From f6737618e319b78f874e938c5e68ad70cd7ba746 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Fri, 20 Oct 2017 16:27:00 -0400 Subject: [PATCH] expose state, stdout, stderr, uuid in the API fix few bugs and UI/UX glitches --- .../mvc/library/library-dataset-view.js | 35 +++++++++++++-- .../mvc/library/library-folderlist-view.js | 6 ++- .../mvc/library/library-folderrow-view.js | 44 +++++++++++-------- .../mvc/library/library-foldertoolbar-view.js | 17 ++++--- .../mvc/library/library-libraryrow-view.js | 18 ++++---- .../library/library-librarytoolbar-view.js | 17 ++++--- client/galaxy/style/less/library.less | 2 +- lib/galaxy/managers/library_datasets.py | 19 +++++--- .../webapps/galaxy/api/folder_contents.py | 1 + .../mvc/library/library-dataset-view.js.map | 2 +- .../library/library-folderlist-view.js.map | 2 +- .../mvc/library/library-folderrow-view.js.map | 2 +- .../library/library-foldertoolbar-view.js.map | 2 +- .../library/library-libraryrow-view.js.map | 2 +- .../library-librarytoolbar-view.js.map | 2 +- .../mvc/library/library-dataset-view.js | 2 +- .../mvc/library/library-folderlist-view.js | 2 +- .../mvc/library/library-folderrow-view.js | 2 +- .../mvc/library/library-foldertoolbar-view.js | 2 +- .../mvc/library/library-libraryrow-view.js | 2 +- .../library/library-librarytoolbar-view.js | 2 +- static/style/blue/base.css | 2 +- static/style/blue/library.css | 2 +- 23 files changed, 123 insertions(+), 64 deletions(-) diff --git a/client/galaxy/scripts/mvc/library/library-dataset-view.js b/client/galaxy/scripts/mvc/library/library-dataset-view.js index 7a5ecae7352..9336068eded 100644 --- a/client/galaxy/scripts/mvc/library/library-dataset-view.js +++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js @@ -541,7 +541,8 @@ define( } }, - copyToClipboard: function() { + copyToClipboard: function(e) { + e.preventDefault(); var href = Backbone.history.location.href; if (href.lastIndexOf("/permissions") !== -1) { href = href.substr(0, href.lastIndexOf("/permissions")); @@ -764,7 +765,7 @@ define( '<% if (item.get("is_unrestricted")) { %>', "
", - 'This dataset is unrestricted so everybody with the link can access it. Just share this page.', + 'This dataset is unrestricted so everybody with the link can access it. Just share this page.', "
", "<% } %>", @@ -853,8 +854,34 @@ define( '<%= _.escape(item.get("tags")) %>', "", "<% } %>", + '<% if ( item.get("uuid") !== "ok" ) { %>', + "", + 'UUID', + '<%= _.escape(item.get("uuid")) %>', + "", + "<% } %>", + '<% if ( item.get("state") !== "ok" ) { %>', + "", + 'State', + '<%= _.escape(item.get("state")) %>', + "", + "<% } %>", "", + '<% if (item.get("job_stderr")) { %>', + "

Job Standard Error

", + '
',
+                        '<%= _.escape(item.get("job_stderr")) %>',
+                        "
", + "<% } %>", + + '<% if (item.get("job_stdout")) { %>', + "

Job Standard Output

", + '
',
+                        '<%= _.escape(item.get("job_stdout")) %>',
+                        "
", + "<% } %>", + "
", '
',
                         "
", @@ -1154,9 +1181,9 @@ define( "

Dataset-related permissions

", '
Changes made below will affect every library item that was created from this dataset and also every history this dataset is part of.
', '<% if (!item.get("is_unrestricted")) { %>', - '

You can remove all access restrictions on this dataset.

', + '

You can remove all access restrictions on this dataset.

', "<% } else { %>", - '

You can make this dataset private to you.

', + '

You can make this dataset private to you.

', "<% } %>", "

