [locus_data[4].split(\",\")];\n sample_gts = locus_data[7].split(\",\");\n allele_counts = locus_data.slice(8);\n\n // Process alterate values to derive information about each alt.\n alt = _.map(_.flatten(alt), function(a) {\n var alt_info = {\n type: \"snp\",\n value: a,\n start: 0\n },\n indel_info = get_indel_info(ref, a);\n\n return _.extend(alt_info, indel_info);\n });\n\n // Only draw locus data if it's in viewing region.\n if (pos < this.view_start || pos > this.view_end) {\n continue;\n }\n\n // Draw summary for alleles.\n if (draw_summary) {\n ctx.fillStyle = \"#999999\";\n ctx.globalAlpha = 1;\n for (j = 0; j < alt.length; j++) {\n // Draw background for summary.\n draw_x_start = this.get_start_draw_pos(\n pos + alt[j].start,\n w_scale\n );\n ctx.fillRect(\n draw_x_start,\n 0,\n base_px,\n this.prefs.summary_height\n );\n draw_y_start = this.prefs.summary_height;\n // Draw allele fractions onto summary.\n for (j = 0; j < alt.length; j++) {\n ctx.fillStyle =\n alt[j].type === \"deletion\"\n ? \"black\"\n : this.base_color_fn(alt[j].value);\n var allele_frac = allele_counts / sample_gts.length;\n var draw_height = Math.ceil(\n this.prefs.summary_height * allele_frac\n );\n ctx.fillRect(\n draw_x_start,\n draw_y_start - draw_height,\n base_px,\n draw_height\n );\n draw_y_start -= draw_height;\n }\n }\n }\n\n // Done drawing if not showing samples data.\n if (!this.prefs.show_sample_data) {\n continue;\n }\n\n // Draw sample genotype(s).\n draw_y_start = draw_summary\n ? this.prefs.summary_height + this.divider_height\n : 0;\n for (\n j = 0;\n j < sample_gts.length;\n j++, draw_y_start += row_height\n ) {\n genotype = sample_gts[j]\n ? sample_gts[j].split(/\\/|\\|/)\n : [\"0\", \"0\"];\n\n // Get variant to draw and set drawing properties.\n variant = null;\n if (genotype[0] === genotype[1]) {\n if (genotype[0] === \".\") {\n // TODO: draw uncalled variant.\n } else if (genotype[0] !== \"0\") {\n // Homozygous for variant.\n variant = alt[parseInt(genotype[0], 10) - 1];\n ctx.globalAlpha = 1;\n }\n // else reference\n } else {\n // Heterozygous for variant.\n variant =\n genotype[0] !== \"0\" ? genotype[0] : genotype[1];\n variant = alt[parseInt(variant, 10) - 1];\n ctx.globalAlpha = 0.5;\n }\n\n // If there's a variant, draw it.\n if (variant) {\n draw_x_start = this.get_start_draw_pos(\n pos + variant.start,\n w_scale\n );\n if (variant.type === \"snp\") {\n var snp = variant.value;\n ctx.fillStyle = this.base_color_fn(snp);\n if (paint_utils.draw_details) {\n ctx.fillText(\n snp,\n this.get_draw_pos(pos, w_scale),\n draw_y_start + row_height\n );\n } else {\n ctx.fillRect(\n draw_x_start,\n draw_y_start + 1,\n base_px,\n feature_height\n );\n }\n } else if (variant.type === \"deletion\") {\n paint_utils.draw_deletion(\n draw_x_start,\n draw_y_start + 1,\n variant.len\n );\n } else {\n // TODO: handle insertions.\n }\n }\n }\n }\n\n ctx.restore();\n }\n });\n\n return {\n Scaler: Scaler,\n LinePainter: LinePainter,\n LinkedFeaturePainter: LinkedFeaturePainter,\n 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function(_) {\n /**\n * Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig.\n * The overlap is computed relative to the second region; hence, OVERLAP_START indicates that the first\n * region overlaps the start (but not the end) of the second region.\n * NOTE: Coordinates are assumed to be in BED format: half open (start is closed, end is open).\n */\n var BEFORE = 1001,\n CONTAINS = 1002,\n OVERLAP_START = 1003,\n OVERLAP_END = 1004,\n CONTAINED_BY = 1005,\n AFTER = 1006;\n var compute_overlap = function(first_region, second_region) {\n var first_start = first_region[0],\n first_end = first_region[1],\n second_start = second_region[0],\n second_end = second_region[1],\n overlap;\n if (first_start < second_start) {\n if (first_end <= second_start) {\n overlap = BEFORE;\n } else if (first_end <= second_end) {\n overlap = OVERLAP_START;\n } else {\n // first_end > second_end\n overlap = CONTAINS;\n }\n } else {\n // first_start >= second_start\n if (first_start > second_end) {\n overlap = AFTER;\n } else if (first_end <= second_end) {\n overlap = CONTAINED_BY;\n } else {\n overlap = OVERLAP_END;\n }\n }\n\n return overlap;\n };\n\n /**\n * Returns true if regions overlap.\n */\n var is_overlap = function(first_region, second_region) {\n var overlap = compute_overlap(first_region, second_region);\n return overlap !== BEFORE && overlap !== AFTER;\n };\n\n /**\n * Draw a dashed line on a canvas using filled rectangles. This function is based on:\n * http://vetruvet.blogspot.com/2010/10/drawing-dashed-lines-on-html5-canvas.html\n * However, that approach uses lines, which don't seem to render as well, so use\n * rectangles instead.\n */\n var dashedLine = function(ctx, x1, y1, x2, y2, dashLen) {\n if (dashLen === undefined) {\n dashLen = 4;\n }\n var dX = x2 - x1;\n var dY = y2 - y1;\n var dashes = Math.floor(Math.sqrt(dX * dX + dY * dY) / dashLen);\n var dashX = dX / dashes;\n var dashY = dY / dashes;\n var q;\n\n for (q = 0; q < dashes; q++, x1 += dashX, y1 += dashY) {\n if (q % 2 !== 0) {\n continue;\n }\n ctx.fillRect(x1, y1, dashLen, 1);\n }\n };\n\n /**\n * Draw an isosceles triangle that points down.\n */\n var drawDownwardEquilateralTriangle = function(\n ctx,\n down_vertex_x,\n down_vertex_y,\n side_len\n ) {\n // Compute other two points of triangle.\n var x1 = down_vertex_x - side_len / 2,\n x2 = down_vertex_x + side_len / 2,\n y = down_vertex_y - Math.sqrt(side_len * 3 / 2);\n\n // Draw and fill.\n ctx.beginPath();\n ctx.moveTo(x1, y);\n ctx.lineTo(x2, y);\n ctx.lineTo(down_vertex_x, down_vertex_y);\n ctx.lineTo(x1, y);\n\n ctx.strokeStyle = this.fillStyle;\n ctx.fill();\n ctx.stroke();\n ctx.closePath();\n };\n\n /**\n * Base class for all scalers. Scalers produce values that are used to change (scale) drawing attributes.\n */\n var Scaler = function(default_val) {\n this.default_val = default_val ? default_val : 1;\n };\n\n /**\n * Produce a scaling value.\n */\n Scaler.prototype.gen_val = function(input) {\n return this.default_val;\n };\n\n /**\n * Results from painter.draw()\n */\n var DrawResults = function(options) {\n this.incomplete_features = options.incomplete_features;\n this.feature_mapper = options.feature_mapper;\n };\n\n /**\n * Base class for painters\n *\n * -- Mode and prefs are both optional\n */\n var Painter = function(data, view_start, view_end, prefs, mode) {\n // Data and data properties\n this.data = data;\n // View\n this.view_start = view_start;\n this.view_end = view_end;\n // Drawing prefs\n this.prefs = _.extend({}, this.default_prefs, prefs);\n this.mode = mode;\n };\n\n Painter.prototype.default_prefs = {};\n\n /**\n * Draw on the context using a rectangle of width x height using scale w_scale.\n */\n Painter.prototype.draw = function(ctx, width, height, w_scale) {};\n\n /**\n * Get starting drawing position, which is offset a half-base left of coordinate.\n */\n Painter.prototype.get_start_draw_pos = function(chrom_pos, w_scale) {\n return this._chrom_pos_to_draw_pos(chrom_pos, w_scale, -0.5);\n };\n\n /**\n * Get end drawing position, which is offset a half-base right of coordinate.\n */\n Painter.prototype.get_end_draw_pos = function(chrom_pos, w_scale) {\n return this._chrom_pos_to_draw_pos(chrom_pos, w_scale, 0.5);\n };\n\n /**\n * Get drawing position.\n */\n Painter.prototype.get_draw_pos = function(chrom_pos, w_scale) {\n return this._chrom_pos_to_draw_pos(chrom_pos, w_scale, 0);\n };\n\n /**\n * Convert chromosome position to drawing position.\n */\n Painter.prototype._chrom_pos_to_draw_pos = function(\n chrom_pos,\n w_scale,\n offset\n ) {\n return Math.floor(\n w_scale * (Math.max(0, chrom_pos - this.view_start) + offset)\n );\n };\n\n var LinePainter = function(data, view_start, view_end, prefs, mode) {\n Painter.call(this, data, view_start, view_end, prefs, mode);\n };\n\n LinePainter.prototype.default_prefs = {\n min_value: undefined,\n max_value: undefined,\n mode: \"Histogram\",\n color: \"#000\",\n overflow_color: \"#F66\"\n };\n\n LinePainter.prototype.draw = function(ctx, width, height, w_scale) {\n var in_path = false,\n min_value = this.prefs.min_value,\n max_value = this.prefs.max_value,\n vertical_range = max_value - min_value,\n height_px = height,\n view_start = this.view_start,\n mode = this.mode,\n data = this.data;\n\n ctx.save();\n\n // Pixel position of 0 on the y axis\n var y_zero = Math.round(height + min_value / vertical_range * height);\n\n // Horizontal line to denote x-axis\n if (mode !== \"Intensity\") {\n ctx.fillStyle = \"#aaa\";\n ctx.fillRect(0, y_zero, width, 1);\n }\n\n ctx.beginPath();\n var x_scaled, y, delta_x_pxs;\n if (data.length > 1) {\n delta_x_pxs = _.map(data.slice(0, -1), function(d, i) {\n return Math.ceil((data[i + 1][0] - data[i][0]) * w_scale);\n });\n } else {\n delta_x_pxs = [10];\n }\n\n // Painter color can be in either block_color (FeatureTrack) or color pref (LineTrack).\n var painter_color = this.prefs.block_color || this.prefs.color,\n // Extract RGB from preference color.\n pref_color = parseInt(painter_color.slice(1), 16),\n pref_r = (pref_color & 0xff0000) >> 16,\n pref_g = (pref_color & 0x00ff00) >> 8,\n pref_b = pref_color & 0x0000ff,\n top_overflow = false,\n bot_overflow = false;\n\n // Paint track.\n var delta_x_px;\n for (var i = 0, len = data.length; i < len; i++) {\n // Reset attributes for next point.\n ctx.fillStyle = ctx.strokeStyle = painter_color;\n top_overflow = bot_overflow = false;\n delta_x_px = delta_x_pxs[i];\n\n x_scaled = Math.floor((data[i][0] - view_start - 0.5) * w_scale);\n y = data[i][1];\n\n // Process Y (scaler) value.\n if (y === null) {\n if (in_path && mode === \"Filled\") {\n ctx.lineTo(x_scaled, height_px);\n }\n in_path = false;\n continue;\n }\n\n // Bound Y value by min, max.\n if (y < min_value) {\n bot_overflow = true;\n y = min_value;\n } else if (y > max_value) {\n top_overflow = true;\n y = max_value;\n }\n\n // Draw point.\n if (mode === \"Histogram\") {\n // y becomes the bar height in pixels, which is the negated for canvas coords\n y = Math.round(y / vertical_range * height_px);\n ctx.fillRect(x_scaled, y_zero, delta_x_px, -y);\n } else if (mode === \"Intensity\") {\n var saturation = (y - min_value) / vertical_range,\n // Range is [pref_color, 255] where saturation = 0 --> 255 and saturation = 1 --> pref color\n new_r = Math.round(\n pref_r + (255 - pref_r) * (1 - saturation)\n ),\n new_g = Math.round(\n pref_g + (255 - pref_g) * (1 - saturation)\n ),\n new_b = Math.round(\n pref_b + (255 - pref_b) * (1 - saturation)\n );\n ctx.fillStyle =\n \"rgb(\" + new_r + \",\" + new_g + \",\" + new_b + \")\";\n ctx.fillRect(x_scaled, 0, delta_x_px, height_px);\n } else {\n // mode is Coverage/Line or Filled.\n\n // Scale Y value.\n y = Math.round(\n height_px - (y - min_value) / vertical_range * height_px\n );\n if (in_path) {\n ctx.lineTo(x_scaled, y);\n } else {\n in_path = true;\n if (mode === \"Filled\") {\n ctx.moveTo(x_scaled, height_px);\n ctx.lineTo(x_scaled, y);\n } else {\n ctx.moveTo(x_scaled, y);\n // Use this approach (note: same as for filled) to draw line from 0 to\n // first data point.\n //ctx.moveTo(x_scaled, height_px);\n //ctx.lineTo(x_scaled, y);\n }\n }\n }\n\n // Draw lines at boundaries if overflowing min or max\n ctx.fillStyle = this.prefs.overflow_color;\n if (top_overflow || bot_overflow) {\n var overflow_x;\n if (mode === \"Histogram\" || mode === \"Intensity\") {\n overflow_x = delta_x_px;\n } else {\n // Line and Filled, which are points\n x_scaled -= 2; // Move it over to the left so it's centered on the point\n overflow_x = 4;\n }\n if (top_overflow) {\n ctx.fillRect(x_scaled, 0, overflow_x, 3);\n }\n if (bot_overflow) {\n ctx.fillRect(x_scaled, height_px - 3, overflow_x, 3);\n }\n }\n ctx.fillStyle = painter_color;\n }\n if (mode === \"Filled\") {\n if (in_path) {\n ctx.lineTo(x_scaled, y_zero);\n ctx.lineTo(0, y_zero);\n }\n ctx.fill();\n } else {\n ctx.stroke();\n }\n\n ctx.restore();\n };\n\n /**\n * Mapper that contains information about feature locations and data.\n */\n var FeaturePositionMapper = function(slot_height) {\n this.feature_positions = {};\n this.slot_height = slot_height;\n this.translation = 0;\n this.y_translation = 0;\n };\n\n /**\n * Map feature data to a position defined by \n var x_center = s_start - (s_end - s_start) / 2;\n if (\n (mode === \"Pack\" || this.mode === \"Auto\") &&\n read_seq !== undefined &&\n w_scale > char_width_px\n ) {\n // Draw sequence container.\n ctx.fillStyle = \"yellow\";\n ctx.fillRect(\n x_center - gap,\n y_start - 9,\n s_end - s_start,\n 9\n );\n draw_last[draw_last.length] = {\n type: \"triangle\",\n data: [insert_x_coord, y_start + 4, 5]\n };\n ctx.fillStyle = CONNECTOR_COLOR;\n // Based on overlap b/t sequence and tile, get sequence to be drawn.\n switch (compute_overlap(\n [seq_start, seq_start + cig_len],\n tile_region\n )) {\n case OVERLAP_START:\n seq = seq.slice(\n tile_low - seq_start\n );\n break;\n case OVERLAP_END:\n seq = seq.slice(\n 0,\n seq_start - tile_high\n );\n break;\n case CONTAINED_BY:\n // All of sequence drawn.\n break;\n case CONTAINS:\n seq = seq.slice(\n tile_low - seq_start,\n seq_start - tile_high\n );\n break;\n }\n // Draw sequence.\n for (\n var c = 0, str_len = seq.length;\n c < str_len;\n c++\n ) {\n var c_start = Math.floor(\n Math.max(\n 0,\n (seq_start + c - tile_low) *\n w_scale\n )\n );\n ctx.fillText(\n seq[c],\n c_start - (s_end - s_start) / 2,\n y_start\n );\n }\n } else {\n // Draw block.\n ctx.fillStyle = \"yellow\";\n // TODO: This is a pretty hack-ish way to fill rectangle based on mode.\n ctx.fillRect(\n x_center,\n y_start +\n (this.mode !== \"Dense\" ? 2 : 5),\n s_end - s_start,\n mode !== \"Dense\"\n ? SQUISH_FEATURE_HEIGHT\n : DENSE_FEATURE_HEIGHT\n );\n }\n } else {\n if (\n (mode === \"Pack\" || this.mode === \"Auto\") &&\n read_seq !== undefined &&\n w_scale > char_width_px\n ) {\n // Show insertions with a single number at the insertion point.\n draw_last.push({\n type: \"text\",\n data: [\n seq.length,\n insert_x_coord,\n y_start + 9\n ]\n });\n } else {\n // TODO: probably can merge this case with code above.\n }\n }\n }\n seq_offset += cig_len;\n // No change to base offset because insertions are drawn above sequence/read.\n break;\n }\n }\n\n //\n // Draw last items.\n //\n ctx.fillStyle = \"yellow\";\n var item, type, data;\n for (var i = 0; i < draw_last.length; i++) {\n item = draw_last[i];\n type = item.type;\n data = item.data;\n if (type === \"text\") {\n ctx.save();\n ctx.font = \"bold \" + ctx.font;\n ctx.fillText(data[0], data[1], data[2]);\n ctx.restore();\n } else if (type === \"triangle\") {\n drawDownwardEquilateralTriangle(\n ctx,\n data[0],\n data[1],\n data[2]\n );\n }\n }\n },\n\n /**\n * Draw a complete read pair\n */\n draw_element: function(\n ctx,\n mode,\n feature,\n slot,\n tile_low,\n tile_high,\n w_scale,\n y_scale,\n width\n ) {\n // All features need a start, end, and vertical center.\n var feature_uid = feature[0],\n feature_start = feature[1],\n feature_end = feature[2],\n feature_name = feature[3],\n // -0.5 to put element between bases.\n f_start = Math.floor(\n Math.max(\n -0.5 * w_scale,\n (feature_start - tile_low - 0.5) * w_scale\n )\n ),\n f_end = Math.ceil(\n Math.min(\n width,\n Math.max(0, (feature_end - tile_low - 0.5) * w_scale)\n )\n ),\n y_start = (mode === \"Dense\" ? 0 : 0 + slot) * y_scale,\n draw_height =\n mode === \"Pack\"\n ? PACK_FEATURE_HEIGHT\n : SQUISH_FEATURE_HEIGHT,\n label_color = this.prefs.label_color;\n\n // Draw read.\n if (feature[5] instanceof Array) {\n // Read is paired.\n var connector = true;\n\n // Draw left/forward read.\n if (\n feature[4][1] >= tile_low &&\n feature[4][0] <= tile_high &&\n feature[4][2]\n ) {\n this.draw_read(\n ctx,\n mode,\n w_scale,\n y_start,\n tile_low,\n tile_high,\n feature[4][0],\n feature[4][2],\n feature[4][3],\n feature[4][4]\n );\n } else {\n connector = false;\n }\n\n // Draw right/reverse read.\n if (\n feature[5][1] >= tile_low &&\n feature[5][0] <= tile_high &&\n feature[5][2]\n ) {\n this.draw_read(\n ctx,\n mode,\n w_scale,\n y_start,\n tile_low,\n tile_high,\n feature[5][0],\n feature[5][2],\n feature[5][3],\n feature[5][4]\n );\n } else {\n connector = false;\n }\n\n // Draw connector if both reads were drawn.\n // TODO: currently, there is no way to connect reads drawn on different tiles; to connect reads on different tiles, data manager\n // code is needed to join mate pairs from different regions. Alternatively, requesting multiple regions of data at once would\n // make it possible to put together more easily.\n // -0.5 to position connector correctly between reads.\n var b1_end = Math.ceil(\n Math.min(\n width,\n Math.max(\n -0.5 * w_scale,\n (feature[4][1] - tile_low - 0.5) * w_scale\n )\n )\n ),\n b2_start = Math.floor(\n Math.max(\n -0.5 * w_scale,\n (feature[5][0] - tile_low - 0.5) * w_scale\n )\n );\n if (connector && b2_start > b1_end) {\n ctx.fillStyle = CONNECTOR_COLOR;\n var line_height = y_start + 1 + (draw_height - 1) / 2;\n dashedLine(ctx, b1_end, line_height, b2_start, line_height);\n }\n } else {\n // Read is single.\n this.draw_read(\n ctx,\n mode,\n w_scale,\n y_start,\n tile_low,\n tile_high,\n feature_start,\n feature[4],\n feature[5],\n feature[6]\n );\n }\n if (\n mode === \"Pack\" &&\n feature_start >= tile_low &&\n feature_name !== \".\"\n ) {\n // Draw label.\n ctx.fillStyle = this.prefs.label_color;\n if (\n tile_low === 0 &&\n f_start - ctx.measureText(feature_name).width < 0\n ) {\n ctx.textAlign = \"left\";\n ctx.fillText(\n feature_name,\n f_end + LABEL_SPACING,\n y_start + 9,\n this.max_label_length\n );\n } else {\n ctx.textAlign = \"right\";\n ctx.fillText(\n feature_name,\n f_start - LABEL_SPACING,\n y_start + 9,\n this.max_label_length\n );\n }\n }\n\n // FIXME: provide actual coordinates for drawn read.\n return [0, 0];\n }\n });\n\n var ArcLinkedFeaturePainter = function(\n data,\n view_start,\n view_end,\n prefs,\n mode,\n alpha_scaler,\n height_scaler\n ) {\n LinkedFeaturePainter.call(\n this,\n data,\n view_start,\n view_end,\n prefs,\n mode,\n alpha_scaler,\n height_scaler\n );\n // Need to know the longest feature length for adding spacing\n this.longest_feature_length = this.calculate_longest_feature_length();\n this.draw_background_connector = false;\n this.draw_individual_connectors = true;\n };\n\n _.extend(\n ArcLinkedFeaturePainter.prototype,\n FeaturePainter.prototype,\n LinkedFeaturePainter.prototype,\n {\n calculate_longest_feature_length: function() {\n var longest_feature_length = 0;\n for (var i = 0, len = this.data.length; i < len; i++) {\n var feature = this.data[i],\n feature_start = feature[1],\n feature_end = feature[2];\n longest_feature_length = Math.max(\n longest_feature_length,\n feature_end - feature_start\n );\n }\n return longest_feature_length;\n },\n\n get_top_padding: function(width) {\n var view_range = this.view_end - this.view_start,\n w_scale = width / view_range;\n return Math.min(\n 128,\n Math.ceil(this.longest_feature_length / 2 * w_scale)\n );\n },\n\n draw_connector: function(\n ctx,\n block1_start,\n block1_end,\n block2_start,\n block2_end,\n y_start\n ) {\n // Arc drawing -- from closest endpoints\n var x_center = (block1_end + block2_start) / 2,\n radius = block2_start - x_center;\n // For full half circles\n var angle1 = Math.PI,\n angle2 = 0;\n if (radius > 0) {\n ctx.beginPath();\n ctx.arc(\n x_center,\n y_start,\n block2_start - x_center,\n Math.PI,\n 0\n );\n ctx.stroke();\n }\n }\n }\n );\n\n // Color stuff from less.js\n\n var Color = function(rgb, a) {\n /**\n * The end goal here, is to parse the arguments\n * into an integer triplet, such as `128, 255, 0`\n *\n * This facilitates operations and conversions.\n */\n if (Array.isArray(rgb)) {\n this.rgb = rgb;\n } else if (rgb.length == 6) {\n this.rgb = rgb.match(/.{2}/g).map(function(c) {\n return parseInt(c, 16);\n });\n } else if (rgb.length == 7) {\n this.rgb = rgb\n .substring(1, 7)\n .match(/.{2}/g)\n .map(function(c) {\n return parseInt(c, 16);\n });\n } else {\n this.rgb = rgb.split(\"\").map(function(c) {\n return parseInt(c + c, 16);\n });\n }\n this.alpha = typeof a === \"number\" ? a : 1;\n };\n Color.prototype = {\n eval: function() {\n return this;\n },\n\n //\n // If we have some transparency, the only way to represent it\n // is via `rgba`. Otherwise, we use the hex representation,\n // which has better compatibility with older browsers.\n // Values are capped between `0` and `255`, rounded and zero-padded.\n //\n toCSS: function() {\n if (this.alpha < 1.0) {\n return (\n \"rgba(\" +\n this.rgb\n .map(function(c) {\n return Math.round(c);\n })\n .concat(this.alpha)\n .join(\", \") +\n \")\"\n );\n } else {\n return (\n \"#\" +\n this.rgb\n .map(function(i) {\n i = Math.round(i);\n i = (i > 255 ? 255 : i < 0 ? 0 : i).toString(16);\n return i.length === 1 ? \"0\" + i : i;\n })\n .join(\"\")\n );\n }\n },\n\n toHSL: function() {\n var r = this.rgb[0] / 255,\n g = this.rgb[1] / 255,\n b = this.rgb[2] / 255,\n a = this.alpha;\n\n var max = Math.max(r, g, b),\n min = Math.min(r, g, b);\n var h,\n s,\n l = (max + min) / 2,\n d = max - min;\n\n if (max === min) {\n h = s = 0;\n } else {\n s = l > 0.5 ? d / (2 - max - min) : d / (max + min);\n\n switch (max) {\n case r:\n h = (g - b) / d + (g < b ? 6 : 0);\n break;\n case g:\n h = (b - r) / d + 2;\n break;\n case b:\n h = (r - g) / d + 4;\n break;\n }\n h /= 6;\n }\n return { h: h * 360, s: s, l: l, a: a };\n },\n\n toARGB: function() {\n var argb = [Math.round(this.alpha * 255)].concat(this.rgb);\n return (\n \"#\" +\n argb\n .map(function(i) {\n i = Math.round(i);\n i = (i > 255 ? 255 : i < 0 ? 0 : i).toString(16);\n return i.length === 1 ? \"0\" + i : i;\n })\n .join(\"\")\n );\n },\n\n mix: function(color2, weight) {\n var color1 = this;\n\n var p = weight; // .value / 100.0;\n var w = p * 2 - 1;\n var a = color1.toHSL().a - color2.toHSL().a;\n\n var w1 = ((w * a == -1 ? w : (w + a) / (1 + w * a)) + 1) / 2.0;\n var w2 = 1 - w1;\n\n var rgb = [\n color1.rgb[0] * w1 + color2.rgb[0] * w2,\n color1.rgb[1] * w1 + color2.rgb[1] * w2,\n color1.rgb[2] * w1 + color2.rgb[2] * w2\n ];\n\n var alpha = color1.alpha * p + color2.alpha * (1 - p);\n\n return new Color(rgb, alpha);\n }\n };\n\n // End colors from less.js\n\n var LinearRamp = function(start_color, end_color, start_value, end_value) {\n /**\n * Simple linear gradient\n */\n this.start_color = new Color(start_color);\n this.end_color = new Color(end_color);\n this.start_value = start_value;\n this.end_value = end_value;\n this.value_range = end_value - start_value;\n };\n\n LinearRamp.prototype.map_value = function(value) {\n value = Math.max(value, this.start_value);\n value = Math.min(value, this.end_value);\n value = (value - this.start_value) / this.value_range;\n // HACK: just red for now\n // return \"hsl(0,100%,\" + (value * 100) + \"%)\"\n return this.start_color.mix(this.end_color, 1 - value).toCSS();\n };\n\n var SplitRamp = function(\n start_color,\n middle_color,\n end_color,\n start_value,\n end_value\n ) {\n /**\n * Two gradients split away from 0\n */\n this.positive_ramp = new LinearRamp(\n middle_color,\n end_color,\n 0,\n end_value\n );\n this.negative_ramp = new LinearRamp(\n middle_color,\n start_color,\n 0,\n -start_value\n );\n this.start_value = start_value;\n this.end_value = end_value;\n };\n\n SplitRamp.prototype.map_value = function(value) {\n value = Math.max(value, this.start_value);\n value = Math.min(value, this.end_value);\n if (value >= 0) {\n return this.positive_ramp.map_value(value);\n } else {\n return this.negative_ramp.map_value(-value);\n }\n };\n\n var DiagonalHeatmapPainter = function(\n data,\n view_start,\n view_end,\n prefs,\n mode\n ) {\n Painter.call(this, data, view_start, view_end, prefs, mode);\n var i, len;\n\n if (this.prefs.min_value === undefined) {\n var min_value = Infinity;\n for (i = 0, len = this.data.length; i < len; i++) {\n min_value = Math.min(min_value, this.data[i][6]);\n }\n this.prefs.min_value = min_value;\n }\n if (this.prefs.max_value === undefined) {\n var max_value = -Infinity;\n for (i = 0, len = this.data.length; i < len; i++) {\n max_value = Math.max(max_value, this.data[i][6]);\n }\n this.prefs.max_value = max_value;\n }\n };\n\n DiagonalHeatmapPainter.prototype.default_prefs = {\n min_value: undefined,\n max_value: undefined,\n mode: \"Heatmap\",\n pos_color: \"#FF8C00\",\n neg_color: \"#4169E1\"\n };\n\n DiagonalHeatmapPainter.prototype.draw = function(\n ctx,\n width,\n height,\n w_scale\n ) {\n var min_value = this.prefs.min_value,\n max_value = this.prefs.max_value,\n value_range = max_value - min_value,\n height_px = height,\n view_start = this.view_start,\n mode = this.mode,\n data = this.data,\n invsqrt2 = 1 / Math.sqrt(2);\n\n var ramp = new SplitRamp(\n this.prefs.neg_color,\n \"#FFFFFF\",\n this.prefs.pos_color,\n min_value,\n max_value\n );\n\n var d, s1, e1, s2, e2, value;\n\n var scale = function(p) {\n return (p - view_start) * w_scale;\n };\n\n ctx.save();\n\n // Draw into triangle, then rotate and scale\n ctx.rotate(-45 * Math.PI / 180);\n ctx.scale(invsqrt2, invsqrt2);\n\n // Paint track.\n for (var i = 0, len = data.length; i < len; i++) {\n d = data[i];\n\n s1 = scale(d[1]);\n e1 = scale(d[2]);\n s2 = scale(d[4]);\n e2 = scale(d[5]);\n value = d[6];\n\n ctx.fillStyle = ramp.map_value(value);\n ctx.fillRect(s1, s2, e1 - s1, e2 - s2);\n }\n\n ctx.restore();\n };\n\n /**\n * Utilities for painting reads.\n */\n var ReadPainterUtils = function(ctx, row_height, px_per_base, mode) {\n this.ctx = ctx;\n this.row_height = row_height;\n this.px_per_base = px_per_base;\n this.draw_details =\n (mode === \"Pack\" || mode === \"Auto\") &&\n px_per_base >= ctx.canvas.manager.char_width_px;\n this.delete_details_thickness = 0.2;\n };\n\n _.extend(ReadPainterUtils.prototype, {\n /**\n * Draw deletion of base(s).\n * @param draw_detail if true, drawing in detail and deletion is drawn more subtly\n */\n draw_deletion: function(x, y, len) {\n this.ctx.fillStyle = \"black\";\n var thickness =\n (this.draw_details ? this.delete_details_thickness : 1) *\n this.row_height;\n y += 0.5 * (this.row_height - thickness);\n this.ctx.fillRect(x, y, len * this.px_per_base, thickness);\n }\n });\n\n /**\n * Paints variant data onto canvas.\n */\n var VariantPainter = function(\n data,\n view_start,\n view_end,\n prefs,\n mode,\n base_color_fn\n ) {\n Painter.call(this, data, view_start, view_end, prefs, mode);\n this.base_color_fn = base_color_fn;\n this.divider_height = 1;\n };\n\n _.extend(VariantPainter.prototype, Painter.prototype, {\n /**\n * Height of a single row, depends on mode\n */\n get_row_height: function() {\n var mode = this.mode,\n height;\n if (mode === \"Dense\") {\n height = DENSE_TRACK_HEIGHT;\n } else if (mode === \"Squish\") {\n height = SQUISH_TRACK_HEIGHT;\n } else {\n // mode === \"Pack\"\n height = PACK_TRACK_HEIGHT;\n }\n return height;\n },\n\n /**\n * Returns required height to draw a particular number of samples in a given mode.\n */\n get_required_height: function(num_samples) {\n // FIXME: for single-sample data, height should be summary_height when zoomed out and\n // row_height when zoomed in.\n var height = this.prefs.summary_height;\n\n // If showing sample data, height is summary + divider + samples.\n if (num_samples > 1 && this.prefs.show_sample_data) {\n height +=\n this.divider_height + num_samples * this.get_row_height();\n }\n return height;\n },\n\n /**\n * Draw on the context using a rectangle of width x height with scale w_scale.\n */\n draw: function(ctx, width, height, w_scale) {\n ctx.save();\n\n var /**\n * Returns dictionary of information about an indel; returns empty if there no indel. Assumes indel is left-aligned.\n * Dict attributes:\n * -type: 'insertion' or 'deletion'\n * -start: where the deletion starts relative to reference start\n * -len: how long the deletion is\n */\n get_indel_info = function(ref, alt) {\n var ref_len = ref.length,\n alt_len = alt.length,\n start = 0,\n len = 1,\n type = null;\n if (alt === \"-\") {\n type = \"deletion\";\n len = ref.length;\n } else if (ref.indexOf(alt) === 0 && ref_len > alt_len) {\n type = \"deletion\";\n len = ref_len - alt_len;\n start = alt_len;\n } else if (alt.indexOf(ref) === 0 && ref_len < alt_len) {\n // Insertion.\n type = \"insertion\";\n len = alt_len - ref_len;\n start = alt_len;\n }\n\n return type !== null\n ? { type: type, start: start, len: len }\n : {};\n };\n\n // Draw.\n var locus_data,\n pos,\n id,\n ref,\n alt,\n qual,\n filter,\n sample_gts,\n allele_counts,\n variant,\n draw_x_start,\n draw_y_start,\n genotype,\n // Always draw variants at least 1 pixel wide.\n base_px = Math.max(1, Math.floor(w_scale)),\n // Determine number of samples.\n num_samples = this.data.length\n ? this.data[0][7].split(\",\").length\n : 0,\n row_height =\n this.mode === \"Squish\"\n ? SQUISH_TRACK_HEIGHT\n : PACK_TRACK_HEIGHT,\n // If zoomed out, fill the whole row with feature to make it easier to read;\n // when zoomed in, use feature height so that there are gaps in sample rows.\n feature_height =\n w_scale < 0.1\n ? row_height\n : this.mode === \"Squish\"\n ? SQUISH_FEATURE_HEIGHT\n : PACK_FEATURE_HEIGHT,\n draw_summary = true,\n paint_utils = new ReadPainterUtils(\n ctx,\n row_height,\n w_scale,\n this.mode\n ),\n j;\n\n // If there's a single sample, update drawing variables.\n if (num_samples === 1) {\n row_height = feature_height =\n w_scale < ctx.canvas.manager.char_width_px\n ? this.prefs.summary_height\n : row_height;\n paint_utils.row_height = row_height;\n // No summary when there's a single sample.\n draw_summary = false;\n }\n\n // Draw divider between summary and samples.\n if (this.prefs.show_sample_data && draw_summary) {\n ctx.fillStyle = \"#F3F3F3\";\n ctx.globalAlpha = 1;\n ctx.fillRect(\n 0,\n this.prefs.summary_height - this.divider_height,\n width,\n this.divider_height\n );\n }\n\n // Draw variants.\n ctx.textAlign = \"center\";\n for (var i = 0; i < this.data.length; i++) {\n // Get locus data.\n locus_data = this.data[i];\n pos = locus_data[1];\n ref = locus_data[3];\n alt = [locus_data[4].split(\",\")];\n sample_gts = locus_data[7].split(\",\");\n allele_counts = locus_data.slice(8);\n\n // Process alterate values to derive information about each alt.\n alt = _.map(_.flatten(alt), function(a) {\n var alt_info = {\n type: \"snp\",\n value: a,\n start: 0\n },\n indel_info = get_indel_info(ref, a);\n\n return _.extend(alt_info, indel_info);\n });\n\n // Only draw locus data if it's in viewing region.\n if (pos < this.view_start || pos > this.view_end) {\n continue;\n }\n\n // Draw summary for alleles.\n if (draw_summary) {\n ctx.fillStyle = \"#999999\";\n ctx.globalAlpha = 1;\n for (j = 0; j < alt.length; j++) {\n // Draw background for summary.\n draw_x_start = this.get_start_draw_pos(\n pos + alt[j].start,\n w_scale\n );\n ctx.fillRect(\n draw_x_start,\n 0,\n base_px,\n this.prefs.summary_height\n );\n draw_y_start = this.prefs.summary_height;\n // Draw allele fractions onto summary.\n for (j = 0; j < alt.length; j++) {\n ctx.fillStyle =\n alt[j].type === \"deletion\"\n ? \"black\"\n : this.base_color_fn(alt[j].value);\n var allele_frac = allele_counts / sample_gts.length;\n var draw_height = Math.ceil(\n this.prefs.summary_height * allele_frac\n );\n ctx.fillRect(\n draw_x_start,\n draw_y_start - draw_height,\n base_px,\n draw_height\n );\n draw_y_start -= draw_height;\n }\n }\n }\n\n // Done drawing if not showing samples data.\n if (!this.prefs.show_sample_data) {\n continue;\n }\n\n // Draw sample genotype(s).\n draw_y_start = draw_summary\n ? this.prefs.summary_height + this.divider_height\n : 0;\n for (\n j = 0;\n j < sample_gts.length;\n j++, draw_y_start += row_height\n ) {\n genotype = sample_gts[j]\n ? sample_gts[j].split(/\\/|\\|/)\n : [\"0\", \"0\"];\n\n // Get variant to draw and set drawing properties.\n variant = null;\n if (genotype[0] === genotype[1]) {\n if (genotype[0] === \".\") {\n // TODO: draw uncalled variant.\n } else if (genotype[0] !== \"0\") {\n // Homozygous for variant.\n variant = alt[parseInt(genotype[0], 10) - 1];\n ctx.globalAlpha = 1;\n }\n // else reference\n } else {\n // Heterozygous for variant.\n variant =\n genotype[0] !== \"0\" ? genotype[0] : genotype[1];\n variant = alt[parseInt(variant, 10) - 1];\n ctx.globalAlpha = 0.5;\n }\n\n // If there's a variant, draw it.\n if (variant) {\n draw_x_start = this.get_start_draw_pos(\n pos + variant.start,\n w_scale\n );\n if (variant.type === \"snp\") {\n var snp = variant.value;\n ctx.fillStyle = this.base_color_fn(snp);\n if (paint_utils.draw_details) {\n ctx.fillText(\n snp,\n this.get_draw_pos(pos, w_scale),\n draw_y_start + row_height\n );\n } else {\n ctx.fillRect(\n draw_x_start,\n draw_y_start + 1,\n base_px,\n feature_height\n );\n }\n } else if (variant.type === \"deletion\") {\n paint_utils.draw_deletion(\n draw_x_start,\n draw_y_start + 1,\n variant.len\n );\n } else {\n // TODO: handle insertions.\n }\n }\n }\n }\n\n ctx.restore();\n }\n });\n\n return {\n Scaler: Scaler,\n LinePainter: LinePainter,\n LinkedFeaturePainter: LinkedFeaturePainter,\n ReadPainter: ReadPainter,\n ArcLinkedFeaturePainter: ArcLinkedFeaturePainter,\n DiagonalHeatmapPainter: DiagonalHeatmapPainter,\n VariantPainter: VariantPainter\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/viz/trackster/slotting.js.map b/static/maps/viz/trackster/slotting.js.map index a4ae409a6a3..6907d06122b 100644 --- a/static/maps/viz/trackster/slotting.js.map +++ b/static/maps/viz/trackster/slotting.js.map @@ -1 +1 @@ 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function(_) {\n var extend = _.extend;\n\n // HACK: LABEL_SPACING is currently duplicated between here and painters\n var LABEL_SPACING = 2,\n PACK_SPACING = 5;\n\n /**\n * Hold slotting information for a feature.\n */\n var SlottedInfo = function(slot, feature) {\n this.slot = slot;\n this.feature = feature;\n };\n\n /**\n * FeatureSlotter determines slots in which to draw features for vertical\n * packing.\n *\n * This implementation is incremental, any feature assigned a slot will be\n * retained for slotting future features.\n */\n var FeatureSlotter = function(w_scale, mode, max_rows, measureText) {\n this.slots = {};\n this.start_end_dct = {};\n this.w_scale = w_scale;\n this.mode = mode;\n this.include_label = mode === \"Pack\";\n this.max_rows = max_rows;\n this.measureText = measureText;\n };\n\n /**\n * Slot a set of features, `this.slots` will be updated with slots by id, and\n * the largest slot required for the passed set of features is returned\n */\n extend(FeatureSlotter.prototype, {\n /**\n * Get drawing coordinate for a feature.\n */\n _get_draw_coords: function(feature) {\n // Get initial draw coordinates using w_scale.\n var draw_start = Math.floor(feature[1] * this.w_scale),\n draw_end = Math.ceil(feature[2] * this.w_scale),\n f_name = feature[3],\n text_align;\n\n // Update start, end drawing locations to include feature name.\n // Try to put the name on the left, if not, put on right.\n if (f_name !== undefined && this.include_label) {\n // Add gap for label spacing and extra pack space padding\n // TODO: Fix constants\n var text_len =\n this.measureText(f_name).width +\n (LABEL_SPACING + PACK_SPACING);\n if (draw_start - text_len >= 0) {\n draw_start -= text_len;\n text_align = \"left\";\n } else {\n draw_end += text_len;\n text_align = \"right\";\n }\n }\n\n /*\n if (slot_num < 0) {\n \n TODO: this is not yet working --\n console.log(feature_uid, \"looking for slot with text on the right\");\n // Slot not found. If text was on left, try on right and see\n // if slot can be found.\n // TODO: are there any checks we need to do to ensure that text\n // will fit on tile?\n if (text_align === \"left\") {\n draw_start -= text_len;\n draw_end -= text_len;\n text_align = \"right\";\n slot_num = find_slot(draw_start, draw_end);\n }\n if (slot_num >= 0) {\n console.log(feature_uid, \"found slot with text on the right\");\n }\n\n }\n */\n\n return [draw_start, draw_end];\n },\n\n /**\n * Find the first slot such that current feature doesn't overlap any other features in that slot.\n * Returns -1 if no slot was found.\n */\n _find_slot: function(draw_coords) {\n // TODO: Use a data structure for faster searching of available slots.\n var draw_start = draw_coords[0],\n draw_end = draw_coords[1];\n for (var slot_num = 0; slot_num <= this.max_rows; slot_num++) {\n var has_overlap = false,\n slot = this.start_end_dct[slot_num];\n if (slot !== undefined) {\n // Iterate through features already in slot to see if current feature will fit.\n for (var k = 0, k_len = slot.length; k < k_len; k++) {\n var s_e = slot[k];\n if (draw_end > s_e[0] && draw_start < s_e[1]) {\n // There is overlap\n has_overlap = true;\n break;\n }\n }\n }\n if (!has_overlap) {\n return slot_num;\n }\n }\n return -1;\n },\n\n /**\n * Slot features.\n */\n slot_features: function(features) {\n var start_end_dct = this.start_end_dct,\n undone = [],\n highest_slot = 0,\n feature,\n feature_uid;\n\n // Loop through features to (a) find those that are not yet slotted and (b) update\n // those that are slotted if new information is availabe. 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function(_) {\n var extend = _.extend;\n\n // HACK: LABEL_SPACING is currently duplicated between here and painters\n var LABEL_SPACING = 2,\n PACK_SPACING = 5;\n\n /**\n * Hold slotting information for a feature.\n */\n var SlottedInfo = function(slot, feature) {\n this.slot = slot;\n this.feature = feature;\n };\n\n /**\n * FeatureSlotter determines slots in which to draw features for vertical\n * packing.\n *\n * This implementation is incremental, any feature assigned a slot will be\n * retained for slotting future features.\n */\n var FeatureSlotter = function(w_scale, mode, max_rows, measureText) {\n this.slots = {};\n this.start_end_dct = {};\n this.w_scale = w_scale;\n this.mode = mode;\n this.include_label = mode === \"Pack\";\n this.max_rows = max_rows;\n this.measureText = measureText;\n };\n\n /**\n * Slot a set of features, `this.slots` will be updated with slots by id, and\n * the largest slot required for the passed set of features is returned\n */\n extend(FeatureSlotter.prototype, {\n /**\n * Get drawing coordinate for a feature.\n */\n _get_draw_coords: function(feature) {\n // Get initial draw coordinates using w_scale.\n var draw_start = Math.floor(feature[1] * this.w_scale),\n draw_end = Math.ceil(feature[2] * this.w_scale),\n f_name = feature[3],\n text_align;\n\n // Update start, end drawing locations to include feature name.\n // Try to put the name on the left, if not, put on right.\n if (f_name !== undefined && this.include_label) {\n // Add gap for label spacing and extra pack space padding\n // TODO: Fix constants\n var text_len =\n this.measureText(f_name).width +\n (LABEL_SPACING + PACK_SPACING);\n if (draw_start - text_len >= 0) {\n draw_start -= text_len;\n text_align = \"left\";\n } else {\n draw_end += text_len;\n text_align = \"right\";\n }\n }\n\n /*\n if (slot_num < 0) {\n \n TODO: this is not yet working --\n console.log(feature_uid, \"looking for slot with text on the right\");\n // Slot not found. If text was on left, try on right and see\n // if slot can be found.\n // TODO: are there any checks we need to do to ensure that text\n // will fit on tile?\n if (text_align === \"left\") {\n draw_start -= text_len;\n draw_end -= text_len;\n text_align = \"right\";\n slot_num = find_slot(draw_start, draw_end);\n }\n if (slot_num >= 0) {\n console.log(feature_uid, \"found slot with text on the right\");\n }\n\n }\n */\n\n return [draw_start, draw_end];\n },\n\n /**\n * Find the first slot such that current feature doesn't overlap any other features in that slot.\n * Returns -1 if no slot was found.\n */\n _find_slot: function(draw_coords) {\n // TODO: Use a data structure for faster searching of available slots.\n var draw_start = draw_coords[0],\n draw_end = draw_coords[1];\n for (var slot_num = 0; slot_num <= this.max_rows; slot_num++) {\n var has_overlap = false,\n slot = this.start_end_dct[slot_num];\n if (slot !== undefined) {\n // Iterate through features already in slot to see if current feature will fit.\n for (var k = 0, k_len = slot.length; k < k_len; k++) {\n var s_e = slot[k];\n if (draw_end > s_e[0] && draw_start < s_e[1]) {\n // There is overlap\n has_overlap = true;\n break;\n }\n }\n }\n if (!has_overlap) {\n return slot_num;\n }\n }\n return -1;\n },\n\n /**\n * Slot features.\n */\n slot_features: function(features) {\n var start_end_dct = this.start_end_dct,\n undone = [],\n highest_slot = 0,\n feature,\n feature_uid;\n\n // Loop through features to (a) find those that are not yet slotted and (b) update\n // those that are slotted if new information is availabe. For (a), features already\n // slotted (based on slotting from other tiles) will retain their current slot.\n for (var i = 0, len = features.length; i < len; i++) {\n feature = features[i];\n feature_uid = feature[0];\n var slotted_info = this.slots[feature_uid];\n\n // Separate and handle slotted vs. unslotted features.\n if (slotted_info) {\n // Feature is slotted; if feature now has larger start/end coordinates,\n // update drawing coordinates.\n if (\n feature[1] < slotted_info.feature[1] ||\n slotted_info.feature[2] < feature[2]\n ) {\n // Feature has changed (e.g. a single read now has its pair), so recalculate its\n // drawing coordinates.\n var old_draw_coords = this._get_draw_coords(\n slotted_info.feature\n ),\n new_draw_coords = this._get_draw_coords(feature),\n slotted_coords = this.start_end_dct[\n slotted_info.slot\n ];\n for (var k = 0; k < slotted_coords.length; k++) {\n var dc = slotted_coords[k];\n if (\n dc[0] === old_draw_coords[0] &&\n dc[1] === old_draw_coords[1]\n ) {\n // Replace old drawing coordinates with new ones.\n slotted_coords[k] = new_draw_coords;\n }\n }\n }\n highest_slot = Math.max(\n highest_slot,\n this.slots[feature_uid].slot\n );\n } else {\n undone.push(i);\n }\n }\n\n // Slot unslotted features.\n\n // Do slotting.\n for (var i = 0, len = undone.length; i < len; i++) {\n feature = features[undone[i]];\n feature_uid = feature[0];\n var draw_coords = this._get_draw_coords(feature);\n\n // Find slot.\n var slot_num = this._find_slot(draw_coords);\n\n // Do slotting.\n if (slot_num >= 0) {\n // Add current feature to slot.\n if (start_end_dct[slot_num] === undefined) {\n start_end_dct[slot_num] = [];\n }\n start_end_dct[slot_num].push(draw_coords);\n this.slots[feature_uid] = new SlottedInfo(\n slot_num,\n feature\n );\n highest_slot = Math.max(highest_slot, slot_num);\n }\n }\n\n // Debugging: view slots data.\n /*\n for (var i = 0; i < MAX_FEATURE_DEPTH; i++) {\n var slot = start_end_dct[i];\n if (slot !== 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[\n \"libs/underscore\",\n \"viz/visualization\",\n \"viz/viz_views\",\n \"viz/trackster/util\",\n \"viz/trackster/slotting\",\n \"viz/trackster/painters\",\n \"viz/trackster/filters\",\n \"mvc/dataset/data\",\n \"mvc/tool/tools\",\n \"utils/config\",\n \"viz/bbi-data-manager\",\n \"ui/editable-text\"\n ],\n function(\n _,\n visualization,\n viz_views,\n util,\n slotting,\n painters,\n filters_mod,\n data,\n tools_mod,\n config_mod,\n bbi\n ) {\n var extend = _.extend;\n\n // ---- Web UI specific utilities ----\n\n /**\n * Dictionary of HTML element-JavaScript object relationships.\n */\n // TODO: probably should separate moveable objects from containers.\n var html_elt_js_obj_dict = {};\n\n /**\n * Designates an HTML as a container.\n */\n var is_container = function(element, obj) {\n html_elt_js_obj_dict[element.attr(\"id\")] = obj;\n };\n\n /**\n * Make `element` moveable within parent and sibling elements by dragging `handle` (a selector).\n * Function manages JS objects, containers as well.\n *\n * @param element HTML element to make moveable\n * @param handle_class classname that denotes HTML element to be used as handle\n * @param container_selector selector used to identify possible containers for this element\n * @param element_js_obj JavaScript object associated with element; used\n */\n var moveable = function(\n element,\n handle_class,\n container_selector,\n element_js_obj\n ) {\n // HACK: set default value for container selector.\n container_selector = \".group\";\n\n // Register element with its object.\n html_elt_js_obj_dict[element.attr(\"id\")] = element_js_obj;\n\n // Need to provide selector for handle, not class.\n element\n .bind(\n \"drag\",\n { handle: \".\" + handle_class, relative: true },\n function(e, d) {\n var element = $(this),\n parent = $(this).parent(),\n // Only sorting amongst tracks and groups.\n children = parent.children(\".track,.group\"),\n this_obj = html_elt_js_obj_dict[$(this).attr(\"id\")],\n child,\n container,\n top,\n bottom,\n i;\n\n //\n // Enable three types of dragging: (a) out of container; (b) into container;\n // (c) sibling movement, aka sorting. Handle in this order for simplicity.\n //\n\n // Handle dragging out of container.\n container = $(this).parents(container_selector);\n if (container.length !== 0) {\n top = container.position().top;\n bottom = top + container.outerHeight();\n var cur_container =\n html_elt_js_obj_dict[container.attr(\"id\")];\n if (d.offsetY < top) {\n // Moving above container.\n $(this).insertBefore(container);\n cur_container.remove_drawable(this_obj);\n cur_container.container.add_drawable_before(\n this_obj,\n cur_container\n );\n return;\n } else if (d.offsetY > bottom) {\n // Moving below container.\n $(this).insertAfter(container);\n cur_container.remove_drawable(this_obj);\n cur_container.container.add_drawable(this_obj);\n return;\n }\n }\n\n // Handle dragging into container. Child is appended to container's content_div.\n container = null;\n for (i = 0; i < children.length; i++) {\n child = $(children.get(i));\n top = child.position().top;\n bottom = top + child.outerHeight();\n // Dragging into container if child is a container and offset is inside container.\n if (\n child.is(container_selector) &&\n this !== child.get(0) &&\n d.offsetY >= top &&\n d.offsetY <= bottom\n ) {\n // Append/prepend based on where offsetY is closest to and return.\n if (d.offsetY - top < bottom - d.offsetY) {\n child.find(\".content-div\").prepend(this);\n } else {\n child.find(\".content-div\").append(this);\n }\n // Update containers. Object may not have container if it is being moved quickly.\n if (this_obj.container) {\n this_obj.container.remove_drawable(\n this_obj\n );\n }\n html_elt_js_obj_dict[\n child.attr(\"id\")\n ].add_drawable(this_obj);\n return;\n }\n }\n\n // Handle sibling movement, aka sorting.\n\n // Determine new position\n for (i = 0; i < children.length; i++) {\n child = $(children.get(i));\n if (\n d.offsetY < child.position().top &&\n // Cannot move tracks above reference track or intro div.\n !(\n child.hasClass(\"reference-track\") ||\n child.hasClass(\"intro\")\n )\n ) {\n break;\n }\n }\n\n // If not already in the right place, move. Need\n // to handle the end specially since we don't have\n // insert at index\n if (i === children.length) {\n if (this !== children.get(i - 1)) {\n parent.append(this);\n html_elt_js_obj_dict[\n parent.attr(\"id\")\n ].move_drawable(this_obj, i);\n }\n } else if (this !== children.get(i)) {\n $(this).insertBefore(children.get(i));\n // Need to adjust insert position if moving down because move is changing\n // indices of all list items.\n html_elt_js_obj_dict[\n parent.attr(\"id\")\n ].move_drawable(this_obj, d.deltaY > 0 ? i - 1 : i);\n }\n }\n )\n .bind(\"dragstart\", function() {\n $(this).addClass(\"dragging\");\n })\n .bind(\"dragend\", function() {\n $(this).removeClass(\"dragging\");\n });\n };\n\n /**\n * Init constants & functions used throughout trackster.\n */\n var // Padding at the top of tracks for error messages\n ERROR_PADDING = 20,\n // Maximum number of rows un a slotted track\n MAX_FEATURE_DEPTH = 100,\n // Minimum width for window for squish to be used.\n MIN_SQUISH_VIEW_WIDTH = 12000,\n // Number of pixels per tile, not including left offset.\n TILE_SIZE = 400,\n DEFAULT_DATA_QUERY_WAIT = 5000,\n // Maximum number of chromosomes that are selectable at any one time.\n MAX_CHROMS_SELECTABLE = 100,\n DATA_ERROR = \"Cannot display dataset due to an error. \",\n DATA_NOCONVERTER =\n \"A converter for this dataset is not installed. Please check your datatypes_conf.xml file.\",\n DATA_NONE = \"No data for this chrom/contig.\",\n DATA_PENDING =\n \"Preparing data. This can take a while for a large dataset. \" +\n \"If the visualization is saved and closed, preparation will continue in the background.\",\n DATA_CANNOT_RUN_TOOL = \"Tool cannot be rerun: \",\n DATA_LOADING = \"Loading data...\",\n DATA_OK = \"Ready for display\",\n TILE_CACHE_SIZE = 10,\n DATA_CACHE_SIZE = 20,\n // Numerical/continuous data display modes.\n CONTINUOUS_DATA_MODES = [\n \"Histogram\",\n \"Line\",\n \"Filled\",\n \"Intensity\"\n ];\n\n /**\n * Round a number to a given number of decimal places.\n */\n function round(num, places) {\n // Default rounding is to integer.\n if (!places) {\n places = 0;\n }\n\n var val = Math.pow(10, places);\n return Math.round(num * val) / val;\n }\n\n /**\n * Check if a server can do byte range requests.\n */\n function supportsByteRanges(url) {\n var promise = $.Deferred();\n $.ajax({\n type: \"HEAD\",\n url: url,\n beforeSend: function(xhr) {\n xhr.setRequestHeader(\"Range\", \"bytes=0-10\");\n },\n success: function(result, status, xhr) {\n promise.resolve(xhr.status === 206);\n }\n });\n\n return promise;\n }\n\n /**\n * Drawables hierarchy:\n *\n * Drawable\n * --> DrawableCollection\n * --> DrawableGroup\n * --> View\n * --> Track\n */\n\n /**\n * Base class for all drawable objects. Drawable objects are associated with a view and live in a\n * container. They have the following HTML elements and structure:\n * \n * \n * \n *\n * They optionally have a drag handle class.\n */\n var Drawable = function(view, container, obj_dict) {\n if (!Drawable.id_counter) {\n Drawable.id_counter = 0;\n }\n this.id = Drawable.id_counter++;\n this.view = view;\n this.container = container;\n this.drag_handle_class = obj_dict.drag_handle_class;\n this.is_overview = false;\n this.action_icons = {};\n\n // -- Set up drawable configuration. --\n this.config = config_mod.ConfigSettingCollection.from_models_and_saved_values(\n this.config_params,\n obj_dict.prefs\n );\n\n // If there's no saved name, use object name.\n if (!this.config.get_value(\"name\")) {\n this.config.set_value(\"name\", obj_dict.name);\n }\n if (this.config_onchange) {\n this.config.on(\"change\", this.config_onchange, this);\n }\n\n // Build Drawable HTML and behaviors.\n this.container_div = this.build_container_div();\n this.header_div = null;\n\n // Use opt-out policy on header creation because this is the more frequent approach:\n // unless flag set, create header.\n if (obj_dict.header !== false) {\n var header_view = new viz_views.TrackHeaderView({\n model: this,\n id: this.id\n });\n\n this.header_div = header_view.$el;\n this.container_div.append(this.header_div);\n\n // Show icons when users is hovering over track.\n var icons_div = header_view.icons_div;\n this.action_icons = header_view.action_icons;\n this.container_div.hover(\n function() {\n icons_div.show();\n },\n function() {\n icons_div.hide();\n }\n );\n }\n };\n\n Drawable.prototype.action_icons_def = [\n // Hide/show drawable content.\n // FIXME: make this an odict for easier lookup.\n {\n name: \"toggle_icon\",\n title: \"Hide/show content\",\n css_class: \"toggle\",\n on_click_fn: function(drawable) {\n if (drawable.config.get_value(\"content_visible\")) {\n drawable.action_icons.toggle_icon\n .addClass(\"toggle-expand\")\n .removeClass(\"toggle\");\n drawable.hide_contents();\n drawable.config.set_value(\"content_visible\", false);\n } else {\n drawable.action_icons.toggle_icon\n .addClass(\"toggle\")\n .removeClass(\"toggle-expand\");\n drawable.config.set_value(\"content_visible\", true);\n drawable.show_contents();\n }\n }\n },\n // Edit settings.\n {\n name: \"settings_icon\",\n title: \"Edit settings\",\n css_class: \"gear\",\n on_click_fn: function(drawable) {\n var view = new config_mod.ConfigSettingCollectionView({\n collection: drawable.config\n });\n view.render_in_modal(\"Configure Track\");\n }\n },\n // Remove.\n {\n name: \"remove_icon\",\n title: \"Remove\",\n css_class: \"remove-icon\",\n on_click_fn: function(drawable) {\n // Tooltip for remove icon must be deleted when drawable is deleted.\n $(\".tooltip\").remove();\n drawable.remove();\n }\n }\n ];\n\n extend(Drawable.prototype, {\n config_params: [\n { key: \"name\", label: \"Name\", type: \"text\", default_value: \"\" },\n {\n key: \"content_visible\",\n type: \"bool\",\n default_value: true,\n hidden: true\n }\n ],\n\n config_onchange: function() {},\n\n init: function() {},\n\n changed: function() {\n this.view.changed();\n },\n\n can_draw: function() {\n if (this.enabled && this.config.get_value(\"content_visible\")) {\n return true;\n }\n\n return false;\n },\n\n request_draw: function() {},\n\n _draw: function(options) {},\n\n /**\n * Returns representation of object in a dictionary for easy saving.\n * Use from_dict to recreate object.\n */\n to_dict: function() {},\n\n /**\n * Set drawable name.\n */\n set_name: function(new_name) {\n this.old_name = this.config.get_value(\"name\");\n this.config.set_value(\"name\", new_name);\n },\n\n /**\n * Revert track name; currently name can be reverted only once.\n */\n revert_name: function() {\n if (this.old_name) {\n this.config.set_value(\"name\", this.old_name);\n }\n },\n\n /**\n * Remove drawable (a) from its container and (b) from the HTML.\n */\n remove: function() {\n this.changed();\n\n this.container.remove_drawable(this);\n var view = this.view;\n this.container_div.hide(0, function() {\n $(this).remove();\n // HACK: is there a better way to update the view?\n view.update_intro_div();\n });\n },\n\n /**\n * Build drawable's container div; this is the parent div for all drawable's elements.\n */\n build_container_div: function() {},\n\n /**\n * Update icons.\n */\n update_icons: function() {},\n\n /**\n * Hide drawable's contents.\n */\n hide_contents: function() {},\n\n /**\n * Show drawable's contents.\n */\n show_contents: function() {},\n\n /**\n * Returns a shallow copy of all drawables in this drawable.\n */\n get_drawables: function() {}\n });\n\n /**\n * A collection of drawable objects.\n */\n var DrawableCollection = function(view, container, obj_dict) {\n Drawable.call(this, view, container, obj_dict);\n\n // Attribute init.\n this.obj_type = obj_dict.obj_type;\n this.drawables = [];\n };\n\n extend(DrawableCollection.prototype, Drawable.prototype, {\n /**\n * Unpack and add drawables to the collection.\n */\n unpack_drawables: function(drawables_array) {\n // Add drawables to collection.\n this.drawables = [];\n var drawable;\n for (var i = 0; i < drawables_array.length; i++) {\n drawable = object_from_template(\n drawables_array[i],\n this.view,\n this\n );\n this.add_drawable(drawable);\n }\n },\n\n /**\n * Init each drawable in the collection.\n */\n init: function() {\n for (var i = 0; i < this.drawables.length; i++) {\n this.drawables[i].init();\n }\n },\n\n /**\n * Draw each drawable in the collection.\n */\n _draw: function(options) {\n for (var i = 0; i < this.drawables.length; i++) {\n this.drawables[i]._draw(options);\n }\n },\n\n /**\n * Returns representation of object in a dictionary for easy saving.\n * Use from_dict to recreate object.\n */\n to_dict: function() {\n var dictified_drawables = [];\n for (var i = 0; i < this.drawables.length; i++) {\n dictified_drawables.push(this.drawables[i].to_dict());\n }\n return {\n prefs: this.config.to_key_value_dict(),\n obj_type: this.obj_type,\n drawables: dictified_drawables\n };\n },\n\n /**\n * Add a drawable to the end of the collection.\n */\n add_drawable: function(drawable) {\n this.drawables.push(drawable);\n drawable.container = this;\n this.changed();\n },\n\n /**\n * Add a drawable before another drawable.\n */\n add_drawable_before: function(drawable, other) {\n this.changed();\n var index = this.drawables.indexOf(other);\n if (index !== -1) {\n this.drawables.splice(index, 0, drawable);\n return true;\n }\n return false;\n },\n\n /**\n * Replace one drawable with another.\n */\n replace_drawable: function(\n old_drawable,\n new_drawable,\n update_html\n ) {\n var index = this.drawables.indexOf(old_drawable);\n if (index !== -1) {\n this.drawables[index] = new_drawable;\n if (update_html) {\n old_drawable.container_div.replaceWith(\n new_drawable.container_div\n );\n }\n this.changed();\n }\n return index;\n },\n\n /**\n * Remove drawable from this collection.\n */\n remove_drawable: function(drawable) {\n var index = this.drawables.indexOf(drawable);\n if (index !== -1) {\n // Found drawable to remove.\n this.drawables.splice(index, 1);\n drawable.container = null;\n this.changed();\n return true;\n }\n return false;\n },\n\n /**\n * Move drawable to another location in collection.\n */\n move_drawable: function(drawable, new_position) {\n var index = this.drawables.indexOf(drawable);\n if (index !== -1) {\n // Remove from current position:\n this.drawables.splice(index, 1);\n // insert into new position:\n this.drawables.splice(new_position, 0, drawable);\n this.changed();\n return true;\n }\n return false;\n },\n\n /**\n * Returns all drawables in this drawable.\n */\n get_drawables: function() {\n return this.drawables;\n },\n\n /**\n * Returns all tracks in collection.\n */\n get_tracks: function(track_type) {\n // Initialize queue with copy of drawables array.\n var queue = this.drawables.slice(0),\n tracks = [],\n drawable;\n while (queue.length !== 0) {\n drawable = queue.shift();\n if (drawable instanceof track_type) {\n tracks.push(drawable);\n } else if (drawable.drawables) {\n queue = queue.concat(drawable.drawables);\n }\n }\n return tracks;\n }\n });\n\n /**\n * A group of drawables that are moveable, visible.\n */\n var DrawableGroup = function(view, container, obj_dict) {\n extend(obj_dict, {\n obj_type: \"DrawableGroup\",\n drag_handle_class: \"group-handle\"\n });\n DrawableCollection.call(this, view, container, obj_dict);\n\n // Set up containers/moving for group: register both container_div and content div as container\n // because both are used as containers (container div to recognize container, content_div to\n // store elements). Group can be moved.\n this.content_div = $(\"\")\n .addClass(\"content-div\")\n .attr(\"id\", \"group_\" + this.id + \"_content_div\")\n .appendTo(this.container_div);\n is_container(this.container_div, this);\n is_container(this.content_div, this);\n moveable(\n this.container_div,\n this.drag_handle_class,\n \".group\",\n this\n );\n\n // Set up filters.\n this.filters_manager = new filters_mod.FiltersManager(this);\n this.header_div.after(this.filters_manager.parent_div);\n\n // HACK: add div to clear floating elements.\n this.filters_manager.parent_div.after(\n $(\"\")\n );\n\n // For saving drawables' filter managers when group-level filtering is done:\n this.saved_filters_managers = [];\n\n // Add drawables.\n if (\"drawables\" in obj_dict) {\n this.unpack_drawables(obj_dict.drawables);\n }\n\n // Restore filters.\n if (\"filters\" in obj_dict) {\n // FIXME: Pass collection_dict to DrawableCollection/Drawable will make this easier.\n var old_manager = this.filters_manager;\n this.filters_manager = new filters_mod.FiltersManager(\n this,\n obj_dict.filters\n );\n old_manager.parent_div.replaceWith(\n this.filters_manager.parent_div\n );\n\n if (obj_dict.filters.visible) {\n this.setup_multitrack_filtering();\n }\n }\n };\n\n extend(\n DrawableGroup.prototype,\n Drawable.prototype,\n DrawableCollection.prototype,\n {\n action_icons_def: [\n Drawable.prototype.action_icons_def[0],\n Drawable.prototype.action_icons_def[1],\n // Replace group with composite track.\n {\n name: \"composite_icon\",\n title: \"Show composite track\",\n css_class: \"layers-stack\",\n on_click_fn: function(group) {\n $(\".tooltip\").remove();\n group.show_composite_track();\n }\n },\n // Toggle track filters.\n {\n name: \"filters_icon\",\n title: \"Filters\",\n css_class: \"ui-slider-050\",\n on_click_fn: function(group) {\n // TODO: update Tooltip text.\n if (group.filters_manager.visible()) {\n // Hiding filters.\n group.filters_manager.clear_filters();\n group._restore_filter_managers();\n // TODO: maintain current filter by restoring and setting saved manager's\n // settings to current/shared manager's settings.\n // TODO: need to restore filter managers when moving drawable outside group.\n } else {\n // Showing filters.\n group.setup_multitrack_filtering();\n group.request_draw({ clear_tile_cache: true });\n }\n group.filters_manager.toggle();\n }\n },\n Drawable.prototype.action_icons_def[2]\n ],\n\n build_container_div: function() {\n var container_div = $(\"\")\n .addClass(\"group\")\n .attr(\"id\", \"group_\" + this.id);\n if (this.container) {\n this.container.content_div.append(container_div);\n }\n return container_div;\n },\n\n hide_contents: function() {\n this.tiles_div.hide();\n },\n\n show_contents: function() {\n // Show the contents div and labels (if present)\n this.tiles_div.show();\n // Request a redraw of the content\n this.request_draw();\n },\n\n update_icons: function() {\n //\n // Handle update when there are no tracks.\n //\n var num_drawables = this.drawables.length;\n if (num_drawables === 0) {\n this.action_icons.composite_icon.hide();\n this.action_icons.filters_icon.hide();\n } else if (num_drawables === 1) {\n this.action_icons.composite_icon.toggle(\n this.drawables[0] instanceof CompositeTrack\n );\n this.action_icons.filters_icon.hide();\n } else {\n // There are 2 or more tracks.\n\n //\n // Determine if a composite track can be created. Current criteria:\n // (a) all tracks are line tracks;\n // OR\n // FIXME: this is not enabled right now because it has not been well tested:\n // (b) there is a single FeatureTrack.\n //\n\n // All tracks the same?\n var i,\n j,\n drawable,\n same_type = true,\n a_type = this.drawables[0].get_type(),\n num_feature_tracks = 0;\n for (i = 0; i < num_drawables; i++) {\n drawable = this.drawables[i];\n if (drawable.get_type() !== a_type) {\n can_composite = false;\n break;\n }\n if (drawable instanceof FeatureTrack) {\n num_feature_tracks++;\n }\n }\n\n if (\n same_type &&\n this.drawables[0] instanceof LineTrack\n ) {\n this.action_icons.composite_icon.show();\n } else {\n this.action_icons.composite_icon.hide();\n $(\".tooltip\").remove();\n }\n\n //\n // Set up group-level filtering and update filter icon.\n //\n if (\n num_feature_tracks > 1 &&\n num_feature_tracks === this.drawables.length\n ) {\n //\n // Find shared filters.\n //\n var shared_filters = {},\n filter;\n\n // Init shared filters with filters from first drawable.\n drawable = this.drawables[0];\n for (\n j = 0;\n j < drawable.filters_manager.filters.length;\n j++\n ) {\n filter = drawable.filters_manager.filters[j];\n shared_filters[filter.name] = [filter];\n }\n\n // Create lists of shared filters.\n for (i = 1; i < this.drawables.length; i++) {\n drawable = this.drawables[i];\n for (\n j = 0;\n j < drawable.filters_manager.filters.length;\n j++\n ) {\n filter =\n drawable.filters_manager.filters[j];\n if (filter.name in shared_filters) {\n shared_filters[filter.name].push(\n filter\n );\n }\n }\n }\n\n //\n // Create filters for shared filters manager. Shared filters manager is group's\n // manager.\n //\n this.filters_manager.remove_all();\n var filters, new_filter, min, max;\n for (var filter_name in shared_filters) {\n filters = shared_filters[filter_name];\n if (filters.length === num_feature_tracks) {\n // Add new filter.\n // FIXME: can filter.copy() be used?\n new_filter = new filters_mod.NumberFilter({\n name: filters[0].name,\n index: filters[0].index\n });\n this.filters_manager.add_filter(new_filter);\n }\n }\n\n // Show/hide icon based on filter availability.\n this.action_icons.filters_icon.toggle(\n this.filters_manager.filters.length > 0\n );\n } else {\n this.action_icons.filters_icon.hide();\n }\n }\n },\n\n /**\n * Restore individual track filter managers.\n */\n _restore_filter_managers: function() {\n for (var i = 0; i < this.drawables.length; i++) {\n this.drawables[\n i\n ].filters_manager = this.saved_filters_managers[i];\n }\n this.saved_filters_managers = [];\n },\n\n /**\n *\n */\n setup_multitrack_filtering: function() {\n // Save tracks' managers and set up shared manager.\n if (this.filters_manager.filters.length > 0) {\n // For all tracks, save current filter manager and set manager to shared (this object's) manager.\n this.saved_filters_managers = [];\n for (var i = 0; i < this.drawables.length; i++) {\n var drawable = this.drawables[i];\n this.saved_filters_managers.push(\n drawable.filters_manager\n );\n drawable.filters_manager = this.filters_manager;\n }\n\n //TODO: hide filters icons for each drawable?\n }\n this.filters_manager.init_filters();\n },\n\n /**\n * Replace group with a single composite track that includes all group's tracks.\n */\n show_composite_track: function() {\n var composite_track = new CompositeTrack(\n this.view,\n this.view,\n {\n name: this.config.get_value(\"name\"),\n drawables: this.drawables\n }\n );\n var index = this.container.replace_drawable(\n this,\n composite_track,\n true\n );\n composite_track.request_draw();\n },\n\n add_drawable: function(drawable) {\n DrawableCollection.prototype.add_drawable.call(\n this,\n drawable\n );\n this.update_icons();\n },\n\n remove_drawable: function(drawable) {\n DrawableCollection.prototype.remove_drawable.call(\n this,\n drawable\n );\n this.update_icons();\n },\n\n to_dict: function() {\n // If filters are visible, need to restore original filter managers before converting to dict.\n if (this.filters_manager.visible()) {\n this._restore_filter_managers();\n }\n\n var obj_dict = extend(\n DrawableCollection.prototype.to_dict.call(this),\n { filters: this.filters_manager.to_dict() }\n );\n\n // Setup multi-track filtering again.\n if (this.filters_manager.visible()) {\n this.setup_multitrack_filtering();\n }\n\n return obj_dict;\n },\n\n request_draw: function(options) {\n _.each(this.drawables, function(d) {\n d.request_draw(options);\n });\n }\n }\n );\n\n /**\n * View object manages a trackster visualization, including tracks and user interactions.\n * Events triggered:\n * navigate: when browser view changes to a new locations\n */\n var TracksterView = Backbone.View.extend({\n initialize: function(obj_dict) {\n extend(obj_dict, {\n obj_type: \"View\"\n });\n DrawableCollection.call(\n this,\n \"View\",\n obj_dict.container,\n obj_dict\n );\n this.chrom = null;\n this.vis_id = obj_dict.vis_id;\n this.dbkey = obj_dict.dbkey;\n this.stand_alone =\n obj_dict.stand_alone !== undefined\n ? obj_dict.stand_alone\n : true;\n this.label_tracks = [];\n this.tracks_to_be_redrawn = [];\n this.max_low = 0;\n this.max_high = 0;\n this.zoom_factor = 3;\n this.min_separation = 30;\n this.has_changes = false;\n // Deferred object that indicates when view's chrom data has been loaded.\n this.load_chroms_deferred = null;\n this.render();\n this.canvas_manager = new visualization.CanvasManager(\n this.container.get(0).ownerDocument\n );\n this.reset();\n\n // Define track configuration\n this.config = config_mod.ConfigSettingCollection.from_models_and_saved_values(\n [\n {\n key: \"name\",\n label: \"Name\",\n type: \"text\",\n default_value: \"\"\n },\n {\n key: \"a_color\",\n label: \"A Color\",\n type: \"color\",\n default_value: \"#FF0000\"\n },\n {\n key: \"c_color\",\n label: \"C Color\",\n type: \"color\",\n default_value: \"#00FF00\"\n },\n {\n key: \"g_color\",\n label: \"G Color\",\n type: \"color\",\n default_value: \"#0000FF\"\n },\n {\n key: \"t_color\",\n label: \"T Color\",\n type: \"color\",\n default_value: \"#FF00FF\"\n },\n {\n key: \"n_color\",\n label: \"N Color\",\n type: \"color\",\n default_value: \"#AAAAAA\"\n }\n ],\n { name: obj_dict.name }\n );\n },\n\n render: function() {\n // Attribute init.\n this.requested_redraw = false;\n\n // Create DOM elements\n var parent_element = this.container,\n view = this;\n // Top container for things that are fixed at the top\n this.top_container = $(\"\")\n .addClass(\"top-container\")\n .appendTo(parent_element);\n // Browser content, primary tracks are contained in here\n this.browser_content_div = $(\"\")\n .addClass(\"content\")\n .appendTo(parent_element);\n // Bottom container for things that are fixed at the bottom\n this.bottom_container = $(\"\")\n .addClass(\"bottom-container\")\n .appendTo(parent_element);\n // Label track fixed at top\n this.top_labeltrack = $(\"\")\n .addClass(\"top-labeltrack\")\n .appendTo(this.top_container);\n // Viewport for dragging tracks in center\n this.viewport_container = $(\"\")\n .addClass(\"viewport-container\")\n .attr(\"id\", \"viewport-container\")\n .appendTo(this.browser_content_div);\n // Alias viewport_container as content_div so that it matches function of DrawableCollection/Group content_div.