Roles that can access the dataset

", '
', diff --git a/client/galaxy/scripts/mvc/library/library-folderlist-view.js b/client/galaxy/scripts/mvc/library/library-folderlist-view.js index 694de517443..4d7bfa86b65 100644 --- a/client/galaxy/scripts/mvc/library/library-folderlist-view.js +++ b/client/galaxy/scripts/mvc/library/library-folderlist-view.js @@ -467,11 +467,12 @@ define( '', '', 'name ', - 'description', + 'description', 'data type', 'size', 'time updated (UTC)', - ' ', + 'state ', + ' ', "", '', '', @@ -485,6 +486,7 @@ define( "", "", "", + "", "", "", "", diff --git a/client/galaxy/scripts/mvc/library/library-folderrow-view.js b/client/galaxy/scripts/mvc/library/library-folderrow-view.js index 2cef1d8cc61..8a391714ce4 100644 --- a/client/galaxy/scripts/mvc/library/library-folderrow-view.js +++ b/client/galaxy/scripts/mvc/library/library-folderrow-view.js @@ -17,10 +17,10 @@ define( defaults: { type: null, visibility_config: { - edit_folder_btn: true, + edit_folder_btn: false, save_folder_btn: false, cancel_folder_btn: false, - permission_folder_btn: true + permission_folder_btn: false }, edit_mode: false }, @@ -306,32 +306,31 @@ define( "", '<%- content_item.get("description") %>', "", + "", "<% } else if(edit_mode){ %>", '', '', "<% } %>", "folder", - "", "", '<%= _.escape(content_item.get("update_time")) %>', "", + "", "", "<% if(edit_mode) { %>", // start edit mode '", '", "<% } else if (!edit_mode){%>", // start no edit mode '", '', - '", "", "<% } %>", //end no edit mode @@ -361,6 +360,11 @@ define( '<%= _.escape(content_item.get("file_size")) %>', '<%= _.escape(content_item.get("update_time")) %>', "", + '<% if ( content_item.get("state") !== "ok" ) { %>', + '<%= _.escape(content_item.get("state")) %>', + "<% } %>", + "", + "", '<% if (content_item.get("is_unrestricted")) { %>', '', "<% } %>", @@ -372,8 +376,8 @@ define( "<% } %>", '<% if (content_item.get("can_manage")) { %>', '/datasets/<%- content_item.id %>/permissions">', - '", "", "<% } %>", @@ -407,10 +411,14 @@ define( '<%= _.escape(content_item.get("update_time")) %>', "", "", + '<% if ( content_item.get("state") !== "ok" ) { %>', + '<%= _.escape(content_item.get("state")) %>', + "<% } %>", + "", + "", '', - '", "", "" @@ -439,11 +447,11 @@ define( "", '<%= _.escape(content_item.get("update_time")) %>', "", + "", "", '', - '", "", "" diff --git a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js index fa3c358415a..c4ffaa5025d 100644 --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -112,7 +112,10 @@ define( show_page: parseInt(this.options.show_page), page_count: parseInt(this.options.page_count), total_items_count: this.options.total_items_count, - items_shown: this.options.items_shown + items_shown: this.options.items_shown, + folder_page_size: Galaxy.libraries.preferences.get( + "folder_page_size" + ) }) ); }, @@ -1432,7 +1435,8 @@ define( /** * Show user the prompt to change the number of items shown on page. */ - showPageSizePrompt: function() { + showPageSizePrompt: function(e) { + e.preventDefault(); var folder_page_size = prompt( "How many items per page do you want to see?", Galaxy.libraries.preferences.get("folder_page_size") @@ -1886,11 +1890,10 @@ define( "<% } %>", "", "", - " showing ", - '', - "<%- items_shown %>", - "", - " of <%- total_items_count %> items", + ' <%- items_shown %> items shown (change)', + "", + "", + " <%- total_items_count %> total", "" ].join("") ); diff --git a/client/galaxy/scripts/mvc/library/library-libraryrow-view.js b/client/galaxy/scripts/mvc/library/library-libraryrow-view.js index 951d395c6da..47531c39cfb 100644 --- a/client/galaxy/scripts/mvc/library/library-libraryrow-view.js +++ b/client/galaxy/scripts/mvc/library/library-libraryrow-view.js @@ -264,7 +264,7 @@ define(["layout/masthead", "utils/utils", "libs/toastr"], function( '" style="display:none;" data-id="<%- library.get("id") %>">', "<% if(!edit_mode) { %>", '<% if(library.get("deleted")) { %>', - ' <%- library.get("name") %>', + '<%- library.get("name") %>', "<% } else { %>", '"><%- library.get("name") %>', "<% } %>", @@ -293,14 +293,16 @@ define(["layout/masthead", "utils/utils", "libs/toastr"], function( "<% } %>", '', '<% if( (library.get("public")) && (library.get("deleted") === false) ) { %>', - ' ', + ' ', "<% }%>", - '', - '/permissions">', - '', - '', - '', - '', + '', + '/permissions">', + '', + '', + '', + // For deleted libraries + '" class="fa fa-ban fa-lg">', + '', "", "" ].join("") diff --git a/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js b/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js index 5d008d4bcca..ef599d1026a 100644 --- a/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js @@ -17,7 +17,7 @@ define(["libs/toastr", "mvc/library/library-model"], function( "click #create_new_library_btn": "createLibraryFromModal", "click #include_deleted_chk": "includeDeletedChecked", "click #exclude_restricted_chk": "excludeRestrictedChecked", - "click #lib_page_size_prompt": "showPageSizePrompt", + "click .page_size_prompt": "showPageSizePrompt", "keyup .library-search-input": "searchLibraries" }, @@ -64,7 +64,10 @@ define(["libs/toastr", "mvc/library/library-model"], function( show_page: parseInt(this.options.show_page), page_count: parseInt(this.options.page_count), total_libraries_count: this.options.total_libraries_count, - libraries_shown: this.options.libraries_shown + libraries_shown: this.options.libraries_shown, + library_page_size: Galaxy.libraries.preferences.get( + "library_page_size" + ) }) ); }, @@ -128,7 +131,8 @@ define(["libs/toastr", "mvc/library/library-model"], function( /** * Show user the propmpt to change the number of libs shown on page. */ - showPageSizePrompt: function() { + showPageSizePrompt: function(e) { + e.preventDefault(); var library_page_size = prompt( "How many libraries per page do you want to see?", Galaxy.libraries.preferences.get("library_page_size") @@ -281,8 +285,11 @@ define(["libs/toastr", "mvc/library/library-model"], function( '
    • ', "<% } %>", "", - '', - ' showing <%- libraries_shown %> of <%- total_libraries_count %> libraries', + "", + ' <%- libraries_shown %> libraries shown (change)', + "", + "", + " <%- total_libraries_count %> total", "" ].join("") ); diff --git a/client/galaxy/style/less/library.less b/client/galaxy/style/less/library.less index 91614c3a048..ccebc0e528c 100644 --- a/client/galaxy/style/less/library.less +++ b/client/galaxy/style/less/library.less @@ -11,7 +11,7 @@ overflow: auto !important; .fa{ font-size: 12px; } -.fa-globe{ +.fa-globe, .fa-shield, .fa-key, .fa-ban{ font-size: initial; margin-left: 0.6em; } diff --git a/lib/galaxy/managers/library_datasets.py b/lib/galaxy/managers/library_datasets.py index 20ce8c3789a..de968e748a0 100644 --- a/lib/galaxy/managers/library_datasets.py +++ b/lib/galaxy/managers/library_datasets.py @@ -195,17 +195,26 @@ class LibraryDatasetsManager(object): if len(expired_ldda_versions) > 0: rval['has_versions'] = True rval['expired_versions'] = expired_ldda_versions + + ldda = ld.library_dataset_dataset_association + if ldda.creating_job_associations: + if ldda.creating_job_associations[0].job.stdout: + rval['job_stdout'] = ldda.creating_job_associations[0].job.stdout.strip() + if ldda.creating_job_associations[0].job.stderr: + rval['job_stderr'] = ldda.creating_job_associations[0].job.stderr.strip() + if ldda.dataset.uuid: + rval['uuid'] = str(ldda.dataset.uuid) rval['deleted'] = ld.deleted rval['folder_id'] = 'F' + rval['folder_id'] rval['full_path'] = full_path - rval['file_size'] = util.nice_size(int(ld.library_dataset_dataset_association.get_size())) - rval['date_uploaded'] = ld.library_dataset_dataset_association.create_time.strftime("%Y-%m-%d %I:%M %p") + rval['file_size'] = util.nice_size(int(ldda.get_size())) + rval['date_uploaded'] = ldda.create_time.strftime("%Y-%m-%d %I:%M %p") rval['can_user_modify'] = trans.app.security_agent.can_modify_library_item(current_user_roles, ld) or trans.user_is_admin() - rval['is_unrestricted'] = trans.app.security_agent.dataset_is_public(ld.library_dataset_dataset_association.dataset) - rval['tags'] = self.tag_manager.get_tags_str(ld.library_dataset_dataset_association.tags) + rval['is_unrestricted'] = trans.app.security_agent.dataset_is_public(ldda.dataset) + rval['tags'] = self.tag_manager.get_tags_str(ldda.tags) # Manage dataset permission is always attached to the dataset itself, not the the ld or ldda to maintain consistency - rval['can_user_manage'] = trans.app.security_agent.can_manage_dataset(current_user_roles, ld.library_dataset_dataset_association.dataset) or trans.user_is_admin() + rval['can_user_manage'] = trans.app.security_agent.can_manage_dataset(current_user_roles, ldda.dataset) or trans.user_is_admin() return rval def _build_path(self, trans, folder): diff --git a/lib/galaxy/webapps/galaxy/api/folder_contents.py b/lib/galaxy/webapps/galaxy/api/folder_contents.py index 3ff8c2e0629..63ff60d4564 100644 --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -109,6 +109,7 @@ class FolderContentsController(BaseAPIController, UsesLibraryMixin, UsesLibraryM is_unrestricted=is_unrestricted, is_private=is_private, can_manage=can_manage, + state=library_dataset_dict['state'], file_size=nice_size)) if content_item.library_dataset_dataset_association.message: return_item.update(dict(message=content_item.library_dataset_dataset_association.message)) diff --git a/static/maps/mvc/library/library-dataset-view.js.map b/static/maps/mvc/library/library-dataset-view.js.map index 025124c3906..48ff6ceb1f6 100644 --- a/static/maps/mvc/library/library-dataset-view.js.map +++ b/static/maps/mvc/library/library-dataset-view.js.map @@ -1 +1 @@ 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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 $(\n '
    ' +\n inputs +\n \"
    \"\n )\n .appendTo(\"body\")\n .submit()\n .remove();\n\n mod_toastr.info(\"Your download will begin soon.\");\n }\n },\n\n importIntoHistory: function() {\n this.refreshUserHistoriesList(function(self) {\n var template = self.templateBulkImportInModal();\n self.modal = Galaxy.modal;\n self.modal.show({\n closing_events: true,\n title: \"Import into History\",\n body: template({ histories: self.histories.models }),\n buttons: {\n Import: function() {\n self.importCurrentIntoHistory();\n },\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n });\n },\n\n refreshUserHistoriesList: function(callback) {\n var self = this;\n this.histories = new mod_library_model.GalaxyHistories();\n this.histories.fetch({\n success: function(histories) {\n if (histories.length === 0) {\n mod_toastr.warning(\n \"You have to create history first. Click this to do so.\",\n \"\",\n {\n onclick: function() {\n window.location = Galaxy.root;\n }\n }\n );\n } else {\n callback(self);\n }\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n }\n });\n },\n\n importCurrentIntoHistory: function() {\n this.modal.disableButton(\"Import\");\n var new_history_name = this.modal\n .$(\"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 '\",\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 '
    1. Libraries
      2. ',\n '<% _.each(item.get(\"full_path\"), function(path_item) { %>',\n \"<% if (path_item[0] != item.id) { %>\",\n '
    2. \"><%- path_item[1] %>
      3. ',\n \"<% } else { %>\",\n '
    3. <%- path_item[1] %>
      4. ',\n \"<% } %>\",\n \"<% }); %>\",\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 \"\",\n '',\n '',\n \"\",\n '<% if (item.get(\"file_ext\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"genome_build\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"file_size\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"date_uploaded\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"uploaded_by\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"metadata_data_lines\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"metadata_comment_lines\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"metadata_columns\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"metadata_column_types\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"message\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"misc_blurb\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"misc_info\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"tags\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n \"
    \">Name<%= _.escape(item.get(\"name\")) %>
    Data type<%= _.escape(item.get(\"file_ext\")) %>
    Genome build<%= _.escape(item.get(\"genome_build\")) %>
    Size<%= _.escape(item.get(\"file_size\")) %>
    Date uploaded (UTC)<%= _.escape(item.get(\"date_uploaded\")) %>
    Uploaded by<%= _.escape(item.get(\"uploaded_by\")) %>
    Data Lines<%= _.escape(item.get(\"metadata_data_lines\")) %>
    Comment Lines<%= _.escape(item.get(\"metadata_comment_lines\")) %>
    Number of Columns<%= _.escape(item.get(\"metadata_columns\")) %>
    Column Types<%= _.escape(item.get(\"metadata_column_types\")) %>
    Message<%= _.escape(item.get(\"message\")) %>
    Misc. blurb<%= _.escape(item.get(\"misc_blurb\")) %>
    Misc. info<%= _.escape(item.get(\"misc_info\")) %>
    Tags<%= _.escape(item.get(\"tags\")) %>
    \",\n\n \"
    \",\n '
    ',\n                        \"
    \",\n \"
    \",\n\n '<% if (item.get(\"has_versions\")) { %>',\n \"
    \",\n \"

    Expired versions:

    \",\n \"
    \",\n \"<% } %>\",\n // TABLE END\n \"
    \",\n // CONTAINER END\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateVersion: function() {\n return _.template(\n [\n // CONTAINER START\n '
    ',\n '\",\n\n // BREADCRUMBS\n '
      ',\n '
    1. Libraries
      2. ',\n '<% _.each(item.get(\"full_path\"), function(path_item) { %>',\n \"<% if (path_item[0] != item.id) { %>\",\n '
    2. \"><%- path_item[1] %>
      3. ',\n \"<% } else { %>\",\n '
    3. <%- path_item[1] %>
      4. ',\n \"<% } %>\",\n \"<% }); %>\",\n \"
    \",\n\n '
    This is an expired version of the library dataset: <%= _.escape(item.get(\"name\")) %>
    ',\n // DATASET START\n '
    ',\n '',\n \"\",\n '',\n '',\n \"\",\n '<% if (ldda.get(\"file_ext\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"genome_build\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"file_size\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"date_uploaded\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"uploaded_by\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"metadata_data_lines\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"metadata_comment_lines\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"metadata_columns\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"metadata_column_types\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"message\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"misc_blurb\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"misc_info\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"tags\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n \"
    \">Name<%= _.escape(ldda.get(\"name\")) %>
    Data type<%= _.escape(ldda.get(\"file_ext\")) %>
    Genome build<%= _.escape(ldda.get(\"genome_build\")) %>
    Size<%= _.escape(ldda.get(\"file_size\")) %>
    Date uploaded (UTC)<%= _.escape(ldda.get(\"date_uploaded\")) %>
    Uploaded by<%= _.escape(ldda.get(\"uploaded_by\")) %>
    Data Lines<%= _.escape(ldda.get(\"metadata_data_lines\")) %>
    Comment Lines<%= _.escape(ldda.get(\"metadata_comment_lines\")) %>
    Number of Columns<%= _.escape(ldda.get(\"metadata_columns\")) %>
    Column Types<%= _.escape(ldda.get(\"metadata_column_types\")) %>
    Message<%= _.escape(ldda.get(\"message\")) %>
    Miscellaneous blurb<%= _.escape(ldda.get(\"misc_blurb\")) %>
    Miscellaneous information<%= _.escape(ldda.get(\"misc_info\")) %>
    Tags<%= _.escape(item.get(\"tags\")) %>
    \",\n \"
    \",\n '
    ',\n                        \"
    \",\n \"
    \",\n // DATASET END\n \"
    \",\n // CONTAINER END\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateModifyDataset: function() {\n return _.template(\n [\n // CONTAINER START\n '
    ',\n '
    ',\n '\",\n '\",\n \"
    \",\n\n // BREADCRUMBS\n '
      ',\n '
    1. Libraries
      2. ',\n '<% _.each(item.get(\"full_path\"), function(path_item) { %>',\n \"<% if (path_item[0] != item.id) { %>\",\n '
    2. \"><%- path_item[1] %>
      3. ',\n \"<% } else { %>\",\n '
    3. <%- path_item[1] %>
      4. ',\n \"<% } %>\",\n \"<% }); %>\",\n \"
    \",\n\n '
    ',\n '',\n \"\",\n '',\n '',\n \"\",\n \"\",\n '',\n \"\",\n \"\",\n \"\",\n '',\n \"\",\n \"\",\n \"\",\n '',\n '',\n \"\",\n \"\",\n '',\n '',\n \"\",\n \"\",\n '',\n '',\n \"\",\n '',\n '',\n '',\n \"\",\n '',\n '<% if (item.get(\"metadata_comment_lines\") === \"\") { %>',\n '',\n \"<% } else { %>\",\n '',\n \"<% } %>\",\n \"\",\n \"\",\n '',\n '',\n \"\",\n \"\",\n '',\n '',\n \"\",\n \"\",\n '',\n '',\n \"\",\n \"\",\n '',\n '',\n \"\",\n \"\",\n '',\n '',\n \"\",\n //TODO: add functionality to modify tags here\n '<% if (item.get(\"tags\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n \"
    \">Name\">
    Data type\",\n '',\n \"
    Genome build\",\n '',\n \"
    Size<%= _.escape(item.get(\"file_size\")) %>
    Date uploaded (UTC)<%= _.escape(item.get(\"date_uploaded\")) %>
    Uploaded by<%= _.escape(item.get(\"uploaded_by\")) %>
    Data Lines<%= _.escape(item.get(\"metadata_data_lines\")) %>
    Comment Lines<%= _.escape(item.get(\"metadata_comment_lines\")) %>unknown
    Number of Columns<%= _.escape(item.get(\"metadata_columns\")) %>
    Column Types<%= _.escape(item.get(\"metadata_column_types\")) %>
    Message<%= _.escape(item.get(\"message\")) %>
    Misc. blurb<%= _.escape(item.get(\"misc_blurb\")) %>
    Misc. information\">
    Tags<%= _.escape(item.get(\"tags\")) %>
    \",\n \"
    \",\n '
    ',\n                        \"
    \",\n \"
    \",\n \"
    \",\n // CONTAINER END\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateDatasetPermissions: function() {\n return _.template(\n [\n // CONTAINER START\n '
    ',\n '\",\n\n // BREADCRUMBS\n '
      ',\n '
    1. Libraries
      2. ',\n '<% _.each(item.get(\"full_path\"), function(path_item) { %>',\n \"<% if (path_item[0] != item.id) { %>\",\n '
    2. \"><%- path_item[1] %>
      3. ',\n \"<% } else { %>\",\n '
    3. <%- path_item[1] %>
      4. ',\n \"<% } %>\",\n \"<% }); %>\",\n \"
    \",\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 \"

    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 // CONTAINER END\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateBulkImportInModal: function() {\n return _.template(\n [\n \"
    \",\n '
    ',\n \"Select history: \",\n '\",\n \"
    \",\n '
    ',\n \"or create new: \",\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 +{"version":3,"sources":["mvc/library/library-dataset-view.js"],"names":["define","LibraryDatasetView","el","mod_toastr","mod_library_model","mod_utils","mod_select","Backbone","View","extend","edit_mode","options","defaults","events","click .toolbtn_modify_dataset","click .toolbtn_cancel_modifications","click .toolbtn-download-dataset","click .toolbtn-import-dataset","click .copy-link-to-clipboard","click .make-private","click .remove-restrictions","select_genome","click 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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 $(\n '
    ' +\n inputs +\n \"
    \"\n )\n .appendTo(\"body\")\n .submit()\n .remove();\n\n mod_toastr.info(\"Your download will begin soon.\");\n }\n },\n\n importIntoHistory: function() {\n this.refreshUserHistoriesList(function(self) {\n var template = self.templateBulkImportInModal();\n self.modal = Galaxy.modal;\n self.modal.show({\n closing_events: true,\n title: \"Import into History\",\n body: template({ histories: self.histories.models }),\n buttons: {\n Import: function() {\n self.importCurrentIntoHistory();\n },\n Close: function() {\n Galaxy.modal.hide();\n }\n }\n });\n });\n },\n\n refreshUserHistoriesList: function(callback) {\n var self = this;\n this.histories = new mod_library_model.GalaxyHistories();\n this.histories.fetch({\n success: function(histories) {\n if (histories.length === 0) {\n mod_toastr.warning(\n \"You have to create history first. Click this to do so.\",\n \"\",\n {\n onclick: function() {\n window.location = Galaxy.root;\n }\n }\n );\n } else {\n callback(self);\n }\n },\n error: function(model, response) {\n if (typeof response.responseJSON !== \"undefined\") {\n mod_toastr.error(response.responseJSON.err_msg);\n } else {\n mod_toastr.error(\"An error occurred.\");\n }\n }\n });\n },\n\n importCurrentIntoHistory: function() {\n this.modal.disableButton(\"Import\");\n var new_history_name = this.modal\n .$(\"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(e) {\n e.preventDefault();\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 '\",\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 '
    1. Libraries
      2. ',\n '<% _.each(item.get(\"full_path\"), function(path_item) { %>',\n \"<% if (path_item[0] != item.id) { %>\",\n '
    2. \"><%- path_item[1] %>
      3. ',\n \"<% } else { %>\",\n '
    3. <%- path_item[1] %>
      4. ',\n \"<% } %>\",\n \"<% }); %>\",\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 \"\",\n '',\n '',\n \"\",\n '<% if (item.get(\"file_ext\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"genome_build\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"file_size\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"date_uploaded\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"uploaded_by\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"metadata_data_lines\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"metadata_comment_lines\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"metadata_columns\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"metadata_column_types\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"message\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"misc_blurb\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"misc_info\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"tags\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if ( item.get(\"uuid\") !== \"ok\" ) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if ( item.get(\"state\") !== \"ok\" ) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n \"
    \">Name<%= _.escape(item.get(\"name\")) %>
    Data type<%= _.escape(item.get(\"file_ext\")) %>
    Genome build<%= _.escape(item.get(\"genome_build\")) %>
    Size<%= _.escape(item.get(\"file_size\")) %>
    Date uploaded (UTC)<%= _.escape(item.get(\"date_uploaded\")) %>
    Uploaded by<%= _.escape(item.get(\"uploaded_by\")) %>
    Data Lines<%= _.escape(item.get(\"metadata_data_lines\")) %>
    Comment Lines<%= _.escape(item.get(\"metadata_comment_lines\")) %>
    Number of Columns<%= _.escape(item.get(\"metadata_columns\")) %>
    Column Types<%= _.escape(item.get(\"metadata_column_types\")) %>
    Message<%= _.escape(item.get(\"message\")) %>
    Misc. blurb<%= _.escape(item.get(\"misc_blurb\")) %>
    Misc. info<%= _.escape(item.get(\"misc_info\")) %>
    Tags<%= _.escape(item.get(\"tags\")) %>
    UUID<%= _.escape(item.get(\"uuid\")) %>
    State<%= _.escape(item.get(\"state\")) %>
    \",\n\n '<% if (item.get(\"job_stderr\")) { %>',\n \"

    Job Standard Error

    \",\n '
    ',\n                        '<%= _.escape(item.get(\"job_stderr\")) %>',\n                        \"
    \",\n \"<% } %>\",\n\n '<% if (item.get(\"job_stdout\")) { %>',\n \"

    Job Standard Output

    \",\n '
    ',\n                        '<%= _.escape(item.get(\"job_stdout\")) %>',\n                        \"
    \",\n \"<% } %>\",\n\n \"
    \",\n '
    ',\n                        \"
    \",\n \"
    \",\n\n '<% if (item.get(\"has_versions\")) { %>',\n \"
    \",\n \"

    Expired versions:

    \",\n \"
    \",\n \"<% } %>\",\n // TABLE END\n \"
    \",\n // CONTAINER END\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateVersion: function() {\n return _.template(\n [\n // CONTAINER START\n '
    ',\n '\",\n\n // BREADCRUMBS\n '
      ',\n '
    1. Libraries
      2. ',\n '<% _.each(item.get(\"full_path\"), function(path_item) { %>',\n \"<% if (path_item[0] != item.id) { %>\",\n '
    2. \"><%- path_item[1] %>
      3. ',\n \"<% } else { %>\",\n '
    3. <%- path_item[1] %>
      4. ',\n \"<% } %>\",\n \"<% }); %>\",\n \"
    \",\n\n '
    This is an expired version of the library dataset: <%= _.escape(item.get(\"name\")) %>
    ',\n // DATASET START\n '
    ',\n '',\n \"\",\n '',\n '',\n \"\",\n '<% if (ldda.get(\"file_ext\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"genome_build\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"file_size\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"date_uploaded\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"uploaded_by\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"metadata_data_lines\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"metadata_comment_lines\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"metadata_columns\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"metadata_column_types\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"message\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"misc_blurb\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (ldda.get(\"misc_info\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n '<% if (item.get(\"tags\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n \"
    \">Name<%= _.escape(ldda.get(\"name\")) %>
    Data type<%= _.escape(ldda.get(\"file_ext\")) %>
    Genome build<%= _.escape(ldda.get(\"genome_build\")) %>
    Size<%= _.escape(ldda.get(\"file_size\")) %>
    Date uploaded (UTC)<%= _.escape(ldda.get(\"date_uploaded\")) %>
    Uploaded by<%= _.escape(ldda.get(\"uploaded_by\")) %>
    Data Lines<%= _.escape(ldda.get(\"metadata_data_lines\")) %>
    Comment Lines<%= _.escape(ldda.get(\"metadata_comment_lines\")) %>
    Number of Columns<%= _.escape(ldda.get(\"metadata_columns\")) %>
    Column Types<%= _.escape(ldda.get(\"metadata_column_types\")) %>
    Message<%= _.escape(ldda.get(\"message\")) %>
    Miscellaneous blurb<%= _.escape(ldda.get(\"misc_blurb\")) %>
    Miscellaneous information<%= _.escape(ldda.get(\"misc_info\")) %>
    Tags<%= _.escape(item.get(\"tags\")) %>
    \",\n \"
    \",\n '
    ',\n                        \"
    \",\n \"
    \",\n // DATASET END\n \"
    \",\n // CONTAINER END\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateModifyDataset: function() {\n return _.template(\n [\n // CONTAINER START\n '
    ',\n '
    ',\n '\",\n '\",\n \"
    \",\n\n // BREADCRUMBS\n '
      ',\n '
    1. Libraries
      2. ',\n '<% _.each(item.get(\"full_path\"), function(path_item) { %>',\n \"<% if (path_item[0] != item.id) { %>\",\n '
    2. \"><%- path_item[1] %>
      3. ',\n \"<% } else { %>\",\n '
    3. <%- path_item[1] %>
      4. ',\n \"<% } %>\",\n \"<% }); %>\",\n \"
    \",\n\n '
    ',\n '',\n \"\",\n '',\n '',\n \"\",\n \"\",\n '',\n \"\",\n \"\",\n \"\",\n '',\n \"\",\n \"\",\n \"\",\n '',\n '',\n \"\",\n \"\",\n '',\n '',\n \"\",\n \"\",\n '',\n '',\n \"\",\n '',\n '',\n '',\n \"\",\n '',\n '<% if (item.get(\"metadata_comment_lines\") === \"\") { %>',\n '',\n \"<% } else { %>\",\n '',\n \"<% } %>\",\n \"\",\n \"\",\n '',\n '',\n \"\",\n \"\",\n '',\n '',\n \"\",\n \"\",\n '',\n '',\n \"\",\n \"\",\n '',\n '',\n \"\",\n \"\",\n '',\n '',\n \"\",\n //TODO: add functionality to modify tags here\n '<% if (item.get(\"tags\")) { %>',\n \"\",\n '',\n '',\n \"\",\n \"<% } %>\",\n \"
    \">Name\">
    Data type\",\n '',\n \"
    Genome build\",\n '',\n \"
    Size<%= _.escape(item.get(\"file_size\")) %>
    Date uploaded (UTC)<%= _.escape(item.get(\"date_uploaded\")) %>
    Uploaded by<%= _.escape(item.get(\"uploaded_by\")) %>
    Data Lines<%= _.escape(item.get(\"metadata_data_lines\")) %>
    Comment Lines<%= _.escape(item.get(\"metadata_comment_lines\")) %>unknown
    Number of Columns<%= _.escape(item.get(\"metadata_columns\")) %>
    Column Types<%= _.escape(item.get(\"metadata_column_types\")) %>
    Message<%= _.escape(item.get(\"message\")) %>
    Misc. blurb<%= _.escape(item.get(\"misc_blurb\")) %>
    Misc. information\">
    Tags<%= _.escape(item.get(\"tags\")) %>
    \",\n \"
    \",\n '
    ',\n                        \"
    \",\n \"
    \",\n \"
    \",\n // CONTAINER END\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateDatasetPermissions: function() {\n return _.template(\n [\n // CONTAINER START\n '
    ',\n '\",\n\n // BREADCRUMBS\n '
      ',\n '
    1. Libraries
      2. ',\n '<% _.each(item.get(\"full_path\"), function(path_item) { %>',\n \"<% if (path_item[0] != item.id) { %>\",\n '
    2. \"><%- path_item[1] %>
      3. ',\n \"<% } else { %>\",\n '
    3. <%- path_item[1] %>
      4. ',\n \"<% } %>\",\n \"<% }); %>\",\n \"
    \",\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 \"