\n this.content_div = this.viewport_container;\n is_container(this.viewport_container, view);\n // Introduction div shown when there are no tracks.\n this.intro_div = $(\"\")\n .addClass(\"intro\")\n .appendTo(this.viewport_container);\n var add_tracks_button = $(\"\")\n .text(\"Add Datasets to Visualization\")\n .addClass(\"action-button\")\n .appendTo(this.intro_div)\n .click(function() {\n visualization.select_datasets(\n { dbkey: view.dbkey },\n function(tracks) {\n _.each(tracks, function(track) {\n view.add_drawable(\n object_from_template(track, view, view)\n );\n });\n }\n );\n });\n\n // Navigation at top\n this.nav_container = $(\"\")\n .addClass(\"trackster-nav-container\")\n .prependTo(this.top_container);\n this.nav = $(\"\")\n .addClass(\"trackster-nav\")\n .appendTo(this.nav_container);\n\n if (this.stand_alone) {\n this.nav_container.addClass(\"stand-alone\");\n this.nav.addClass(\"stand-alone\");\n }\n\n // Overview (scrollbar and overview plot) at bottom\n this.overview = $(\"\")\n .addClass(\"overview\")\n .appendTo(this.bottom_container);\n this.overview_viewport = $(\"\")\n .addClass(\"overview-viewport\")\n .appendTo(this.overview);\n this.overview_close = $(\"\")\n .attr(\"title\", \"Close overview\")\n .addClass(\"icon-button overview-close tooltip\")\n .hide()\n .appendTo(this.overview_viewport);\n this.overview_highlight = $(\"\")\n .addClass(\"overview-highlight\")\n .hide()\n .appendTo(this.overview_viewport);\n this.overview_box_background = $(\"\")\n .addClass(\"overview-boxback\")\n .appendTo(this.overview_viewport);\n this.overview_box = $(\"\")\n .addClass(\"overview-box\")\n .appendTo(this.overview_viewport);\n this.default_overview_height = this.overview_box.height();\n\n this.nav_controls = $(\"\")\n .addClass(\"nav-controls\")\n .appendTo(this.nav);\n this.chrom_select = $(\"\")\n .attr({ name: \"chrom\" })\n .addClass(\"chrom-nav\")\n .append(\"\")\n .appendTo(this.nav_controls);\n var submit_nav = function(e) {\n if (\n e.type === \"focusout\" ||\n (e.keyCode || e.which) === 13 ||\n (e.keyCode || e.which) === 27\n ) {\n if ((e.keyCode || e.which) !== 27) {\n // Not escape key\n view.go_to($(this).val());\n }\n $(this).hide();\n $(this).val(\"\");\n view.location_span.show();\n view.chrom_select.show();\n }\n\n // Suppress key presses so that they do impact viz.\n e.stopPropagation();\n };\n this.nav_input = $(\"\")\n .addClass(\"nav-input\")\n .hide()\n .bind(\"keyup focusout\", submit_nav)\n .appendTo(this.nav_controls);\n this.location_span = $(\"\")\n .addClass(\"location\")\n .attr(\"title\", \"Click to change location\")\n .tooltip({ placement: \"bottom\" })\n .appendTo(this.nav_controls);\n this.location_span.click(function() {\n view.location_span.hide();\n view.chrom_select.hide();\n view.nav_input.val(\n view.chrom + \":\" + view.low + \"-\" + view.high\n );\n view.nav_input.css(\"display\", \"inline-block\");\n view.nav_input.select();\n view.nav_input.focus();\n // Set up autocomplete for tracks' features.\n view.nav_input.autocomplete({\n source: function(request, response) {\n // Using current text, query each track and create list of all matching features.\n var all_features = [],\n feature_search_deferreds = $.map(\n view.get_tracks(FeatureTrack),\n function(t) {\n return t.data_manager\n .search_features(request.term)\n .success(function(\n dataset_features\n ) {\n all_features = all_features.concat(\n dataset_features\n );\n });\n }\n );\n\n // When all searching is done, fill autocomplete.\n $.when\n .apply($, feature_search_deferreds)\n .done(function() {\n response(\n $.map(all_features, function(feature) {\n return {\n label: feature[0],\n value: feature[1]\n };\n })\n );\n });\n },\n minLength: 2\n });\n });\n if (this.vis_id !== undefined) {\n this.hidden_input = $(\"\")\n .attr(\"type\", \"hidden\")\n .val(this.vis_id)\n .appendTo(this.nav_controls);\n }\n\n this.zo_link = $(\"\")\n .attr(\"id\", \"zoom-out\")\n .attr(\"title\", \"Zoom out\")\n .tooltip({ placement: \"bottom\" })\n .click(function() {\n view.zoom_out();\n })\n .appendTo(this.nav_controls);\n this.zi_link = $(\"\")\n .attr(\"id\", \"zoom-in\")\n .attr(\"title\", \"Zoom in\")\n .tooltip({ placement: \"bottom\" })\n .click(function() {\n view.zoom_in();\n })\n .appendTo(this.nav_controls);\n\n // Get initial set of chroms.\n this.load_chroms_deferred = this.load_chroms({ low: 0 });\n this.chrom_select.bind(\"change\", function() {\n view.change_chrom(view.chrom_select.val());\n });\n\n /*\n this.browser_content_div.bind(\"mousewheel\", function( e, delta ) {\n if (Math.abs(delta) < 0.5) {\n return;\n }\n if (delta > 0) {\n view.zoom_in(e.pageX, this.viewport_container);\n } else {\n view.zoom_out();\n }\n e.preventDefault();\n });\n */\n\n // Blur tool/filter inputs when user clicks on content div.\n this.browser_content_div.click(function(e) {\n $(this)\n .find(\"input\")\n .trigger(\"blur\");\n });\n\n // Double clicking zooms in\n this.browser_content_div.bind(\"dblclick\", function(e) {\n view.zoom_in(e.pageX, this.viewport_container);\n });\n\n // Dragging the overview box (~ horizontal scroll bar)\n this.overview_box\n .bind(\"dragstart\", function(e, d) {\n this.current_x = d.offsetX;\n })\n .bind(\"drag\", function(e, d) {\n var delta = d.offsetX - this.current_x;\n this.current_x = d.offsetX;\n var delta_chrom = Math.round(\n delta /\n view.viewport_container.width() *\n (view.max_high - view.max_low)\n );\n view.move_delta(-delta_chrom);\n });\n\n this.overview_close.click(function() {\n view.reset_overview();\n });\n\n // Dragging in the viewport scrolls\n this.viewport_container\n .bind(\"draginit\", function(e, d) {\n // Disable interaction if started in scrollbar (for webkit)\n if (e.clientX > view.viewport_container.width() - 16) {\n return false;\n }\n })\n .bind(\"dragstart\", function(e, d) {\n d.original_low = view.low;\n d.current_height = e.clientY;\n d.current_x = d.offsetX;\n })\n .bind(\"drag\", function(e, d) {\n var container = $(this);\n var delta = d.offsetX - d.current_x;\n var new_scroll =\n container.scrollTop() -\n (e.clientY - d.current_height);\n container.scrollTop(new_scroll);\n d.current_height = e.clientY;\n d.current_x = d.offsetX;\n var delta_chrom = Math.round(\n delta /\n view.viewport_container.width() *\n (view.high - view.low)\n );\n view.move_delta(delta_chrom);\n });\n /*\n FIXME: Do not do this for now because it's too jittery. Some kind of gravity approach is\n needed here because moving left/right should be difficult.\n\n // Also capture mouse wheel for left/right scrolling\n }).bind( 'mousewheel', function( e, d, dx, dy ) {\n // Only handle x axis scrolling; y axis scrolling is\n // handled by the browser when the event bubbles up.\n if (dx) {\n var delta_chrom = Math.round( - dx / view.viewport_container.width() * (view.high - view.low) );\n view.move_delta( delta_chrom );\n }\n });\n */\n\n // Dragging in the top label track allows selecting a region to zoom in on selected region.\n this.top_labeltrack\n .bind(\"dragstart\", function(e, d) {\n return $(\"\")\n .addClass(\"zoom-area\")\n .css(\n \"height\",\n view.browser_content_div.height() +\n view.top_labeltrack.height() +\n 1\n )\n .appendTo($(this));\n })\n .bind(\"drag\", function(e, d) {\n $(d.proxy).css({\n left:\n Math.min(e.pageX, d.startX) -\n view.container.offset().left,\n width: Math.abs(e.pageX - d.startX)\n });\n var min =\n Math.min(e.pageX, d.startX) -\n view.container.offset().left,\n max =\n Math.max(e.pageX, d.startX) -\n view.container.offset().left,\n span = view.high - view.low,\n width = view.viewport_container.width();\n view.update_location(\n Math.round(min / width * span) + view.low,\n Math.round(max / width * span) + view.low\n );\n })\n .bind(\"dragend\", function(e, d) {\n var min = Math.min(e.pageX, d.startX),\n max = Math.max(e.pageX, d.startX),\n span = view.high - view.low,\n width = view.viewport_container.width(),\n old_low = view.low;\n view.low = Math.round(min / width * span) + old_low;\n view.high = Math.round(max / width * span) + old_low;\n $(d.proxy).remove();\n view.request_redraw();\n });\n\n // FIXME: this is still wonky for embedded visualizations.\n /*\n // For vertical alignment, track mouse with simple line.\n var mouse_tracker_div = $('').addClass('mouse-pos').appendTo(parent_element);\n\n // Show tracker only when hovering over view.\n parent_element.hover(\n function() {\n mouse_tracker_div.show();\n parent_element.mousemove(function(e) {\n mouse_tracker_div.css({\n // -1 makes line appear next to the mouse w/o preventing mouse actions.\n left: e.pageX - parent_element.offset().left - 1\n });\n });\n },\n function() {\n parent_element.off('mousemove');\n mouse_tracker_div.hide();\n }\n );\n */\n\n this.add_label_track(\n new LabelTrack(this, { content_div: this.top_labeltrack })\n );\n\n $(window).bind(\"resize\", function() {\n // Stop previous timer.\n if (this.resize_timer) {\n clearTimeout(this.resize_timer);\n }\n\n // When function activated, resize window and redraw.\n this.resize_timer = setTimeout(function() {\n view.resize_window();\n }, 500);\n });\n $(document).bind(\"redraw\", function() {\n view.redraw();\n });\n\n this.reset();\n $(window).trigger(\"resize\");\n },\n\n get_base_color: function(base) {\n return (\n this.config.get_value(base.toLowerCase() + \"_color\") ||\n this.config.get_value(\"n_color\")\n );\n }\n });\n\n // FIXME: need to use this approach to enable inheritance of DrawableCollection functions.\n extend(TracksterView.prototype, DrawableCollection.prototype, {\n changed: function() {\n this.has_changes = true;\n },\n\n /** Add or remove intro div depending on view state. */\n update_intro_div: function() {\n this.intro_div.toggle(this.drawables.length === 0);\n },\n\n /**\n * Triggers navigate events as needed. If there is a delay,\n * then event is triggered only after navigation has stopped.\n */\n trigger_navigate: function(new_chrom, new_low, new_high, delay) {\n // Stop previous timer.\n if (this.timer) {\n clearTimeout(this.timer);\n }\n\n if (delay) {\n // To aggregate calls, use timer and only navigate once\n // location has stabilized.\n var self = this;\n this.timer = setTimeout(function() {\n self.trigger(\n \"navigate\",\n new_chrom + \":\" + new_low + \"-\" + new_high\n );\n }, 500);\n } else {\n view.trigger(\n \"navigate\",\n new_chrom + \":\" + new_low + \"-\" + new_high\n );\n }\n },\n\n update_location: function(low, high) {\n this.location_span.text(\n util.commatize(low) + \" - \" + util.commatize(high)\n );\n this.nav_input.val(\n this.chrom +\n \":\" +\n util.commatize(low) +\n \"-\" +\n util.commatize(high)\n );\n\n // Update location. Only update when there is a valid chrom; when loading vis, there may\n // not be a valid chrom.\n var chrom = this.chrom_select.val();\n if (chrom !== \"\") {\n this.trigger_navigate(chrom, this.low, this.high, true);\n }\n },\n\n /**\n * Load chrom data for the view. Returns a jQuery Deferred.\n */\n // FIXME: instead of loading chrom data, should load and store genome object.\n load_chroms: function(url_parms) {\n url_parms.num = MAX_CHROMS_SELECTABLE;\n\n var view = this,\n chrom_data = $.Deferred();\n $.ajax({\n url: Galaxy.root + \"api/genomes/\" + this.dbkey,\n data: url_parms,\n dataType: \"json\",\n success: function(result) {\n // Do nothing if could not load chroms.\n if (result.chrom_info.length === 0) {\n return;\n }\n\n // Load chroms.\n if (result.reference) {\n var ref_track = new ReferenceTrack(view);\n view.add_label_track(ref_track);\n view.reference_track = ref_track;\n }\n view.chrom_data = result.chrom_info;\n\n view.chrom_select.html(\"\");\n view.chrom_select.append(\n $('')\n );\n\n for (\n var i = 0, len = view.chrom_data.length;\n i < len;\n i++\n ) {\n var chrom = view.chrom_data[i].chrom;\n var chrom_option = $(\"\"\n )\n );\n }\n if (result.next_chroms) {\n view.chrom_select.append(\n $(\n '\"\n )\n );\n }\n view.chrom_start_index = result.start_index;\n\n chrom_data.resolve(result.chrom_info);\n },\n error: function() {\n alert(\n \"Could not load chroms for this dbkey: \" +\n view.dbkey\n );\n }\n });\n return chrom_data;\n },\n\n change_chrom: function(chrom, low, high) {\n var view = this;\n // If chrom data is still loading, wait for it.\n if (!view.chrom_data) {\n view.load_chroms_deferred.then(function() {\n view.change_chrom(chrom, low, high);\n });\n return;\n }\n\n // Don't do anything if chrom is \"None\" (hackish but some browsers already have this set), or null/blank\n if (!chrom || chrom === \"None\") {\n return;\n }\n\n //\n // If user is navigating to previous/next set of chroms, load new chrom set and return.\n //\n if (chrom === \"previous\") {\n view.load_chroms({\n low: this.chrom_start_index - MAX_CHROMS_SELECTABLE\n });\n return;\n }\n if (chrom === \"next\") {\n view.load_chroms({\n low: this.chrom_start_index + MAX_CHROMS_SELECTABLE\n });\n return;\n }\n\n //\n // User is loading a particular chrom. Look first in current set; if not in current set, load new\n // chrom set.\n //\n var found = $.grep(view.chrom_data, function(v, i) {\n return v.chrom === chrom;\n })[0];\n if (found === undefined) {\n // Try to load chrom and then change to chrom.\n view.load_chroms({ chrom: chrom }, function() {\n view.change_chrom(chrom, low, high);\n });\n return;\n } else {\n // Switching to local chrom.\n if (chrom !== view.chrom) {\n view.chrom = chrom;\n view.chrom_select.val(view.chrom);\n view.max_high = found.len - 1; // -1 because we're using 0-based indexing.\n view.reset();\n\n for (\n var i = 0, len = view.drawables.length;\n i < len;\n i++\n ) {\n var drawable = view.drawables[i];\n if (drawable.init) {\n drawable.init();\n }\n }\n if (view.reference_track) {\n view.reference_track.init();\n }\n }\n\n // Resolve low, high.\n if (low === undefined && high === undefined) {\n // Both are undefined, so view is whole chromosome.\n view.low = 0;\n view.high = view.max_high;\n } else {\n // Low and/or high is defined.\n view.low = low !== undefined ? Math.max(low, 0) : 0;\n if (high === undefined) {\n // Center visualization around low.\n // HACK: max resolution is currently 30 bases.\n view.low = Math.max(view.low - 15, 0);\n view.high = view.low + 30;\n } else {\n // High is defined.\n view.high = Math.min(high, view.max_high);\n }\n }\n\n view.request_redraw();\n }\n },\n\n /**\n * Change viewing region to that denoted by string. General format of string is:\n *\n * [ {separator} [- ] ]\n *\n * where separator can be whitespace or a colon. Examples:\n *\n * chr22\n * chr1:100-200\n * chr7 89999\n * chr8 90000 990000\n */\n go_to: function(str) {\n // Remove commas.\n str = str.replace(/,/g, \"\");\n\n // Replace colons and hyphens with space for easy parsing.\n str = str.replace(/:|\\-/g, \" \");\n\n // Parse new location.\n var chrom_pos = str.split(/\\s+/),\n chrom = chrom_pos[0],\n new_low = chrom_pos[1]\n ? parseInt(chrom_pos[1], 10)\n : undefined,\n new_high = chrom_pos[2]\n ? parseInt(chrom_pos[2], 10)\n : undefined;\n\n this.change_chrom(chrom, new_low, new_high);\n },\n\n move_fraction: function(fraction) {\n var view = this;\n var span = view.high - view.low;\n this.move_delta(fraction * span);\n },\n\n move_delta: function(delta_chrom) {\n //\n // Update low, high.\n //\n\n var view = this;\n var current_chrom_span = view.high - view.low;\n // Check for left and right boundaries\n if (view.low - delta_chrom < view.max_low) {\n view.low = view.max_low;\n view.high = view.max_low + current_chrom_span;\n } else if (view.high - delta_chrom > view.max_high) {\n view.high = view.max_high;\n view.low = view.max_high - current_chrom_span;\n } else {\n view.high -= delta_chrom;\n view.low -= delta_chrom;\n }\n\n //\n // Redraw view.\n //\n\n // Redraw without requesting more data immediately.\n view.request_redraw({ data_fetch: false });\n\n // Set up timeout to redraw with more data when moving stops.\n if (this.redraw_on_move_fn) {\n clearTimeout(this.redraw_on_move_fn);\n }\n\n this.redraw_on_move_fn = setTimeout(function() {\n view.request_redraw();\n }, 200);\n\n // Navigate.\n var chrom = view.chrom_select.val();\n this.trigger_navigate(chrom, view.low, view.high, true);\n },\n\n /**\n * Add a drawable to the view.\n */\n add_drawable: function(drawable) {\n DrawableCollection.prototype.add_drawable.call(this, drawable);\n drawable.init();\n this.changed();\n this.update_intro_div();\n\n // When drawable config changes, mark view as changed. This\n // captures most (all?) state change that needs to be saved.\n var self = this;\n drawable.config.on(\"change\", function() {\n self.changed();\n });\n },\n\n add_label_track: function(label_track) {\n label_track.view = this;\n label_track.init();\n this.label_tracks.push(label_track);\n },\n\n /**\n * Remove drawable from the view.\n */\n remove_drawable: function(drawable, hide) {\n DrawableCollection.prototype.remove_drawable.call(\n this,\n drawable\n );\n if (hide) {\n var view = this;\n drawable.container_div.hide(0, function() {\n $(this).remove();\n view.update_intro_div();\n });\n }\n },\n\n reset: function() {\n this.low = this.max_low;\n this.high = this.max_high;\n this.viewport_container.find(\".yaxislabel\").remove();\n },\n\n /**\n * Request that view redraw one or more of view's drawables. If drawable is not specified,\n * all drawables are redrawn.\n */\n request_redraw: function(options, drawable) {\n var view = this,\n // Either redrawing a single drawable or all view's drawables.\n track_list = drawable ? [drawable] : view.drawables;\n\n // Add/update tracks in track list to redraw list.\n _.each(track_list, function(track) {\n var track_options = _.find(\n view.tracks_to_be_redrawn,\n function(to) {\n return to[0] === track;\n }\n );\n\n if (track_options) {\n // Track already in list; update options.\n track_options[1] = options;\n } else {\n // Track not in list yet.\n view.tracks_to_be_redrawn.push([track, options]);\n }\n });\n\n // Set up redraw if it has not been requested since last redraw.\n if (!this.requested_redraw) {\n requestAnimationFrame(function() {\n view._redraw();\n });\n this.requested_redraw = true;\n }\n },\n\n /**\n * Redraws view and tracks.\n * NOTE: this method should never be called directly; request_redraw() should be used so\n * that requestAnimationFrame can manage redrawing.\n */\n _redraw: function() {\n // TODO: move this code to function that does location setting.\n\n // Clear because requested redraw is being handled now.\n this.requested_redraw = false;\n\n var low = this.low,\n high = this.high;\n\n if (low < this.max_low) {\n low = this.max_low;\n }\n if (high > this.max_high) {\n high = this.max_high;\n }\n var span = this.high - this.low;\n if (this.high !== 0 && span < this.min_separation) {\n high = low + this.min_separation;\n }\n this.low = Math.floor(low);\n this.high = Math.ceil(high);\n\n this.update_location(this.low, this.high);\n\n // -- Drawing code --\n\n // Resolution is a pixel density.\n this.resolution_px_b =\n this.viewport_container.width() / (this.high - this.low);\n\n // Overview\n var left_px =\n this.low /\n (this.max_high - this.max_low) *\n this.overview_viewport.width() || 0;\n var width_px =\n (this.high - this.low) /\n (this.max_high - this.max_low) *\n this.overview_viewport.width() || 0;\n var min_width_px = 13;\n\n this.overview_box\n .css({\n left: left_px,\n width: Math.max(min_width_px, width_px)\n })\n .show();\n if (width_px < min_width_px) {\n this.overview_box.css(\n \"left\",\n left_px - (min_width_px - width_px) / 2\n );\n }\n if (this.overview_highlight) {\n this.overview_highlight.css({\n left: left_px,\n width: width_px\n });\n }\n\n // Draw data tracks.\n _.each(this.tracks_to_be_redrawn, function(track_options) {\n var track = track_options[0],\n options = track_options[1];\n if (track) {\n track._draw(options);\n }\n });\n this.tracks_to_be_redrawn = [];\n\n // Draw label tracks.\n _.each(this.label_tracks, function(label_track) {\n label_track._draw();\n });\n },\n\n zoom_in: function(point, container) {\n if (\n this.max_high === 0 ||\n this.high - this.low <= this.min_separation\n ) {\n return;\n }\n var span = this.high - this.low,\n cur_center = span / 2 + this.low,\n new_half = span / this.zoom_factor / 2;\n if (point) {\n cur_center =\n point /\n this.viewport_container.width() *\n (this.high - this.low) +\n this.low;\n }\n this.low = Math.round(cur_center - new_half);\n this.high = Math.round(cur_center + new_half);\n\n this.changed();\n this.request_redraw();\n },\n\n zoom_out: function() {\n if (this.max_high === 0) {\n return;\n }\n var span = this.high - this.low,\n cur_center = span / 2 + this.low,\n new_half = span * this.zoom_factor / 2;\n this.low = Math.round(cur_center - new_half);\n this.high = Math.round(cur_center + new_half);\n this.changed();\n this.request_redraw();\n },\n\n /** Resize viewport. Use this method if header/footer content has changed in size. */\n resize_viewport: function() {\n this.viewport_container.height(\n this.container.height() -\n this.top_container.height() -\n this.bottom_container.height()\n );\n },\n\n /** Called when window is resized. */\n resize_window: function() {\n this.resize_viewport();\n this.request_redraw();\n },\n\n /** Show a Drawable in the overview. */\n set_overview: function(drawable) {\n if (this.overview_drawable) {\n // If drawable to be set as overview is already in overview, do nothing.\n // Otherwise, remove overview.\n if (\n this.overview_drawable.dataset.id ===\n drawable.dataset.id\n ) {\n return;\n }\n this.overview_viewport.find(\".track\").remove();\n }\n\n // Set new overview.\n var overview_drawable = drawable.copy({\n content_div: this.overview_viewport\n }),\n view = this;\n overview_drawable.header_div.hide();\n overview_drawable.is_overview = true;\n view.overview_drawable = overview_drawable;\n this.overview_drawable.postdraw_actions = function() {\n view.overview_highlight\n .show()\n .height(view.overview_drawable.content_div.height());\n view.overview_viewport.height(\n view.overview_drawable.content_div.height() +\n view.overview_box.outerHeight()\n );\n view.overview_close.show();\n view.resize_window();\n };\n view.overview_drawable.request_draw();\n this.changed();\n },\n\n /** Close and reset overview. */\n reset_overview: function() {\n // Update UI.\n $(\".tooltip\").remove();\n this.overview_viewport.find(\".track-tile\").remove();\n this.overview_viewport.height(this.default_overview_height);\n this.overview_box.height(this.default_overview_height);\n this.overview_close.hide();\n this.overview_highlight.hide();\n view.resize_window();\n view.overview_drawable = null;\n }\n });\n\n /**\n * Encapsulation of a tool that users can apply to tracks/datasets.\n */\n var TracksterTool = tools_mod.Tool.extend({\n defaults: {\n track: null\n },\n\n initialize: function(options) {\n tools_mod.Tool.prototype.initialize.call(this, options);\n\n // Restore tool visibility from state; default to hidden.\n var hidden = true;\n if (\n options.tool_state !== undefined &&\n options.tool_state.hidden !== undefined\n ) {\n hidden = options.tool_state.hidden;\n }\n this.set(\"hidden\", hidden);\n\n // FIXME: need to restore tool values from options.tool_state\n\n // HACK: remove some inputs because Trackster does yet not work with them.\n this.remove_inputs([\"data\", \"hidden_data\", \"conditional\"]);\n },\n\n state_dict: function(options) {\n return _.extend(this.get_inputs_dict(), {\n hidden: !this.is_visible()\n });\n }\n });\n\n /**\n * View renders tool parameter HTML and updates parameter value as it is changed in the HTML.\n */\n var ToolParameterView = Backbone.View.extend({\n events: {\n \"change :input\": \"update_value\"\n },\n\n render: function() {\n var param_div = this.$el.addClass(\"param-row\"),\n param = this.model;\n\n // Param label.\n var label_div = $(\" \")\n .addClass(\"param-label\")\n .text(param.get(\"label\"))\n .appendTo(param_div);\n // Param HTML.\n var html_div = $(\"\")\n .addClass(\"param-input\")\n .html(param.get(\"html\"))\n .appendTo(param_div);\n // Set initial value.\n html_div.find(\":input\").val(param.get(\"value\"));\n\n // Add to clear floating layout.\n $(\"\").appendTo(param_div);\n },\n\n update_value: function(update_event) {\n this.model.set_value($(update_event.target).val());\n }\n });\n\n /**\n * View for TracksterTool.\n */\n var TracksterToolView = Backbone.View.extend({\n initialize: function(options) {\n this.model.on(\"change:hidden\", this.set_visible, this);\n },\n\n /**\n * Render tool UI.\n */\n render: function() {\n var self = this,\n tool = this.model,\n parent_div = this.$el.addClass(\"dynamic-tool\").hide();\n\n // Prevent div events from propogating to other elements.\n parent_div\n .bind(\"drag\", function(e) {\n e.stopPropagation();\n })\n .click(function(e) {\n e.stopPropagation();\n })\n .bind(\"dblclick\", function(e) {\n e.stopPropagation();\n })\n .keydown(function(e) {\n e.stopPropagation();\n });\n\n // Add name, inputs.\n var name_div = $(\"\")\n .appendTo(parent_div)\n .text(tool.get(\"name\"));\n tool.get(\"inputs\").each(function(param) {\n // Render parameter.\n var param_view = new ToolParameterView({ model: param });\n param_view.render();\n parent_div.append(param_view.$el);\n });\n\n // Highlight value for inputs for easy replacement.\n parent_div.find(\"input\").click(function() {\n $(this).select();\n });\n\n // Add buttons for running on dataset, region.\n var run_tool_row = $(\"\")\n .addClass(\"param-row\")\n .appendTo(parent_div);\n var run_on_dataset_button = $(\"\")\n .attr(\"value\", \"Run on complete dataset\")\n .appendTo(run_tool_row);\n var run_on_region_button = $(\"\")\n .attr(\"value\", \"Run on visible region\")\n .appendTo(run_tool_row);\n run_on_region_button.click(function() {\n // Run tool to create new track.\n self.run_on_region();\n });\n run_on_dataset_button.click(function() {\n self.run_on_dataset();\n });\n\n if (tool.is_visible()) {\n this.$el.show();\n }\n },\n\n /**\n * Show or hide tool depending on tool visibility state.\n */\n set_visible: function() {\n this.$el.toggle(this.model.is_visible());\n },\n\n /**\n * Update tool parameters.\n */\n update_params: function() {\n for (var i = 0; i < this.params.length; i++) {\n this.params[i].update_value();\n }\n },\n\n /**\n * Run tool on dataset. Output is placed in dataset's history and no changes to viz are made.\n */\n run_on_dataset: function() {\n var tool = this.model;\n this.run(\n // URL params.\n {\n target_dataset_id: this.model.get(\"track\").dataset.id,\n action: \"rerun\",\n tool_id: tool.id\n },\n null,\n // Success callback.\n function(track_data) {\n Galaxy.modal.show({\n title: tool.get(\"name\") + \" is Running\",\n body:\n tool.get(\"name\") +\n \" is running on the complete dataset. Tool outputs are in dataset's history.\",\n buttons: {\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n }\n );\n },\n\n /**\n * Run dataset on visible region. This creates a new track and sets the track's contents\n * to the tool's output.\n */\n run_on_region: function() {\n //\n // Create track for tool's output immediately to provide user feedback.\n //\n var track = this.model.get(\"track\"),\n tool = this.model,\n region = new visualization.GenomeRegion({\n chrom: track.view.chrom,\n start: track.view.low,\n end: track.view.high\n }),\n url_params = {\n target_dataset_id: track.dataset.id,\n action: \"rerun\",\n tool_id: tool.id,\n regions: [region.toJSON()]\n },\n current_track = track,\n // Set name of track to include tool name, parameters, and region used.\n track_name =\n tool.get(\"name\") +\n current_track.tool_region_and_parameters_str(region),\n container;\n\n // If track not in a group, create a group for it and add new track to group. If track\n // already in group, add track to group.\n if (current_track.container === view) {\n // Create new group.\n var group = new DrawableGroup(view, view, {\n name: track.config.get_value(\"name\")\n });\n\n // Replace track with group.\n var index = current_track.container.replace_drawable(\n current_track,\n group,\n false\n );\n\n // Update HTML.\n // FIXME: this is ugly way to replace a track with a group -- make this easier via\n // a Drawable or DrawableCollection function.\n group.container_div.insertBefore(\n current_track.view.content_div.children()[index]\n );\n group.add_drawable(current_track);\n current_track.container_div.appendTo(group.content_div);\n container = group;\n } else {\n // Use current group.\n container = current_track.container;\n }\n\n // Create and init new track.\n var new_track = new current_track.constructor(view, container, {\n name: track_name,\n hda_ldda: \"hda\"\n });\n new_track.init_for_tool_data();\n new_track.change_mode(current_track.mode);\n new_track.set_filters_manager(\n current_track.filters_manager.copy(new_track)\n );\n new_track.update_icons();\n container.add_drawable(new_track);\n new_track.tiles_div.text(\"Starting job.\");\n\n // Run tool.\n this.run(\n url_params,\n new_track,\n // Success callback.\n function(track_data) {\n new_track.set_dataset(new data.Dataset(track_data));\n new_track.tiles_div.text(\"Running job.\");\n new_track.init();\n }\n );\n },\n\n /**\n * Run tool using a set of URL params and a success callback.\n */\n run: function(url_params, new_track, success_callback) {\n // Run tool.\n url_params.inputs = this.model.get_inputs_dict();\n var ss_deferred = new util.ServerStateDeferred({\n ajax_settings: {\n url: Galaxy.root + \"api/tools\",\n data: JSON.stringify(url_params),\n dataType: \"json\",\n contentType: \"application/json\",\n type: \"POST\"\n },\n interval: 2000,\n success_fn: function(response) {\n return response !== \"pending\";\n }\n });\n\n // Start with this status message.\n //new_track.container_div.addClass(\"pending\");\n //new_track.content_div.html(DATA_PENDING);\n\n $.when(ss_deferred.go()).then(function(response) {\n if (response === \"no converter\") {\n // No converter available for input datasets, so cannot run tool.\n new_track.container_div.addClass(\"error\");\n new_track.content_div.text(DATA_NOCONVERTER);\n } else if (response.error) {\n // General error.\n new_track.container_div.addClass(\"error\");\n new_track.content_div.text(\n DATA_CANNOT_RUN_TOOL + response.message\n );\n } else {\n // Job submitted and running.\n success_callback(response);\n }\n });\n }\n });\n\n /**\n * Generates scale values based on filter and feature's value for filter.\n */\n var FilterScaler = function(filter, default_val) {\n painters.Scaler.call(this, default_val);\n this.filter = filter;\n };\n\n FilterScaler.prototype.gen_val = function(feature_data) {\n // If filter is not initalized yet, return default val.\n if (\n this.filter.high === Number.MAX_VALUE ||\n this.filter.low === -Number.MAX_VALUE ||\n this.filter.low === this.filter.high\n ) {\n return this.default_val;\n }\n\n // Scaling value is ratio of (filter's value compared to low) to (complete filter range).\n return (\n (parseFloat(feature_data[this.filter.index]) -\n this.filter.low) /\n (this.filter.high - this.filter.low)\n );\n };\n\n /**\n * Tiles drawn by tracks.\n */\n var Tile = function(track, region, w_scale, canvas, data) {\n this.track = track;\n this.region = region;\n this.low = region.get(\"start\");\n this.high = region.get(\"end\");\n this.w_scale = w_scale;\n this.canvas = canvas;\n // Wrap element in div for background and to provide container for tile-specific elements.\n this.html_elt = $(\"\").append(canvas);\n this.data = data;\n this.stale = false;\n };\n\n /**\n * Perform pre-display actions.\n */\n Tile.prototype.predisplay_actions = function() {};\n\n var LineTrackTile = function(track, region, w_scale, canvas, data) {\n Tile.call(this, track, region, w_scale, canvas, data);\n };\n LineTrackTile.prototype.predisplay_actions = function() {};\n\n var FeatureTrackTile = function(\n track,\n region,\n w_scale,\n canvas,\n data,\n mode,\n message,\n all_slotted,\n feature_mapper,\n incomplete_features,\n seq_data\n ) {\n // Attribute init.\n Tile.call(this, track, region, w_scale, canvas, data);\n this.mode = mode;\n this.all_slotted = all_slotted;\n this.feature_mapper = feature_mapper;\n this.has_icons = false;\n this.incomplete_features = incomplete_features;\n // Features drawn based on data from other tiles.\n this.other_tiles_features_drawn = {};\n this.seq_data = seq_data;\n\n // Add message + action icons to tile's html.\n /*\n This does not work right now because a random set of reads is returned by the server.\n When the server can respond with more data systematically, renable these icons.\n if (message) {\n this.has_icons = true;\n\n var\n tile = this;\n canvas = this.html_elt.children()[0],\n message_div = $(\"\").addClass(\"tile-message\")\n // -1 to account for border.\n .css({'height': ERROR_PADDING, 'width': canvas.width}).prependTo(this.html_elt);\n\n // Handle message; only message currently is that only the first N elements are displayed.\n var tile_region = new visualization.GenomeRegion({\n chrom: track.view.chrom,\n start: this.low,\n end: this.high\n }),\n num_features = data.length,\n more_down_icon = $(\"\").addClass(\"icon more-down\")\n .attr(\"title\", \"For speed, only the first \" + num_features + \" features in this region were obtained from server. Click to get more data including depth\")\n .tooltip().appendTo(message_div),\n more_across_icon = $(\"\").addClass(\"icon more-across\")\n .attr(\"title\", \"For speed, only the first \" + num_features + \" features in this region were obtained from server. Click to get more data excluding depth\")\n .tooltip().appendTo(message_div);\n\n // Set up actions for icons.\n more_down_icon.click(function() {\n // Mark tile as stale, request more data, and redraw track.\n tile.stale = true;\n track.data_manager.get_more_data(tile_region, track.mode, 1 / tile.w_scale, {}, track.data_manager.DEEP_DATA_REQ);\n $(\".tooltip\").hide();\n track.request_draw();\n }).dblclick(function(e) {\n // Do not propogate as this would normally zoom in.\n e.stopPropagation();\n });\n\n more_across_icon.click(function() {\n // Mark tile as stale, request more data, and redraw track.\n tile.stale = true;\n track.data_manager.get_more_data(tile_region, track.mode, 1 / tile.w_scale, {}, track.data_manager.BROAD_DATA_REQ);\n $(\".tooltip\").hide();\n track.request_draw();\n }).dblclick(function(e) {\n // Do not propogate as this would normally zoom in.\n e.stopPropagation();\n });\n }\n */\n };\n extend(FeatureTrackTile.prototype, Tile.prototype);\n\n /**\n * Sets up support for popups.\n */\n FeatureTrackTile.prototype.predisplay_actions = function() {\n /*\n FIXME: use a canvas library to handle popups.\n //\n // Add support for popups.\n //\n var tile = this,\n popups = {};\n\n // Only show popups in Pack mode.\n if (tile.mode !== \"Pack\") { return; }\n\n $(this.html_elt).hover(\n function() {\n this.hovered = true;\n $(this).mousemove();\n },\n function() {\n this.hovered = false;\n // Clear popup if it is still hanging around (this is probably not needed)\n $(this).parents(\".track-content\").children(\".overlay\").children(\".feature-popup\").remove();\n } ).mousemove(function (e) {\n // Use the hover plugin to get a delay before showing popup\n if ( !this.hovered ) { return; }\n // Get feature data for position.\n var\n this_offset = $(this).offset(),\n offsetX = e.pageX - this_offset.left,\n offsetY = e.pageY - this_offset.top,\n feature_data = tile.feature_mapper.get_feature_data(offsetX, offsetY),\n feature_uid = (feature_data ? feature_data[0] : null);\n // Hide visible popup if not over a feature or over a different feature.\n $(this).parents(\".track-content\").children(\".overlay\").children(\".feature-popup\").each(function() {\n if ( !feature_uid ||\n $(this).attr(\"id\") !== feature_uid.toString() ) {\n $(this).remove();\n }\n });\n\n if (feature_data) {\n // Get or create popup.\n var popup = popups[feature_uid];\n if (!popup) {\n // Create feature's popup element.\n var feature_dict = {\n name: feature_data[3],\n start: feature_data[1],\n end: feature_data[2],\n strand: feature_data[4]\n },\n filters = tile.track.filters_manager.filters,\n filter;\n\n // Add filter values to feature dict.\n for (var i = 0; i < filters.length; i++) {\n filter = filters[i];\n feature_dict[filter.name] = feature_data[filter.index];\n }\n\n // Build popup.\n popup = $(\"\").attr(\"id\", feature_uid).addClass(\"feature-popup\");\n var table = $(\"\"),\n key, value, row;\n for (key in feature_dict) {\n value = feature_dict[key];\n row = $(\"
\").appendTo(table);\n $(\" \").appendTo(row).text(key);\n $(\" \").attr(\"align\", \"left\").appendTo(row)\n .text(typeof(value) === 'number' ? round(value, 2) : value);\n }\n popup.append( $(\" \").append( table ) );\n popups[feature_uid] = popup;\n }\n\n // Attach popup to track's overlay.\n popup.appendTo( $(this).parents(\".track-content\").children(\".overlay\") );\n\n // Offsets are within canvas, but popup must be positioned relative to parent element.\n // parseInt strips \"px\" from left, top measurements. +7 so that mouse pointer does not\n // overlap popup.\n var\n popupX = offsetX + parseInt( tile.html_elt.css(\"left\"), 10 ) - popup.width() / 2,\n popupY = offsetY + parseInt( tile.html_elt.css(\"top\"), 10 ) + 7;\n popup.css(\"left\", popupX + \"px\").css(\"top\", popupY + \"px\");\n }\n else if (!e.isPropagationStopped()) {\n // Propogate event to other tiles because overlapping tiles prevent mousemove from being\n // called on tiles under this tile.\n e.stopPropagation();\n $(this).siblings().each(function() {\n $(this).trigger(e);\n });\n }\n })\n .mouseleave(function() {\n $(this).parents(\".track-content\").children(\".overlay\").children(\".feature-popup\").remove();\n });\n */\n };\n\n /**\n * Tracks are objects can be added to the View.\n *\n * Track object hierarchy:\n * Track\n * -> LabelTrack\n * -> TiledTrack\n * ----> LineTrack\n * ----> ReferenceTrack\n * ----> FeatureTrack\n * -------> ReadTrack\n * ----> VariantTrack\n */\n var Track = function(view, container, obj_dict) {\n // For now, track's container is always view.\n extend(obj_dict, {\n drag_handle_class: \"draghandle\"\n });\n Drawable.call(this, view, container, obj_dict);\n\n //\n // Attribute init.\n //\n\n // Set or create dataset.\n this.dataset = null;\n if (obj_dict.dataset) {\n // Dataset can be a Backbone model or a dict that can be used to create a model.\n this.dataset =\n obj_dict.dataset instanceof Backbone.Model\n ? obj_dict.dataset\n : new data.Dataset(obj_dict.dataset);\n }\n this.dataset_check_type = \"converted_datasets_state\";\n this.data_url_extra_params = {};\n this.data_query_wait =\n \"data_query_wait\" in obj_dict\n ? obj_dict.data_query_wait\n : DEFAULT_DATA_QUERY_WAIT;\n // A little ugly creating data manager right now due to transition to Backbone-based objects.\n this.data_manager =\n \"data_manager\" in obj_dict\n ? obj_dict.data_manager\n : new visualization.GenomeDataManager({\n dataset: this.dataset,\n // HACK: simulate 'genome' attributes from view for now.\n // View should eventually use Genome object.\n genome: new visualization.Genome({\n key: view.dbkey,\n chroms_info: {\n chrom_info: view.chrom_data\n }\n }),\n data_mode_compatible: this.data_and_mode_compatible,\n can_subset: this.can_subset\n });\n\n // Height attributes: min height, max height, and visible height.\n this.min_height_px = 16;\n this.max_height_px = 800;\n this.visible_height_px = this.config.get_value(\"height\");\n\n //\n // Create content div, which is where track is displayed, and add to container if available.\n //\n this.content_div = $(\"\").appendTo(\n this.container_div\n );\n if (this.container) {\n this.container.content_div.append(this.container_div);\n if (!(\"resize\" in obj_dict) || obj_dict.resize) {\n this.add_resize_handle();\n }\n }\n };\n\n extend(Track.prototype, Drawable.prototype, {\n action_icons_def: [\n // Change track mode.\n {\n name: \"mode_icon\",\n title: \"Set display mode\",\n css_class: \"chevron-expand\",\n on_click_fn: function() {}\n },\n // Hide/show content.\n Drawable.prototype.action_icons_def[0],\n // Set track as overview.\n {\n name: \"overview_icon\",\n title: \"Set as overview\",\n css_class: \"application-dock-270\",\n on_click_fn: function(track) {\n track.view.set_overview(track);\n }\n },\n // Edit config.\n Drawable.prototype.action_icons_def[1],\n // Toggle track filters.\n {\n name: \"filters_icon\",\n title: \"Filters\",\n css_class: \"ui-slider-050\",\n on_click_fn: function(drawable) {\n // TODO: update Tooltip text.\n if (drawable.filters_manager.visible()) {\n drawable.filters_manager.clear_filters();\n } else {\n drawable.filters_manager.init_filters();\n }\n drawable.filters_manager.toggle();\n }\n },\n // Toggle track tool.\n {\n name: \"tools_icon\",\n title: \"Tool\",\n css_class: \"hammer\",\n on_click_fn: function(track) {\n // TODO: update Tooltip text.\n\n track.tool.toggle();\n\n // Update track name.\n if (track.tool.is_visible()) {\n track.set_name(\n track.config.get_value(\"name\") +\n track.tool_region_and_parameters_str()\n );\n } else {\n track.revert_name();\n }\n // HACK: name change modifies icon placement, which leaves tooltip incorrectly placed.\n $(\".tooltip\").remove();\n }\n },\n // Go to parameter exploration visualization.\n {\n name: \"param_space_viz_icon\",\n title: \"Tool parameter space visualization\",\n css_class: \"arrow-split\",\n on_click_fn: function(track) {\n var html =\n \"Tool:\" +\n track.tool.get(\"name\") +\n \"
\" +\n \"Dataset:\" +\n track.config.get_value(\"name\") +\n \"
\" +\n 'Region(s): \";\n var cancel_fn = function() {\n Galaxy.modal.hide();\n $(window).unbind(\"keypress.check_enter_esc\");\n },\n ok_fn = function() {\n var regions_to_use = $(\n 'select[name=\"regions\"] option:selected'\n ).val(),\n regions,\n view_region = new visualization.GenomeRegion(\n {\n chrom: view.chrom,\n start: view.low,\n end: view.high\n }\n ),\n bookmarked_regions = _.map(\n $(\".bookmark\"),\n function(elt) {\n return new visualization.GenomeRegion(\n {\n from_str: $(elt)\n .children(\".position\")\n .text()\n }\n );\n }\n );\n\n // Get regions for visualization.\n if (regions_to_use === \"cur\") {\n // Use only current region.\n regions = [view_region];\n } else if (regions_to_use === \"bookmarks\") {\n // Use only bookmarks.\n regions = bookmarked_regions;\n } else {\n // Use both current region and bookmarks.\n regions = [view_region].concat(\n bookmarked_regions\n );\n }\n\n Galaxy.modal.hide();\n\n // Go to visualization.\n window.location.href =\n Galaxy.root +\n \"visualization/sweepster\" +\n \"?\" +\n $.param({\n dataset_id: track.dataset.id,\n hda_ldda: track.dataset.get(\"hda_ldda\"),\n regions: JSON.stringify(\n new Backbone.Collection(\n regions\n ).toJSON()\n )\n });\n },\n check_enter_esc = function(e) {\n if ((e.keyCode || e.which) === 27) {\n // Escape key\n cancel_fn();\n } else if ((e.keyCode || e.which) === 13) {\n // Enter key\n ok_fn();\n }\n };\n\n // show dialog\n Galaxy.modal.show({\n title:\n \"Visualize tool parameter space and output from different parameter settings?\",\n body: html,\n buttons: { No: cancel_fn, Yes: ok_fn }\n });\n }\n },\n // Remove track.\n Drawable.prototype.action_icons_def[2]\n ],\n\n can_draw: function() {\n return this.dataset && Drawable.prototype.can_draw.call(this);\n },\n\n build_container_div: function() {\n return $(\"\")\n .addClass(\"track\")\n .attr(\"id\", \"track_\" + this.id);\n },\n\n /**\n * Set track's dataset.\n */\n set_dataset: function(dataset) {\n this.dataset = dataset;\n this.data_manager.set(\"dataset\", dataset);\n },\n\n /**\n * Action to take during resize.\n */\n on_resize: function() {\n this.request_draw({ clear_tile_cache: true });\n },\n\n /**\n * Add resizing handle to drawable's container_div.\n */\n add_resize_handle: function() {\n var track = this;\n var in_handle = false;\n var in_drag = false;\n var drag_control = $(\"\");\n // Control shows on hover over track, stays while dragging\n $(track.container_div).hover(\n function() {\n if (track.config.get_value(\"content_visible\")) {\n in_handle = true;\n drag_control.show();\n }\n },\n function() {\n in_handle = false;\n if (!in_drag) {\n drag_control.hide();\n }\n }\n );\n // Update height and force redraw of current view while dragging,\n // clear cache to force redraw of other tiles.\n drag_control\n .hide()\n .bind(\"dragstart\", function(e, d) {\n in_drag = true;\n d.original_height = $(track.content_div).height();\n })\n .bind(\"drag\", function(e, d) {\n var new_height = Math.min(\n Math.max(\n d.original_height + d.deltaY,\n track.min_height_px\n ),\n track.max_height_px\n );\n $(track.tiles_div).css(\"height\", new_height);\n track.visible_height_px =\n track.max_height_px === new_height ? 0 : new_height;\n track.on_resize();\n })\n .bind(\"dragend\", function(e, d) {\n track.tile_cache.clear();\n in_drag = false;\n if (!in_handle) {\n drag_control.hide();\n }\n track.config.set_value(\n \"height\",\n track.visible_height_px\n );\n track.changed();\n })\n .appendTo(track.container_div);\n },\n\n /**\n * Hide any elements that are part of the tracks contents area. Should\n * remove as approprite, the track will be redrawn by show_contents.\n */\n hide_contents: function() {\n // Hide tiles.\n this.tiles_div.hide();\n // Hide any y axis labels (common to several track types)\n this.container_div.find(\".yaxislabel, .track-resize\").hide();\n },\n\n show_contents: function() {\n // Show the contents div and labels (if present)\n this.tiles_div.show();\n this.container_div.find(\".yaxislabel, .track-resize\").show();\n // Request a redraw of the content\n this.request_draw();\n },\n\n /**\n * Returns track type.\n */\n get_type: function() {\n // Order is important: start with most-specific classes and go up the track hierarchy.\n if (this instanceof LabelTrack) {\n return \"LabelTrack\";\n } else if (this instanceof ReferenceTrack) {\n return \"ReferenceTrack\";\n } else if (this instanceof LineTrack) {\n return \"LineTrack\";\n } else if (this instanceof ReadTrack) {\n return \"ReadTrack\";\n } else if (this instanceof VariantTrack) {\n return \"VariantTrack\";\n } else if (this instanceof CompositeTrack) {\n return \"CompositeTrack\";\n } else if (this instanceof FeatureTrack) {\n return \"FeatureTrack\";\n }\n return \"\";\n },\n\n /**\n * Remove visualization content and display message.\n */\n show_message: function(msg_html) {\n this.tiles_div.remove();\n return $(\"\")\n .addClass(\"message\")\n .html(msg_html)\n .appendTo(this.content_div);\n },\n\n /**\n * Initialize and draw the track.\n */\n init: function(retry) {\n // FIXME: track should have a 'state' attribute that is checked on load; this state attribute should be\n // used in this function to determine what action(s) to take.\n\n var track = this;\n track.enabled = false;\n track.tile_cache.clear();\n track.data_manager.clear();\n /*\n if (!track.content_div.text()) {\n track.content_div.text(DATA_LOADING);\n }\n */\n // Remove old track content (e.g. tiles, messages).\n track.content_div.children().remove();\n track.container_div.removeClass(\"nodata error pending\");\n\n track.tiles_div = $(\"\")\n .addClass(\"tiles\")\n .appendTo(track.content_div);\n\n //\n // Tracks with no dataset id are handled differently.\n // FIXME: is this really necessary?\n //\n if (!track.dataset.id) {\n return;\n }\n\n // Get dataset state; if state is fine, enable and draw track. Otherwise, show message\n // about track status.\n var init_deferred = $.Deferred(),\n params = {\n hda_ldda: track.dataset.get(\"hda_ldda\"),\n data_type: this.dataset_check_type,\n chrom: track.view.chrom,\n retry: retry\n };\n $.getJSON(this.dataset.url(), params, function(result) {\n if (\n !result ||\n result === \"error\" ||\n result.kind === \"error\"\n ) {\n // Dataset is in error state.\n track.container_div.addClass(\"error\");\n var msg_elt = track.show_message(DATA_ERROR);\n if (result.message) {\n // Add links to (a) show error and (b) try again.\n msg_elt.append(\n $(\"\")\n .text(\"View error\")\n .click(function() {\n Galaxy.modal.show({\n title: \"Trackster Error\",\n body:\n \"\" +\n result.message +\n \"
\",\n buttons: {\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n })\n );\n msg_elt.append($(\"\").text(\" \"));\n msg_elt.append(\n $(\"\")\n .text(\"Try again\")\n .click(function() {\n track.init(true);\n })\n );\n }\n } else if (result === \"no converter\") {\n track.container_div.addClass(\"error\");\n track.show_message(DATA_NOCONVERTER);\n } else if (\n result === \"no data\" ||\n (result.data !== undefined &&\n (result.data === null || result.data.length === 0))\n ) {\n track.container_div.addClass(\"nodata\");\n track.show_message(DATA_NONE);\n } else if (result === \"pending\") {\n track.container_div.addClass(\"pending\");\n track.show_message(DATA_PENDING);\n //$(\"\").attr(\"src\", image_path + \"/yui/rel_interstitial_loading.gif\").appendTo(track.tiles_div);\n setTimeout(function() {\n track.init();\n }, track.data_query_wait);\n } else if (result === \"data\" || result.status === \"data\") {\n if (result.valid_chroms) {\n track.valid_chroms = result.valid_chroms;\n track.update_icons();\n }\n track.tiles_div.text(DATA_OK);\n if (track.view.chrom) {\n track.tiles_div.text(\"\");\n track.tiles_div.css(\n \"height\",\n track.visible_height_px + \"px\"\n );\n track.enabled = true;\n // predraw_init may be asynchronous, wait for it and then draw\n $.when\n .apply($, track.predraw_init())\n .done(function() {\n init_deferred.resolve();\n track.container_div.removeClass(\n \"nodata error pending\"\n );\n track.request_draw();\n });\n } else {\n init_deferred.resolve();\n }\n }\n });\n\n this.update_icons();\n return init_deferred;\n },\n\n /**\n * Additional initialization required before drawing track for the first time.\n */\n predraw_init: function() {\n var track = this;\n return $.getJSON(\n track.dataset.url(),\n {\n data_type: \"data\",\n stats: true,\n chrom: track.view.chrom,\n low: 0,\n high: track.view.max_high,\n hda_ldda: track.dataset.get(\"hda_ldda\")\n },\n function(result) {\n var data = result.data;\n\n // Tracks may not have stat data either because there is no data or data is not yet ready.\n if (\n data &&\n data.min !== undefined &&\n data.max !== undefined\n ) {\n // Compute default minimum and maximum values\n var min_value = data.min,\n max_value = data.max;\n // If mean and sd are present, use them to compute a ~95% window\n // but only if it would shrink the range on one side\n min_value = Math.floor(\n Math.min(\n 0,\n Math.max(min_value, data.mean - 2 * data.sd)\n )\n );\n max_value = Math.ceil(\n Math.max(\n 0,\n Math.min(max_value, data.mean + 2 * data.sd)\n )\n );\n // Update config, prefs\n track.config.set_default_value(\n \"min_value\",\n min_value\n );\n track.config.set_default_value(\n \"max_value\",\n max_value\n );\n track.config.set_value(\"min_value\", min_value);\n track.config.set_value(\"max_value\", max_value);\n }\n }\n );\n },\n\n /**\n * Returns all drawables in this drawable.\n */\n get_drawables: function() {\n return this;\n }\n });\n\n var TiledTrack = function(view, container, obj_dict) {\n Track.call(this, view, container, obj_dict);\n\n var track = this;\n\n // Make track moveable.\n moveable(\n track.container_div,\n track.drag_handle_class,\n \".group\",\n track\n );\n\n // Attribute init.\n this.filters_manager = new filters_mod.FiltersManager(\n this,\n \"filters\" in obj_dict ? obj_dict.filters : null\n );\n // HACK: set filters manager for data manager.\n // FIXME: prolly need function to set filters and update data_manager reference.\n this.data_manager.set(\"filters_manager\", this.filters_manager);\n this.filters_available = false;\n this.tool = obj_dict.tool\n ? new TracksterTool(\n _.extend(obj_dict.tool, {\n track: this,\n tool_state: obj_dict.tool_state\n })\n )\n : null;\n this.tile_cache = new visualization.Cache(TILE_CACHE_SIZE);\n this.left_offset = 0;\n\n if (this.header_div) {\n //\n // Setup filters.\n //\n this.set_filters_manager(this.filters_manager);\n\n //\n // Create dynamic tool view.\n //\n if (this.tool) {\n var tool_view = new TracksterToolView({ model: this.tool });\n tool_view.render();\n this.dynamic_tool_div = tool_view.$el;\n this.header_div.after(this.dynamic_tool_div);\n }\n }\n\n // Add tiles_div, overlay_div to content_div.\n this.tiles_div = $(\"\")\n .addClass(\"tiles\")\n .appendTo(this.content_div);\n if (!this.config.get_value(\"content_visible\")) {\n this.tiles_div.hide();\n }\n this.overlay_div = $(\"\")\n .addClass(\"overlay\")\n .appendTo(this.content_div);\n\n if (obj_dict.mode) {\n this.change_mode(obj_dict.mode);\n }\n };\n extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {\n action_icons_def: Track.prototype.action_icons_def.concat([\n // Show more rows when all features are not slotted.\n {\n name: \"show_more_rows_icon\",\n title:\n \"To minimize track height, not all feature rows are displayed. Click to display more rows.\",\n css_class: \"exclamation\",\n on_click_fn: function(track) {\n $(\".tooltip\").remove();\n track.slotters[\n track.view.resolution_px_b\n ].max_rows *= 2;\n track.request_draw({ clear_tile_cache: true });\n },\n hide: true\n }\n ]),\n\n /**\n * Returns a copy of the track. The copy uses the same data manager so that the tracks can share data.\n */\n copy: function(container) {\n // Create copy.\n var obj_dict = this.to_dict();\n extend(obj_dict, {\n data_manager: this.data_manager\n });\n var new_track = new this.constructor(\n this.view,\n container,\n obj_dict\n );\n // Misc. init and return.\n new_track.change_mode(this.mode);\n new_track.enabled = this.enabled;\n return new_track;\n },\n\n /**\n * Set filters manager + HTML elements.\n */\n set_filters_manager: function(filters_manager) {\n this.filters_manager = filters_manager;\n this.header_div.after(this.filters_manager.parent_div);\n },\n\n /**\n * Returns representation of object in a dictionary for easy saving.\n * Use from_dict to recreate object.\n */\n to_dict: function() {\n return {\n track_type: this.get_type(),\n dataset: {\n id: this.dataset.id,\n hda_ldda: this.dataset.get(\"hda_ldda\")\n },\n prefs: this.config.to_key_value_dict(),\n mode: this.mode,\n filters: this.filters_manager.to_dict(),\n tool_state: this.tool ? this.tool.state_dict() : {}\n };\n },\n\n /**\n * Set track bounds for current chromosome.\n */\n set_min_max: function() {\n var track = this;\n\n return $.getJSON(\n track.dataset.url(),\n {\n data_type: \"data\",\n stats: true,\n chrom: track.view.chrom,\n low: 0,\n high: track.view.max_high,\n hda_ldda: track.dataset.get(\"hda_ldda\")\n },\n function(result) {\n var data = result.data;\n if (\n isNaN(\n parseFloat(track.config.get_value(\"min_value\"))\n ) ||\n isNaN(\n parseFloat(track.config.get_value(\"max_value\"))\n )\n ) {\n // Compute default minimum and maximum values\n var min_value = data.min,\n max_value = data.max;\n // If mean and sd are present, use them to compute a ~95% window\n // but only if it would shrink the range on one side\n min_value = Math.floor(\n Math.min(\n 0,\n Math.max(min_value, data.mean - 2 * data.sd)\n )\n );\n max_value = Math.ceil(\n Math.max(\n 0,\n Math.min(max_value, data.mean + 2 * data.sd)\n )\n );\n // Update the prefs\n track.config.set_value(\"min_value\", min_value);\n track.config.set_value(\"max_value\", max_value);\n }\n }\n );\n },\n\n /**\n * Change track's mode.\n */\n change_mode: function(new_mode) {\n var track = this;\n // TODO: is it necessary to store the mode in two places (.mode and track_config)?\n track.mode = new_mode;\n track.config.set_value(\"mode\", new_mode);\n // FIXME: find a better way to get Auto data w/o clearing cache; using mode in the\n // data manager would work if Auto data were checked for compatibility when a specific\n // mode is chosen.\n if (new_mode === \"Auto\") {\n this.data_manager.clear();\n }\n track.request_draw({ clear_tile_cache: true });\n this.action_icons.mode_icon.attr(\n \"title\",\n \"Set display mode (now: \" + track.mode + \")\"\n );\n return track;\n },\n\n /**\n * Update track's buttons.\n */\n update_icons: function() {\n var track = this;\n\n //\n // Show/hide filter icon.\n //\n track.action_icons.filters_icon.toggle(track.filters_available);\n\n //\n // Show/hide tool icons.\n //\n track.action_icons.tools_icon.toggle(track.tool !== null);\n track.action_icons.param_space_viz_icon.toggle(\n track.tool !== null\n );\n },\n\n /**\n * Generate a key for the tile cache.\n * TODO: create a TileCache object (like DataCache) and generate key internally.\n */\n _gen_tile_cache_key: function(w_scale, tile_region) {\n return w_scale + \"_\" + tile_region;\n },\n\n /**\n * Request that track be drawn.\n */\n request_draw: function(options) {\n if (options && options.clear_tile_cache) {\n this.tile_cache.clear();\n }\n this.view.request_redraw(options, this);\n },\n\n /**\n * Actions to be taken before drawing.\n */\n before_draw: function() {\n // Clear because this is set when drawing.\n this.max_height_px = 0;\n },\n\n /**\n * Draw track. Options include:\n * -force: force a redraw rather than use cached tiles (default: false)\n * -clear_after: clear old tiles after drawing new tiles (default: false)\n * -data_fetch: fetch data if necessary (default: true)\n *\n * NOTE: this function should never be called directly; use request_draw() so that drawing\n * management can be used.\n */\n _draw: function(options) {\n if (!this.can_draw()) {\n return;\n }\n\n var clear_after = options && options.clear_after,\n low = this.view.low,\n high = this.view.high,\n range = high - low,\n width = this.view.container.width(),\n w_scale = this.view.resolution_px_b,\n resolution = 1 / w_scale;\n\n // For overview, adjust high, low, resolution, and w_scale.\n if (this.is_overview) {\n low = this.view.max_low;\n high = this.view.max_high;\n w_scale = width / (view.max_high - view.max_low);\n resolution = 1 / w_scale;\n }\n\n this.before_draw();\n\n //\n // Method for moving and/or removing tiles:\n // (a) mark all elements for removal using class 'remove'\n // (b) during tile drawing/placement, remove class for elements that are moved;\n // this occurs in show_tile()\n // (c) after drawing tiles, remove elements still marked for removal\n // (i.e. that still have class 'remove').\n //\n\n // Step (a) for (re)moving tiles.\n this.tiles_div.children().addClass(\"remove\");\n\n var // Tile width in bases.\n tile_width = Math.floor(TILE_SIZE * resolution),\n // Index of first tile that overlaps visible region.\n tile_index = Math.floor(low / tile_width),\n tile_region,\n tile_promise,\n tile_promises = [],\n tiles = [];\n // Draw tiles.\n while (tile_index * tile_width < high) {\n // Get tile region.\n tile_region = new visualization.GenomeRegion({\n chrom: this.view.chrom,\n start: tile_index * tile_width,\n // Tile high cannot be larger than view.max_high, which the chromosome length.\n end: Math.min(\n (tile_index + 1) * tile_width,\n this.view.max_high\n )\n });\n tile_promise = this.draw_helper(\n tile_region,\n w_scale,\n options\n );\n tile_promises.push(tile_promise);\n $.when(tile_promise).then(function(tile) {\n tiles.push(tile);\n });\n\n // Go to next tile.\n tile_index += 1;\n }\n\n // Step (c) for (re)moving tiles when clear_after is false.\n if (!clear_after) {\n this.tiles_div\n .children(\".remove\")\n .removeClass(\"remove\")\n .remove();\n }\n\n // When all tiles are drawn, call post-draw actions.\n var track = this;\n $.when.apply($, tile_promises).then(function() {\n // Step (c) for (re)moving tiles when clear_after is true:\n track.tiles_div.children(\".remove\").remove();\n\n // Only do postdraw actions for tiles; instances where tiles may not be drawn include:\n // (a) ReferenceTrack without sufficient resolution;\n // (b) data_fetch = false.\n tiles = _.filter(tiles, function(t) {\n return t !== null;\n });\n if (tiles.length !== 0) {\n track.postdraw_actions(\n tiles,\n width,\n w_scale,\n clear_after\n );\n }\n });\n },\n\n /**\n * Add a maximum/minimum label to track.\n */\n _add_yaxis_label: function(type, on_change) {\n var track = this,\n css_class = type === \"max\" ? \"top\" : \"bottom\",\n text = type === \"max\" ? \"max\" : \"min\",\n pref_name = type === \"max\" ? \"max_value\" : \"min_value\",\n label = this.container_div.find(\".yaxislabel.\" + css_class),\n value = round(track.config.get_value(pref_name), 1);\n\n // Default action for on_change is to redraw track.\n on_change =\n on_change ||\n function() {\n track.request_draw({ clear_tile_cache: true });\n };\n\n if (label.length !== 0) {\n // Label already exists, so update value.\n label.text(value);\n } else {\n // Add label.\n label = $(\"\")\n .text(value)\n .make_text_editable({\n num_cols: 12,\n on_finish: function(new_val) {\n $(\".tooltip\").remove();\n track.config.set_value(\n pref_name,\n round(new_val, 1)\n );\n on_change();\n },\n help_text: \"Set \" + text + \" value\"\n })\n .addClass(\"yaxislabel \" + css_class)\n .css(\"color\", this.config.get_value(\"label_color\"));\n this.container_div.prepend(label);\n }\n },\n\n /**\n * Actions to be taken after draw has been completed. Draw is completed when all tiles have been\n * drawn/fetched and shown.\n */\n postdraw_actions: function(tiles, width, w_scale, clear_after) {\n var line_track_tiles = _.filter(tiles, function(tile) {\n return tile instanceof LineTrackTile;\n });\n\n //\n // Take different actions depending on whether there are LineTrack/Coverage tiles.\n //\n\n if (line_track_tiles.length > 0) {\n // -- Drawing in Coverage mode. --\n\n // Clear because this is set when drawing.\n this.max_height_px = 0;\n var track = this;\n _.each(tiles, function(tile) {\n if (!(tile instanceof LineTrackTile)) {\n tile.html_elt.remove();\n track.draw_helper(tile.region, w_scale, {\n force: true,\n mode: \"Coverage\"\n });\n }\n });\n\n track._add_yaxis_label(\"max\");\n } else {\n // -- Drawing in non-Coverage mode. --\n\n // Remove Y-axis labels because there are no line track tiles.\n this.container_div.find(\".yaxislabel\").remove();\n\n //\n // If some tiles have icons, set padding of tiles without icons so features and rows align.\n //\n var icons_present = _.find(tiles, function(tile) {\n return tile.has_icons;\n });\n\n if (icons_present) {\n _.each(tiles, function(tile) {\n if (!tile.has_icons) {\n // Need to align with other tile(s) that have icons.\n tile.html_elt.css(\"padding-top\", ERROR_PADDING);\n }\n });\n }\n }\n },\n\n /**\n * Returns appropriate display mode based on data.\n */\n get_mode: function(data) {\n return this.mode;\n },\n\n /**\n * Update track interface to show display mode being used.\n */\n update_auto_mode: function(display_mode) {\n // FIXME: needs to be implemented.\n },\n\n /**\n * Returns a list of drawables to draw. Defaults to current track.\n */\n _get_drawables: function() {\n return [this];\n },\n\n /**\n * Retrieves from cache, draws, or sets up drawing for a single tile. Returns either a Tile object or a\n * jQuery.Deferred object that is fulfilled when tile can be drawn again. Options include:\n * -force: force a redraw rather than use cached tiles (default: false)\n * -data_fetch: fetch data if necessary (default: true)\n */\n draw_helper: function(region, w_scale, options) {\n // Init options if necessary to avoid having to check if options defined.\n if (!options) {\n options = {};\n }\n\n var force = options.force,\n mode = options.mode || this.mode,\n resolution = 1 / w_scale,\n // Useful vars.\n track = this,\n drawables = this._get_drawables(),\n key = this._gen_tile_cache_key(w_scale, region),\n is_tile = function(o) {\n return o && \"track\" in o;\n };\n\n // Check tile cache, if found show existing tile in correct position\n var tile = force ? undefined : track.tile_cache.get_elt(key);\n if (tile) {\n if (is_tile(tile)) {\n track.show_tile(tile, w_scale);\n }\n return tile;\n }\n\n // If not fetching data, nothing more to do because data is needed to draw tile.\n if (options.data_fetch === false) {\n return null;\n }\n\n // Function that returns data/Deferreds needed to draw tile.\n var get_tile_data = function() {\n // HACK: if display mode (mode) is in continuous data modes, data mode must be coverage to get coverage data.\n var data_mode = _.find(CONTINUOUS_DATA_MODES, function(m) {\n return m === mode;\n })\n ? \"Coverage\"\n : mode;\n\n // Map drawable object to data needed for drawing.\n var tile_data = _.map(drawables, function(d) {\n // Get the track data/promise.\n return d.data_manager.get_data(\n region,\n data_mode,\n resolution,\n track.data_url_extra_params\n );\n });\n\n // Get reference data/promise.\n if (view.reference_track) {\n tile_data.push(\n view.reference_track.data_manager.get_data(\n region,\n mode,\n resolution,\n view.reference_track.data_url_extra_params\n )\n );\n }\n\n return tile_data;\n };\n\n //\n // When data is available, draw tile.\n //\n var tile_drawn = $.Deferred();\n track.tile_cache.set_elt(key, tile_drawn);\n $.when.apply($, get_tile_data()).then(function() {\n var tile_data = get_tile_data(),\n tracks_data = tile_data,\n seq_data;\n\n // Deferreds may show up here if trying to fetch a subset of data from a superset data chunk\n // that cannot be subsetted. This may occur if the superset has a message. If there is a\n // Deferred, try again from the top. NOTE: this condition could (should?) be handled by the\n // GenomeDataManager in visualization module.\n if (\n _.find(tile_data, function(d) {\n return util.is_deferred(d);\n })\n ) {\n track.tile_cache.set_elt(key, undefined);\n $.when(\n track.draw_helper(region, w_scale, options)\n ).then(function(tile) {\n tile_drawn.resolve(tile);\n });\n return;\n }\n\n // If sequence data is available, subset to get only data in region.\n if (view.reference_track) {\n seq_data = view.reference_track.data_manager.subset_entry(\n tile_data.pop(),\n region\n );\n }\n\n // Get drawing modes, heights for all tracks.\n var drawing_modes = [],\n drawing_heights = [];\n\n _.each(drawables, function(d, i) {\n var mode = d.mode,\n data = tracks_data[i];\n if (mode === \"Auto\") {\n mode = d.get_mode(data);\n d.update_auto_mode(mode);\n }\n drawing_modes.push(mode);\n drawing_heights.push(\n d.get_canvas_height(data, mode, w_scale, width)\n );\n });\n\n var canvas = track.view.canvas_manager.new_canvas(),\n tile_low = region.get(\"start\"),\n tile_high = region.get(\"end\"),\n all_data_index = 0,\n width =\n Math.ceil((tile_high - tile_low) * w_scale) +\n track.left_offset,\n height = _.max(drawing_heights),\n tile;\n\n //\n // Draw all tracks on tile.\n //\n canvas.width = width;\n // Height is specified in options or is the height found above.\n canvas.height = options.height || height;\n var ctx = canvas.getContext(\"2d\");\n ctx.translate(track.left_offset, 0);\n if (drawables.length > 1) {\n ctx.globalAlpha = 0.5;\n ctx.globalCompositeOperation = \"source-over\";\n }\n _.each(drawables, function(d, i) {\n tile = d.draw_tile(\n tracks_data[i],\n ctx,\n drawing_modes[i],\n region,\n w_scale,\n seq_data\n );\n });\n\n // Don't cache, show if no tile.\n if (tile !== undefined) {\n track.tile_cache.set_elt(key, tile);\n track.show_tile(tile, w_scale);\n }\n\n tile_drawn.resolve(tile);\n });\n\n return tile_drawn;\n },\n\n /**\n * Returns canvas height needed to display data; return value is an integer that denotes the\n * number of pixels required.\n */\n get_canvas_height: function(result, mode, w_scale, canvas_width) {\n return this.visible_height_px;\n },\n\n /**\n * Draw line (bigwig) data onto tile.\n */\n _draw_line_track_tile: function(\n result,\n ctx,\n mode,\n region,\n w_scale\n ) {\n // Set min/max if they are not already set.\n // FIXME: checking for different null/undefined/0 is messy; it would be nice to\n // standardize this.\n if (\n [undefined, null].indexOf(\n this.config.get_value(\"min_value\")\n ) !== -1\n ) {\n this.config.set_value(\"min_value\", 0);\n }\n if (\n [undefined, null, 0].indexOf(\n this.config.get_value(\"max_value\")\n ) !== -1\n ) {\n this.config.set_value(\n \"max_value\",\n _.max(\n _.map(result.data, function(d) {\n return d[1];\n })\n ) || 0\n );\n }\n\n var canvas = ctx.canvas,\n painter = new painters.LinePainter(\n result.data,\n region.get(\"start\"),\n region.get(\"end\"),\n this.config.to_key_value_dict(),\n mode\n );\n painter.draw(ctx, canvas.width, canvas.height, w_scale);\n\n return new LineTrackTile(\n this,\n region,\n w_scale,\n canvas,\n result.data\n );\n },\n\n /**\n * Draw a track tile.