    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 // CONTAINER END\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateBulkImportInModal: function() {\n return _.template(\n [\n \"
    \",\n '
    ',\n \"Select history: \",\n '\",\n \"
    \",\n '
    ',\n \"or create new: \",\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-folderlist-view.js.map b/static/maps/mvc/library/library-folderlist-view.js.map index 6b0b70b4ff2..98b94d40337 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 '
    1. Libraries
      2. ',\n \"<% _.each(path, function(path_item) { %>\",\n \"<% if (path_item[0] != id) { %>\",\n '
    2. \"><%- path_item[1] %>
      3. ',\n \"<% } else { %>\",\n '
    3. <%- path_item[1] %>
      4. ',\n \"<% } %>\",\n \"<% }); %>\",\n \"
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    name \">descriptiondata typesizetime updated (UTC)
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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 '
    1. Libraries
      2. ',\n \"<% _.each(path, function(path_item) { %>\",\n \"<% if (path_item[0] != id) { %>\",\n '
    2. \"><%- path_item[1] %>
      3. ',\n \"<% } else { %>\",\n '
    3. <%- path_item[1] %>
      4. ',\n \"<% } %>\",\n \"<% }); %>\",\n \"
    \",\n\n // FOLDER CONTENT\n '\" class=\"grid table table-condensed\">',\n \"\",\n '',\n '',\n '',\n '',\n '',\n '',\n '',\n ' ',\n ' ',\n \"\",\n '',\n '',\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n \"
    name \">descriptiondata typesizetime updated (UTC)state
    \",\n '\" title=\"Go to parent folder\" class=\"btn_open_folder btn btn-default btn-xs\">..',\n \"
    \",\n '
    ',\n \"This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up\",\n ' please consult the library security wikipage',\n ' or visit the Galaxy support site.',\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..5339009ddda 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 '',\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 ].join(\"\")\n );\n },\n\n templateRowFile: function() {\n return _.template(\n [\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 ].join(\"\")\n );\n },\n\n templateRowDeletedFile: function() {\n return _.template(\n [\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 ].join(\"\")\n );\n },\n\n templateRowDeletedFolder: function() {\n return _.template(\n [\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 ].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: false,\n save_folder_btn: false,\n cancel_folder_btn: false,\n permission_folder_btn: false\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 \"<% if(!edit_mode) { %>\",\n \"\",\n '\"><%- content_item.get(\"name\") %>',\n \"\",\n \"\",\n '<%- content_item.get(\"description\") %>',\n \"\",\n \"\",\n \"<% } else if(edit_mode){ %>\",\n '',\n '',\n \"<% } %>\",\n \"folder\",\n \"\",\n '<%= _.escape(content_item.get(\"update_time\")) %>',\n \"\",\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 ].join(\"\")\n );\n },\n\n templateRowFile: function() {\n return _.template(\n [\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(\"state\") !== \"ok\" ) { %>',\n '<%= _.escape(content_item.get(\"state\")) %>',\n \"<% } %>\",\n \"\",\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 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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 inputs +\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 // toolbar start\n '
    ',\n '
    ',\n \"DATA LIBRARIES\",\n // paginator will append here\n '',\n '
    ',\n \"\",\n \"
    \",\n '\",\n \"<% if(mutiple_add_dataset_options) { %>\",\n '
    ',\n '\",\n '\",\n \"
    \",\n \"<% } else { %>\",\n '/import/history\" role=\"button\">',\n '',\n \"\",\n \"<% } %>\",\n '\",\n '
    ',\n '\",\n '\",\n \"
    \",\n '',\n '\",\n '',\n '',\n '\",\n \"\",\n \"\",\n \"
    \",\n \"\",\n // toolbar end\n '
    ',\n \"
    \",\n // paginator will append here\n '
    ',\n // container end\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateLocInfoInModal: function() {\n return _.template(\n [\n \"
    \",\n '',\n \"\",\n '',\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n '',\n \"\",\n '<% if(library.get(\"description\") !== \"\") { %>',\n \"\",\n \"\",\n '',\n \"\",\n \"<% } %>\",\n '<% if(library.get(\"synopsis\") !== \"\") { %>',\n \"\",\n \"\",\n '',\n \"\",\n \"<% } %>\",\n '<% if(library.get(\"create_time_pretty\") !== \"\") { %>',\n \"\",\n \"\",\n '',\n \"\",\n \"<% } %>\",\n \"\",\n \"\",\n '',\n \"\",\n \"\",\n \"
    library
    name<%- library.get(\"name\") %>
    description<%- library.get(\"description\") %>
    synopsis<%- library.get(\"synopsis\") %>
    created\"><%- library.get(\"create_time_pretty\") %>
    id<%- library.get(\"id\") %>
    \",\n '',\n \"\",\n '',\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n '<% if(options.folder_description !== \"\") { %>',\n \"\",\n \"\",\n \"\",\n \"\",\n \"<% } %>\",\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n \"
    folder
    name<%- options.folder_name %>
    description<%- options.folder_description %>
    id<%- options.id %>
    \",\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateNewFolderInModal: function() {\n return _.template(\n [\n '
    ',\n \"
    \",\n '',\n '',\n \"
    \",\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateBulkImportInModal: function() {\n return _.template(\n [\n \"
    \",\n '
    ',\n \"Select history: \",\n '\",\n \"
    \",\n '
    ',\n \"or create new: \",\n '',\n \"\",\n \"
    \",\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateImportIntoHistoryProgressBar: function() {\n return _.template(\n [\n '
    ',\n \"Importing selected items to history <%= _.escape(history_name) %>\",\n \"
    \",\n '
    ',\n '
    ',\n '0% Complete',\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 '0% Complete',\n \"
    \",\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateDeletingItemsProgressBar: function() {\n return _.template(\n [\n '
    ',\n \"
    \",\n '
    ',\n '
    ',\n '0% Complete',\n \"
    \",\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateBrowserModal: function() {\n return _.template(\n [\n '
    ',\n '
    All files you select will be imported into the current folder ignoring their folder structure.
    ',\n '
    All files within the selected folders and their subfolders will be imported into the current folder.
    ',\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 ].join(\"\")\n );\n },\n\n templateImportPathModal: function() {\n return _.template(\n [\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 ].join(\"\")\n );\n },\n\n templateAddFilesFromHistory: function() {\n return _.template(\n [\n '
    ',\n \"
    \",\n \"1. Select history: \",\n '\",\n \"
    \",\n \"
    \",\n '
    ',\n \"
    \",\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateHistoryContents: function() {\n return _.template(\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 '
    • \" 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 \"
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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 folder_page_size: Galaxy.libraries.preferences.get(\n \"folder_page_size\"\n )\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 inputs +\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(e) {\n e.preventDefault();\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 // toolbar start\n '
    ',\n '
    ',\n \"DATA LIBRARIES\",\n // paginator will append here\n '',\n '
    ',\n \"\",\n \"
    \",\n '\",\n \"<% if(mutiple_add_dataset_options) { %>\",\n '
    ',\n '\",\n '\",\n \"
    \",\n \"<% } else { %>\",\n '/import/history\" role=\"button\">',\n '',\n \"\",\n \"<% } %>\",\n '\",\n '
    ',\n '\",\n '\",\n \"
    \",\n '',\n '\",\n '',\n '',\n '\",\n \"\",\n \"\",\n \"
    \",\n \"\",\n // toolbar end\n '
    ',\n \"
    \",\n // paginator will append here\n '
    ',\n // container end\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateLocInfoInModal: function() {\n return _.template(\n [\n \"
    \",\n '',\n \"\",\n '',\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n '',\n \"\",\n '<% if(library.get(\"description\") !== \"\") { %>',\n \"\",\n \"\",\n '',\n \"\",\n \"<% } %>\",\n '<% if(library.get(\"synopsis\") !== \"\") { %>',\n \"\",\n \"\",\n '',\n \"\",\n \"<% } %>\",\n '<% if(library.get(\"create_time_pretty\") !== \"\") { %>',\n \"\",\n \"\",\n '',\n \"\",\n \"<% } %>\",\n \"\",\n \"\",\n '',\n \"\",\n \"\",\n \"
    library
    name<%- library.get(\"name\") %>
    description<%- library.get(\"description\") %>
    synopsis<%- library.get(\"synopsis\") %>
    created\"><%- library.get(\"create_time_pretty\") %>
    id<%- library.get(\"id\") %>
    \",\n '',\n \"\",\n '',\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n '<% if(options.folder_description !== \"\") { %>',\n \"\",\n \"\",\n \"\",\n \"\",\n \"<% } %>\",\n \"\",\n \"\",\n \"\",\n \"\",\n \"\",\n \"
    folder
    name<%- options.folder_name %>
    description<%- options.folder_description %>
    id<%- options.id %>
    \",\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateNewFolderInModal: function() {\n return _.template(\n [\n '
    ',\n \"
    \",\n '',\n '',\n \"
    \",\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateBulkImportInModal: function() {\n return _.template(\n [\n \"
    \",\n '
    ',\n \"Select history: \",\n '\",\n \"
    \",\n '
    ',\n \"or create new: \",\n '',\n \"\",\n \"
    \",\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateImportIntoHistoryProgressBar: function() {\n return _.template(\n [\n '
    ',\n \"Importing selected items to history <%= _.escape(history_name) %>\",\n \"
    \",\n '
    ',\n '
    ',\n '0% Complete',\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 '0% Complete',\n \"
    \",\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateDeletingItemsProgressBar: function() {\n return _.template(\n [\n '
    ',\n \"
    \",\n '
    ',\n '
    ',\n '0% Complete',\n \"
    \",\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateBrowserModal: function() {\n return _.template(\n [\n '
    ',\n '
    All files you select will be imported into the current folder ignoring their folder structure.
    ',\n '
    All files within the selected folders and their subfolders will be imported into the current folder.
    ',\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 ].join(\"\")\n );\n },\n\n templateImportPathModal: function() {\n return _.template(\n [\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 ].join(\"\")\n );\n },\n\n templateAddFilesFromHistory: function() {\n return _.template(\n [\n '
    ',\n \"
    \",\n \"1. Select history: \",\n '\",\n \"
    \",\n \"
    \",\n '
    ',\n \"
    \",\n \"
    \"\n ].join(\"\")\n );\n },\n\n templateHistoryContents: function() {\n return _.template(\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 '
    • \" 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 \"