\n * @param result result from server\n * @param ctx canvas context to draw on\n * @param mode mode to draw in\n * @param region region to draw on tile\n * @param w_scale pixels per base\n * @param ref_seq reference sequence data\n */\n draw_tile: function(result, ctx, mode, region, w_scale, ref_seq) {},\n\n /**\n * Show track tile and perform associated actions. Showing tile may actually move\n * an existing tile rather than reshowing it.\n */\n show_tile: function(tile, w_scale) {\n var track = this,\n tile_element = tile.html_elt;\n\n // -- Show/move tile element. --\n\n tile.predisplay_actions();\n\n // Position tile element based on current viewport.\n var left = Math.round(\n (tile.low -\n (this.is_overview\n ? this.view.max_low\n : this.view.low)) *\n w_scale\n );\n if (this.left_offset) {\n left -= this.left_offset;\n }\n tile_element.css(\"left\", left);\n\n if (tile_element.hasClass(\"remove\")) {\n // Step (b) for (re)moving tiles. See _draw() function for description of algorithm\n // for removing tiles.\n tile_element.removeClass(\"remove\");\n } else {\n // Showing new tile.\n this.tiles_div.append(tile_element);\n }\n\n // -- Update track, tile heights based on new tile. --\n\n tile_element.css(\"height\", \"auto\");\n\n // Update max height based on current tile's height.\n // BUG/HACK: tile_element.height() returns a height that is always 2 pixels too big, so\n // -2 to get the correct height.\n this.max_height_px = Math.max(\n this.max_height_px,\n tile_element.height() - 2\n );\n\n // Update height for all tiles based on max height.\n tile_element\n .parent()\n .children()\n .css(\"height\", this.max_height_px + \"px\");\n\n // Update track height based on max height and visible height.\n var track_height = this.max_height_px;\n if (this.visible_height_px !== 0) {\n track_height = Math.min(\n this.max_height_px,\n this.visible_height_px\n );\n }\n this.tiles_div.css(\"height\", track_height + \"px\");\n },\n\n /**\n * Utility function that creates a label string describing the region and parameters of a track's tool.\n */\n tool_region_and_parameters_str: function(region) {\n var track = this,\n region_str =\n region !== undefined ? region.toString() : \"all\",\n param_str = _.values(track.tool.get_inputs_dict()).join(\n \", \"\n );\n return (\n \" - region=[\" +\n region_str +\n \"], parameters=[\" +\n param_str +\n \"]\"\n );\n },\n\n /**\n * Returns true if data is compatible with a given mode.\n */\n data_and_mode_compatible: function(data, mode) {\n // Only handle modes that user can set.\n if (mode === \"Auto\") {\n return true;\n } else if (mode === \"Coverage\") {\n // Histogram mode requires bigwig data.\n return data.dataset_type === \"bigwig\";\n } else if (\n data.dataset_type === \"bigwig\" ||\n data.extra_info === \"no_detail\"\n ) {\n // All other modes--Dense, Squish, Pack--require data + details.\n return false;\n } else {\n return true;\n }\n },\n\n /**\n * Returns true if entry can be subsetted.\n */\n can_subset: function(entry) {\n // Do not subset entries with a message or data with no detail.\n if (entry.message || entry.extra_info === \"no_detail\") {\n return false;\n } else if (entry.dataset_type === \"bigwig\") {\n // Subset only if data is single-bp resolution.\n return entry.data[1][0] - entry.data[0][0] === 1;\n }\n\n return true;\n },\n\n /**\n * Set up track to receive tool data.\n */\n init_for_tool_data: function() {\n // Set up track to fetch raw data rather than converted data.\n this.data_manager.set(\"data_type\", \"raw_data\");\n this.data_query_wait = 1000;\n this.dataset_check_type = \"state\";\n\n // FIXME: this is optional and is disabled for now because it creates\n // additional converter jobs without a clear benefit because indexing\n // such a small dataset provides little benefit.\n //\n // Set up one-time, post-draw to clear tool execution settings.\n //\n /*\n this.normal_postdraw_actions = this.postdraw_actions;\n this.postdraw_actions = function(tiles, width, w_scale, clear_after) {\n var self = this;\n\n // Do normal postdraw init.\n self.normal_postdraw_actions(tiles, width, w_scale, clear_after);\n\n // Tool-execution specific post-draw init:\n\n // Reset dataset check, wait time.\n self.dataset_check_type = 'converted_datasets_state';\n self.data_query_wait = DEFAULT_DATA_QUERY_WAIT;\n\n // Reset data URL when dataset indexing has completed/when not pending.\n var ss_deferred = new util.ServerStateDeferred({\n url: self.dataset_state_url,\n url_params: {dataset_id : self.dataset.id, hda_ldda: self.dataset.get('hda_ldda')},\n interval: self.data_query_wait,\n // Set up deferred to check dataset state until it is not pending.\n success_fn: function(result) { return result !== \"pending\"; }\n });\n $.when(ss_deferred.go()).then(function() {\n // Dataset is indexed, so use converted data.\n self.data_manager.set('data_type', 'data');\n });\n\n // Reset post-draw actions function.\n self.postdraw_actions = self.normal_postdraw_actions;\n };\n */\n }\n });\n\n var LabelTrack = function(view, container) {\n Track.call(this, view, container, {\n resize: false,\n header: false\n });\n this.container_div.addClass(\"label-track\");\n };\n extend(LabelTrack.prototype, Track.prototype, {\n init: function() {\n // Enable by default because there should always be data when drawing track.\n this.enabled = true;\n },\n\n /**\n * Additional initialization required before drawing track for the first time.\n */\n predraw_init: function() {},\n\n _draw: function(options) {\n var view = this.view,\n range = view.high - view.low,\n tickDistance = Math.floor(\n Math.pow(10, Math.floor(Math.log(range) / Math.log(10)))\n ),\n position =\n Math.floor(view.low / tickDistance) * tickDistance,\n width = this.view.container.width(),\n new_div = $(\"\").addClass(\"label-container\");\n while (position < view.high) {\n var screenPosition = Math.floor(\n (position - view.low) / range * width\n );\n new_div.append(\n $(\"\")\n .addClass(\"pos-label\")\n .text(util.commatize(position))\n .css({\n left: screenPosition\n })\n );\n position += tickDistance;\n }\n this.content_div.children(\":first\").remove();\n this.content_div.append(new_div);\n }\n });\n\n // FIXME: Composite tracks have code for showing composite tracks with line tracks and\n // composite tracks with line + feature tracks. It's probably best if different classes\n // are created for each type of composite track.\n\n /**\n * A tiled track composed of multiple other tracks. Composite tracks only work with\n * bigwig data for now.\n */\n var CompositeTrack = function(view, container, obj_dict) {\n TiledTrack.call(this, view, container, obj_dict);\n\n // Init drawables; each drawable is a copy so that config/preferences\n // are independent of each other. Also init left offset.\n this.drawables = [];\n if (\"drawables\" in obj_dict) {\n var drawable;\n for (var i = 0; i < obj_dict.drawables.length; i++) {\n drawable = obj_dict.drawables[i];\n this.drawables[i] = object_from_template(\n drawable,\n view,\n null\n );\n\n // Track's left offset is the max of all tracks.\n if (drawable.left_offset > this.left_offset) {\n this.left_offset = drawable.left_offset;\n }\n }\n this.enabled = true;\n }\n\n // Set all feature tracks to use Coverage mode.\n _.each(this.drawables, function(d) {\n if (d instanceof FeatureTrack || d instanceof ReadTrack) {\n d.change_mode(\"Coverage\");\n }\n });\n\n this.update_icons();\n\n // HACK: needed for saving object for now. Need to generalize get_type() to all Drawables and use\n // that for object type.\n this.obj_type = \"CompositeTrack\";\n };\n\n extend(CompositeTrack.prototype, TiledTrack.prototype, {\n display_modes: CONTINUOUS_DATA_MODES,\n\n build_config_params: function() {\n return _.union(Drawable.prototype.config_params, [\n {\n key: \"min_value\",\n label: \"Min Value\",\n type: \"float\",\n default_value: undefined\n },\n {\n key: \"max_value\",\n label: \"Max Value\",\n type: \"float\",\n default_value: undefined\n },\n {\n key: \"mode\",\n type: \"string\",\n default_value: this.mode,\n hidden: true\n },\n {\n key: \"height\",\n type: \"int\",\n default_value: 30,\n hidden: true\n }\n ]);\n },\n\n action_icons_def: [\n // Create composite track from group's tracks.\n {\n name: \"composite_icon\",\n title: \"Show individual tracks\",\n css_class: \"layers-stack\",\n on_click_fn: function(track) {\n $(\".tooltip\").remove();\n track.show_group();\n }\n }\n ].concat(TiledTrack.prototype.action_icons_def),\n\n // HACK: CompositeTrack should inherit from DrawableCollection as well.\n /**\n * Returns representation of object in a dictionary for easy saving.\n * Use from_dict to recreate object.\n */\n to_dict: DrawableCollection.prototype.to_dict,\n\n add_drawable: DrawableCollection.prototype.add_drawable,\n\n unpack_drawables: DrawableCollection.prototype.unpack_drawables,\n\n config_onchange: function() {\n this.set_name(this.config.get_value(\"name\"));\n this.request_draw({ clear_tile_cache: true });\n },\n\n /**\n * Action to take during resize.\n */\n on_resize: function() {\n // Propogate visible height to other tracks.\n var visible_height = this.visible_height_px;\n _.each(this.drawables, function(d) {\n d.visible_height_px = visible_height;\n });\n Track.prototype.on_resize.call(this);\n },\n\n /**\n * Change mode for all tracks.\n */\n change_mode: function(new_mode) {\n TiledTrack.prototype.change_mode.call(this, new_mode);\n for (var i = 0; i < this.drawables.length; i++) {\n this.drawables[i].change_mode(new_mode);\n }\n },\n\n /**\n * Initialize component tracks and draw composite track when all components are initialized.\n */\n init: function() {\n // Init components.\n var init_deferreds = [];\n for (var i = 0; i < this.drawables.length; i++) {\n init_deferreds.push(this.drawables[i].init());\n }\n\n // Draw composite when all tracks available.\n var track = this;\n $.when.apply($, init_deferreds).then(function() {\n track.enabled = true;\n track.request_draw();\n });\n },\n\n update_icons: function() {\n // For now, hide filters and tool.\n this.action_icons.filters_icon.hide();\n this.action_icons.tools_icon.hide();\n this.action_icons.param_space_viz_icon.hide();\n },\n\n can_draw: Drawable.prototype.can_draw,\n\n _get_drawables: function() {\n return this.drawables;\n },\n\n /**\n * Replace this track with group that includes individual tracks.\n */\n show_group: function() {\n // Create group with individual tracks.\n var group = new DrawableGroup(this.view, this.container, {\n name: this.config.get_value(\"name\")\n }),\n track;\n for (var i = 0; i < this.drawables.length; i++) {\n track = this.drawables[i];\n track.update_icons();\n group.add_drawable(track);\n track.container = group;\n group.content_div.append(track.container_div);\n }\n\n // Replace track with group.\n var index = this.container.replace_drawable(this, group, true);\n group.request_draw({ clear_tile_cache: true });\n },\n\n /**\n * Actions taken before drawing.\n */\n before_draw: function() {\n // FIXME: this is needed only if there are feature tracks in the composite track.\n // TiledTrack.prototype.before_draw.call(this);\n\n //\n // Set min, max for tracks to be largest min, max.\n //\n\n // Get smallest min, biggest max.\n var min = _.min(\n _.map(this.drawables, function(d) {\n return d.config.get_value(\"min_value\");\n })\n ),\n max = _.max(\n _.map(this.drawables, function(d) {\n return d.config.get_value(\"max_value\");\n })\n );\n\n this.config.set_value(\"min_value\", min);\n this.config.set_value(\"max_value\", max);\n\n // Set all tracks to smallest min, biggest max.\n _.each(this.drawables, function(d) {\n d.config.set_value(\"min_value\", min);\n d.config.set_value(\"max_value\", max);\n });\n },\n\n /**\n * Update minimum, maximum for component tracks.\n */\n update_all_min_max: function() {\n var track = this,\n min_value = this.config.get_value(\"min_value\"),\n max_value = this.config.get_value(\"max_value\");\n _.each(this.drawables, function(d) {\n d.config.set_value(\"min_value\", min_value);\n d.config.set_value(\"max_value\", max_value);\n });\n this.request_draw({ clear_tile_cache: true });\n },\n\n /**\n * Actions to be taken after draw has been completed. Draw is completed when all tiles have been\n * drawn/fetched and shown.\n */\n postdraw_actions: function(tiles, width, w_scale, clear_after) {\n // All tiles must be the same height in order to draw LineTracks, so redraw tiles as needed.\n var max_height = -1,\n i;\n for (i = 0; i < tiles.length; i++) {\n var height = tiles[i].html_elt.find(\"canvas\").height();\n if (height > max_height) {\n max_height = height;\n }\n }\n\n for (i = 0; i < tiles.length; i++) {\n var tile = tiles[i];\n if (tile.html_elt.find(\"canvas\").height() !== max_height) {\n this.draw_helper(tile.region, w_scale, {\n force: true,\n height: max_height\n });\n tile.html_elt.remove();\n }\n }\n\n // Wrap function so that it can be called without object reference.\n var track = this,\n t = function() {\n track.update_all_min_max();\n };\n\n // Add min, max labels.\n this._add_yaxis_label(\"min\", t);\n this._add_yaxis_label(\"max\", t);\n }\n });\n\n /**\n * Displays reference genome data.\n */\n var ReferenceTrack = function(view) {\n TiledTrack.call(\n this,\n view,\n { content_div: view.top_labeltrack },\n { resize: false, header: false }\n );\n\n // Use offset to ensure that bases at tile edges are drawn.\n this.left_offset = view.canvas_manager.char_width_px;\n this.container_div.addClass(\"reference-track\");\n this.data_url = Galaxy.root + \"api/genomes/\" + this.view.dbkey;\n this.data_url_extra_params = { reference: true };\n this.data_manager = new visualization.GenomeReferenceDataManager({\n data_url: this.data_url,\n can_subset: this.can_subset\n });\n this.hide_contents();\n };\n extend(\n ReferenceTrack.prototype,\n Drawable.prototype,\n TiledTrack.prototype,\n {\n build_config_params: function() {\n return _.union(Drawable.prototype.config_params, [\n {\n key: \"height\",\n type: \"int\",\n default_value: 13,\n hidden: true\n }\n ]);\n },\n\n init: function() {\n this.data_manager.clear();\n // Enable by default because there should always be data when drawing track.\n this.enabled = true;\n },\n\n /**\n * Additional initialization required before drawing track for the first time.\n */\n predraw_init: function() {},\n\n can_draw: Drawable.prototype.can_draw,\n\n /**\n * Draws and shows tile if reference data can be displayed; otherwise track is hidden.\n */\n draw_helper: function(region, w_scale, options) {\n var cur_visible = this.tiles_div.is(\":visible\"),\n new_visible,\n tile = null;\n if (w_scale > this.view.canvas_manager.char_width_px) {\n this.tiles_div.show();\n new_visible = true;\n tile = TiledTrack.prototype.draw_helper.call(\n this,\n region,\n w_scale,\n options\n );\n } else {\n new_visible = false;\n this.tiles_div.hide();\n }\n\n // NOTE: viewport resizing conceptually belongs in postdraw_actions(), but currently\n // postdraw_actions is not called when reference track not shown due to no tiles. If\n // it is moved to postdraw_actions, resize must be called each time because cannot\n // easily detect showing/hiding.\n\n // If showing or hiding reference track, resize viewport.\n if (cur_visible !== new_visible) {\n this.view.resize_viewport();\n }\n\n return tile;\n },\n\n can_subset: function(entry) {\n return true;\n },\n\n /**\n * Draw ReferenceTrack tile.\n */\n draw_tile: function(data, ctx, mode, region, w_scale) {\n // Try to subset data.\n var subset = this.data_manager.subset_entry(data, region),\n seq_data = subset.data;\n\n // Draw sequence data.\n var canvas = ctx.canvas;\n ctx.font = ctx.canvas.manager.default_font;\n ctx.textAlign = \"center\";\n for (\n var c = 0, str_len = seq_data.length;\n c < str_len;\n c++\n ) {\n ctx.fillStyle = this.view.get_base_color(seq_data[c]);\n ctx.fillText(seq_data[c], Math.floor(c * w_scale), 10);\n }\n return new Tile(this, region, w_scale, canvas, subset);\n }\n }\n );\n\n /**\n * Track displays continuous/numerical data. Track expects position data in 1-based format, i.e. wiggle format.\n */\n var LineTrack = function(view, container, obj_dict) {\n this.mode = \"Histogram\";\n TiledTrack.call(this, view, container, obj_dict);\n // Need left offset for drawing overlap near tile boundaries.\n this.left_offset = 30;\n\n // If server has byte-range support, use BBI data manager to read directly from the BBI file.\n // FIXME: there should be a flag to wait for this check to complete before loading the track.\n var self = this;\n $.when(\n supportsByteRanges(\n Galaxy.root + \"datasets/\" + this.dataset.id + \"/display\"\n )\n ).then(function(supportsByteRanges) {\n if (supportsByteRanges) {\n self.data_manager = new bbi.BBIDataManager({\n dataset: self.dataset\n });\n }\n });\n };\n\n extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {\n display_modes: CONTINUOUS_DATA_MODES,\n\n build_config_params: function() {\n return _.union(Drawable.prototype.config_params, [\n { key: \"color\", label: \"Color\", type: \"color\" },\n {\n key: \"min_value\",\n label: \"Min Value\",\n type: \"float\",\n default_value: undefined\n },\n {\n key: \"max_value\",\n label: \"Max Value\",\n type: \"float\",\n default_value: undefined\n },\n {\n key: \"mode\",\n type: \"string\",\n default_value: this.mode,\n hidden: true\n },\n {\n key: \"height\",\n type: \"int\",\n default_value: 30,\n hidden: true\n }\n ]);\n },\n\n config_onchange: function() {\n this.set_name(this.config.get_value(\"name\"));\n this.request_draw({ clear_tile_cache: true });\n },\n\n /**\n * Actions to be taken before drawing.\n */\n // FIXME: can the default behavior be used; right now it breaks during resize.\n before_draw: function() {},\n\n /**\n * Draw track tile.\n */\n draw_tile: function(result, ctx, mode, region, w_scale) {\n return this._draw_line_track_tile(\n result,\n ctx,\n mode,\n region,\n w_scale\n );\n },\n\n /**\n * Subset data only if data is at single-base pair resolution.\n */\n can_subset: function(entry) {\n return entry.data[1][0] - entry.data[0][0] === 1;\n },\n\n /**\n * Add min, max labels.\n */\n postdraw_actions: function(tiles, width, w_scale, clear_after) {\n // Add min, max labels.\n this._add_yaxis_label(\"max\");\n this._add_yaxis_label(\"min\");\n }\n });\n\n /**\n * Diagonal heatmap for showing interactions data.\n */\n var DiagonalHeatmapTrack = function(view, container, obj_dict) {\n this.mode = \"Heatmap\";\n TiledTrack.call(this, view, container, obj_dict);\n };\n\n extend(\n DiagonalHeatmapTrack.prototype,\n Drawable.prototype,\n TiledTrack.prototype,\n {\n display_modes: [\"Heatmap\"],\n\n build_config_params: function() {\n return _.union(Drawable.prototype.config_params, [\n {\n key: \"pos_color\",\n label: \"Positive Color\",\n type: \"color\",\n default_value: \"#FF8C00\"\n },\n {\n key: \"neg_color\",\n label: \"Negative Color\",\n type: \"color\",\n default_value: \"#4169E1\"\n },\n {\n key: \"min_value\",\n label: \"Min Value\",\n type: \"int\",\n default_value: undefined\n },\n {\n key: \"max_value\",\n label: \"Max Value\",\n type: \"int\",\n default_value: undefined\n },\n {\n key: \"mode\",\n type: \"string\",\n default_value: this.mode,\n hidden: true\n },\n {\n key: \"height\",\n type: \"int\",\n default_value: 500,\n hidden: true\n }\n ]);\n },\n\n config_onchange: function() {\n this.set_name(this.config.get_value(\"name\"));\n this.request_draw({ clear_tile_cache: true });\n },\n\n /**\n * Additional initialization required before drawing track for the first time.\n */\n predraw_init: function() {\n var track = this;\n return $.getJSON(\n track.dataset.url(),\n {\n data_type: \"data\",\n stats: true,\n chrom: track.view.chrom,\n low: 0,\n high: track.view.max_high,\n hda_ldda: track.dataset.get(\"hda_ldda\")\n },\n function(result) {\n var data = result.data;\n }\n );\n },\n\n /**\n * Draw tile.\n */\n draw_tile: function(result, ctx, mode, region, w_scale) {\n // Paint onto canvas.\n var canvas = ctx.canvas,\n painter = new painters.DiagonalHeatmapPainter(\n result.data,\n region.get(\"start\"),\n region.get(\"end\"),\n this.config.to_key_value_dict(),\n mode\n );\n painter.draw(ctx, canvas.width, canvas.height, w_scale);\n\n return new Tile(this, region, w_scale, canvas, result.data);\n }\n }\n );\n\n /**\n * A track that displays features/regions. Track expects position data in BED format, i.e. 0-based, half-open.\n */\n var FeatureTrack = function(view, container, obj_dict) {\n TiledTrack.call(this, view, container, obj_dict);\n this.container_div.addClass(\"feature-track\");\n this.summary_draw_height = 30;\n this.slotters = {};\n this.start_end_dct = {};\n this.left_offset = 200;\n\n // this.painter = painters.LinkedFeaturePainter;\n this.set_painter_from_config();\n };\n extend(\n FeatureTrack.prototype,\n Drawable.prototype,\n TiledTrack.prototype,\n {\n display_modes: [\"Auto\", \"Coverage\", \"Dense\", \"Squish\", \"Pack\"],\n\n build_config_params: function() {\n return _.union(Drawable.prototype.config_params, [\n {\n key: \"block_color\",\n label: \"Block color\",\n type: \"color\"\n },\n {\n key: \"reverse_strand_color\",\n label: \"Antisense strand color\",\n type: \"color\"\n },\n {\n key: \"label_color\",\n label: \"Label color\",\n type: \"color\",\n default_value: \"black\"\n },\n {\n key: \"show_counts\",\n label: \"Show summary counts\",\n type: \"bool\",\n default_value: true,\n help:\n \"Show the number of items in each bin when drawing summary histogram\"\n },\n {\n key: \"min_value\",\n label: \"Histogram minimum\",\n type: \"float\",\n default_value: undefined,\n help: \"clear value to set automatically\"\n },\n {\n key: \"max_value\",\n label: \"Histogram maximum\",\n type: \"float\",\n default_value: undefined,\n help: \"clear value to set automatically\"\n },\n {\n key: \"connector_style\",\n label: \"Connector style\",\n type: \"select\",\n default_value: \"fishbones\",\n options: [\n {\n label: \"Line with arrows\",\n value: \"fishbone\"\n },\n { label: \"Arcs\", value: \"arcs\" }\n ]\n },\n {\n key: \"mode\",\n type: \"string\",\n default_value: this.mode,\n hidden: true\n },\n {\n key: \"height\",\n type: \"int\",\n default_value: 0,\n hidden: true\n }\n ]);\n },\n\n config_onchange: function() {\n this.set_name(this.config.get_value(\"name\"));\n this.set_painter_from_config();\n this.request_draw({ clear_tile_cache: true });\n },\n\n set_painter_from_config: function() {\n if (this.config.get_value(\"connector_style\") === \"arcs\") {\n this.painter = painters.ArcLinkedFeaturePainter;\n } else {\n this.painter = painters.LinkedFeaturePainter;\n }\n },\n\n /**\n * Actions to be taken after draw has been completed. Draw is completed when all tiles have been\n * drawn/fetched and shown.\n */\n postdraw_actions: function(tiles, width, w_scale, clear_after) {\n TiledTrack.prototype.postdraw_actions.call(\n this,\n tiles,\n width,\n w_scale,\n clear_after\n );\n\n var track = this,\n i,\n line_track_tiles = _.filter(tiles, function(t) {\n return t instanceof LineTrackTile;\n });\n\n //\n // Finish drawing of features that span multiple tiles. Features that span multiple tiles\n // are labeled incomplete on the tile level because they cannot be completely drawn.\n //\n if (line_track_tiles.length === 0) {\n // Gather incomplete features together.\n var all_incomplete_features = {};\n _.each(_.pluck(tiles, \"incomplete_features\"), function(\n inc_features\n ) {\n _.each(inc_features, function(feature) {\n all_incomplete_features[feature[0]] = feature;\n });\n });\n\n // Draw incomplete features on each tile.\n var self = this;\n _.each(tiles, function(tile) {\n // Remove features already drawn on tile originally.\n var tile_incomplete_features = _.omit(\n all_incomplete_features,\n _.map(tile.incomplete_features, function(f) {\n return f[0];\n })\n );\n\n // Remove features already drawn on tile in past postdraw actions.\n tile_incomplete_features = _.omit(\n tile_incomplete_features,\n _.keys(tile.other_tiles_features_drawn)\n );\n\n // Draw tile's incomplete features.\n if (_.size(tile_incomplete_features) !== 0) {\n // To draw incomplete features, create new canvas, copy original canvas/tile onto new\n // canvas, and then draw incomplete features on the new canvas.\n var features = {\n data: _.values(tile_incomplete_features)\n },\n new_canvas = self.view.canvas_manager.new_canvas(),\n new_canvas_ctx = new_canvas.getContext(\n \"2d\"\n );\n new_canvas.height = Math.max(\n tile.canvas.height,\n self.get_canvas_height(\n features,\n tile.mode,\n tile.w_scale,\n 100\n )\n );\n new_canvas.width = tile.canvas.width;\n new_canvas_ctx.drawImage(tile.canvas, 0, 0);\n new_canvas_ctx.translate(track.left_offset, 0);\n var new_tile = self.draw_tile(\n features,\n new_canvas_ctx,\n tile.mode,\n tile.region,\n tile.w_scale,\n tile.seq_data\n );\n $(tile.canvas).replaceWith($(new_tile.canvas));\n tile.canvas = new_canvas;\n _.extend(\n tile.other_tiles_features_drawn,\n all_incomplete_features\n );\n }\n });\n }\n\n // If mode is Coverage and tiles do not share max, redraw tiles as necessary using new max.\n /*\n This code isn't used right now because Coverage mode uses predefined max in preferences.\n if (track.mode === \"Coverage\") {\n // Get global max.\n var global_max = -1;\n for (i = 0; i < tiles.length; i++) {\n var cur_max = tiles[i].max_val;\n if (cur_max > global_max) {\n global_max = cur_max;\n }\n }\n\n for (i = 0; i < tiles.length; i++) {\n var tile = tiles[i];\n if (tile.max_val !== global_max) {\n tile.html_elt.remove();\n track.draw_helper(tile.index, w_scale, { more_tile_data: { force: true, max: global_max } } );\n }\n }\n }\n */\n\n //\n // Update filter attributes, UI.\n //\n\n // Update filtering UI.\n if (track.filters_manager) {\n var filters = track.filters_manager.filters,\n f;\n for (f = 0; f < filters.length; f++) {\n filters[f].update_ui_elt();\n }\n\n // Determine if filters are available; this is based on the tiles' data.\n // Criteria for filter to be available: (a) it is applicable to tile data and (b) filter min != filter max.\n var filters_available = false,\n example_feature,\n filter;\n for (i = 0; i < tiles.length; i++) {\n if (tiles[i].data.length) {\n example_feature = tiles[i].data[0];\n for (f = 0; f < filters.length; f++) {\n filter = filters[f];\n if (\n filter.applies_to(example_feature) &&\n filter.min !== filter.max\n ) {\n filters_available = true;\n break;\n }\n }\n }\n }\n\n // If filter availability changed, hide filter div if necessary and update menu.\n if (track.filters_available !== filters_available) {\n track.filters_available = filters_available;\n if (!track.filters_available) {\n track.filters_manager.hide();\n }\n track.update_icons();\n }\n }\n\n //\n // If not all features slotted, show icon for showing more rows (slots).\n //\n if (tiles[0] instanceof FeatureTrackTile) {\n var all_slotted = true;\n for (i = 0; i < tiles.length; i++) {\n if (!tiles[i].all_slotted) {\n all_slotted = false;\n break;\n }\n }\n this.action_icons.show_more_rows_icon.toggle(\n !all_slotted\n );\n } else {\n this.action_icons.show_more_rows_icon.hide();\n }\n },\n\n /**\n * Update track interface to show display mode being used.\n */\n update_auto_mode: function(mode) {\n if (this.mode === \"Auto\") {\n if (mode === \"no_detail\") {\n mode = \"feature spans\";\n }\n this.action_icons.mode_icon.attr(\n \"title\",\n \"Set display mode (now: Auto/\" + mode + \")\"\n );\n }\n },\n\n /**\n * Place features in slots for drawing (i.e. pack features).\n * this.slotters[level] is created in this method. this.slotters[level]\n * is a Slotter object. Returns the number of slots used to pack features.\n */\n incremental_slots: function(level, features, mode) {\n // Get/create incremental slots for level. If display mode changed,\n // need to create new slots.\n\n var dummy_context = this.view.canvas_manager.dummy_context,\n slotter = this.slotters[level];\n if (!slotter || slotter.mode !== mode) {\n slotter = new slotting.FeatureSlotter(\n level,\n mode,\n MAX_FEATURE_DEPTH,\n function(x) {\n return dummy_context.measureText(x);\n }\n );\n this.slotters[level] = slotter;\n }\n\n return slotter.slot_features(features);\n },\n\n /**\n * Returns appropriate display mode based on data.\n */\n get_mode: function(data) {\n var mode;\n // HACK: use no_detail mode track is in overview to prevent overview from being too large.\n if (data.extra_info === \"no_detail\" || this.is_overview) {\n mode = \"no_detail\";\n } else {\n // Choose b/t Squish and Pack.\n // Proxy measures for using Squish:\n // (a) error message re: limiting number of features shown;\n // (b) X number of features shown;\n // (c) size of view shown.\n // TODO: cannot use (a) and (b) because it requires coordinating mode across tiles;\n // fix this so that tiles are redrawn as necessary to use the same mode.\n //if ( (result.message && result.message.match(/^Only the first [\\d]+/)) ||\n // (result.data && result.data.length > 2000) ||\n //var data = result.data;\n // if ( (data.length && data.length < 4) ||\n // (this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH) ) {\n if (\n this.view.high - this.view.low >\n MIN_SQUISH_VIEW_WIDTH\n ) {\n mode = \"Squish\";\n } else {\n mode = \"Pack\";\n }\n }\n return mode;\n },\n\n /**\n * Returns canvas height needed to display data; return value is an integer that denotes the\n * number of pixels required.\n */\n get_canvas_height: function(\n result,\n mode,\n w_scale,\n canvas_width\n ) {\n if (\n mode === \"Coverage\" ||\n result.dataset_type === \"bigwig\"\n ) {\n return this.summary_draw_height;\n } else {\n // All other modes require slotting.\n var rows_required = this.incremental_slots(\n w_scale,\n result.data,\n mode\n );\n // HACK: use dummy painter to get required height. Painter should be extended so that get_required_height\n // works as a static function.\n var dummy_painter = new this.painter(\n null,\n null,\n null,\n this.config.to_key_value_dict(),\n mode\n );\n return Math.max(\n this.min_height_px,\n dummy_painter.get_required_height(\n rows_required,\n canvas_width\n )\n );\n }\n },\n\n /**\n * Draw FeatureTrack tile.\n * @param result result from server\n * @param cxt canvas context to draw on\n * @param mode mode to draw in\n * @param region region to draw on tile\n * @param w_scale pixels per base\n * @param ref_seq reference sequence data\n * @param cur_tile true if drawing is occurring on a currently visible tile.\n */\n draw_tile: function(\n result,\n ctx,\n mode,\n region,\n w_scale,\n ref_seq,\n cur_tile\n ) {\n var track = this,\n canvas = ctx.canvas,\n tile_low = region.get(\"start\"),\n tile_high = region.get(\"end\"),\n left_offset = this.left_offset;\n\n // If data is line track data, draw line track tile.\n if (result.dataset_type === \"bigwig\") {\n return this._draw_line_track_tile(\n result,\n ctx,\n mode,\n region,\n w_scale\n );\n }\n\n // Handle row-by-row tracks\n\n // Preprocessing: filter features and determine whether all unfiltered features have been slotted.\n var filtered = [],\n slots = this.slotters[w_scale].slots,\n all_slotted = true;\n if (result.data) {\n var filters = this.filters_manager.filters;\n for (\n var i = 0, len = result.data.length;\n i < len;\n i++\n ) {\n var feature = result.data[i];\n var hide_feature = false;\n var filter;\n for (\n var f = 0, flen = filters.length;\n f < flen;\n f++\n ) {\n filter = filters[f];\n filter.update_attrs(feature);\n if (!filter.keep(feature)) {\n hide_feature = true;\n break;\n }\n }\n if (!hide_feature) {\n // Feature visible.\n filtered.push(feature);\n // Set flag if not slotted.\n if (!(feature[0] in slots)) {\n all_slotted = false;\n }\n }\n }\n }\n\n // Create painter.\n var filter_alpha_scaler = this.filters_manager.alpha_filter\n ? new FilterScaler(\n this.filters_manager.alpha_filter\n )\n : null,\n filter_height_scaler = this.filters_manager\n .height_filter\n ? new FilterScaler(\n this.filters_manager.height_filter\n )\n : null,\n painter = new this.painter(\n filtered,\n tile_low,\n tile_high,\n this.config.to_key_value_dict(),\n mode,\n filter_alpha_scaler,\n filter_height_scaler,\n // HACK: ref_seq only be defined for ReadTracks, and only the ReadPainter accepts that argument\n ref_seq,\n // Only the ReadPainer will use this function\n function(b) {\n return track.view.get_base_color(b);\n }\n );\n var feature_mapper = null;\n\n ctx.fillStyle = this.config.get_value(\"block_color\");\n ctx.font = ctx.canvas.manager.default_font;\n ctx.textAlign = \"right\";\n\n if (result.data) {\n // Draw features.\n var draw_results = painter.draw(\n ctx,\n canvas.width,\n canvas.height,\n w_scale,\n slots\n );\n feature_mapper = draw_results.feature_mapper;\n incomplete_features = draw_results.incomplete_features;\n feature_mapper.translation = -left_offset;\n }\n\n // If not drawing on current tile, create new tile.\n if (!cur_tile) {\n return new FeatureTrackTile(\n track,\n region,\n w_scale,\n canvas,\n result.data,\n mode,\n result.message,\n all_slotted,\n feature_mapper,\n incomplete_features,\n ref_seq\n );\n }\n }\n }\n );\n\n /**\n * Displays variant data.\n */\n var VariantTrack = function(view, container, obj_dict) {\n TiledTrack.call(this, view, container, obj_dict);\n this.painter = painters.VariantPainter;\n this.summary_draw_height = 30;\n\n // Maximum resolution is ~45 pixels/base, so use this size left offset to ensure that full\n // variant is drawn when variant is at start of tile.\n this.left_offset = 30;\n };\n\n extend(\n VariantTrack.prototype,\n Drawable.prototype,\n TiledTrack.prototype,\n {\n display_modes: [\"Auto\", \"Coverage\", \"Dense\", \"Squish\", \"Pack\"],\n\n build_config_params: function() {\n return _.union(Drawable.prototype.config_params, [\n {\n key: \"color\",\n label: \"Histogram color\",\n type: \"color\"\n },\n {\n key: \"show_sample_data\",\n label: \"Show sample data\",\n type: \"bool\",\n default_value: true\n },\n {\n key: \"show_labels\",\n label: \"Show summary and sample labels\",\n type: \"bool\",\n default_value: true\n },\n {\n key: \"summary_height\",\n label: \"Locus summary height\",\n type: \"float\",\n default_value: 20\n },\n {\n key: \"mode\",\n type: \"string\",\n default_value: this.mode,\n hidden: true\n },\n {\n key: \"height\",\n type: \"int\",\n default_value: 0,\n hidden: true\n }\n ]);\n },\n\n config_onchange: function() {\n this.set_name(this.config.get_value(\"name\"));\n this.request_draw({ clear_tile_cache: true });\n },\n\n /**\n * Draw tile.\n */\n draw_tile: function(result, ctx, mode, region, w_scale) {\n // Data could be coverage data or variant data.\n if (result.dataset_type === \"bigwig\") {\n return this._draw_line_track_tile(\n result,\n ctx,\n \"Histogram\",\n region,\n w_scale\n );\n } else {\n // result.dataset_type === 'variant'\n var view = this.view,\n painter = new this.painter(\n result.data,\n region.get(\"start\"),\n region.get(\"end\"),\n this.config.to_key_value_dict(),\n mode,\n function(b) {\n return view.get_base_color(b);\n }\n );\n painter.draw(\n ctx,\n ctx.canvas.width,\n ctx.canvas.height,\n w_scale\n );\n return new Tile(\n this,\n region,\n w_scale,\n ctx.canvas,\n result.data\n );\n }\n },\n\n /**\n * Returns canvas height needed to display data; return value is an integer that denotes the\n * number of pixels required.\n */\n get_canvas_height: function(\n result,\n mode,\n w_scale,\n canvas_width\n ) {\n if (result.dataset_type === \"bigwig\") {\n return this.summary_draw_height;\n } else {\n // HACK: sample_names is not be defined when dataset definition is fetched before\n // dataset is complete (as is done when running tools). In that case, fall back on\n // # of samples in data. This can be fixed by re-requesting dataset definition\n // in init.\n var num_samples = this.dataset.get_metadata(\n \"sample_names\"\n )\n ? this.dataset.get_metadata(\"sample_names\").length\n : 0;\n if (num_samples === 0 && result.data.length !== 0) {\n // Sample data is separated by commas, so this computes # of samples:\n num_samples = result.data[0][7].match(/,/g);\n if (num_samples === null) {\n num_samples = 1;\n } else {\n num_samples = num_samples.length + 1;\n }\n }\n\n var dummy_painter = new this.painter(\n null,\n null,\n null,\n this.config.to_key_value_dict(),\n mode\n );\n return dummy_painter.get_required_height(num_samples);\n }\n },\n\n /**\n * Additional initialization required before drawing track for the first time.\n */\n predraw_init: function() {\n var deferreds = [Track.prototype.predraw_init.call(this)];\n // FIXME: updating dataset metadata is only needed for visual analysis. Can\n // this be moved somewhere else?\n if (!this.dataset.get_metadata(\"sample_names\")) {\n deferreds.push(this.dataset.fetch());\n }\n return deferreds;\n },\n\n /**\n * Actions to be taken after draw has been completed. 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Track expects position data in 1-based, closed format, i.e. SAM/BAM format.\n */\n var ReadTrack = function(view, container, obj_dict) {\n FeatureTrack.call(this, view, container, obj_dict);\n this.painter = painters.ReadPainter;\n this.update_icons();\n };\n\n extend(\n ReadTrack.prototype,\n Drawable.prototype,\n TiledTrack.prototype,\n FeatureTrack.prototype,\n {\n build_config_params: function() {\n return _.union(Drawable.prototype.config_params, [\n {\n key: \"block_color\",\n label: \"Histogram color\",\n type: \"color\"\n },\n {\n key: \"detail_block_color\",\n label: \"Sense strand block color\",\n type: \"color\",\n default_value: \"#AAAAAA\"\n },\n {\n key: \"reverse_strand_color\",\n label: \"Antisense strand block color\",\n type: \"color\",\n default_value: \"#DDDDDD\"\n },\n {\n key: \"label_color\",\n label: \"Label color\",\n type: \"color\",\n default_value: \"black\"\n },\n {\n key: \"show_insertions\",\n label: \"Show insertions\",\n type: \"bool\",\n default_value: false\n },\n {\n key: \"show_differences\",\n label: \"Show differences only\",\n type: \"bool\",\n default_value: true\n },\n {\n key: \"show_counts\",\n label: \"Show summary counts\",\n type: \"bool\",\n default_value: true\n },\n {\n key: \"mode\",\n type: \"string\",\n default_value: this.mode,\n hidden: true\n },\n {\n key: \"min_value\",\n label: \"Histogram minimum\",\n type: \"float\",\n default_value: undefined,\n help: \"clear value to set automatically\"\n },\n {\n key: \"max_value\",\n label: \"Histogram maximum\",\n type: \"float\",\n default_value: undefined,\n help: \"clear value to set automatically\"\n },\n {\n key: \"height\",\n type: \"int\",\n default_value: 0,\n hidden: true\n }\n ]);\n },\n\n config_onchange: function() {\n this.set_name(this.config.get_value(\"name\"));\n this.request_draw({ clear_tile_cache: true });\n }\n }\n );\n\n /**\n * Objects that can be added to a view.\n */\n var addable_objects = {\n CompositeTrack: CompositeTrack,\n DrawableGroup: DrawableGroup,\n DiagonalHeatmapTrack: DiagonalHeatmapTrack,\n FeatureTrack: FeatureTrack,\n LineTrack: LineTrack,\n ReadTrack: ReadTrack,\n VariantTrack: VariantTrack,\n // For backward compatibility, map vcf track to variant.\n VcfTrack: VariantTrack\n };\n\n /**\n * Create new object from a template. 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[\n \"libs/underscore\",\n \"viz/visualization\",\n \"viz/viz_views\",\n \"viz/trackster/util\",\n \"viz/trackster/slotting\",\n \"viz/trackster/painters\",\n \"viz/trackster/filters\",\n \"mvc/dataset/data\",\n \"mvc/tool/tools\",\n \"utils/config\",\n \"viz/bbi-data-manager\",\n \"ui/editable-text\"\n ],\n function(\n _,\n visualization,\n viz_views,\n util,\n slotting,\n painters,\n filters_mod,\n data,\n tools_mod,\n config_mod,\n bbi\n ) {\n var extend = _.extend;\n\n // ---- Web UI specific utilities ----\n\n /**\n * Dictionary of HTML element-JavaScript object relationships.\n */\n // TODO: probably should separate moveable objects from containers.\n var html_elt_js_obj_dict = {};\n\n /**\n * Designates an HTML as a container.\n */\n var is_container = function(element, obj) {\n html_elt_js_obj_dict[element.attr(\"id\")] = obj;\n };\n\n /**\n * Make `element` moveable within parent and sibling elements by dragging `handle` (a selector).\n * Function manages JS objects, containers as well.\n *\n * @param element HTML element to make moveable\n * @param handle_class classname that denotes HTML element to be used as handle\n * @param container_selector selector used to identify possible containers for this element\n * @param element_js_obj JavaScript object associated with element; used\n */\n var moveable = function(\n element,\n handle_class,\n container_selector,\n element_js_obj\n ) {\n // HACK: set default value for container selector.\n container_selector = \".group\";\n\n // Register element with its object.\n html_elt_js_obj_dict[element.attr(\"id\")] = element_js_obj;\n\n // Need to provide selector for handle, not class.\n element\n .bind(\n \"drag\",\n { handle: \".\" + handle_class, relative: true },\n function(e, d) {\n var element = $(this),\n parent = $(this).parent(),\n // Only sorting amongst tracks and groups.\n children = parent.children(\".track,.group\"),\n this_obj = html_elt_js_obj_dict[$(this).attr(\"id\")],\n child,\n container,\n top,\n bottom,\n i;\n\n //\n // Enable three types of dragging: (a) out of container; (b) into container;\n // (c) sibling movement, aka sorting. Handle in this order for simplicity.\n //\n\n // Handle dragging out of container.\n container = $(this).parents(container_selector);\n if (container.length !== 0) {\n top = container.position().top;\n bottom = top + container.outerHeight();\n var cur_container =\n html_elt_js_obj_dict[container.attr(\"id\")];\n if (d.offsetY < top) {\n // Moving above container.\n $(this).insertBefore(container);\n cur_container.remove_drawable(this_obj);\n cur_container.container.add_drawable_before(\n this_obj,\n cur_container\n );\n return;\n } else if (d.offsetY > bottom) {\n // Moving below container.\n $(this).insertAfter(container);\n cur_container.remove_drawable(this_obj);\n cur_container.container.add_drawable(this_obj);\n return;\n }\n }\n\n // Handle dragging into container. Child is appended to container's content_div.\n container = null;\n for (i = 0; i < children.length; i++) {\n child = $(children.get(i));\n top = child.position().top;\n bottom = top + child.outerHeight();\n // Dragging into container if child is a container and offset is inside container.\n if (\n child.is(container_selector) &&\n this !== child.get(0) &&\n d.offsetY >= top &&\n d.offsetY <= bottom\n ) {\n // Append/prepend based on where offsetY is closest to and return.\n if (d.offsetY - top < bottom - d.offsetY) {\n child.find(\".content-div\").prepend(this);\n } else {\n child.find(\".content-div\").append(this);\n }\n // Update containers. Object may not have container if it is being moved quickly.\n if (this_obj.container) {\n this_obj.container.remove_drawable(\n this_obj\n );\n }\n html_elt_js_obj_dict[\n child.attr(\"id\")\n ].add_drawable(this_obj);\n return;\n }\n }\n\n // Handle sibling movement, aka sorting.\n\n // Determine new position\n for (i = 0; i < children.length; i++) {\n child = $(children.get(i));\n if (\n d.offsetY < child.position().top &&\n // Cannot move tracks above reference track or intro div.\n !(\n child.hasClass(\"reference-track\") ||\n child.hasClass(\"intro\")\n )\n ) {\n break;\n }\n }\n\n // If not already in the right place, move. Need\n // to handle the end specially since we don't have\n // insert at index\n if (i === children.length) {\n if (this !== children.get(i - 1)) {\n parent.append(this);\n html_elt_js_obj_dict[\n parent.attr(\"id\")\n ].move_drawable(this_obj, i);\n }\n } else if (this !== children.get(i)) {\n $(this).insertBefore(children.get(i));\n // Need to adjust insert position if moving down because move is changing\n // indices of all list items.\n html_elt_js_obj_dict[\n parent.attr(\"id\")\n ].move_drawable(this_obj, d.deltaY > 0 ? i - 1 : i);\n }\n }\n )\n .bind(\"dragstart\", function() {\n $(this).addClass(\"dragging\");\n })\n .bind(\"dragend\", function() {\n $(this).removeClass(\"dragging\");\n });\n };\n\n /**\n * Init constants & functions used throughout trackster.\n */\n var // Padding at the top of tracks for error messages\n ERROR_PADDING = 20,\n // Maximum number of rows un a slotted track\n MAX_FEATURE_DEPTH = 100,\n // Minimum width for window for squish to be used.\n MIN_SQUISH_VIEW_WIDTH = 12000,\n // Number of pixels per tile, not including left offset.\n TILE_SIZE = 400,\n DEFAULT_DATA_QUERY_WAIT = 5000,\n // Maximum number of chromosomes that are selectable at any one time.\n MAX_CHROMS_SELECTABLE = 100,\n DATA_ERROR = \"Cannot display dataset due to an error. \",\n DATA_NOCONVERTER =\n \"A converter for this dataset is not installed. Please check your datatypes_conf.xml file.\",\n DATA_NONE = \"No data for this chrom/contig.\",\n DATA_PENDING =\n \"Preparing data. This can take a while for a large dataset. \" +\n \"If the visualization is saved and closed, preparation will continue in the background.\",\n DATA_CANNOT_RUN_TOOL = \"Tool cannot be rerun: \",\n DATA_LOADING = \"Loading data...\",\n DATA_OK = \"Ready for display\",\n TILE_CACHE_SIZE = 10,\n DATA_CACHE_SIZE = 20,\n // Numerical/continuous data display modes.\n CONTINUOUS_DATA_MODES = [\n \"Histogram\",\n \"Line\",\n \"Filled\",\n \"Intensity\"\n ];\n\n /**\n * Round a number to a given number of decimal places.\n */\n function round(num, places) {\n // Default rounding is to integer.\n if (!places) {\n places = 0;\n }\n\n var val = Math.pow(10, places);\n return Math.round(num * val) / val;\n }\n\n /**\n * Check if a server can do byte range requests.\n */\n function supportsByteRanges(url) {\n var promise = $.Deferred();\n $.ajax({\n type: \"HEAD\",\n url: url,\n beforeSend: function(xhr) {\n xhr.setRequestHeader(\"Range\", \"bytes=0-10\");\n },\n success: function(result, status, xhr) {\n promise.resolve(xhr.status === 206);\n }\n });\n\n return promise;\n }\n\n /**\n * Drawables hierarchy:\n *\n * Drawable\n * --> DrawableCollection\n * --> DrawableGroup\n * --> View\n * --> Track\n */\n\n /**\n * Base class for all drawable objects. Drawable objects are associated with a view and live in a\n * container. They have the following HTML elements and structure:\n *\n * \n * \n *\n * They optionally have a drag handle class.\n */\n var Drawable = function(view, container, obj_dict) {\n if (!Drawable.id_counter) {\n Drawable.id_counter = 0;\n }\n this.id = Drawable.id_counter++;\n this.view = view;\n this.container = container;\n this.drag_handle_class = obj_dict.drag_handle_class;\n this.is_overview = false;\n this.action_icons = {};\n\n // -- Set up drawable configuration. --\n this.config = config_mod.ConfigSettingCollection.from_models_and_saved_values(\n this.config_params,\n obj_dict.prefs\n );\n\n // If there's no saved name, use object name.\n if (!this.config.get_value(\"name\")) {\n this.config.set_value(\"name\", obj_dict.name);\n }\n if (this.config_onchange) {\n this.config.on(\"change\", this.config_onchange, this);\n }\n\n // Build Drawable HTML and behaviors.\n this.container_div = this.build_container_div();\n this.header_div = null;\n\n // Use opt-out policy on header creation because this is the more frequent approach:\n // unless flag set, create header.\n if (obj_dict.header !== false) {\n var header_view = new viz_views.TrackHeaderView({\n model: this,\n id: this.id\n });\n\n this.header_div = header_view.$el;\n this.container_div.append(this.header_div);\n\n // Show icons when users is hovering over track.\n var icons_div = header_view.icons_div;\n this.action_icons = header_view.action_icons;\n this.container_div.hover(\n function() {\n icons_div.show();\n },\n function() {\n icons_div.hide();\n }\n );\n }\n };\n\n Drawable.prototype.action_icons_def = [\n // Hide/show drawable content.\n // FIXME: make this an odict for easier lookup.\n {\n name: \"toggle_icon\",\n title: \"Hide/show content\",\n css_class: \"toggle\",\n on_click_fn: function(drawable) {\n if (drawable.config.get_value(\"content_visible\")) {\n drawable.action_icons.toggle_icon\n .addClass(\"toggle-expand\")\n .removeClass(\"toggle\");\n drawable.hide_contents();\n drawable.config.set_value(\"content_visible\", false);\n } else {\n drawable.action_icons.toggle_icon\n .addClass(\"toggle\")\n .removeClass(\"toggle-expand\");\n drawable.config.set_value(\"content_visible\", true);\n drawable.show_contents();\n }\n }\n },\n // Edit settings.\n {\n name: \"settings_icon\",\n title: \"Edit settings\",\n css_class: \"gear\",\n on_click_fn: function(drawable) {\n var view = new config_mod.ConfigSettingCollectionView({\n collection: drawable.config\n });\n view.render_in_modal(\"Configure Track\");\n }\n },\n // Remove.\n {\n name: \"remove_icon\",\n title: \"Remove\",\n css_class: \"remove-icon\",\n on_click_fn: function(drawable) {\n // Tooltip for remove icon must be deleted when drawable is deleted.\n $(\".tooltip\").remove();\n drawable.remove();\n }\n }\n ];\n\n extend(Drawable.prototype, {\n config_params: [\n { key: \"name\", label: \"Name\", type: \"text\", default_value: \"\" },\n {\n key: \"content_visible\",\n type: \"bool\",\n default_value: true,\n hidden: true\n }\n ],\n\n config_onchange: function() {},\n\n init: function() {},\n\n changed: function() {\n this.view.changed();\n },\n\n can_draw: function() {\n if (this.enabled && this.config.get_value(\"content_visible\")) {\n return true;\n }\n\n return false;\n },\n\n request_draw: function() {},\n\n _draw: function(options) {},\n\n /**\n * Returns representation of object in a dictionary for easy saving.\n * Use from_dict to recreate object.\n */\n to_dict: function() {},\n\n /**\n * Set drawable name.\n */\n set_name: function(new_name) {\n this.old_name = this.config.get_value(\"name\");\n this.config.set_value(\"name\", new_name);\n },\n\n /**\n * Revert track name; currently name can be reverted only once.\n */\n revert_name: function() {\n if (this.old_name) {\n this.config.set_value(\"name\", this.old_name);\n }\n },\n\n /**\n * Remove drawable (a) from its container and (b) from the HTML.\n */\n remove: function() {\n this.changed();\n\n this.container.remove_drawable(this);\n var view = this.view;\n this.container_div.hide(0, function() {\n $(this).remove();\n // HACK: is there a better way to update the view?\n view.update_intro_div();\n });\n },\n\n /**\n * Build drawable's container div; this is the parent div for all drawable's elements.\n */\n build_container_div: function() {},\n\n /**\n * Update icons.\n */\n update_icons: function() {},\n\n /**\n * Hide drawable's contents.\n */\n hide_contents: function() {},\n\n /**\n * Show drawable's contents.\n */\n show_contents: function() {},\n\n /**\n * Returns a shallow copy of all drawables in this drawable.\n */\n get_drawables: function() {}\n });\n\n /**\n * A collection of drawable objects.\n */\n var DrawableCollection = function(view, container, obj_dict) {\n Drawable.call(this, view, container, obj_dict);\n\n // Attribute init.\n this.obj_type = obj_dict.obj_type;\n this.drawables = [];\n };\n\n extend(DrawableCollection.prototype, Drawable.prototype, {\n /**\n * Unpack and add drawables to the collection.\n */\n unpack_drawables: function(drawables_array) {\n // Add drawables to collection.\n this.drawables = [];\n var drawable;\n for (var i = 0; i < drawables_array.length; i++) {\n drawable = object_from_template(\n drawables_array[i],\n this.view,\n this\n );\n this.add_drawable(drawable);\n }\n },\n\n /**\n * Init each drawable in the collection.\n */\n init: function() {\n for (var i = 0; i < this.drawables.length; i++) {\n this.drawables[i].init();\n }\n },\n\n /**\n * Draw each drawable in the collection.\n */\n _draw: function(options) {\n for (var i = 0; i < this.drawables.length; i++) {\n this.drawables[i]._draw(options);\n }\n },\n\n /**\n * Returns representation of object in a dictionary for easy saving.\n * Use from_dict to recreate object.\n */\n to_dict: function() {\n var dictified_drawables = [];\n for (var i = 0; i < this.drawables.length; i++) {\n dictified_drawables.push(this.drawables[i].to_dict());\n }\n return {\n prefs: this.config.to_key_value_dict(),\n obj_type: this.obj_type,\n drawables: dictified_drawables\n };\n },\n\n /**\n * Add a drawable to the end of the collection.\n */\n add_drawable: function(drawable) {\n this.drawables.push(drawable);\n drawable.container = this;\n this.changed();\n },\n\n /**\n * Add a drawable before another drawable.\n */\n add_drawable_before: function(drawable, other) {\n this.changed();\n var index = this.drawables.indexOf(other);\n if (index !== -1) {\n this.drawables.splice(index, 0, drawable);\n return true;\n }\n return false;\n },\n\n /**\n * Replace one drawable with another.\n */\n replace_drawable: function(\n old_drawable,\n new_drawable,\n update_html\n ) {\n var index = this.drawables.indexOf(old_drawable);\n if (index !== -1) {\n this.drawables[index] = new_drawable;\n if (update_html) {\n old_drawable.container_div.replaceWith(\n new_drawable.container_div\n );\n }\n this.changed();\n }\n return index;\n },\n\n /**\n * Remove drawable from this collection.\n */\n remove_drawable: function(drawable) {\n var index = this.drawables.indexOf(drawable);\n if (index !== -1) {\n // Found drawable to remove.\n this.drawables.splice(index, 1);\n drawable.container = null;\n this.changed();\n return true;\n }\n return false;\n },\n\n /**\n * Move drawable to another location in collection.\n */\n move_drawable: function(drawable, new_position) {\n var index = this.drawables.indexOf(drawable);\n if (index !== -1) {\n // Remove from current position:\n this.drawables.splice(index, 1);\n // insert into new position:\n this.drawables.splice(new_position, 0, drawable);\n this.changed();\n return true;\n }\n return false;\n },\n\n /**\n * Returns all drawables in this drawable.\n */\n get_drawables: function() {\n return this.drawables;\n },\n\n /**\n * Returns all tracks in collection.\n */\n get_tracks: function(track_type) {\n // Initialize queue with copy of drawables array.\n var queue = this.drawables.slice(0),\n tracks = [],\n drawable;\n while (queue.length !== 0) {\n drawable = queue.shift();\n if (drawable instanceof track_type) {\n tracks.push(drawable);\n } else if (drawable.drawables) {\n queue = queue.concat(drawable.drawables);\n }\n }\n return tracks;\n }\n });\n\n /**\n * A group of drawables that are moveable, visible.\n */\n var DrawableGroup = function(view, container, obj_dict) {\n extend(obj_dict, {\n obj_type: \"DrawableGroup\",\n drag_handle_class: \"group-handle\"\n });\n DrawableCollection.call(this, view, container, obj_dict);\n\n // Set up containers/moving for group: register both container_div and content div as container\n // because both are used as containers (container div to recognize container, content_div to\n // store elements). Group can be moved.\n this.content_div = $(\"\")\n .addClass(\"content-div\")\n .attr(\"id\", \"group_\" + this.id + \"_content_div\")\n .appendTo(this.container_div);\n is_container(this.container_div, this);\n is_container(this.content_div, this);\n moveable(\n this.container_div,\n this.drag_handle_class,\n \".group\",\n this\n );\n\n // Set up filters.\n this.filters_manager = new filters_mod.FiltersManager(this);\n this.header_div.after(this.filters_manager.parent_div);\n\n // HACK: add div to clear floating elements.\n this.filters_manager.parent_div.after(\n $(\"\")\n );\n\n // For saving drawables' filter managers when group-level filtering is done:\n this.saved_filters_managers = [];\n\n // Add drawables.\n if (\"drawables\" in obj_dict) {\n this.unpack_drawables(obj_dict.drawables);\n }\n\n // Restore filters.\n if (\"filters\" in obj_dict) {\n // FIXME: Pass collection_dict to DrawableCollection/Drawable will make this easier.\n var old_manager = this.filters_manager;\n this.filters_manager = new filters_mod.FiltersManager(\n this,\n obj_dict.filters\n );\n old_manager.parent_div.replaceWith(\n this.filters_manager.parent_div\n );\n\n if (obj_dict.filters.visible) {\n this.setup_multitrack_filtering();\n }\n }\n };\n\n extend(\n DrawableGroup.prototype,\n Drawable.prototype,\n DrawableCollection.prototype,\n {\n action_icons_def: [\n Drawable.prototype.action_icons_def[0],\n Drawable.prototype.action_icons_def[1],\n // Replace group with composite track.\n {\n name: \"composite_icon\",\n title: \"Show composite track\",\n css_class: \"layers-stack\",\n on_click_fn: function(group) {\n $(\".tooltip\").remove();\n group.show_composite_track();\n }\n },\n // Toggle track filters.\n {\n name: \"filters_icon\",\n title: \"Filters\",\n css_class: \"ui-slider-050\",\n on_click_fn: function(group) {\n // TODO: update Tooltip text.\n if (group.filters_manager.visible()) {\n // Hiding filters.\n group.filters_manager.clear_filters();\n group._restore_filter_managers();\n // TODO: maintain current filter by restoring and setting saved manager's\n // settings to current/shared manager's settings.\n // TODO: need to restore filter managers when moving drawable outside group.\n } else {\n // Showing filters.\n group.setup_multitrack_filtering();\n group.request_draw({ clear_tile_cache: true });\n }\n group.filters_manager.toggle();\n }\n },\n Drawable.prototype.action_icons_def[2]\n ],\n\n build_container_div: function() {\n var container_div = $(\"\")\n .addClass(\"group\")\n .attr(\"id\", \"group_\" + this.id);\n if (this.container) {\n this.container.content_div.append(container_div);\n }\n return container_div;\n },\n\n hide_contents: function() {\n this.tiles_div.hide();\n },\n\n show_contents: function() {\n // Show the contents div and labels (if present)\n this.tiles_div.show();\n // Request a redraw of the content\n this.request_draw();\n },\n\n update_icons: function() {\n //\n // Handle update when there are no tracks.\n //\n var num_drawables = this.drawables.length;\n if (num_drawables === 0) {\n this.action_icons.composite_icon.hide();\n this.action_icons.filters_icon.hide();\n } else if (num_drawables === 1) {\n this.action_icons.composite_icon.toggle(\n this.drawables[0] instanceof CompositeTrack\n );\n this.action_icons.filters_icon.hide();\n } else {\n // There are 2 or more tracks.\n\n //\n // Determine if a composite track can be created. Current criteria:\n // (a) all tracks are line tracks;\n // OR\n // FIXME: this is not enabled right now because it has not been well tested:\n // (b) there is a single FeatureTrack.\n //\n\n // All tracks the same?\n var i,\n j,\n drawable,\n same_type = true,\n a_type = this.drawables[0].get_type(),\n num_feature_tracks = 0;\n for (i = 0; i < num_drawables; i++) {\n drawable = this.drawables[i];\n if (drawable.get_type() !== a_type) {\n can_composite = false;\n break;\n }\n if (drawable instanceof FeatureTrack) {\n num_feature_tracks++;\n }\n }\n\n if (\n same_type &&\n this.drawables[0] instanceof LineTrack\n ) {\n this.action_icons.composite_icon.show();\n } else {\n this.action_icons.composite_icon.hide();\n $(\".tooltip\").remove();\n }\n\n //\n // Set up group-level filtering and update filter icon.\n //\n if (\n num_feature_tracks > 1 &&\n num_feature_tracks === this.drawables.length\n ) {\n //\n // Find shared filters.\n //\n var shared_filters = {},\n filter;\n\n // Init shared filters with filters from first drawable.\n drawable = this.drawables[0];\n for (\n j = 0;\n j < drawable.filters_manager.filters.length;\n j++\n ) {\n filter = drawable.filters_manager.filters[j];\n shared_filters[filter.name] = [filter];\n }\n\n // Create lists of shared filters.\n for (i = 1; i < this.drawables.length; i++) {\n drawable = this.drawables[i];\n for (\n j = 0;\n j < drawable.filters_manager.filters.length;\n j++\n ) {\n filter =\n drawable.filters_manager.filters[j];\n if (filter.name in shared_filters) {\n shared_filters[filter.name].push(\n filter\n );\n }\n }\n }\n\n //\n // Create filters for shared filters manager. Shared filters manager is group's\n // manager.\n //\n this.filters_manager.remove_all();\n var filters, new_filter, min, max;\n for (var filter_name in shared_filters) {\n filters = shared_filters[filter_name];\n if (filters.length === num_feature_tracks) {\n // Add new filter.\n // FIXME: can filter.copy() be used?\n new_filter = new filters_mod.NumberFilter({\n name: filters[0].name,\n index: filters[0].index\n });\n this.filters_manager.add_filter(new_filter);\n }\n }\n\n // Show/hide icon based on filter availability.\n this.action_icons.filters_icon.toggle(\n this.filters_manager.filters.length > 0\n );\n } else {\n this.action_icons.filters_icon.hide();\n }\n }\n },\n\n /**\n * Restore individual track filter managers.\n */\n _restore_filter_managers: function() {\n for (var i = 0; i < this.drawables.length; i++) {\n this.drawables[\n i\n ].filters_manager = this.saved_filters_managers[i];\n }\n this.saved_filters_managers = [];\n },\n\n /**\n *\n */\n setup_multitrack_filtering: function() {\n // Save tracks' managers and set up shared manager.\n if (this.filters_manager.filters.length > 0) {\n // For all tracks, save current filter manager and set manager to shared (this object's) manager.\n this.saved_filters_managers = [];\n for (var i = 0; i < this.drawables.length; i++) {\n var drawable = this.drawables[i];\n this.saved_filters_managers.push(\n drawable.filters_manager\n );\n drawable.filters_manager = this.filters_manager;\n }\n\n //TODO: hide filters icons for each drawable?\n }\n this.filters_manager.init_filters();\n },\n\n /**\n * Replace group with a single composite track that includes all group's tracks.\n */\n show_composite_track: function() {\n var composite_track = new CompositeTrack(\n this.view,\n this.view,\n {\n name: this.config.get_value(\"name\"),\n drawables: this.drawables\n }\n );\n var index = this.container.replace_drawable(\n this,\n composite_track,\n true\n );\n composite_track.request_draw();\n },\n\n add_drawable: function(drawable) {\n DrawableCollection.prototype.add_drawable.call(\n this,\n drawable\n );\n this.update_icons();\n },\n\n remove_drawable: function(drawable) {\n DrawableCollection.prototype.remove_drawable.call(\n this,\n drawable\n );\n this.update_icons();\n },\n\n to_dict: function() {\n // If filters are visible, need to restore original filter managers before converting to dict.\n if (this.filters_manager.visible()) {\n this._restore_filter_managers();\n }\n\n var obj_dict = extend(\n DrawableCollection.prototype.to_dict.call(this),\n { filters: this.filters_manager.to_dict() }\n );\n\n // Setup multi-track filtering again.\n if (this.filters_manager.visible()) {\n this.setup_multitrack_filtering();\n }\n\n return obj_dict;\n },\n\n request_draw: function(options) {\n _.each(this.drawables, function(d) {\n d.request_draw(options);\n });\n }\n }\n );\n\n /**\n * View object manages a trackster visualization, including tracks and user interactions.\n * Events triggered:\n * navigate: when browser view changes to a new locations\n */\n var TracksterView = Backbone.View.extend({\n initialize: function(obj_dict) {\n extend(obj_dict, {\n obj_type: \"View\"\n });\n DrawableCollection.call(\n this,\n \"View\",\n obj_dict.container,\n obj_dict\n );\n this.chrom = null;\n this.vis_id = obj_dict.vis_id;\n this.dbkey = obj_dict.dbkey;\n this.stand_alone =\n obj_dict.stand_alone !== undefined\n ? obj_dict.stand_alone\n : true;\n this.label_tracks = [];\n this.tracks_to_be_redrawn = [];\n this.max_low = 0;\n this.max_high = 0;\n this.zoom_factor = 3;\n this.min_separation = 30;\n this.has_changes = false;\n // Deferred object that indicates when view's chrom data has been loaded.\n this.load_chroms_deferred = null;\n this.render();\n this.canvas_manager = new visualization.CanvasManager(\n this.container.get(0).ownerDocument\n );\n this.reset();\n\n // Define track configuration\n this.config = config_mod.ConfigSettingCollection.from_models_and_saved_values(\n [\n {\n key: \"name\",\n label: \"Name\",\n type: \"text\",\n default_value: \"\"\n },\n {\n key: \"a_color\",\n label: \"A Color\",\n type: \"color\",\n default_value: \"#FF0000\"\n },\n {\n key: \"c_color\",\n label: \"C Color\",\n type: \"color\",\n default_value: \"#00FF00\"\n },\n {\n key: \"g_color\",\n label: \"G Color\",\n type: \"color\",\n default_value: \"#0000FF\"\n },\n {\n key: \"t_color\",\n label: \"T Color\",\n type: \"color\",\n default_value: \"#FF00FF\"\n },\n {\n key: \"n_color\",\n label: \"N Color\",\n type: \"color\",\n default_value: \"#AAAAAA\"\n }\n ],\n { name: obj_dict.name }\n );\n },\n\n render: function() {\n // Attribute init.\n this.requested_redraw = false;\n\n // Create DOM elements\n var parent_element = this.container,\n view = this;\n // Top container for things that are fixed at the top\n this.top_container = $(\"\")\n .addClass(\"top-container\")\n .appendTo(parent_element);\n // Browser content, primary tracks are contained in here\n this.browser_content_div = $(\"\")\n .addClass(\"content\")\n .appendTo(parent_element);\n // Bottom container for things that are fixed at the bottom\n this.bottom_container = $(\"\")\n .addClass(\"bottom-container\")\n .appendTo(parent_element);\n // Label track fixed at top\n this.top_labeltrack = $(\"\")\n .addClass(\"top-labeltrack\")\n .appendTo(this.top_container);\n // Viewport for dragging tracks in center\n this.viewport_container = $(\"\")\n .addClass(\"viewport-container\")\n .attr(\"id\", \"viewport-container\")\n .appendTo(this.browser_content_div);\n // Alias viewport_container as content_div so that it matches function of DrawableCollection/Group content_div.\n this.content_div = this.viewport_container;\n is_container(this.viewport_container, view);\n // Introduction div shown when there are no tracks.\n this.intro_div = $(\"\")\n .addClass(\"intro\")\n .appendTo(this.viewport_container);\n var add_tracks_button = $(\"\")\n .text(\"Add Datasets to Visualization\")\n .addClass(\"action-button\")\n .appendTo(this.intro_div)\n .click(function() {\n visualization.select_datasets(\n { dbkey: view.dbkey },\n function(tracks) {\n _.each(tracks, function(track) {\n view.add_drawable(\n object_from_template(track, view, view)\n );\n });\n }\n );\n });\n\n // Navigation at top\n this.nav_container = $(\"\")\n .addClass(\"trackster-nav-container\")\n .prependTo(this.top_container);\n this.nav = $(\"\")\n .addClass(\"trackster-nav\")\n .appendTo(this.nav_container);\n\n if (this.stand_alone) {\n this.nav_container.addClass(\"stand-alone\");\n this.nav.addClass(\"stand-alone\");\n }\n\n // Overview (scrollbar and overview plot) at bottom\n this.overview = $(\"\")\n .addClass(\"overview\")\n .appendTo(this.bottom_container);\n this.overview_viewport = $(\"\")\n .addClass(\"overview-viewport\")\n .appendTo(this.overview);\n this.overview_close = $(\"\")\n .attr(\"title\", \"Close overview\")\n .addClass(\"icon-button overview-close tooltip\")\n .hide()\n .appendTo(this.overview_viewport);\n this.overview_highlight = $(\"\")\n .addClass(\"overview-highlight\")\n .hide()\n .appendTo(this.overview_viewport);\n this.overview_box_background = $(\"\")\n .addClass(\"overview-boxback\")\n .appendTo(this.overview_viewport);\n this.overview_box = $(\"\")\n .addClass(\"overview-box\")\n .appendTo(this.overview_viewport);\n this.default_overview_height = this.overview_box.height();\n\n this.nav_controls = $(\"\")\n .addClass(\"nav-controls\")\n .appendTo(this.nav);\n this.chrom_select = $(\"\")\n .attr({ name: \"chrom\" })\n .addClass(\"chrom-nav\")\n .append(\"\")\n .appendTo(this.nav_controls);\n var submit_nav = function(e) {\n if (\n e.type === \"focusout\" ||\n (e.keyCode || e.which) === 13 ||\n (e.keyCode || e.which) === 27\n ) {\n if ((e.keyCode || e.which) !== 27) {\n // Not escape key\n view.go_to($(this).val());\n }\n $(this).hide();\n $(this).val(\"\");\n view.location_span.show();\n view.chrom_select.show();\n }\n\n // Suppress key presses so that they do impact viz.\n e.stopPropagation();\n };\n this.nav_input = $(\"\")\n .addClass(\"nav-input\")\n .hide()\n .bind(\"keyup focusout\", submit_nav)\n .appendTo(this.nav_controls);\n this.location_span = $(\"\")\n .addClass(\"location\")\n .attr(\"title\", \"Click to change location\")\n .tooltip({ placement: \"bottom\" })\n .appendTo(this.nav_controls);\n this.location_span.click(function() {\n view.location_span.hide();\n view.chrom_select.hide();\n view.nav_input.val(\n view.chrom + \":\" + view.low + \"-\" + view.high\n );\n view.nav_input.css(\"display\", \"inline-block\");\n view.nav_input.select();\n view.nav_input.focus();\n // Set up autocomplete for tracks' features.\n view.nav_input.autocomplete({\n source: function(request, response) {\n // Using current text, query each track and create list of all matching features.\n var all_features = [],\n feature_search_deferreds = $.map(\n view.get_tracks(FeatureTrack),\n function(t) {\n return t.data_manager\n .search_features(request.term)\n .success(function(\n dataset_features\n ) {\n all_features = all_features.concat(\n dataset_features\n );\n });\n }\n );\n\n // When all searching is done, fill autocomplete.\n $.when\n .apply($, feature_search_deferreds)\n .done(function() {\n response(\n $.map(all_features, function(feature) {\n return {\n label: feature[0],\n value: feature[1]\n };\n })\n );\n });\n },\n minLength: 2\n });\n });\n if (this.vis_id !== undefined) {\n this.hidden_input = $(\"\")\n .attr(\"type\", \"hidden\")\n .val(this.vis_id)\n .appendTo(this.nav_controls);\n }\n\n this.zo_link = $(\"\")\n .attr(\"id\", \"zoom-out\")\n .attr(\"title\", \"Zoom out\")\n .tooltip({ placement: \"bottom\" })\n .click(function() {\n view.zoom_out();\n })\n .appendTo(this.nav_controls);\n this.zi_link = $(\"\")\n .attr(\"id\", \"zoom-in\")\n .attr(\"title\", \"Zoom in\")\n .tooltip({ placement: \"bottom\" })\n .click(function() {\n view.zoom_in();\n })\n .appendTo(this.nav_controls);\n\n // Get initial set of chroms.\n this.load_chroms_deferred = this.load_chroms({ low: 0 });\n this.chrom_select.bind(\"change\", function() {\n view.change_chrom(view.chrom_select.val());\n });\n\n /*\n this.browser_content_div.bind(\"mousewheel\", function( e, delta ) {\n if (Math.abs(delta) < 0.5) {\n return;\n }\n if (delta > 0) {\n view.zoom_in(e.pageX, this.viewport_container);\n } else {\n view.zoom_out();\n }\n e.preventDefault();\n });\n */\n\n // Blur tool/filter inputs when user clicks on content div.\n this.browser_content_div.click(function(e) {\n $(this)\n .find(\"input\")\n .trigger(\"blur\");\n });\n\n // Double clicking zooms in\n this.browser_content_div.bind(\"dblclick\", function(e) {\n view.zoom_in(e.pageX, this.viewport_container);\n });\n\n // Dragging the overview box (~ horizontal scroll bar)\n this.overview_box\n .bind(\"dragstart\", function(e, d) {\n this.current_x = d.offsetX;\n })\n .bind(\"drag\", function(e, d) {\n var delta = d.offsetX - this.current_x;\n this.current_x = d.offsetX;\n var delta_chrom = Math.round(\n delta /\n view.viewport_container.width() *\n (view.max_high - view.max_low)\n );\n view.move_delta(-delta_chrom);\n });\n\n this.overview_close.click(function() {\n view.reset_overview();\n });\n\n // Dragging in the viewport scrolls\n this.viewport_container\n .bind(\"draginit\", function(e, d) {\n // Disable interaction if started in scrollbar (for webkit)\n if (e.clientX > view.viewport_container.width() - 16) {\n return false;\n }\n })\n .bind(\"dragstart\", function(e, d) {\n d.original_low = view.low;\n d.current_height = e.clientY;\n d.current_x = d.offsetX;\n })\n .bind(\"drag\", function(e, d) {\n var container = $(this);\n var delta = d.offsetX - d.current_x;\n var new_scroll =\n container.scrollTop() -\n (e.clientY - d.current_height);\n container.scrollTop(new_scroll);\n d.current_height = e.clientY;\n d.current_x = d.offsetX;\n var delta_chrom = Math.round(\n delta /\n view.viewport_container.width() *\n (view.high - view.low)\n );\n view.move_delta(delta_chrom);\n });\n /*\n FIXME: Do not do this for now because it's too jittery. Some kind of gravity approach is\n needed here because moving left/right should be difficult.\n\n // Also capture mouse wheel for left/right scrolling\n }).bind( 'mousewheel', function( e, d, dx, dy ) {\n // Only handle x axis scrolling; y axis scrolling is\n // handled by the browser when the event bubbles up.\n if (dx) {\n var delta_chrom = Math.round( - dx / view.viewport_container.width() * (view.high - view.low) );\n view.move_delta( delta_chrom );\n }\n });\n */\n\n // Dragging in the top label track allows selecting a region to zoom in on selected region.\n this.top_labeltrack\n .bind(\"dragstart\", function(e, d) {\n return $(\"\")\n .addClass(\"zoom-area\")\n .css(\n \"height\",\n view.browser_content_div.height() +\n view.top_labeltrack.height() +\n 1\n )\n .appendTo($(this));\n })\n .bind(\"drag\", function(e, d) {\n $(d.proxy).css({\n left:\n Math.min(e.pageX, d.startX) -\n view.container.offset().left,\n width: Math.abs(e.pageX - d.startX)\n });\n var min =\n Math.min(e.pageX, d.startX) -\n view.container.offset().left,\n max =\n Math.max(e.pageX, d.startX) -\n view.container.offset().left,\n span = view.high - view.low,\n width = view.viewport_container.width();\n view.update_location(\n Math.round(min / width * span) + view.low,\n Math.round(max / width * span) + view.low\n );\n })\n .bind(\"dragend\", function(e, d) {\n var min = Math.min(e.pageX, d.startX),\n max = Math.max(e.pageX, d.startX),\n span = view.high - view.low,\n width = view.viewport_container.width(),\n old_low = view.low;\n view.low = Math.round(min / width * span) + old_low;\n view.high = Math.round(max / width * span) + old_low;\n $(d.proxy).remove();\n view.request_redraw();\n });\n\n // FIXME: this is still wonky for embedded visualizations.\n /*\n // For vertical alignment, track mouse with simple line.\n var mouse_tracker_div = $('').addClass('mouse-pos').appendTo(parent_element);\n\n // Show tracker only when hovering over view.\n parent_element.hover(\n function() {\n mouse_tracker_div.show();\n parent_element.mousemove(function(e) {\n mouse_tracker_div.css({\n // -1 makes line appear next to the mouse w/o preventing mouse actions.\n left: e.pageX - parent_element.offset().left - 1\n });\n });\n },\n function() {\n parent_element.off('mousemove');\n mouse_tracker_div.hide();\n }\n );\n */\n\n this.add_label_track(\n new LabelTrack(this, { content_div: this.top_labeltrack })\n );\n\n $(window).bind(\"resize\", function() {\n // Stop previous timer.\n if (this.resize_timer) {\n clearTimeout(this.resize_timer);\n }\n\n // When function activated, resize window and redraw.\n this.resize_timer = setTimeout(function() {\n view.resize_window();\n }, 500);\n });\n $(document).bind(\"redraw\", function() {\n view.redraw();\n });\n\n this.reset();\n $(window).trigger(\"resize\");\n },\n\n get_base_color: function(base) {\n return (\n this.config.get_value(base.toLowerCase() + \"_color\") ||\n this.config.get_value(\"n_color\")\n );\n }\n });\n\n // FIXME: need to use this approach to enable inheritance of DrawableCollection functions.\n extend(TracksterView.prototype, DrawableCollection.prototype, {\n changed: function() {\n this.has_changes = true;\n },\n\n /** Add or remove intro div depending on view state. */\n update_intro_div: function() {\n this.intro_div.toggle(this.drawables.length === 0);\n },\n\n /**\n * Triggers navigate events as needed. If there is a delay,\n * then event is triggered only after navigation has stopped.\n */\n trigger_navigate: function(new_chrom, new_low, new_high, delay) {\n // Stop previous timer.\n if (this.timer) {\n clearTimeout(this.timer);\n }\n\n if (delay) {\n // To aggregate calls, use timer and only navigate once\n // location has stabilized.\n var self = this;\n this.timer = setTimeout(function() {\n self.trigger(\n \"navigate\",\n new_chrom + \":\" + new_low + \"-\" + new_high\n );\n }, 500);\n } else {\n view.trigger(\n \"navigate\",\n new_chrom + \":\" + new_low + \"-\" + new_high\n );\n }\n },\n\n update_location: function(low, high) {\n this.location_span.text(\n util.commatize(low) + \" - \" + util.commatize(high)\n );\n this.nav_input.val(\n this.chrom +\n \":\" +\n util.commatize(low) +\n \"-\" +\n util.commatize(high)\n );\n\n // Update location. Only update when there is a valid chrom; when loading vis, there may\n // not be a valid chrom.\n var chrom = this.chrom_select.val();\n if (chrom !== \"\") {\n this.trigger_navigate(chrom, this.low, this.high, true);\n }\n },\n\n /**\n * Load chrom data for the view. Returns a jQuery Deferred.\n */\n // FIXME: instead of loading chrom data, should load and store genome object.\n load_chroms: function(url_parms) {\n url_parms.num = MAX_CHROMS_SELECTABLE;\n\n var view = this,\n chrom_data = $.Deferred();\n $.ajax({\n url: Galaxy.root + \"api/genomes/\" + this.dbkey,\n data: url_parms,\n dataType: \"json\",\n success: function(result) {\n // Do nothing if could not load chroms.\n if (result.chrom_info.length === 0) {\n return;\n }\n\n // Load chroms.\n if (result.reference) {\n var ref_track = new ReferenceTrack(view);\n view.add_label_track(ref_track);\n view.reference_track = ref_track;\n }\n view.chrom_data = result.chrom_info;\n\n view.chrom_select.html(\"\");\n view.chrom_select.append(\n $('')\n );\n\n for (\n var i = 0, len = view.chrom_data.length;\n i < len;\n i++\n ) {\n var chrom = view.chrom_data[i].chrom;\n var chrom_option = $(\"\"\n )\n );\n }\n if (result.next_chroms) {\n view.chrom_select.append(\n $(\n '\"\n )\n );\n }\n view.chrom_start_index = result.start_index;\n\n chrom_data.resolve(result.chrom_info);\n },\n error: function() {\n alert(\n \"Could not load chroms for this dbkey: \" +\n view.dbkey\n );\n }\n });\n return chrom_data;\n },\n\n change_chrom: function(chrom, low, high) {\n var view = this;\n // If chrom data is still loading, wait for it.\n if (!view.chrom_data) {\n view.load_chroms_deferred.then(function() {\n view.change_chrom(chrom, low, high);\n });\n return;\n }\n\n // Don't do anything if chrom is \"None\" (hackish but some browsers already have this set), or null/blank\n if (!chrom || chrom === \"None\") {\n return;\n }\n\n //\n // If user is navigating to previous/next set of chroms, load new chrom set and return.\n //\n if (chrom === \"previous\") {\n view.load_chroms({\n low: this.chrom_start_index - MAX_CHROMS_SELECTABLE\n });\n return;\n }\n if (chrom === \"next\") {\n view.load_chroms({\n low: this.chrom_start_index + MAX_CHROMS_SELECTABLE\n });\n return;\n }\n\n //\n // User is loading a particular chrom. Look first in current set; if not in current set, load new\n // chrom set.\n //\n var found = $.grep(view.chrom_data, function(v, i) {\n return v.chrom === chrom;\n })[0];\n if (found === undefined) {\n // Try to load chrom and then change to chrom.\n view.load_chroms({ chrom: chrom }, function() {\n view.change_chrom(chrom, low, high);\n });\n return;\n } else {\n // Switching to local chrom.\n if (chrom !== view.chrom) {\n view.chrom = chrom;\n view.chrom_select.val(view.chrom);\n view.max_high = found.len - 1; // -1 because we're using 0-based indexing.\n view.reset();\n\n for (\n var i = 0, len = view.drawables.length;\n i < len;\n i++\n ) {\n var drawable = view.drawables[i];\n if (drawable.init) {\n drawable.init();\n }\n }\n if (view.reference_track) {\n view.reference_track.init();\n }\n }\n\n // Resolve low, high.\n if (low === undefined && high === undefined) {\n // Both are undefined, so view is whole chromosome.\n view.low = 0;\n view.high = view.max_high;\n } else {\n // Low and/or high is defined.\n view.low = low !== undefined ? Math.max(low, 0) : 0;\n if (high === undefined) {\n // Center visualization around low.\n // HACK: max resolution is currently 30 bases.\n view.low = Math.max(view.low - 15, 0);\n view.high = view.low + 30;\n } else {\n // High is defined.\n view.high = Math.min(high, view.max_high);\n }\n }\n\n view.request_redraw();\n }\n },\n\n /**\n * Change viewing region to that denoted by string. General format of string is:\n *\n * [ {separator} [- ] ]\n *\n * where separator can be whitespace or a colon. Examples:\n *\n * chr22\n * chr1:100-200\n * chr7 89999\n * chr8 90000 990000\n */\n go_to: function(str) {\n // Remove commas.\n str = str.replace(/,/g, \"\");\n\n // Replace colons and hyphens with space for easy parsing.\n str = str.replace(/:|\\-/g, \" \");\n\n // Parse new location.\n var chrom_pos = str.split(/\\s+/),\n chrom = chrom_pos[0],\n new_low = chrom_pos[1]\n ? parseInt(chrom_pos[1], 10)\n : undefined,\n new_high = chrom_pos[2]\n ? parseInt(chrom_pos[2], 10)\n : undefined;\n\n this.change_chrom(chrom, new_low, new_high);\n },\n\n move_fraction: function(fraction) {\n var view = this;\n var span = view.high - view.low;\n this.move_delta(fraction * span);\n },\n\n move_delta: function(delta_chrom) {\n //\n // Update low, high.\n //\n\n var view = this;\n var current_chrom_span = view.high - view.low;\n // Check for left and right boundaries\n if (view.low - delta_chrom < view.max_low) {\n view.low = view.max_low;\n view.high = view.max_low + current_chrom_span;\n } else if (view.high - delta_chrom > view.max_high) {\n view.high = view.max_high;\n view.low = view.max_high - current_chrom_span;\n } else {\n view.high -= delta_chrom;\n view.low -= delta_chrom;\n }\n\n //\n // Redraw view.\n //\n\n // Redraw without requesting more data immediately.\n view.request_redraw({ data_fetch: false });\n\n // Set up timeout to redraw with more data when moving stops.\n if (this.redraw_on_move_fn) {\n clearTimeout(this.redraw_on_move_fn);\n }\n\n this.redraw_on_move_fn = setTimeout(function() {\n view.request_redraw();\n }, 200);\n\n // Navigate.\n var chrom = view.chrom_select.val();\n this.trigger_navigate(chrom, view.low, view.high, true);\n },\n\n /**\n * Add a drawable to the view.\n */\n add_drawable: function(drawable) {\n DrawableCollection.prototype.add_drawable.call(this, drawable);\n drawable.init();\n this.changed();\n this.update_intro_div();\n\n // When drawable config changes, mark view as changed. This\n // captures most (all?) state change that needs to be saved.\n var self = this;\n drawable.config.on(\"change\", function() {\n self.changed();\n });\n },\n\n add_label_track: function(label_track) {\n label_track.view = this;\n label_track.init();\n this.label_tracks.push(label_track);\n },\n\n /**\n * Remove drawable from the view.\n */\n remove_drawable: function(drawable, hide) {\n DrawableCollection.prototype.remove_drawable.call(\n this,\n drawable\n );\n if (hide) {\n var view = this;\n drawable.container_div.hide(0, function() {\n $(this).remove();\n view.update_intro_div();\n });\n }\n },\n\n reset: function() {\n this.low = this.max_low;\n this.high = this.max_high;\n this.viewport_container.find(\".yaxislabel\").remove();\n },\n\n /**\n * Request that view redraw one or more of view's drawables. If drawable is not specified,\n * all drawables are redrawn.\n */\n request_redraw: function(options, drawable) {\n var view = this,\n // Either redrawing a single drawable or all view's drawables.\n track_list = drawable ? [drawable] : view.drawables;\n\n // Add/update tracks in track list to redraw list.\n _.each(track_list, function(track) {\n var track_options = _.find(\n view.tracks_to_be_redrawn,\n function(to) {\n return to[0] === track;\n }\n );\n\n if (track_options) {\n // Track already in list; update options.\n track_options[1] = options;\n } else {\n // Track not in list yet.\n view.tracks_to_be_redrawn.push([track, options]);\n }\n });\n\n // Set up redraw if it has not been requested since last redraw.\n if (!this.requested_redraw) {\n requestAnimationFrame(function() {\n view._redraw();\n });\n this.requested_redraw = true;\n }\n },\n\n /**\n * Redraws view and tracks.\n * NOTE: this method should never be called directly; request_redraw() should be used so\n * that requestAnimationFrame can manage redrawing.\n */\n _redraw: function() {\n // TODO: move this code to function that does location setting.\n\n // Clear because requested redraw is being handled now.\n this.requested_redraw = false;\n\n var low = this.low,\n high = this.high;\n\n if (low < this.max_low) {\n low = this.max_low;\n }\n if (high > this.max_high) {\n high = this.max_high;\n }\n var span = this.high - this.low;\n if (this.high !== 0 && span < this.min_separation) {\n high = low + this.min_separation;\n }\n this.low = Math.floor(low);\n this.high = Math.ceil(high);\n\n this.update_location(this.low, this.high);\n\n // -- Drawing code --\n\n // Resolution is a pixel density.\n this.resolution_px_b =\n this.viewport_container.width() / (this.high - this.low);\n\n // Overview\n var left_px =\n this.low /\n (this.max_high - this.max_low) *\n this.overview_viewport.width() || 0;\n var width_px =\n (this.high - this.low) /\n (this.max_high - this.max_low) *\n this.overview_viewport.width() || 0;\n var min_width_px = 13;\n\n this.overview_box\n .css({\n left: left_px,\n width: Math.max(min_width_px, width_px)\n })\n .show();\n if (width_px < min_width_px) {\n this.overview_box.css(\n \"left\",\n left_px - (min_width_px - width_px) / 2\n );\n }\n if (this.overview_highlight) {\n this.overview_highlight.css({\n left: left_px,\n width: width_px\n });\n }\n\n // Draw data tracks.\n _.each(this.tracks_to_be_redrawn, function(track_options) {\n var track = track_options[0],\n options = track_options[1];\n if (track) {\n track._draw(options);\n }\n });\n this.tracks_to_be_redrawn = [];\n\n // Draw label tracks.\n _.each(this.label_tracks, function(label_track) {\n label_track._draw();\n });\n },\n\n zoom_in: function(point, container) {\n if (\n this.max_high === 0 ||\n this.high - this.low <= this.min_separation\n ) {\n return;\n }\n var span = this.high - this.low,\n cur_center = span / 2 + this.low,\n new_half = span / this.zoom_factor / 2;\n if (point) {\n cur_center =\n point /\n this.viewport_container.width() *\n (this.high - this.low) +\n this.low;\n }\n this.low = Math.round(cur_center - new_half);\n this.high = Math.round(cur_center + new_half);\n\n this.changed();\n this.request_redraw();\n },\n\n zoom_out: function() {\n if (this.max_high === 0) {\n return;\n }\n var span = this.high - this.low,\n cur_center = span / 2 + this.low,\n new_half = span * this.zoom_factor / 2;\n this.low = Math.round(cur_center - new_half);\n this.high = Math.round(cur_center + new_half);\n this.changed();\n this.request_redraw();\n },\n\n /** Resize viewport. Use this method if header/footer content has changed in size. */\n resize_viewport: function() {\n this.viewport_container.height(\n this.container.height() -\n this.top_container.height() -\n this.bottom_container.height()\n );\n },\n\n /** Called when window is resized. */\n resize_window: function() {\n this.resize_viewport();\n this.request_redraw();\n },\n\n /** Show a Drawable in the overview. */\n set_overview: function(drawable) {\n if (this.overview_drawable) {\n // If drawable to be set as overview is already in overview, do nothing.\n // Otherwise, remove overview.\n if (\n this.overview_drawable.dataset.id ===\n drawable.dataset.id\n ) {\n return;\n }\n this.overview_viewport.find(\".track\").remove();\n }\n\n // Set new overview.\n var overview_drawable = drawable.copy({\n content_div: this.overview_viewport\n }),\n view = this;\n overview_drawable.header_div.hide();\n overview_drawable.is_overview = true;\n view.overview_drawable = overview_drawable;\n this.overview_drawable.postdraw_actions = function() {\n view.overview_highlight\n .show()\n .height(view.overview_drawable.content_div.height());\n view.overview_viewport.height(\n view.overview_drawable.content_div.height() +\n view.overview_box.outerHeight()\n );\n view.overview_close.show();\n view.resize_window();\n };\n view.overview_drawable.request_draw();\n this.changed();\n },\n\n /** Close and reset overview. */\n reset_overview: function() {\n // Update UI.\n $(\".tooltip\").remove();\n this.overview_viewport.find(\".track-tile\").remove();\n this.overview_viewport.height(this.default_overview_height);\n this.overview_box.height(this.default_overview_height);\n this.overview_close.hide();\n this.overview_highlight.hide();\n view.resize_window();\n view.overview_drawable = null;\n }\n });\n\n /**\n * Encapsulation of a tool that users can apply to tracks/datasets.\n */\n var TracksterTool = tools_mod.Tool.extend({\n defaults: {\n track: null\n },\n\n initialize: function(options) {\n tools_mod.Tool.prototype.initialize.call(this, options);\n\n // Restore tool visibility from state; default to hidden.\n var hidden = true;\n if (\n options.tool_state !== undefined &&\n options.tool_state.hidden !== undefined\n ) {\n hidden = options.tool_state.hidden;\n }\n this.set(\"hidden\", hidden);\n\n // FIXME: need to restore tool values from options.tool_state\n\n // HACK: remove some inputs because Trackster does yet not work with them.\n this.remove_inputs([\"data\", \"hidden_data\", \"conditional\"]);\n },\n\n state_dict: function(options) {\n return _.extend(this.get_inputs_dict(), {\n hidden: !this.is_visible()\n });\n }\n });\n\n /**\n * View renders tool parameter HTML and updates parameter value as it is changed in the HTML.\n */\n var ToolParameterView = Backbone.View.extend({\n events: {\n \"change :input\": \"update_value\"\n },\n\n render: function() {\n var param_div = this.$el.addClass(\"param-row\"),\n param = this.model;\n\n // Param label.\n var label_div = $(\" \")\n .addClass(\"param-label\")\n .text(param.get(\"label\"))\n .appendTo(param_div);\n // Param HTML.\n var html_div = $(\"\")\n .addClass(\"param-input\")\n .html(param.get(\"html\"))\n .appendTo(param_div);\n // Set initial value.\n html_div.find(\":input\").val(param.get(\"value\"));\n\n // Add to clear floating layout.\n $(\"\").appendTo(param_div);\n },\n\n update_value: function(update_event) {\n this.model.set_value($(update_event.target).val());\n }\n });\n\n /**\n * View for TracksterTool.\n */\n var TracksterToolView = Backbone.View.extend({\n initialize: function(options) {\n this.model.on(\"change:hidden\", this.set_visible, this);\n },\n\n /**\n * Render tool UI.\n */\n render: function() {\n var self = this,\n tool = this.model,\n parent_div = this.$el.addClass(\"dynamic-tool\").hide();\n\n // Prevent div events from propogating to other elements.\n parent_div\n .bind(\"drag\", function(e) {\n e.stopPropagation();\n })\n .click(function(e) {\n e.stopPropagation();\n })\n .bind(\"dblclick\", function(e) {\n e.stopPropagation();\n })\n .keydown(function(e) {\n e.stopPropagation();\n });\n\n // Add name, inputs.\n var name_div = $(\"'}),e.prototype=t.extend({},t.fn.tooltip.Constructor.prototype),e.prototype.constructor=e,e.prototype.getDefaults=function(){return e.DEFAULTS},e.prototype.setContent=function(){var t=this.tip(),e=this.getTitle(),i=this.getContent();t.find(".popover-title")[this.options.html?"html":"text"](e),t.find(".popover-content")[this.options.html?"html":"text"](i),t.removeClass("fade top bottom left right in"),t.find(".popover-title").html()||t.find(".popover-title").hide()},e.prototype.hasContent=function(){return this.getTitle()||this.getContent()},e.prototype.getContent=function(){var t=this.$element,e=this.options;return t.attr("data-content")||("function"==typeof e.content?e.content.call(t[0]):e.content)},e.prototype.arrow=function(){return this.$arrow=this.$arrow||this.tip().find(".arrow")},e.prototype.tip=function(){return this.$tip||(this.$tip=t(this.options.template)),this.$tip};var i=t.fn.popover;t.fn.popover=function(i){return this.each(function(){var n=t(this),o=n.data("bs.popover"),s="object"==typeof i&&i;o||n.data("bs.popover",o=new e(this,s)),"string"==typeof i&&o[i]()})},t.fn.popover.Constructor=e,t.fn.popover.noConflict=function(){return t.fn.popover=i,this}}(e)}).call(e,i(0),i(0))},function(t,e){var i;i=function(){return this}();try{i=i||Function("return this")()||(0,eval)("this")}catch(t){"object"==typeof window&&(i=window)}t.exports=i},function(t,e){t.exports=function(){throw new Error("define cannot be used indirect")}},function(t,e,i){"use strict";(function(t,e,n,o,s){function r(t){return t&&t.__esModule?t:{default:t}}function a(e,i,n){function o(t){var e=s(t),i={placeholder:"Click to select",closeOnSelect:!e.is("[MULTIPLE]"),dropdownAutoWidth:!0,containerCssClass:"select2-minwidth"};return t.select2(i)}t.fn.select2&&(void 0===e&&(e=20),void 0===i&&(i=3e3),n=n||s("select"),n.each(function(){var t=s(this).not("[multiple]"),n=t.find("option").length;n\")\n .appendTo(parent_div)\n .text(tool.get(\"name\"));\n tool.get(\"inputs\").each(function(param) {\n // Render parameter.\n var param_view = new ToolParameterView({ model: param });\n param_view.render();\n parent_div.append(param_view.$el);\n });\n\n // Highlight value for inputs for easy replacement.\n parent_div.find(\"input\").click(function() {\n $(this).select();\n });\n\n // Add buttons for running on dataset, region.\n var run_tool_row = $(\""));return y.length?v+y.join("\n"):""},getCurrentRegionFields:function(){},calcHighlightColor:function(t,e){var i,n,s,r,l=e.get("highlightColor"),u=e.get("highlightLighten");if(l)return l;if(u&&(i=/^#([0-9a-f])([0-9a-f])([0-9a-f])$/i.exec(t)||/^#([0-9a-f]{2})([0-9a-f]{2})([0-9a-f]{2})$/i.exec(t))){for(s=[],n=4===t.length?16:1,r=0;r<3;r++)s[r]=o(a.round(parseInt(i[r+1],16)*n*u),0,255);return"rgb("+s.join(",")+")"}return t}}),b={changeHighlight:function(e){var i,n=this.currentRegion,o=this.target,s=this.regionShapes[n];s&&(i=this.renderRegion(n,e),t.isArray(i)||t.isArray(s)?(o.replaceWithShapes(s,i),this.regionShapes[n]=t.map(i,function(t){return t.id})):(o.replaceWithShape(s,i),this.regionShapes[n]=i.id))},render:function(){var e,i,n,o,s=this.values,r=this.target,a=this.regionShapes;if(this.cls._super.render.call(this)){for(n=s.length;n--;)if(e=this.renderRegion(n))if(t.isArray(e)){for(i=[],o=e.length;o--;)e[o].append(),i.push(e[o].id);a[n]=i}else e.append(),a[n]=e.id;else a[n]=null;r.render()}}},t.fn.sparkline.line=w=i(t.fn.sparkline._base,{type:"line",init:function(t,e,i,n,o){w._super.init.call(this,t,e,i,n,o),this.vertices=[],this.regionMap=[],this.xvalues=[],this.yvalues=[],this.yminmax=[],this.hightlightSpotId=null,this.lastShapeId=null,this.initTarget()},getRegion:function(t,e,i){var n,o=this.regionMap;for(n=o.length;n--;)if(null!==o[n]&&e>=o[n][0]&&e<=o[n][1])return o[n][2]},getCurrentRegionFields:function(){var t=this.currentRegion;return{isNull:null===this.yvalues[t],x:this.xvalues[t],y:this.yvalues[t],color:this.options.get("lineColor"),fillColor:this.options.get("fillColor"),offset:t}},renderHighlight:function(){var t,e,i=this.currentRegion,n=this.target,o=this.vertices[i],s=this.options,r=s.get("spotRadius"),a=s.get("highlightSpotColor"),l=s.get("highlightLineColor");o&&(r&&a&&(t=n.drawCircle(o[0],o[1],r,void 0,a),this.highlightSpotId=t.id,n.insertAfterShape(this.lastShapeId,t)),l&&(e=n.drawLine(o[0],this.canvasTop,o[0],this.canvasTop+this.canvasHeight,l),this.highlightLineId=e.id,n.insertAfterShape(this.lastShapeId,e)))},removeHighlight:function(){var t=this.target;this.highlightSpotId&&(t.removeShapeId(this.highlightSpotId),this.highlightSpotId=null),this.highlightLineId&&(t.removeShapeId(this.highlightLineId),this.highlightLineId=null)},scanValues:function(){var t,e,i,n,o,s=this.values,r=s.length,l=this.xvalues,u=this.yvalues,c=this.yminmax;for(t=0;t\")\n .addClass(\"param-row\")\n .appendTo(parent_div);\n var run_on_dataset_button = $(\"\")\n .attr(\"value\", \"Run on complete dataset\")\n .appendTo(run_tool_row);\n var run_on_region_button = $(\"\")\n .attr(\"value\", \"Run on visible region\")\n .appendTo(run_tool_row);\n run_on_region_button.click(function() {\n // Run tool to create new track.\n self.run_on_region();\n });\n run_on_dataset_button.click(function() {\n self.run_on_dataset();\n });\n\n if (tool.is_visible()) {\n this.$el.show();\n }\n },\n\n /**\n * Show or hide tool depending on tool visibility state.\n */\n set_visible: function() {\n this.$el.toggle(this.model.is_visible());\n },\n\n /**\n * Update tool parameters.\n */\n update_params: function() {\n for (var i = 0; i < this.params.length; i++) {\n this.params[i].update_value();\n }\n },\n\n /**\n * Run tool on dataset. Output is placed in dataset's history and no changes to viz are made.\n */\n run_on_dataset: function() {\n var tool = this.model;\n this.run(\n // URL params.\n {\n target_dataset_id: this.model.get(\"track\").dataset.id,\n action: \"rerun\",\n tool_id: tool.id\n },\n null,\n // Success callback.\n function(track_data) {\n Galaxy.modal.show({\n title: tool.get(\"name\") + \" is Running\",\n body:\n tool.get(\"name\") +\n \" is running on the complete dataset. Tool outputs are in dataset's history.\",\n buttons: {\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n }\n );\n },\n\n /**\n * Run dataset on visible region. This creates a new track and sets the track's contents\n * to the tool's output.\n */\n run_on_region: function() {\n //\n // Create track for tool's output immediately to provide user feedback.\n //\n var track = this.model.get(\"track\"),\n tool = this.model,\n region = new visualization.GenomeRegion({\n chrom: track.view.chrom,\n start: track.view.low,\n end: track.view.high\n }),\n url_params = {\n target_dataset_id: track.dataset.id,\n action: \"rerun\",\n tool_id: tool.id,\n regions: [region.toJSON()]\n },\n current_track = track,\n // Set name of track to include tool name, parameters, and region used.\n track_name =\n tool.get(\"name\") +\n current_track.tool_region_and_parameters_str(region),\n container;\n\n // If track not in a group, create a group for it and add new track to group. If track\n // already in group, add track to group.\n if (current_track.container === view) {\n // Create new group.\n var group = new DrawableGroup(view, view, {\n name: track.config.get_value(\"name\")\n });\n\n // Replace track with group.\n var index = current_track.container.replace_drawable(\n current_track,\n group,\n false\n );\n\n // Update HTML.\n // FIXME: this is ugly way to replace a track with a group -- make this easier via\n // a Drawable or DrawableCollection function.\n group.container_div.insertBefore(\n current_track.view.content_div.children()[index]\n );\n group.add_drawable(current_track);\n current_track.container_div.appendTo(group.content_div);\n container = group;\n } else {\n // Use current group.\n container = current_track.container;\n }\n\n // Create and init new track.\n var new_track = new current_track.constructor(view, container, {\n name: track_name,\n hda_ldda: \"hda\"\n });\n new_track.init_for_tool_data();\n new_track.change_mode(current_track.mode);\n new_track.set_filters_manager(\n current_track.filters_manager.copy(new_track)\n );\n new_track.update_icons();\n container.add_drawable(new_track);\n new_track.tiles_div.text(\"Starting job.\");\n\n // Run tool.\n this.run(\n url_params,\n new_track,\n // Success callback.\n function(track_data) {\n new_track.set_dataset(new data.Dataset(track_data));\n new_track.tiles_div.text(\"Running job.\");\n new_track.init();\n }\n );\n },\n\n /**\n * Run tool using a set of URL params and a success callback.\n */\n run: function(url_params, new_track, success_callback) {\n // Run tool.\n url_params.inputs = this.model.get_inputs_dict();\n var ss_deferred = new util.ServerStateDeferred({\n ajax_settings: {\n url: Galaxy.root + \"api/tools\",\n data: JSON.stringify(url_params),\n dataType: \"json\",\n contentType: \"application/json\",\n type: \"POST\"\n },\n interval: 2000,\n success_fn: function(response) {\n return response !== \"pending\";\n }\n });\n\n // Start with this status message.\n //new_track.container_div.addClass(\"pending\");\n //new_track.content_div.html(DATA_PENDING);\n\n $.when(ss_deferred.go()).then(function(response) {\n if (response === \"no converter\") {\n // No converter available for input datasets, so cannot run tool.\n new_track.container_div.addClass(\"error\");\n new_track.content_div.text(DATA_NOCONVERTER);\n } else if (response.error) {\n // General error.\n new_track.container_div.addClass(\"error\");\n new_track.content_div.text(\n DATA_CANNOT_RUN_TOOL + response.message\n );\n } else {\n // Job submitted and running.\n success_callback(response);\n }\n });\n }\n });\n\n /**\n * Generates scale values based on filter and feature's value for filter.\n */\n var FilterScaler = function(filter, default_val) {\n painters.Scaler.call(this, default_val);\n this.filter = filter;\n };\n\n FilterScaler.prototype.gen_val = function(feature_data) {\n // If filter is not initalized yet, return default val.\n if (\n this.filter.high === Number.MAX_VALUE ||\n this.filter.low === -Number.MAX_VALUE ||\n this.filter.low === this.filter.high\n ) {\n return this.default_val;\n }\n\n // Scaling value is ratio of (filter's value compared to low) to (complete filter range).\n return (\n (parseFloat(feature_data[this.filter.index]) -\n this.filter.low) /\n (this.filter.high - this.filter.low)\n );\n };\n\n /**\n * Tiles drawn by tracks.\n */\n var Tile = function(track, region, w_scale, canvas, data) {\n this.track = track;\n this.region = region;\n this.low = region.get(\"start\");\n this.high = region.get(\"end\");\n this.w_scale = w_scale;\n this.canvas = canvas;\n // Wrap element in div for background and to provide container for tile-specific elements.\n this.html_elt = $(\"\").append(canvas);\n this.data = data;\n this.stale = false;\n };\n\n /**\n * Perform pre-display actions.\n */\n Tile.prototype.predisplay_actions = function() {};\n\n var LineTrackTile = function(track, region, w_scale, canvas, data) {\n Tile.call(this, track, region, w_scale, canvas, data);\n };\n LineTrackTile.prototype.predisplay_actions = function() {};\n\n var FeatureTrackTile = function(\n track,\n region,\n w_scale,\n canvas,\n data,\n mode,\n message,\n all_slotted,\n feature_mapper,\n incomplete_features,\n seq_data\n ) {\n // Attribute init.\n Tile.call(this, track, region, w_scale, canvas, data);\n this.mode = mode;\n this.all_slotted = all_slotted;\n this.feature_mapper = feature_mapper;\n this.has_icons = false;\n this.incomplete_features = incomplete_features;\n // Features drawn based on data from other tiles.\n this.other_tiles_features_drawn = {};\n this.seq_data = seq_data;\n\n // Add message + action icons to tile's html.\n /*\n This does not work right now because a random set of reads is returned by the server.\n When the server can respond with more data systematically, renable these icons.\n if (message) {\n this.has_icons = true;\n\n var\n tile = this;\n canvas = this.html_elt.children()[0],\n message_div = $(\"\").addClass(\"tile-message\")\n // -1 to account for border.\n .css({'height': ERROR_PADDING, 'width': canvas.width}).prependTo(this.html_elt);\n\n // Handle message; only message currently is that only the first N elements are displayed.\n var tile_region = new visualization.GenomeRegion({\n chrom: track.view.chrom,\n start: this.low,\n end: this.high\n }),\n num_features = data.length,\n more_down_icon = $(\"\").addClass(\"icon more-down\")\n .attr(\"title\", \"For speed, only the first \" + num_features + \" features in this region were obtained from server. Click to get more data including depth\")\n .tooltip().appendTo(message_div),\n more_across_icon = $(\"\").addClass(\"icon more-across\")\n .attr(\"title\", \"For speed, only the first \" + num_features + \" features in this region were obtained from server. Click to get more data excluding depth\")\n .tooltip().appendTo(message_div);\n\n // Set up actions for icons.\n more_down_icon.click(function() {\n // Mark tile as stale, request more data, and redraw track.\n tile.stale = true;\n track.data_manager.get_more_data(tile_region, track.mode, 1 / tile.w_scale, {}, track.data_manager.DEEP_DATA_REQ);\n $(\".tooltip\").hide();\n track.request_draw();\n }).dblclick(function(e) {\n // Do not propogate as this would normally zoom in.\n e.stopPropagation();\n });\n\n more_across_icon.click(function() {\n // Mark tile as stale, request more data, and redraw track.\n tile.stale = true;\n track.data_manager.get_more_data(tile_region, track.mode, 1 / tile.w_scale, {}, track.data_manager.BROAD_DATA_REQ);\n $(\".tooltip\").hide();\n track.request_draw();\n }).dblclick(function(e) {\n // Do not propogate as this would normally zoom in.\n e.stopPropagation();\n });\n }\n */\n };\n extend(FeatureTrackTile.prototype, Tile.prototype);\n\n /**\n * Sets up support for popups.\n */\n FeatureTrackTile.prototype.predisplay_actions = function() {\n /*\n FIXME: use a canvas library to handle popups.\n //\n // Add support for popups.\n //\n var tile = this,\n popups = {};\n\n // Only show popups in Pack mode.\n if (tile.mode !== \"Pack\") { return; }\n\n $(this.html_elt).hover(\n function() {\n this.hovered = true;\n $(this).mousemove();\n },\n function() {\n this.hovered = false;\n // Clear popup if it is still hanging around (this is probably not needed)\n $(this).parents(\".track-content\").children(\".overlay\").children(\".feature-popup\").remove();\n } ).mousemove(function (e) {\n // Use the hover plugin to get a delay before showing popup\n if ( !this.hovered ) { return; }\n // Get feature data for position.\n var\n this_offset = $(this).offset(),\n offsetX = e.pageX - this_offset.left,\n offsetY = e.pageY - this_offset.top,\n feature_data = tile.feature_mapper.get_feature_data(offsetX, offsetY),\n feature_uid = (feature_data ? feature_data[0] : null);\n // Hide visible popup if not over a feature or over a different feature.\n $(this).parents(\".track-content\").children(\".overlay\").children(\".feature-popup\").each(function() {\n if ( !feature_uid ||\n $(this).attr(\"id\") !== feature_uid.toString() ) {\n $(this).remove();\n }\n });\n\n if (feature_data) {\n // Get or create popup.\n var popup = popups[feature_uid];\n if (!popup) {\n // Create feature's popup element.\n var feature_dict = {\n name: feature_data[3],\n start: feature_data[1],\n end: feature_data[2],\n strand: feature_data[4]\n },\n filters = tile.track.filters_manager.filters,\n filter;\n\n // Add filter values to feature dict.\n for (var i = 0; i < filters.length; i++) {\n filter = filters[i];\n feature_dict[filter.name] = feature_data[filter.index];\n }\n\n // Build popup.\n popup = $(\"\").attr(\"id\", feature_uid).addClass(\"feature-popup\");\n var table = $(\"").hide().addClass(this.options.resultsClass).css({position:"absolute"}),t("body").append(this.dom.$results),e.keydown(function(t){switch(o.lastKeyPressed_=t.keyCode,o.lastKeyPressed_){case o.options.delimiterKeyCode:o.options.useDelimiter&&o.active_&&o.selectCurrent();break;case 35:case 36:case 16:case 17:case 18:case 37:case 39:break;case 38:return t.preventDefault(),o.active_?o.focusPrev():o.activate(),!1;case 40:return t.preventDefault(),o.active_?o.focusNext():o.activate(),!1;case 9:if(o.active_&&(o.selectCurrent(),o.options.preventDefaultTab))return t.preventDefault(),!1;if(2===o.options.preventDefaultTab)return t.preventDefault(),!1;break;case 13:if(o.active_&&(o.selectCurrent(),o.options.preventDefaultReturn))return t.preventDefault(),!1;if(2===o.options.preventDefaultReturn)return t.preventDefault(),!1;break;case 27:if(o.active_)return t.preventDefault(),o.deactivate(!0),!1;break;default:o.activate()}}),e.on("paste",function(){o.activate()});var s=function(){o.deactivate(!0)};e.blur(function(){o.finishOnBlur_&&(o.finishTimeout_=setTimeout(s,200))}),e.parents("form").on("submit",s)},t.Autocompleter.prototype.position=function(){var e=this.dom.$elem.offset(),i=this.dom.$results.outerHeight(),n=t(window).outerHeight(),o=e.top+this.dom.$elem.outerHeight(),s=o+i,r={top:o,left:e.left};if(s>n){var a=e.top-i;a>=0&&(r.top=a)}this.dom.$results.css(r)},t.Autocompleter.prototype.cacheRead=function(t){var e,i,n,o,s;if(this.options.useCache)for(t=String(t),e=t.length,i=this.options.matchSubset?1:e;i<=e;){for(o=this.options.matchInside?e-i:0,s=0;s<=o;){if(n=t.substr(0,i),void 0!==this.cacheData_[n])return this.cacheData_[n];s++}i++}return!1},t.Autocompleter.prototype.cacheWrite=function(t,e){return!!this.options.useCache&&(this.cacheLength_>=this.options.maxCacheLength&&this.cacheFlush(),t=String(t),void 0!==this.cacheData_[t]&&this.cacheLength_++,this.cacheData_[t]=e,this.cacheData_[t])},t.Autocompleter.prototype.cacheFlush=function(){this.cacheData_={},this.cacheLength_=0},t.Autocompleter.prototype.callHook=function(e,i){var n=this.options[e];return!(!n||!t.isFunction(n))&&n(i,this)},t.Autocompleter.prototype.activate=function(){if(this.options.enabled){var t=this;this.keyTimeout_&&clearTimeout(this.keyTimeout_),this.keyTimeout_=setTimeout(function(){t.activateNow()},this.options.delay)}},t.Autocompleter.prototype.activateNow=function(){var t=this.beforeUseConverter(this.dom.$elem.val());t!==this.lastProcessedValue_&&t!==this.lastSelectedValue_&&this.fetchData(t)},t.Autocompleter.prototype.fetchData=function(t){var e=this,i=function(t,i){e.options.processData&&(t=e.options.processData(t)),e.showResults(e.filterResults(t,i),i)};this.lastProcessedValue_=t,t.length\"),\n key, value, row;\n for (key in feature_dict) {\n value = feature_dict[key];\n row = $(\"
\").appendTo(table);\n $(\" \").appendTo(row).text(key);\n $(\" \").attr(\"align\", \"left\").appendTo(row)\n .text(typeof(value) === 'number' ? round(value, 2) : value);\n }\n popup.append( $(\" \").append( table ) );\n popups[feature_uid] = popup;\n }\n\n // Attach popup to track's overlay.\n popup.appendTo( $(this).parents(\".track-content\").children(\".overlay\") );\n\n // Offsets are within canvas, but popup must be positioned relative to parent element.\n // parseInt strips \"px\" from left, top measurements. +7 so that mouse pointer does not\n // overlap popup.\n var\n popupX = offsetX + parseInt( tile.html_elt.css(\"left\"), 10 ) - popup.width() / 2,\n popupY = offsetY + parseInt( tile.html_elt.css(\"top\"), 10 ) + 7;\n popup.css(\"left\", popupX + \"px\").css(\"top\", popupY + \"px\");\n }\n else if (!e.isPropagationStopped()) {\n // Propogate event to other tiles because overlapping tiles prevent mousemove from being\n // called on tiles under this tile.\n e.stopPropagation();\n $(this).siblings().each(function() {\n $(this).trigger(e);\n });\n }\n })\n .mouseleave(function() {\n $(this).parents(\".track-content\").children(\".overlay\").children(\".feature-popup\").remove();\n });\n */\n };\n\n /**\n * Tracks are objects can be added to the View.\n *\n * Track object hierarchy:\n * Track\n * -> LabelTrack\n * -> TiledTrack\n * ----> LineTrack\n * ----> ReferenceTrack\n * ----> FeatureTrack\n * -------> ReadTrack\n * ----> VariantTrack\n */\n var Track = function(view, container, obj_dict) {\n // For now, track's container is always view.\n extend(obj_dict, {\n drag_handle_class: \"draghandle\"\n });\n Drawable.call(this, view, container, obj_dict);\n\n //\n // Attribute init.\n //\n\n // Set or create dataset.\n this.dataset = null;\n if (obj_dict.dataset) {\n // Dataset can be a Backbone model or a dict that can be used to create a model.\n this.dataset =\n obj_dict.dataset instanceof Backbone.Model\n ? obj_dict.dataset\n : new data.Dataset(obj_dict.dataset);\n }\n this.dataset_check_type = \"converted_datasets_state\";\n this.data_url_extra_params = {};\n this.data_query_wait =\n \"data_query_wait\" in obj_dict\n ? obj_dict.data_query_wait\n : DEFAULT_DATA_QUERY_WAIT;\n // A little ugly creating data manager right now due to transition to Backbone-based objects.\n this.data_manager =\n \"data_manager\" in obj_dict\n ? obj_dict.data_manager\n : new visualization.GenomeDataManager({\n dataset: this.dataset,\n // HACK: simulate 'genome' attributes from view for now.\n // View should eventually use Genome object.\n genome: new visualization.Genome({\n key: view.dbkey,\n chroms_info: {\n chrom_info: view.chrom_data\n }\n }),\n data_mode_compatible: this.data_and_mode_compatible,\n can_subset: this.can_subset\n });\n\n // Height attributes: min height, max height, and visible height.\n this.min_height_px = 16;\n this.max_height_px = 800;\n this.visible_height_px = this.config.get_value(\"height\");\n\n //\n // Create content div, which is where track is displayed, and add to container if available.\n //\n this.content_div = $(\"'}),e.prototype=t.extend({},t.fn.tooltip.Constructor.prototype),e.prototype.constructor=e,e.prototype.getDefaults=function(){return e.DEFAULTS},e.prototype.setContent=function(){var t=this.tip(),e=this.getTitle(),i=this.getContent();t.find(".popover-title")[this.options.html?"html":"text"](e),t.find(".popover-content")[this.options.html?"html":"text"](i),t.removeClass("fade top bottom left right in"),t.find(".popover-title").html()||t.find(".popover-title").hide()},e.prototype.hasContent=function(){return this.getTitle()||this.getContent()},e.prototype.getContent=function(){var t=this.$element,e=this.options;return t.attr("data-content")||("function"==typeof e.content?e.content.call(t[0]):e.content)},e.prototype.arrow=function(){return this.$arrow=this.$arrow||this.tip().find(".arrow")},e.prototype.tip=function(){return this.$tip||(this.$tip=t(this.options.template)),this.$tip};var i=t.fn.popover;t.fn.popover=function(i){return this.each(function(){var n=t(this),o=n.data("bs.popover"),s="object"==typeof i&&i;o||n.data("bs.popover",o=new e(this,s)),"string"==typeof i&&o[i]()})},t.fn.popover.Constructor=e,t.fn.popover.noConflict=function(){return t.fn.popover=i,this}}(e)}).call(e,i(0),i(0))},function(t,e){var i;i=function(){return this}();try{i=i||Function("return this")()||(0,eval)("this")}catch(t){"object"==typeof window&&(i=window)}t.exports=i},function(t,e){t.exports=function(){throw new Error("define cannot be used indirect")}},function(t,e,i){"use strict";(function(t,e,n,o,s){function r(t){return t&&t.__esModule?t:{default:t}}function a(e,i,n){function o(t){var e=s(t),i={placeholder:"Click to select",closeOnSelect:!e.is("[MULTIPLE]"),dropdownAutoWidth:!0,containerCssClass:"select2-minwidth"};return t.select2(i)}t.fn.select2&&(void 0===e&&(e=20),void 0===i&&(i=3e3),n=n||s("select"),n.each(function(){var t=s(this).not("[multiple]"),n=t.find("option").length;n\").appendTo(\n this.container_div\n );\n if (this.container) {\n this.container.content_div.append(this.container_div);\n if (!(\"resize\" in obj_dict) || obj_dict.resize) {\n this.add_resize_handle();\n }\n }\n };\n\n extend(Track.prototype, Drawable.prototype, {\n action_icons_def: [\n // Change track mode.\n {\n name: \"mode_icon\",\n title: \"Set display mode\",\n css_class: \"chevron-expand\",\n on_click_fn: function() {}\n },\n // Hide/show content.\n Drawable.prototype.action_icons_def[0],\n // Set track as overview.\n {\n name: \"overview_icon\",\n title: \"Set as overview\",\n css_class: \"application-dock-270\",\n on_click_fn: function(track) {\n track.view.set_overview(track);\n }\n },\n // Edit config.\n Drawable.prototype.action_icons_def[1],\n // Toggle track filters.\n {\n name: \"filters_icon\",\n title: \"Filters\",\n css_class: \"ui-slider-050\",\n on_click_fn: function(drawable) {\n // TODO: update Tooltip text.\n if (drawable.filters_manager.visible()) {\n drawable.filters_manager.clear_filters();\n } else {\n drawable.filters_manager.init_filters();\n }\n drawable.filters_manager.toggle();\n }\n },\n // Toggle track tool.\n {\n name: \"tools_icon\",\n title: \"Tool\",\n css_class: \"hammer\",\n on_click_fn: function(track) {\n // TODO: update Tooltip text.\n\n track.tool.toggle();\n\n // Update track name.\n if (track.tool.is_visible()) {\n track.set_name(\n track.config.get_value(\"name\") +\n track.tool_region_and_parameters_str()\n );\n } else {\n track.revert_name();\n }\n // HACK: name change modifies icon placement, which leaves tooltip incorrectly placed.\n $(\".tooltip\").remove();\n }\n },\n // Go to parameter exploration visualization.\n {\n name: \"param_space_viz_icon\",\n title: \"Tool parameter space visualization\",\n css_class: \"arrow-split\",\n on_click_fn: function(track) {\n var html =\n \"Tool:\" +\n track.tool.get(\"name\") +\n \""));return y.length?v+y.join("\n"):""},getCurrentRegionFields:function(){},calcHighlightColor:function(t,e){var i,n,s,r,l=e.get("highlightColor"),u=e.get("highlightLighten");if(l)return l;if(u&&(i=/^#([0-9a-f])([0-9a-f])([0-9a-f])$/i.exec(t)||/^#([0-9a-f]{2})([0-9a-f]{2})([0-9a-f]{2})$/i.exec(t))){for(s=[],n=4===t.length?16:1,r=0;r<3;r++)s[r]=o(a.round(parseInt(i[r+1],16)*n*u),0,255);return"rgb("+s.join(",")+")"}return t}}),b={changeHighlight:function(e){var i,n=this.currentRegion,o=this.target,s=this.regionShapes[n];s&&(i=this.renderRegion(n,e),t.isArray(i)||t.isArray(s)?(o.replaceWithShapes(s,i),this.regionShapes[n]=t.map(i,function(t){return t.id})):(o.replaceWithShape(s,i),this.regionShapes[n]=i.id))},render:function(){var e,i,n,o,s=this.values,r=this.target,a=this.regionShapes;if(this.cls._super.render.call(this)){for(n=s.length;n--;)if(e=this.renderRegion(n))if(t.isArray(e)){for(i=[],o=e.length;o--;)e[o].append(),i.push(e[o].id);a[n]=i}else e.append(),a[n]=e.id;else a[n]=null;r.render()}}},t.fn.sparkline.line=w=i(t.fn.sparkline._base,{type:"line",init:function(t,e,i,n,o){w._super.init.call(this,t,e,i,n,o),this.vertices=[],this.regionMap=[],this.xvalues=[],this.yvalues=[],this.yminmax=[],this.hightlightSpotId=null,this.lastShapeId=null,this.initTarget()},getRegion:function(t,e,i){var n,o=this.regionMap;for(n=o.length;n--;)if(null!==o[n]&&e>=o[n][0]&&e<=o[n][1])return o[n][2]},getCurrentRegionFields:function(){var t=this.currentRegion;return{isNull:null===this.yvalues[t],x:this.xvalues[t],y:this.yvalues[t],color:this.options.get("lineColor"),fillColor:this.options.get("fillColor"),offset:t}},renderHighlight:function(){var t,e,i=this.currentRegion,n=this.target,o=this.vertices[i],s=this.options,r=s.get("spotRadius"),a=s.get("highlightSpotColor"),l=s.get("highlightLineColor");o&&(r&&a&&(t=n.drawCircle(o[0],o[1],r,void 0,a),this.highlightSpotId=t.id,n.insertAfterShape(this.lastShapeId,t)),l&&(e=n.drawLine(o[0],this.canvasTop,o[0],this.canvasTop+this.canvasHeight,l),this.highlightLineId=e.id,n.insertAfterShape(this.lastShapeId,e)))},removeHighlight:function(){var t=this.target;this.highlightSpotId&&(t.removeShapeId(this.highlightSpotId),this.highlightSpotId=null),this.highlightLineId&&(t.removeShapeId(this.highlightLineId),this.highlightLineId=null)},scanValues:function(){var t,e,i,n,o,s=this.values,r=s.length,l=this.xvalues,u=this.yvalues,c=this.yminmax;for(t=0;t
\" +\n \"Dataset:\" +\n track.config.get_value(\"name\") +\n \"
\" +\n 'Region(s): \";\n var cancel_fn = function() {\n Galaxy.modal.hide();\n $(window).unbind(\"keypress.check_enter_esc\");\n },\n ok_fn = function() {\n var regions_to_use = $(\n 'select[name=\"regions\"] option:selected'\n ).val(),\n regions,\n view_region = new visualization.GenomeRegion(\n {\n chrom: view.chrom,\n start: view.low,\n end: view.high\n }\n ),\n bookmarked_regions = _.map(\n $(\".bookmark\"),\n function(elt) {\n return new visualization.GenomeRegion(\n {\n from_str: $(elt)\n .children(\".position\")\n .text()\n }\n );\n }\n );\n\n // Get regions for visualization.\n if (regions_to_use === \"cur\") {\n // Use only current region.\n regions = [view_region];\n } else if (regions_to_use === \"bookmarks\") {\n // Use only bookmarks.\n regions = bookmarked_regions;\n } else {\n // Use both current region and bookmarks.\n regions = [view_region].concat(\n bookmarked_regions\n );\n }\n\n Galaxy.modal.hide();\n\n // Go to visualization.\n window.location.href =\n Galaxy.root +\n \"visualization/sweepster\" +\n \"?\" +\n $.param({\n dataset_id: track.dataset.id,\n hda_ldda: track.dataset.get(\"hda_ldda\"),\n regions: JSON.stringify(\n new Backbone.Collection(\n regions\n ).toJSON()\n )\n });\n },\n check_enter_esc = function(e) {\n if ((e.keyCode || e.which) === 27) {\n // Escape key\n cancel_fn();\n } else if ((e.keyCode || e.which) === 13) {\n // Enter key\n ok_fn();\n }\n };\n\n // show dialog\n Galaxy.modal.show({\n title:\n \"Visualize tool parameter space and output from different parameter settings?\",\n body: html,\n buttons: { No: cancel_fn, Yes: ok_fn }\n });\n }\n },\n // Remove track.\n Drawable.prototype.action_icons_def[2]\n ],\n\n can_draw: function() {\n return this.dataset && Drawable.prototype.can_draw.call(this);\n },\n\n build_container_div: function() {\n return $(\"\")\n .addClass(\"track\")\n .attr(\"id\", \"track_\" + this.id);\n },\n\n /**\n * Set track's dataset.\n */\n set_dataset: function(dataset) {\n this.dataset = dataset;\n this.data_manager.set(\"dataset\", dataset);\n },\n\n /**\n * Action to take during resize.\n */\n on_resize: function() {\n this.request_draw({ clear_tile_cache: true });\n },\n\n /**\n * Add resizing handle to drawable's container_div.\n */\n add_resize_handle: function() {\n var track = this;\n var in_handle = false;\n var in_drag = false;\n var drag_control = $(\"\");\n // Control shows on hover over track, stays while dragging\n $(track.container_div).hover(\n function() {\n if (track.config.get_value(\"content_visible\")) {\n in_handle = true;\n drag_control.show();\n }\n },\n function() {\n in_handle = false;\n if (!in_drag) {\n drag_control.hide();\n }\n }\n );\n // Update height and force redraw of current view while dragging,\n // clear cache to force redraw of other tiles.\n drag_control\n .hide()\n .bind(\"dragstart\", function(e, d) {\n in_drag = true;\n d.original_height = $(track.content_div).height();\n })\n .bind(\"drag\", function(e, d) {\n var new_height = Math.min(\n Math.max(\n d.original_height + d.deltaY,\n track.min_height_px\n ),\n track.max_height_px\n );\n $(track.tiles_div).css(\"height\", new_height);\n track.visible_height_px =\n track.max_height_px === new_height ? 0 : new_height;\n track.on_resize();\n })\n .bind(\"dragend\", function(e, d) {\n track.tile_cache.clear();\n in_drag = false;\n if (!in_handle) {\n drag_control.hide();\n }\n track.config.set_value(\n \"height\",\n track.visible_height_px\n );\n track.changed();\n })\n .appendTo(track.container_div);\n },\n\n /**\n * Hide any elements that are part of the tracks contents area. Should\n * remove as approprite, the track will be redrawn by show_contents.\n */\n hide_contents: function() {\n // Hide tiles.\n this.tiles_div.hide();\n // Hide any y axis labels (common to several track types)\n this.container_div.find(\".yaxislabel, .track-resize\").hide();\n },\n\n show_contents: function() {\n // Show the contents div and labels (if present)\n this.tiles_div.show();\n this.container_div.find(\".yaxislabel, .track-resize\").show();\n // Request a redraw of the content\n this.request_draw();\n },\n\n /**\n * Returns track type.\n */\n get_type: function() {\n // Order is important: start with most-specific classes and go up the track hierarchy.\n if (this instanceof LabelTrack) {\n return \"LabelTrack\";\n } else if (this instanceof ReferenceTrack) {\n return \"ReferenceTrack\";\n } else if (this instanceof LineTrack) {\n return \"LineTrack\";\n } else if (this instanceof ReadTrack) {\n return \"ReadTrack\";\n } else if (this instanceof VariantTrack) {\n return \"VariantTrack\";\n } else if (this instanceof CompositeTrack) {\n return \"CompositeTrack\";\n } else if (this instanceof FeatureTrack) {\n return \"FeatureTrack\";\n }\n return \"\";\n },\n\n /**\n * Remove visualization content and display message.\n */\n show_message: function(msg_html) {\n this.tiles_div.remove();\n return $(\"\")\n .addClass(\"message\")\n .html(msg_html)\n .appendTo(this.content_div);\n },\n\n /**\n * Initialize and draw the track.\n */\n init: function(retry) {\n // FIXME: track should have a 'state' attribute that is checked on load; this state attribute should be\n // used in this function to determine what action(s) to take.\n\n var track = this;\n track.enabled = false;\n track.tile_cache.clear();\n track.data_manager.clear();\n /*\n if (!track.content_div.text()) {\n track.content_div.text(DATA_LOADING);\n }\n */\n // Remove old track content (e.g. tiles, messages).\n track.content_div.children().remove();\n track.container_div.removeClass(\"nodata error pending\");\n\n track.tiles_div = $(\"\")\n .addClass(\"tiles\")\n .appendTo(track.content_div);\n\n //\n // Tracks with no dataset id are handled differently.\n // FIXME: is this really necessary?\n //\n if (!track.dataset.id) {\n return;\n }\n\n // Get dataset state; if state is fine, enable and draw track. Otherwise, show message\n // about track status.\n var init_deferred = $.Deferred(),\n params = {\n hda_ldda: track.dataset.get(\"hda_ldda\"),\n data_type: this.dataset_check_type,\n chrom: track.view.chrom,\n retry: retry\n };\n $.getJSON(this.dataset.url(), params, function(result) {\n if (\n !result ||\n result === \"error\" ||\n result.kind === \"error\"\n ) {\n // Dataset is in error state.\n track.container_div.addClass(\"error\");\n var msg_elt = track.show_message(DATA_ERROR);\n if (result.message) {\n // Add links to (a) show error and (b) try again.\n msg_elt.append(\n $(\"\")\n .text(\"View error\")\n .click(function() {\n Galaxy.modal.show({\n title: \"Trackster Error\",\n body:\n \"").hide().addClass(this.options.resultsClass).css({position:"absolute"}),t("body").append(this.dom.$results),e.keydown(function(t){switch(o.lastKeyPressed_=t.keyCode,o.lastKeyPressed_){case o.options.delimiterKeyCode:o.options.useDelimiter&&o.active_&&o.selectCurrent();break;case 35:case 36:case 16:case 17:case 18:case 37:case 39:break;case 38:return t.preventDefault(),o.active_?o.focusPrev():o.activate(),!1;case 40:return t.preventDefault(),o.active_?o.focusNext():o.activate(),!1;case 9:if(o.active_&&(o.selectCurrent(),o.options.preventDefaultTab))return t.preventDefault(),!1;if(2===o.options.preventDefaultTab)return t.preventDefault(),!1;break;case 13:if(o.active_&&(o.selectCurrent(),o.options.preventDefaultReturn))return t.preventDefault(),!1;if(2===o.options.preventDefaultReturn)return t.preventDefault(),!1;break;case 27:if(o.active_)return t.preventDefault(),o.deactivate(!0),!1;break;default:o.activate()}}),e.on("paste",function(){o.activate()});var s=function(){o.deactivate(!0)};e.blur(function(){o.finishOnBlur_&&(o.finishTimeout_=setTimeout(s,200))}),e.parents("form").on("submit",s)},t.Autocompleter.prototype.position=function(){var e=this.dom.$elem.offset(),i=this.dom.$results.outerHeight(),n=t(window).outerHeight(),o=e.top+this.dom.$elem.outerHeight(),s=o+i,r={top:o,left:e.left};if(s>n){var a=e.top-i;a>=0&&(r.top=a)}this.dom.$results.css(r)},t.Autocompleter.prototype.cacheRead=function(t){var e,i,n,o,s;if(this.options.useCache)for(t=String(t),e=t.length,i=this.options.matchSubset?1:e;i<=e;){for(o=this.options.matchInside?e-i:0,s=0;s<=o;){if(n=t.substr(0,i),void 0!==this.cacheData_[n])return this.cacheData_[n];s++}i++}return!1},t.Autocompleter.prototype.cacheWrite=function(t,e){return!!this.options.useCache&&(this.cacheLength_>=this.options.maxCacheLength&&this.cacheFlush(),t=String(t),void 0!==this.cacheData_[t]&&this.cacheLength_++,this.cacheData_[t]=e,this.cacheData_[t])},t.Autocompleter.prototype.cacheFlush=function(){this.cacheData_={},this.cacheLength_=0},t.Autocompleter.prototype.callHook=function(e,i){var n=this.options[e];return!(!n||!t.isFunction(n))&&n(i,this)},t.Autocompleter.prototype.activate=function(){if(this.options.enabled){var t=this;this.keyTimeout_&&clearTimeout(this.keyTimeout_),this.keyTimeout_=setTimeout(function(){t.activateNow()},this.options.delay)}},t.Autocompleter.prototype.activateNow=function(){var t=this.beforeUseConverter(this.dom.$elem.val());t!==this.lastProcessedValue_&&t!==this.lastSelectedValue_&&this.fetchData(t)},t.Autocompleter.prototype.fetchData=function(t){var e=this,i=function(t,i){e.options.processData&&(t=e.options.processData(t)),e.showResults(e.filterResults(t,i),i)};this.lastProcessedValue_=t,t.length\" +\n result.message +\n \"