    \"\n ].join(\"\")\n );\n },\n\n templatePaginator: function() {\n return _.template(\n [\n '\",\n \"\",\n ' <%- items_shown %> items shown per page\" class=\"page_size_prompt\">(change)',\n \"\",\n \"\",\n \" <%- total_items_count %> total\",\n \"\"\n ].join(\"\")\n );\n }\n });\n\n return {\n FolderToolbarView: FolderToolbarView\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..16b56b95c6c 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 '\" style=\"display:none;\" data-id=\"<%- library.get(\"id\") %>\">',\n \"<% if(!edit_mode) { %>\",\n '<% if(library.get(\"deleted\")) { %>',\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 '\"><%= 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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 '\" style=\"display:none;\" data-id=\"<%- library.get(\"id\") %>\">',\n \"<% if(!edit_mode) { %>\",\n '<% if(library.get(\"deleted\")) { %>',\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 // For deleted libraries\n '\" class=\"fa fa-ban fa-lg\">',\n '',\n \"\",\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..02e1d604d3c 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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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 library_page_size: Galaxy.libraries.preferences.get(\n \"library_page_size\"\n )\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(e) {\n e.preventDefault();\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 '
    ',\n '
    ',\n 'DATA LIBRARIES',\n '',\n // paginator will append here\n \"\",\n '
    ',\n '',\n \"
    \",\n // only admins see the following\n \"<% if(admin_user === true) { %>\",\n '
    ',\n \"\",\n \"\",\n \"
    \",\n '',\n '',\n \"\",\n \"<% } %>\",\n '',\n '',\n '',\n \"\",\n \"\",\n \"
    \",\n \"
    \",\n \"
    \",\n '
    ',\n // table with libraries will append here\n \"
    \",\n \"
    \"\n ].join(\"\")\n );\n },\n\n templatePaginator: function() {\n return _.template(\n [\n '\",\n \"\",\n ' <%- libraries_shown %> libraries shown per page\" class=\"page_size_prompt\">(change)',\n \"\",\n \"\",\n \" <%- total_libraries_count %> total\",\n \"\"\n ].join(\"\")\n );\n },\n\n templateNewLibraryInModal: function() {\n return _.template(\n [\n '
    ',\n \"
    \",\n '',\n '',\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/scripts/mvc/library/library-dataset-view.js b/static/scripts/mvc/library/library-dataset-view.js index 518209b75af..1cd1d4a8b56 100644 --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -1,2 +1,2 @@ -"use strict";define(["libs/toastr","mvc/library/library-model","utils/utils","mvc/ui/ui-select"],function(t,e,s,i){return{LibraryDatasetView:Backbone.View.extend({el:"#center",model:null,options:{},defaults:{edit_mode:!1},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .copy-link-to-clipboard":"copyToClipboard","click .make-private":"makeDatasetPrivate","click .remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"saveModifications"},select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"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."},list_genomes:[],initialize:function(t){this.options=_.extend(this.options,t),this.fetchExtAndGenomes(),this.options.id&&this.fetchDataset()},fetchDataset:function(s){this.options=_.extend(this.options,s),this.model=new e.Item({id:this.options.id});var i=this;this.model.fetch({success:function(){i.options.show_permissions?i.showPermissions():i.options.show_version?i.fetchVersion():i.render()},error:function(e,s){void 0!==s.responseJSON?t.error(s.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}}):t.error("An error occurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}})},render:function(t){this.options=_.extend(this.options,t),$(".tooltip").remove();var e=this.templateDataset();this.$el.html(e({item:this.model})),$(".peek").html(this.model.get("peek")),$("#center [data-toggle]").tooltip()},fetchVersion:function(s){this.options=_.extend(this.options,s),that=this,this.options.ldda_id?(this.ldda=new e.Ldda({id:this.options.ldda_id}),this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id,this.ldda.fetch({success:function(){that.renderVersion()},error:function(e,s){void 0!==s.responseJSON?t.error(s.responseJSON.err_msg):t.error("An error occurred.")}})):(this.render(),t.error("Library dataset version requested but no id provided."))},renderVersion:function(){$(".tooltip").remove();var t=this.templateVersion();this.$el.html(t({item:this.model,ldda:this.ldda})),$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var t=this.templateModifyDataset();this.$el.html(t({item:this.model})),this.renderSelectBoxes({genome_build:this.model.get("genome_build"),file_ext:this.model.get("file_ext")}),$(".peek").html(this.model.get("peek")),$("#center [data-toggle]").tooltip()},downloadDataset:function(){var t=Galaxy.root+"api/libraries/datasets/download/uncompressed",e={ld_ids:this.id};this.processDownload(t,e)},processDownload:function(e,s,i){if(e&&s){s="string"==typeof s?s:$.param(s);var a="";$.each(s.split("&"),function(){var t=this.split("=");a+=''}),$('
    '+a+"
    ").appendTo("body").submit().remove(),t.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(t){var e=t.templateBulkImportInModal();t.modal=Galaxy.modal,t.modal.show({closing_events:!0,title:"Import into History",body:e({histories:t.histories.models}),buttons:{Import:function(){t.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(s){var i=this;this.histories=new e.GalaxyHistories,this.histories.fetch({success:function(e){0===e.length?t.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location=Galaxy.root}}):s(i)},error:function(e,s){void 0!==s.responseJSON?t.error(s.responseJSON.err_msg):t.error("An error occurred.")}})},importCurrentIntoHistory:function(){this.modal.disableButton("Import");var e=this.modal.$("input[name=history_name]").val(),s=this;if(""!==e)$.post(Galaxy.root+"api/histories",{name:e}).done(function(t){s.processImportToHistory(t.id)}).fail(function(e,s,i){t.error("An error occurred.")}).always(function(){s.modal.enableButton("Import")});else{var i=$(this.modal.$el).find("select[name=dataset_import_single] option:selected").val();this.processImportToHistory(i),this.modal.enableButton("Import")}},processImportToHistory:function(s){var i=new e.HistoryItem;i.url=i.urlRoot+s+"/contents",jQuery.getJSON(Galaxy.root+"history/set_as_current?id="+s),i.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide(),t.success("Dataset imported. Click this to start analyzing it.","",{onclick:function(){window.location=Galaxy.root}})},error:function(e,s){void 0!==s.responseJSON?t.error("Dataset not imported. "+s.responseJSON.err_msg):t.error("An error occured. Dataset not imported. Please try again.")}})},showPermissions:function(e){var s=this.templateDatasetPermissions(),i=this;this.options=_.extend(this.options,e),$(".tooltip").remove(),void 0!==this.options.fetched_permissions&&(0===this.options.fetched_permissions.access_dataset_roles.length?this.model.set({is_unrestricted:!0}):this.model.set({is_unrestricted:!1})),this.$el.html(s({item:this.model,is_admin:Galaxy.config.is_admin_user})),$.get(Galaxy.root+"api/libraries/datasets/"+i.id+"/permissions?scope=current").done(function(t){i.prepareSelectBoxes({fetched_permissions:t,is_admin:Galaxy.config.is_admin_user})}).fail(function(){t.error("An error occurred while attempting to fetch dataset permissions.")}),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},_serializeRoles:function(t){for(var e=[],s=0;s0))return void t.warning("Library dataset name has to be at least 1 character long.");i.set("name",a),s=!0}var o=this.$el.find(".input_dataset_misc_info").val();void 0!==o&&o!==i.get("misc_info")&&(i.set("misc_info",o),s=!0);var r=this.select_genome.$el.select2("data").id;void 0!==r&&r!==i.get("genome_build")&&(i.set("genome_build",r),s=!0);var n=this.select_extension.$el.select2("data").id;void 0!==n&&n!==i.get("file_ext")&&(i.set("file_ext",n),s=!0);var l=this;s?i.save(null,{patch:!0,success:function(e){l.render(),t.success("Changes to library dataset saved.")},error:function(e,s){void 0!==s.responseJSON?t.error(s.responseJSON.err_msg):t.error("An error occured while attempting to update the library dataset.")}}):(l.render(),t.info("Nothing has changed."))},copyToClipboard:function(){var t=Backbone.history.location.href;-1!==t.lastIndexOf("/permissions")&&(t=t.substr(0,t.lastIndexOf("/permissions"))),window.prompt("Copy to clipboard: Ctrl+C, Enter",t)},makeDatasetPrivate:function(){var e=this;$.post(Galaxy.root+"api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(s){e.model.set({is_unrestricted:!1}),e.showPermissions({fetched_permissions:s}),t.success("The dataset is now private to you.")}).fail(function(){t.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post(Galaxy.root+"api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(s){e.model.set({is_unrestricted:!0}),e.showPermissions({fetched_permissions:s}),t.success("Access to this dataset is now unrestricted.")}).fail(function(){t.error("An error occurred while attempting to make dataset unrestricted.")})},_extractIds:function(t){for(var e=[],s=t.length-1;s>=0;s--)e.push(t[s].id);return e},savePermissions:function(e){var s=this,i=this._extractIds(this.accessSelectObject.$el.select2("data")),a=this._extractIds(this.manageSelectObject.$el.select2("data")),o=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post(Galaxy.root+"api/libraries/datasets/"+s.id+"/permissions?action=set_permissions",{"access_ids[]":i,"manage_ids[]":a,"modify_ids[]":o}).done(function(e){s.showPermissions({fetched_permissions:e}),t.success("Permissions saved.")}).fail(function(){t.error("An error occurred while attempting to set dataset permissions.")})},fetchExtAndGenomes:function(){var t=this;0==this.list_genomes.length&&s.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(e){for(var s in e)t.list_extensions.push({id:e[s].extension,text:e[s].extension,description:e[s].description,description_url:e[s].description_url});t.list_extensions.sort(function(t,e){return t.id>e.id?1:t.ide.id?1:t.id','
    ','",'",'<% if (item.get("can_user_modify")) { %>','","<% } %>",'<% if (item.get("can_user_manage")) { %>','/datasets/<%- item.id %>/permissions">','","","<% } %>","
    ",'
      ','
    1. Libraries
      2. ','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'
    2. <%- path_item[1] %>
      3. ',"<% } else { %>",'
    3. <%- path_item[1] %>
      4. ',"<% } %>","<% }); %>","
    ",'<% if (item.get("is_unrestricted")) { %>',"
    ",'This dataset is unrestricted so everybody with the link can access it. Just share this page.',"
    ","<% } %>",'
    ','',"",'','',"",'<% if (item.get("file_ext")) { %>',"",'','',"","<% } %>",'<% if (item.get("genome_build")) { %>',"",'','',"","<% } %>",'<% if (item.get("file_size")) { %>',"",'','',"","<% } %>",'<% if (item.get("date_uploaded")) { %>',"",'','',"","<% } %>",'<% if (item.get("uploaded_by")) { %>',"",'','',"","<% } %>",'<% if (item.get("metadata_data_lines")) { %>',"",'','',"","<% } %>",'<% if (item.get("metadata_comment_lines")) { %>',"",'','',"","<% } %>",'<% if (item.get("metadata_columns")) { %>',"",'','',"","<% } %>",'<% if (item.get("metadata_column_types")) { %>',"",'','',"","<% } %>",'<% if (item.get("message")) { %>',"",'','',"","<% } %>",'<% if (item.get("misc_blurb")) { %>',"",'','',"","<% } %>",'<% if (item.get("misc_info")) { %>',"",'','',"","<% } %>",'<% if (item.get("tags")) { %>',"",'','',"","<% } %>","
    ">Name<%= _.escape(item.get("name")) %>
    Data type<%= _.escape(item.get("file_ext")) %>
    Genome build<%= _.escape(item.get("genome_build")) %>
    Size<%= _.escape(item.get("file_size")) %>
    Date uploaded (UTC)<%= _.escape(item.get("date_uploaded")) %>
    Uploaded by<%= _.escape(item.get("uploaded_by")) %>
    Data Lines<%= _.escape(item.get("metadata_data_lines")) %>
    Comment Lines<%= _.escape(item.get("metadata_comment_lines")) %>
    Number of Columns<%= _.escape(item.get("metadata_columns")) %>
    Column Types<%= _.escape(item.get("metadata_column_types")) %>
    Message<%= _.escape(item.get("message")) %>
    Misc. blurb<%= _.escape(item.get("misc_blurb")) %>
    Misc. info<%= _.escape(item.get("misc_info")) %>
    Tags<%= _.escape(item.get("tags")) %>
    ","
    ",'
    ',"
    ","
    ",'<% if (item.get("has_versions")) { %>',"
    ","