\",\n buttons: {\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n })\n );\n msg_elt.append($(\"\").text(\" \"));\n msg_elt.append(\n $(\"\")\n .text(\"Try again\")\n .click(function() {\n track.init(true);\n })\n );\n }\n } else if (result === \"no converter\") {\n track.container_div.addClass(\"error\");\n track.show_message(DATA_NOCONVERTER);\n } else if (\n result === \"no data\" ||\n (result.data !== undefined &&\n (result.data === null || result.data.length === 0))\n ) {\n track.container_div.addClass(\"nodata\");\n track.show_message(DATA_NONE);\n } else if (result === \"pending\") {\n track.container_div.addClass(\"pending\");\n track.show_message(DATA_PENDING);\n //$(\"\").attr(\"src\", image_path + \"/yui/rel_interstitial_loading.gif\").appendTo(track.tiles_div);\n setTimeout(function() {\n track.init();\n }, track.data_query_wait);\n } else if (result === \"data\" || result.status === \"data\") {\n if (result.valid_chroms) {\n track.valid_chroms = result.valid_chroms;\n track.update_icons();\n }\n track.tiles_div.text(DATA_OK);\n if (track.view.chrom) {\n track.tiles_div.text(\"\");\n track.tiles_div.css(\n \"height\",\n track.visible_height_px + \"px\"\n );\n track.enabled = true;\n // predraw_init may be asynchronous, wait for it and then draw\n $.when\n .apply($, track.predraw_init())\n .done(function() {\n init_deferred.resolve();\n track.container_div.removeClass(\n \"nodata error pending\"\n );\n track.request_draw();\n });\n } else {\n init_deferred.resolve();\n }\n }\n });\n\n this.update_icons();\n return init_deferred;\n },\n\n /**\n * Additional initialization required before drawing track for the first time.\n */\n predraw_init: function() {\n var track = this;\n return $.getJSON(\n track.dataset.url(),\n {\n data_type: \"data\",\n stats: true,\n chrom: track.view.chrom,\n low: 0,\n high: track.view.max_high,\n hda_ldda: track.dataset.get(\"hda_ldda\")\n },\n function(result) {\n var data = result.data;\n\n // Tracks may not have stat data either because there is no data or data is not yet ready.\n if (\n data &&\n data.min !== undefined &&\n data.max !== undefined\n ) {\n // Compute default minimum and maximum values\n var min_value = data.min,\n max_value = data.max;\n // If mean and sd are present, use them to compute a ~95% window\n // but only if it would shrink the range on one side\n min_value = Math.floor(\n Math.min(\n 0,\n Math.max(min_value, data.mean - 2 * data.sd)\n )\n );\n max_value = Math.ceil(\n Math.max(\n 0,\n Math.min(max_value, data.mean + 2 * data.sd)\n )\n );\n // Update config, prefs\n track.config.set_default_value(\n \"min_value\",\n min_value\n );\n track.config.set_default_value(\n \"max_value\",\n max_value\n );\n track.config.set_value(\"min_value\", min_value);\n track.config.set_value(\"max_value\", max_value);\n }\n }\n );\n },\n\n /**\n * Returns all drawables in this drawable.\n */\n get_drawables: function() {\n return this;\n }\n });\n\n var TiledTrack = function(view, container, obj_dict) {\n Track.call(this, view, container, obj_dict);\n\n var track = this;\n\n // Make track moveable.\n moveable(\n track.container_div,\n track.drag_handle_class,\n \".group\",\n track\n );\n\n // Attribute init.\n this.filters_manager = new filters_mod.FiltersManager(\n this,\n \"filters\" in obj_dict ? obj_dict.filters : null\n );\n // HACK: set filters manager for data manager.\n // FIXME: prolly need function to set filters and update data_manager reference.\n this.data_manager.set(\"filters_manager\", this.filters_manager);\n this.filters_available = false;\n this.tool = obj_dict.tool\n ? new TracksterTool(\n _.extend(obj_dict.tool, {\n track: this,\n tool_state: obj_dict.tool_state\n })\n )\n : null;\n this.tile_cache = new visualization.Cache(TILE_CACHE_SIZE);\n this.left_offset = 0;\n\n if (this.header_div) {\n //\n // Setup filters.\n //\n this.set_filters_manager(this.filters_manager);\n\n //\n // Create dynamic tool view.\n //\n if (this.tool) {\n var tool_view = new TracksterToolView({ model: this.tool });\n tool_view.render();\n this.dynamic_tool_div = tool_view.$el;\n this.header_div.after(this.dynamic_tool_div);\n }\n }\n\n // Add tiles_div, overlay_div to content_div.\n this.tiles_div = $(\"\")\n .addClass(\"tiles\")\n .appendTo(this.content_div);\n if (!this.config.get_value(\"content_visible\")) {\n this.tiles_div.hide();\n }\n this.overlay_div = $(\"\")\n .addClass(\"overlay\")\n .appendTo(this.content_div);\n\n if (obj_dict.mode) {\n this.change_mode(obj_dict.mode);\n }\n };\n extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, {\n action_icons_def: Track.prototype.action_icons_def.concat([\n // Show more rows when all features are not slotted.\n {\n name: \"show_more_rows_icon\",\n title:\n \"To minimize track height, not all feature rows are displayed. Click to display more rows.\",\n css_class: \"exclamation\",\n on_click_fn: function(track) {\n $(\".tooltip\").remove();\n track.slotters[\n track.view.resolution_px_b\n ].max_rows *= 2;\n track.request_draw({ clear_tile_cache: true });\n },\n hide: true\n }\n ]),\n\n /**\n * Returns a copy of the track. The copy uses the same data manager so that the tracks can share data.\n */\n copy: function(container) {\n // Create copy.\n var obj_dict = this.to_dict();\n extend(obj_dict, {\n data_manager: this.data_manager\n });\n var new_track = new this.constructor(\n this.view,\n container,\n obj_dict\n );\n // Misc. init and return.\n new_track.change_mode(this.mode);\n new_track.enabled = this.enabled;\n return new_track;\n },\n\n /**\n * Set filters manager + HTML elements.\n */\n set_filters_manager: function(filters_manager) {\n this.filters_manager = filters_manager;\n this.header_div.after(this.filters_manager.parent_div);\n },\n\n /**\n * Returns representation of object in a dictionary for easy saving.\n * Use from_dict to recreate object.\n */\n to_dict: function() {\n return {\n track_type: this.get_type(),\n dataset: {\n id: this.dataset.id,\n hda_ldda: this.dataset.get(\"hda_ldda\")\n },\n prefs: this.config.to_key_value_dict(),\n mode: this.mode,\n filters: this.filters_manager.to_dict(),\n tool_state: this.tool ? this.tool.state_dict() : {}\n };\n },\n\n /**\n * Set track bounds for current chromosome.\n */\n set_min_max: function() {\n var track = this;\n\n return $.getJSON(\n track.dataset.url(),\n {\n data_type: \"data\",\n stats: true,\n chrom: track.view.chrom,\n low: 0,\n high: track.view.max_high,\n hda_ldda: track.dataset.get(\"hda_ldda\")\n },\n function(result) {\n var data = result.data;\n if (\n isNaN(\n parseFloat(track.config.get_value(\"min_value\"))\n ) ||\n isNaN(\n parseFloat(track.config.get_value(\"max_value\"))\n )\n ) {\n // Compute default minimum and maximum values\n var min_value = data.min,\n max_value = data.max;\n // If mean and sd are present, use them to compute a ~95% window\n // but only if it would shrink the range on one side\n min_value = Math.floor(\n Math.min(\n 0,\n Math.max(min_value, data.mean - 2 * data.sd)\n )\n );\n max_value = Math.ceil(\n Math.max(\n 0,\n Math.min(max_value, data.mean + 2 * data.sd)\n )\n );\n // Update the prefs\n track.config.set_value(\"min_value\", min_value);\n track.config.set_value(\"max_value\", max_value);\n }\n }\n );\n },\n\n /**\n * Change track's mode.\n */\n change_mode: function(new_mode) {\n var track = this;\n // TODO: is it necessary to store the mode in two places (.mode and track_config)?\n track.mode = new_mode;\n track.config.set_value(\"mode\", new_mode);\n // FIXME: find a better way to get Auto data w/o clearing cache; using mode in the\n // data manager would work if Auto data were checked for compatibility when a specific\n // mode is chosen.\n if (new_mode === \"Auto\") {\n this.data_manager.clear();\n }\n track.request_draw({ clear_tile_cache: true });\n this.action_icons.mode_icon.attr(\n \"title\",\n \"Set display mode (now: \" + track.mode + \")\"\n );\n return track;\n },\n\n /**\n * Update track's buttons.\n */\n update_icons: function() {\n var track = this;\n\n //\n // Show/hide filter icon.\n //\n track.action_icons.filters_icon.toggle(track.filters_available);\n\n //\n // Show/hide tool icons.\n //\n track.action_icons.tools_icon.toggle(track.tool !== null);\n track.action_icons.param_space_viz_icon.toggle(\n track.tool !== null\n );\n },\n\n /**\n * Generate a key for the tile cache.\n * TODO: create a TileCache object (like DataCache) and generate key internally.\n */\n _gen_tile_cache_key: function(w_scale, tile_region) {\n return w_scale + \"_\" + tile_region;\n },\n\n /**\n * Request that track be drawn.\n */\n request_draw: function(options) {\n if (options && options.clear_tile_cache) {\n this.tile_cache.clear();\n }\n this.view.request_redraw(options, this);\n },\n\n /**\n * Actions to be taken before drawing.\n */\n before_draw: function() {\n // Clear because this is set when drawing.\n this.max_height_px = 0;\n },\n\n /**\n * Draw track. Options include:\n * -force: force a redraw rather than use cached tiles (default: false)\n * -clear_after: clear old tiles after drawing new tiles (default: false)\n * -data_fetch: fetch data if necessary (default: true)\n *\n * NOTE: this function should never be called directly; use request_draw() so that drawing\n * management can be used.\n */\n _draw: function(options) {\n if (!this.can_draw()) {\n return;\n }\n\n var clear_after = options && options.clear_after,\n low = this.view.low,\n high = this.view.high,\n range = high - low,\n width = this.view.container.width(),\n w_scale = this.view.resolution_px_b,\n resolution = 1 / w_scale;\n\n // For overview, adjust high, low, resolution, and w_scale.\n if (this.is_overview) {\n low = this.view.max_low;\n high = this.view.max_high;\n w_scale = width / (view.max_high - view.max_low);\n resolution = 1 / w_scale;\n }\n\n this.before_draw();\n\n //\n // Method for moving and/or removing tiles:\n // (a) mark all elements for removal using class 'remove'\n // (b) during tile drawing/placement, remove class for elements that are moved;\n // this occurs in show_tile()\n // (c) after drawing tiles, remove elements still marked for removal\n // (i.e. that still have class 'remove').\n //\n\n // Step (a) for (re)moving tiles.\n this.tiles_div.children().addClass(\"remove\");\n\n var // Tile width in bases.\n tile_width = Math.floor(TILE_SIZE * resolution),\n // Index of first tile that overlaps visible region.\n tile_index = Math.floor(low / tile_width),\n tile_region,\n tile_promise,\n tile_promises = [],\n tiles = [];\n // Draw tiles.\n while (tile_index * tile_width < high) {\n // Get tile region.\n tile_region = new visualization.GenomeRegion({\n chrom: this.view.chrom,\n start: tile_index * tile_width,\n // Tile high cannot be larger than view.max_high, which the chromosome length.\n end: Math.min(\n (tile_index + 1) * tile_width,\n this.view.max_high\n )\n });\n tile_promise = this.draw_helper(\n tile_region,\n w_scale,\n options\n );\n tile_promises.push(tile_promise);\n $.when(tile_promise).then(function(tile) {\n tiles.push(tile);\n });\n\n // Go to next tile.\n tile_index += 1;\n }\n\n // Step (c) for (re)moving tiles when clear_after is false.\n if (!clear_after) {\n this.tiles_div\n .children(\".remove\")\n .removeClass(\"remove\")\n .remove();\n }\n\n // When all tiles are drawn, call post-draw actions.\n var track = this;\n $.when.apply($, tile_promises).then(function() {\n // Step (c) for (re)moving tiles when clear_after is true:\n track.tiles_div.children(\".remove\").remove();\n\n // Only do postdraw actions for tiles; instances where tiles may not be drawn include:\n // (a) ReferenceTrack without sufficient resolution;\n // (b) data_fetch = false.\n tiles = _.filter(tiles, function(t) {\n return t !== null;\n });\n if (tiles.length !== 0) {\n track.postdraw_actions(\n tiles,\n width,\n w_scale,\n clear_after\n );\n }\n });\n },\n\n /**\n * Add a maximum/minimum label to track.\n */\n _add_yaxis_label: function(type, on_change) {\n var track = this,\n css_class = type === \"max\" ? \"top\" : \"bottom\",\n text = type === \"max\" ? \"max\" : \"min\",\n pref_name = type === \"max\" ? \"max_value\" : \"min_value\",\n label = this.container_div.find(\".yaxislabel.\" + css_class),\n value = round(track.config.get_value(pref_name), 1);\n\n // Default action for on_change is to redraw track.\n on_change =\n on_change ||\n function() {\n track.request_draw({ clear_tile_cache: true });\n };\n\n if (label.length !== 0) {\n // Label already exists, so update value.\n label.text(value);\n } else {\n // Add label.\n label = $(\"\")\n .text(value)\n .make_text_editable({\n num_cols: 12,\n on_finish: function(new_val) {\n $(\".tooltip\").remove();\n track.config.set_value(\n pref_name,\n round(new_val, 1)\n );\n on_change();\n },\n help_text: \"Set \" + text + \" value\"\n })\n .addClass(\"yaxislabel \" + css_class)\n .css(\"color\", this.config.get_value(\"label_color\"));\n this.container_div.prepend(label);\n }\n },\n\n /**\n * Actions to be taken after draw has been completed. Draw is completed when all tiles have been\n * drawn/fetched and shown.\n */\n postdraw_actions: function(tiles, width, w_scale, clear_after) {\n var line_track_tiles = _.filter(tiles, function(tile) {\n return tile instanceof LineTrackTile;\n });\n\n //\n // Take different actions depending on whether there are LineTrack/Coverage tiles.\n //\n\n if (line_track_tiles.length > 0) {\n // -- Drawing in Coverage mode. --\n\n // Clear because this is set when drawing.\n this.max_height_px = 0;\n var track = this;\n _.each(tiles, function(tile) {\n if (!(tile instanceof LineTrackTile)) {\n tile.html_elt.remove();\n track.draw_helper(tile.region, w_scale, {\n force: true,\n mode: \"Coverage\"\n });\n }\n });\n\n track._add_yaxis_label(\"max\");\n } else {\n // -- Drawing in non-Coverage mode. --\n\n // Remove Y-axis labels because there are no line track tiles.\n this.container_div.find(\".yaxislabel\").remove();\n\n //\n // If some tiles have icons, set padding of tiles without icons so features and rows align.\n //\n var icons_present = _.find(tiles, function(tile) {\n return tile.has_icons;\n });\n\n if (icons_present) {\n _.each(tiles, function(tile) {\n if (!tile.has_icons) {\n // Need to align with other tile(s) that have icons.\n tile.html_elt.css(\"padding-top\", ERROR_PADDING);\n }\n });\n }\n }\n },\n\n /**\n * Returns appropriate display mode based on data.\n */\n get_mode: function(data) {\n return this.mode;\n },\n\n /**\n * Update track interface to show display mode being used.\n */\n update_auto_mode: function(display_mode) {\n // FIXME: needs to be implemented.\n },\n\n /**\n * Returns a list of drawables to draw. Defaults to current track.\n */\n _get_drawables: function() {\n return [this];\n },\n\n /**\n * Retrieves from cache, draws, or sets up drawing for a single tile. Returns either a Tile object or a\n * jQuery.Deferred object that is fulfilled when tile can be drawn again. Options include:\n * -force: force a redraw rather than use cached tiles (default: false)\n * -data_fetch: fetch data if necessary (default: true)\n */\n draw_helper: function(region, w_scale, options) {\n // Init options if necessary to avoid having to check if options defined.\n if (!options) {\n options = {};\n }\n\n var force = options.force,\n mode = options.mode || this.mode,\n resolution = 1 / w_scale,\n // Useful vars.\n track = this,\n drawables = this._get_drawables(),\n key = this._gen_tile_cache_key(w_scale, region),\n is_tile = function(o) {\n return o && \"track\" in o;\n };\n\n // Check tile cache, if found show existing tile in correct position\n var tile = force ? undefined : track.tile_cache.get_elt(key);\n if (tile) {\n if (is_tile(tile)) {\n track.show_tile(tile, w_scale);\n }\n return tile;\n }\n\n // If not fetching data, nothing more to do because data is needed to draw tile.\n if (options.data_fetch === false) {\n return null;\n }\n\n // Function that returns data/Deferreds needed to draw tile.\n var get_tile_data = function() {\n // HACK: if display mode (mode) is in continuous data modes, data mode must be coverage to get coverage data.\n var data_mode = _.find(CONTINUOUS_DATA_MODES, function(m) {\n return m === mode;\n })\n ? \"Coverage\"\n : mode;\n\n // Map drawable object to data needed for drawing.\n var tile_data = _.map(drawables, function(d) {\n // Get the track data/promise.\n return d.data_manager.get_data(\n region,\n data_mode,\n resolution,\n track.data_url_extra_params\n );\n });\n\n // Get reference data/promise.\n if (view.reference_track) {\n tile_data.push(\n view.reference_track.data_manager.get_data(\n region,\n mode,\n resolution,\n view.reference_track.data_url_extra_params\n )\n );\n }\n\n return tile_data;\n };\n\n //\n // When data is available, draw tile.\n //\n var tile_drawn = $.Deferred();\n track.tile_cache.set_elt(key, tile_drawn);\n $.when.apply($, get_tile_data()).then(function() {\n var tile_data = get_tile_data(),\n tracks_data = tile_data,\n seq_data;\n\n // Deferreds may show up here if trying to fetch a subset of data from a superset data chunk\n // that cannot be subsetted. This may occur if the superset has a message. If there is a\n // Deferred, try again from the top. NOTE: this condition could (should?) be handled by the\n // GenomeDataManager in visualization module.\n if (\n _.find(tile_data, function(d) {\n return util.is_deferred(d);\n })\n ) {\n track.tile_cache.set_elt(key, undefined);\n $.when(\n track.draw_helper(region, w_scale, options)\n ).then(function(tile) {\n tile_drawn.resolve(tile);\n });\n return;\n }\n\n // If sequence data is available, subset to get only data in region.\n if (view.reference_track) {\n seq_data = view.reference_track.data_manager.subset_entry(\n tile_data.pop(),\n region\n );\n }\n\n // Get drawing modes, heights for all tracks.\n var drawing_modes = [],\n drawing_heights = [];\n\n _.each(drawables, function(d, i) {\n var mode = d.mode,\n data = tracks_data[i];\n if (mode === \"Auto\") {\n mode = d.get_mode(data);\n d.update_auto_mode(mode);\n }\n drawing_modes.push(mode);\n drawing_heights.push(\n d.get_canvas_height(data, mode, w_scale, width)\n );\n });\n\n var canvas = track.view.canvas_manager.new_canvas(),\n tile_low = region.get(\"start\"),\n tile_high = region.get(\"end\"),\n all_data_index = 0,\n width =\n Math.ceil((tile_high - tile_low) * w_scale) +\n track.left_offset,\n height = _.max(drawing_heights),\n tile;\n\n //\n // Draw all tracks on tile.\n //\n canvas.width = width;\n // Height is specified in options or is the height found above.\n canvas.height = options.height || height;\n var ctx = canvas.getContext(\"2d\");\n ctx.translate(track.left_offset, 0);\n if (drawables.length > 1) {\n ctx.globalAlpha = 0.5;\n ctx.globalCompositeOperation = \"source-over\";\n }\n _.each(drawables, function(d, i) {\n tile = d.draw_tile(\n tracks_data[i],\n ctx,\n drawing_modes[i],\n region,\n w_scale,\n seq_data\n );\n });\n\n // Don't cache, show if no tile.\n if (tile !== undefined) {\n track.tile_cache.set_elt(key, tile);\n track.show_tile(tile, w_scale);\n }\n\n tile_drawn.resolve(tile);\n });\n\n return tile_drawn;\n },\n\n /**\n * Returns canvas height needed to display data; return value is an integer that denotes the\n * number of pixels required.\n */\n get_canvas_height: function(result, mode, w_scale, canvas_width) {\n return this.visible_height_px;\n },\n\n /**\n * Draw line (bigwig) data onto tile.\n */\n _draw_line_track_tile: function(\n result,\n ctx,\n mode,\n region,\n w_scale\n ) {\n // Set min/max if they are not already set.\n // FIXME: checking for different null/undefined/0 is messy; it would be nice to\n // standardize this.\n if (\n [undefined, null].indexOf(\n this.config.get_value(\"min_value\")\n ) !== -1\n ) {\n this.config.set_value(\"min_value\", 0);\n }\n if (\n [undefined, null, 0].indexOf(\n this.config.get_value(\"max_value\")\n ) !== -1\n ) {\n this.config.set_value(\n \"max_value\",\n _.max(\n _.map(result.data, function(d) {\n return d[1];\n })\n ) || 0\n );\n }\n\n var canvas = ctx.canvas,\n painter = new painters.LinePainter(\n result.data,\n region.get(\"start\"),\n region.get(\"end\"),\n this.config.to_key_value_dict(),\n mode\n );\n painter.draw(ctx, canvas.width, canvas.height, w_scale);\n\n return new LineTrackTile(\n this,\n region,\n w_scale,\n canvas,\n result.data\n );\n },\n\n /**\n * Draw a track tile.\n * @param result result from server\n * @param ctx canvas context to draw on\n * @param mode mode to draw in\n * @param region region to draw on tile\n * @param w_scale pixels per base\n * @param ref_seq reference sequence data\n */\n draw_tile: function(result, ctx, mode, region, w_scale, ref_seq) {},\n\n /**\n * Show track tile and perform associated actions. Showing tile may actually move\n * an existing tile rather than reshowing it.\n */\n show_tile: function(tile, w_scale) {\n var track = this,\n tile_element = tile.html_elt;\n\n // -- Show/move tile element. --\n\n tile.predisplay_actions();\n\n // Position tile element based on current viewport.\n var left = Math.round(\n (tile.low -\n (this.is_overview\n ? this.view.max_low\n : this.view.low)) *\n w_scale\n );\n if (this.left_offset) {\n left -= this.left_offset;\n }\n tile_element.css(\"left\", left);\n\n if (tile_element.hasClass(\"remove\")) {\n // Step (b) for (re)moving tiles. See _draw() function for description of algorithm\n // for removing tiles.\n tile_element.removeClass(\"remove\");\n } else {\n // Showing new tile.\n this.tiles_div.append(tile_element);\n }\n\n // -- Update track, tile heights based on new tile. --\n\n tile_element.css(\"height\", \"auto\");\n\n // Update max height based on current tile's height.\n // BUG/HACK: tile_element.height() returns a height that is always 2 pixels too big, so\n // -2 to get the correct height.\n this.max_height_px = Math.max(\n this.max_height_px,\n tile_element.height() - 2\n );\n\n // Update height for all tiles based on max height.\n tile_element\n .parent()\n .children()\n .css(\"height\", this.max_height_px + \"px\");\n\n // Update track height based on max height and visible height.\n var track_height = this.max_height_px;\n if (this.visible_height_px !== 0) {\n track_height = Math.min(\n this.max_height_px,\n this.visible_height_px\n );\n }\n this.tiles_div.css(\"height\", track_height + \"px\");\n },\n\n /**\n * Utility function that creates a label string describing the region and parameters of a track's tool.\n */\n tool_region_and_parameters_str: function(region) {\n var track = this,\n region_str =\n region !== undefined ? region.toString() : \"all\",\n param_str = _.values(track.tool.get_inputs_dict()).join(\n \", \"\n );\n return (\n \" - region=[\" +\n region_str +\n \"], parameters=[\" +\n param_str +\n \"]\"\n );\n },\n\n /**\n * Returns true if data is compatible with a given mode.\n */\n data_and_mode_compatible: function(data, mode) {\n // Only handle modes that user can set.\n if (mode === \"Auto\") {\n return true;\n } else if (mode === \"Coverage\") {\n // Histogram mode requires bigwig data.\n return data.dataset_type === \"bigwig\";\n } else if (\n data.dataset_type === \"bigwig\" ||\n data.extra_info === \"no_detail\"\n ) {\n // All other modes--Dense, Squish, Pack--require data + details.\n return false;\n } else {\n return true;\n }\n },\n\n /**\n * Returns true if entry can be subsetted.\n */\n can_subset: function(entry) {\n // Do not subset entries with a message or data with no detail.\n if (entry.message || entry.extra_info === \"no_detail\") {\n return false;\n } else if (entry.dataset_type === \"bigwig\") {\n // Subset only if data is single-bp resolution.\n return entry.data[1][0] - entry.data[0][0] === 1;\n }\n\n return true;\n },\n\n /**\n * Set up track to receive tool data.\n */\n init_for_tool_data: function() {\n // Set up track to fetch raw data rather than converted data.\n this.data_manager.set(\"data_type\", \"raw_data\");\n this.data_query_wait = 1000;\n this.dataset_check_type = \"state\";\n\n // FIXME: this is optional and is disabled for now because it creates\n // additional converter jobs without a clear benefit because indexing\n // such a small dataset provides little benefit.\n //\n // Set up one-time, post-draw to clear tool execution settings.\n //\n /*\n this.normal_postdraw_actions = this.postdraw_actions;\n this.postdraw_actions = function(tiles, width, w_scale, clear_after) {\n var self = this;\n\n // Do normal postdraw init.\n self.normal_postdraw_actions(tiles, width, w_scale, clear_after);\n\n // Tool-execution specific post-draw init:\n\n // Reset dataset check, wait time.\n self.dataset_check_type = 'converted_datasets_state';\n self.data_query_wait = DEFAULT_DATA_QUERY_WAIT;\n\n // Reset data URL when dataset indexing has completed/when not pending.\n var ss_deferred = new util.ServerStateDeferred({\n url: self.dataset_state_url,\n url_params: {dataset_id : self.dataset.id, hda_ldda: self.dataset.get('hda_ldda')},\n interval: self.data_query_wait,\n // Set up deferred to check dataset state until it is not pending.\n success_fn: function(result) { return result !== \"pending\"; }\n });\n $.when(ss_deferred.go()).then(function() {\n // Dataset is indexed, so use converted data.\n self.data_manager.set('data_type', 'data');\n });\n\n // Reset post-draw actions function.\n self.postdraw_actions = self.normal_postdraw_actions;\n };\n */\n }\n });\n\n var LabelTrack = function(view, container) {\n Track.call(this, view, container, {\n resize: false,\n header: false\n });\n this.container_div.addClass(\"label-track\");\n };\n extend(LabelTrack.prototype, Track.prototype, {\n init: function() {\n // Enable by default because there should always be data when drawing track.\n this.enabled = true;\n },\n\n /**\n * Additional initialization required before drawing track for the first time.\n */\n predraw_init: function() {},\n\n _draw: function(options) {\n var view = this.view,\n range = view.high - view.low,\n tickDistance = Math.floor(\n Math.pow(10, Math.floor(Math.log(range) / Math.log(10)))\n ),\n position =\n Math.floor(view.low / tickDistance) * tickDistance,\n width = this.view.container.width(),\n new_div = $(\"\").addClass(\"label-container\");\n while (position < view.high) {\n var screenPosition = Math.floor(\n (position - view.low) / range * width\n );\n new_div.append(\n $(\"\")\n .addClass(\"pos-label\")\n .text(util.commatize(position))\n .css({\n left: screenPosition\n })\n );\n position += tickDistance;\n }\n this.content_div.children(\":first\").remove();\n this.content_div.append(new_div);\n }\n });\n\n // FIXME: Composite tracks have code for showing composite tracks with line tracks and\n // composite tracks with line + feature tracks. It's probably best if different classes\n // are created for each type of composite track.\n\n /**\n * A tiled track composed of multiple other tracks. Composite tracks only work with\n * bigwig data for now.\n */\n var CompositeTrack = function(view, container, obj_dict) {\n TiledTrack.call(this, view, container, obj_dict);\n\n // Init drawables; each drawable is a copy so that config/preferences\n // are independent of each other. Also init left offset.\n this.drawables = [];\n if (\"drawables\" in obj_dict) {\n var drawable;\n for (var i = 0; i < obj_dict.drawables.length; i++) {\n drawable = obj_dict.drawables[i];\n this.drawables[i] = object_from_template(\n drawable,\n view,\n null\n );\n\n // Track's left offset is the max of all tracks.\n if (drawable.left_offset > this.left_offset) {\n this.left_offset = drawable.left_offset;\n }\n }\n this.enabled = true;\n }\n\n // Set all feature tracks to use Coverage mode.\n _.each(this.drawables, function(d) {\n if (d instanceof FeatureTrack || d instanceof ReadTrack) {\n d.change_mode(\"Coverage\");\n }\n });\n\n this.update_icons();\n\n // HACK: needed for saving object for now. Need to generalize get_type() to all Drawables and use\n // that for object type.\n this.obj_type = \"CompositeTrack\";\n };\n\n extend(CompositeTrack.prototype, TiledTrack.prototype, {\n display_modes: CONTINUOUS_DATA_MODES,\n\n build_config_params: function() {\n return _.union(Drawable.prototype.config_params, [\n {\n key: \"min_value\",\n label: \"Min Value\",\n type: \"float\",\n default_value: undefined\n },\n {\n key: \"max_value\",\n label: \"Max Value\",\n type: \"float\",\n default_value: undefined\n },\n {\n key: \"mode\",\n type: \"string\",\n default_value: this.mode,\n hidden: true\n },\n {\n key: \"height\",\n type: \"int\",\n default_value: 30,\n hidden: true\n }\n ]);\n },\n\n action_icons_def: [\n // Create composite track from group's tracks.\n {\n name: \"composite_icon\",\n title: \"Show individual tracks\",\n css_class: \"layers-stack\",\n on_click_fn: function(track) {\n $(\".tooltip\").remove();\n track.show_group();\n }\n }\n ].concat(TiledTrack.prototype.action_icons_def),\n\n // HACK: CompositeTrack should inherit from DrawableCollection as well.\n /**\n * Returns representation of object in a dictionary for easy saving.\n * Use from_dict to recreate object.\n */\n to_dict: DrawableCollection.prototype.to_dict,\n\n add_drawable: DrawableCollection.prototype.add_drawable,\n\n unpack_drawables: DrawableCollection.prototype.unpack_drawables,\n\n config_onchange: function() {\n this.set_name(this.config.get_value(\"name\"));\n this.request_draw({ clear_tile_cache: true });\n },\n\n /**\n * Action to take during resize.\n */\n on_resize: function() {\n // Propogate visible height to other tracks.\n var visible_height = this.visible_height_px;\n _.each(this.drawables, function(d) {\n d.visible_height_px = visible_height;\n });\n Track.prototype.on_resize.call(this);\n },\n\n /**\n * Change mode for all tracks.\n */\n change_mode: function(new_mode) {\n TiledTrack.prototype.change_mode.call(this, new_mode);\n for (var i = 0; i < this.drawables.length; i++) {\n this.drawables[i].change_mode(new_mode);\n }\n },\n\n /**\n * Initialize component tracks and draw composite track when all components are initialized.\n */\n init: function() {\n // Init components.\n var init_deferreds = [];\n for (var i = 0; i < this.drawables.length; i++) {\n init_deferreds.push(this.drawables[i].init());\n }\n\n // Draw composite when all tracks available.\n var track = this;\n $.when.apply($, init_deferreds).then(function() {\n track.enabled = true;\n track.request_draw();\n });\n },\n\n update_icons: function() {\n // For now, hide filters and tool.\n this.action_icons.filters_icon.hide();\n this.action_icons.tools_icon.hide();\n this.action_icons.param_space_viz_icon.hide();\n },\n\n can_draw: Drawable.prototype.can_draw,\n\n _get_drawables: function() {\n return this.drawables;\n },\n\n /**\n * Replace this track with group that includes individual tracks.\n */\n show_group: function() {\n // Create group with individual tracks.\n var group = new DrawableGroup(this.view, this.container, {\n name: this.config.get_value(\"name\")\n }),\n track;\n for (var i = 0; i < this.drawables.length; i++) {\n track = this.drawables[i];\n track.update_icons();\n group.add_drawable(track);\n track.container = group;\n group.content_div.append(track.container_div);\n }\n\n // Replace track with group.\n var index = this.container.replace_drawable(this, group, true);\n group.request_draw({ clear_tile_cache: true });\n },\n\n /**\n * Actions taken before drawing.\n */\n before_draw: function() {\n // FIXME: this is needed only if there are feature tracks in the composite track.\n // TiledTrack.prototype.before_draw.call(this);\n\n //\n // Set min, max for tracks to be largest min, max.\n //\n\n // Get smallest min, biggest max.\n var min = _.min(\n _.map(this.drawables, function(d) {\n return d.config.get_value(\"min_value\");\n })\n ),\n max = _.max(\n _.map(this.drawables, function(d) {\n return d.config.get_value(\"max_value\");\n })\n );\n\n this.config.set_value(\"min_value\", min);\n this.config.set_value(\"max_value\", max);\n\n // Set all tracks to smallest min, biggest max.\n _.each(this.drawables, function(d) {\n d.config.set_value(\"min_value\", min);\n d.config.set_value(\"max_value\", max);\n });\n },\n\n /**\n * Update minimum, maximum for component tracks.\n */\n update_all_min_max: function() {\n var track = this,\n min_value = this.config.get_value(\"min_value\"),\n max_value = this.config.get_value(\"max_value\");\n _.each(this.drawables, function(d) {\n d.config.set_value(\"min_value\", min_value);\n d.config.set_value(\"max_value\", max_value);\n });\n this.request_draw({ clear_tile_cache: true });\n },\n\n /**\n * Actions to be taken after draw has been completed. Draw is completed when all tiles have been\n * drawn/fetched and shown.\n */\n postdraw_actions: function(tiles, width, w_scale, clear_after) {\n // All tiles must be the same height in order to draw LineTracks, so redraw tiles as needed.\n var max_height = -1,\n i;\n for (i = 0; i < tiles.length; i++) {\n var height = tiles[i].html_elt.find(\"canvas\").height();\n if (height > max_height) {\n max_height = height;\n }\n }\n\n for (i = 0; i < tiles.length; i++) {\n var tile = tiles[i];\n if (tile.html_elt.find(\"canvas\").height() !== max_height) {\n this.draw_helper(tile.region, w_scale, {\n force: true,\n height: max_height\n });\n tile.html_elt.remove();\n }\n }\n\n // Wrap function so that it can be called without object reference.\n var track = this,\n t = function() {\n track.update_all_min_max();\n };\n\n // Add min, max labels.\n this._add_yaxis_label(\"min\", t);\n this._add_yaxis_label(\"max\", t);\n }\n });\n\n /**\n * Displays reference genome data.\n */\n var ReferenceTrack = function(view) {\n TiledTrack.call(\n this,\n view,\n { content_div: view.top_labeltrack },\n { resize: false, header: false }\n );\n\n // Use offset to ensure that bases at tile edges are drawn.\n this.left_offset = view.canvas_manager.char_width_px;\n this.container_div.addClass(\"reference-track\");\n this.data_url = Galaxy.root + \"api/genomes/\" + this.view.dbkey;\n this.data_url_extra_params = { reference: true };\n this.data_manager = new visualization.GenomeReferenceDataManager({\n data_url: this.data_url,\n can_subset: this.can_subset\n });\n this.hide_contents();\n };\n extend(\n ReferenceTrack.prototype,\n Drawable.prototype,\n TiledTrack.prototype,\n {\n build_config_params: function() {\n return _.union(Drawable.prototype.config_params, [\n {\n key: \"height\",\n type: \"int\",\n default_value: 13,\n hidden: true\n }\n ]);\n },\n\n init: function() {\n this.data_manager.clear();\n // Enable by default because there should always be data when drawing track.\n this.enabled = true;\n },\n\n /**\n * Additional initialization required before drawing track for the first time.\n */\n predraw_init: function() {},\n\n can_draw: Drawable.prototype.can_draw,\n\n /**\n * Draws and shows tile if reference data can be displayed; otherwise track is hidden.\n */\n draw_helper: function(region, w_scale, options) {\n var cur_visible = this.tiles_div.is(\":visible\"),\n new_visible,\n tile = null;\n if (w_scale > this.view.canvas_manager.char_width_px) {\n this.tiles_div.show();\n new_visible = true;\n tile = TiledTrack.prototype.draw_helper.call(\n this,\n region,\n w_scale,\n options\n );\n } else {\n new_visible = false;\n this.tiles_div.hide();\n }\n\n // NOTE: viewport resizing conceptually belongs in postdraw_actions(), but currently\n // postdraw_actions is not called when reference track not shown due to no tiles. If\n // it is moved to postdraw_actions, resize must be called each time because cannot\n // easily detect showing/hiding.\n\n // If showing or hiding reference track, resize viewport.\n if (cur_visible !== new_visible) {\n this.view.resize_viewport();\n }\n\n return tile;\n },\n\n can_subset: function(entry) {\n return true;\n },\n\n /**\n * Draw ReferenceTrack tile.\n */\n draw_tile: function(data, ctx, mode, region, w_scale) {\n // Try to subset data.\n var subset = this.data_manager.subset_entry(data, region),\n seq_data = subset.data;\n\n // Draw sequence data.\n var canvas = ctx.canvas;\n ctx.font = ctx.canvas.manager.default_font;\n ctx.textAlign = \"center\";\n for (\n var c = 0, str_len = seq_data.length;\n c < str_len;\n c++\n ) {\n ctx.fillStyle = this.view.get_base_color(seq_data[c]);\n ctx.fillText(seq_data[c], Math.floor(c * w_scale), 10);\n }\n return new Tile(this, region, w_scale, canvas, subset);\n }\n }\n );\n\n /**\n * Track displays continuous/numerical data. Track expects position data in 1-based format, i.e. wiggle format.\n */\n var LineTrack = function(view, container, obj_dict) {\n this.mode = \"Histogram\";\n TiledTrack.call(this, view, container, obj_dict);\n // Need left offset for drawing overlap near tile boundaries.\n this.left_offset = 30;\n\n // If server has byte-range support, use BBI data manager to read directly from the BBI file.\n // FIXME: there should be a flag to wait for this check to complete before loading the track.\n var self = this;\n $.when(\n supportsByteRanges(\n Galaxy.root + \"datasets/\" + this.dataset.id + \"/display\"\n )\n ).then(function(supportsByteRanges) {\n if (supportsByteRanges) {\n self.data_manager = new bbi.BBIDataManager({\n dataset: self.dataset\n });\n }\n });\n };\n\n extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {\n display_modes: CONTINUOUS_DATA_MODES,\n\n build_config_params: function() {\n return _.union(Drawable.prototype.config_params, [\n { key: \"color\", label: \"Color\", type: \"color\" },\n {\n key: \"min_value\",\n label: \"Min Value\",\n type: \"float\",\n default_value: undefined\n },\n {\n key: \"max_value\",\n label: \"Max Value\",\n type: \"float\",\n default_value: undefined\n },\n {\n key: \"mode\",\n type: \"string\",\n default_value: this.mode,\n hidden: true\n },\n {\n key: \"height\",\n type: \"int\",\n default_value: 30,\n hidden: true\n }\n ]);\n },\n\n config_onchange: function() {\n this.set_name(this.config.get_value(\"name\"));\n this.request_draw({ clear_tile_cache: true });\n },\n\n /**\n * Actions to be taken before drawing.\n */\n // FIXME: can the default behavior be used; right now it breaks during resize.\n before_draw: function() {},\n\n /**\n * Draw track tile.\n */\n draw_tile: function(result, ctx, mode, region, w_scale) {\n return this._draw_line_track_tile(\n result,\n ctx,\n mode,\n region,\n w_scale\n );\n },\n\n /**\n * Subset data only if data is at single-base pair resolution.\n */\n can_subset: function(entry) {\n return entry.data[1][0] - entry.data[0][0] === 1;\n },\n\n /**\n * Add min, max labels.\n */\n postdraw_actions: function(tiles, width, w_scale, clear_after) {\n // Add min, max labels.\n this._add_yaxis_label(\"max\");\n this._add_yaxis_label(\"min\");\n }\n });\n\n /**\n * Diagonal heatmap for showing interactions data.\n */\n var DiagonalHeatmapTrack = function(view, container, obj_dict) {\n this.mode = \"Heatmap\";\n TiledTrack.call(this, view, container, obj_dict);\n };\n\n extend(\n DiagonalHeatmapTrack.prototype,\n Drawable.prototype,\n TiledTrack.prototype,\n {\n display_modes: [\"Heatmap\"],\n\n build_config_params: function() {\n return _.union(Drawable.prototype.config_params, [\n {\n key: \"pos_color\",\n label: \"Positive Color\",\n type: \"color\",\n default_value: \"#FF8C00\"\n },\n {\n key: \"neg_color\",\n label: \"Negative Color\",\n type: \"color\",\n default_value: \"#4169E1\"\n },\n {\n key: \"min_value\",\n label: \"Min Value\",\n type: \"int\",\n default_value: undefined\n },\n {\n key: \"max_value\",\n label: \"Max Value\",\n type: \"int\",\n default_value: undefined\n },\n {\n key: \"mode\",\n type: \"string\",\n default_value: this.mode,\n hidden: true\n },\n {\n key: \"height\",\n type: \"int\",\n default_value: 500,\n hidden: true\n }\n ]);\n },\n\n config_onchange: function() {\n this.set_name(this.config.get_value(\"name\"));\n this.request_draw({ clear_tile_cache: true });\n },\n\n /**\n * Additional initialization required before drawing track for the first time.\n */\n predraw_init: function() {\n var track = this;\n return $.getJSON(\n track.dataset.url(),\n {\n data_type: \"data\",\n stats: true,\n chrom: track.view.chrom,\n low: 0,\n high: track.view.max_high,\n hda_ldda: track.dataset.get(\"hda_ldda\")\n },\n function(result) {\n var data = result.data;\n }\n );\n },\n\n /**\n * Draw tile.\n */\n draw_tile: function(result, ctx, mode, region, w_scale) {\n // Paint onto canvas.\n var canvas = ctx.canvas,\n painter = new painters.DiagonalHeatmapPainter(\n result.data,\n region.get(\"start\"),\n region.get(\"end\"),\n this.config.to_key_value_dict(),\n mode\n );\n painter.draw(ctx, canvas.width, canvas.height, w_scale);\n\n return new Tile(this, region, w_scale, canvas, result.data);\n }\n }\n );\n\n /**\n * A track that displays features/regions. Track expects position data in BED format, i.e. 0-based, half-open.\n */\n var FeatureTrack = function(view, container, obj_dict) {\n TiledTrack.call(this, view, container, obj_dict);\n this.container_div.addClass(\"feature-track\");\n this.summary_draw_height = 30;\n this.slotters = {};\n this.start_end_dct = {};\n this.left_offset = 200;\n\n // this.painter = painters.LinkedFeaturePainter;\n this.set_painter_from_config();\n };\n extend(\n FeatureTrack.prototype,\n Drawable.prototype,\n TiledTrack.prototype,\n {\n display_modes: [\"Auto\", \"Coverage\", \"Dense\", \"Squish\", \"Pack\"],\n\n build_config_params: function() {\n return _.union(Drawable.prototype.config_params, [\n {\n key: \"block_color\",\n label: \"Block color\",\n type: \"color\"\n },\n {\n key: \"reverse_strand_color\",\n label: \"Antisense strand color\",\n type: \"color\"\n },\n {\n key: \"label_color\",\n label: \"Label color\",\n type: \"color\",\n default_value: \"black\"\n },\n {\n key: \"show_counts\",\n label: \"Show summary counts\",\n type: \"bool\",\n default_value: true,\n help:\n \"Show the number of items in each bin when drawing summary histogram\"\n },\n {\n key: \"min_value\",\n label: \"Histogram minimum\",\n type: \"float\",\n default_value: undefined,\n help: \"clear value to set automatically\"\n },\n {\n key: \"max_value\",\n label: \"Histogram maximum\",\n type: \"float\",\n default_value: undefined,\n help: \"clear value to set automatically\"\n },\n {\n key: \"connector_style\",\n label: \"Connector style\",\n type: \"select\",\n default_value: \"fishbones\",\n options: [\n {\n label: \"Line with arrows\",\n value: \"fishbone\"\n },\n { label: \"Arcs\", value: \"arcs\" }\n ]\n },\n {\n key: \"mode\",\n type: \"string\",\n default_value: this.mode,\n hidden: true\n },\n {\n key: \"height\",\n type: \"int\",\n default_value: 0,\n hidden: true\n }\n ]);\n },\n\n config_onchange: function() {\n this.set_name(this.config.get_value(\"name\"));\n this.set_painter_from_config();\n this.request_draw({ clear_tile_cache: true });\n },\n\n set_painter_from_config: function() {\n if (this.config.get_value(\"connector_style\") === \"arcs\") {\n this.painter = painters.ArcLinkedFeaturePainter;\n } else {\n this.painter = painters.LinkedFeaturePainter;\n }\n },\n\n /**\n * Actions to be taken after draw has been completed. Draw is completed when all tiles have been\n * drawn/fetched and shown.\n */\n postdraw_actions: function(tiles, width, w_scale, clear_after) {\n TiledTrack.prototype.postdraw_actions.call(\n this,\n tiles,\n width,\n w_scale,\n clear_after\n );\n\n var track = this,\n i,\n line_track_tiles = _.filter(tiles, function(t) {\n return t instanceof LineTrackTile;\n });\n\n //\n // Finish drawing of features that span multiple tiles. Features that span multiple tiles\n // are labeled incomplete on the tile level because they cannot be completely drawn.\n //\n if (line_track_tiles.length === 0) {\n // Gather incomplete features together.\n var all_incomplete_features = {};\n _.each(_.pluck(tiles, \"incomplete_features\"), function(\n inc_features\n ) {\n _.each(inc_features, function(feature) {\n all_incomplete_features[feature[0]] = feature;\n });\n });\n\n // Draw incomplete features on each tile.\n var self = this;\n _.each(tiles, function(tile) {\n // Remove features already drawn on tile originally.\n var tile_incomplete_features = _.omit(\n all_incomplete_features,\n _.map(tile.incomplete_features, function(f) {\n return f[0];\n })\n );\n\n // Remove features already drawn on tile in past postdraw actions.\n tile_incomplete_features = _.omit(\n tile_incomplete_features,\n _.keys(tile.other_tiles_features_drawn)\n );\n\n // Draw tile's incomplete features.\n if (_.size(tile_incomplete_features) !== 0) {\n // To draw incomplete features, create new canvas, copy original canvas/tile onto new\n // canvas, and then draw incomplete features on the new canvas.\n var features = {\n data: _.values(tile_incomplete_features)\n },\n new_canvas = self.view.canvas_manager.new_canvas(),\n new_canvas_ctx = new_canvas.getContext(\n \"2d\"\n );\n new_canvas.height = Math.max(\n tile.canvas.height,\n self.get_canvas_height(\n features,\n tile.mode,\n tile.w_scale,\n 100\n )\n );\n new_canvas.width = tile.canvas.width;\n new_canvas_ctx.drawImage(tile.canvas, 0, 0);\n new_canvas_ctx.translate(track.left_offset, 0);\n var new_tile = self.draw_tile(\n features,\n new_canvas_ctx,\n tile.mode,\n tile.region,\n tile.w_scale,\n tile.seq_data\n );\n $(tile.canvas).replaceWith($(new_tile.canvas));\n tile.canvas = new_canvas;\n _.extend(\n tile.other_tiles_features_drawn,\n all_incomplete_features\n );\n }\n });\n }\n\n // If mode is Coverage and tiles do not share max, redraw tiles as necessary using new max.\n /*\n This code isn't used right now because Coverage mode uses predefined max in preferences.\n if (track.mode === \"Coverage\") {\n // Get global max.\n var global_max = -1;\n for (i = 0; i < tiles.length; i++) {\n var cur_max = tiles[i].max_val;\n if (cur_max > global_max) {\n global_max = cur_max;\n }\n }\n\n for (i = 0; i < tiles.length; i++) {\n var tile = tiles[i];\n if (tile.max_val !== global_max) {\n tile.html_elt.remove();\n track.draw_helper(tile.index, w_scale, { more_tile_data: { force: true, max: global_max } } );\n }\n }\n }\n */\n\n //\n // Update filter attributes, UI.\n //\n\n // Update filtering UI.\n if (track.filters_manager) {\n var filters = track.filters_manager.filters,\n f;\n for (f = 0; f < filters.length; f++) {\n filters[f].update_ui_elt();\n }\n\n // Determine if filters are available; this is based on the tiles' data.\n // Criteria for filter to be available: (a) it is applicable to tile data and (b) filter min != filter max.\n var filters_available = false,\n example_feature,\n filter;\n for (i = 0; i < tiles.length; i++) {\n if (tiles[i].data.length) {\n example_feature = tiles[i].data[0];\n for (f = 0; f < filters.length; f++) {\n filter = filters[f];\n if (\n filter.applies_to(example_feature) &&\n filter.min !== filter.max\n ) {\n filters_available = true;\n break;\n }\n }\n }\n }\n\n // If filter availability changed, hide filter div if necessary and update menu.\n if (track.filters_available !== filters_available) {\n track.filters_available = filters_available;\n if (!track.filters_available) {\n track.filters_manager.hide();\n }\n track.update_icons();\n }\n }\n\n //\n // If not all features slotted, show icon for showing more rows (slots).\n //\n if (tiles[0] instanceof FeatureTrackTile) {\n var all_slotted = true;\n for (i = 0; i < tiles.length; i++) {\n if (!tiles[i].all_slotted) {\n all_slotted = false;\n break;\n }\n }\n this.action_icons.show_more_rows_icon.toggle(\n !all_slotted\n );\n } else {\n this.action_icons.show_more_rows_icon.hide();\n }\n },\n\n /**\n * Update track interface to show display mode being used.\n */\n update_auto_mode: function(mode) {\n if (this.mode === \"Auto\") {\n if (mode === \"no_detail\") {\n mode = \"feature spans\";\n }\n this.action_icons.mode_icon.attr(\n \"title\",\n \"Set display mode (now: Auto/\" + mode + \")\"\n );\n }\n },\n\n /**\n * Place features in slots for drawing (i.e. pack features).\n * this.slotters[level] is created in this method. this.slotters[level]\n * is a Slotter object. Returns the number of slots used to pack features.\n */\n incremental_slots: function(level, features, mode) {\n // Get/create incremental slots for level. If display mode changed,\n // need to create new slots.\n\n var dummy_context = this.view.canvas_manager.dummy_context,\n slotter = this.slotters[level];\n if (!slotter || slotter.mode !== mode) {\n slotter = new slotting.FeatureSlotter(\n level,\n mode,\n MAX_FEATURE_DEPTH,\n function(x) {\n return dummy_context.measureText(x);\n }\n );\n this.slotters[level] = slotter;\n }\n\n return slotter.slot_features(features);\n },\n\n /**\n * Returns appropriate display mode based on data.\n */\n get_mode: function(data) {\n var mode;\n // HACK: use no_detail mode track is in overview to prevent overview from being too large.\n if (data.extra_info === \"no_detail\" || this.is_overview) {\n mode = \"no_detail\";\n } else {\n // Choose b/t Squish and Pack.\n // Proxy measures for using Squish:\n // (a) error message re: limiting number of features shown;\n // (b) X number of features shown;\n // (c) size of view shown.\n // TODO: cannot use (a) and (b) because it requires coordinating mode across tiles;\n // fix this so that tiles are redrawn as necessary to use the same mode.\n //if ( (result.message && result.message.match(/^Only the first [\\d]+/)) ||\n // (result.data && result.data.length > 2000) ||\n //var data = result.data;\n // if ( (data.length && data.length < 4) ||\n // (this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH) ) {\n if (\n this.view.high - this.view.low >\n MIN_SQUISH_VIEW_WIDTH\n ) {\n mode = \"Squish\";\n } else {\n mode = \"Pack\";\n }\n }\n return mode;\n },\n\n /**\n * Returns canvas height needed to display data; return value is an integer that denotes the\n * number of pixels required.\n */\n get_canvas_height: function(\n result,\n mode,\n w_scale,\n canvas_width\n ) {\n if (\n mode === \"Coverage\" ||\n result.dataset_type === \"bigwig\"\n ) {\n return this.summary_draw_height;\n } else {\n // All other modes require slotting.\n var rows_required = this.incremental_slots(\n w_scale,\n result.data,\n mode\n );\n // HACK: use dummy painter to get required height. Painter should be extended so that get_required_height\n // works as a static function.\n var dummy_painter = new this.painter(\n null,\n null,\n null,\n this.config.to_key_value_dict(),\n mode\n );\n return Math.max(\n this.min_height_px,\n dummy_painter.get_required_height(\n rows_required,\n canvas_width\n )\n );\n }\n },\n\n /**\n * Draw FeatureTrack tile.\n * @param result result from server\n * @param cxt canvas context to draw on\n * @param mode mode to draw in\n * @param region region to draw on tile\n * @param w_scale pixels per base\n * @param ref_seq reference sequence data\n * @param cur_tile true if drawing is occurring on a currently visible tile.\n */\n draw_tile: function(\n result,\n ctx,\n mode,\n region,\n w_scale,\n ref_seq,\n cur_tile\n ) {\n var track = this,\n canvas = ctx.canvas,\n tile_low = region.get(\"start\"),\n tile_high = region.get(\"end\"),\n left_offset = this.left_offset;\n\n // If data is line track data, draw line track tile.\n if (result.dataset_type === \"bigwig\") {\n return this._draw_line_track_tile(\n result,\n ctx,\n mode,\n region,\n w_scale\n );\n }\n\n // Handle row-by-row tracks\n\n // Preprocessing: filter features and determine whether all unfiltered features have been slotted.\n var filtered = [],\n slots = this.slotters[w_scale].slots,\n all_slotted = true;\n if (result.data) {\n var filters = this.filters_manager.filters;\n for (\n var i = 0, len = result.data.length;\n i < len;\n i++\n ) {\n var feature = result.data[i];\n var hide_feature = false;\n var filter;\n for (\n var f = 0, flen = filters.length;\n f < flen;\n f++\n ) {\n filter = filters[f];\n filter.update_attrs(feature);\n if (!filter.keep(feature)) {\n hide_feature = true;\n break;\n }\n }\n if (!hide_feature) {\n // Feature visible.\n filtered.push(feature);\n // Set flag if not slotted.\n if (!(feature[0] in slots)) {\n all_slotted = false;\n }\n }\n }\n }\n\n // Create painter.\n var filter_alpha_scaler = this.filters_manager.alpha_filter\n ? new FilterScaler(\n this.filters_manager.alpha_filter\n )\n : null,\n filter_height_scaler = this.filters_manager\n .height_filter\n ? new FilterScaler(\n this.filters_manager.height_filter\n )\n : null,\n painter = new this.painter(\n filtered,\n tile_low,\n tile_high,\n this.config.to_key_value_dict(),\n mode,\n filter_alpha_scaler,\n filter_height_scaler,\n // HACK: ref_seq only be defined for ReadTracks, and only the ReadPainter accepts that argument\n ref_seq,\n // Only the ReadPainer will use this function\n function(b) {\n return track.view.get_base_color(b);\n }\n );\n var feature_mapper = null;\n\n ctx.fillStyle = this.config.get_value(\"block_color\");\n ctx.font = ctx.canvas.manager.default_font;\n ctx.textAlign = \"right\";\n\n if (result.data) {\n // Draw features.\n var draw_results = painter.draw(\n ctx,\n canvas.width,\n canvas.height,\n w_scale,\n slots\n );\n feature_mapper = draw_results.feature_mapper;\n incomplete_features = draw_results.incomplete_features;\n feature_mapper.translation = -left_offset;\n }\n\n // If not drawing on current tile, create new tile.\n if (!cur_tile) {\n return new FeatureTrackTile(\n track,\n region,\n w_scale,\n canvas,\n result.data,\n mode,\n result.message,\n all_slotted,\n feature_mapper,\n incomplete_features,\n ref_seq\n );\n }\n }\n }\n );\n\n /**\n * Displays variant data.\n */\n var VariantTrack = function(view, container, obj_dict) {\n TiledTrack.call(this, view, container, obj_dict);\n this.painter = painters.VariantPainter;\n this.summary_draw_height = 30;\n\n // Maximum resolution is ~45 pixels/base, so use this size left offset to ensure that full\n // variant is drawn when variant is at start of tile.\n this.left_offset = 30;\n };\n\n extend(\n VariantTrack.prototype,\n Drawable.prototype,\n TiledTrack.prototype,\n {\n display_modes: [\"Auto\", \"Coverage\", \"Dense\", \"Squish\", \"Pack\"],\n\n build_config_params: function() {\n return _.union(Drawable.prototype.config_params, [\n {\n key: \"color\",\n label: \"Histogram color\",\n type: \"color\"\n },\n {\n key: \"show_sample_data\",\n label: \"Show sample data\",\n type: \"bool\",\n default_value: true\n },\n {\n key: \"show_labels\",\n label: \"Show summary and sample labels\",\n type: \"bool\",\n default_value: true\n },\n {\n key: \"summary_height\",\n label: \"Locus summary height\",\n type: \"float\",\n default_value: 20\n },\n {\n key: \"mode\",\n type: \"string\",\n default_value: this.mode,\n hidden: true\n },\n {\n key: \"height\",\n type: \"int\",\n default_value: 0,\n hidden: true\n }\n ]);\n },\n\n config_onchange: function() {\n this.set_name(this.config.get_value(\"name\"));\n this.request_draw({ clear_tile_cache: true });\n },\n\n /**\n * Draw tile.\n */\n draw_tile: function(result, ctx, mode, region, w_scale) {\n // Data could be coverage data or variant data.\n if (result.dataset_type === \"bigwig\") {\n return this._draw_line_track_tile(\n result,\n ctx,\n \"Histogram\",\n region,\n w_scale\n );\n } else {\n // result.dataset_type === 'variant'\n var view = this.view,\n painter = new this.painter(\n result.data,\n region.get(\"start\"),\n region.get(\"end\"),\n this.config.to_key_value_dict(),\n mode,\n function(b) {\n return view.get_base_color(b);\n }\n );\n painter.draw(\n ctx,\n ctx.canvas.width,\n ctx.canvas.height,\n w_scale\n );\n return new Tile(\n this,\n region,\n w_scale,\n ctx.canvas,\n result.data\n );\n }\n },\n\n /**\n * Returns canvas height needed to display data; return value is an integer that denotes the\n * number of pixels required.\n */\n get_canvas_height: function(\n result,\n mode,\n w_scale,\n canvas_width\n ) {\n if (result.dataset_type === \"bigwig\") {\n return this.summary_draw_height;\n } else {\n // HACK: sample_names is not be defined when dataset definition is fetched before\n // dataset is complete (as is done when running tools). In that case, fall back on\n // # of samples in data. This can be fixed by re-requesting dataset definition\n // in init.\n var num_samples = this.dataset.get_metadata(\n \"sample_names\"\n )\n ? this.dataset.get_metadata(\"sample_names\").length\n : 0;\n if (num_samples === 0 && result.data.length !== 0) {\n // Sample data is separated by commas, so this computes # of samples:\n num_samples = result.data[0][7].match(/,/g);\n if (num_samples === null) {\n num_samples = 1;\n } else {\n num_samples = num_samples.length + 1;\n }\n }\n\n var dummy_painter = new this.painter(\n null,\n null,\n null,\n this.config.to_key_value_dict(),\n mode\n );\n return dummy_painter.get_required_height(num_samples);\n }\n },\n\n /**\n * Additional initialization required before drawing track for the first time.\n */\n predraw_init: function() {\n var deferreds = [Track.prototype.predraw_init.call(this)];\n // FIXME: updating dataset metadata is only needed for visual analysis. Can\n // this be moved somewhere else?\n if (!this.dataset.get_metadata(\"sample_names\")) {\n deferreds.push(this.dataset.fetch());\n }\n return deferreds;\n },\n\n /**\n * Actions to be taken after draw has been completed. Draw is completed when all tiles have been\n * drawn/fetched and shown.\n */\n postdraw_actions: function(tiles, width, w_scale, clear_after) {\n TiledTrack.prototype.postdraw_actions.call(\n this,\n tiles,\n width,\n w_scale,\n clear_after\n );\n\n var line_track_tiles = _.filter(tiles, function(t) {\n return t instanceof LineTrackTile;\n });\n\n // Add summary/sample labels if needed and not already included.\n var sample_names = this.dataset.get_metadata(\n \"sample_names\"\n );\n if (\n line_track_tiles.length === 0 &&\n this.config.get_value(\"show_labels\") &&\n sample_names &&\n sample_names.length > 1\n ) {\n var font_size;\n\n // Add and/or style labels.\n if (\n this.container_div.find(\".yaxislabel.variant\")\n .length === 0\n ) {\n // Add summary and sample labels.\n\n // Add summary label to middle of summary area.\n font_size =\n this.config.get_value(\"summary_height\") / 2;\n this.tiles_div.prepend(\n $(\"\")\n .text(\"Summary\")\n .addClass(\"yaxislabel variant top\")\n .css({\n \"font-size\": font_size + \"px\",\n top:\n (this.config.get_value(\n \"summary_height\"\n ) -\n font_size) /\n 2 +\n \"px\"\n })\n );\n\n // Show sample labels.\n if (this.config.get_value(\"show_sample_data\")) {\n var samples_div_html = sample_names.join(\n \"
\"\n );\n\n this.tiles_div.prepend(\n $(\"\")\n .html(samples_div_html)\n .addClass(\n \"yaxislabel variant top sample\"\n )\n .css({\n top: this.config.get_value(\n \"summary_height\"\n )\n })\n );\n }\n }\n\n // Style labels.\n\n // Match sample font size to mode.\n font_size = (this.mode === \"Squish\" ? 5 : 10) + \"px\";\n $(this.tiles_div)\n .find(\".sample\")\n .css({\n \"font-size\": font_size,\n \"line-height\": font_size\n });\n // Color labels to preference color.\n $(this.tiles_div)\n .find(\".yaxislabel\")\n .css(\"color\", this.config.get_value(\"label_color\"));\n } else {\n // Remove all labels.\n this.container_div.find(\".yaxislabel.variant\").remove();\n }\n }\n }\n );\n\n /**\n * Track that displays mapped reads. Track expects position data in 1-based, closed format, i.e. SAM/BAM format.\n */\n var ReadTrack = function(view, container, obj_dict) {\n FeatureTrack.call(this, view, container, obj_dict);\n this.painter = painters.ReadPainter;\n this.update_icons();\n };\n\n extend(\n ReadTrack.prototype,\n Drawable.prototype,\n TiledTrack.prototype,\n FeatureTrack.prototype,\n {\n build_config_params: function() {\n return _.union(Drawable.prototype.config_params, [\n {\n key: \"block_color\",\n label: \"Histogram color\",\n type: \"color\"\n },\n {\n key: \"detail_block_color\",\n label: \"Sense strand block color\",\n type: \"color\",\n default_value: \"#AAAAAA\"\n },\n {\n key: \"reverse_strand_color\",\n label: \"Antisense strand block color\",\n type: \"color\",\n default_value: \"#DDDDDD\"\n },\n {\n key: \"label_color\",\n label: \"Label color\",\n type: \"color\",\n default_value: \"black\"\n },\n {\n key: \"show_insertions\",\n label: \"Show insertions\",\n type: \"bool\",\n default_value: false\n },\n {\n key: \"show_differences\",\n label: \"Show differences only\",\n type: \"bool\",\n default_value: true\n },\n {\n key: \"show_counts\",\n label: \"Show summary counts\",\n type: \"bool\",\n default_value: true\n },\n {\n key: \"mode\",\n type: \"string\",\n default_value: this.mode,\n hidden: true\n },\n {\n key: \"min_value\",\n label: \"Histogram minimum\",\n type: \"float\",\n default_value: undefined,\n help: \"clear value to set automatically\"\n },\n {\n key: \"max_value\",\n label: \"Histogram maximum\",\n type: \"float\",\n default_value: undefined,\n help: \"clear value to set automatically\"\n },\n {\n key: \"height\",\n type: \"int\",\n default_value: 0,\n hidden: true\n }\n ]);\n },\n\n config_onchange: function() {\n this.set_name(this.config.get_value(\"name\"));\n this.request_draw({ clear_tile_cache: true });\n }\n }\n );\n\n /**\n * Objects that can be added to a view.\n */\n var addable_objects = {\n CompositeTrack: CompositeTrack,\n DrawableGroup: DrawableGroup,\n DiagonalHeatmapTrack: DiagonalHeatmapTrack,\n FeatureTrack: FeatureTrack,\n LineTrack: LineTrack,\n ReadTrack: ReadTrack,\n VariantTrack: VariantTrack,\n // For backward compatibility, map vcf track to variant.\n VcfTrack: VariantTrack\n };\n\n /**\n * Create new object from a template. 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Server is repeatedly polled, and when\n * condition is met, deferred is resolved.\n */\n var ServerStateDeferred = Backbone.Model.extend({\n defaults: {\n ajax_settings: {},\n interval: 1000,\n success_fn: function(result) {\n return true;\n }\n },\n\n /**\n * Returns a deferred that resolves when success function returns true.\n */\n go: function() {\n var deferred = $.Deferred(),\n self = this,\n ajax_settings = self.get(\"ajax_settings\"),\n success_fn = self.get(\"success_fn\"),\n interval = self.get(\"interval\"),\n _go = function() {\n $.ajax(ajax_settings).success(function(result) {\n if (success_fn(result)) {\n // Result is good, so resolve.\n deferred.resolve(result);\n } else {\n // Result not good, try again.\n setTimeout(_go, interval);\n }\n });\n };\n _go();\n return deferred;\n }\n });\n\n /**\n * Returns a random color in hexadecimal format that is sufficiently different from a single color\n * or set of colors.\n * @param colors a color or list of colors in the format '#RRGGBB'\n */\n var get_random_color = function(colors) {\n // Default for colors is white.\n if (!colors) {\n colors = \"#ffffff\";\n }\n\n // If needed, create list of colors.\n if (typeof colors === \"string\") {\n colors = [colors];\n }\n\n // Convert colors to numbers.\n for (var i = 0; i < colors.length; i++) {\n colors[i] = parseInt(colors[i].slice(1), 16);\n }\n\n // -- Perceived brightness and difference formulas are from\n // -- http://www.w3.org/WAI/ER/WD-AERT/#color-contrast\n\n // Compute perceived color brightness (based on RGB-YIQ transformation):\n var brightness = function(r, g, b) {\n return (r * 299 + g * 587 + b * 114) / 1000;\n };\n\n // Compute color difference:\n var difference = function(r1, g1, b1, r2, g2, b2) {\n return (\n Math.max(r1, r2) -\n Math.min(r1, r2) +\n (Math.max(g1, g2) - Math.min(g1, g2)) +\n (Math.max(b1, b2) - Math.min(b1, b2))\n );\n };\n\n // Create new random color.\n var new_color,\n nr,\n ng,\n nb,\n other_color,\n or,\n og,\n ob,\n n_brightness,\n o_brightness,\n diff,\n ok = false,\n num_tries = 0;\n do {\n // New color is never white b/c random in [0,1)\n new_color = Math.round(Math.random() * 0xffffff);\n nr = (new_color & 0xff0000) >> 16;\n ng = (new_color & 0x00ff00) >> 8;\n nb = new_color & 0x0000ff;\n n_brightness = brightness(nr, ng, nb);\n ok = true;\n for (i = 0; i < colors.length; i++) {\n other_color = colors[i];\n or = (other_color & 0xff0000) >> 16;\n og = (other_color & 0x00ff00) >> 8;\n ob = other_color & 0x0000ff;\n o_brightness = brightness(or, og, ob);\n diff = difference(nr, ng, nb, or, og, ob);\n // These thresholds may need to be adjusted. 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Brightness difference range is 125;\n // color difference range is 500.\n if (Math.abs(n_brightness - o_brightness) < 40 || diff < 200) {\n ok = false;\n break;\n }\n }\n\n num_tries++;\n } while (!ok && num_tries <= 10);\n\n // Add 0x1000000 to left pad number with 0s.\n return \"#\" + (0x1000000 + new_color).toString(16).substr(1, 6);\n };\n\n return {\n commatize: commatize,\n is_deferred: is_deferred,\n ServerStateDeferred: ServerStateDeferred,\n get_random_color: get_random_color\n };\n});\n"]} \ No newline at end of file diff --git a/static/maps/viz/visualization.js.map b/static/maps/viz/visualization.js.map index 40505dcfd08..d77ca7e15be 100644 --- a/static/maps/viz/visualization.js.map +++ b/static/maps/viz/visualization.js.map @@ -1 +1 @@ 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[\n \"libs/underscore\",\n \"mvc/dataset/data\",\n \"viz/trackster/util\",\n \"utils/config\",\n \"mvc/grid/grid-view\",\n \"mvc/ui/ui-tabs\",\n \"mvc/ui/ui-misc\"\n ],\n function(_, data_mod, util_mod, config_mod, GridView, Tabs, Ui) {\n /**\n * Mixin for returning custom JSON representation from toJSON. Class attribute to_json_keys defines a set of attributes\n * to include in the representation; to_json_mappers defines mappers for returned objects.\n */\n var CustomToJSON = {\n /**\n * Returns JSON representation of object using to_json_keys and to_json_mappers.\n */\n toJSON: function() {\n var self = this,\n json = {};\n _.each(self.constructor.to_json_keys, function(k) {\n var val = self.get(k);\n if (k in self.constructor.to_json_mappers) {\n val = self.constructor.to_json_mappers[k](val, self);\n }\n json[k] = val;\n });\n return json;\n }\n };\n\n /**\n * Model, view, and controller objects for Galaxy visualization framework.\n *\n * Models have no references to views, instead using events to indicate state\n * changes; this is advantageous because multiple views can use the same object\n * and models can be used without views.\n */\n\n /**\n * Use a popup grid to select datasets from histories or libraries. After datasets are selected,\n * track definitions are obtained from the server and the success_fn is called with the list of\n * definitions for selected datasets.\n */\n var select_datasets = function(filters, success_fn) {\n // history dataset selection tab\n var history_grid = new GridView({\n url_base: Galaxy.root + \"visualization/list_history_datasets\",\n filters: filters,\n dict_format: true,\n embedded: true\n });\n\n // library dataset selection tab\n var library_grid = new GridView({\n url_base: Galaxy.root + \"visualization/list_library_datasets\",\n dict_format: true,\n embedded: true\n });\n\n // build tabs\n var tabs = new Tabs.View();\n tabs.add({\n id: \"histories\",\n title: \"Histories\",\n $el: $(\"\").append(history_grid.$el)\n });\n tabs.add({\n id: \"libraries\",\n title: \"Libraries\",\n $el: $(\"\").append(library_grid.$el)\n });\n\n // modal\n Galaxy.modal.show({\n title: \"Select datasets for new tracks\",\n body: tabs.$el,\n closing_events: true,\n buttons: {\n Cancel: function() {\n Galaxy.modal.hide();\n },\n Add: function() {\n var requests = [];\n tabs\n .$(\n \"input.grid-row-select-checkbox[name=id]:checked\"\n )\n .each(function() {\n window.console.log($(this).val());\n requests[requests.length] = $.ajax({\n url:\n Galaxy.root +\n \"api/datasets/\" +\n $(this).val(),\n dataType: \"json\",\n data: {\n data_type: \"track_config\",\n hda_ldda:\n tabs.current() == \"histories\"\n ? \"hda\"\n : \"ldda\"\n }\n });\n });\n // To preserve order, wait until there are definitions for all tracks and then add\n // them sequentially.\n $.when.apply($, requests).then(function() {\n // jQuery always returns an Array for arguments, so need to look at first element\n // to determine whether multiple requests were made and consequently how to\n // map arguments to track definitions.\n var track_defs =\n arguments[0] instanceof Array\n ? $.map(arguments, function(arg) {\n return arg[0];\n })\n : [arguments[0]];\n success_fn(track_defs);\n });\n Galaxy.modal.hide();\n }\n }\n });\n };\n\n // --------- Models ---------\n\n /**\n * Canvas manager is used to create canvases for browsers as well as providing a pattern cache\n */\n var CanvasManager = function(default_font) {\n this.default_font =\n default_font !== undefined\n ? default_font\n : \"9px Monaco, Lucida Console, monospace\";\n\n this.dummy_canvas = this.new_canvas();\n this.dummy_context = this.dummy_canvas.getContext(\"2d\");\n this.dummy_context.font = this.default_font;\n\n this.char_width_px = this.dummy_context.measureText(\"A\").width;\n\n this.patterns = {};\n\n // FIXME: move somewhere to make this more general\n this.load_pattern(\n \"right_strand\",\n \"/visualization/strand_right.png\"\n );\n this.load_pattern(\"left_strand\", \"/visualization/strand_left.png\");\n this.load_pattern(\n \"right_strand_inv\",\n \"/visualization/strand_right_inv.png\"\n );\n this.load_pattern(\n \"left_strand_inv\",\n \"/visualization/strand_left_inv.png\"\n );\n };\n\n _.extend(CanvasManager.prototype, {\n load_pattern: function(key, path) {\n var patterns = this.patterns,\n dummy_context = this.dummy_context,\n image = new Image();\n image.src = Galaxy.root + \"static/images\" + path;\n image.onload = function() {\n patterns[key] = dummy_context.createPattern(\n image,\n \"repeat\"\n );\n };\n },\n get_pattern: function(key) {\n return this.patterns[key];\n },\n new_canvas: function() {\n var canvas = $(\"\")[0];\n // Keep a reference back to the manager\n canvas.manager = this;\n return canvas;\n }\n });\n\n /**\n * Generic cache that handles key/value pairs. Keys can be any object that can be\n * converted to a String and compared.\n */\n var Cache = Backbone.Model.extend({\n defaults: {\n num_elements: 20,\n // Objects in cache; indexes into cache are strings of keys.\n obj_cache: null,\n // key_ary contains keys for objects in cache.\n key_ary: null\n },\n\n initialize: function(options) {\n this.clear();\n },\n\n /**\n * Get an element from the cache using its key.\n */\n get_elt: function(key) {\n var obj_cache = this.attributes.obj_cache,\n key_ary = this.attributes.key_ary,\n key_str = key.toString(),\n index = _.indexOf(key_ary, function(k) {\n return k.toString() === key_str;\n });\n\n // Update cache.\n if (index !== -1) {\n // Object is in cache, so update it.\n if (obj_cache[key_str].stale) {\n // Object is stale: remove key and object.\n key_ary.splice(index, 1);\n delete obj_cache[key_str];\n } else {\n // Move key to back because it is most recently used.\n this.move_key_to_end(key, index);\n }\n }\n\n return obj_cache[key_str];\n },\n\n /**\n * Put an element into the cache.\n */\n set_elt: function(key, value) {\n var obj_cache = this.attributes.obj_cache,\n key_ary = this.attributes.key_ary,\n key_str = key.toString(),\n num_elements = this.attributes.num_elements;\n\n // Update keys, objects.\n if (!obj_cache[key_str]) {\n // Add object to cache.\n\n if (key_ary.length >= num_elements) {\n // Cache full, so remove first element.\n var deleted_key = key_ary.shift();\n delete obj_cache[deleted_key.toString()];\n }\n\n // Add key.\n key_ary.push(key);\n }\n\n // Add object.\n obj_cache[key_str] = value;\n return value;\n },\n\n /**\n * Move key to end of cache. Keys are removed from the front, so moving a key to the end\n * delays the key's removal.\n */\n move_key_to_end: function(key, index) {\n this.attributes.key_ary.splice(index, 1);\n this.attributes.key_ary.push(key);\n },\n\n /**\n * Clear all elements from the cache.\n */\n clear: function() {\n this.attributes.obj_cache = {};\n this.attributes.key_ary = [];\n },\n\n /** Returns the number of elements in the cache. */\n size: function() {\n return this.attributes.key_ary.length;\n },\n\n /** Returns key most recently added to cache. */\n most_recently_added: function() {\n return this.size() === 0\n ? null\n : // Most recent key is at the end of key array.\n this.attributes.key_ary[\n this.attributes.key_ary.length - 1\n ];\n }\n });\n\n /**\n * Data manager for genomic data. Data is connected to and queryable by genomic regions.\n */\n var GenomeDataManager = Cache.extend({\n defaults: _.extend({}, Cache.prototype.defaults, {\n dataset: null,\n genome: null,\n init_data: null,\n min_region_size: 200,\n filters_manager: null,\n data_type: \"data\",\n data_mode_compatible: function(entry, mode) {\n return true;\n },\n can_subset: function(entry) {\n return false;\n }\n }),\n\n /**\n * Initialization.\n */\n initialize: function(options) {\n Cache.prototype.initialize.call(this);\n\n // Set initial entries in data manager.\n var initial_entries = this.get(\"init_data\");\n if (initial_entries) {\n this.add_data(initial_entries);\n }\n },\n\n /**\n * Add data entries to manager; each entry should be a dict with attributes region (key), data, and data_type.\n * If necessary, manager size is increased to hold all data.\n */\n add_data: function(entries) {\n // Increase size to accomodate all entries.\n if (this.get(\"num_elements\") < entries.length) {\n this.set(\"num_elements\", entries.length);\n }\n\n // Put data into manager.\n var self = this;\n _.each(entries, function(entry) {\n self.set_data(entry.region, entry);\n });\n },\n\n /**\n * Returns deferred that resolves to true when dataset is ready (or false if dataset\n * cannot be used).\n */\n data_is_ready: function() {\n var dataset = this.get(\"dataset\"),\n ready_deferred = $.Deferred(),\n // If requesting raw data, query dataset state; if requesting (converted) data,\n // need to query converted datasets state.\n query_type =\n this.get(\"data_type\") === \"raw_data\"\n ? \"state\"\n : this.get(\"data_type\") === \"data\"\n ? \"converted_datasets_state\"\n : \"error\",\n ss_deferred = new util_mod.ServerStateDeferred({\n ajax_settings: {\n url: this.get(\"dataset\").url(),\n data: {\n hda_ldda: dataset.get(\"hda_ldda\"),\n data_type: query_type\n },\n dataType: \"json\"\n },\n interval: 5000,\n success_fn: function(response) {\n return response !== \"pending\";\n }\n });\n\n $.when(ss_deferred.go()).then(function(response) {\n ready_deferred.resolve(\n response === \"ok\" || response === \"data\"\n );\n });\n return ready_deferred;\n },\n\n /**\n * Perform a feature search from server; returns Deferred object that resolves when data is available.\n */\n search_features: function(query) {\n var dataset = this.get(\"dataset\"),\n params = {\n query: query,\n hda_ldda: dataset.get(\"hda_ldda\"),\n data_type: \"features\"\n };\n return $.getJSON(dataset.url(), params);\n },\n\n /**\n * Load data from server and manages data entries. Adds a Deferred to manager\n * for region; when data becomes available, replaces Deferred with data.\n * Returns the Deferred that resolves when data is available.\n */\n load_data: function(region, mode, resolution, extra_params) {\n // Setup data request params.\n var dataset = this.get(\"dataset\"),\n params = {\n data_type: this.get(\"data_type\"),\n chrom: region.get(\"chrom\"),\n low: region.get(\"start\"),\n high: region.get(\"end\"),\n mode: mode,\n resolution: resolution,\n hda_ldda: dataset.get(\"hda_ldda\")\n };\n\n $.extend(params, extra_params);\n\n // Add track filters to params.\n var filters_manager = this.get(\"filters_manager\");\n if (filters_manager) {\n var filter_names = [];\n var filters = filters_manager.filters;\n for (var i = 0; i < filters.length; i++) {\n filter_names.push(filters[i].name);\n }\n params.filter_cols = JSON.stringify(filter_names);\n }\n\n // Do request.\n var manager = this,\n entry = $.getJSON(dataset.url(), params, function(result) {\n // Add region to the result.\n result.region = region;\n manager.set_data(region, result);\n });\n\n this.set_data(region, entry);\n return entry;\n },\n\n /**\n * Get data from dataset.\n */\n get_data: function(region, mode, resolution, extra_params) {\n // Look for entry and return if it's a deferred or if data available is compatible with mode.\n var entry = this.get_elt(region);\n if (\n entry &&\n (util_mod.is_deferred(entry) ||\n this.get(\"data_mode_compatible\")(entry, mode))\n ) {\n return entry;\n }\n\n //\n // Look in cache for data that can be used.\n // TODO: this logic could be improved if the visualization knew whether\n // the data was \"index\" or \"data.\"\n //\n var key_ary = this.get(\"key_ary\"),\n obj_cache = this.get(\"obj_cache\"),\n entry_region,\n is_subregion;\n for (var i = 0; i < key_ary.length; i++) {\n entry_region = key_ary[i];\n\n if (entry_region.contains(region)) {\n is_subregion = true;\n\n // This entry has data in the requested range. Return if data\n // is compatible and can be subsetted.\n entry = obj_cache[entry_region.toString()];\n if (\n util_mod.is_deferred(entry) ||\n (this.get(\"data_mode_compatible\")(entry, mode) &&\n this.get(\"can_subset\")(entry))\n ) {\n this.move_key_to_end(entry_region, i);\n\n // If there's data, subset it.\n if (!util_mod.is_deferred(entry)) {\n var subset_entry = this.subset_entry(\n entry,\n region\n );\n this.set_data(region, subset_entry);\n entry = subset_entry;\n }\n\n return entry;\n }\n }\n }\n\n // FIXME: There _may_ be instances where region is a subregion of another entry but cannot be\n // subsetted. For these cases, do not increase length because region will never be found (and\n // an infinite loop will occur.)\n // If needed, extend region to make it minimum size.\n if (\n !is_subregion &&\n region.length() < this.attributes.min_region_size\n ) {\n // IDEA: alternative heuristic is to find adjacent cache entry to region and use that to extend.\n // This would prevent bad extensions when zooming in/out while still preserving the behavior\n // below.\n\n // Use copy of region to avoid changing actual region.\n region = region.copy();\n\n // Use heuristic to extend region: extend relative to last data request.\n var last_request = this.most_recently_added();\n if (\n !last_request ||\n region.get(\"start\") > last_request.get(\"start\")\n ) {\n // This request is after the last request, so extend right.\n region.set(\n \"end\",\n region.get(\"start\") +\n this.attributes.min_region_size\n );\n } else {\n // This request is after the last request, so extend left.\n region.set(\n \"start\",\n region.get(\"end\") - this.attributes.min_region_size\n );\n }\n\n // Trim region to avoid invalid coordinates.\n region.set(\"genome\", this.attributes.genome);\n region.trim();\n }\n\n return this.load_data(region, mode, resolution, extra_params);\n },\n\n /**\n * Alias for set_elt for readbility.\n */\n set_data: function(region, entry) {\n this.set_elt(region, entry);\n },\n\n /** \"Deep\" data request; used as a parameter for DataManager.get_more_data() */\n DEEP_DATA_REQ: \"deep\",\n\n /** \"Broad\" data request; used as a parameter for DataManager.get_more_data() */\n BROAD_DATA_REQ: \"breadth\",\n\n /**\n * Gets more data for a region using either a depth-first or a breadth-first approach.\n */\n get_more_data: function(\n region,\n mode,\n resolution,\n extra_params,\n req_type\n ) {\n var cur_data = this._mark_stale(region);\n if (\n !(\n cur_data &&\n this.get(\"data_mode_compatible\")(cur_data, mode)\n )\n ) {\n console.log(\n \"ERROR: problem with getting more data: current data is not compatible\"\n );\n return;\n }\n\n //\n // Set parameters based on request type.\n //\n var query_low = region.get(\"start\");\n if (req_type === this.DEEP_DATA_REQ) {\n // Use same interval but set start_val to skip data that's already in cur_data.\n $.extend(extra_params, {\n start_val: cur_data.data.length + 1\n });\n } else if (req_type === this.BROAD_DATA_REQ) {\n // To get past an area of extreme feature depth, set query low to be after either\n // (a) the maximum high or HACK/FIXME (b) the end of the last feature returned.\n query_low =\n (cur_data.max_high\n ? cur_data.max_high\n : cur_data.data[cur_data.data.length - 1][2]) + 1;\n }\n var query_region = region.copy().set(\"start\", query_low);\n\n //\n // Get additional data, append to current data, and set new data. Use a custom deferred object\n // to signal when new data is available.\n //\n var data_manager = this,\n new_data_request = this.load_data(\n query_region,\n mode,\n resolution,\n extra_params\n ),\n new_data_available = $.Deferred();\n // load_data sets cache to new_data_request, but use custom deferred object so that signal and data\n // is all data, not just new data.\n this.set_data(region, new_data_available);\n $.when(new_data_request).then(function(result) {\n // Update data and message.\n if (result.data) {\n result.data = cur_data.data.concat(result.data);\n if (result.max_low) {\n result.max_low = cur_data.max_low;\n }\n if (result.message) {\n // HACK: replace number in message with current data length. Works but is ugly.\n result.message = result.message.replace(\n /[0-9]+/,\n result.data.length\n );\n }\n }\n data_manager.set_data(region, result);\n new_data_available.resolve(result);\n });\n return new_data_available;\n },\n\n /**\n * Returns true if more detailed data can be obtained for entry.\n */\n can_get_more_detailed_data: function(region) {\n var cur_data = this.get_elt(region);\n\n // Can only get more detailed data for bigwig data that has less than 8000 data points.\n // Summary tree returns *way* too much data, and 8000 data points ~ 500KB.\n return (\n cur_data.dataset_type === \"bigwig\" &&\n cur_data.data.length < 8000\n );\n },\n\n /**\n * Returns more detailed data for an entry.\n */\n get_more_detailed_data: function(\n region,\n mode,\n resolution,\n detail_multiplier,\n extra_params\n ) {\n // Mark current entry as stale.\n var cur_data = this._mark_stale(region);\n if (!cur_data) {\n console.log(\n \"ERROR getting more detailed data: no current data\"\n );\n return;\n }\n\n if (!extra_params) {\n extra_params = {};\n }\n\n // Use additional parameters to get more detailed data.\n if (cur_data.dataset_type === \"bigwig\") {\n // FIXME: constant should go somewhere.\n extra_params.num_samples = 1000 * detail_multiplier;\n }\n\n return this.load_data(region, mode, resolution, extra_params);\n },\n\n /**\n * Marks cache data as stale.\n */\n _mark_stale: function(region) {\n var entry = this.get_elt(region);\n if (!entry) {\n console.log(\n \"ERROR: no data to mark as stale: \",\n this.get(\"dataset\"),\n region.toString()\n );\n }\n entry.stale = true;\n return entry;\n },\n\n /**\n * Returns an array of data with each entry representing one chromosome/contig\n * of data or, if data is not available, returns a Deferred that resolves to the\n * data when it becomes available.\n */\n get_genome_wide_data: function(genome) {\n // -- Get all data. --\n\n var self = this,\n all_data_available = true,\n // Map chromosome info into genome data.\n gw_data = _.map(\n genome.get(\"chroms_info\").chrom_info,\n function(chrom_info) {\n var chrom_data = self.get_elt(\n new GenomeRegion({\n chrom: chrom_info.chrom,\n start: 0,\n end: chrom_info.len\n })\n );\n\n // Set flag if data is not available.\n if (!chrom_data) {\n all_data_available = false;\n }\n\n return chrom_data;\n }\n );\n\n // -- If all data is available, return it. --\n if (all_data_available) {\n return gw_data;\n }\n\n // -- All data is not available, so load from server. --\n\n var deferred = $.Deferred();\n $.getJSON(\n this.get(\"dataset\").url(),\n { data_type: \"genome_data\" },\n function(genome_wide_data) {\n self.add_data(genome_wide_data.data);\n deferred.resolve(genome_wide_data.data);\n }\n );\n\n return deferred;\n },\n\n /**\n * Returns entry with only data in the subregion.\n */\n subset_entry: function(entry, subregion) {\n // Dictionary from entry type to function for subsetting data.\n var subset_fns = {\n bigwig: function(data, subregion) {\n return _.filter(data, function(data_point) {\n return (\n data_point[0] >= subregion.get(\"start\") &&\n data_point[0] <= subregion.get(\"end\")\n );\n });\n },\n refseq: function(data, subregion) {\n var seq_start =\n subregion.get(\"start\") - entry.region.get(\"start\");\n return entry.data.slice(\n seq_start,\n seq_start + subregion.length()\n );\n }\n };\n\n // Subset entry if there is a function for subsetting and regions are not the same.\n var subregion_data = entry.data;\n if (\n !entry.region.same(subregion) &&\n entry.dataset_type in subset_fns\n ) {\n subregion_data = subset_fns[entry.dataset_type](\n entry.data,\n subregion\n );\n }\n\n // Return entry with subregion's data.\n return {\n region: subregion,\n data: subregion_data,\n dataset_type: entry.dataset_type\n };\n }\n });\n\n var GenomeReferenceDataManager = GenomeDataManager.extend({\n initialize: function(options) {\n // Use generic object in place of dataset and set urlRoot to fetch data.\n var dataset_placeholder = new Backbone.Model();\n dataset_placeholder.urlRoot = options.data_url;\n this.set(\"dataset\", dataset_placeholder);\n },\n\n load_data: function(region, mode, resolution, extra_params) {\n // Fetch data if region is not too large.\n return region.length() <= 100000\n ? GenomeDataManager.prototype.load_data.call(\n this,\n region,\n mode,\n resolution,\n extra_params\n )\n : { data: null, region: region };\n }\n });\n\n /**\n * A genome build.\n */\n var Genome = Backbone.Model.extend({\n defaults: {\n name: null,\n key: null,\n chroms_info: null\n },\n\n initialize: function(options) {\n this.id = options.dbkey;\n },\n\n /**\n * Shorthand for getting to chromosome information.\n */\n get_chroms_info: function() {\n return this.attributes.chroms_info.chrom_info;\n },\n\n /**\n * Returns a GenomeRegion object denoting a complete chromosome.\n */\n get_chrom_region: function(chr_name) {\n // FIXME: use findWhere in underscore 1.4\n var chrom_info = _.find(this.get_chroms_info(), function(\n chrom_info\n ) {\n return chrom_info.chrom === chr_name;\n });\n return new GenomeRegion({\n chrom: chrom_info.chrom,\n end: chrom_info.len\n });\n },\n\n /** Returns the length of a chromosome. */\n get_chrom_len: function(chr_name) {\n // FIXME: use findWhere in underscore 1.4\n return _.find(this.get_chroms_info(), function(chrom_info) {\n return chrom_info.chrom === chr_name;\n }).len;\n }\n });\n\n /**\n * A genomic region.\n */\n var GenomeRegion = Backbone.Model.extend(\n {\n defaults: {\n chrom: null,\n start: 0,\n end: 0,\n str_val: null,\n genome: null\n },\n\n /**\n * Returns true if this region is the same as a given region.\n * It does not test the genome right now.\n */\n same: function(region) {\n return (\n this.attributes.chrom === region.get(\"chrom\") &&\n this.attributes.start === region.get(\"start\") &&\n this.attributes.end === region.get(\"end\")\n );\n },\n\n /**\n * If from_str specified, use it to initialize attributes.\n */\n initialize: function(options) {\n if (options.from_str) {\n var pieces = options.from_str.split(\":\"),\n chrom = pieces[0],\n start_end = pieces[1].split(\"-\");\n this.set({\n chrom: chrom,\n start: parseInt(start_end[0], 10),\n end: parseInt(start_end[1], 10)\n });\n }\n\n // Keep a copy of region's string value for fast lookup.\n this.attributes.str_val =\n this.get(\"chrom\") +\n \":\" +\n this.get(\"start\") +\n \"-\" +\n this.get(\"end\");\n\n // Set str_val on attribute change.\n this.on(\n \"change\",\n function() {\n this.attributes.str_val =\n this.get(\"chrom\") +\n \":\" +\n this.get(\"start\") +\n \"-\" +\n this.get(\"end\");\n },\n this\n );\n },\n\n copy: function() {\n return new GenomeRegion({\n chrom: this.get(\"chrom\"),\n start: this.get(\"start\"),\n end: this.get(\"end\")\n });\n },\n\n length: function() {\n return this.get(\"end\") - this.get(\"start\");\n },\n\n /** Returns region in canonical form chrom:start-end */\n toString: function() {\n return this.attributes.str_val;\n },\n\n toJSON: function() {\n return {\n chrom: this.get(\"chrom\"),\n start: this.get(\"start\"),\n end: this.get(\"end\")\n };\n },\n\n /**\n * Compute the type of overlap between this region and another region. The overlap is computed relative to the given/second region;\n * hence, OVERLAP_START indicates that the first region overlaps the start (but not the end) of the second region.\n */\n compute_overlap: function(a_region) {\n var first_chrom = this.get(\"chrom\"),\n second_chrom = a_region.get(\"chrom\"),\n first_start = this.get(\"start\"),\n second_start = a_region.get(\"start\"),\n first_end = this.get(\"end\"),\n second_end = a_region.get(\"end\"),\n overlap;\n\n // Compare chroms.\n if (\n first_chrom &&\n second_chrom &&\n first_chrom !== second_chrom\n ) {\n return GenomeRegion.overlap_results.DIF_CHROMS;\n }\n\n // Compare regions.\n if (first_start < second_start) {\n if (first_end < second_start) {\n overlap = GenomeRegion.overlap_results.BEFORE;\n } else if (first_end < second_end) {\n overlap =\n GenomeRegion.overlap_results.OVERLAP_START;\n } else {\n // first_end >= second_end\n overlap = GenomeRegion.overlap_results.CONTAINS;\n }\n } else if (first_start > second_start) {\n if (first_start > second_end) {\n overlap = GenomeRegion.overlap_results.AFTER;\n } else if (first_end <= second_end) {\n overlap = GenomeRegion.overlap_results.CONTAINED_BY;\n } else {\n overlap = GenomeRegion.overlap_results.OVERLAP_END;\n }\n } else {\n // first_start === second_start\n overlap =\n first_end >= second_end\n ? GenomeRegion.overlap_results.CONTAINS\n : GenomeRegion.overlap_results.CONTAINED_BY;\n }\n\n return overlap;\n },\n\n /**\n * Trim a region to match genome's constraints.\n */\n trim: function(genome) {\n // Assume that all chromosome/contigs start at 0.\n if (this.attributes.start < 0) {\n this.attributes.start = 0;\n }\n\n // Only try to trim the end if genome is set.\n if (this.attributes.genome) {\n var chrom_len = this.attributes.genome.get_chrom_len(\n this.attributes.chrom\n );\n if (this.attributes.end > chrom_len) {\n this.attributes.end = chrom_len - 1;\n }\n }\n\n return this;\n },\n\n /**\n * Returns true if this region contains a given region.\n */\n contains: function(a_region) {\n return (\n this.compute_overlap(a_region) ===\n GenomeRegion.overlap_results.CONTAINS\n );\n },\n\n /**\n * Returns true if regions overlap.\n */\n overlaps: function(a_region) {\n return (\n _.intersection(\n [this.compute_overlap(a_region)],\n [\n GenomeRegion.overlap_results.DIF_CHROMS,\n GenomeRegion.overlap_results.BEFORE,\n GenomeRegion.overlap_results.AFTER\n ]\n ).length === 0\n );\n }\n },\n {\n overlap_results: {\n DIF_CHROMS: 1000,\n BEFORE: 1001,\n CONTAINS: 1002,\n OVERLAP_START: 1003,\n OVERLAP_END: 1004,\n CONTAINED_BY: 1005,\n AFTER: 1006\n }\n }\n );\n\n var GenomeRegionCollection = Backbone.Collection.extend({\n model: GenomeRegion\n });\n\n /**\n * A genome browser bookmark.\n */\n var BrowserBookmark = Backbone.Model.extend({\n defaults: {\n region: null,\n note: \"\"\n },\n\n initialize: function(options) {\n this.set(\"region\", new GenomeRegion(options.region));\n }\n });\n\n /**\n * Bookmarks collection.\n */\n var BrowserBookmarkCollection = Backbone.Collection.extend({\n model: BrowserBookmark\n });\n\n /**\n * A track of data in a genome visualization.\n */\n // TODO: rename to Track and merge with Trackster's Track object.\n var BackboneTrack = Backbone.Model.extend(CustomToJSON).extend(\n {\n defaults: {\n mode: \"Auto\"\n },\n\n initialize: function(options) {\n this.set(\"dataset\", new data_mod.Dataset(options.dataset));\n\n // -- Set up config settings. --\n var models = [\n {\n key: \"name\",\n default_value: this.get(\"dataset\").get(\"name\")\n },\n { key: \"color\" },\n {\n key: \"min_value\",\n label: \"Min Value\",\n type: \"float\",\n default_value: 0\n },\n {\n key: \"max_value\",\n label: \"Max Value\",\n type: \"float\",\n default_value: 1\n }\n ];\n\n this.set(\n \"config\",\n config_mod.ConfigSettingCollection.from_models_and_saved_values(\n models,\n options.prefs\n )\n );\n\n // -- Set up data manager. --\n var preloaded_data = this.get(\"preloaded_data\");\n if (preloaded_data) {\n preloaded_data = preloaded_data.data;\n } else {\n preloaded_data = [];\n }\n this.set(\n \"data_manager\",\n new GenomeDataManager({\n dataset: this.get(\"dataset\"),\n init_data: preloaded_data\n })\n );\n }\n },\n {\n // This definition matches that produced by to_dict() methods in tracks.js\n to_json_keys: [\n \"track_type\",\n \"dataset\",\n \"prefs\",\n \"mode\",\n \"filters\",\n \"tool_state\"\n ],\n to_json_mappers: {\n prefs: function(p, self) {\n if (_.size(p) === 0) {\n p = {\n name: self\n .get(\"config\")\n .get(\"name\")\n .get(\"value\"),\n color: self\n .get(\"config\")\n .get(\"color\")\n .get(\"value\")\n };\n }\n return p;\n },\n dataset: function(d) {\n return {\n id: d.id,\n hda_ldda: d.get(\"hda_ldda\")\n };\n }\n }\n }\n );\n\n var BackboneTrackCollection = Backbone.Collection.extend({\n model: BackboneTrack\n });\n\n /**\n * A visualization.\n */\n var Visualization = Backbone.Model.extend({\n defaults: {\n title: \"\",\n type: \"\"\n },\n\n urlRoot: Galaxy.root + \"api/visualizations\",\n\n /**\n * POSTs visualization's JSON to its URL using the parameter 'vis_json'\n * Note: This is necessary because (a) Galaxy requires keyword args and\n * (b) Galaxy does not handle PUT now.\n */\n save: function() {\n return $.ajax({\n url: this.url(),\n type: \"POST\",\n dataType: \"json\",\n data: {\n vis_json: JSON.stringify(this)\n }\n });\n }\n });\n\n /**\n * A visualization of genome data.\n */\n var GenomeVisualization = Visualization.extend(CustomToJSON).extend(\n {\n defaults: _.extend({}, Visualization.prototype.defaults, {\n dbkey: \"\",\n drawables: null,\n bookmarks: null,\n viewport: null\n }),\n\n initialize: function(options) {\n // Replace drawables with tracks.\n this.set(\n \"drawables\",\n new BackboneTrackCollection(options.tracks)\n );\n\n var models = [];\n this.set(\n \"config\",\n config_mod.ConfigSettingCollection.from_models_and_saved_values(\n models,\n options.prefs\n )\n );\n\n // Clear track and data definitions to avoid storing large objects.\n this.unset(\"tracks\");\n this.get(\"drawables\").each(function(d) {\n d.unset(\"preloaded_data\");\n });\n },\n\n /**\n * Add a track or array of tracks to the visualization.\n */\n add_tracks: function(tracks) {\n this.get(\"drawables\").add(tracks);\n }\n },\n {\n // This definition matches that produced by to_dict() methods in tracks.js\n to_json_keys: [\"view\", \"viewport\", \"bookmarks\"],\n\n to_json_mappers: {\n view: function(dummy, self) {\n return {\n obj_type: \"View\",\n prefs: {\n name: self.get(\"title\"),\n content_visible: true\n },\n drawables: self.get(\"drawables\")\n };\n }\n }\n }\n );\n\n /**\n * -- Routers --\n */\n\n /**\n * Router for track browser.\n */\n var TrackBrowserRouter = Backbone.Router.extend({\n initialize: function(options) {\n this.view = options.view;\n\n // Can't put regular expression in routes dictionary.\n // NOTE: parentheses are used to denote parameters returned to callback.\n this.route(/([\\w]+)$/, \"change_location\");\n this.route(/([\\w\\+]+\\:[\\d,]+-[\\d,]+)$/, \"change_location\");\n\n // Handle navigate events from view.\n var self = this;\n self.view.on(\"navigate\", function(new_loc) {\n self.navigate(new_loc);\n });\n },\n\n change_location: function(new_loc) {\n this.view.go_to(new_loc);\n }\n });\n\n return {\n BackboneTrack: BackboneTrack,\n BrowserBookmark: BrowserBookmark,\n BrowserBookmarkCollection: BrowserBookmarkCollection,\n Cache: Cache,\n CanvasManager: CanvasManager,\n Genome: Genome,\n GenomeDataManager: GenomeDataManager,\n GenomeRegion: GenomeRegion,\n GenomeRegionCollection: GenomeRegionCollection,\n GenomeVisualization: GenomeVisualization,\n GenomeReferenceDataManager: GenomeReferenceDataManager,\n TrackBrowserRouter: TrackBrowserRouter,\n Visualization: Visualization,\n select_datasets: select_datasets\n };\n }\n);\n"]} \ No newline at end of file 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[\n \"libs/underscore\",\n \"mvc/dataset/data\",\n \"viz/trackster/util\",\n \"utils/config\",\n \"mvc/grid/grid-view\",\n \"mvc/ui/ui-tabs\",\n \"mvc/ui/ui-misc\"\n ],\n function(_, data_mod, util_mod, config_mod, GridView, Tabs, Ui) {\n /**\n * Mixin for returning custom JSON representation from toJSON. Class attribute to_json_keys defines a set of attributes\n * to include in the representation; to_json_mappers defines mappers for returned objects.\n */\n var CustomToJSON = {\n /**\n * Returns JSON representation of object using to_json_keys and to_json_mappers.\n */\n toJSON: function() {\n var self = this,\n json = {};\n _.each(self.constructor.to_json_keys, function(k) {\n var val = self.get(k);\n if (k in self.constructor.to_json_mappers) {\n val = self.constructor.to_json_mappers[k](val, self);\n }\n json[k] = val;\n });\n return json;\n }\n };\n\n /**\n * Model, view, and controller objects for Galaxy visualization framework.\n *\n * Models have no references to views, instead using events to indicate state\n * changes; this is advantageous because multiple views can use the same object\n * and models can be used without views.\n */\n\n /**\n * Use a popup grid to select datasets from histories or libraries. After datasets are selected,\n * track definitions are obtained from the server and the success_fn is called with the list of\n * definitions for selected datasets.\n */\n var select_datasets = function(filters, success_fn) {\n // history dataset selection tab\n var history_grid = new GridView({\n url_base: Galaxy.root + \"visualization/list_history_datasets\",\n filters: filters,\n dict_format: true,\n embedded: true\n });\n\n // library dataset selection tab\n var library_grid = new GridView({\n url_base: Galaxy.root + \"visualization/list_library_datasets\",\n dict_format: true,\n embedded: true\n });\n\n // build tabs\n var tabs = new Tabs.View();\n tabs.add({\n id: \"histories\",\n title: \"Histories\",\n $el: $(\"\").append(history_grid.$el)\n });\n tabs.add({\n id: \"libraries\",\n title: \"Libraries\",\n $el: $(\"\").append(library_grid.$el)\n });\n\n // modal\n Galaxy.modal.show({\n title: \"Select datasets for new tracks\",\n body: tabs.$el,\n closing_events: true,\n buttons: {\n Cancel: function() {\n Galaxy.modal.hide();\n },\n Add: function() {\n var requests = [];\n tabs\n .$(\n \"input.grid-row-select-checkbox[name=id]:checked\"\n )\n .each(function() {\n window.console.log($(this).val());\n requests[requests.length] = $.ajax({\n url:\n Galaxy.root +\n \"api/datasets/\" +\n $(this).val(),\n dataType: \"json\",\n data: {\n data_type: \"track_config\",\n hda_ldda:\n tabs.current() == \"histories\"\n ? \"hda\"\n : \"ldda\"\n }\n });\n });\n // To preserve order, wait until there are definitions for all tracks and then add\n // them sequentially.\n $.when.apply($, requests).then(function() {\n // jQuery always returns an Array for arguments, so need to look at first element\n // to determine whether multiple requests were made and consequently how to\n // map arguments to track definitions.\n var track_defs =\n arguments[0] instanceof Array\n ? $.map(arguments, function(arg) {\n return arg[0];\n })\n : [arguments[0]];\n success_fn(track_defs);\n });\n Galaxy.modal.hide();\n }\n }\n });\n };\n\n // --------- Models ---------\n\n /**\n * Canvas manager is used to create canvases for browsers as well as providing a pattern cache\n */\n var CanvasManager = function(default_font) {\n this.default_font =\n default_font !== undefined\n ? default_font\n : \"9px Monaco, Lucida Console, monospace\";\n\n this.dummy_canvas = this.new_canvas();\n this.dummy_context = this.dummy_canvas.getContext(\"2d\");\n this.dummy_context.font = this.default_font;\n\n this.char_width_px = this.dummy_context.measureText(\"A\").width;\n\n this.patterns = {};\n\n // FIXME: move somewhere to make this more general\n this.load_pattern(\n \"right_strand\",\n \"/visualization/strand_right.png\"\n );\n this.load_pattern(\"left_strand\", \"/visualization/strand_left.png\");\n this.load_pattern(\n \"right_strand_inv\",\n \"/visualization/strand_right_inv.png\"\n );\n this.load_pattern(\n \"left_strand_inv\",\n \"/visualization/strand_left_inv.png\"\n );\n };\n\n _.extend(CanvasManager.prototype, {\n load_pattern: function(key, path) {\n var patterns = this.patterns,\n dummy_context = this.dummy_context,\n image = new Image();\n image.src = Galaxy.root + \"static/images\" + path;\n image.onload = function() {\n patterns[key] = dummy_context.createPattern(\n image,\n \"repeat\"\n );\n };\n },\n get_pattern: function(key) {\n return this.patterns[key];\n },\n new_canvas: function() {\n var canvas = $(\"\")[0];\n // Keep a reference back to the manager\n canvas.manager = this;\n return canvas;\n }\n });\n\n /**\n * Generic cache that handles key/value pairs. Keys can be any object that can be\n * converted to a String and compared.\n */\n var Cache = Backbone.Model.extend({\n defaults: {\n num_elements: 20,\n // Objects in cache; indexes into cache are strings of keys.\n obj_cache: null,\n // key_ary contains keys for objects in cache.\n key_ary: null\n },\n\n initialize: function(options) {\n this.clear();\n },\n\n /**\n * Get an element from the cache using its key.\n */\n get_elt: function(key) {\n var obj_cache = this.attributes.obj_cache,\n key_ary = this.attributes.key_ary,\n key_str = key.toString(),\n index = _.indexOf(key_ary, function(k) {\n return k.toString() === key_str;\n });\n\n // Update cache.\n if (index !== -1) {\n // Object is in cache, so update it.\n if (obj_cache[key_str].stale) {\n // Object is stale: remove key and object.\n key_ary.splice(index, 1);\n delete obj_cache[key_str];\n } else {\n // Move key to back because it is most recently used.\n this.move_key_to_end(key, index);\n }\n }\n\n return obj_cache[key_str];\n },\n\n /**\n * Put an element into the cache.\n */\n set_elt: function(key, value) {\n var obj_cache = this.attributes.obj_cache,\n key_ary = this.attributes.key_ary,\n key_str = key.toString(),\n num_elements = this.attributes.num_elements;\n\n // Update keys, objects.\n if (!obj_cache[key_str]) {\n // Add object to cache.\n\n if (key_ary.length >= num_elements) {\n // Cache full, so remove first element.\n var deleted_key = key_ary.shift();\n delete obj_cache[deleted_key.toString()];\n }\n\n // Add key.\n key_ary.push(key);\n }\n\n // Add object.\n obj_cache[key_str] = value;\n return value;\n },\n\n /**\n * Move key to end of cache. Keys are removed from the front, so moving a key to the end\n * delays the key's removal.\n */\n move_key_to_end: function(key, index) {\n this.attributes.key_ary.splice(index, 1);\n this.attributes.key_ary.push(key);\n },\n\n /**\n * Clear all elements from the cache.\n */\n clear: function() {\n this.attributes.obj_cache = {};\n this.attributes.key_ary = [];\n },\n\n /** Returns the number of elements in the cache. */\n size: function() {\n return this.attributes.key_ary.length;\n },\n\n /** Returns key most recently added to cache. */\n most_recently_added: function() {\n return this.size() === 0\n ? null\n : // Most recent key is at the end of key array.\n this.attributes.key_ary[\n this.attributes.key_ary.length - 1\n ];\n }\n });\n\n /**\n * Data manager for genomic data. Data is connected to and queryable by genomic regions.\n */\n var GenomeDataManager = Cache.extend({\n defaults: _.extend({}, Cache.prototype.defaults, {\n dataset: null,\n genome: null,\n init_data: null,\n min_region_size: 200,\n filters_manager: null,\n data_type: \"data\",\n data_mode_compatible: function(entry, mode) {\n return true;\n },\n can_subset: function(entry) {\n return false;\n }\n }),\n\n /**\n * Initialization.\n */\n initialize: function(options) {\n Cache.prototype.initialize.call(this);\n\n // Set initial entries in data manager.\n var initial_entries = this.get(\"init_data\");\n if (initial_entries) {\n this.add_data(initial_entries);\n }\n },\n\n /**\n * Add data entries to manager; each entry should be a dict with attributes region (key), data, and data_type.\n * If necessary, manager size is increased to hold all data.\n */\n add_data: function(entries) {\n // Increase size to accomodate all entries.\n if (this.get(\"num_elements\") < entries.length) {\n this.set(\"num_elements\", entries.length);\n }\n\n // Put data into manager.\n var self = this;\n _.each(entries, function(entry) {\n self.set_data(entry.region, entry);\n });\n },\n\n /**\n * Returns deferred that resolves to true when dataset is ready (or false if dataset\n * cannot be used).\n */\n data_is_ready: function() {\n var dataset = this.get(\"dataset\"),\n ready_deferred = $.Deferred(),\n // If requesting raw data, query dataset state; if requesting (converted) data,\n // need to query converted datasets state.\n query_type =\n this.get(\"data_type\") === \"raw_data\"\n ? \"state\"\n : this.get(\"data_type\") === \"data\"\n ? \"converted_datasets_state\"\n : \"error\",\n ss_deferred = new util_mod.ServerStateDeferred({\n ajax_settings: {\n url: this.get(\"dataset\").url(),\n data: {\n hda_ldda: dataset.get(\"hda_ldda\"),\n data_type: query_type\n },\n dataType: \"json\"\n },\n interval: 5000,\n success_fn: function(response) {\n return response !== \"pending\";\n }\n });\n\n $.when(ss_deferred.go()).then(function(response) {\n ready_deferred.resolve(\n response === \"ok\" || response === \"data\"\n );\n });\n return ready_deferred;\n },\n\n /**\n * Perform a feature search from server; returns Deferred object that resolves when data is available.\n */\n search_features: function(query) {\n var dataset = this.get(\"dataset\"),\n params = {\n query: query,\n hda_ldda: dataset.get(\"hda_ldda\"),\n data_type: \"features\"\n };\n return $.getJSON(dataset.url(), params);\n },\n\n /**\n * Load data from server and manages data entries. Adds a Deferred to manager\n * for region; when data becomes available, replaces Deferred with data.\n * Returns the Deferred that resolves when data is available.\n */\n load_data: function(region, mode, resolution, extra_params) {\n // Setup data request params.\n var dataset = this.get(\"dataset\"),\n params = {\n data_type: this.get(\"data_type\"),\n chrom: region.get(\"chrom\"),\n low: region.get(\"start\"),\n high: region.get(\"end\"),\n mode: mode,\n resolution: resolution,\n hda_ldda: dataset.get(\"hda_ldda\")\n };\n\n $.extend(params, extra_params);\n\n // Add track filters to params.\n var filters_manager = this.get(\"filters_manager\");\n if (filters_manager) {\n var filter_names = [];\n var filters = filters_manager.filters;\n for (var i = 0; i < filters.length; i++) {\n filter_names.push(filters[i].name);\n }\n params.filter_cols = JSON.stringify(filter_names);\n }\n\n // Do request.\n var manager = this,\n entry = $.getJSON(dataset.url(), params, function(result) {\n // Add region to the result.\n result.region = region;\n manager.set_data(region, result);\n });\n\n this.set_data(region, entry);\n return entry;\n },\n\n /**\n * Get data from dataset.\n */\n get_data: function(region, mode, resolution, extra_params) {\n // Look for entry and return if it's a deferred or if data available is compatible with mode.\n var entry = this.get_elt(region);\n if (\n entry &&\n (util_mod.is_deferred(entry) ||\n this.get(\"data_mode_compatible\")(entry, mode))\n ) {\n return entry;\n }\n\n //\n // Look in cache for data that can be used.\n // TODO: this logic could be improved if the visualization knew whether\n // the data was \"index\" or \"data.\"\n //\n var key_ary = this.get(\"key_ary\"),\n obj_cache = this.get(\"obj_cache\"),\n entry_region,\n is_subregion;\n for (var i = 0; i < key_ary.length; i++) {\n entry_region = key_ary[i];\n\n if (entry_region.contains(region)) {\n is_subregion = true;\n\n // This entry has data in the requested range. Return if data\n // is compatible and can be subsetted.\n entry = obj_cache[entry_region.toString()];\n if (\n util_mod.is_deferred(entry) ||\n (this.get(\"data_mode_compatible\")(entry, mode) &&\n this.get(\"can_subset\")(entry))\n ) {\n this.move_key_to_end(entry_region, i);\n\n // If there's data, subset it.\n if (!util_mod.is_deferred(entry)) {\n var subset_entry = this.subset_entry(\n entry,\n region\n );\n this.set_data(region, subset_entry);\n entry = subset_entry;\n }\n\n return entry;\n }\n }\n }\n\n // FIXME: There _may_ be instances where region is a subregion of another entry but cannot be\n // subsetted. For these cases, do not increase length because region will never be found (and\n // an infinite loop will occur.)\n // If needed, extend region to make it minimum size.\n if (\n !is_subregion &&\n region.length() < this.attributes.min_region_size\n ) {\n // IDEA: alternative heuristic is to find adjacent cache entry to region and use that to extend.\n // This would prevent bad extensions when zooming in/out while still preserving the behavior\n // below.\n\n // Use copy of region to avoid changing actual region.\n region = region.copy();\n\n // Use heuristic to extend region: extend relative to last data request.\n var last_request = this.most_recently_added();\n if (\n !last_request ||\n region.get(\"start\") > last_request.get(\"start\")\n ) {\n // This request is after the last request, so extend right.\n region.set(\n \"end\",\n region.get(\"start\") +\n this.attributes.min_region_size\n );\n } else {\n // This request is after the last request, so extend left.\n region.set(\n \"start\",\n region.get(\"end\") - this.attributes.min_region_size\n );\n }\n\n // Trim region to avoid invalid coordinates.\n region.set(\"genome\", this.attributes.genome);\n region.trim();\n }\n\n return this.load_data(region, mode, resolution, extra_params);\n },\n\n /**\n * Alias for set_elt for readbility.\n */\n set_data: function(region, entry) {\n this.set_elt(region, entry);\n },\n\n /** \"Deep\" data request; used as a parameter for DataManager.get_more_data() */\n DEEP_DATA_REQ: \"deep\",\n\n /** \"Broad\" data request; used as a parameter for DataManager.get_more_data() */\n BROAD_DATA_REQ: \"breadth\",\n\n /**\n * Gets more data for a region using either a depth-first or a breadth-first approach.\n */\n get_more_data: function(\n region,\n mode,\n resolution,\n extra_params,\n req_type\n ) {\n var cur_data = this._mark_stale(region);\n if (\n !(\n cur_data &&\n this.get(\"data_mode_compatible\")(cur_data, mode)\n )\n ) {\n console.log(\n \"ERROR: problem with getting more data: current data is not compatible\"\n );\n return;\n }\n\n //\n // Set parameters based on request type.\n //\n var query_low = region.get(\"start\");\n if (req_type === this.DEEP_DATA_REQ) {\n // Use same interval but set start_val to skip data that's already in cur_data.\n $.extend(extra_params, {\n start_val: cur_data.data.length + 1\n });\n } else if (req_type === this.BROAD_DATA_REQ) {\n // To get past an area of extreme feature depth, set query low to be after either\n // (a) the maximum high or HACK/FIXME (b) the end of the last feature returned.\n query_low =\n (cur_data.max_high\n ? cur_data.max_high\n : cur_data.data[cur_data.data.length - 1][2]) + 1;\n }\n var query_region = region.copy().set(\"start\", query_low);\n\n //\n // Get additional data, append to current data, and set new data. Use a custom deferred object\n // to signal when new data is available.\n //\n var data_manager = this,\n new_data_request = this.load_data(\n query_region,\n mode,\n resolution,\n extra_params\n ),\n new_data_available = $.Deferred();\n // load_data sets cache to new_data_request, but use custom deferred object so that signal and data\n // is all data, not just new data.\n this.set_data(region, new_data_available);\n $.when(new_data_request).then(function(result) {\n // Update data and message.\n if (result.data) {\n result.data = cur_data.data.concat(result.data);\n if (result.max_low) {\n result.max_low = cur_data.max_low;\n }\n if (result.message) {\n // HACK: replace number in message with current data length. Works but is ugly.\n result.message = result.message.replace(\n /[0-9]+/,\n result.data.length\n );\n }\n }\n data_manager.set_data(region, result);\n new_data_available.resolve(result);\n });\n return new_data_available;\n },\n\n /**\n * Returns true if more detailed data can be obtained for entry.\n */\n can_get_more_detailed_data: function(region) {\n var cur_data = this.get_elt(region);\n\n // Can only get more detailed data for bigwig data that has less than 8000 data points.\n // Summary tree returns *way* too much data, and 8000 data points ~ 500KB.\n return (\n cur_data.dataset_type === \"bigwig\" &&\n cur_data.data.length < 8000\n );\n },\n\n /**\n * Returns more detailed data for an entry.\n */\n get_more_detailed_data: function(\n region,\n mode,\n resolution,\n detail_multiplier,\n extra_params\n ) {\n // Mark current entry as stale.\n var cur_data = this._mark_stale(region);\n if (!cur_data) {\n console.log(\n \"ERROR getting more detailed data: no current data\"\n );\n return;\n }\n\n if (!extra_params) {\n extra_params = {};\n }\n\n // Use additional parameters to get more detailed data.\n if (cur_data.dataset_type === \"bigwig\") {\n // FIXME: constant should go somewhere.\n extra_params.num_samples = 1000 * detail_multiplier;\n }\n\n return this.load_data(region, mode, resolution, extra_params);\n },\n\n /**\n * Marks cache data as stale.\n */\n _mark_stale: function(region) {\n var entry = this.get_elt(region);\n if (!entry) {\n console.log(\n \"ERROR: no data to mark as stale: \",\n this.get(\"dataset\"),\n region.toString()\n );\n }\n entry.stale = true;\n return entry;\n },\n\n /**\n * Returns an array of data with each entry representing one chromosome/contig\n * of data or, if data is not available, returns a Deferred that resolves to the\n * data when it becomes available.\n */\n get_genome_wide_data: function(genome) {\n // -- Get all data. --\n\n var self = this,\n all_data_available = true,\n // Map chromosome info into genome data.\n gw_data = _.map(\n genome.get(\"chroms_info\").chrom_info,\n function(chrom_info) {\n var chrom_data = self.get_elt(\n new GenomeRegion({\n chrom: chrom_info.chrom,\n start: 0,\n end: chrom_info.len\n })\n );\n\n // Set flag if data is not available.\n if (!chrom_data) {\n all_data_available = false;\n }\n\n return chrom_data;\n }\n );\n\n // -- If all data is available, return it. --\n if (all_data_available) {\n return gw_data;\n }\n\n // -- All data is not available, so load from server. --\n\n var deferred = $.Deferred();\n $.getJSON(\n this.get(\"dataset\").url(),\n { data_type: \"genome_data\" },\n function(genome_wide_data) {\n self.add_data(genome_wide_data.data);\n deferred.resolve(genome_wide_data.data);\n }\n );\n\n return deferred;\n },\n\n /**\n * Returns entry with only data in the subregion.\n */\n subset_entry: function(entry, subregion) {\n // Dictionary from entry type to function for subsetting data.\n var subset_fns = {\n bigwig: function(data, subregion) {\n return _.filter(data, function(data_point) {\n return (\n data_point[0] >= subregion.get(\"start\") &&\n data_point[0] <= subregion.get(\"end\")\n );\n });\n },\n refseq: function(data, subregion) {\n var seq_start =\n subregion.get(\"start\") - entry.region.get(\"start\");\n return entry.data.slice(\n seq_start,\n seq_start + subregion.length()\n );\n }\n };\n\n // Subset entry if there is a function for subsetting and regions are not the same.\n var subregion_data = entry.data;\n if (\n !entry.region.same(subregion) &&\n entry.dataset_type in subset_fns\n ) {\n subregion_data = subset_fns[entry.dataset_type](\n entry.data,\n subregion\n );\n }\n\n // Return entry with subregion's data.\n return {\n region: subregion,\n data: subregion_data,\n dataset_type: entry.dataset_type\n };\n }\n });\n\n var GenomeReferenceDataManager = GenomeDataManager.extend({\n initialize: function(options) {\n // Use generic object in place of dataset and set urlRoot to fetch data.\n var dataset_placeholder = new Backbone.Model();\n dataset_placeholder.urlRoot = options.data_url;\n this.set(\"dataset\", dataset_placeholder);\n },\n\n load_data: function(region, mode, resolution, extra_params) {\n // Fetch data if region is not too large.\n return region.length() <= 100000\n ? GenomeDataManager.prototype.load_data.call(\n this,\n region,\n mode,\n resolution,\n extra_params\n )\n : { data: null, region: region };\n }\n });\n\n /**\n * A genome build.\n */\n var Genome = Backbone.Model.extend({\n defaults: {\n name: null,\n key: null,\n chroms_info: null\n },\n\n initialize: function(options) {\n this.id = options.dbkey;\n },\n\n /**\n * Shorthand for getting to chromosome information.\n */\n get_chroms_info: function() {\n return this.attributes.chroms_info.chrom_info;\n },\n\n /**\n * Returns a GenomeRegion object denoting a complete chromosome.\n */\n get_chrom_region: function(chr_name) {\n // FIXME: use findWhere in underscore 1.4\n var chrom_info = _.find(this.get_chroms_info(), function(\n chrom_info\n ) {\n return chrom_info.chrom === chr_name;\n });\n return new GenomeRegion({\n chrom: chrom_info.chrom,\n end: chrom_info.len\n });\n },\n\n /** Returns the length of a chromosome. */\n get_chrom_len: function(chr_name) {\n // FIXME: use findWhere in underscore 1.4\n return _.find(this.get_chroms_info(), function(chrom_info) {\n return chrom_info.chrom === chr_name;\n }).len;\n }\n });\n\n /**\n * A genomic region.\n */\n var GenomeRegion = Backbone.Model.extend(\n {\n defaults: {\n chrom: null,\n start: 0,\n end: 0,\n str_val: null,\n genome: null\n },\n\n /**\n * Returns true if this region is the same as a given region.\n * It does not test the genome right now.\n */\n same: function(region) {\n return (\n this.attributes.chrom === region.get(\"chrom\") &&\n this.attributes.start === region.get(\"start\") &&\n this.attributes.end === region.get(\"end\")\n );\n },\n\n /**\n * If from_str specified, use it to initialize attributes.\n */\n initialize: function(options) {\n if (options.from_str) {\n var pieces = options.from_str.split(\":\"),\n chrom = pieces[0],\n start_end = pieces[1].split(\"-\");\n this.set({\n chrom: chrom,\n start: parseInt(start_end[0], 10),\n end: parseInt(start_end[1], 10)\n });\n }\n\n // Keep a copy of region's string value for fast lookup.\n this.attributes.str_val =\n this.get(\"chrom\") +\n \":\" +\n this.get(\"start\") +\n \"-\" +\n this.get(\"end\");\n\n // Set str_val on attribute change.\n this.on(\n \"change\",\n function() {\n this.attributes.str_val =\n this.get(\"chrom\") +\n \":\" +\n this.get(\"start\") +\n \"-\" +\n this.get(\"end\");\n },\n this\n );\n },\n\n copy: function() {\n return new GenomeRegion({\n chrom: this.get(\"chrom\"),\n start: this.get(\"start\"),\n end: this.get(\"end\")\n });\n },\n\n length: function() {\n return this.get(\"end\") - this.get(\"start\");\n },\n\n /** Returns region in canonical form chrom:start-end */\n toString: function() {\n return this.attributes.str_val;\n },\n\n toJSON: function() {\n return {\n chrom: this.get(\"chrom\"),\n start: this.get(\"start\"),\n end: this.get(\"end\")\n };\n },\n\n /**\n * Compute the type of overlap between this region and another region. The overlap is computed relative to the given/second region;\n * hence, OVERLAP_START indicates that the first region overlaps the start (but not the end) of the second region.\n */\n compute_overlap: function(a_region) {\n var first_chrom = this.get(\"chrom\"),\n second_chrom = a_region.get(\"chrom\"),\n first_start = this.get(\"start\"),\n second_start = a_region.get(\"start\"),\n first_end = this.get(\"end\"),\n second_end = a_region.get(\"end\"),\n overlap;\n\n // Compare chroms.\n if (\n first_chrom &&\n second_chrom &&\n first_chrom !== second_chrom\n ) {\n return GenomeRegion.overlap_results.DIF_CHROMS;\n }\n\n // Compare regions.\n if (first_start < second_start) {\n if (first_end < second_start) {\n overlap = GenomeRegion.overlap_results.BEFORE;\n } else if (first_end < second_end) {\n overlap =\n GenomeRegion.overlap_results.OVERLAP_START;\n } else {\n // first_end >= second_end\n overlap = GenomeRegion.overlap_results.CONTAINS;\n }\n } else if (first_start > second_start) {\n if (first_start > second_end) {\n overlap = GenomeRegion.overlap_results.AFTER;\n } else if (first_end <= second_end) {\n overlap = GenomeRegion.overlap_results.CONTAINED_BY;\n } else {\n overlap = GenomeRegion.overlap_results.OVERLAP_END;\n }\n } else {\n // first_start === second_start\n overlap =\n first_end >= second_end\n ? GenomeRegion.overlap_results.CONTAINS\n : GenomeRegion.overlap_results.CONTAINED_BY;\n }\n\n return overlap;\n },\n\n /**\n * Trim a region to match genome's constraints.\n */\n trim: function(genome) {\n // Assume that all chromosome/contigs start at 0.\n if (this.attributes.start < 0) {\n this.attributes.start = 0;\n }\n\n // Only try to trim the end if genome is set.\n if (this.attributes.genome) {\n var chrom_len = this.attributes.genome.get_chrom_len(\n this.attributes.chrom\n );\n if (this.attributes.end > chrom_len) {\n this.attributes.end = chrom_len - 1;\n }\n }\n\n return this;\n },\n\n /**\n * Returns true if this region contains a given region.\n */\n contains: function(a_region) {\n return (\n this.compute_overlap(a_region) ===\n GenomeRegion.overlap_results.CONTAINS\n );\n },\n\n /**\n * Returns true if regions overlap.\n */\n overlaps: function(a_region) {\n return (\n _.intersection(\n [this.compute_overlap(a_region)],\n [\n GenomeRegion.overlap_results.DIF_CHROMS,\n GenomeRegion.overlap_results.BEFORE,\n GenomeRegion.overlap_results.AFTER\n ]\n ).length === 0\n );\n }\n },\n {\n overlap_results: {\n DIF_CHROMS: 1000,\n BEFORE: 1001,\n CONTAINS: 1002,\n OVERLAP_START: 1003,\n OVERLAP_END: 1004,\n CONTAINED_BY: 1005,\n AFTER: 1006\n }\n }\n );\n\n var GenomeRegionCollection = Backbone.Collection.extend({\n model: GenomeRegion\n });\n\n /**\n * A genome browser bookmark.\n */\n var BrowserBookmark = Backbone.Model.extend({\n defaults: {\n region: null,\n note: \"\"\n },\n\n initialize: function(options) {\n this.set(\"region\", new GenomeRegion(options.region));\n }\n });\n\n /**\n * Bookmarks collection.\n */\n var BrowserBookmarkCollection = Backbone.Collection.extend({\n model: BrowserBookmark\n });\n\n /**\n * A track of data in a genome visualization.\n */\n // TODO: rename to Track and merge with Trackster's Track object.\n var BackboneTrack = Backbone.Model.extend(CustomToJSON).extend(\n {\n defaults: {\n mode: \"Auto\"\n },\n\n initialize: function(options) {\n this.set(\"dataset\", new data_mod.Dataset(options.dataset));\n\n // -- Set up config settings. --\n var models = [\n {\n key: \"name\",\n default_value: this.get(\"dataset\").get(\"name\")\n },\n { key: \"color\" },\n {\n key: \"min_value\",\n label: \"Min Value\",\n type: \"float\",\n default_value: 0\n },\n {\n key: \"max_value\",\n label: \"Max Value\",\n type: \"float\",\n default_value: 1\n }\n ];\n\n this.set(\n \"config\",\n config_mod.ConfigSettingCollection.from_models_and_saved_values(\n models,\n options.prefs\n )\n );\n\n // -- Set up data manager. --\n var preloaded_data = this.get(\"preloaded_data\");\n if (preloaded_data) {\n preloaded_data = preloaded_data.data;\n } else {\n preloaded_data = [];\n }\n this.set(\n \"data_manager\",\n new GenomeDataManager({\n dataset: this.get(\"dataset\"),\n init_data: preloaded_data\n })\n );\n }\n },\n {\n // This definition matches that produced by to_dict() methods in tracks.js\n to_json_keys: [\n \"track_type\",\n \"dataset\",\n \"prefs\",\n \"mode\",\n \"filters\",\n \"tool_state\"\n ],\n to_json_mappers: {\n prefs: function(p, self) {\n if (_.size(p) === 0) {\n p = {\n name: self\n .get(\"config\")\n .get(\"name\")\n .get(\"value\"),\n color: self\n .get(\"config\")\n .get(\"color\")\n .get(\"value\")\n };\n }\n return p;\n },\n dataset: function(d) {\n return {\n id: d.id,\n hda_ldda: d.get(\"hda_ldda\")\n };\n }\n }\n }\n );\n\n var BackboneTrackCollection = Backbone.Collection.extend({\n model: BackboneTrack\n });\n\n /**\n * A visualization.\n */\n var Visualization = Backbone.Model.extend({\n defaults: {\n title: \"\",\n type: \"\"\n },\n\n urlRoot: Galaxy.root + \"api/visualizations\",\n\n /**\n * POSTs visualization's JSON to its URL using the parameter 'vis_json'\n * Note: This is necessary because (a) Galaxy requires keyword args and\n * (b) Galaxy does not handle PUT now.\n */\n save: function() {\n return $.ajax({\n url: this.url(),\n type: \"POST\",\n dataType: \"json\",\n data: {\n vis_json: JSON.stringify(this)\n }\n });\n }\n });\n\n /**\n * A visualization of genome data.\n */\n var GenomeVisualization = Visualization.extend(CustomToJSON).extend(\n {\n defaults: _.extend({}, Visualization.prototype.defaults, {\n dbkey: \"\",\n drawables: null,\n bookmarks: null,\n viewport: null\n }),\n\n initialize: function(options) {\n // Replace drawables with tracks.\n this.set(\n \"drawables\",\n new BackboneTrackCollection(options.tracks)\n );\n\n var models = [];\n this.set(\n \"config\",\n config_mod.ConfigSettingCollection.from_models_and_saved_values(\n models,\n options.prefs\n )\n );\n\n // Clear track and data definitions to avoid storing large objects.\n this.unset(\"tracks\");\n this.get(\"drawables\").each(function(d) {\n d.unset(\"preloaded_data\");\n });\n },\n\n /**\n * Add a track or array of tracks to the visualization.\n */\n add_tracks: function(tracks) {\n this.get(\"drawables\").add(tracks);\n }\n },\n {\n // This definition matches that produced by to_dict() methods in tracks.js\n to_json_keys: [\"view\", \"viewport\", \"bookmarks\"],\n\n to_json_mappers: {\n view: function(dummy, self) {\n return {\n obj_type: \"View\",\n prefs: {\n name: self.get(\"title\"),\n content_visible: true\n },\n drawables: self.get(\"drawables\")\n };\n }\n }\n }\n );\n\n /**\n * -- Routers --\n */\n\n /**\n * Router for track browser.\n */\n var TrackBrowserRouter = Backbone.Router.extend({\n initialize: function(options) {\n this.view = options.view;\n\n // Can't put regular expression in routes dictionary.\n // NOTE: parentheses are used to denote parameters returned to callback.\n this.route(/([\\w]+)$/, \"change_location\");\n this.route(/([\\w\\+]+\\:[\\d,]+-[\\d,]+)$/, \"change_location\");\n\n // Handle navigate events from view.\n var self = this;\n self.view.on(\"navigate\", function(new_loc) {\n self.navigate(new_loc);\n });\n },\n\n change_location: function(new_loc) {\n this.view.go_to(new_loc);\n }\n });\n\n return {\n BackboneTrack: BackboneTrack,\n BrowserBookmark: BrowserBookmark,\n BrowserBookmarkCollection: BrowserBookmarkCollection,\n Cache: Cache,\n CanvasManager: CanvasManager,\n Genome: Genome,\n GenomeDataManager: GenomeDataManager,\n GenomeRegion: GenomeRegion,\n GenomeRegionCollection: GenomeRegionCollection,\n GenomeVisualization: GenomeVisualization,\n GenomeReferenceDataManager: GenomeReferenceDataManager,\n TrackBrowserRouter: TrackBrowserRouter,\n Visualization: Visualization,\n select_datasets: select_datasets\n };\n }\n);\n"]} \ No newline at end of file diff --git a/static/maps/viz/viz_views.js.map b/static/maps/viz/viz_views.js.map index 65f00eee60c..33b095f6c12 100644 --- a/static/maps/viz/viz_views.js.map +++ b/static/maps/viz/viz_views.js.map @@ -1 +1 @@ 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function(_) {\n /**\n * View for track/group header.\n */\n var TrackHeaderView = Backbone.View.extend({\n className: \"track-header\",\n\n initialize: function() {\n // Watch and update name changes.\n this.model.config\n .get(\"name\")\n .on(\"change:value\", this.update_name, this);\n this.render();\n },\n\n render: function() {\n this.$el.append($(\"\").addClass(this.model.drag_handle_class));\n this.$el.append(\n $(\"\")\n .addClass(\"track-name\")\n .text(this.model.config.get_value(\"name\"))\n );\n\n // Icons container.\n this.action_icons = {};\n this.render_action_icons();\n\n // Suppress double clicks in header so that they do not impact viz under header.\n this.$el.dblclick(function(e) {\n e.stopPropagation();\n });\n\n // Needed for floating elts in header.\n this.$el.append($(\"\"));\n },\n\n update_name: function() {\n this.$el\n .find(\".track-name\")\n .text(this.model.config.get_value(\"name\"));\n },\n\n render_action_icons: function() {\n var self = this;\n 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Appends icon unless prepend flag is specified.\n */\n add_action_icon: function(\n name,\n title,\n css_class,\n on_click_fn,\n prepend,\n hide\n ) {\n var self = this;\n this.action_icons[name] = $(\"\")\n .attr(\"title\", title)\n .addClass(\"icon-button\")\n .addClass(css_class)\n .tooltip()\n .click(function() {\n on_click_fn(self.model);\n })\n .appendTo(this.icons_div);\n if (hide) {\n this.action_icons[name].hide();\n }\n },\n\n /**\n * Set track's modes and update mode icon popup.\n */\n set_display_modes: function(new_modes, init_mode) {\n if (!new_modes) {\n return;\n }\n\n // HACK: move this out of view and into track.\n\n // Set modes, init mode.\n this.model.display_modes = new_modes;\n this.model.mode =\n init_mode ||\n this.model.config.get_value(\"mode\") ||\n this.model.display_modes[0];\n\n this.action_icons.mode_icon.attr(\n \"title\",\n \"Set display mode (now: \" + this.mode + \")\"\n );\n\n // Setup popup menu for changing modes.\n var self = this,\n track = this.model,\n mode_mapping = {};\n for (var i = 0, len = track.display_modes.length; i < len; i++) {\n var mode = track.display_modes[i];\n mode_mapping[mode] = (function(mode) {\n return function() {\n track.change_mode(mode);\n // HACK: the popup menu messes with the track's hover event, so manually show/hide\n // icons div for now.\n //self.icons_div.show();\n //track.container_div.mouseleave(function() { track.icons_div.hide(); } );\n };\n })(mode);\n }\n\n make_popupmenu(this.action_icons.mode_icon, mode_mapping);\n }\n });\n\n return {\n TrackHeaderView: TrackHeaderView\n };\n});\n"]} \ No newline at end of file +{"version":3,"sources":["viz/viz_views.js"],"names":["define","_","TrackHeaderView","Backbone","View","extend","className","initialize","this","model","config","on","update_name","render","append","$","addClass","drag_handle_class","$el","text","get_value","action_icons","render_action_icons","dblclick","e","stopPropagation","find","self","icons_div","set_display_modes","hide","appendTo","each","action_icons_def","icon_dict","add_action_icon","name","title","css_class","on_click_fn","display_modes","prepend","mode_icon","attr","tooltip","click","mode_mapping","len","track","change_mode","new_modes","init_mode","mode","i","length","make_popupmenu"],"mappings":"kCAAAA,QAAQ,mBAAoB,SAASC,GAoIjC,OACIC,gBApIJC,SAAAC,KAAAC,QAIIC,UAAW,eADfC,WAAIL,WAKIM,KAAKC,MAAMC,OAFfH,IAAAA,QACII,GAAA,eAAAH,KAAAI,YAAAJ,MACAA,KAAAK,UAMJA,OAAQ,WAARA,KAAAA,IAAQC,OAAAC,EAAA,UAAWC,SAAAR,KAAAC,MAAAQ,oBACfT,KAAAU,IAAKA,OACLH,EAAA,UAESC,SAAS,cAIlBG,KAAAX,KAAAC,MAAAC,OAAAU,UAAA,UAIAZ,KAAAa,gBACAb,KAAAc,sBAAAd,KAAKU,IAAIK,SAAS,SAASC,GAI3BA,EAAAC,oBAIJb,KAAAA,IAAAA,OAAaG,EAAA,gCAAbH,YAAa,WAMbU,KAAAA,IACII,KAAIC,eACJR,KAAKS,KAAAA,MAAYb,OAAEK,UACdJ,UAYJM,oBATD,WALA,IAAIK,EAAOnB,KAgBXA,KAAAoB,UAAAb,EAAA,UACAC,SAAKa,eAxD8BC,OA2C9BC,SAASvB,KAAKU,KAgBvBjB,EAAA+B,KAAAxB,KAAAC,MAAAwB,iBAAA,SAAAC,GAdQP,EAAKQ,gBACDD,EAAUE,KAgBtBD,EAAiBE,MAQTV,EAAOW,UACXJ,EAAKb,YAMGkB,EAAAA,QAEHR,EAASD,QAvBdtB,KAAKqB,kBAAkBrB,KAAKC,MAAM+B,gBAkC9BL,gBAAA,SACHC,EA3BDC,EA6BAC,EA3BAC,EA6BAE,EACAX,GA1BA,IAAIH,EAAOnB,KAgCXA,KAAAa,aAAKA,GAAaqB,EAAAA,QA9BbC,KAAK,QAASN,GAmCnBrB,SAAA,eACAA,SAAIW,GAAJiB,UAAAC,MAEIC,WACJP,EAAgBQ,EAAAA,SAEZD,SAAAA,KAAAA,WACIhB,GACIkB,KAAAA,aAAMC,GAAAA,QAOjBpB,kBAAA,SAAAqB,EAAAC,GAjCD,GAAKD,EAAL,CAuCR1C,KAAAC,MAAA+B,cAAAU,EApIJ1C,KAAAC,MAAA2C,KAsGgBD,GACA3C,KAAKC,MAAMC,OAAOU,UAAU,SAC5BZ,KAAKC,MAAM+B,cAAc,GAE7BhC,KAAKa,aAAaqB,UAAUC,KACxB,QACA,0BAA4BnC,KAAK4C,KAAO,KAO5C,IAAK,IAFDJ,EAAQxC,KAAKC,MACbqC,KACKO,EAAI,EAAGN,EAAMC,EAAMR,cAAcc,OAAQD,EAAIN,EAAKM,IAAK,CAC5D,IAAID,EAAOJ,EAAMR,cAAca,GAC/BP,EAAaM,GAAS,SAASA,GAC3B,OAAO,WACHJ,EAAMC,YAAYG,IAFJ,CAQnBA,GAGPG,eAAe/C,KAAKa,aAAaqB,UAAWI","file":"../../scripts/viz/viz_views.js","sourcesContent":["define([\"libs/underscore\"], function(_) {\n /**\n * View for track/group header.\n */\n var TrackHeaderView = Backbone.View.extend({\n className: \"track-header\",\n\n initialize: function() {\n // Watch and update name changes.\n this.model.config\n .get(\"name\")\n .on(\"change:value\", this.update_name, this);\n this.render();\n },\n\n render: function() {\n this.$el.append($(\"\").addClass(this.model.drag_handle_class));\n this.$el.append(\n $(\"\")\n .addClass(\"track-name\")\n .text(this.model.config.get_value(\"name\"))\n );\n\n // Icons container.\n this.action_icons = {};\n this.render_action_icons();\n\n // Suppress double clicks in header so that they do not impact viz under header.\n this.$el.dblclick(function(e) {\n e.stopPropagation();\n });\n\n // Needed for floating elts in header.\n this.$el.append($(\"\"));\n },\n\n update_name: function() {\n this.$el\n .find(\".track-name\")\n .text(this.model.config.get_value(\"name\"));\n },\n\n render_action_icons: function() {\n var self = this;\n this.icons_div = $(\"\")\n .addClass(\"track-icons\")\n .hide()\n .appendTo(this.$el);\n _.each(this.model.action_icons_def, function(icon_dict) {\n self.add_action_icon(\n icon_dict.name,\n icon_dict.title,\n icon_dict.css_class,\n icon_dict.on_click_fn,\n icon_dict.prepend,\n icon_dict.hide\n );\n });\n\n // Set up behavior for modes popup.\n this.set_display_modes(this.model.display_modes);\n },\n\n /**\n * Add an action icon to this object. Appends icon unless prepend flag is specified.\n */\n add_action_icon: function(\n name,\n title,\n css_class,\n on_click_fn,\n prepend,\n hide\n ) {\n var self = this;\n this.action_icons[name] = $(\"\")\n .attr(\"title\", title)\n .addClass(\"icon-button\")\n .addClass(css_class)\n .tooltip()\n .click(function() {\n on_click_fn(self.model);\n })\n .appendTo(this.icons_div);\n if (hide) {\n this.action_icons[name].hide();\n }\n },\n\n /**\n * Set track's modes and update mode icon popup.\n */\n set_display_modes: function(new_modes, init_mode) {\n if (!new_modes) {\n return;\n }\n\n // HACK: move this out of view and into track.\n\n // Set modes, init mode.\n this.model.display_modes = new_modes;\n this.model.mode =\n init_mode ||\n this.model.config.get_value(\"mode\") ||\n this.model.display_modes[0];\n\n this.action_icons.mode_icon.attr(\n \"title\",\n \"Set display mode (now: \" + this.mode + \")\"\n );\n\n // Setup popup menu for changing modes.\n var self = this,\n track = this.model,\n mode_mapping = {};\n for (var i = 0, len = track.display_modes.length; i < len; i++) {\n var mode = track.display_modes[i];\n mode_mapping[mode] = (function(mode) {\n return function() {\n track.change_mode(mode);\n // HACK: the popup menu messes with the track's hover event, so manually show/hide\n // icons div for now.\n //self.icons_div.show();\n //track.container_div.mouseleave(function() { track.icons_div.hide(); } );\n };\n })(mode);\n }\n\n make_popupmenu(this.action_icons.mode_icon, mode_mapping);\n }\n });\n\n return {\n TrackHeaderView: TrackHeaderView\n };\n});\n"]} \ No newline at end of file diff --git a/static/scripts/admin.toolshed.js b/static/scripts/admin.toolshed.js index 7436ca71121..495c628315a 100644 --- a/static/scripts/admin.toolshed.js +++ b/static/scripts/admin.toolshed.js @@ -1,2 +1,2 @@ -"use strict";define(["mvc/toolshed/shed-list-view","mvc/toolshed/categories-view","mvc/toolshed/repositories-view","mvc/toolshed/repository-view","mvc/toolshed/repository-queue-view","mvc/toolshed/repo-status-view","mvc/toolshed/workflows-view"],function(e,o,t,i,a,s,r){var d=Backbone.Router.extend({initialize:function(){this.routesHit=0,Backbone.history.on("route",function(){this.routesHit++},this),this.bind("route",this.trackPageview)},routes:{"":"toolsheds",sheds:"toolsheds",queue:"queue",workflows:"workflows","status/r/:repositories":"status",status:"status","categories/s/:tool_shed":"categories","category/s/:tool_shed/c/:cateory_id":"repositories","repository/s/:tool_shed/r/:repository_id":"repository"},back:function(){this.routesHit>1?window.history.back():this.navigate("#",{trigger:!0,replace:!0})}});return{GalaxyApp:Backbone.View.extend({app_config:{known_views:["toolsheds","queue","status","categories","repositories","repoository"]},initialize:function(){Galaxy.admintoolshedapp=this,this.admin_toolshed_router=new d,this.admin_toolshed_router.on("route:queue",function(){Galaxy.admintoolshedapp.adminRepoQueueView?Galaxy.admintoolshedapp.adminRepoQueueView.reDraw():Galaxy.admintoolshedapp.adminRepoQueueView=new a.RepoQueueView}),this.admin_toolshed_router.on("route:toolsheds",function(){Galaxy.admintoolshedapp.adminShedListView?Galaxy.admintoolshedapp.adminShedListView.reDraw():Galaxy.admintoolshedapp.adminShedListView=new e.ShedListView}),this.admin_toolshed_router.on("route:categories",function(e){Galaxy.admintoolshedapp.adminShedCategoriesView?Galaxy.admintoolshedapp.adminShedCategoriesView.reDraw({tool_shed:e.replace(/\//g,"%2f")}):Galaxy.admintoolshedapp.adminShedCategoriesView=new o.CategoryView({tool_shed:e.replace(/\//g,"%2f")})}),this.admin_toolshed_router.on("route:repositories",function(e,o){Galaxy.admintoolshedapp.adminShedCategoryView?Galaxy.admintoolshedapp.adminShedCategoryView.reDraw({tool_shed:e.replace(/\//g,"%2f"),category_id:o}):Galaxy.admintoolshedapp.adminShedCategoryView=new t.Category({tool_shed:e.replace(/\//g,"%2f"),category_id:o})}),this.admin_toolshed_router.on("route:repository",function(e,o){Galaxy.admintoolshedapp.adminRepositoryView?Galaxy.admintoolshedapp.adminRepositoryView.reDraw({tool_shed:e.replace(/\//g,"%2f"),repository_id:o}):Galaxy.admintoolshedapp.adminRepositoryView=new i.RepoDetails({tool_shed:e.replace(/\//g,"%2f"),repository_id:o})}),this.admin_toolshed_router.on("route:status",function(e){Galaxy.admintoolshedapp.adminRepoStatusView?Galaxy.admintoolshedapp.adminRepoStatusView.reDraw({repositories:e.split("|")}):Galaxy.admintoolshedapp.adminRepoStatusView=new s.RepoStatus({repositories:e.split("|")})}),this.admin_toolshed_router.on("route:workflows",function(){Galaxy.admintoolshedapp.adminWorkflowsView?Galaxy.admintoolshedapp.adminWorkflowsView.reDraw():Galaxy.admintoolshedapp.adminWorkflowsView=new r.Workflows}),Backbone.history.start({pushState:!1})}})}}); +define([],function(){"use strict";define(["mvc/toolshed/shed-list-view","mvc/toolshed/categories-view","mvc/toolshed/repositories-view","mvc/toolshed/repository-view","mvc/toolshed/repository-queue-view","mvc/toolshed/repo-status-view","mvc/toolshed/workflows-view"],function(e,o,t,i,a,s,d){var r=Backbone.Router.extend({initialize:function(){this.routesHit=0,Backbone.history.on("route",function(){this.routesHit++},this),this.bind("route",this.trackPageview)},routes:{"":"toolsheds",sheds:"toolsheds",queue:"queue",workflows:"workflows","status/r/:repositories":"status",status:"status","categories/s/:tool_shed":"categories","category/s/:tool_shed/c/:cateory_id":"repositories","repository/s/:tool_shed/r/:repository_id":"repository"},back:function(){this.routesHit>1?window.history.back():this.navigate("#",{trigger:!0,replace:!0})}});return{GalaxyApp:Backbone.View.extend({app_config:{known_views:["toolsheds","queue","status","categories","repositories","repoository"]},initialize:function(){Galaxy.admintoolshedapp=this,this.admin_toolshed_router=new r,this.admin_toolshed_router.on("route:queue",function(){Galaxy.admintoolshedapp.adminRepoQueueView?Galaxy.admintoolshedapp.adminRepoQueueView.reDraw():Galaxy.admintoolshedapp.adminRepoQueueView=new a.RepoQueueView}),this.admin_toolshed_router.on("route:toolsheds",function(){Galaxy.admintoolshedapp.adminShedListView?Galaxy.admintoolshedapp.adminShedListView.reDraw():Galaxy.admintoolshedapp.adminShedListView=new e.ShedListView}),this.admin_toolshed_router.on("route:categories",function(e){Galaxy.admintoolshedapp.adminShedCategoriesView?Galaxy.admintoolshedapp.adminShedCategoriesView.reDraw({tool_shed:e.replace(/\//g,"%2f")}):Galaxy.admintoolshedapp.adminShedCategoriesView=new o.CategoryView({tool_shed:e.replace(/\//g,"%2f")})}),this.admin_toolshed_router.on("route:repositories",function(e,o){Galaxy.admintoolshedapp.adminShedCategoryView?Galaxy.admintoolshedapp.adminShedCategoryView.reDraw({tool_shed:e.replace(/\//g,"%2f"),category_id:o}):Galaxy.admintoolshedapp.adminShedCategoryView=new t.Category({tool_shed:e.replace(/\//g,"%2f"),category_id:o})}),this.admin_toolshed_router.on("route:repository",function(e,o){Galaxy.admintoolshedapp.adminRepositoryView?Galaxy.admintoolshedapp.adminRepositoryView.reDraw({tool_shed:e.replace(/\//g,"%2f"),repository_id:o}):Galaxy.admintoolshedapp.adminRepositoryView=new i.RepoDetails({tool_shed:e.replace(/\//g,"%2f"),repository_id:o})}),this.admin_toolshed_router.on("route:status",function(e){Galaxy.admintoolshedapp.adminRepoStatusView?Galaxy.admintoolshedapp.adminRepoStatusView.reDraw({repositories:e.split("|")}):Galaxy.admintoolshedapp.adminRepoStatusView=new s.RepoStatus({repositories:e.split("|")})}),this.admin_toolshed_router.on("route:workflows",function(){Galaxy.admintoolshedapp.adminWorkflowsView?Galaxy.admintoolshedapp.adminWorkflowsView.reDraw():Galaxy.admintoolshedapp.adminWorkflowsView=new d.Workflows}),Backbone.history.start({pushState:!1})}})}})}); //# sourceMappingURL=../maps/admin.toolshed.js.map diff --git a/static/scripts/bundled/libs.bundled.js b/static/scripts/bundled/libs.bundled.js index e6a41fa89ad..4c86ce27ee7 100644 --- a/static/scripts/bundled/libs.bundled.js +++ b/static/scripts/bundled/libs.bundled.js @@ -48,5 +48,5 @@ return s&&(a.length<4&&n("jQuery.fn.attr( props, pass ) is deprecated"),e&&!h.te * @license MIT | GPL | Apache 2.0, see LICENSE.txt * @see https://github.com/dyve/jquery-autocomplete */ -!function(t){"use strict";t.fn.autocomplete_verheul=function(e){var i;arguments.length>1?(i=e,e=arguments[1],e.url=i):"string"==typeof e&&(i=e,e={url:i});var n=t.extend({},t.fn.autocomplete_verheul.defaults,e);return this.each(function(){var e=t(this);e.data("autocompleter",new 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(#13335)\n//\"use strict\";\nvar arr = [];\n\nvar document = window.document;\n\nvar slice = arr.slice;\n\nvar concat = arr.concat;\n\nvar push = arr.push;\n\nvar indexOf = arr.indexOf;\n\nvar class2type = {};\n\nvar toString = class2type.toString;\n\nvar hasOwn = class2type.hasOwnProperty;\n\nvar support = {};\n\n\n\nvar\n\tversion = \"2.2.4\",\n\n\t// Define a local copy of jQuery\n\tjQuery = function( selector, context ) {\n\n\t\t// The jQuery object is actually just the init constructor 'enhanced'\n\t\t// Need init if jQuery is called (just allow error to be thrown if not included)\n\t\treturn new jQuery.fn.init( selector, context );\n\t},\n\n\t// Support: Android<4.1\n\t// Make sure we trim BOM and NBSP\n\trtrim = /^[\\s\\uFEFF\\xA0]+|[\\s\\uFEFF\\xA0]+$/g,\n\n\t// Matches dashed string for camelizing\n\trmsPrefix = /^-ms-/,\n\trdashAlpha = /-([\\da-z])/gi,\n\n\t// Used by jQuery.camelCase as callback to replace()\n\tfcamelCase = function( all, letter ) {\n\t\treturn letter.toUpperCase();\n\t};\n\njQuery.fn = jQuery.prototype = {\n\n\t// The current version of jQuery being used\n\tjquery: version,\n\n\tconstructor: jQuery,\n\n\t// Start with an empty selector\n\tselector: \"\",\n\n\t// The default length of a jQuery object is 0\n\tlength: 0,\n\n\ttoArray: function() {\n\t\treturn slice.call( this );\n\t},\n\n\t// Get the Nth element in the matched element set OR\n\t// Get the whole matched element set as a clean array\n\tget: function( num ) {\n\t\treturn num != null ?\n\n\t\t\t// Return just the one element from the set\n\t\t\t( num < 0 ? this[ num + this.length ] : this[ num ] ) :\n\n\t\t\t// Return all the elements in a clean array\n\t\t\tslice.call( this );\n\t},\n\n\t// Take an array of elements and push it onto the stack\n\t// (returning the new matched element set)\n\tpushStack: function( elems ) {\n\n\t\t// Build a new jQuery matched element set\n\t\tvar ret = jQuery.merge( this.constructor(), elems );\n\n\t\t// Add the old object onto the stack (as a reference)\n\t\tret.prevObject = this;\n\t\tret.context = this.context;\n\n\t\t// Return the newly-formed element set\n\t\treturn ret;\n\t},\n\n\t// Execute a callback for every element in the matched set.\n\teach: function( callback ) {\n\t\treturn jQuery.each( this, callback );\n\t},\n\n\tmap: function( callback ) {\n\t\treturn this.pushStack( jQuery.map( this, function( elem, i ) {\n\t\t\treturn callback.call( elem, i, elem );\n\t\t} ) );\n\t},\n\n\tslice: function() {\n\t\treturn this.pushStack( slice.apply( this, arguments ) );\n\t},\n\n\tfirst: function() {\n\t\treturn this.eq( 0 );\n\t},\n\n\tlast: function() {\n\t\treturn this.eq( -1 );\n\t},\n\n\teq: function( i ) {\n\t\tvar len = this.length,\n\t\t\tj = +i + ( i < 0 ? len : 0 );\n\t\treturn this.pushStack( j >= 0 && j < len ? [ this[ j ] ] : [] );\n\t},\n\n\tend: function() {\n\t\treturn this.prevObject || this.constructor();\n\t},\n\n\t// For internal use only.\n\t// Behaves like an Array's method, not like a jQuery method.\n\tpush: push,\n\tsort: arr.sort,\n\tsplice: arr.splice\n};\n\njQuery.extend = jQuery.fn.extend = function() {\n\tvar options, name, src, copy, copyIsArray, clone,\n\t\ttarget = arguments[ 0 ] || {},\n\t\ti = 1,\n\t\tlength = arguments.length,\n\t\tdeep = false;\n\n\t// Handle a deep copy situation\n\tif ( typeof target === \"boolean\" ) {\n\t\tdeep = target;\n\n\t\t// Skip the boolean and the target\n\t\ttarget = arguments[ i ] || {};\n\t\ti++;\n\t}\n\n\t// Handle case when target is a string or something (possible in deep copy)\n\tif ( typeof target !== \"object\" && !jQuery.isFunction( target ) ) {\n\t\ttarget = {};\n\t}\n\n\t// Extend jQuery itself if only one argument is passed\n\tif ( i === length ) {\n\t\ttarget = this;\n\t\ti--;\n\t}\n\n\tfor ( ; i < length; i++ ) {\n\n\t\t// Only deal with non-null/undefined values\n\t\tif ( ( options = arguments[ i ] ) != null ) {\n\n\t\t\t// Extend the base object\n\t\t\tfor ( name in options ) {\n\t\t\t\tsrc = target[ name ];\n\t\t\t\tcopy = options[ name ];\n\n\t\t\t\t// Prevent never-ending loop\n\t\t\t\tif ( target === copy ) {\n\t\t\t\t\tcontinue;\n\t\t\t\t}\n\n\t\t\t\t// Recurse if we're merging plain objects or arrays\n\t\t\t\tif ( deep && copy && ( jQuery.isPlainObject( copy ) ||\n\t\t\t\t\t( copyIsArray = jQuery.isArray( copy ) ) ) ) {\n\n\t\t\t\t\tif ( copyIsArray ) {\n\t\t\t\t\t\tcopyIsArray = false;\n\t\t\t\t\t\tclone = src && jQuery.isArray( src ) ? src : [];\n\n\t\t\t\t\t} else {\n\t\t\t\t\t\tclone = src && jQuery.isPlainObject( src ) ? src : {};\n\t\t\t\t\t}\n\n\t\t\t\t\t// Never move original objects, clone them\n\t\t\t\t\ttarget[ name ] = jQuery.extend( deep, clone, copy );\n\n\t\t\t\t// Don't bring in undefined values\n\t\t\t\t} else if ( copy !== undefined ) {\n\t\t\t\t\ttarget[ name ] = copy;\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\t// Return the modified object\n\treturn target;\n};\n\njQuery.extend( {\n\n\t// Unique for each copy of jQuery on the page\n\texpando: \"jQuery\" + ( version + Math.random() ).replace( /\\D/g, \"\" ),\n\n\t// Assume jQuery is ready without the ready module\n\tisReady: true,\n\n\terror: function( msg ) {\n\t\tthrow new Error( msg );\n\t},\n\n\tnoop: function() {},\n\n\tisFunction: function( obj ) {\n\t\treturn jQuery.type( obj ) === \"function\";\n\t},\n\n\tisArray: Array.isArray,\n\n\tisWindow: function( obj ) {\n\t\treturn obj != null && obj === obj.window;\n\t},\n\n\tisNumeric: function( obj ) {\n\n\t\t// parseFloat NaNs numeric-cast false positives (null|true|false|\"\")\n\t\t// ...but misinterprets leading-number strings, particularly hex literals (\"0x...