    Expired versions:

    ","
    ","<% } %>","
    ","
    "].join(""))},templateVersion:function(){return _.template(['
    ','",'
      ','
    1. Libraries
      2. ','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'
    2. <%- path_item[1] %>
      3. ',"<% } else { %>",'
    3. <%- path_item[1] %>
      4. ',"<% } %>","<% }); %>","
    ",'
    This is an expired version of the library dataset: <%= _.escape(item.get("name")) %>
    ','
    ','',"",'','',"",'<% if (ldda.get("file_ext")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("genome_build")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("file_size")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("date_uploaded")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("uploaded_by")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("metadata_data_lines")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("metadata_comment_lines")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("metadata_columns")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("metadata_column_types")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("message")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("misc_blurb")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("misc_info")) { %>',"",'','',"","<% } %>",'<% if (item.get("tags")) { %>',"",'','',"","<% } %>","
    Name<%= _.escape(ldda.get("name")) %>
    Data type<%= _.escape(ldda.get("file_ext")) %>
    Genome build<%= _.escape(ldda.get("genome_build")) %>
    Size<%= _.escape(ldda.get("file_size")) %>
    Date uploaded (UTC)<%= _.escape(ldda.get("date_uploaded")) %>
    Uploaded by<%= _.escape(ldda.get("uploaded_by")) %>
    Data Lines<%= _.escape(ldda.get("metadata_data_lines")) %>
    Comment Lines<%= _.escape(ldda.get("metadata_comment_lines")) %>
    Number of Columns<%= _.escape(ldda.get("metadata_columns")) %>
    Column Types<%= _.escape(ldda.get("metadata_column_types")) %>
    Message<%= _.escape(ldda.get("message")) %>
    Miscellaneous blurb<%= _.escape(ldda.get("misc_blurb")) %>
    Miscellaneous information<%= _.escape(ldda.get("misc_info")) %>
    Tags<%= _.escape(item.get("tags")) %>
    ","
    ",'
    ',"
    ","
    ","
    ","
    "].join(""))},templateModifyDataset:function(){return _.template(['
    ','
    ','",'","
    ",'
      ','
    1. Libraries
      2. ','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'
    2. <%- path_item[1] %>
      3. ',"<% } else { %>",'
    3. <%- path_item[1] %>
      4. ',"<% } %>","<% }); %>","
    ",'
    ','',"",'','',"","",'',"","","",'',"","","",'','',"","",'','',"","",'','',"",'','','',"",'','<% if (item.get("metadata_comment_lines") === "") { %>','',"<% } else { %>",'',"<% } %>","","",'','',"","",'','',"","",'','',"","",'','',"","",'','',"",'<% if (item.get("tags")) { %>',"",'','',"","<% } %>","
    ">Name">
    Data type",'',"
    Genome build",'',"
    Size<%= _.escape(item.get("file_size")) %>
    Date uploaded (UTC)<%= _.escape(item.get("date_uploaded")) %>
    Uploaded by<%= _.escape(item.get("uploaded_by")) %>
    Data Lines<%= _.escape(item.get("metadata_data_lines")) %>
    Comment Lines<%= _.escape(item.get("metadata_comment_lines")) %>unknown
    Number of Columns<%= _.escape(item.get("metadata_columns")) %>
    Column Types<%= _.escape(item.get("metadata_column_types")) %>
    Message<%= _.escape(item.get("message")) %>
    Misc. blurb<%= _.escape(item.get("misc_blurb")) %>
    Misc. information">
    Tags<%= _.escape(item.get("tags")) %>
    ","
    ",'
    ',"
    ","
    ","
    ","
    "].join(""))},templateDatasetPermissions:function(){return _.template(['
    ','",'
      ','
    1. Libraries
      2. ','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'
    2. <%- path_item[1] %>
      3. ',"<% } else { %>",'
    3. <%- path_item[1] %>
      4. ',"<% } %>","<% }); %>","
    ",'

    Dataset: <%= _.escape(item.get("name")) %>

    ','
    ',"<% if (is_admin) { %>","You are logged in as an administrator therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.","<% } else { %>","You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.","<% } %>","
    ",'
    ',"

    Library-related permissions

    ","

    Roles that can modify the library item

    ",'
    ','
    User with any of these roles can modify name, metadata, and other information about this library item.
    ',"
    ","

    Dataset-related permissions

    ",'
    Changes made below will affect every library item that was created from this dataset and also every history this dataset is part of.
    ','<% if (!item.get("is_unrestricted")) { %>','

    You can remove all access restrictions on this dataset.

    ',"<% } else { %>",'

    You can make this dataset private to you.

    ',"<% } %>","

    Roles that can access the dataset

    ",'
    ','
    ',"User has to have all these roles in order to access this dataset."," Users without access permission cannot have other permissions on this dataset."," If there are no access roles set on the dataset it is considered unrestricted.","
    ","