\")\n\t\t// subtraction forces infinities to NaN\n\t\t// adding 1 corrects loss of precision from parseFloat (#15100)\n\t\tvar realStringObj = obj && obj.toString();\n\t\treturn !jQuery.isArray( obj ) && ( realStringObj - parseFloat( realStringObj ) + 1 ) >= 0;\n\t},\n\n\tisPlainObject: function( obj ) {\n\t\tvar key;\n\n\t\t// Not plain objects:\n\t\t// - Any object or value whose internal [[Class]] property is not \"[object Object]\"\n\t\t// - DOM nodes\n\t\t// - window\n\t\tif ( jQuery.type( obj ) !== \"object\" || obj.nodeType || jQuery.isWindow( obj ) ) {\n\t\t\treturn false;\n\t\t}\n\n\t\t// Not own constructor property must be Object\n\t\tif ( obj.constructor &&\n\t\t\t\t!hasOwn.call( obj, \"constructor\" ) &&\n\t\t\t\t!hasOwn.call( obj.constructor.prototype || {}, \"isPrototypeOf\" ) ) {\n\t\t\treturn false;\n\t\t}\n\n\t\t// Own properties are enumerated firstly, so to speed up,\n\t\t// if last one is own, then all properties are own\n\t\tfor ( key in obj ) {}\n\n\t\treturn key === undefined || hasOwn.call( obj, key );\n\t},\n\n\tisEmptyObject: function( obj ) {\n\t\tvar name;\n\t\tfor ( name in obj ) {\n\t\t\treturn false;\n\t\t}\n\t\treturn true;\n\t},\n\n\ttype: function( obj ) {\n\t\tif ( obj == null ) {\n\t\t\treturn obj + \"\";\n\t\t}\n\n\t\t// Support: Android<4.0, iOS<6 (functionish RegExp)\n\t\treturn typeof obj === \"object\" || typeof obj === \"function\" ?\n\t\t\tclass2type[ toString.call( obj ) ] || \"object\" :\n\t\t\ttypeof obj;\n\t},\n\n\t// Evaluates a script in a global context\n\tglobalEval: function( code ) {\n\t\tvar script,\n\t\t\tindirect = eval;\n\n\t\tcode = jQuery.trim( code );\n\n\t\tif ( code ) {\n\n\t\t\t// If the code includes a valid, prologue position\n\t\t\t// strict mode pragma, execute code by injecting a\n\t\t\t// script tag into the document.\n\t\t\tif ( code.indexOf( \"use strict\" ) === 1 ) {\n\t\t\t\tscript = document.createElement( \"script\" );\n\t\t\t\tscript.text = code;\n\t\t\t\tdocument.head.appendChild( script ).parentNode.removeChild( script );\n\t\t\t} else {\n\n\t\t\t\t// Otherwise, avoid the DOM node creation, insertion\n\t\t\t\t// and removal by using an indirect global eval\n\n\t\t\t\tindirect( code );\n\t\t\t}\n\t\t}\n\t},\n\n\t// Convert dashed to camelCase; used by the css and data modules\n\t// Support: IE9-11+\n\t// Microsoft forgot to hump their vendor prefix (#9572)\n\tcamelCase: function( string ) {\n\t\treturn string.replace( rmsPrefix, \"ms-\" ).replace( rdashAlpha, fcamelCase );\n\t},\n\n\tnodeName: function( elem, name ) {\n\t\treturn elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase();\n\t},\n\n\teach: function( obj, callback ) {\n\t\tvar length, i = 0;\n\n\t\tif ( isArrayLike( obj ) ) {\n\t\t\tlength = obj.length;\n\t\t\tfor ( ; i < length; i++ ) {\n\t\t\t\tif ( callback.call( obj[ i ], i, obj[ i ] ) === false ) {\n\t\t\t\t\tbreak;\n\t\t\t\t}\n\t\t\t}\n\t\t} else {\n\t\t\tfor ( i in obj ) {\n\t\t\t\tif ( callback.call( obj[ i ], i, obj[ i ] ) === false ) {\n\t\t\t\t\tbreak;\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\treturn obj;\n\t},\n\n\t// Support: Android<4.1\n\ttrim: function( text ) {\n\t\treturn text == null ?\n\t\t\t\"\" :\n\t\t\t( text + \"\" ).replace( rtrim, \"\" );\n\t},\n\n\t// results is for internal usage only\n\tmakeArray: function( arr, results ) {\n\t\tvar ret = results || [];\n\n\t\tif ( arr != null ) {\n\t\t\tif ( isArrayLike( Object( arr ) ) ) {\n\t\t\t\tjQuery.merge( ret,\n\t\t\t\t\ttypeof arr === \"string\" ?\n\t\t\t\t\t[ arr ] : arr\n\t\t\t\t);\n\t\t\t} else {\n\t\t\t\tpush.call( ret, arr );\n\t\t\t}\n\t\t}\n\n\t\treturn ret;\n\t},\n\n\tinArray: function( elem, arr, i ) {\n\t\treturn arr == null ? -1 : indexOf.call( arr, elem, i );\n\t},\n\n\tmerge: function( first, second ) {\n\t\tvar len = +second.length,\n\t\t\tj = 0,\n\t\t\ti = first.length;\n\n\t\tfor ( ; j < len; j++ ) {\n\t\t\tfirst[ i++ ] = second[ j ];\n\t\t}\n\n\t\tfirst.length = i;\n\n\t\treturn first;\n\t},\n\n\tgrep: function( elems, callback, invert ) {\n\t\tvar callbackInverse,\n\t\t\tmatches = [],\n\t\t\ti = 0,\n\t\t\tlength = elems.length,\n\t\t\tcallbackExpect = !invert;\n\n\t\t// Go through the array, only saving the items\n\t\t// that pass the validator function\n\t\tfor ( ; i < length; i++ ) {\n\t\t\tcallbackInverse = !callback( elems[ i ], i );\n\t\t\tif ( callbackInverse !== callbackExpect ) {\n\t\t\t\tmatches.push( elems[ i ] );\n\t\t\t}\n\t\t}\n\n\t\treturn matches;\n\t},\n\n\t// arg is for internal usage only\n\tmap: function( elems, callback, arg ) {\n\t\tvar length, value,\n\t\t\ti = 0,\n\t\t\tret = [];\n\n\t\t// Go through the array, translating each of the items to their new values\n\t\tif ( isArrayLike( elems ) ) {\n\t\t\tlength = elems.length;\n\t\t\tfor ( ; i < length; i++ ) {\n\t\t\t\tvalue = callback( elems[ i ], i, arg );\n\n\t\t\t\tif ( value != null ) {\n\t\t\t\t\tret.push( value );\n\t\t\t\t}\n\t\t\t}\n\n\t\t// Go through every key on the object,\n\t\t} else {\n\t\t\tfor ( i in elems ) {\n\t\t\t\tvalue = callback( elems[ i ], i, arg );\n\n\t\t\t\tif ( value != null ) {\n\t\t\t\t\tret.push( value );\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\t// Flatten any nested arrays\n\t\treturn concat.apply( [], ret );\n\t},\n\n\t// A global GUID counter for objects\n\tguid: 1,\n\n\t// Bind a function to a context, optionally partially applying any\n\t// arguments.\n\tproxy: function( fn, context ) {\n\t\tvar tmp, args, proxy;\n\n\t\tif ( typeof context === \"string\" ) {\n\t\t\ttmp = fn[ context ];\n\t\t\tcontext = fn;\n\t\t\tfn = tmp;\n\t\t}\n\n\t\t// Quick check to determine if target is callable, in the spec\n\t\t// this throws a TypeError, but we will just return undefined.\n\t\tif ( !jQuery.isFunction( fn ) ) {\n\t\t\treturn undefined;\n\t\t}\n\n\t\t// Simulated bind\n\t\targs = slice.call( arguments, 2 );\n\t\tproxy = function() {\n\t\t\treturn fn.apply( context || this, args.concat( slice.call( arguments ) ) );\n\t\t};\n\n\t\t// Set the guid of unique handler to the same of original handler, so it can be removed\n\t\tproxy.guid = fn.guid = fn.guid || jQuery.guid++;\n\n\t\treturn proxy;\n\t},\n\n\tnow: Date.now,\n\n\t// jQuery.support is not used in Core but other projects attach their\n\t// properties to it so it needs to exist.\n\tsupport: support\n} );\n\n// JSHint would error on this code due to the Symbol not being defined in ES5.\n// Defining this global in .jshintrc would create a danger of using the global\n// unguarded in another place, it seems safer to just disable JSHint for these\n// three lines.\n/* jshint ignore: start */\nif ( typeof Symbol === \"function\" ) {\n\tjQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ];\n}\n/* jshint ignore: end */\n\n// Populate the class2type map\njQuery.each( \"Boolean Number String Function Array Date RegExp Object Error Symbol\".split( \" \" ),\nfunction( i, name ) {\n\tclass2type[ \"[object \" + name + \"]\" ] = name.toLowerCase();\n} );\n\nfunction isArrayLike( obj ) {\n\n\t// Support: iOS 8.2 (not reproducible in simulator)\n\t// `in` check used to prevent JIT error (gh-2145)\n\t// hasOwn isn't used here due to false negatives\n\t// regarding Nodelist length in IE\n\tvar length = !!obj && \"length\" in obj && obj.length,\n\t\ttype = jQuery.type( obj );\n\n\tif ( type === \"function\" || jQuery.isWindow( obj ) ) {\n\t\treturn false;\n\t}\n\n\treturn type === \"array\" || length === 0 ||\n\t\ttypeof length === \"number\" && length > 0 && ( length - 1 ) in obj;\n}\nvar Sizzle =\n/*!\n * Sizzle CSS Selector Engine v2.2.1\n * http://sizzlejs.com/\n *\n * Copyright jQuery Foundation and other contributors\n * Released under the MIT license\n * http://jquery.org/license\n *\n * Date: 2015-10-17\n */\n(function( window ) {\n\nvar i,\n\tsupport,\n\tExpr,\n\tgetText,\n\tisXML,\n\ttokenize,\n\tcompile,\n\tselect,\n\toutermostContext,\n\tsortInput,\n\thasDuplicate,\n\n\t// Local document vars\n\tsetDocument,\n\tdocument,\n\tdocElem,\n\tdocumentIsHTML,\n\trbuggyQSA,\n\trbuggyMatches,\n\tmatches,\n\tcontains,\n\n\t// Instance-specific data\n\texpando = \"sizzle\" + 1 * new Date(),\n\tpreferredDoc = window.document,\n\tdirruns = 0,\n\tdone = 0,\n\tclassCache = createCache(),\n\ttokenCache = createCache(),\n\tcompilerCache = createCache(),\n\tsortOrder = function( a, b ) {\n\t\tif ( a === b ) {\n\t\t\thasDuplicate = true;\n\t\t}\n\t\treturn 0;\n\t},\n\n\t// General-purpose constants\n\tMAX_NEGATIVE = 1 << 31,\n\n\t// Instance methods\n\thasOwn = ({}).hasOwnProperty,\n\tarr = [],\n\tpop = arr.pop,\n\tpush_native = arr.push,\n\tpush = arr.push,\n\tslice = arr.slice,\n\t// Use a stripped-down indexOf as it's faster than native\n\t// http://jsperf.com/thor-indexof-vs-for/5\n\tindexOf = function( list, elem ) {\n\t\tvar i = 0,\n\t\t\tlen = list.length;\n\t\tfor ( ; i < len; i++ ) {\n\t\t\tif ( list[i] === elem ) {\n\t\t\t\treturn i;\n\t\t\t}\n\t\t}\n\t\treturn -1;\n\t},\n\n\tbooleans = \"checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped\",\n\n\t// Regular expressions\n\n\t// http://www.w3.org/TR/css3-selectors/#whitespace\n\twhitespace = \"[\\\\x20\\\\t\\\\r\\\\n\\\\f]\",\n\n\t// http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier\n\tidentifier = \"(?:\\\\\\\\.|[\\\\w-]|[^\\\\x00-\\\\xa0])+\",\n\n\t// Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors\n\tattributes = \"\\\\[\" + whitespace + \"*(\" + identifier + \")(?:\" + whitespace +\n\t\t// Operator (capture 2)\n\t\t\"*([*^$|!~]?=)\" + whitespace +\n\t\t// \"Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]\"\n\t\t\"*(?:'((?:\\\\\\\\.|[^\\\\\\\\'])*)'|\\\"((?:\\\\\\\\.|[^\\\\\\\\\\\"])*)\\\"|(\" + identifier + \"))|)\" + whitespace +\n\t\t\"*\\\\]\",\n\n\tpseudos = \":(\" + identifier + \")(?:\\\\((\" +\n\t\t// To reduce the number of selectors needing tokenize in the preFilter, prefer arguments:\n\t\t// 1. quoted (capture 3; capture 4 or capture 5)\n\t\t\"('((?:\\\\\\\\.|[^\\\\\\\\'])*)'|\\\"((?:\\\\\\\\.|[^\\\\\\\\\\\"])*)\\\")|\" +\n\t\t// 2. simple (capture 6)\n\t\t\"((?:\\\\\\\\.|[^\\\\\\\\()[\\\\]]|\" + attributes + \")*)|\" +\n\t\t// 3. anything else (capture 2)\n\t\t\".*\" +\n\t\t\")\\\\)|)\",\n\n\t// Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter\n\trwhitespace = new RegExp( whitespace + \"+\", \"g\" ),\n\trtrim = new RegExp( \"^\" + whitespace + \"+|((?:^|[^\\\\\\\\])(?:\\\\\\\\.)*)\" + whitespace + \"+$\", \"g\" ),\n\n\trcomma = new RegExp( \"^\" + whitespace + \"*,\" + whitespace + \"*\" ),\n\trcombinators = new RegExp( \"^\" + whitespace + \"*([>+~]|\" + whitespace + \")\" + whitespace + \"*\" ),\n\n\trattributeQuotes = new RegExp( \"=\" + whitespace + \"*([^\\\\]'\\\"]*?)\" + whitespace + \"*\\\\]\", \"g\" ),\n\n\trpseudo = new RegExp( pseudos ),\n\tridentifier = new RegExp( \"^\" + identifier + \"$\" ),\n\n\tmatchExpr = {\n\t\t\"ID\": new RegExp( \"^#(\" + identifier + \")\" ),\n\t\t\"CLASS\": new RegExp( \"^\\\\.(\" + identifier + \")\" ),\n\t\t\"TAG\": new RegExp( \"^(\" + identifier + \"|[*])\" ),\n\t\t\"ATTR\": new RegExp( \"^\" + attributes ),\n\t\t\"PSEUDO\": new RegExp( \"^\" + pseudos ),\n\t\t\"CHILD\": new RegExp( \"^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\\\(\" + whitespace +\n\t\t\t\"*(even|odd|(([+-]|)(\\\\d*)n|)\" + whitespace + \"*(?:([+-]|)\" + whitespace +\n\t\t\t\"*(\\\\d+)|))\" + whitespace + \"*\\\\)|)\", \"i\" ),\n\t\t\"bool\": new RegExp( \"^(?:\" + booleans + \")$\", \"i\" ),\n\t\t// For use in libraries implementing .is()\n\t\t// We use this for POS matching in `select`\n\t\t\"needsContext\": new RegExp( \"^\" + whitespace + \"*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\\\(\" +\n\t\t\twhitespace + \"*((?:-\\\\d)?\\\\d*)\" + whitespace + \"*\\\\)|)(?=[^-]|$)\", \"i\" )\n\t},\n\n\trinputs = /^(?:input|select|textarea|button)$/i,\n\trheader = /^h\\d$/i,\n\n\trnative = /^[^{]+\\{\\s*\\[native \\w/,\n\n\t// Easily-parseable/retrievable ID or TAG or CLASS selectors\n\trquickExpr = /^(?:#([\\w-]+)|(\\w+)|\\.([\\w-]+))$/,\n\n\trsibling = /[+~]/,\n\trescape = /'|\\\\/g,\n\n\t// CSS escapes http://www.w3.org/TR/CSS21/syndata.html#escaped-characters\n\trunescape = new RegExp( \"\\\\\\\\([\\\\da-f]{1,6}\" + whitespace + \"?|(\" + whitespace + \")|.)\", \"ig\" ),\n\tfunescape = function( _, escaped, escapedWhitespace ) {\n\t\tvar high = \"0x\" + escaped - 0x10000;\n\t\t// NaN means non-codepoint\n\t\t// Support: Firefox<24\n\t\t// Workaround erroneous numeric interpretation of +\"0x\"\n\t\treturn high !== high || escapedWhitespace ?\n\t\t\tescaped :\n\t\t\thigh < 0 ?\n\t\t\t\t// BMP codepoint\n\t\t\t\tString.fromCharCode( high + 0x10000 ) :\n\t\t\t\t// Supplemental Plane codepoint (surrogate pair)\n\t\t\t\tString.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 );\n\t},\n\n\t// Used for iframes\n\t// See setDocument()\n\t// Removing the function wrapper causes a \"Permission Denied\"\n\t// error in IE\n\tunloadHandler = function() {\n\t\tsetDocument();\n\t};\n\n// Optimize for push.apply( _, NodeList )\ntry {\n\tpush.apply(\n\t\t(arr = slice.call( preferredDoc.childNodes )),\n\t\tpreferredDoc.childNodes\n\t);\n\t// Support: Android<4.0\n\t// Detect silently failing push.apply\n\tarr[ preferredDoc.childNodes.length ].nodeType;\n} catch ( e ) {\n\tpush = { apply: arr.length ?\n\n\t\t// Leverage slice if possible\n\t\tfunction( target, els ) {\n\t\t\tpush_native.apply( target, slice.call(els) );\n\t\t} :\n\n\t\t// Support: IE<9\n\t\t// Otherwise append directly\n\t\tfunction( target, els ) {\n\t\t\tvar j = target.length,\n\t\t\t\ti = 0;\n\t\t\t// Can't trust NodeList.length\n\t\t\twhile ( (target[j++] = els[i++]) ) {}\n\t\t\ttarget.length = j - 1;\n\t\t}\n\t};\n}\n\nfunction Sizzle( selector, context, results, seed ) {\n\tvar m, i, elem, nid, nidselect, match, groups, newSelector,\n\t\tnewContext = context && context.ownerDocument,\n\n\t\t// nodeType defaults to 9, since context defaults to document\n\t\tnodeType = context ? context.nodeType : 9;\n\n\tresults = results || [];\n\n\t// Return early from calls with invalid selector or context\n\tif ( typeof selector !== \"string\" || !selector ||\n\t\tnodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) {\n\n\t\treturn results;\n\t}\n\n\t// Try to shortcut find operations (as opposed to filters) in HTML documents\n\tif ( !seed ) {\n\n\t\tif ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) {\n\t\t\tsetDocument( context );\n\t\t}\n\t\tcontext = context || document;\n\n\t\tif ( documentIsHTML ) {\n\n\t\t\t// If the selector is sufficiently simple, try using a \"get*By*\" DOM method\n\t\t\t// (excepting DocumentFragment context, where the methods don't exist)\n\t\t\tif ( nodeType !== 11 && (match = rquickExpr.exec( selector )) ) {\n\n\t\t\t\t// ID selector\n\t\t\t\tif ( (m = match[1]) ) {\n\n\t\t\t\t\t// Document context\n\t\t\t\t\tif ( nodeType === 9 ) {\n\t\t\t\t\t\tif ( (elem = context.getElementById( m )) ) {\n\n\t\t\t\t\t\t\t// Support: IE, Opera, Webkit\n\t\t\t\t\t\t\t// TODO: identify versions\n\t\t\t\t\t\t\t// getElementById can match elements by name instead of ID\n\t\t\t\t\t\t\tif ( elem.id === m ) {\n\t\t\t\t\t\t\t\tresults.push( elem );\n\t\t\t\t\t\t\t\treturn results;\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\treturn results;\n\t\t\t\t\t\t}\n\n\t\t\t\t\t// Element context\n\t\t\t\t\t} else {\n\n\t\t\t\t\t\t// Support: IE, Opera, Webkit\n\t\t\t\t\t\t// TODO: identify versions\n\t\t\t\t\t\t// getElementById can match elements by name instead of ID\n\t\t\t\t\t\tif ( newContext && (elem = newContext.getElementById( m )) &&\n\t\t\t\t\t\t\tcontains( context, elem ) &&\n\t\t\t\t\t\t\telem.id === m ) {\n\n\t\t\t\t\t\t\tresults.push( elem );\n\t\t\t\t\t\t\treturn results;\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\n\t\t\t\t// Type selector\n\t\t\t\t} else if ( match[2] ) {\n\t\t\t\t\tpush.apply( results, context.getElementsByTagName( selector ) );\n\t\t\t\t\treturn results;\n\n\t\t\t\t// Class selector\n\t\t\t\t} else if ( (m = match[3]) && support.getElementsByClassName &&\n\t\t\t\t\tcontext.getElementsByClassName ) {\n\n\t\t\t\t\tpush.apply( results, context.getElementsByClassName( m ) );\n\t\t\t\t\treturn results;\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// Take advantage of querySelectorAll\n\t\t\tif ( support.qsa &&\n\t\t\t\t!compilerCache[ selector + \" \" ] &&\n\t\t\t\t(!rbuggyQSA || !rbuggyQSA.test( selector )) ) {\n\n\t\t\t\tif ( nodeType !== 1 ) {\n\t\t\t\t\tnewContext = context;\n\t\t\t\t\tnewSelector = selector;\n\n\t\t\t\t// qSA looks outside Element context, which is not what we want\n\t\t\t\t// Thanks to Andrew Dupont for this workaround technique\n\t\t\t\t// Support: IE <=8\n\t\t\t\t// Exclude object elements\n\t\t\t\t} else if ( context.nodeName.toLowerCase() !== \"object\" ) {\n\n\t\t\t\t\t// Capture the context ID, setting it first if necessary\n\t\t\t\t\tif ( (nid = context.getAttribute( \"id\" )) ) {\n\t\t\t\t\t\tnid = nid.replace( rescape, \"\\\\$&\" );\n\t\t\t\t\t} else {\n\t\t\t\t\t\tcontext.setAttribute( \"id\", (nid = expando) );\n\t\t\t\t\t}\n\n\t\t\t\t\t// Prefix every selector in the list\n\t\t\t\t\tgroups = tokenize( selector );\n\t\t\t\t\ti = groups.length;\n\t\t\t\t\tnidselect = ridentifier.test( nid ) ? \"#\" + nid : \"[id='\" + nid + \"']\";\n\t\t\t\t\twhile ( i-- ) {\n\t\t\t\t\t\tgroups[i] = nidselect + \" \" + toSelector( groups[i] );\n\t\t\t\t\t}\n\t\t\t\t\tnewSelector = groups.join( \",\" );\n\n\t\t\t\t\t// Expand context for sibling selectors\n\t\t\t\t\tnewContext = rsibling.test( selector ) && testContext( context.parentNode ) ||\n\t\t\t\t\t\tcontext;\n\t\t\t\t}\n\n\t\t\t\tif ( newSelector ) {\n\t\t\t\t\ttry {\n\t\t\t\t\t\tpush.apply( results,\n\t\t\t\t\t\t\tnewContext.querySelectorAll( newSelector )\n\t\t\t\t\t\t);\n\t\t\t\t\t\treturn results;\n\t\t\t\t\t} catch ( qsaError ) {\n\t\t\t\t\t} finally {\n\t\t\t\t\t\tif ( nid === expando ) {\n\t\t\t\t\t\t\tcontext.removeAttribute( \"id\" );\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\t// All others\n\treturn select( selector.replace( rtrim, \"$1\" ), context, results, seed );\n}\n\n/**\n * Create key-value caches of limited size\n * @returns {function(string, object)} Returns the Object data after storing it on itself with\n *\tproperty name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength)\n *\tdeleting the oldest entry\n */\nfunction createCache() {\n\tvar keys = [];\n\n\tfunction cache( key, value ) {\n\t\t// Use (key + \" \") to avoid collision with native prototype properties (see Issue #157)\n\t\tif ( keys.push( key + \" \" ) > Expr.cacheLength ) {\n\t\t\t// Only keep the most recent entries\n\t\t\tdelete cache[ keys.shift() ];\n\t\t}\n\t\treturn (cache[ key + \" \" ] = value);\n\t}\n\treturn cache;\n}\n\n/**\n * Mark a function for special use by Sizzle\n * @param {Function} fn The function to mark\n */\nfunction markFunction( fn ) {\n\tfn[ expando ] = true;\n\treturn fn;\n}\n\n/**\n * Support testing using an element\n * @param {Function} fn Passed the created div and expects a boolean result\n */\nfunction assert( fn ) {\n\tvar div = document.createElement(\"div\");\n\n\ttry {\n\t\treturn !!fn( div );\n\t} catch (e) {\n\t\treturn false;\n\t} finally {\n\t\t// Remove from its parent by default\n\t\tif ( div.parentNode ) {\n\t\t\tdiv.parentNode.removeChild( div );\n\t\t}\n\t\t// release memory in IE\n\t\tdiv = null;\n\t}\n}\n\n/**\n * Adds the same handler for all of the specified attrs\n * @param {String} attrs Pipe-separated list of attributes\n * @param {Function} handler The method that will be applied\n */\nfunction addHandle( attrs, handler ) {\n\tvar arr = attrs.split(\"|\"),\n\t\ti = arr.length;\n\n\twhile ( i-- ) {\n\t\tExpr.attrHandle[ arr[i] ] = handler;\n\t}\n}\n\n/**\n * Checks document order of two siblings\n * @param {Element} a\n * @param {Element} b\n * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b\n */\nfunction siblingCheck( a, b ) {\n\tvar cur = b && a,\n\t\tdiff = cur && a.nodeType === 1 && b.nodeType === 1 &&\n\t\t\t( ~b.sourceIndex || MAX_NEGATIVE ) -\n\t\t\t( ~a.sourceIndex || MAX_NEGATIVE );\n\n\t// Use IE sourceIndex if available on both nodes\n\tif ( diff ) {\n\t\treturn diff;\n\t}\n\n\t// Check if b follows a\n\tif ( cur ) {\n\t\twhile ( (cur = cur.nextSibling) ) {\n\t\t\tif ( cur === b ) {\n\t\t\t\treturn -1;\n\t\t\t}\n\t\t}\n\t}\n\n\treturn a ? 1 : -1;\n}\n\n/**\n * Returns a function to use in pseudos for input types\n * @param {String} type\n */\nfunction createInputPseudo( type ) {\n\treturn function( elem ) {\n\t\tvar name = elem.nodeName.toLowerCase();\n\t\treturn name === \"input\" && elem.type === type;\n\t};\n}\n\n/**\n * Returns a function to use in pseudos for buttons\n * @param {String} type\n */\nfunction createButtonPseudo( type ) {\n\treturn function( elem ) {\n\t\tvar name = elem.nodeName.toLowerCase();\n\t\treturn (name === \"input\" || name === \"button\") && elem.type === type;\n\t};\n}\n\n/**\n * Returns a function to use in pseudos for positionals\n * @param {Function} fn\n */\nfunction createPositionalPseudo( fn ) {\n\treturn markFunction(function( argument ) {\n\t\targument = +argument;\n\t\treturn markFunction(function( seed, matches ) {\n\t\t\tvar j,\n\t\t\t\tmatchIndexes = fn( [], seed.length, argument ),\n\t\t\t\ti = matchIndexes.length;\n\n\t\t\t// Match elements found at the specified indexes\n\t\t\twhile ( i-- ) {\n\t\t\t\tif ( seed[ (j = matchIndexes[i]) ] ) {\n\t\t\t\t\tseed[j] = !(matches[j] = seed[j]);\n\t\t\t\t}\n\t\t\t}\n\t\t});\n\t});\n}\n\n/**\n * Checks a node for validity as a Sizzle context\n * @param {Element|Object=} context\n * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value\n */\nfunction testContext( context ) {\n\treturn context && typeof context.getElementsByTagName !== \"undefined\" && context;\n}\n\n// Expose support vars for convenience\nsupport = Sizzle.support = {};\n\n/**\n * Detects XML nodes\n * @param {Element|Object} elem An element or a document\n * @returns {Boolean} True iff elem is a non-HTML XML node\n */\nisXML = Sizzle.isXML = function( elem ) {\n\t// documentElement is verified for cases where it doesn't yet exist\n\t// (such as loading iframes in IE - #4833)\n\tvar documentElement = elem && (elem.ownerDocument || elem).documentElement;\n\treturn documentElement ? documentElement.nodeName !== \"HTML\" : false;\n};\n\n/**\n * Sets document-related variables once based on the current document\n * @param {Element|Object} [doc] An element or document object to use to set the document\n * @returns {Object} Returns the current document\n */\nsetDocument = Sizzle.setDocument = function( node ) {\n\tvar hasCompare, parent,\n\t\tdoc = node ? node.ownerDocument || node : preferredDoc;\n\n\t// Return early if doc is invalid or already selected\n\tif ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) {\n\t\treturn document;\n\t}\n\n\t// Update global variables\n\tdocument = doc;\n\tdocElem = document.documentElement;\n\tdocumentIsHTML = !isXML( document );\n\n\t// Support: IE 9-11, Edge\n\t// Accessing iframe documents after unload throws \"permission denied\" errors (jQuery #13936)\n\tif ( (parent = document.defaultView) && parent.top !== parent ) {\n\t\t// Support: IE 11\n\t\tif ( parent.addEventListener ) {\n\t\t\tparent.addEventListener( \"unload\", unloadHandler, false );\n\n\t\t// Support: IE 9 - 10 only\n\t\t} else if ( parent.attachEvent ) {\n\t\t\tparent.attachEvent( \"onunload\", unloadHandler );\n\t\t}\n\t}\n\n\t/* Attributes\n\t---------------------------------------------------------------------- */\n\n\t// Support: IE<8\n\t// Verify that getAttribute really returns attributes and not properties\n\t// (excepting IE8 booleans)\n\tsupport.attributes = assert(function( div ) {\n\t\tdiv.className = \"i\";\n\t\treturn !div.getAttribute(\"className\");\n\t});\n\n\t/* getElement(s)By*\n\t---------------------------------------------------------------------- */\n\n\t// Check if getElementsByTagName(\"*\") returns only elements\n\tsupport.getElementsByTagName = assert(function( div ) {\n\t\tdiv.appendChild( document.createComment(\"\") );\n\t\treturn !div.getElementsByTagName(\"*\").length;\n\t});\n\n\t// Support: IE<9\n\tsupport.getElementsByClassName = rnative.test( document.getElementsByClassName );\n\n\t// Support: IE<10\n\t// Check if getElementById returns elements by name\n\t// The broken getElementById methods don't pick up programatically-set names,\n\t// so use a roundabout getElementsByName test\n\tsupport.getById = assert(function( div ) {\n\t\tdocElem.appendChild( div ).id = expando;\n\t\treturn !document.getElementsByName || !document.getElementsByName( expando ).length;\n\t});\n\n\t// ID find and filter\n\tif ( support.getById ) {\n\t\tExpr.find[\"ID\"] = function( id, context ) {\n\t\t\tif ( typeof context.getElementById !== \"undefined\" && documentIsHTML ) {\n\t\t\t\tvar m = context.getElementById( id );\n\t\t\t\treturn m ? [ m ] : [];\n\t\t\t}\n\t\t};\n\t\tExpr.filter[\"ID\"] = function( id ) {\n\t\t\tvar attrId = id.replace( runescape, funescape );\n\t\t\treturn function( elem ) {\n\t\t\t\treturn elem.getAttribute(\"id\") === attrId;\n\t\t\t};\n\t\t};\n\t} else {\n\t\t// Support: IE6/7\n\t\t// getElementById is not reliable as a find shortcut\n\t\tdelete Expr.find[\"ID\"];\n\n\t\tExpr.filter[\"ID\"] = function( id ) {\n\t\t\tvar attrId = id.replace( runescape, funescape );\n\t\t\treturn function( elem ) {\n\t\t\t\tvar node = typeof elem.getAttributeNode !== \"undefined\" &&\n\t\t\t\t\telem.getAttributeNode(\"id\");\n\t\t\t\treturn node && node.value === attrId;\n\t\t\t};\n\t\t};\n\t}\n\n\t// Tag\n\tExpr.find[\"TAG\"] = support.getElementsByTagName ?\n\t\tfunction( tag, context ) {\n\t\t\tif ( typeof context.getElementsByTagName !== \"undefined\" ) {\n\t\t\t\treturn context.getElementsByTagName( tag );\n\n\t\t\t// DocumentFragment nodes don't have gEBTN\n\t\t\t} else if ( support.qsa ) {\n\t\t\t\treturn context.querySelectorAll( tag );\n\t\t\t}\n\t\t} :\n\n\t\tfunction( tag, context ) {\n\t\t\tvar elem,\n\t\t\t\ttmp = [],\n\t\t\t\ti = 0,\n\t\t\t\t// By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too\n\t\t\t\tresults = context.getElementsByTagName( tag );\n\n\t\t\t// Filter out possible comments\n\t\t\tif ( tag === \"*\" ) {\n\t\t\t\twhile ( (elem = results[i++]) ) {\n\t\t\t\t\tif ( elem.nodeType === 1 ) {\n\t\t\t\t\t\ttmp.push( elem );\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\treturn tmp;\n\t\t\t}\n\t\t\treturn results;\n\t\t};\n\n\t// Class\n\tExpr.find[\"CLASS\"] = support.getElementsByClassName && function( className, context ) {\n\t\tif ( typeof context.getElementsByClassName !== \"undefined\" && documentIsHTML ) {\n\t\t\treturn context.getElementsByClassName( className );\n\t\t}\n\t};\n\n\t/* QSA/matchesSelector\n\t---------------------------------------------------------------------- */\n\n\t// QSA and matchesSelector support\n\n\t// matchesSelector(:active) reports false when true (IE9/Opera 11.5)\n\trbuggyMatches = [];\n\n\t// qSa(:focus) reports false when true (Chrome 21)\n\t// We allow this because of a bug in IE8/9 that throws an error\n\t// whenever `document.activeElement` is accessed on an iframe\n\t// So, we allow :focus to pass through QSA all the time to avoid the IE error\n\t// See http://bugs.jquery.com/ticket/13378\n\trbuggyQSA = [];\n\n\tif ( (support.qsa = rnative.test( document.querySelectorAll )) ) {\n\t\t// Build QSA regex\n\t\t// Regex strategy adopted from Diego Perini\n\t\tassert(function( div ) {\n\t\t\t// Select is set to empty string on purpose\n\t\t\t// This is to test IE's treatment of not explicitly\n\t\t\t// setting a boolean content attribute,\n\t\t\t// since its presence should be enough\n\t\t\t// http://bugs.jquery.com/ticket/12359\n\t\t\tdocElem.appendChild( div ).innerHTML = \"\" +\n\t\t\t\t\"\";\n\n\t\t\t// Support: IE8, Opera 11-12.16\n\t\t\t// Nothing should be selected when empty strings follow ^= or $= or *=\n\t\t\t// The test attribute must be unknown in Opera but \"safe\" for WinRT\n\t\t\t// http://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section\n\t\t\tif ( div.querySelectorAll(\"[msallowcapture^='']\").length ) {\n\t\t\t\trbuggyQSA.push( \"[*^$]=\" + whitespace + \"*(?:''|\\\"\\\")\" );\n\t\t\t}\n\n\t\t\t// Support: IE8\n\t\t\t// Boolean attributes and \"value\" are not treated correctly\n\t\t\tif ( !div.querySelectorAll(\"[selected]\").length ) {\n\t\t\t\trbuggyQSA.push( \"\\\\[\" + whitespace + \"*(?:value|\" + booleans + \")\" );\n\t\t\t}\n\n\t\t\t// Support: Chrome<29, Android<4.4, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.8+\n\t\t\tif ( !div.querySelectorAll( \"[id~=\" + expando + \"-]\" ).length ) {\n\t\t\t\trbuggyQSA.push(\"~=\");\n\t\t\t}\n\n\t\t\t// Webkit/Opera - :checked should return selected option elements\n\t\t\t// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked\n\t\t\t// IE8 throws error here and will not see later tests\n\t\t\tif ( !div.querySelectorAll(\":checked\").length ) {\n\t\t\t\trbuggyQSA.push(\":checked\");\n\t\t\t}\n\n\t\t\t// Support: Safari 8+, iOS 8+\n\t\t\t// https://bugs.webkit.org/show_bug.cgi?id=136851\n\t\t\t// In-page `selector#id sibing-combinator selector` fails\n\t\t\tif ( !div.querySelectorAll( \"a#\" + expando + \"+*\" ).length ) {\n\t\t\t\trbuggyQSA.push(\".#.+[+~]\");\n\t\t\t}\n\t\t});\n\n\t\tassert(function( div ) {\n\t\t\t// Support: Windows 8 Native Apps\n\t\t\t// The type and name attributes are restricted during .innerHTML assignment\n\t\t\tvar input = document.createElement(\"input\");\n\t\t\tinput.setAttribute( \"type\", \"hidden\" );\n\t\t\tdiv.appendChild( input ).setAttribute( \"name\", \"D\" );\n\n\t\t\t// Support: IE8\n\t\t\t// Enforce case-sensitivity of name attribute\n\t\t\tif ( div.querySelectorAll(\"[name=d]\").length ) {\n\t\t\t\trbuggyQSA.push( \"name\" + whitespace + \"*[*^$|!~]?=\" );\n\t\t\t}\n\n\t\t\t// FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled)\n\t\t\t// IE8 throws error here and will not see later tests\n\t\t\tif ( !div.querySelectorAll(\":enabled\").length ) {\n\t\t\t\trbuggyQSA.push( \":enabled\", \":disabled\" );\n\t\t\t}\n\n\t\t\t// Opera 10-11 does not throw on post-comma invalid pseudos\n\t\t\tdiv.querySelectorAll(\"*,:x\");\n\t\t\trbuggyQSA.push(\",.*:\");\n\t\t});\n\t}\n\n\tif ( (support.matchesSelector = rnative.test( (matches = docElem.matches ||\n\t\tdocElem.webkitMatchesSelector ||\n\t\tdocElem.mozMatchesSelector ||\n\t\tdocElem.oMatchesSelector ||\n\t\tdocElem.msMatchesSelector) )) ) {\n\n\t\tassert(function( div ) {\n\t\t\t// Check to see if it's possible to do matchesSelector\n\t\t\t// on a disconnected node (IE 9)\n\t\t\tsupport.disconnectedMatch = matches.call( div, \"div\" );\n\n\t\t\t// This should fail with an exception\n\t\t\t// Gecko does not error, returns false instead\n\t\t\tmatches.call( div, \"[s!='']:x\" );\n\t\t\trbuggyMatches.push( \"!=\", pseudos );\n\t\t});\n\t}\n\n\trbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join(\"|\") );\n\trbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join(\"|\") );\n\n\t/* Contains\n\t---------------------------------------------------------------------- */\n\thasCompare = rnative.test( docElem.compareDocumentPosition );\n\n\t// Element contains another\n\t// Purposefully self-exclusive\n\t// As in, an element does not contain itself\n\tcontains = hasCompare || rnative.test( docElem.contains ) ?\n\t\tfunction( a, b ) {\n\t\t\tvar adown = a.nodeType === 9 ? a.documentElement : a,\n\t\t\t\tbup = b && b.parentNode;\n\t\t\treturn a === bup || !!( bup && bup.nodeType === 1 && (\n\t\t\t\tadown.contains ?\n\t\t\t\t\tadown.contains( bup ) :\n\t\t\t\t\ta.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16\n\t\t\t));\n\t\t} :\n\t\tfunction( a, b ) {\n\t\t\tif ( b ) {\n\t\t\t\twhile ( (b = b.parentNode) ) {\n\t\t\t\t\tif ( b === a ) {\n\t\t\t\t\t\treturn true;\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn false;\n\t\t};\n\n\t/* Sorting\n\t---------------------------------------------------------------------- */\n\n\t// Document order sorting\n\tsortOrder = hasCompare ?\n\tfunction( a, b ) {\n\n\t\t// Flag for duplicate removal\n\t\tif ( a === b ) {\n\t\t\thasDuplicate = true;\n\t\t\treturn 0;\n\t\t}\n\n\t\t// Sort on method existence if only one input has compareDocumentPosition\n\t\tvar compare = !a.compareDocumentPosition - !b.compareDocumentPosition;\n\t\tif ( compare ) {\n\t\t\treturn compare;\n\t\t}\n\n\t\t// Calculate position if both inputs belong to the same document\n\t\tcompare = ( a.ownerDocument || a ) === ( b.ownerDocument || b ) ?\n\t\t\ta.compareDocumentPosition( b ) :\n\n\t\t\t// Otherwise we know they are disconnected\n\t\t\t1;\n\n\t\t// Disconnected nodes\n\t\tif ( compare & 1 ||\n\t\t\t(!support.sortDetached && b.compareDocumentPosition( a ) === compare) ) {\n\n\t\t\t// Choose the first element that is related to our preferred document\n\t\t\tif ( a === document || a.ownerDocument === preferredDoc && contains(preferredDoc, a) ) {\n\t\t\t\treturn -1;\n\t\t\t}\n\t\t\tif ( b === document || b.ownerDocument === preferredDoc && contains(preferredDoc, b) ) {\n\t\t\t\treturn 1;\n\t\t\t}\n\n\t\t\t// Maintain original order\n\t\t\treturn sortInput ?\n\t\t\t\t( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) :\n\t\t\t\t0;\n\t\t}\n\n\t\treturn compare & 4 ? -1 : 1;\n\t} :\n\tfunction( a, b ) {\n\t\t// Exit early if the nodes are identical\n\t\tif ( a === b ) {\n\t\t\thasDuplicate = true;\n\t\t\treturn 0;\n\t\t}\n\n\t\tvar cur,\n\t\t\ti = 0,\n\t\t\taup = a.parentNode,\n\t\t\tbup = b.parentNode,\n\t\t\tap = [ a ],\n\t\t\tbp = [ b ];\n\n\t\t// Parentless nodes are either documents or disconnected\n\t\tif ( !aup || !bup ) {\n\t\t\treturn a === document ? -1 :\n\t\t\t\tb === document ? 1 :\n\t\t\t\taup ? -1 :\n\t\t\t\tbup ? 1 :\n\t\t\t\tsortInput ?\n\t\t\t\t( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) :\n\t\t\t\t0;\n\n\t\t// If the nodes are siblings, we can do a quick check\n\t\t} else if ( aup === bup ) {\n\t\t\treturn siblingCheck( a, b );\n\t\t}\n\n\t\t// Otherwise we need full lists of their ancestors for comparison\n\t\tcur = a;\n\t\twhile ( (cur = cur.parentNode) ) {\n\t\t\tap.unshift( cur );\n\t\t}\n\t\tcur = b;\n\t\twhile ( (cur = cur.parentNode) ) {\n\t\t\tbp.unshift( cur );\n\t\t}\n\n\t\t// Walk down the tree looking for a discrepancy\n\t\twhile ( ap[i] === bp[i] ) {\n\t\t\ti++;\n\t\t}\n\n\t\treturn i ?\n\t\t\t// Do a sibling check if the nodes have a common ancestor\n\t\t\tsiblingCheck( ap[i], bp[i] ) :\n\n\t\t\t// Otherwise nodes in our document sort first\n\t\t\tap[i] === preferredDoc ? -1 :\n\t\t\tbp[i] === preferredDoc ? 1 :\n\t\t\t0;\n\t};\n\n\treturn document;\n};\n\nSizzle.matches = function( expr, elements ) {\n\treturn Sizzle( expr, null, null, elements );\n};\n\nSizzle.matchesSelector = function( elem, expr ) {\n\t// Set document vars if needed\n\tif ( ( elem.ownerDocument || elem ) !== document ) {\n\t\tsetDocument( elem );\n\t}\n\n\t// Make sure that attribute selectors are quoted\n\texpr = expr.replace( rattributeQuotes, \"='$1']\" );\n\n\tif ( support.matchesSelector && documentIsHTML &&\n\t\t!compilerCache[ expr + \" \" ] &&\n\t\t( !rbuggyMatches || !rbuggyMatches.test( expr ) ) &&\n\t\t( !rbuggyQSA || !rbuggyQSA.test( expr ) ) ) {\n\n\t\ttry {\n\t\t\tvar ret = matches.call( elem, expr );\n\n\t\t\t// IE 9's matchesSelector returns false on disconnected nodes\n\t\t\tif ( ret || support.disconnectedMatch ||\n\t\t\t\t\t// As well, disconnected nodes are said to be in a document\n\t\t\t\t\t// fragment in IE 9\n\t\t\t\t\telem.document && elem.document.nodeType !== 11 ) {\n\t\t\t\treturn ret;\n\t\t\t}\n\t\t} catch (e) {}\n\t}\n\n\treturn Sizzle( expr, document, null, [ elem ] ).length > 0;\n};\n\nSizzle.contains = function( context, elem ) {\n\t// Set document vars if needed\n\tif ( ( context.ownerDocument || context ) !== document ) {\n\t\tsetDocument( context );\n\t}\n\treturn contains( context, elem );\n};\n\nSizzle.attr = function( elem, name ) {\n\t// Set document vars if needed\n\tif ( ( elem.ownerDocument || elem ) !== document ) {\n\t\tsetDocument( elem );\n\t}\n\n\tvar fn = Expr.attrHandle[ name.toLowerCase() ],\n\t\t// Don't get fooled by Object.prototype properties (jQuery #13807)\n\t\tval = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ?\n\t\t\tfn( elem, name, !documentIsHTML ) :\n\t\t\tundefined;\n\n\treturn val !== undefined ?\n\t\tval :\n\t\tsupport.attributes || !documentIsHTML ?\n\t\t\telem.getAttribute( name ) :\n\t\t\t(val = elem.getAttributeNode(name)) && val.specified ?\n\t\t\t\tval.value :\n\t\t\t\tnull;\n};\n\nSizzle.error = function( msg ) {\n\tthrow new Error( \"Syntax error, unrecognized expression: \" + msg );\n};\n\n/**\n * Document sorting and removing duplicates\n * @param {ArrayLike} results\n */\nSizzle.uniqueSort = function( results ) {\n\tvar elem,\n\t\tduplicates = [],\n\t\tj = 0,\n\t\ti = 0;\n\n\t// Unless we *know* we can detect duplicates, assume their presence\n\thasDuplicate = !support.detectDuplicates;\n\tsortInput = !support.sortStable && results.slice( 0 );\n\tresults.sort( sortOrder );\n\n\tif ( hasDuplicate ) {\n\t\twhile ( (elem = results[i++]) ) {\n\t\t\tif ( elem === results[ i ] ) {\n\t\t\t\tj = duplicates.push( i );\n\t\t\t}\n\t\t}\n\t\twhile ( j-- ) {\n\t\t\tresults.splice( duplicates[ j ], 1 );\n\t\t}\n\t}\n\n\t// Clear input after sorting to release objects\n\t// See https://github.com/jquery/sizzle/pull/225\n\tsortInput = null;\n\n\treturn results;\n};\n\n/**\n * Utility function for retrieving the text value of an array of DOM nodes\n * @param {Array|Element} elem\n */\ngetText = Sizzle.getText = function( elem ) {\n\tvar node,\n\t\tret = \"\",\n\t\ti = 0,\n\t\tnodeType = elem.nodeType;\n\n\tif ( !nodeType ) {\n\t\t// If no nodeType, this is expected to be an array\n\t\twhile ( (node = elem[i++]) ) {\n\t\t\t// Do not traverse comment nodes\n\t\t\tret += getText( node );\n\t\t}\n\t} else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) {\n\t\t// Use textContent for elements\n\t\t// innerText usage removed for consistency of new lines (jQuery #11153)\n\t\tif ( typeof elem.textContent === \"string\" ) {\n\t\t\treturn elem.textContent;\n\t\t} else {\n\t\t\t// Traverse its children\n\t\t\tfor ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {\n\t\t\t\tret += getText( elem );\n\t\t\t}\n\t\t}\n\t} else if ( nodeType === 3 || nodeType === 4 ) {\n\t\treturn elem.nodeValue;\n\t}\n\t// Do not include comment or processing instruction nodes\n\n\treturn ret;\n};\n\nExpr = Sizzle.selectors = {\n\n\t// Can be adjusted by the user\n\tcacheLength: 50,\n\n\tcreatePseudo: markFunction,\n\n\tmatch: matchExpr,\n\n\tattrHandle: {},\n\n\tfind: {},\n\n\trelative: {\n\t\t\">\": { dir: \"parentNode\", first: true },\n\t\t\" \": { dir: \"parentNode\" },\n\t\t\"+\": { dir: \"previousSibling\", first: true },\n\t\t\"~\": { dir: \"previousSibling\" }\n\t},\n\n\tpreFilter: {\n\t\t\"ATTR\": function( match ) {\n\t\t\tmatch[1] = match[1].replace( runescape, funescape );\n\n\t\t\t// Move the given value to match[3] whether quoted or unquoted\n\t\t\tmatch[3] = ( match[3] || match[4] || match[5] || \"\" ).replace( runescape, funescape );\n\n\t\t\tif ( match[2] === \"~=\" ) {\n\t\t\t\tmatch[3] = \" \" + match[3] + \" \";\n\t\t\t}\n\n\t\t\treturn match.slice( 0, 4 );\n\t\t},\n\n\t\t\"CHILD\": function( match ) {\n\t\t\t/* matches from matchExpr[\"CHILD\"]\n\t\t\t\t1 type (only|nth|...)\n\t\t\t\t2 what (child|of-type)\n\t\t\t\t3 argument (even|odd|\\d*|\\d*n([+-]\\d+)?|...)\n\t\t\t\t4 xn-component of xn+y argument ([+-]?\\d*n|)\n\t\t\t\t5 sign of xn-component\n\t\t\t\t6 x of xn-component\n\t\t\t\t7 sign of y-component\n\t\t\t\t8 y of y-component\n\t\t\t*/\n\t\t\tmatch[1] = match[1].toLowerCase();\n\n\t\t\tif ( match[1].slice( 0, 3 ) === \"nth\" ) {\n\t\t\t\t// nth-* requires argument\n\t\t\t\tif ( !match[3] ) {\n\t\t\t\t\tSizzle.error( match[0] );\n\t\t\t\t}\n\n\t\t\t\t// numeric x and y parameters for Expr.filter.CHILD\n\t\t\t\t// remember that false/true cast respectively to 0/1\n\t\t\t\tmatch[4] = +( match[4] ? match[5] + (match[6] || 1) : 2 * ( match[3] === \"even\" || match[3] === \"odd\" ) );\n\t\t\t\tmatch[5] = +( ( match[7] + match[8] ) || match[3] === \"odd\" );\n\n\t\t\t// other types prohibit arguments\n\t\t\t} else if ( match[3] ) {\n\t\t\t\tSizzle.error( match[0] );\n\t\t\t}\n\n\t\t\treturn match;\n\t\t},\n\n\t\t\"PSEUDO\": function( match ) {\n\t\t\tvar excess,\n\t\t\t\tunquoted = !match[6] && match[2];\n\n\t\t\tif ( matchExpr[\"CHILD\"].test( match[0] ) ) {\n\t\t\t\treturn null;\n\t\t\t}\n\n\t\t\t// Accept quoted arguments as-is\n\t\t\tif ( match[3] ) {\n\t\t\t\tmatch[2] = match[4] || match[5] || \"\";\n\n\t\t\t// Strip excess characters from unquoted arguments\n\t\t\t} else if ( unquoted && rpseudo.test( unquoted ) &&\n\t\t\t\t// Get excess from tokenize (recursively)\n\t\t\t\t(excess = tokenize( unquoted, true )) &&\n\t\t\t\t// advance to the next closing parenthesis\n\t\t\t\t(excess = unquoted.indexOf( \")\", unquoted.length - excess ) - unquoted.length) ) {\n\n\t\t\t\t// excess is a negative index\n\t\t\t\tmatch[0] = match[0].slice( 0, excess );\n\t\t\t\tmatch[2] = unquoted.slice( 0, excess );\n\t\t\t}\n\n\t\t\t// Return only captures needed by the pseudo filter method (type and argument)\n\t\t\treturn match.slice( 0, 3 );\n\t\t}\n\t},\n\n\tfilter: {\n\n\t\t\"TAG\": function( nodeNameSelector ) {\n\t\t\tvar nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase();\n\t\t\treturn nodeNameSelector === \"*\" ?\n\t\t\t\tfunction() { return true; } :\n\t\t\t\tfunction( elem ) {\n\t\t\t\t\treturn elem.nodeName && elem.nodeName.toLowerCase() === nodeName;\n\t\t\t\t};\n\t\t},\n\n\t\t\"CLASS\": function( className ) {\n\t\t\tvar pattern = classCache[ className + \" \" ];\n\n\t\t\treturn pattern ||\n\t\t\t\t(pattern = new RegExp( \"(^|\" + whitespace + \")\" + className + \"(\" + whitespace + \"|$)\" )) &&\n\t\t\t\tclassCache( className, function( elem ) {\n\t\t\t\t\treturn pattern.test( typeof elem.className === \"string\" && elem.className || typeof elem.getAttribute !== \"undefined\" && elem.getAttribute(\"class\") || \"\" );\n\t\t\t\t});\n\t\t},\n\n\t\t\"ATTR\": function( name, operator, check ) {\n\t\t\treturn function( elem ) {\n\t\t\t\tvar result = Sizzle.attr( elem, name );\n\n\t\t\t\tif ( result == null ) {\n\t\t\t\t\treturn operator === \"!=\";\n\t\t\t\t}\n\t\t\t\tif ( !operator ) {\n\t\t\t\t\treturn true;\n\t\t\t\t}\n\n\t\t\t\tresult += \"\";\n\n\t\t\t\treturn operator === \"=\" ? result === check :\n\t\t\t\t\toperator === \"!=\" ? result !== check :\n\t\t\t\t\toperator === \"^=\" ? check && result.indexOf( check ) === 0 :\n\t\t\t\t\toperator === \"*=\" ? check && result.indexOf( check ) > -1 :\n\t\t\t\t\toperator === \"$=\" ? check && result.slice( -check.length ) === check :\n\t\t\t\t\toperator === \"~=\" ? ( \" \" + result.replace( rwhitespace, \" \" ) + \" \" ).indexOf( check ) > -1 :\n\t\t\t\t\toperator === \"|=\" ? result === check || result.slice( 0, check.length + 1 ) === check + \"-\" :\n\t\t\t\t\tfalse;\n\t\t\t};\n\t\t},\n\n\t\t\"CHILD\": function( type, what, argument, first, last ) {\n\t\t\tvar simple = type.slice( 0, 3 ) !== \"nth\",\n\t\t\t\tforward = type.slice( -4 ) !== \"last\",\n\t\t\t\tofType = what === \"of-type\";\n\n\t\t\treturn first === 1 && last === 0 ?\n\n\t\t\t\t// Shortcut for :nth-*(n)\n\t\t\t\tfunction( elem ) {\n\t\t\t\t\treturn !!elem.parentNode;\n\t\t\t\t} :\n\n\t\t\t\tfunction( elem, context, xml ) {\n\t\t\t\t\tvar cache, uniqueCache, outerCache, node, nodeIndex, start,\n\t\t\t\t\t\tdir = simple !== forward ? \"nextSibling\" : \"previousSibling\",\n\t\t\t\t\t\tparent = elem.parentNode,\n\t\t\t\t\t\tname = ofType && elem.nodeName.toLowerCase(),\n\t\t\t\t\t\tuseCache = !xml && !ofType,\n\t\t\t\t\t\tdiff = false;\n\n\t\t\t\t\tif ( parent ) {\n\n\t\t\t\t\t\t// :(first|last|only)-(child|of-type)\n\t\t\t\t\t\tif ( simple ) {\n\t\t\t\t\t\t\twhile ( dir ) {\n\t\t\t\t\t\t\t\tnode = elem;\n\t\t\t\t\t\t\t\twhile ( (node = node[ dir ]) ) {\n\t\t\t\t\t\t\t\t\tif ( ofType ?\n\t\t\t\t\t\t\t\t\t\tnode.nodeName.toLowerCase() === name :\n\t\t\t\t\t\t\t\t\t\tnode.nodeType === 1 ) {\n\n\t\t\t\t\t\t\t\t\t\treturn false;\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t// Reverse direction for :only-* (if we haven't yet done so)\n\t\t\t\t\t\t\t\tstart = dir = type === \"only\" && !start && \"nextSibling\";\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\treturn true;\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\tstart = [ forward ? parent.firstChild : parent.lastChild ];\n\n\t\t\t\t\t\t// non-xml :nth-child(...) stores cache data on `parent`\n\t\t\t\t\t\tif ( forward && useCache ) {\n\n\t\t\t\t\t\t\t// Seek `elem` from a previously-cached index\n\n\t\t\t\t\t\t\t// ...in a gzip-friendly way\n\t\t\t\t\t\t\tnode = parent;\n\t\t\t\t\t\t\touterCache = node[ expando ] || (node[ expando ] = {});\n\n\t\t\t\t\t\t\t// Support: IE <9 only\n\t\t\t\t\t\t\t// Defend against cloned attroperties (jQuery gh-1709)\n\t\t\t\t\t\t\tuniqueCache = outerCache[ node.uniqueID ] ||\n\t\t\t\t\t\t\t\t(outerCache[ node.uniqueID ] = {});\n\n\t\t\t\t\t\t\tcache = uniqueCache[ type ] || [];\n\t\t\t\t\t\t\tnodeIndex = cache[ 0 ] === dirruns && cache[ 1 ];\n\t\t\t\t\t\t\tdiff = nodeIndex && cache[ 2 ];\n\t\t\t\t\t\t\tnode = nodeIndex && parent.childNodes[ nodeIndex ];\n\n\t\t\t\t\t\t\twhile ( (node = ++nodeIndex && node && node[ dir ] ||\n\n\t\t\t\t\t\t\t\t// Fallback to seeking `elem` from the start\n\t\t\t\t\t\t\t\t(diff = nodeIndex = 0) || start.pop()) ) {\n\n\t\t\t\t\t\t\t\t// When found, cache indexes on `parent` and break\n\t\t\t\t\t\t\t\tif ( node.nodeType === 1 && ++diff && node === elem ) {\n\t\t\t\t\t\t\t\t\tuniqueCache[ type ] = [ dirruns, nodeIndex, diff ];\n\t\t\t\t\t\t\t\t\tbreak;\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t// Use previously-cached element index if available\n\t\t\t\t\t\t\tif ( useCache ) {\n\t\t\t\t\t\t\t\t// ...in a gzip-friendly way\n\t\t\t\t\t\t\t\tnode = elem;\n\t\t\t\t\t\t\t\touterCache = node[ expando ] || (node[ expando ] = {});\n\n\t\t\t\t\t\t\t\t// Support: IE <9 only\n\t\t\t\t\t\t\t\t// Defend against cloned attroperties (jQuery gh-1709)\n\t\t\t\t\t\t\t\tuniqueCache = outerCache[ node.uniqueID ] ||\n\t\t\t\t\t\t\t\t\t(outerCache[ node.uniqueID ] = {});\n\n\t\t\t\t\t\t\t\tcache = uniqueCache[ type ] || [];\n\t\t\t\t\t\t\t\tnodeIndex = cache[ 0 ] === dirruns && cache[ 1 ];\n\t\t\t\t\t\t\t\tdiff = nodeIndex;\n\t\t\t\t\t\t\t}\n\n\t\t\t\t\t\t\t// xml :nth-child(...)\n\t\t\t\t\t\t\t// or :nth-last-child(...) or :nth(-last)?-of-type(...)\n\t\t\t\t\t\t\tif ( diff === false ) {\n\t\t\t\t\t\t\t\t// Use the same loop as above to seek `elem` from the start\n\t\t\t\t\t\t\t\twhile ( (node = ++nodeIndex && node && node[ dir ] ||\n\t\t\t\t\t\t\t\t\t(diff = nodeIndex = 0) || start.pop()) ) {\n\n\t\t\t\t\t\t\t\t\tif ( ( ofType ?\n\t\t\t\t\t\t\t\t\t\tnode.nodeName.toLowerCase() === name :\n\t\t\t\t\t\t\t\t\t\tnode.nodeType === 1 ) &&\n\t\t\t\t\t\t\t\t\t\t++diff ) {\n\n\t\t\t\t\t\t\t\t\t\t// Cache the index of each encountered element\n\t\t\t\t\t\t\t\t\t\tif ( useCache ) {\n\t\t\t\t\t\t\t\t\t\t\touterCache = node[ expando ] || (node[ expando ] = {});\n\n\t\t\t\t\t\t\t\t\t\t\t// Support: IE <9 only\n\t\t\t\t\t\t\t\t\t\t\t// Defend against cloned attroperties (jQuery gh-1709)\n\t\t\t\t\t\t\t\t\t\t\tuniqueCache = outerCache[ node.uniqueID ] ||\n\t\t\t\t\t\t\t\t\t\t\t\t(outerCache[ node.uniqueID ] = {});\n\n\t\t\t\t\t\t\t\t\t\t\tuniqueCache[ type ] = [ dirruns, diff ];\n\t\t\t\t\t\t\t\t\t\t}\n\n\t\t\t\t\t\t\t\t\t\tif ( node === elem ) {\n\t\t\t\t\t\t\t\t\t\t\tbreak;\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\n\t\t\t\t\t\t// Incorporate the offset, then check against cycle size\n\t\t\t\t\t\tdiff -= last;\n\t\t\t\t\t\treturn diff === first || ( diff % first === 0 && diff / first >= 0 );\n\t\t\t\t\t}\n\t\t\t\t};\n\t\t},\n\n\t\t\"PSEUDO\": function( pseudo, argument ) {\n\t\t\t// pseudo-class names are case-insensitive\n\t\t\t// http://www.w3.org/TR/selectors/#pseudo-classes\n\t\t\t// Prioritize by case sensitivity in case custom pseudos are added with uppercase letters\n\t\t\t// Remember that setFilters inherits from pseudos\n\t\t\tvar args,\n\t\t\t\tfn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] ||\n\t\t\t\t\tSizzle.error( \"unsupported pseudo: \" + pseudo );\n\n\t\t\t// The user may use createPseudo to indicate that\n\t\t\t// arguments are needed to create the filter function\n\t\t\t// just as Sizzle does\n\t\t\tif ( fn[ expando ] ) {\n\t\t\t\treturn fn( argument );\n\t\t\t}\n\n\t\t\t// But maintain support for old signatures\n\t\t\tif ( fn.length > 1 ) {\n\t\t\t\targs = [ pseudo, pseudo, \"\", argument ];\n\t\t\t\treturn Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ?\n\t\t\t\t\tmarkFunction(function( seed, matches ) {\n\t\t\t\t\t\tvar idx,\n\t\t\t\t\t\t\tmatched = fn( seed, argument ),\n\t\t\t\t\t\t\ti = matched.length;\n\t\t\t\t\t\twhile ( i-- ) {\n\t\t\t\t\t\t\tidx = indexOf( seed, matched[i] );\n\t\t\t\t\t\t\tseed[ idx ] = !( matches[ idx ] = matched[i] );\n\t\t\t\t\t\t}\n\t\t\t\t\t}) :\n\t\t\t\t\tfunction( elem ) {\n\t\t\t\t\t\treturn fn( elem, 0, args );\n\t\t\t\t\t};\n\t\t\t}\n\n\t\t\treturn fn;\n\t\t}\n\t},\n\n\tpseudos: {\n\t\t// Potentially complex pseudos\n\t\t\"not\": markFunction(function( selector ) {\n\t\t\t// Trim the selector passed to compile\n\t\t\t// to avoid treating leading and trailing\n\t\t\t// spaces as combinators\n\t\t\tvar input = [],\n\t\t\t\tresults = [],\n\t\t\t\tmatcher = compile( selector.replace( rtrim, \"$1\" ) );\n\n\t\t\treturn matcher[ expando ] ?\n\t\t\t\tmarkFunction(function( seed, matches, context, xml ) {\n\t\t\t\t\tvar elem,\n\t\t\t\t\t\tunmatched = matcher( seed, null, xml, [] ),\n\t\t\t\t\t\ti = seed.length;\n\n\t\t\t\t\t// Match elements unmatched by `matcher`\n\t\t\t\t\twhile ( i-- ) {\n\t\t\t\t\t\tif ( (elem = unmatched[i]) ) {\n\t\t\t\t\t\t\tseed[i] = !(matches[i] = elem);\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}) :\n\t\t\t\tfunction( elem, context, xml ) {\n\t\t\t\t\tinput[0] = elem;\n\t\t\t\t\tmatcher( input, null, xml, results );\n\t\t\t\t\t// Don't keep the element (issue #299)\n\t\t\t\t\tinput[0] = null;\n\t\t\t\t\treturn !results.pop();\n\t\t\t\t};\n\t\t}),\n\n\t\t\"has\": markFunction(function( selector ) {\n\t\t\treturn function( elem ) {\n\t\t\t\treturn Sizzle( selector, elem ).length > 0;\n\t\t\t};\n\t\t}),\n\n\t\t\"contains\": markFunction(function( text ) {\n\t\t\ttext = text.replace( runescape, funescape );\n\t\t\treturn function( elem ) {\n\t\t\t\treturn ( elem.textContent || elem.innerText || getText( elem ) ).indexOf( text ) > -1;\n\t\t\t};\n\t\t}),\n\n\t\t// \"Whether an element is represented by a :lang() selector\n\t\t// is based solely on the element's language value\n\t\t// being equal to the identifier C,\n\t\t// or beginning with the identifier C immediately followed by \"-\".\n\t\t// The matching of C against the element's language value is performed case-insensitively.\n\t\t// The identifier C does not have to be a valid language name.\"\n\t\t// http://www.w3.org/TR/selectors/#lang-pseudo\n\t\t\"lang\": markFunction( function( lang ) {\n\t\t\t// lang value must be a valid identifier\n\t\t\tif ( !ridentifier.test(lang || \"\") ) {\n\t\t\t\tSizzle.error( \"unsupported lang: \" + lang );\n\t\t\t}\n\t\t\tlang = lang.replace( runescape, funescape ).toLowerCase();\n\t\t\treturn function( elem ) {\n\t\t\t\tvar elemLang;\n\t\t\t\tdo {\n\t\t\t\t\tif ( (elemLang = documentIsHTML ?\n\t\t\t\t\t\telem.lang :\n\t\t\t\t\t\telem.getAttribute(\"xml:lang\") || elem.getAttribute(\"lang\")) ) {\n\n\t\t\t\t\t\telemLang = elemLang.toLowerCase();\n\t\t\t\t\t\treturn elemLang === lang || elemLang.indexOf( lang + \"-\" ) === 0;\n\t\t\t\t\t}\n\t\t\t\t} while ( (elem = elem.parentNode) && elem.nodeType === 1 );\n\t\t\t\treturn false;\n\t\t\t};\n\t\t}),\n\n\t\t// Miscellaneous\n\t\t\"target\": function( elem ) {\n\t\t\tvar hash = window.location && window.location.hash;\n\t\t\treturn hash && hash.slice( 1 ) === elem.id;\n\t\t},\n\n\t\t\"root\": function( elem ) {\n\t\t\treturn elem === docElem;\n\t\t},\n\n\t\t\"focus\": function( elem ) {\n\t\t\treturn elem === document.activeElement && (!document.hasFocus || document.hasFocus()) && !!(elem.type || elem.href || ~elem.tabIndex);\n\t\t},\n\n\t\t// Boolean properties\n\t\t\"enabled\": function( elem ) {\n\t\t\treturn elem.disabled === false;\n\t\t},\n\n\t\t\"disabled\": function( elem ) {\n\t\t\treturn elem.disabled === true;\n\t\t},\n\n\t\t\"checked\": function( elem ) {\n\t\t\t// In CSS3, :checked should return both checked and selected elements\n\t\t\t// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked\n\t\t\tvar nodeName = elem.nodeName.toLowerCase();\n\t\t\treturn (nodeName === \"input\" && !!elem.checked) || (nodeName === \"option\" && !!elem.selected);\n\t\t},\n\n\t\t\"selected\": function( elem ) {\n\t\t\t// Accessing this property makes selected-by-default\n\t\t\t// options in Safari work properly\n\t\t\tif ( elem.parentNode ) {\n\t\t\t\telem.parentNode.selectedIndex;\n\t\t\t}\n\n\t\t\treturn elem.selected === true;\n\t\t},\n\n\t\t// Contents\n\t\t\"empty\": function( elem ) {\n\t\t\t// http://www.w3.org/TR/selectors/#empty-pseudo\n\t\t\t// :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5),\n\t\t\t// but not by others (comment: 8; processing instruction: 7; etc.)\n\t\t\t// nodeType < 6 works because attributes (2) do not appear as children\n\t\t\tfor ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {\n\t\t\t\tif ( elem.nodeType < 6 ) {\n\t\t\t\t\treturn false;\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn true;\n\t\t},\n\n\t\t\"parent\": function( elem ) {\n\t\t\treturn !Expr.pseudos[\"empty\"]( elem );\n\t\t},\n\n\t\t// Element/input types\n\t\t\"header\": function( elem ) {\n\t\t\treturn rheader.test( elem.nodeName );\n\t\t},\n\n\t\t\"input\": function( elem ) {\n\t\t\treturn rinputs.test( elem.nodeName );\n\t\t},\n\n\t\t\"button\": function( elem ) {\n\t\t\tvar name = elem.nodeName.toLowerCase();\n\t\t\treturn name === \"input\" && elem.type === \"button\" || name === \"button\";\n\t\t},\n\n\t\t\"text\": function( elem ) {\n\t\t\tvar attr;\n\t\t\treturn elem.nodeName.toLowerCase() === \"input\" &&\n\t\t\t\telem.type === \"text\" &&\n\n\t\t\t\t// Support: IE<8\n\t\t\t\t// New HTML5 attribute values (e.g., \"search\") appear with elem.type === \"text\"\n\t\t\t\t( (attr = elem.getAttribute(\"type\")) == null || attr.toLowerCase() === \"text\" );\n\t\t},\n\n\t\t// Position-in-collection\n\t\t\"first\": createPositionalPseudo(function() {\n\t\t\treturn [ 0 ];\n\t\t}),\n\n\t\t\"last\": createPositionalPseudo(function( matchIndexes, length ) {\n\t\t\treturn [ length - 1 ];\n\t\t}),\n\n\t\t\"eq\": createPositionalPseudo(function( matchIndexes, length, argument ) {\n\t\t\treturn [ argument < 0 ? argument + length : argument ];\n\t\t}),\n\n\t\t\"even\": createPositionalPseudo(function( matchIndexes, length ) {\n\t\t\tvar i = 0;\n\t\t\tfor ( ; i < length; i += 2 ) {\n\t\t\t\tmatchIndexes.push( i );\n\t\t\t}\n\t\t\treturn matchIndexes;\n\t\t}),\n\n\t\t\"odd\": createPositionalPseudo(function( matchIndexes, length ) {\n\t\t\tvar i = 1;\n\t\t\tfor ( ; i < length; i += 2 ) {\n\t\t\t\tmatchIndexes.push( i );\n\t\t\t}\n\t\t\treturn matchIndexes;\n\t\t}),\n\n\t\t\"lt\": createPositionalPseudo(function( matchIndexes, length, argument ) {\n\t\t\tvar i = argument < 0 ? argument + length : argument;\n\t\t\tfor ( ; --i >= 0; ) {\n\t\t\t\tmatchIndexes.push( i );\n\t\t\t}\n\t\t\treturn matchIndexes;\n\t\t}),\n\n\t\t\"gt\": createPositionalPseudo(function( matchIndexes, length, argument ) {\n\t\t\tvar i = argument < 0 ? argument + length : argument;\n\t\t\tfor ( ; ++i < length; ) {\n\t\t\t\tmatchIndexes.push( i );\n\t\t\t}\n\t\t\treturn matchIndexes;\n\t\t})\n\t}\n};\n\nExpr.pseudos[\"nth\"] = Expr.pseudos[\"eq\"];\n\n// Add button/input type pseudos\nfor ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) {\n\tExpr.pseudos[ i ] = createInputPseudo( i );\n}\nfor ( i in { submit: true, reset: true } ) {\n\tExpr.pseudos[ i ] = createButtonPseudo( i );\n}\n\n// Easy API for creating new setFilters\nfunction setFilters() {}\nsetFilters.prototype = Expr.filters = Expr.pseudos;\nExpr.setFilters = new setFilters();\n\ntokenize = Sizzle.tokenize = function( selector, parseOnly ) {\n\tvar matched, match, tokens, type,\n\t\tsoFar, groups, preFilters,\n\t\tcached = tokenCache[ selector + \" \" ];\n\n\tif ( cached ) {\n\t\treturn parseOnly ? 0 : cached.slice( 0 );\n\t}\n\n\tsoFar = selector;\n\tgroups = [];\n\tpreFilters = Expr.preFilter;\n\n\twhile ( soFar ) {\n\n\t\t// Comma and first run\n\t\tif ( !matched || (match = rcomma.exec( soFar )) ) {\n\t\t\tif ( match ) {\n\t\t\t\t// Don't consume trailing commas as valid\n\t\t\t\tsoFar = soFar.slice( match[0].length ) || soFar;\n\t\t\t}\n\t\t\tgroups.push( (tokens = []) );\n\t\t}\n\n\t\tmatched = false;\n\n\t\t// Combinators\n\t\tif ( (match = rcombinators.exec( soFar )) ) {\n\t\t\tmatched = match.shift();\n\t\t\ttokens.push({\n\t\t\t\tvalue: matched,\n\t\t\t\t// Cast descendant combinators to space\n\t\t\t\ttype: match[0].replace( rtrim, \" \" )\n\t\t\t});\n\t\t\tsoFar = soFar.slice( matched.length );\n\t\t}\n\n\t\t// Filters\n\t\tfor ( type in Expr.filter ) {\n\t\t\tif ( (match = matchExpr[ type ].exec( soFar )) && (!preFilters[ type ] ||\n\t\t\t\t(match = preFilters[ type ]( match ))) ) {\n\t\t\t\tmatched = match.shift();\n\t\t\t\ttokens.push({\n\t\t\t\t\tvalue: matched,\n\t\t\t\t\ttype: type,\n\t\t\t\t\tmatches: match\n\t\t\t\t});\n\t\t\t\tsoFar = soFar.slice( matched.length );\n\t\t\t}\n\t\t}\n\n\t\tif ( !matched ) {\n\t\t\tbreak;\n\t\t}\n\t}\n\n\t// Return the length of the invalid excess\n\t// if we're just parsing\n\t// Otherwise, throw an error or return tokens\n\treturn parseOnly ?\n\t\tsoFar.length :\n\t\tsoFar ?\n\t\t\tSizzle.error( selector ) :\n\t\t\t// Cache the tokens\n\t\t\ttokenCache( selector, groups ).slice( 0 );\n};\n\nfunction toSelector( tokens ) {\n\tvar i = 0,\n\t\tlen = tokens.length,\n\t\tselector = \"\";\n\tfor ( ; i < len; i++ ) {\n\t\tselector += tokens[i].value;\n\t}\n\treturn selector;\n}\n\nfunction addCombinator( matcher, combinator, base ) {\n\tvar dir = combinator.dir,\n\t\tcheckNonElements = base && dir === \"parentNode\",\n\t\tdoneName = done++;\n\n\treturn combinator.first ?\n\t\t// Check against closest ancestor/preceding element\n\t\tfunction( elem, context, xml ) {\n\t\t\twhile ( (elem = elem[ dir ]) ) {\n\t\t\t\tif ( elem.nodeType === 1 || checkNonElements ) {\n\t\t\t\t\treturn matcher( elem, context, xml );\n\t\t\t\t}\n\t\t\t}\n\t\t} :\n\n\t\t// Check against all ancestor/preceding elements\n\t\tfunction( elem, context, xml ) {\n\t\t\tvar oldCache, uniqueCache, outerCache,\n\t\t\t\tnewCache = [ dirruns, doneName ];\n\n\t\t\t// We can't set arbitrary data on XML nodes, so they don't benefit from combinator caching\n\t\t\tif ( xml ) {\n\t\t\t\twhile ( (elem = elem[ dir ]) ) {\n\t\t\t\t\tif ( elem.nodeType === 1 || checkNonElements ) {\n\t\t\t\t\t\tif ( matcher( elem, context, xml ) ) {\n\t\t\t\t\t\t\treturn true;\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\twhile ( (elem = elem[ dir ]) ) {\n\t\t\t\t\tif ( elem.nodeType === 1 || checkNonElements ) {\n\t\t\t\t\t\touterCache = elem[ expando ] || (elem[ expando ] = {});\n\n\t\t\t\t\t\t// Support: IE <9 only\n\t\t\t\t\t\t// Defend against cloned attroperties (jQuery gh-1709)\n\t\t\t\t\t\tuniqueCache = outerCache[ elem.uniqueID ] || (outerCache[ elem.uniqueID ] = {});\n\n\t\t\t\t\t\tif ( (oldCache = uniqueCache[ dir ]) &&\n\t\t\t\t\t\t\toldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) {\n\n\t\t\t\t\t\t\t// Assign to newCache so results back-propagate to previous elements\n\t\t\t\t\t\t\treturn (newCache[ 2 ] = oldCache[ 2 ]);\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t// Reuse newcache so results back-propagate to previous elements\n\t\t\t\t\t\t\tuniqueCache[ dir ] = newCache;\n\n\t\t\t\t\t\t\t// A match means we're done; a fail means we have to keep checking\n\t\t\t\t\t\t\tif ( (newCache[ 2 ] = matcher( elem, context, xml )) ) {\n\t\t\t\t\t\t\t\treturn true;\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t};\n}\n\nfunction elementMatcher( matchers ) {\n\treturn matchers.length > 1 ?\n\t\tfunction( elem, context, xml ) {\n\t\t\tvar i = matchers.length;\n\t\t\twhile ( i-- ) {\n\t\t\t\tif ( !matchers[i]( elem, context, xml ) ) {\n\t\t\t\t\treturn false;\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn true;\n\t\t} :\n\t\tmatchers[0];\n}\n\nfunction multipleContexts( selector, contexts, results ) {\n\tvar i = 0,\n\t\tlen = contexts.length;\n\tfor ( ; i < len; i++ ) {\n\t\tSizzle( selector, contexts[i], results );\n\t}\n\treturn results;\n}\n\nfunction condense( unmatched, map, filter, context, xml ) {\n\tvar elem,\n\t\tnewUnmatched = [],\n\t\ti = 0,\n\t\tlen = unmatched.length,\n\t\tmapped = map != null;\n\n\tfor ( ; i < len; i++ ) {\n\t\tif ( (elem = unmatched[i]) ) {\n\t\t\tif ( !filter || filter( elem, context, xml ) ) {\n\t\t\t\tnewUnmatched.push( elem );\n\t\t\t\tif ( mapped ) {\n\t\t\t\t\tmap.push( i );\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\treturn newUnmatched;\n}\n\nfunction setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) {\n\tif ( postFilter && !postFilter[ expando ] ) {\n\t\tpostFilter = setMatcher( postFilter );\n\t}\n\tif ( postFinder && !postFinder[ expando ] ) {\n\t\tpostFinder = setMatcher( postFinder, postSelector );\n\t}\n\treturn markFunction(function( seed, results, context, xml ) {\n\t\tvar temp, i, elem,\n\t\t\tpreMap = [],\n\t\t\tpostMap = [],\n\t\t\tpreexisting = results.length,\n\n\t\t\t// Get initial elements from seed or context\n\t\t\telems = seed || multipleContexts( selector || \"*\", context.nodeType ? [ context ] : context, [] ),\n\n\t\t\t// Prefilter to get matcher input, preserving a map for seed-results synchronization\n\t\t\tmatcherIn = preFilter && ( seed || !selector ) ?\n\t\t\t\tcondense( elems, preMap, preFilter, context, xml ) :\n\t\t\t\telems,\n\n\t\t\tmatcherOut = matcher ?\n\t\t\t\t// If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results,\n\t\t\t\tpostFinder || ( seed ? preFilter : preexisting || postFilter ) ?\n\n\t\t\t\t\t// ...intermediate processing is necessary\n\t\t\t\t\t[] :\n\n\t\t\t\t\t// ...otherwise use results directly\n\t\t\t\t\tresults :\n\t\t\t\tmatcherIn;\n\n\t\t// Find primary matches\n\t\tif ( matcher ) {\n\t\t\tmatcher( matcherIn, matcherOut, context, xml );\n\t\t}\n\n\t\t// Apply postFilter\n\t\tif ( postFilter ) {\n\t\t\ttemp = condense( matcherOut, postMap );\n\t\t\tpostFilter( temp, [], context, xml );\n\n\t\t\t// Un-match failing elements by moving them back to matcherIn\n\t\t\ti = temp.length;\n\t\t\twhile ( i-- ) {\n\t\t\t\tif ( (elem = temp[i]) ) {\n\t\t\t\t\tmatcherOut[ postMap[i] ] = !(matcherIn[ postMap[i] ] = elem);\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif ( seed ) {\n\t\t\tif ( postFinder || preFilter ) {\n\t\t\t\tif ( postFinder ) {\n\t\t\t\t\t// Get the final matcherOut by condensing this intermediate into postFinder contexts\n\t\t\t\t\ttemp = [];\n\t\t\t\t\ti = matcherOut.length;\n\t\t\t\t\twhile ( i-- ) {\n\t\t\t\t\t\tif ( (elem = matcherOut[i]) ) {\n\t\t\t\t\t\t\t// Restore matcherIn since elem is not yet a final match\n\t\t\t\t\t\t\ttemp.push( (matcherIn[i] = elem) );\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tpostFinder( null, (matcherOut = []), temp, xml );\n\t\t\t\t}\n\n\t\t\t\t// Move matched elements from seed to results to keep them synchronized\n\t\t\t\ti = matcherOut.length;\n\t\t\t\twhile ( i-- ) {\n\t\t\t\t\tif ( (elem = matcherOut[i]) &&\n\t\t\t\t\t\t(temp = postFinder ? indexOf( seed, elem ) : preMap[i]) > -1 ) {\n\n\t\t\t\t\t\tseed[temp] = !(results[temp] = elem);\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t// Add elements to results, through postFinder if defined\n\t\t} else {\n\t\t\tmatcherOut = condense(\n\t\t\t\tmatcherOut === results ?\n\t\t\t\t\tmatcherOut.splice( preexisting, matcherOut.length ) :\n\t\t\t\t\tmatcherOut\n\t\t\t);\n\t\t\tif ( postFinder ) {\n\t\t\t\tpostFinder( null, results, matcherOut, xml );\n\t\t\t} else {\n\t\t\t\tpush.apply( results, matcherOut );\n\t\t\t}\n\t\t}\n\t});\n}\n\nfunction matcherFromTokens( tokens ) {\n\tvar checkContext, matcher, j,\n\t\tlen = tokens.length,\n\t\tleadingRelative = Expr.relative[ tokens[0].type ],\n\t\timplicitRelative = leadingRelative || Expr.relative[\" \"],\n\t\ti = leadingRelative ? 1 : 0,\n\n\t\t// The foundational matcher ensures that elements are reachable from top-level context(s)\n\t\tmatchContext = addCombinator( function( elem ) {\n\t\t\treturn elem === checkContext;\n\t\t}, implicitRelative, true ),\n\t\tmatchAnyContext = addCombinator( function( elem ) {\n\t\t\treturn indexOf( checkContext, elem ) > -1;\n\t\t}, implicitRelative, true ),\n\t\tmatchers = [ function( elem, context, xml ) {\n\t\t\tvar ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || (\n\t\t\t\t(checkContext = context).nodeType ?\n\t\t\t\t\tmatchContext( elem, context, xml ) :\n\t\t\t\t\tmatchAnyContext( elem, context, xml ) );\n\t\t\t// Avoid hanging onto element (issue #299)\n\t\t\tcheckContext = null;\n\t\t\treturn ret;\n\t\t} ];\n\n\tfor ( ; i < len; i++ ) {\n\t\tif ( (matcher = Expr.relative[ tokens[i].type ]) ) {\n\t\t\tmatchers = [ addCombinator(elementMatcher( matchers ), matcher) ];\n\t\t} else {\n\t\t\tmatcher = Expr.filter[ tokens[i].type ].apply( null, tokens[i].matches );\n\n\t\t\t// Return special upon seeing a positional matcher\n\t\t\tif ( matcher[ expando ] ) {\n\t\t\t\t// Find the next relative operator (if any) for proper handling\n\t\t\t\tj = ++i;\n\t\t\t\tfor ( ; j < len; j++ ) {\n\t\t\t\t\tif ( Expr.relative[ tokens[j].type ] ) {\n\t\t\t\t\t\tbreak;\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\treturn setMatcher(\n\t\t\t\t\ti > 1 && elementMatcher( matchers ),\n\t\t\t\t\ti > 1 && toSelector(\n\t\t\t\t\t\t// If the preceding token was a descendant combinator, insert an implicit any-element `*`\n\t\t\t\t\t\ttokens.slice( 0, i - 1 ).concat({ value: tokens[ i - 2 ].type === \" \" ? \"*\" : \"\" })\n\t\t\t\t\t).replace( rtrim, \"$1\" ),\n\t\t\t\t\tmatcher,\n\t\t\t\t\ti < j && matcherFromTokens( tokens.slice( i, j ) ),\n\t\t\t\t\tj < len && matcherFromTokens( (tokens = tokens.slice( j )) ),\n\t\t\t\t\tj < len && toSelector( tokens )\n\t\t\t\t);\n\t\t\t}\n\t\t\tmatchers.push( matcher );\n\t\t}\n\t}\n\n\treturn elementMatcher( matchers );\n}\n\nfunction matcherFromGroupMatchers( elementMatchers, setMatchers ) {\n\tvar bySet = setMatchers.length > 0,\n\t\tbyElement = elementMatchers.length > 0,\n\t\tsuperMatcher = function( seed, context, xml, results, outermost ) {\n\t\t\tvar elem, j, matcher,\n\t\t\t\tmatchedCount = 0,\n\t\t\t\ti = \"0\",\n\t\t\t\tunmatched = seed && [],\n\t\t\t\tsetMatched = [],\n\t\t\t\tcontextBackup = outermostContext,\n\t\t\t\t// We must always have either seed elements or outermost context\n\t\t\t\telems = seed || byElement && Expr.find[\"TAG\"]( \"*\", outermost ),\n\t\t\t\t// Use integer dirruns iff this is the outermost matcher\n\t\t\t\tdirrunsUnique = (dirruns += contextBackup == null ? 1 : Math.random() || 0.1),\n\t\t\t\tlen = elems.length;\n\n\t\t\tif ( outermost ) {\n\t\t\t\toutermostContext = context === document || context || outermost;\n\t\t\t}\n\n\t\t\t// Add elements passing elementMatchers directly to results\n\t\t\t// Support: IE<9, Safari\n\t\t\t// Tolerate NodeList properties (IE: \"length\"; Safari:',t.nice_total_disk_usage?(0,u.default)("Using ")+t.nice_total_disk_usage:"","",") matching elements by id\n\t\t\tfor ( ; i !== len && (elem = elems[i]) != null; i++ ) {\n\t\t\t\tif ( byElement && elem ) {\n\t\t\t\t\tj = 0;\n\t\t\t\t\tif ( !context && elem.ownerDocument !== document ) {\n\t\t\t\t\t\tsetDocument( elem );\n\t\t\t\t\t\txml = !documentIsHTML;\n\t\t\t\t\t}\n\t\t\t\t\twhile ( (matcher = elementMatchers[j++]) ) {\n\t\t\t\t\t\tif ( matcher( elem, context || document, xml) ) {\n\t\t\t\t\t\t\tresults.push( elem );\n\t\t\t\t\t\t\tbreak;\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif ( outermost ) {\n\t\t\t\t\t\tdirruns = dirrunsUnique;\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\t// Track unmatched elements for set filters\n\t\t\t\tif ( bySet ) {\n\t\t\t\t\t// They will have gone through all possible matchers\n\t\t\t\t\tif ( (elem = !matcher && elem) ) {\n\t\t\t\t\t\tmatchedCount--;\n\t\t\t\t\t}\n\n\t\t\t\t\t// Lengthen the array for every element, matched or not\n\t\t\t\t\tif ( seed ) {\n\t\t\t\t\t\tunmatched.push( elem );\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// `i` is now the count of elements visited above, and adding it to `matchedCount`\n\t\t\t// makes the latter nonnegative.\n\t\t\tmatchedCount += i;\n\n\t\t\t// Apply set filters to unmatched elements\n\t\t\t// NOTE: This can be skipped if there are no unmatched elements (i.e., `matchedCount`\n\t\t\t// equals `i`), unless we didn't visit _any_ elements in the above loop because we have\n\t\t\t// no element matchers and no seed.\n\t\t\t// Incrementing an initially-string \"0\" `i` allows `i` to remain a string only in that\n\t\t\t// case, which will result in a \"00\" `matchedCount` that differs from `i` but is also\n\t\t\t// numerically zero.\n\t\t\tif ( bySet && i !== matchedCount ) {\n\t\t\t\tj = 0;\n\t\t\t\twhile ( (matcher = setMatchers[j++]) ) {\n\t\t\t\t\tmatcher( unmatched, setMatched, context, xml );\n\t\t\t\t}\n\n\t\t\t\tif ( seed ) {\n\t\t\t\t\t// Reintegrate element matches to eliminate the need for sorting\n\t\t\t\t\tif ( matchedCount > 0 ) {\n\t\t\t\t\t\twhile ( i-- ) {\n\t\t\t\t\t\t\tif ( !(unmatched[i] || setMatched[i]) ) {\n\t\t\t\t\t\t\t\tsetMatched[i] = pop.call( results );\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\n\t\t\t\t\t// Discard index placeholder values to get only actual matches\n\t\t\t\t\tsetMatched = condense( setMatched );\n\t\t\t\t}\n\n\t\t\t\t// Add matches to results\n\t\t\t\tpush.apply( results, setMatched );\n\n\t\t\t\t// Seedless set matches succeeding multiple successful matchers stipulate sorting\n\t\t\t\tif ( outermost && !seed && setMatched.length > 0 &&\n\t\t\t\t\t( matchedCount + setMatchers.length ) > 1 ) {\n\n\t\t\t\t\tSizzle.uniqueSort( results );\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// Override manipulation of globals by nested matchers\n\t\t\tif ( outermost ) {\n\t\t\t\tdirruns = dirrunsUnique;\n\t\t\t\toutermostContext = contextBackup;\n\t\t\t}\n\n\t\t\treturn unmatched;\n\t\t};\n\n\treturn bySet ?\n\t\tmarkFunction( superMatcher ) :\n\t\tsuperMatcher;\n}\n\ncompile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) {\n\tvar i,\n\t\tsetMatchers = [],\n\t\telementMatchers = [],\n\t\tcached = compilerCache[ selector + \" \" ];\n\n\tif ( !cached ) {\n\t\t// Generate a function of recursive functions that can be used to check each element\n\t\tif ( !match ) {\n\t\t\tmatch = tokenize( selector );\n\t\t}\n\t\ti = match.length;\n\t\twhile ( i-- ) {\n\t\t\tcached = matcherFromTokens( match[i] );\n\t\t\tif ( cached[ expando ] ) {\n\t\t\t\tsetMatchers.push( cached );\n\t\t\t} else {\n\t\t\t\telementMatchers.push( cached );\n\t\t\t}\n\t\t}\n\n\t\t// Cache the compiled function\n\t\tcached = compilerCache( selector, matcherFromGroupMatchers( elementMatchers, setMatchers ) );\n\n\t\t// Save selector and tokenization\n\t\tcached.selector = selector;\n\t}\n\treturn cached;\n};\n\n/**\n * A low-level selection function that works with Sizzle's compiled\n * selector functions\n * @param {String|Function} selector A selector or a pre-compiled\n * selector function built with Sizzle.compile\n * @param {Element} context\n * @param {Array} [results]\n * @param {Array} [seed] A set of elements to match against\n */\nselect = Sizzle.select = function( selector, context, results, seed ) {\n\tvar i, tokens, token, type, find,\n\t\tcompiled = typeof selector === \"function\" && selector,\n\t\tmatch = !seed && tokenize( (selector = compiled.selector || selector) );\n\n\tresults = results || [];\n\n\t// Try to minimize operations if there is only one selector in the list and no seed\n\t// (the latter of which guarantees us context)\n\tif ( match.length === 1 ) {\n\n\t\t// Reduce context if the leading compound selector is an ID\n\t\ttokens = match[0] = match[0].slice( 0 );\n\t\tif ( tokens.length > 2 && (token = tokens[0]).type === \"ID\" &&\n\t\t\t\tsupport.getById && context.nodeType === 9 && documentIsHTML &&\n\t\t\t\tExpr.relative[ tokens[1].type ] ) {\n\n\t\t\tcontext = ( Expr.find[\"ID\"]( token.matches[0].replace(runescape, funescape), context ) || [] )[0];\n\t\t\tif ( !context ) {\n\t\t\t\treturn results;\n\n\t\t\t// Precompiled matchers will still verify ancestry, so step up a level\n\t\t\t} else if ( compiled ) {\n\t\t\t\tcontext = context.parentNode;\n\t\t\t}\n\n\t\t\tselector = selector.slice( tokens.shift().value.length );\n\t\t}\n\n\t\t// Fetch a seed set for right-to-left matching\n\t\ti = matchExpr[\"needsContext\"].test( selector ) ? 0 : tokens.length;\n\t\twhile ( i-- ) {\n\t\t\ttoken = tokens[i];\n\n\t\t\t// Abort if we hit a combinator\n\t\t\tif ( Expr.relative[ (type = token.type) ] ) {\n\t\t\t\tbreak;\n\t\t\t}\n\t\t\tif ( (find = Expr.find[ type ]) ) {\n\t\t\t\t// Search, expanding context for leading sibling combinators\n\t\t\t\tif ( (seed = find(\n\t\t\t\t\ttoken.matches[0].replace( runescape, funescape ),\n\t\t\t\t\trsibling.test( tokens[0].type ) && testContext( context.parentNode ) || context\n\t\t\t\t)) ) {\n\n\t\t\t\t\t// If seed is empty or no tokens remain, we can return early\n\t\t\t\t\ttokens.splice( i, 1 );\n\t\t\t\t\tselector = seed.length && toSelector( tokens );\n\t\t\t\t\tif ( !selector ) {\n\t\t\t\t\t\tpush.apply( results, seed );\n\t\t\t\t\t\treturn results;\n\t\t\t\t\t}\n\n\t\t\t\t\tbreak;\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\t// Compile and execute a filtering function if one is not provided\n\t// Provide `match` to avoid retokenization if we modified the selector above\n\t( compiled || compile( selector, match ) )(\n\t\tseed,\n\t\tcontext,\n\t\t!documentIsHTML,\n\t\tresults,\n\t\t!context || rsibling.test( selector ) && testContext( context.parentNode ) || context\n\t);\n\treturn results;\n};\n\n// One-time assignments\n\n// Sort stability\nsupport.sortStable = expando.split(\"\").sort( sortOrder ).join(\"\") === expando;\n\n// Support: Chrome 14-35+\n// Always assume duplicates if they aren't passed to the comparison function\nsupport.detectDuplicates = !!hasDuplicate;\n\n// Initialize against the default document\nsetDocument();\n\n// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27)\n// Detached nodes confoundingly follow *each other*\nsupport.sortDetached = assert(function( div1 ) {\n\t// Should return 1, but returns 4 (following)\n\treturn div1.compareDocumentPosition( document.createElement(\"div\") ) & 1;\n});\n\n// Support: IE<8\n// Prevent attribute/property \"interpolation\"\n// http://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx\nif ( !assert(function( div ) {\n\tdiv.innerHTML = \"\";\n\treturn div.firstChild.getAttribute(\"href\") === \"#\" ;\n}) ) {\n\taddHandle( \"type|href|height|width\", function( elem, name, isXML ) {\n\t\tif ( !isXML ) {\n\t\t\treturn elem.getAttribute( name, name.toLowerCase() === \"type\" ? 1 : 2 );\n\t\t}\n\t});\n}\n\n// Support: IE<9\n// Use defaultValue in place of getAttribute(\"value\")\nif ( !support.attributes || !assert(function( div ) {\n\tdiv.innerHTML = \"\";\n\tdiv.firstChild.setAttribute( \"value\", \"\" );\n\treturn div.firstChild.getAttribute( \"value\" ) === \"\";\n}) ) {\n\taddHandle( \"value\", function( elem, name, isXML ) {\n\t\tif ( !isXML && elem.nodeName.toLowerCase() === \"input\" ) {\n\t\t\treturn elem.defaultValue;\n\t\t}\n\t});\n}\n\n// Support: IE<9\n// Use getAttributeNode to fetch booleans when getAttribute lies\nif ( !assert(function( div ) {\n\treturn div.getAttribute(\"disabled\") == null;\n}) ) {\n\taddHandle( booleans, function( elem, name, isXML ) {\n\t\tvar val;\n\t\tif ( !isXML ) {\n\t\t\treturn elem[ name ] === true ? name.toLowerCase() :\n\t\t\t\t\t(val = elem.getAttributeNode( name )) && val.specified ?\n\t\t\t\t\tval.value :\n\t\t\t\tnull;\n\t\t}\n\t});\n}\n\nreturn Sizzle;\n\n})( window );\n\n\n\njQuery.find = Sizzle;\njQuery.expr = Sizzle.selectors;\njQuery.expr[ \":\" ] = jQuery.expr.pseudos;\njQuery.uniqueSort = jQuery.unique = Sizzle.uniqueSort;\njQuery.text = Sizzle.getText;\njQuery.isXMLDoc = Sizzle.isXML;\njQuery.contains = Sizzle.contains;\n\n\n\nvar dir = function( elem, dir, until ) {\n\tvar matched = [],\n\t\ttruncate = until !== undefined;\n\n\twhile ( ( elem = elem[ dir ] ) && elem.nodeType !== 9 ) {\n\t\tif ( elem.nodeType === 1 ) {\n\t\t\tif ( truncate && jQuery( elem ).is( until ) ) {\n\t\t\t\tbreak;\n\t\t\t}\n\t\t\tmatched.push( elem );\n\t\t}\n\t}\n\treturn matched;\n};\n\n\nvar siblings = function( n, elem ) {\n\tvar matched = [];\n\n\tfor ( ; n; n = n.nextSibling ) {\n\t\tif ( n.nodeType === 1 && n !== elem ) {\n\t\t\tmatched.push( n );\n\t\t}\n\t}\n\n\treturn matched;\n};\n\n\nvar rneedsContext = jQuery.expr.match.needsContext;\n\nvar rsingleTag = ( /^<([\\w-]+)\\s*\\/?>(?:<\\/\\1>|)$/ );\n\n\n\nvar risSimple = /^.[^:#\\[\\.,]*$/;\n\n// Implement the identical functionality for filter and not\nfunction winnow( elements, qualifier, not ) {\n\tif ( jQuery.isFunction( qualifier ) ) {\n\t\treturn jQuery.grep( elements, function( elem, i ) {\n\t\t\t/* jshint -W018 */\n\t\t\treturn !!qualifier.call( elem, i, elem ) !== not;\n\t\t} );\n\n\t}\n\n\tif ( qualifier.nodeType ) {\n\t\treturn jQuery.grep( elements, function( elem ) {\n\t\t\treturn ( elem === qualifier ) !== not;\n\t\t} );\n\n\t}\n\n\tif ( typeof qualifier === \"string\" ) {\n\t\tif ( risSimple.test( qualifier ) ) {\n\t\t\treturn jQuery.filter( qualifier, elements, not );\n\t\t}\n\n\t\tqualifier = jQuery.filter( qualifier, elements );\n\t}\n\n\treturn jQuery.grep( elements, function( elem ) {\n\t\treturn ( indexOf.call( qualifier, elem ) > -1 ) !== not;\n\t} );\n}\n\njQuery.filter = function( expr, elems, not ) {\n\tvar elem = elems[ 0 ];\n\n\tif ( not ) {\n\t\texpr = \":not(\" + expr + \")\";\n\t}\n\n\treturn elems.length === 1 && elem.nodeType === 1 ?\n\t\tjQuery.find.matchesSelector( elem, expr ) ? [ elem ] : [] :\n\t\tjQuery.find.matches( expr, jQuery.grep( elems, function( elem ) {\n\t\t\treturn elem.nodeType === 1;\n\t\t} ) );\n};\n\njQuery.fn.extend( {\n\tfind: function( selector ) {\n\t\tvar i,\n\t\t\tlen = this.length,\n\t\t\tret = [],\n\t\t\tself = this;\n\n\t\tif ( typeof selector !== \"string\" ) {\n\t\t\treturn this.pushStack( jQuery( selector ).filter( function() {\n\t\t\t\tfor ( i = 0; i < len; i++ ) {\n\t\t\t\t\tif ( jQuery.contains( self[ i ], this ) ) {\n\t\t\t\t\t\treturn true;\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} ) );\n\t\t}\n\n\t\tfor ( i = 0; i < len; i++ ) {\n\t\t\tjQuery.find( selector, self[ i ], ret );\n\t\t}\n\n\t\t// Needed because $( selector, context ) becomes $( context ).find( selector )\n\t\tret = this.pushStack( len > 1 ? jQuery.unique( ret ) : ret );\n\t\tret.selector = this.selector ? this.selector + \" \" + selector : selector;\n\t\treturn ret;\n\t},\n\tfilter: function( selector ) {\n\t\treturn this.pushStack( winnow( this, selector || [], false ) );\n\t},\n\tnot: function( selector ) {\n\t\treturn this.pushStack( winnow( this, selector || [], true ) );\n\t},\n\tis: function( selector ) {\n\t\treturn !!winnow(\n\t\t\tthis,\n\n\t\t\t// If this is a positional/relative selector, check membership in the returned set\n\t\t\t// so $(\"p:first\").is(\"p:last\") won't return true for a doc with two \"p\".\n\t\t\ttypeof selector === \"string\" && rneedsContext.test( selector ) ?\n\t\t\t\tjQuery( selector ) :\n\t\t\t\tselector || [],\n\t\t\tfalse\n\t\t).length;\n\t}\n} );\n\n\n// Initialize a jQuery object\n\n\n// A central reference to the root jQuery(document)\nvar rootjQuery,\n\n\t// A simple way to check for HTML strings\n\t// Prioritize #id over to avoid XSS via location.hash (#9521)\n\t// Strict HTML recognition (#11290: must start with <)\n\trquickExpr = /^(?:\\s*(<[\\w\\W]+>)[^>]*|#([\\w-]*))$/,\n\n\tinit = jQuery.fn.init = function( selector, context, root ) {\n\t\tvar match, elem;\n\n\t\t// HANDLE: $(\"\"), $(null), $(undefined), $(false)\n\t\tif ( !selector ) {\n\t\t\treturn this;\n\t\t}\n\n\t\t// Method init() accepts an alternate rootjQuery\n\t\t// so migrate can support jQuery.sub (gh-2101)\n\t\troot = root || rootjQuery;\n\n\t\t// Handle HTML strings\n\t\tif ( typeof selector === \"string\" ) {\n\t\t\tif ( selector[ 0 ] === \"<\" &&\n\t\t\t\tselector[ selector.length - 1 ] === \">\" &&\n\t\t\t\tselector.length >= 3 ) {\n\n\t\t\t\t// Assume that strings that start and end with <> are HTML and skip the regex check\n\t\t\t\tmatch = [ null, selector, null ];\n\n\t\t\t} else {\n\t\t\t\tmatch = rquickExpr.exec( selector );\n\t\t\t}\n\n\t\t\t// Match html or make sure no context is specified for #id\n\t\t\tif ( match && ( match[ 1 ] || !context ) ) {\n\n\t\t\t\t// HANDLE: $(html) -> $(array)\n\t\t\t\tif ( match[ 1 ] ) {\n\t\t\t\t\tcontext = context instanceof jQuery ? context[ 0 ] : context;\n\n\t\t\t\t\t// Option to run scripts is true for back-compat\n\t\t\t\t\t// Intentionally let the error be thrown if parseHTML is not present\n\t\t\t\t\tjQuery.merge( this, jQuery.parseHTML(\n\t\t\t\t\t\tmatch[ 1 ],\n\t\t\t\t\t\tcontext && context.nodeType ? context.ownerDocument || context : document,\n\t\t\t\t\t\ttrue\n\t\t\t\t\t) );\n\n\t\t\t\t\t// HANDLE: $(html, props)\n\t\t\t\t\tif ( rsingleTag.test( match[ 1 ] ) && jQuery.isPlainObject( context ) ) {\n\t\t\t\t\t\tfor ( match in context ) {\n\n\t\t\t\t\t\t\t// Properties of context are called as methods if possible\n\t\t\t\t\t\t\tif ( jQuery.isFunction( this[ match ] ) ) {\n\t\t\t\t\t\t\t\tthis[ match ]( context[ match ] );\n\n\t\t\t\t\t\t\t// ...and otherwise set as attributes\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tthis.attr( match, context[ match ] );\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\n\t\t\t\t\treturn this;\n\n\t\t\t\t// HANDLE: $(#id)\n\t\t\t\t} else {\n\t\t\t\t\telem = document.getElementById( match[ 2 ] );\n\n\t\t\t\t\t// Support: Blackberry 4.6\n\t\t\t\t\t// gEBID returns nodes no longer in the document (#6963)\n\t\t\t\t\tif ( elem && elem.parentNode ) {\n\n\t\t\t\t\t\t// Inject the element directly into the jQuery object\n\t\t\t\t\t\tthis.length = 1;\n\t\t\t\t\t\tthis[ 0 ] = elem;\n\t\t\t\t\t}\n\n\t\t\t\t\tthis.context = document;\n\t\t\t\t\tthis.selector = selector;\n\t\t\t\t\treturn this;\n\t\t\t\t}\n\n\t\t\t// HANDLE: $(expr, $(...))\n\t\t\t} else if ( !context || context.jquery ) {\n\t\t\t\treturn ( context || root ).find( selector );\n\n\t\t\t// HANDLE: $(expr, context)\n\t\t\t// (which is just equivalent to: $(context).find(expr)\n\t\t\t} else {\n\t\t\t\treturn this.constructor( context ).find( selector );\n\t\t\t}\n\n\t\t// HANDLE: $(DOMElement)\n\t\t} else if ( selector.nodeType ) {\n\t\t\tthis.context = this[ 0 ] = selector;\n\t\t\tthis.length = 1;\n\t\t\treturn this;\n\n\t\t// HANDLE: $(function)\n\t\t// Shortcut for document ready\n\t\t} else if ( jQuery.isFunction( selector ) ) {\n\t\t\treturn root.ready !== undefined ?\n\t\t\t\troot.ready( selector ) :\n\n\t\t\t\t// Execute immediately if ready is not present\n\t\t\t\tselector( jQuery );\n\t\t}\n\n\t\tif ( selector.selector !== undefined ) {\n\t\t\tthis.selector = selector.selector;\n\t\t\tthis.context = selector.context;\n\t\t}\n\n\t\treturn jQuery.makeArray( selector, this );\n\t};\n\n// Give the init function the jQuery prototype for later instantiation\ninit.prototype = jQuery.fn;\n\n// Initialize central reference\nrootjQuery = jQuery( document );\n\n\nvar rparentsprev = /^(?:parents|prev(?:Until|All))/,\n\n\t// Methods guaranteed to produce a unique set when starting from a unique set\n\tguaranteedUnique = {\n\t\tchildren: true,\n\t\tcontents: true,\n\t\tnext: true,\n\t\tprev: true\n\t};\n\njQuery.fn.extend( {\n\thas: function( target ) {\n\t\tvar targets = jQuery( target, this ),\n\t\t\tl = targets.length;\n\n\t\treturn this.filter( function() {\n\t\t\tvar i = 0;\n\t\t\tfor ( ; i < l; i++ ) {\n\t\t\t\tif ( jQuery.contains( this, targets[ i ] ) ) {\n\t\t\t\t\treturn true;\n\t\t\t\t}\n\t\t\t}\n\t\t} );\n\t},\n\n\tclosest: function( selectors, context ) {\n\t\tvar cur,\n\t\t\ti = 0,\n\t\t\tl = this.length,\n\t\t\tmatched = [],\n\t\t\tpos = rneedsContext.test( selectors ) || typeof selectors !== \"string\" ?\n\t\t\t\tjQuery( selectors, context || this.context ) :\n\t\t\t\t0;\n\n\t\tfor ( ; i < l; i++ ) {\n\t\t\tfor ( cur = this[ i ]; cur && cur !== context; cur = cur.parentNode ) {\n\n\t\t\t\t// Always skip document fragments\n\t\t\t\tif ( cur.nodeType < 11 && ( pos ?\n\t\t\t\t\tpos.index( cur ) > -1 :\n\n\t\t\t\t\t// Don't pass non-elements to Sizzle\n\t\t\t\t\tcur.nodeType === 1 &&\n\t\t\t\t\t\tjQuery.find.matchesSelector( cur, selectors ) ) ) {\n\n\t\t\t\t\tmatched.push( cur );\n\t\t\t\t\tbreak;\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\treturn this.pushStack( matched.length > 1 ? jQuery.uniqueSort( matched ) : matched );\n\t},\n\n\t// Determine the position of an element within the set\n\tindex: function( elem ) {\n\n\t\t// No argument, return index in parent\n\t\tif ( !elem ) {\n\t\t\treturn ( this[ 0 ] && this[ 0 ].parentNode ) ? this.first().prevAll().length : -1;\n\t\t}\n\n\t\t// Index in selector\n\t\tif ( typeof elem === \"string\" ) {\n\t\t\treturn indexOf.call( jQuery( elem ), this[ 0 ] );\n\t\t}\n\n\t\t// Locate the position of the desired element\n\t\treturn indexOf.call( this,\n\n\t\t\t// If it receives a jQuery object, the first element is used\n\t\t\telem.jquery ? elem[ 0 ] : elem\n\t\t);\n\t},\n\n\tadd: function( selector, context ) {\n\t\treturn this.pushStack(\n\t\t\tjQuery.uniqueSort(\n\t\t\t\tjQuery.merge( this.get(), jQuery( selector, context ) )\n\t\t\t)\n\t\t);\n\t},\n\n\taddBack: function( selector ) {\n\t\treturn this.add( selector == null ?\n\t\t\tthis.prevObject : this.prevObject.filter( selector )\n\t\t);\n\t}\n} );\n\nfunction sibling( cur, dir ) {\n\twhile ( ( cur = cur[ dir ] ) && cur.nodeType !== 1 ) {}\n\treturn cur;\n}\n\njQuery.each( {\n\tparent: function( elem ) {\n\t\tvar parent = elem.parentNode;\n\t\treturn parent && parent.nodeType !== 11 ? parent : null;\n\t},\n\tparents: function( elem ) {\n\t\treturn dir( elem, \"parentNode\" );\n\t},\n\tparentsUntil: function( elem, i, until ) {\n\t\treturn dir( elem, \"parentNode\", until );\n\t},\n\tnext: function( elem ) {\n\t\treturn sibling( elem, \"nextSibling\" );\n\t},\n\tprev: function( elem ) {\n\t\treturn sibling( elem, \"previousSibling\" );\n\t},\n\tnextAll: function( elem ) {\n\t\treturn dir( elem, \"nextSibling\" );\n\t},\n\tprevAll: function( elem ) {\n\t\treturn dir( elem, \"previousSibling\" );\n\t},\n\tnextUntil: function( elem, i, until ) {\n\t\treturn dir( elem, \"nextSibling\", until );\n\t},\n\tprevUntil: function( elem, i, until ) {\n\t\treturn dir( elem, \"previousSibling\", until );\n\t},\n\tsiblings: function( elem ) {\n\t\treturn siblings( ( elem.parentNode || {} ).firstChild, elem );\n\t},\n\tchildren: function( elem ) {\n\t\treturn siblings( elem.firstChild );\n\t},\n\tcontents: function( elem ) {\n\t\treturn elem.contentDocument || jQuery.merge( [], elem.childNodes );\n\t}\n}, function( name, fn ) {\n\tjQuery.fn[ name ] = function( until, selector ) {\n\t\tvar matched = jQuery.map( this, fn, until );\n\n\t\tif ( name.slice( -5 ) !== \"Until\" ) {\n\t\t\tselector = until;\n\t\t}\n\n\t\tif ( selector && typeof selector === \"string\" ) {\n\t\t\tmatched = jQuery.filter( selector, matched );\n\t\t}\n\n\t\tif ( this.length > 1 ) {\n\n\t\t\t// Remove duplicates\n\t\t\tif ( !guaranteedUnique[ name ] ) {\n\t\t\t\tjQuery.uniqueSort( matched );\n\t\t\t}\n\n\t\t\t// Reverse order for parents* and prev-derivatives\n\t\t\tif ( rparentsprev.test( name ) ) {\n\t\t\t\tmatched.reverse();\n\t\t\t}\n\t\t}\n\n\t\treturn this.pushStack( matched );\n\t};\n} );\nvar rnotwhite = ( /\\S+/g );\n\n\n\n// Convert String-formatted options into Object-formatted ones\nfunction createOptions( options ) {\n\tvar object = {};\n\tjQuery.each( options.match( rnotwhite ) || [], function( _, flag ) {\n\t\tobject[ flag ] = true;\n\t} );\n\treturn object;\n}\n\n/*\n * Create a callback list using the following parameters:\n *\n *\toptions: an optional list of space-separated options that will change how\n *\t\t\tthe callback list behaves or a more traditional option object\n *\n * By default a callback list will act like an event callback list and can be\n * \"fired\" multiple times.\n *\n * Possible options:\n *\n *\tonce:\t\t\twill ensure the callback list can only be fired once (like a Deferred)\n *\n *\tmemory:\t\t\twill keep track of previous values and will call any callback added\n *\t\t\t\t\tafter the list has been fired right away with the latest \"memorized\"\n *\t\t\t\t\tvalues (like a Deferred)\n *\n *\tunique:\t\t\twill ensure a callback can only be added once (no duplicate in the list)\n *\n *\tstopOnFalse:\tinterrupt callings when a callback returns false\n *\n */\njQuery.Callbacks = function( options ) {\n\n\t// Convert options from String-formatted to Object-formatted if needed\n\t// (we check in cache first)\n\toptions = typeof options === \"string\" ?\n\t\tcreateOptions( options ) :\n\t\tjQuery.extend( {}, options );\n\n\tvar // Flag to know if list is currently firing\n\t\tfiring,\n\n\t\t// Last fire value for non-forgettable lists\n\t\tmemory,\n\n\t\t// Flag to know if list was already fired\n\t\tfired,\n\n\t\t// Flag to prevent firing\n\t\tlocked,\n\n\t\t// Actual callback list\n\t\tlist = [],\n\n\t\t// Queue of execution data for repeatable lists\n\t\tqueue = [],\n\n\t\t// Index of currently firing callback (modified by add/remove as needed)\n\t\tfiringIndex = -1,\n\n\t\t// Fire callbacks\n\t\tfire = function() {\n\n\t\t\t// Enforce single-firing\n\t\t\tlocked = options.once;\n\n\t\t\t// Execute callbacks for all pending executions,\n\t\t\t// respecting firingIndex overrides and runtime changes\n\t\t\tfired = firing = true;\n\t\t\tfor ( ; queue.length; firingIndex = -1 ) {\n\t\t\t\tmemory = queue.shift();\n\t\t\t\twhile ( ++firingIndex < list.length ) {\n\n\t\t\t\t\t// Run callback and check for early termination\n\t\t\t\t\tif ( list[ firingIndex ].apply( memory[ 0 ], memory[ 1 ] ) === false &&\n\t\t\t\t\t\toptions.stopOnFalse ) {\n\n\t\t\t\t\t\t// Jump to end and forget the data so .add doesn't re-fire\n\t\t\t\t\t\tfiringIndex = list.length;\n\t\t\t\t\t\tmemory = false;\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// Forget the data if we're done with it\n\t\t\tif ( !options.memory ) {\n\t\t\t\tmemory = false;\n\t\t\t}\n\n\t\t\tfiring = false;\n\n\t\t\t// Clean up if we're done firing for good\n\t\t\tif ( locked ) {\n\n\t\t\t\t// Keep an empty list if we have data for future add calls\n\t\t\t\tif ( memory ) {\n\t\t\t\t\tlist = [];\n\n\t\t\t\t// Otherwise, this object is spent\n\t\t\t\t} else {\n\t\t\t\t\tlist = \"\";\n\t\t\t\t}\n\t\t\t}\n\t\t},\n\n\t\t// Actual Callbacks object\n\t\tself = {\n\n\t\t\t// Add a callback or a collection of callbacks to the list\n\t\t\tadd: function() {\n\t\t\t\tif ( list ) {\n\n\t\t\t\t\t// If we have memory from a past run, we should fire after adding\n\t\t\t\t\tif ( memory && !firing ) {\n\t\t\t\t\t\tfiringIndex = list.length - 1;\n\t\t\t\t\t\tqueue.push( memory );\n\t\t\t\t\t}\n\n\t\t\t\t\t( function add( args ) {\n\t\t\t\t\t\tjQuery.each( args, function( _, arg ) {\n\t\t\t\t\t\t\tif ( jQuery.isFunction( arg ) ) {\n\t\t\t\t\t\t\t\tif ( !options.unique || !self.has( arg ) ) {\n\t\t\t\t\t\t\t\t\tlist.push( arg );\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t} else if ( arg && arg.length && jQuery.type( arg ) !== \"string\" ) {\n\n\t\t\t\t\t\t\t\t// Inspect recursively\n\t\t\t\t\t\t\t\tadd( arg );\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t} );\n\t\t\t\t\t} )( arguments );\n\n\t\t\t\t\tif ( memory && !firing ) {\n\t\t\t\t\t\tfire();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\treturn this;\n\t\t\t},\n\n\t\t\t// Remove a callback from the list\n\t\t\tremove: function() {\n\t\t\t\tjQuery.each( arguments, function( _, arg ) {\n\t\t\t\t\tvar index;\n\t\t\t\t\twhile ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) {\n\t\t\t\t\t\tlist.splice( index, 1 );\n\n\t\t\t\t\t\t// Handle firing indexes\n\t\t\t\t\t\tif ( index <= firingIndex ) {\n\t\t\t\t\t\t\tfiringIndex--;\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t} );\n\t\t\t\treturn this;\n\t\t\t},\n\n\t\t\t// Check if a given callback is in the list.\n\t\t\t// If no argument is given, return whether or not list has callbacks attached.\n\t\t\thas: function( fn ) {\n\t\t\t\treturn fn ?\n\t\t\t\t\tjQuery.inArray( fn, list ) > -1 :\n\t\t\t\t\tlist.length > 0;\n\t\t\t},\n\n\t\t\t// Remove all callbacks from the list\n\t\t\tempty: function() {\n\t\t\t\tif ( list ) {\n\t\t\t\t\tlist = [];\n\t\t\t\t}\n\t\t\t\treturn this;\n\t\t\t},\n\n\t\t\t// Disable .fire and .add\n\t\t\t// Abort any current/pending executions\n\t\t\t// Clear all callbacks and values\n\t\t\tdisable: function() {\n\t\t\t\tlocked = queue = [];\n\t\t\t\tlist = memory = \"\";\n\t\t\t\treturn this;\n\t\t\t},\n\t\t\tdisabled: function() {\n\t\t\t\treturn !list;\n\t\t\t},\n\n\t\t\t// Disable .fire\n\t\t\t// Also disable .add unless we have memory (since it would have no effect)\n\t\t\t// Abort any pending executions\n\t\t\tlock: function() {\n\t\t\t\tlocked = queue = [];\n\t\t\t\tif ( !memory ) {\n\t\t\t\t\tlist = memory = \"\";\n\t\t\t\t}\n\t\t\t\treturn this;\n\t\t\t},\n\t\t\tlocked: function() {\n\t\t\t\treturn !!locked;\n\t\t\t},\n\n\t\t\t// Call all callbacks with the given context and arguments\n\t\t\tfireWith: function( context, args ) {\n\t\t\t\tif ( !locked ) {\n\t\t\t\t\targs = args || [];\n\t\t\t\t\targs = [ context, args.slice ? args.slice() : args ];\n\t\t\t\t\tqueue.push( args );\n\t\t\t\t\tif ( !firing ) {\n\t\t\t\t\t\tfire();\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\treturn this;\n\t\t\t},\n\n\t\t\t// Call all the callbacks with the given arguments\n\t\t\tfire: function() {\n\t\t\t\tself.fireWith( this, arguments );\n\t\t\t\treturn this;\n\t\t\t},\n\n\t\t\t// To know if the callbacks have already been called at least once\n\t\t\tfired: function() {\n\t\t\t\treturn !!fired;\n\t\t\t}\n\t\t};\n\n\treturn self;\n};\n\n\njQuery.extend( {\n\n\tDeferred: function( func ) {\n\t\tvar tuples = [\n\n\t\t\t\t// action, add listener, listener list, final state\n\t\t\t\t[ \"resolve\", \"done\", jQuery.Callbacks( \"once memory\" ), \"resolved\" ],\n\t\t\t\t[ \"reject\", \"fail\", jQuery.Callbacks( \"once memory\" ), \"rejected\" ],\n\t\t\t\t[ \"notify\", \"progress\", jQuery.Callbacks( \"memory\" ) ]\n\t\t\t],\n\t\t\tstate = \"pending\",\n\t\t\tpromise = {\n\t\t\t\tstate: function() {\n\t\t\t\t\treturn state;\n\t\t\t\t},\n\t\t\t\talways: function() {\n\t\t\t\t\tdeferred.done( arguments ).fail( arguments );\n\t\t\t\t\treturn this;\n\t\t\t\t},\n\t\t\t\tthen: function( /* fnDone, fnFail, fnProgress */ ) {\n\t\t\t\t\tvar fns = arguments;\n\t\t\t\t\treturn jQuery.Deferred( function( newDefer ) {\n\t\t\t\t\t\tjQuery.each( tuples, function( i, tuple ) {\n\t\t\t\t\t\t\tvar fn = jQuery.isFunction( fns[ i ] ) && fns[ i ];\n\n\t\t\t\t\t\t\t// deferred[ done | fail | progress ] for forwarding actions to newDefer\n\t\t\t\t\t\t\tdeferred[ tuple[ 1 ] ]( function() {\n\t\t\t\t\t\t\t\tvar returned = fn && fn.apply( this, arguments );\n\t\t\t\t\t\t\t\tif ( returned && jQuery.isFunction( returned.promise ) ) {\n\t\t\t\t\t\t\t\t\treturned.promise()\n\t\t\t\t\t\t\t\t\t\t.progress( newDefer.notify )\n\t\t\t\t\t\t\t\t\t\t.done( newDefer.resolve )\n\t\t\t\t\t\t\t\t\t\t.fail( newDefer.reject );\n\t\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\t\tnewDefer[ tuple[ 0 ] + \"With\" ](\n\t\t\t\t\t\t\t\t\t\tthis === promise ? newDefer.promise() : this,\n\t\t\t\t\t\t\t\t\t\tfn ? [ returned ] : arguments\n\t\t\t\t\t\t\t\t\t);\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t} );\n\t\t\t\t\t\t} );\n\t\t\t\t\t\tfns = null;\n\t\t\t\t\t} ).promise();\n\t\t\t\t},\n\n\t\t\t\t// Get a promise for this deferred\n\t\t\t\t// If obj is provided, the promise aspect is added to the object\n\t\t\t\tpromise: function( obj ) {\n\t\t\t\t\treturn obj != null ? jQuery.extend( obj, promise ) : promise;\n\t\t\t\t}\n\t\t\t},\n\t\t\tdeferred = {};\n\n\t\t// Keep pipe for back-compat\n\t\tpromise.pipe = promise.then;\n\n\t\t// Add list-specific methods\n\t\tjQuery.each( tuples, function( i, tuple ) {\n\t\t\tvar list = tuple[ 2 ],\n\t\t\t\tstateString = tuple[ 3 ];\n\n\t\t\t// promise[ done | fail | progress ] = list.add\n\t\t\tpromise[ tuple[ 1 ] ] = list.add;\n\n\t\t\t// Handle state\n\t\t\tif ( stateString ) {\n\t\t\t\tlist.add( function() {\n\n\t\t\t\t\t// state = [ resolved | rejected ]\n\t\t\t\t\tstate = stateString;\n\n\t\t\t\t// [ reject_list | resolve_list ].disable; progress_list.lock\n\t\t\t\t}, tuples[ i ^ 1 ][ 2 ].disable, tuples[ 2 ][ 2 ].lock );\n\t\t\t}\n\n\t\t\t// deferred[ resolve | reject | notify ]\n\t\t\tdeferred[ tuple[ 0 ] ] = function() {\n\t\t\t\tdeferred[ tuple[ 0 ] + \"With\" ]( this === deferred ? promise : this, arguments );\n\t\t\t\treturn this;\n\t\t\t};\n\t\t\tdeferred[ tuple[ 0 ] + \"With\" ] = list.fireWith;\n\t\t} );\n\n\t\t// Make the deferred a promise\n\t\tpromise.promise( deferred );\n\n\t\t// Call given func if any\n\t\tif ( func ) {\n\t\t\tfunc.call( deferred, deferred );\n\t\t}\n\n\t\t// All done!\n\t\treturn deferred;\n\t},\n\n\t// Deferred helper\n\twhen: function( subordinate /* , ..., subordinateN */ ) {\n\t\tvar i = 0,\n\t\t\tresolveValues = slice.call( arguments ),\n\t\t\tlength = resolveValues.length,\n\n\t\t\t// the count of uncompleted subordinates\n\t\t\tremaining = length !== 1 ||\n\t\t\t\t( subordinate && jQuery.isFunction( subordinate.promise ) ) ? length : 0,\n\n\t\t\t// the master Deferred.\n\t\t\t// If resolveValues consist of only a single Deferred, just use that.\n\t\t\tdeferred = remaining === 1 ? subordinate : jQuery.Deferred(),\n\n\t\t\t// Update function for both resolve and progress values\n\t\t\tupdateFunc = function( i, contexts, values ) {\n\t\t\t\treturn function( value ) {\n\t\t\t\t\tcontexts[ i ] = this;\n\t\t\t\t\tvalues[ i ] = arguments.length > 1 ? slice.call( arguments ) : value;\n\t\t\t\t\tif ( values === progressValues ) {\n\t\t\t\t\t\tdeferred.notifyWith( contexts, values );\n\t\t\t\t\t} else if ( !( --remaining ) ) {\n\t\t\t\t\t\tdeferred.resolveWith( contexts, values );\n\t\t\t\t\t}\n\t\t\t\t};\n\t\t\t},\n\n\t\t\tprogressValues, progressContexts, resolveContexts;\n\n\t\t// Add listeners to Deferred subordinates; treat others as resolved\n\t\tif ( length > 1 ) {\n\t\t\tprogressValues = new Array( length );\n\t\t\tprogressContexts = new Array( length );\n\t\t\tresolveContexts = new Array( length );\n\t\t\tfor ( ; i < length; i++ ) {\n\t\t\t\tif ( resolveValues[ i ] && jQuery.isFunction( resolveValues[ i ].promise ) ) {\n\t\t\t\t\tresolveValues[ i ].promise()\n\t\t\t\t\t\t.progress( updateFunc( i, progressContexts, progressValues ) )\n\t\t\t\t\t\t.done( updateFunc( i, resolveContexts, resolveValues ) )\n\t\t\t\t\t\t.fail( deferred.reject );\n\t\t\t\t} else {\n\t\t\t\t\t--remaining;\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\t// If we're not waiting on anything, resolve the master\n\t\tif ( !remaining ) {\n\t\t\tdeferred.resolveWith( resolveContexts, resolveValues );\n\t\t}\n\n\t\treturn deferred.promise();\n\t}\n} );\n\n\n// The deferred used on DOM ready\nvar readyList;\n\njQuery.fn.ready = function( fn ) {\n\n\t// Add the callback\n\tjQuery.ready.promise().done( fn );\n\n\treturn this;\n};\n\njQuery.extend( {\n\n\t// Is the DOM ready to be used? Set to true once it occurs.\n\tisReady: false,\n\n\t// A counter to track how many items to wait for before\n\t// the ready event fires. See #6781\n\treadyWait: 1,\n\n\t// Hold (or release) the ready event\n\tholdReady: function( hold ) {\n\t\tif ( hold ) {\n\t\t\tjQuery.readyWait++;\n\t\t} else {\n\t\t\tjQuery.ready( true );\n\t\t}\n\t},\n\n\t// Handle when the DOM is ready\n\tready: function( wait ) {\n\n\t\t// Abort if there are pending holds or we're already ready\n\t\tif ( wait === true ? --jQuery.readyWait : jQuery.isReady ) {\n\t\t\treturn;\n\t\t}\n\n\t\t// Remember that the DOM is ready\n\t\tjQuery.isReady = true;\n\n\t\t// If a normal DOM Ready event fired, decrement, and wait if need be\n\t\tif ( wait !== true && --jQuery.readyWait > 0 ) {\n\t\t\treturn;\n\t\t}\n\n\t\t// If there are functions bound, to execute\n\t\treadyList.resolveWith( document, [ jQuery ] );\n\n\t\t// Trigger any bound ready events\n\t\tif ( jQuery.fn.triggerHandler ) {\n\t\t\tjQuery( document ).triggerHandler( \"ready\" );\n\t\t\tjQuery( document ).off( \"ready\" );\n\t\t}\n\t}\n} );\n\n/**\n * The ready event handler and self cleanup method\n */\nfunction completed() {\n\tdocument.removeEventListener( \"DOMContentLoaded\", completed );\n\twindow.removeEventListener( \"load\", completed );\n\tjQuery.ready();\n}\n\njQuery.ready.promise = function( obj ) {\n\tif ( !readyList ) {\n\n\t\treadyList = jQuery.Deferred();\n\n\t\t// Catch cases where $(document).ready() is called\n\t\t// after the browser event has already occurred.\n\t\t// Support: IE9-10 only\n\t\t// Older IE sometimes signals \"interactive\" too soon\n\t\tif ( document.readyState === \"complete\" ||\n\t\t\t( document.readyState !== \"loading\" && !document.documentElement.doScroll ) ) {\n\n\t\t\t// Handle it asynchronously to allow scripts the opportunity to delay ready\n\t\t\twindow.setTimeout( jQuery.ready );\n\n\t\t} else {\n\n\t\t\t// Use the handy event callback\n\t\t\tdocument.addEventListener( \"DOMContentLoaded\", completed );\n\n\t\t\t// A fallback to window.onload, that will always work\n\t\t\twindow.addEventListener( \"load\", completed );\n\t\t}\n\t}\n\treturn readyList.promise( obj );\n};\n\n// Kick off the DOM ready check even if the user does not\njQuery.ready.promise();\n\n\n\n\n// Multifunctional method to get and set values of a collection\n// The value/s can optionally be executed if it's a function\nvar access = function( elems, fn, key, value, chainable, emptyGet, raw ) {\n\tvar i = 0,\n\t\tlen = elems.length,\n\t\tbulk = key == null;\n\n\t// Sets many values\n\tif ( jQuery.type( key ) === \"object\" ) {\n\t\tchainable = true;\n\t\tfor ( i in key ) {\n\t\t\taccess( elems, fn, i, key[ i ], true, emptyGet, raw );\n\t\t}\n\n\t// Sets one value\n\t} else if ( value !== undefined ) {\n\t\tchainable = true;\n\n\t\tif ( !jQuery.isFunction( value ) ) {\n\t\t\traw = true;\n\t\t}\n\n\t\tif ( bulk ) {\n\n\t\t\t// Bulk operations run against the entire set\n\t\t\tif ( raw ) {\n\t\t\t\tfn.call( elems, value );\n\t\t\t\tfn = null;\n\n\t\t\t// ...except when executing function values\n\t\t\t} else {\n\t\t\t\tbulk = fn;\n\t\t\t\tfn = function( elem, key, value ) {\n\t\t\t\t\treturn bulk.call( jQuery( elem ), value );\n\t\t\t\t};\n\t\t\t}\n\t\t}\n\n\t\tif ( fn ) {\n\t\t\tfor ( ; i < len; i++ ) {\n\t\t\t\tfn(\n\t\t\t\t\telems[ i ], key, raw ?\n\t\t\t\t\tvalue :\n\t\t\t\t\tvalue.call( elems[ i ], i, fn( elems[ i ], key ) )\n\t\t\t\t);\n\t\t\t}\n\t\t}\n\t}\n\n\treturn chainable ?\n\t\telems :\n\n\t\t// Gets\n\t\tbulk ?\n\t\t\tfn.call( elems ) :\n\t\t\tlen ? fn( elems[ 0 ], key ) : emptyGet;\n};\nvar acceptData = function( owner ) {\n\n\t// Accepts only:\n\t// - Node\n\t// - Node.ELEMENT_NODE\n\t// - Node.DOCUMENT_NODE\n\t// - Object\n\t// - Any\n\t/* jshint -W018 */\n\treturn owner.nodeType === 1 || owner.nodeType === 9 || !( +owner.nodeType );\n};\n\n\n\n\nfunction Data() {\n\tthis.expando = jQuery.expando + Data.uid++;\n}\n\nData.uid = 1;\n\nData.prototype = {\n\n\tregister: function( owner, initial ) {\n\t\tvar value = initial || {};\n\n\t\t// If it is a node unlikely to be stringify-ed or looped over\n\t\t// use plain assignment\n\t\tif ( owner.nodeType ) {\n\t\t\towner[ this.expando ] = value;\n\n\t\t// Otherwise secure it in a non-enumerable, non-writable property\n\t\t// configurability must be true to allow the property to be\n\t\t// deleted with the delete operator\n\t\t} else {\n\t\t\tObject.defineProperty( owner, this.expando, {\n\t\t\t\tvalue: value,\n\t\t\t\twritable: true,\n\t\t\t\tconfigurable: true\n\t\t\t} );\n\t\t}\n\t\treturn owner[ this.expando ];\n\t},\n\tcache: function( owner ) {\n\n\t\t// We can accept data for non-element nodes in modern browsers,\n\t\t// but we should not, see #8335.\n\t\t// Always return an empty object.\n\t\tif ( !acceptData( owner ) ) {\n\t\t\treturn {};\n\t\t}\n\n\t\t// Check if the owner object already has a cache\n\t\tvar value = owner[ this.expando ];\n\n\t\t// If not, create one\n\t\tif ( !value ) {\n\t\t\tvalue = {};\n\n\t\t\t// We can accept data for non-element nodes in modern browsers,\n\t\t\t// but we should not, see #8335.\n\t\t\t// Always return an empty object.\n\t\t\tif ( acceptData( owner ) ) {\n\n\t\t\t\t// If it is a node unlikely to be stringify-ed or looped over\n\t\t\t\t// use plain assignment\n\t\t\t\tif ( owner.nodeType ) {\n\t\t\t\t\towner[ this.expando ] = value;\n\n\t\t\t\t// Otherwise secure it in a non-enumerable property\n\t\t\t\t// configurable must be true to allow the property to be\n\t\t\t\t// deleted when data is removed\n\t\t\t\t} else {\n\t\t\t\t\tObject.defineProperty( owner, this.expando, {\n\t\t\t\t\t\tvalue: value,\n\t\t\t\t\t\tconfigurable: true\n\t\t\t\t\t} );\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\treturn value;\n\t},\n\tset: function( owner, data, value ) {\n\t\tvar prop,\n\t\t\tcache = this.cache( owner );\n\n\t\t// Handle: [ owner, key, value ] args\n\t\tif ( typeof data === \"string\" ) {\n\t\t\tcache[ data ] = value;\n\n\t\t// Handle: [ owner, { properties } ] args\n\t\t} else {\n\n\t\t\t// Copy the properties one-by-one to the cache object\n\t\t\tfor ( prop in data ) {\n\t\t\t\tcache[ prop ] = data[ prop ];\n\t\t\t}\n\t\t}\n\t\treturn cache;\n\t},\n\tget: function( owner, key ) {\n\t\treturn key === undefined ?\n\t\t\tthis.cache( owner ) :\n\t\t\towner[ this.expando ] && owner[ this.expando ][ key ];\n\t},\n\taccess: function( owner, key, value ) {\n\t\tvar stored;\n\n\t\t// In cases where either:\n\t\t//\n\t\t// 1. No key was specified\n\t\t// 2. A string key was specified, but no value provided\n\t\t//\n\t\t// Take the \"read\" path and allow the get method to determine\n\t\t// which value to return, respectively either:\n\t\t//\n\t\t// 1. The entire cache object\n\t\t// 2. The data stored at the key\n\t\t//\n\t\tif ( key === undefined ||\n\t\t\t\t( ( key && typeof key === \"string\" ) && value === undefined ) ) {\n\n\t\t\tstored = this.get( owner, key );\n\n\t\t\treturn stored !== undefined ?\n\t\t\t\tstored : this.get( owner, jQuery.camelCase( key ) );\n\t\t}\n\n\t\t// When the key is not a string, or both a key and value\n\t\t// are specified, set or extend (existing objects) with either:\n\t\t//\n\t\t// 1. An object of properties\n\t\t// 2. A key and value\n\t\t//\n\t\tthis.set( owner, key, value );\n\n\t\t// Since the \"set\" path can have two possible entry points\n\t\t// return the expected data based on which path was taken[*]\n\t\treturn value !== undefined ? value : key;\n\t},\n\tremove: function( owner, key ) {\n\t\tvar i, name, camel,\n\t\t\tcache = owner[ this.expando ];\n\n\t\tif ( cache === undefined ) {\n\t\t\treturn;\n\t\t}\n\n\t\tif ( key === undefined ) {\n\t\t\tthis.register( owner );\n\n\t\t} else {\n\n\t\t\t// Support array or space separated string of keys\n\t\t\tif ( jQuery.isArray( key ) ) {\n\n\t\t\t\t// If \"name\" is an array of keys...\n\t\t\t\t// When data is initially created, via (\"key\", \"val\") signature,\n\t\t\t\t// keys will be converted to camelCase.\n\t\t\t\t// Since there is no way to tell _how_ a key was added, remove\n\t\t\t\t// both plain key and camelCase key. #12786\n\t\t\t\t// This will only penalize the array argument path.\n\t\t\t\tname = key.concat( key.map( jQuery.camelCase ) );\n\t\t\t} else {\n\t\t\t\tcamel = jQuery.camelCase( key );\n\n\t\t\t\t// Try the string as a key before any manipulation\n\t\t\t\tif ( key in cache ) {\n\t\t\t\t\tname = [ key, camel ];\n\t\t\t\t} else {\n\n\t\t\t\t\t// If a key with the spaces exists, use it.\n\t\t\t\t\t// Otherwise, create an array by matching non-whitespace\n\t\t\t\t\tname = camel;\n\t\t\t\t\tname = name in cache ?\n\t\t\t\t\t\t[ name ] : ( name.match( rnotwhite ) || [] );\n\t\t\t\t}\n\t\t\t}\n\n\t\t\ti = name.length;\n\n\t\t\twhile ( i-- ) {\n\t\t\t\tdelete cache[ name[ i ] ];\n\t\t\t}\n\t\t}\n\n\t\t// Remove the expando if there's no more data\n\t\tif ( key === undefined || jQuery.isEmptyObject( cache ) ) {\n\n\t\t\t// Support: Chrome <= 35-45+\n\t\t\t// Webkit & Blink performance suffers when deleting properties\n\t\t\t// from DOM nodes, so set to undefined instead\n\t\t\t// https://code.google.com/p/chromium/issues/detail?id=378607\n\t\t\tif ( owner.nodeType ) {\n\t\t\t\towner[ this.expando ] = undefined;\n\t\t\t} else {\n\t\t\t\tdelete owner[ this.expando ];\n\t\t\t}\n\t\t}\n\t},\n\thasData: function( owner ) {\n\t\tvar cache = owner[ this.expando ];\n\t\treturn cache !== undefined && !jQuery.isEmptyObject( cache );\n\t}\n};\nvar dataPriv = new Data();\n\nvar dataUser = new Data();\n\n\n\n//\tImplementation Summary\n//\n//\t1. Enforce API surface and semantic compatibility with 1.9.x branch\n//\t2. Improve the module's maintainability by reducing the storage\n//\t\tpaths to a single mechanism.\n//\t3. Use the same single mechanism to support \"private\" and \"user\" data.\n//\t4. _Never_ expose \"private\" data to user code (TODO: Drop _data, _removeData)\n//\t5. Avoid exposing implementation details on user objects (eg. expando properties)\n//\t6. Provide a clear path for implementation upgrade to WeakMap in 2014\n\nvar rbrace = /^(?:\\{[\\w\\W]*\\}|\\[[\\w\\W]*\\])$/,\n\trmultiDash = /[A-Z]/g;\n\nfunction dataAttr( elem, key, data ) {\n\tvar name;\n\n\t// If nothing was found internally, try to fetch any\n\t// data from the HTML5 data-* attribute\n\tif ( data === undefined && elem.nodeType === 1 ) {\n\t\tname = \"data-\" + key.replace( rmultiDash, \"-$&\" ).toLowerCase();\n\t\tdata = elem.getAttribute( name );\n\n\t\tif ( typeof data === \"string\" ) {\n\t\t\ttry {\n\t\t\t\tdata = data === \"true\" ? true :\n\t\t\t\t\tdata === \"false\" ? false :\n\t\t\t\t\tdata === \"null\" ? null :\n\n\t\t\t\t\t// Only convert to a number if it doesn't change the string\n\t\t\t\t\t+data + \"\" === data ? +data :\n\t\t\t\t\trbrace.test( data ) ? jQuery.parseJSON( data ) :\n\t\t\t\t\tdata;\n\t\t\t} catch ( e ) {}\n\n\t\t\t// Make sure we set the data so it isn't changed later\n\t\t\tdataUser.set( elem, key, data );\n\t\t} else {\n\t\t\tdata = undefined;\n\t\t}\n\t}\n\treturn data;\n}\n\njQuery.extend( {\n\thasData: function( elem ) {\n\t\treturn dataUser.hasData( elem ) || dataPriv.hasData( elem );\n\t},\n\n\tdata: function( elem, name, data ) {\n\t\treturn dataUser.access( elem, name, data );\n\t},\n\n\tremoveData: function( elem, name ) {\n\t\tdataUser.remove( elem, name );\n\t},\n\n\t// TODO: Now that all calls to _data and _removeData have been replaced\n\t// with direct calls to dataPriv methods, these can be deprecated.\n\t_data: function( elem, name, data ) {\n\t\treturn dataPriv.access( elem, name, data );\n\t},\n\n\t_removeData: function( elem, name ) {\n\t\tdataPriv.remove( elem, name );\n\t}\n} );\n\njQuery.fn.extend( {\n\tdata: function( key, value ) {\n\t\tvar i, name, data,\n\t\t\telem = this[ 0 ],\n\t\t\tattrs = elem && elem.attributes;\n\n\t\t// Gets all values\n\t\tif ( key === undefined ) {\n\t\t\tif ( this.length ) {\n\t\t\t\tdata = dataUser.get( elem );\n\n\t\t\t\tif ( elem.nodeType === 1 && !dataPriv.get( elem, \"hasDataAttrs\" ) ) {\n\t\t\t\t\ti = attrs.length;\n\t\t\t\t\twhile ( i-- ) {\n\n\t\t\t\t\t\t// Support: IE11+\n\t\t\t\t\t\t// The attrs elements can be null (#14894)\n\t\t\t\t\t\tif ( attrs[ i ] ) {\n\t\t\t\t\t\t\tname = attrs[ i ].name;\n\t\t\t\t\t\t\tif ( name.indexOf( \"data-\" ) === 0 ) {\n\t\t\t\t\t\t\t\tname = jQuery.camelCase( name.slice( 5 ) );\n\t\t\t\t\t\t\t\tdataAttr( elem, name, data[ name ] );\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tdataPriv.set( elem, \"hasDataAttrs\", true );\n\t\t\t\t}\n\t\t\t}\n\n\t\t\treturn data;\n\t\t}\n\n\t\t// Sets multiple values\n\t\tif ( typeof key === \"object\" ) {\n\t\t\treturn this.each( function() {\n\t\t\t\tdataUser.set( this, key );\n\t\t\t} );\n\t\t}\n\n\t\treturn access( this, function( value ) {\n\t\t\tvar data, camelKey;\n\n\t\t\t// The calling jQuery object (element matches) is not empty\n\t\t\t// (and therefore has an element appears at this[ 0 ]) and the\n\t\t\t// `value` parameter was not undefined. An empty jQuery object\n\t\t\t// will result in `undefined` for elem = this[ 0 ] which will\n\t\t\t// throw an exception if an attempt to read a data cache is made.\n\t\t\tif ( elem && value === undefined ) {\n\n\t\t\t\t// Attempt to get data from the cache\n\t\t\t\t// with the key as-is\n\t\t\t\tdata = dataUser.get( elem, key ) ||\n\n\t\t\t\t\t// Try to find dashed key if it exists (gh-2779)\n\t\t\t\t\t// This is for 2.2.x only\n\t\t\t\t\tdataUser.get( elem, key.replace( rmultiDash, \"-$&\" ).toLowerCase() );\n\n\t\t\t\tif ( data !== undefined ) {\n\t\t\t\t\treturn data;\n\t\t\t\t}\n\n\t\t\t\tcamelKey = jQuery.camelCase( key );\n\n\t\t\t\t// Attempt to get data from the cache\n\t\t\t\t// with the key camelized\n\t\t\t\tdata = dataUser.get( elem, camelKey );\n\t\t\t\tif ( data !== undefined ) {\n\t\t\t\t\treturn data;\n\t\t\t\t}\n\n\t\t\t\t// Attempt to \"discover\" the data in\n\t\t\t\t// HTML5 custom data-* attrs\n\t\t\t\tdata = dataAttr( elem, camelKey, undefined );\n\t\t\t\tif ( data !== undefined ) {\n\t\t\t\t\treturn data;\n\t\t\t\t}\n\n\t\t\t\t// We tried really hard, but the data doesn't exist.\n\t\t\t\treturn;\n\t\t\t}\n\n\t\t\t// Set the data...\n\t\t\tcamelKey = jQuery.camelCase( key );\n\t\t\tthis.each( function() {\n\n\t\t\t\t// First, attempt to store a copy or reference of any\n\t\t\t\t// data that might've been store with a camelCased key.\n\t\t\t\tvar data = dataUser.get( this, camelKey );\n\n\t\t\t\t// For HTML5 data-* attribute interop, we have to\n\t\t\t\t// store property names with dashes in a camelCase form.\n\t\t\t\t// This might not apply to all properties...*\n\t\t\t\tdataUser.set( this, camelKey, value );\n\n\t\t\t\t// *... In the case of properties that might _actually_\n\t\t\t\t// have dashes, we need to also store a copy of that\n\t\t\t\t// unchanged property.\n\t\t\t\tif ( key.indexOf( \"-\" ) > -1 && data !== undefined ) {\n\t\t\t\t\tdataUser.set( this, key, value );\n\t\t\t\t}\n\t\t\t} );\n\t\t}, null, value, arguments.length > 1, null, true );\n\t},\n\n\tremoveData: function( key ) {\n\t\treturn this.each( function() {\n\t\t\tdataUser.remove( this, key );\n\t\t} );\n\t}\n} );\n\n\njQuery.extend( {\n\tqueue: function( elem, type, data ) {\n\t\tvar queue;\n\n\t\tif ( elem ) {\n\t\t\ttype = ( type || \"fx\" ) + \"queue\";\n\t\t\tqueue = dataPriv.get( elem, type );\n\n\t\t\t// Speed up dequeue by getting out quickly if this is just a lookup\n\t\t\tif ( data ) {\n\t\t\t\tif ( !queue || jQuery.isArray( data ) ) {\n\t\t\t\t\tqueue = dataPriv.access( elem, type, jQuery.makeArray( data ) );\n\t\t\t\t} else {\n\t\t\t\t\tqueue.push( data );\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn queue || [];\n\t\t}\n\t},\n\n\tdequeue: function( elem, type ) {\n\t\ttype = type || \"fx\";\n\n\t\tvar queue = jQuery.queue( elem, type ),\n\t\t\tstartLength = queue.length,\n\t\t\tfn = queue.shift(),\n\t\t\thooks = jQuery._queueHooks( elem, type ),\n\t\t\tnext = function() {\n\t\t\t\tjQuery.dequeue( elem, type );\n\t\t\t};\n\n\t\t// If the fx queue is dequeued, always remove the progress sentinel\n\t\tif ( fn === \"inprogress\" ) {\n\t\t\tfn = queue.shift();\n\t\t\tstartLength--;\n\t\t}\n\n\t\tif ( fn ) {\n\n\t\t\t// Add a progress sentinel to prevent the fx queue from being\n\t\t\t// automatically dequeued\n\t\t\tif ( type === \"fx\" ) {\n\t\t\t\tqueue.unshift( \"inprogress\" );\n\t\t\t}\n\n\t\t\t// Clear up the last queue stop function\n\t\t\tdelete hooks.stop;\n\t\t\tfn.call( elem, next, hooks );\n\t\t}\n\n\t\tif ( !startLength && hooks ) {\n\t\t\thooks.empty.fire();\n\t\t}\n\t},\n\n\t// Not public - generate a queueHooks object, or return the current one\n\t_queueHooks: function( elem, type ) {\n\t\tvar key = type + \"queueHooks\";\n\t\treturn dataPriv.get( elem, key ) || dataPriv.access( elem, key, {\n\t\t\tempty: jQuery.Callbacks( \"once memory\" ).add( function() {\n\t\t\t\tdataPriv.remove( elem, [ type + \"queue\", key ] );\n\t\t\t} )\n\t\t} );\n\t}\n} );\n\njQuery.fn.extend( {\n\tqueue: function( type, data ) {\n\t\tvar setter = 2;\n\n\t\tif ( typeof type !== \"string\" ) {\n\t\t\tdata = type;\n\t\t\ttype = \"fx\";\n\t\t\tsetter--;\n\t\t}\n\n\t\tif ( arguments.length < setter ) {\n\t\t\treturn jQuery.queue( this[ 0 ], type );\n\t\t}\n\n\t\treturn data === undefined ?\n\t\t\tthis :\n\t\t\tthis.each( function() {\n\t\t\t\tvar queue = jQuery.queue( this, type, data );\n\n\t\t\t\t// Ensure a hooks for this queue\n\t\t\t\tjQuery._queueHooks( this, type );\n\n\t\t\t\tif ( type === \"fx\" && queue[ 0 ] !== \"inprogress\" ) {\n\t\t\t\t\tjQuery.dequeue( this, type );\n\t\t\t\t}\n\t\t\t} );\n\t},\n\tdequeue: function( type ) {\n\t\treturn this.each( function() {\n\t\t\tjQuery.dequeue( this, type );\n\t\t} );\n\t},\n\tclearQueue: function( type ) {\n\t\treturn this.queue( type || \"fx\", [] );\n\t},\n\n\t// Get a promise resolved when queues of a certain type\n\t// are emptied (fx is the type by default)\n\tpromise: function( type, obj ) {\n\t\tvar tmp,\n\t\t\tcount = 1,\n\t\t\tdefer = jQuery.Deferred(),\n\t\t\telements = this,\n\t\t\ti = this.length,\n\t\t\tresolve = function() {\n\t\t\t\tif ( !( --count ) ) {\n\t\t\t\t\tdefer.resolveWith( elements, [ elements ] );\n\t\t\t\t}\n\t\t\t};\n\n\t\tif ( typeof type !== \"string\" ) {\n\t\t\tobj = type;\n\t\t\ttype = undefined;\n\t\t}\n\t\ttype = type || \"fx\";\n\n\t\twhile ( i-- ) {\n\t\t\ttmp = dataPriv.get( elements[ i ], type + \"queueHooks\" );\n\t\t\tif ( tmp && tmp.empty ) {\n\t\t\t\tcount++;\n\t\t\t\ttmp.empty.add( resolve );\n\t\t\t}\n\t\t}\n\t\tresolve();\n\t\treturn defer.promise( obj );\n\t}\n} );\nvar pnum = ( /[+-]?(?:\\d*\\.|)\\d+(?:[eE][+-]?\\d+|)/ ).source;\n\nvar rcssNum = new RegExp( \"^(?:([+-])=|)(\" + pnum + \")([a-z%]*)$\", \"i\" );\n\n\nvar cssExpand = [ \"Top\", \"Right\", \"Bottom\", \"Left\" ];\n\nvar isHidden = function( elem, el ) {\n\n\t\t// isHidden might be called from jQuery#filter function;\n\t\t// in that case, element will be second argument\n\t\telem = el || elem;\n\t\treturn jQuery.css( elem, \"display\" ) === \"none\" ||\n\t\t\t!jQuery.contains( elem.ownerDocument, elem );\n\t};\n\n\n\nfunction adjustCSS( elem, prop, valueParts, tween ) {\n\tvar adjusted,\n\t\tscale = 1,\n\t\tmaxIterations = 20,\n\t\tcurrentValue = tween ?\n\t\t\tfunction() { return tween.cur(); } :\n\t\t\tfunction() { return jQuery.css( elem, prop, \"\" ); },\n\t\tinitial = currentValue(),\n\t\tunit = valueParts && valueParts[ 3 ] || ( jQuery.cssNumber[ prop ] ? \"\" : \"px\" ),\n\n\t\t// Starting value computation is required for potential unit mismatches\n\t\tinitialInUnit = ( jQuery.cssNumber[ prop ] || unit !== \"px\" && +initial ) &&\n\t\t\trcssNum.exec( jQuery.css( elem, prop ) );\n\n\tif ( initialInUnit && initialInUnit[ 3 ] !== unit ) {\n\n\t\t// Trust units reported by jQuery.css\n\t\tunit = unit || initialInUnit[ 3 ];\n\n\t\t// Make sure we update the tween properties later on\n\t\tvalueParts = valueParts || [];\n\n\t\t// Iteratively approximate from a nonzero starting point\n\t\tinitialInUnit = +initial || 1;\n\n\t\tdo {\n\n\t\t\t// If previous iteration zeroed out, double until we get *something*.\n\t\t\t// Use string for doubling so we don't accidentally see scale as unchanged below\n\t\t\tscale = scale || \".5\";\n\n\t\t\t// Adjust and apply\n\t\t\tinitialInUnit = initialInUnit / scale;\n\t\t\tjQuery.style( elem, prop, initialInUnit + unit );\n\n\t\t// Update scale, tolerating zero or NaN from tween.cur()\n\t\t// Break the loop if scale is unchanged or perfect, or if we've just had enough.\n\t\t} while (\n\t\t\tscale !== ( scale = currentValue() / initial ) && scale !== 1 && --maxIterations\n\t\t);\n\t}\n\n\tif ( valueParts ) {\n\t\tinitialInUnit = +initialInUnit || +initial || 0;\n\n\t\t// Apply relative offset (+=/-=) if specified\n\t\tadjusted = valueParts[ 1 ] ?\n\t\t\tinitialInUnit + ( valueParts[ 1 ] + 1 ) * valueParts[ 2 ] :\n\t\t\t+valueParts[ 2 ];\n\t\tif ( tween ) {\n\t\t\ttween.unit = unit;\n\t\t\ttween.start = initialInUnit;\n\t\t\ttween.end = adjusted;\n\t\t}\n\t}\n\treturn adjusted;\n}\nvar rcheckableType = ( /^(?:checkbox|radio)$/i );\n\nvar rtagName = ( /<([\\w:-]+)/ );\n\nvar rscriptType = ( /^$|\\/(?:java|ecma)script/i );\n\n\n\n// We have to close these tags to support XHTML (#13200)\nvar wrapMap = {\n\n\t// Support: IE9\n\toption: [ 1, \"\" ],\n\n\t// XHTML parsers do not magically insert elements in the\n\t// same way that tag soup parsers do. So we cannot shorten\n\t// this by omitting or other required elements.\n\tthead: [ 1, \" \", \"
\" ],\n\tcol: [ 2, \"
\" ],\n\ttr: [ 2, \"\", \" \", \"
\" ],\n\ttd: [ 3, \"
\" ],\n\n\t_default: [ 0, \"\", \"\" ]\n};\n\n// Support: IE9\nwrapMap.optgroup = wrapMap.option;\n\nwrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead;\nwrapMap.th = wrapMap.td;\n\n\nfunction getAll( context, tag ) {\n\n\t// Support: IE9-11+\n\t// Use typeof to avoid zero-argument method invocation on host objects (#15151)\n\tvar ret = typeof context.getElementsByTagName !== \"undefined\" ?\n\t\t\tcontext.getElementsByTagName( tag || \"*\" ) :\n\t\t\ttypeof context.querySelectorAll !== \"undefined\" ?\n\t\t\t\tcontext.querySelectorAll( tag || \"*\" ) :\n\t\t\t[];\n\n\treturn tag === undefined || tag && jQuery.nodeName( context, tag ) ?\n\t\tjQuery.merge( [ context ], ret ) :\n\t\tret;\n}\n\n\n// Mark scripts as having already been evaluated\nfunction setGlobalEval( elems, refElements ) {\n\tvar i = 0,\n\t\tl = elems.length;\n\n\tfor ( ; i < l; i++ ) {\n\t\tdataPriv.set(\n\t\t\telems[ i ],\n\t\t\t\"globalEval\",\n\t\t\t!refElements || dataPriv.get( refElements[ i ], \"globalEval\" )\n\t\t);\n\t}\n}\n\n\nvar rhtml = /<|&#?\\w+;/;\n\nfunction buildFragment( elems, context, scripts, selection, ignored ) {\n\tvar elem, tmp, tag, wrap, contains, j,\n\t\tfragment = context.createDocumentFragment(),\n\t\tnodes = [],\n\t\ti = 0,\n\t\tl = elems.length;\n\n\tfor ( ; i < l; i++ ) {\n\t\telem = elems[ i ];\n\n\t\tif ( elem || elem === 0 ) {\n\n\t\t\t// Add nodes directly\n\t\t\tif ( jQuery.type( elem ) === \"object\" ) {\n\n\t\t\t\t// Support: Android<4.1, PhantomJS<2\n\t\t\t\t// push.apply(_, arraylike) throws on ancient WebKit\n\t\t\t\tjQuery.merge( nodes, elem.nodeType ? [ elem ] : elem );\n\n\t\t\t// Convert non-html into a text node\n\t\t\t} else if ( !rhtml.test( elem ) ) {\n\t\t\t\tnodes.push( context.createTextNode( elem ) );\n\n\t\t\t// Convert html into DOM nodes\n\t\t\t} else {\n\t\t\t\ttmp = tmp || fragment.appendChild( context.createElement( \"div\" ) );\n\n\t\t\t\t// Deserialize a standard representation\n\t\t\t\ttag = ( rtagName.exec( elem ) || [ \"\", \"\" ] )[ 1 ].toLowerCase();\n\t\t\t\twrap = wrapMap[ tag ] || wrapMap._default;\n\t\t\t\ttmp.innerHTML = wrap[ 1 ] + jQuery.htmlPrefilter( elem ) + wrap[ 2 ];\n\n\t\t\t\t// Descend through wrappers to the right content\n\t\t\t\tj = wrap[ 0 ];\n\t\t\t\twhile ( j-- ) {\n\t\t\t\t\ttmp = tmp.lastChild;\n\t\t\t\t}\n\n\t\t\t\t// Support: Android<4.1, PhantomJS<2\n\t\t\t\t// push.apply(_, arraylike) throws on ancient WebKit\n\t\t\t\tjQuery.merge( nodes, tmp.childNodes );\n\n\t\t\t\t// Remember the top-level container\n\t\t\t\ttmp = fragment.firstChild;\n\n\t\t\t\t// Ensure the created nodes are orphaned (#12392)\n\t\t\t\ttmp.textContent = \"\";\n\t\t\t}\n\t\t}\n\t}\n\n\t// Remove wrapper from fragment\n\tfragment.textContent = \"\";\n\n\ti = 0;\n\twhile ( ( elem = nodes[ i++ ] ) ) {\n\n\t\t// Skip elements already in the context collection (trac-4087)\n\t\tif ( selection && jQuery.inArray( elem, selection ) > -1 ) {\n\t\t\tif ( ignored ) {\n\t\t\t\tignored.push( elem );\n\t\t\t}\n\t\t\tcontinue;\n\t\t}\n\n\t\tcontains = jQuery.contains( elem.ownerDocument, elem );\n\n\t\t// Append to fragment\n\t\ttmp = getAll( fragment.appendChild( elem ), \"script\" );\n\n\t\t// Preserve script evaluation history\n\t\tif ( contains ) {\n\t\t\tsetGlobalEval( tmp );\n\t\t}\n\n\t\t// Capture executables\n\t\tif ( scripts ) {\n\t\t\tj = 0;\n\t\t\twhile ( ( elem = tmp[ j++ ] ) ) {\n\t\t\t\tif ( rscriptType.test( elem.type || \"\" ) ) {\n\t\t\t\t\tscripts.push( elem );\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\treturn fragment;\n}\n\n\n( function() {\n\tvar fragment = document.createDocumentFragment(),\n\t\tdiv = fragment.appendChild( document.createElement( \"div\" ) ),\n\t\tinput = document.createElement( \"input\" );\n\n\t// Support: Android 4.0-4.3, Safari<=5.1\n\t// Check state lost if the name is set (#11217)\n\t// Support: Windows Web Apps (WWA)\n\t// `name` and `type` must use .setAttribute for WWA (#14901)\n\tinput.setAttribute( \"type\", \"radio\" );\n\tinput.setAttribute( \"checked\", \"checked\" );\n\tinput.setAttribute( \"name\", \"t\" );\n\n\tdiv.appendChild( input );\n\n\t// Support: Safari<=5.1, Android<4.2\n\t// Older WebKit doesn't clone checked state correctly in fragments\n\tsupport.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked;\n\n\t// Support: IE<=11+\n\t// Make sure textarea (and checkbox) defaultValue is properly cloned\n\tdiv.innerHTML = \"\";\n\tsupport.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue;\n} )();\n\n\nvar\n\trkeyEvent = /^key/,\n\trmouseEvent = /^(?:mouse|pointer|contextmenu|drag|drop)|click/,\n\trtypenamespace = /^([^.]*)(?:\\.(.+)|)/;\n\nfunction returnTrue() {\n\treturn true;\n}\n\nfunction returnFalse() {\n\treturn false;\n}\n\n// Support: IE9\n// See #13393 for more info\nfunction safeActiveElement() {\n\ttry {\n\t\treturn document.activeElement;\n\t} catch ( err ) { }\n}\n\nfunction on( elem, types, selector, data, fn, one ) {\n\tvar origFn, type;\n\n\t// Types can be a map of types/handlers\n\tif ( typeof types === \"object\" ) {\n\n\t\t// ( types-Object, selector, data )\n\t\tif ( typeof selector !== \"string\" ) {\n\n\t\t\t// ( types-Object, data )\n\t\t\tdata = data || selector;\n\t\t\tselector = undefined;\n\t\t}\n\t\tfor ( type in types ) {\n\t\t\ton( elem, type, selector, data, types[ type ], one );\n\t\t}\n\t\treturn elem;\n\t}\n\n\tif ( data == null && fn == null ) {\n\n\t\t// ( types, fn )\n\t\tfn = selector;\n\t\tdata = selector = undefined;\n\t} else if ( fn == null ) {\n\t\tif ( typeof selector === \"string\" ) {\n\n\t\t\t// ( types, selector, fn )\n\t\t\tfn = data;\n\t\t\tdata = undefined;\n\t\t} else {\n\n\t\t\t// ( types, data, fn )\n\t\t\tfn = data;\n\t\t\tdata = selector;\n\t\t\tselector = undefined;\n\t\t}\n\t}\n\tif ( fn === false ) {\n\t\tfn = returnFalse;\n\t} else if ( !fn ) {\n\t\treturn elem;\n\t}\n\n\tif ( one === 1 ) {\n\t\torigFn = fn;\n\t\tfn = function( event ) {\n\n\t\t\t// Can use an empty set, since event contains the info\n\t\t\tjQuery().off( event );\n\t\t\treturn origFn.apply( this, arguments );\n\t\t};\n\n\t\t// Use same guid so caller can remove using origFn\n\t\tfn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ );\n\t}\n\treturn elem.each( function() {\n\t\tjQuery.event.add( this, types, fn, data, selector );\n\t} );\n}\n\n/*\n * Helper functions for managing events -- not part of the public interface.\n * Props to Dean Edwards' addEvent library for many of the ideas.\n */\njQuery.event = {\n\n\tglobal: {},\n\n\tadd: function( elem, types, handler, data, selector ) {\n\n\t\tvar handleObjIn, eventHandle, tmp,\n\t\t\tevents, t, handleObj,\n\t\t\tspecial, handlers, type, namespaces, origType,\n\t\t\telemData = dataPriv.get( elem );\n\n\t\t// Don't attach events to noData or text/comment nodes (but allow plain objects)\n\t\tif ( !elemData ) {\n\t\t\treturn;\n\t\t}\n\n\t\t// Caller can pass in an object of custom data in lieu of the handler\n\t\tif ( handler.handler ) {\n\t\t\thandleObjIn = handler;\n\t\t\thandler = handleObjIn.handler;\n\t\t\tselector = handleObjIn.selector;\n\t\t}\n\n\t\t// Make sure that the handler has a unique ID, used to find/remove it later\n\t\tif ( !handler.guid ) {\n\t\t\thandler.guid = jQuery.guid++;\n\t\t}\n\n\t\t// Init the element's event structure and main handler, if this is the first\n\t\tif ( !( events = elemData.events ) ) {\n\t\t\tevents = elemData.events = {};\n\t\t}\n\t\tif ( !( eventHandle = elemData.handle ) ) {\n\t\t\teventHandle = elemData.handle = function( e ) {\n\n\t\t\t\t// Discard the 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Data\"),\n url: \"library/index\",\n tooltip: _l(\"Access published resources\"),\n menu: [\n {\n title: _l(\"Data Libraries\"),\n url: \"library/list\"\n },\n {\n title: _l(\"Histories\"),\n url: \"histories/list_published\"\n },\n {\n title: _l(\"Workflows\"),\n url: \"workflows/list_published\"\n },\n {\n title: _l(\"Visualizations\"),\n url: \"visualizations/list_published\"\n },\n {\n title: _l(\"Pages\"),\n url: \"pages/list_published\"\n }\n ]\n });\n\n //\n // Lab menu.\n //\n options.user_requests &&\n this.add({\n id: \"lab\",\n title: \"Lab\",\n menu: [\n {\n title: \"Sequencing Requests\",\n url: \"requests/index\"\n },\n {\n title: \"Find Samples\",\n url: \"requests/find_samples_index\"\n },\n {\n title: \"Help\",\n url: options.lims_doc_url\n }\n ]\n });\n\n //\n // Visualization tab.\n //\n this.add({\n id: \"visualization\",\n title: _l(\"Visualization\"),\n url: \"visualizations/list\",\n tooltip: _l(\"Visualize datasets\"),\n disabled: !Galaxy.user.id,\n menu: [\n {\n title: _l(\"New Track Browser\"),\n url: \"visualization/trackster\",\n target: \"_frame\"\n },\n {\n title: _l(\"Saved Visualizations\"),\n url: \"visualizations/list\",\n target: \"_frame\"\n },\n {\n title: _l(\"Interactive Environments\"),\n url: \"visualization/gie_list\",\n target: \"galaxy_main\"\n }\n ]\n });\n\n //\n // Webhooks\n //\n Webhooks.add({\n url: \"api/webhooks/masthead/all\",\n callback: function(webhooks) {\n $(document).ready(function() {\n $.each(webhooks.models, function(index, model) {\n var webhook = model.toJSON();\n if (webhook.activate) {\n var obj = {\n id: webhook.name,\n icon: webhook.config.icon,\n url: webhook.config.url,\n tooltip: webhook.config.tooltip,\n onclick:\n webhook.config.function &&\n new Function(\n webhook.config.function\n )\n };\n\n // Galaxy.page is undefined for data libraries, workflows pages\n if (Galaxy.page) {\n Galaxy.page.masthead.collection.add(\n obj\n );\n } else if (Galaxy.masthead) {\n Galaxy.masthead.collection.add(obj);\n }\n\n // Append masthead script and styles to Galaxy main\n Utils.appendScriptStyle(webhook);\n }\n });\n });\n }\n });\n\n //\n // Admin.\n //\n Galaxy.user.get(\"is_admin\") &&\n this.add({\n id: \"admin\",\n title: _l(\"Admin\"),\n url: \"admin\",\n tooltip: _l(\"Administer this Galaxy\"),\n cls: \"admin-only\"\n });\n\n //\n // Help tab.\n //\n var helpTab = {\n id: \"help\",\n title: _l(\"Help\"),\n tooltip: _l(\"Support, contact, and community\"),\n menu: [\n {\n title: _l(\"Support\"),\n url: options.support_url,\n target: \"_blank\"\n },\n {\n title: _l(\"Search\"),\n url: options.search_url,\n target: \"_blank\"\n },\n {\n title: _l(\"Mailing Lists\"),\n url: options.mailing_lists,\n target: \"_blank\"\n },\n {\n title: _l(\"Videos\"),\n url: options.screencasts_url,\n target: \"_blank\"\n },\n {\n title: _l(\"Wiki\"),\n url: options.wiki_url,\n target: \"_blank\"\n },\n {\n title: _l(\"How to Cite Galaxy\"),\n url: options.citation_url,\n target: \"_blank\"\n },\n {\n title: _l(\"Interactive Tours\"),\n url: \"tours\"\n }\n ]\n };\n options.terms_url &&\n helpTab.menu.push({\n title: _l(\"Terms and Conditions\"),\n url: options.terms_url,\n target: \"_blank\"\n });\n options.biostar_url &&\n helpTab.menu.unshift({\n title: _l(\"Ask a question\"),\n url: \"biostar/biostar_question_redirect\",\n target: \"_blank\"\n });\n options.biostar_url &&\n helpTab.menu.unshift({\n title: _l(\"Galaxy Biostar\"),\n url: options.biostar_url_redirect,\n target: \"_blank\"\n });\n this.add(helpTab);\n\n //\n // User tab.\n //\n var userTab = {};\n if (!Galaxy.user.id) {\n if (options.allow_user_creation) {\n userTab = {\n id: \"user\",\n title: _l(\"Login or Register\"),\n cls: \"loggedout-only\",\n tooltip: _l(\"Account registration or login\"),\n menu: [\n {\n title: _l(\"Login\"),\n url: \"user/login\",\n target: \"galaxy_main\",\n noscratchbook: true\n },\n {\n title: _l(\"Register\"),\n url: \"user/create\",\n target: \"galaxy_main\",\n noscratchbook: true\n }\n ]\n };\n } else {\n userTab = {\n id: \"user\",\n title: _l(\"Login\"),\n cls: \"loggedout-only\",\n tooltip: _l(\"Login\"),\n url: \"user/login\",\n target: \"galaxy_main\",\n noscratchbook: true\n };\n }\n } else {\n userTab = {\n id: \"user\",\n title: _l(\"User\"),\n cls: \"loggedin-only\",\n tooltip: _l(\"Account and saved data\"),\n menu: [\n {\n title:\n _l(\"Logged in as\") +\n \" \" +\n Galaxy.user.get(\"email\")\n },\n {\n title: _l(\"Preferences\"),\n url: \"user\"\n },\n {\n title: _l(\"Custom Builds\"),\n url: \"custom_builds\"\n },\n {\n title: _l(\"Logout\"),\n url:\n \"user/logout?session_csrf_token=\" +\n Galaxy.session_csrf_token,\n target: \"_top\",\n divider: true\n },\n {\n title: _l(\"Saved Histories\"),\n url: \"histories/list\",\n target: \"_top\"\n },\n {\n title: _l(\"Saved Datasets\"),\n url: \"datasets/list\",\n target: \"_top\"\n },\n {\n title: _l(\"Saved Pages\"),\n url: \"pages/list\",\n target: \"_top\"\n }\n ]\n };\n }\n this.add(userTab);\n var activeView = this.get(options.active_view);\n activeView && activeView.set(\"active\", true);\n return new jQuery.Deferred().resolve().promise();\n }\n });\n\n /** Masthead tab **/\n var Tab = Backbone.View.extend({\n initialize: function(options) {\n this.model = options.model;\n this.setElement(this._template());\n this.$dropdown = this.$(\".dropdown\");\n this.$toggle = this.$(\".dropdown-toggle\");\n this.$menu = this.$(\".dropdown-menu\");\n this.$note = this.$(\".dropdown-note\");\n this.listenTo(this.model, \"change\", this.render, this);\n },\n\n events: {\n \"click .dropdown-toggle\": \"_toggleClick\"\n },\n\n render: function() {\n var self = this;\n $(\".tooltip\").remove();\n this.$el.attr(\"id\", this.model.id).css({\n visibility:\n (this.model.get(\"visible\") && \"visible\") || \"hidden\"\n });\n this.model.set(\"url\", this._formatUrl(this.model.get(\"url\")));\n this.$note\n .html(this.model.get(\"note\") || \"\")\n .removeClass()\n .addClass(\"dropdown-note\")\n .addClass(this.model.get(\"note_cls\"))\n .css({\n display:\n (this.model.get(\"show_note\") && \"block\") || \"none\"\n });\n this.$toggle\n .html(this.model.get(\"title\") || \"\")\n .removeClass()\n .addClass(\"dropdown-toggle\")\n .addClass(this.model.get(\"cls\"))\n .addClass(\n this.model.get(\"icon\") &&\n \"dropdown-icon fa \" + this.model.get(\"icon\")\n )\n .addClass(this.model.get(\"toggle\") && \"toggle\")\n .attr(\"target\", this.model.get(\"target\"))\n .attr(\"href\", this.model.get(\"url\"))\n .attr(\"title\", this.model.get(\"tooltip\"))\n .tooltip(\"destroy\");\n this.model.get(\"tooltip\") &&\n this.$toggle.tooltip({ placement: \"bottom\" });\n this.$dropdown\n .removeClass()\n .addClass(\"dropdown\")\n .addClass(this.model.get(\"disabled\") && \"disabled\")\n .addClass(this.model.get(\"active\") && \"active\");\n if (this.model.get(\"menu\") && this.model.get(\"show_menu\")) {\n this.$menu.show();\n $(\"#dd-helper\")\n .show()\n .off()\n .on(\"click\", function() {\n $(\"#dd-helper\").hide();\n self.model.set(\"show_menu\", false);\n });\n } else {\n self.$menu.hide();\n $(\"#dd-helper\").hide();\n }\n this.$menu.empty().removeClass(\"dropdown-menu\");\n if (this.model.get(\"menu\")) {\n _.each(this.model.get(\"menu\"), function(menuItem) {\n self.$menu.append(self._buildMenuItem(menuItem));\n menuItem.divider &&\n self.$menu.append($(\"\").addClass(\"divider\"));\n });\n self.$menu.addClass(\"dropdown-menu\");\n self.$toggle.append($(\"\").addClass(\"caret\"));\n }\n return this;\n },\n\n /** Add new menu item */\n _buildMenuItem: function(options) {\n var self = this;\n options = _.defaults(options || {}, {\n title: \"\",\n url: \"\",\n target: \"_parent\",\n noscratchbook: false\n });\n options.url = self._formatUrl(options.url);\n return $(\"\").append(\n $(\"\")\n .attr(\"href\", options.url)\n .attr(\"target\", options.target)\n .html(options.title)\n .on(\"click\", function(e) {\n e.preventDefault();\n self.model.set(\"show_menu\", false);\n if (options.onclick) {\n options.onclick();\n } else {\n Galaxy.frame.add(options);\n }\n })\n );\n },\n\n /** Handle click event */\n _toggleClick: function(e) {\n var self = this;\n var model = this.model;\n e.preventDefault();\n $(\".tooltip\").hide();\n model.trigger(\"dispatch\", function(m) {\n model.id !== m.id &&\n m.get(\"menu\") &&\n m.set(\"show_menu\", false);\n });\n if (!model.get(\"disabled\")) {\n if (!model.get(\"menu\")) {\n model.get(\"onclick\")\n ? model.get(\"onclick\")()\n : Galaxy.frame.add(model.attributes);\n } else {\n model.set(\"show_menu\", true);\n }\n } else {\n function buildLink(label, url) {\n return $(\"\")\n .append(\n $(\"\")\n .attr(\"href\", Galaxy.root + url)\n .html(label)\n )\n .html();\n }\n this.$toggle.popover && this.$toggle.popover(\"destroy\");\n this.$toggle\n .popover({\n html: true,\n placement: \"bottom\",\n content:\n \"Please \" +\n buildLink(\n \"login\",\n \"user/login?use_panels=True\"\n ) +\n \" or \" +\n buildLink(\n \"register\",\n \"user/create?use_panels=True\"\n ) +\n \" to use this feature.\"\n })\n .popover(\"show\");\n setTimeout(function() {\n self.$toggle.popover(\"destroy\");\n }, 5000);\n }\n },\n\n /** Url formatting */\n _formatUrl: function(url) {\n return typeof url == \"string\" &&\n url.indexOf(\"//\") === -1 &&\n url.charAt(0) != \"/\"\n ? Galaxy.root + url\n : url;\n },\n\n /** body tempate */\n _template: function() {\n return (\n '- ' +\n '
- ' +\n '' +\n '