    Roles that can manage permissions on the dataset

    ",'
    ','
    ',"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.","
    ",'","
    ","
    "].join(""))},templateBulkImportInModal:function(){return _.template(["
    ",'
    ',"Select history: ",'","
    ",'
    ',"or create new: ",'',"","
    ","
    "].join(""))}})}}); +"use strict";define(["libs/toastr","mvc/library/library-model","utils/utils","mvc/ui/ui-select"],function(t,e,s,i){return{LibraryDatasetView:Backbone.View.extend({el:"#center",model:null,options:{},defaults:{edit_mode:!1},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .copy-link-to-clipboard":"copyToClipboard","click .make-private":"makeDatasetPrivate","click .remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"saveModifications"},select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"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."},list_genomes:[],initialize:function(t){this.options=_.extend(this.options,t),this.fetchExtAndGenomes(),this.options.id&&this.fetchDataset()},fetchDataset:function(s){this.options=_.extend(this.options,s),this.model=new e.Item({id:this.options.id});var i=this;this.model.fetch({success:function(){i.options.show_permissions?i.showPermissions():i.options.show_version?i.fetchVersion():i.render()},error:function(e,s){void 0!==s.responseJSON?t.error(s.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}}):t.error("An error occurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}})},render:function(t){this.options=_.extend(this.options,t),$(".tooltip").remove();var e=this.templateDataset();this.$el.html(e({item:this.model})),$(".peek").html(this.model.get("peek")),$("#center [data-toggle]").tooltip()},fetchVersion:function(s){this.options=_.extend(this.options,s),that=this,this.options.ldda_id?(this.ldda=new e.Ldda({id:this.options.ldda_id}),this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id,this.ldda.fetch({success:function(){that.renderVersion()},error:function(e,s){void 0!==s.responseJSON?t.error(s.responseJSON.err_msg):t.error("An error occurred.")}})):(this.render(),t.error("Library dataset version requested but no id provided."))},renderVersion:function(){$(".tooltip").remove();var t=this.templateVersion();this.$el.html(t({item:this.model,ldda:this.ldda})),$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var t=this.templateModifyDataset();this.$el.html(t({item:this.model})),this.renderSelectBoxes({genome_build:this.model.get("genome_build"),file_ext:this.model.get("file_ext")}),$(".peek").html(this.model.get("peek")),$("#center [data-toggle]").tooltip()},downloadDataset:function(){var t=Galaxy.root+"api/libraries/datasets/download/uncompressed",e={ld_ids:this.id};this.processDownload(t,e)},processDownload:function(e,s,i){if(e&&s){s="string"==typeof s?s:$.param(s);var a="";$.each(s.split("&"),function(){var t=this.split("=");a+=''}),$('
    '+a+"
    ").appendTo("body").submit().remove(),t.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(t){var e=t.templateBulkImportInModal();t.modal=Galaxy.modal,t.modal.show({closing_events:!0,title:"Import into History",body:e({histories:t.histories.models}),buttons:{Import:function(){t.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(s){var i=this;this.histories=new e.GalaxyHistories,this.histories.fetch({success:function(e){0===e.length?t.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location=Galaxy.root}}):s(i)},error:function(e,s){void 0!==s.responseJSON?t.error(s.responseJSON.err_msg):t.error("An error occurred.")}})},importCurrentIntoHistory:function(){this.modal.disableButton("Import");var e=this.modal.$("input[name=history_name]").val(),s=this;if(""!==e)$.post(Galaxy.root+"api/histories",{name:e}).done(function(t){s.processImportToHistory(t.id)}).fail(function(e,s,i){t.error("An error occurred.")}).always(function(){s.modal.enableButton("Import")});else{var i=$(this.modal.$el).find("select[name=dataset_import_single] option:selected").val();this.processImportToHistory(i),this.modal.enableButton("Import")}},processImportToHistory:function(s){var i=new e.HistoryItem;i.url=i.urlRoot+s+"/contents",jQuery.getJSON(Galaxy.root+"history/set_as_current?id="+s),i.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide(),t.success("Dataset imported. Click this to start analyzing it.","",{onclick:function(){window.location=Galaxy.root}})},error:function(e,s){void 0!==s.responseJSON?t.error("Dataset not imported. "+s.responseJSON.err_msg):t.error("An error occured. Dataset not imported. Please try again.")}})},showPermissions:function(e){var s=this.templateDatasetPermissions(),i=this;this.options=_.extend(this.options,e),$(".tooltip").remove(),void 0!==this.options.fetched_permissions&&(0===this.options.fetched_permissions.access_dataset_roles.length?this.model.set({is_unrestricted:!0}):this.model.set({is_unrestricted:!1})),this.$el.html(s({item:this.model,is_admin:Galaxy.config.is_admin_user})),$.get(Galaxy.root+"api/libraries/datasets/"+i.id+"/permissions?scope=current").done(function(t){i.prepareSelectBoxes({fetched_permissions:t,is_admin:Galaxy.config.is_admin_user})}).fail(function(){t.error("An error occurred while attempting to fetch dataset permissions.")}),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},_serializeRoles:function(t){for(var e=[],s=0;s0))return void t.warning("Library dataset name has to be at least 1 character long.");i.set("name",a),s=!0}var o=this.$el.find(".input_dataset_misc_info").val();void 0!==o&&o!==i.get("misc_info")&&(i.set("misc_info",o),s=!0);var r=this.select_genome.$el.select2("data").id;void 0!==r&&r!==i.get("genome_build")&&(i.set("genome_build",r),s=!0);var n=this.select_extension.$el.select2("data").id;void 0!==n&&n!==i.get("file_ext")&&(i.set("file_ext",n),s=!0);var l=this;s?i.save(null,{patch:!0,success:function(e){l.render(),t.success("Changes to library dataset saved.")},error:function(e,s){void 0!==s.responseJSON?t.error(s.responseJSON.err_msg):t.error("An error occured while attempting to update the library dataset.")}}):(l.render(),t.info("Nothing has changed."))},copyToClipboard:function(t){t.preventDefault();var e=Backbone.history.location.href;-1!==e.lastIndexOf("/permissions")&&(e=e.substr(0,e.lastIndexOf("/permissions"))),window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post(Galaxy.root+"api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(s){e.model.set({is_unrestricted:!1}),e.showPermissions({fetched_permissions:s}),t.success("The dataset is now private to you.")}).fail(function(){t.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post(Galaxy.root+"api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(s){e.model.set({is_unrestricted:!0}),e.showPermissions({fetched_permissions:s}),t.success("Access to this dataset is now unrestricted.")}).fail(function(){t.error("An error occurred while attempting to make dataset unrestricted.")})},_extractIds:function(t){for(var e=[],s=t.length-1;s>=0;s--)e.push(t[s].id);return e},savePermissions:function(e){var s=this,i=this._extractIds(this.accessSelectObject.$el.select2("data")),a=this._extractIds(this.manageSelectObject.$el.select2("data")),o=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post(Galaxy.root+"api/libraries/datasets/"+s.id+"/permissions?action=set_permissions",{"access_ids[]":i,"manage_ids[]":a,"modify_ids[]":o}).done(function(e){s.showPermissions({fetched_permissions:e}),t.success("Permissions saved.")}).fail(function(){t.error("An error occurred while attempting to set dataset permissions.")})},fetchExtAndGenomes:function(){var t=this;0==this.list_genomes.length&&s.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(e){for(var s in e)t.list_extensions.push({id:e[s].extension,text:e[s].extension,description:e[s].description,description_url:e[s].description_url});t.list_extensions.sort(function(t,e){return t.id>e.id?1:t.ide.id?1:t.id','
    ','",'",'<% if (item.get("can_user_modify")) { %>','","<% } %>",'<% if (item.get("can_user_manage")) { %>','/datasets/<%- item.id %>/permissions">','","","<% } %>","
    ",'
      ','
    1. Libraries
      2. ','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'
    2. <%- path_item[1] %>
      3. ',"<% } else { %>",'
    3. <%- path_item[1] %>
      4. ',"<% } %>","<% }); %>","
    ",'<% if (item.get("is_unrestricted")) { %>',"
    ",'This dataset is unrestricted so everybody with the link can access it. Just share this page.',"
    ","<% } %>",'
    ','',"",'','',"",'<% if (item.get("file_ext")) { %>',"",'','',"","<% } %>",'<% if (item.get("genome_build")) { %>',"",'','',"","<% } %>",'<% if (item.get("file_size")) { %>',"",'','',"","<% } %>",'<% if (item.get("date_uploaded")) { %>',"",'','',"","<% } %>",'<% if (item.get("uploaded_by")) { %>',"",'','',"","<% } %>",'<% if (item.get("metadata_data_lines")) { %>',"",'','',"","<% } %>",'<% if (item.get("metadata_comment_lines")) { %>',"",'','',"","<% } %>",'<% if (item.get("metadata_columns")) { %>',"",'','',"","<% } %>",'<% if (item.get("metadata_column_types")) { %>',"",'','',"","<% } %>",'<% if (item.get("message")) { %>',"",'','',"","<% } %>",'<% if (item.get("misc_blurb")) { %>',"",'','',"","<% } %>",'<% if (item.get("misc_info")) { %>',"",'','',"","<% } %>",'<% if (item.get("tags")) { %>',"",'','',"","<% } %>",'<% if ( item.get("uuid") !== "ok" ) { %>',"",'','',"","<% } %>",'<% if ( item.get("state") !== "ok" ) { %>',"",'','',"","<% } %>","
    ">Name<%= _.escape(item.get("name")) %>
    Data type<%= _.escape(item.get("file_ext")) %>
    Genome build<%= _.escape(item.get("genome_build")) %>
    Size<%= _.escape(item.get("file_size")) %>
    Date uploaded (UTC)<%= _.escape(item.get("date_uploaded")) %>
    Uploaded by<%= _.escape(item.get("uploaded_by")) %>
    Data Lines<%= _.escape(item.get("metadata_data_lines")) %>
    Comment Lines<%= _.escape(item.get("metadata_comment_lines")) %>
    Number of Columns<%= _.escape(item.get("metadata_columns")) %>
    Column Types<%= _.escape(item.get("metadata_column_types")) %>
    Message<%= _.escape(item.get("message")) %>
    Misc. blurb<%= _.escape(item.get("misc_blurb")) %>
    Misc. info<%= _.escape(item.get("misc_info")) %>
    Tags<%= _.escape(item.get("tags")) %>
    UUID<%= _.escape(item.get("uuid")) %>
    State<%= _.escape(item.get("state")) %>
    ",'<% if (item.get("job_stderr")) { %>',"

    Job Standard Error

    ",'
    ','<%= _.escape(item.get("job_stderr")) %>',"
    ","<% } %>",'<% if (item.get("job_stdout")) { %>',"

    Job Standard Output

    ",'
    ','<%= _.escape(item.get("job_stdout")) %>',"
    ","<% } %>","
    ",'
    ',"
    ","
    ",'<% if (item.get("has_versions")) { %>',"
    ","

    Expired versions:

    ","
    ","<% } %>","
    ",""].join(""))},templateVersion:function(){return _.template(['
    ','",'
      ','
    1. Libraries
      2. ','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'
    2. <%- path_item[1] %>
      3. ',"<% } else { %>",'
    3. <%- path_item[1] %>
      4. ',"<% } %>","<% }); %>","
    ",'
    This is an expired version of the library dataset: <%= _.escape(item.get("name")) %>
    ','
    ','',"",'','',"",'<% if (ldda.get("file_ext")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("genome_build")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("file_size")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("date_uploaded")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("uploaded_by")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("metadata_data_lines")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("metadata_comment_lines")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("metadata_columns")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("metadata_column_types")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("message")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("misc_blurb")) { %>',"",'','',"","<% } %>",'<% if (ldda.get("misc_info")) { %>',"",'','',"","<% } %>",'<% if (item.get("tags")) { %>',"",'','',"","<% } %>","
    Name<%= _.escape(ldda.get("name")) %>
    Data type<%= _.escape(ldda.get("file_ext")) %>
    Genome build<%= _.escape(ldda.get("genome_build")) %>
    Size<%= _.escape(ldda.get("file_size")) %>
    Date uploaded (UTC)<%= _.escape(ldda.get("date_uploaded")) %>
    Uploaded by<%= _.escape(ldda.get("uploaded_by")) %>
    Data Lines<%= _.escape(ldda.get("metadata_data_lines")) %>
    Comment Lines<%= _.escape(ldda.get("metadata_comment_lines")) %>
    Number of Columns<%= _.escape(ldda.get("metadata_columns")) %>
    Column Types<%= _.escape(ldda.get("metadata_column_types")) %>
    Message<%= _.escape(ldda.get("message")) %>
    Miscellaneous blurb<%= _.escape(ldda.get("misc_blurb")) %>
    Miscellaneous information<%= _.escape(ldda.get("misc_info")) %>
    Tags<%= _.escape(item.get("tags")) %>
    ","
    ",'
    ',"
    ","
    ","
    ","
    "].join(""))},templateModifyDataset:function(){return _.template(['
    ','
    ','",'","
    ",'
      ','
    1. Libraries
      2. ','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'
    2. <%- path_item[1] %>
      3. ',"<% } else { %>",'
    3. <%- path_item[1] %>
      4. ',"<% } %>","<% }); %>","
    ",'
    ','',"",'','',"","",'',"","","",'',"","","",'','',"","",'','',"","",'','',"",'','','',"",'','<% if (item.get("metadata_comment_lines") === "") { %>','',"<% } else { %>",'',"<% } %>","","",'','',"","",'','',"","",'','',"","",'','',"","",'','',"",'<% if (item.get("tags")) { %>',"",'','',"","<% } %>","
    ">Name">
    Data type",'',"
    Genome build",'',"
    Size<%= _.escape(item.get("file_size")) %>
    Date uploaded (UTC)<%= _.escape(item.get("date_uploaded")) %>
    Uploaded by<%= _.escape(item.get("uploaded_by")) %>
    Data Lines<%= _.escape(item.get("metadata_data_lines")) %>
    Comment Lines<%= _.escape(item.get("metadata_comment_lines")) %>unknown
    Number of Columns<%= _.escape(item.get("metadata_columns")) %>
    Column Types<%= _.escape(item.get("metadata_column_types")) %>
    Message<%= _.escape(item.get("message")) %>
    Misc. blurb<%= _.escape(item.get("misc_blurb")) %>
    Misc. information">
    Tags<%= _.escape(item.get("tags")) %>
    ","
    ",'
    ',"
    ","
    ","
    ","
    "].join(""))},templateDatasetPermissions:function(){return _.template(['
    ','",'
      ','
    1. Libraries
      2. ','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'
    2. <%- path_item[1] %>
      3. ',"<% } else { %>",'
    3. <%- path_item[1] %>
      4. ',"<% } %>","<% }); %>","
    ",'

    Dataset: <%= _.escape(item.get("name")) %>

    ','
    ',"<% if (is_admin) { %>","You are logged in as an administrator therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.","<% } else { %>","You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.","<% } %>","
    ",'
    ',"

    Library-related permissions

    ","

    Roles that can modify the library item

    ",'
    ','
    User with any of these roles can modify name, metadata, and other information about this library item.
    ',"
    ","

    Dataset-related permissions

    ",'
    Changes made below will affect every library item that was created from this dataset and also every history this dataset is part of.
    ','<% if (!item.get("is_unrestricted")) { %>','

    You can remove all access restrictions on this dataset.

    ',"<% } else { %>",'

    You can make this dataset private to you.

    ',"<% } %>","

    Roles that can access the dataset

    ",'
    ','
    ',"User has to have all these roles in order to access this dataset."," Users without access permission cannot have other permissions on this dataset."," If there are no access roles set on the dataset it is considered unrestricted.","
    ","

    Roles that can manage permissions on the dataset

    ",'
    ','
    ',"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.","
    ",'","
    ","
    "].join(""))},templateBulkImportInModal:function(){return _.template(["
    ",'
    ',"Select history: ",'","
    ",'
    ',"or create new: ",'',"","
    ","
    "].join(""))}})}}); //# sourceMappingURL=../../../maps/mvc/library/library-dataset-view.js.map diff --git a/static/scripts/mvc/library/library-folderlist-view.js b/static/scripts/mvc/library/library-folderlist-view.js index cd2e136f197..d1e85a4785b 100644 --- a/static/scripts/mvc/library/library-folderlist-view.js +++ b/static/scripts/mvc/library/library-folderlist-view.js @@ -1,2 +1,2 @@ -"use strict";define(["layout/masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view","mvc/library/library-dataset-view"],function(e,t,i,o,s,r){return{FolderListView:Backbone.View.extend({el:"#folder_items_element",progress:0,progressStep:1,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .folder_row":"selectClickedRow","click .sort-folder-link":"sortColumnClicked"},collection:null,defaults:{include_deleted:!1,page_count:null,show_page:null},initialize:function(e){this.options=_.defaults(this.options||{},this.defaults,e),this.modal=null,this.rowViews={},this.collection=new o.Folder,this.listenTo(this.collection,"add",this.renderOne),this.listenTo(this.collection,"remove",this.removeOne),this.listenTo(this.collection,"sort",this.rePaint),this.listenTo(this.collection,"reset",this.rePaint),this.fetchFolder()},fetchFolder:function(e){var e=e||{};this.options.include_deleted=e.include_deleted;var t=this;this.folderContainer=new o.FolderContainer({id:this.options.id}),this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents",this.options.include_deleted&&(this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"),this.folderContainer.fetch({success:function(e){t.folder_container=e,t.render()},error:function(e,t){void 0!==t.responseJSON?i.error(t.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}}):i.error("An error occurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}})},render:function(e){this.options=_.extend(this.options,e);var t=this.templateFolder();$(".tooltip").hide();var o,s=this.folderContainer.attributes.metadata.full_path;if(o=1===s.length?0:s[s.length-2][0],this.$el.html(t({path:this.folderContainer.attributes.metadata.full_path,parent_library_id:this.folderContainer.attributes.metadata.parent_library_id,id:this.options.id,upper_folder_id:o,order:this.sort})),this.options.dataset_id){var r=_.findWhere(that.rowViews,{id:this.options.dataset_id});r?r.showDatasetDetails():i.error("Requested dataset not found. Showing folder instead.")}else(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.paginate();$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},paginate:function(e){this.options=_.extend(this.options,e),(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.options.total_items_count=this.folder_container.get("folder").models.length,this.options.page_count=Math.ceil(this.options.total_items_count/Galaxy.libraries.preferences.get("folder_page_size"));var t=Galaxy.libraries.preferences.get("folder_page_size")*(this.options.show_page-1),i=null;i=this.folder_container.get("folder").models.slice(t,t+Galaxy.libraries.preferences.get("folder_page_size")),this.options.items_shown=i.length,Galaxy.libraries.preferences.get("folder_page_size")*this.options.show_page>this.options.total_items_count+Galaxy.libraries.preferences.get("folder_page_size")&&(i=[]),Galaxy.libraries.folderToolbarView.renderPaginator(this.options),this.collection.reset(i)},rePaint:function(e){this.options=_.extend(this.options,e),this.removeAllRows(),this.renderAll(),this.checkEmptiness()},addAll:function(e){_.each(e,function(e){Galaxy.libraries.folderListView.collection.add(e,{sort:!1})}),$("#center [data-toggle]").tooltip(),this.checkEmptiness(),this.postRender()},postRender:function(){var e=this.folderContainer.attributes.metadata;e.contains_file_or_folder=void 0!==this.collection.findWhere({type:"file"})||void 0!==this.collection.findWhere({type:"folder"}),Galaxy.libraries.folderToolbarView.configureElements(e)},renderAll:function(){var e=this;_.each(this.collection.models.reverse(),function(t){e.renderOne(t)}),this.postRender()},renderOne:function(e){this.options.contains_file_or_folder=!0,e.set("folder_id",this.id);var t=new s.FolderRowView({model:e});this.rowViews[e.get("id")]=t,this.$el.find("#first_folder_item").after(t.el)},removeOne:function(e){this.$el.find("tr").filter(function(){return $(this).data("id")&&$(this).data("id")===e.id}).remove()},removeAllRows:function(){$(".library-row").remove()},checkEmptiness:function(){0===this.$el.find(".dataset_row").length&&0===this.$el.find(".folder_row").length?this.$el.find(".empty-folder-message").show():this.$el.find(".empty-folder-message").hide()},sortColumnClicked:function(e){e.preventDefault(),"asc"===this.sort?(this.sortFolder("name","desc"),this.sort="desc"):(this.sortFolder("name","asc"),this.sort="asc"),this.renderSortIcon()},sortFolder:function(e,t){if("undefined"===e&&"undefined"===t)return this.collection.sortByNameAsc();if("name"===e){if("asc"===t)return this.collection.sortByNameAsc();if("desc"===t)return this.collection.sortByNameDesc()}},selectAll:function(e){var t=e.target.checked;that=this,$(":checkbox","#folder_list_body").each(function(){this.checked=t;var e=$(this).closest("tr");t?that.makeDarkRow(e):that.makeWhiteRow(e)})},selectClickedRow:function(e){var t,i,o="";t=$(e.target).closest("tr"),"input"===e.target.localName?(o=e.target,i="input"):"td"===e.target.localName&&(o=t.find(":checkbox")[0],i="td"),o.checked?"td"===i?(o.checked="",this.makeWhiteRow(t)):"input"===i&&this.makeDarkRow(t):"td"===i?(o.checked="selected",this.makeDarkRow(t)):"input"===i&&this.makeWhiteRow(t)},makeDarkRow:function(e){e.removeClass("light").addClass("dark"),e.find("a").removeClass("light").addClass("dark"),e.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file"),e.find(".fa-folder-o").removeClass("fa-folder-o").addClass("fa-folder")},makeWhiteRow:function(e){e.removeClass("dark").addClass("light"),e.find("a").removeClass("dark").addClass("light"),e.find(".fa-file").removeClass("fa-file").addClass("fa-file-o"),e.find(".fa-folder").removeClass("fa-folder").addClass("fa-folder-o")},renderSortIcon:function(){"asc"===this.sort?$(".sort-icon").removeClass("fa-sort-alpha-desc").addClass("fa-sort-alpha-asc"):$(".sort-icon").removeClass("fa-sort-alpha-asc").addClass("fa-sort-alpha-desc")},templateFolder:function(){return _.template(['
      ','
    1. Libraries
      2. ',"<% _.each(path, function(path_item) { %>","<% if (path_item[0] != id) { %>",'
    2. <%- path_item[1] %>
      3. ',"<% } else { %>",'
    3. <%- path_item[1] %>
      4. ',"<% } %>","<% }); %>","
    ",'',"",'','','','','','','',' ',"",'','',"","","","","","","","","","","
    name descriptiondata typesizetime updated (UTC)
    ",'" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..',"
    ",'"].join(""))}})}}); +"use strict";define(["layout/masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view","mvc/library/library-dataset-view"],function(e,t,i,s,o,r){return{FolderListView:Backbone.View.extend({el:"#folder_items_element",progress:0,progressStep:1,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .folder_row":"selectClickedRow","click .sort-folder-link":"sortColumnClicked"},collection:null,defaults:{include_deleted:!1,page_count:null,show_page:null},initialize:function(e){this.options=_.defaults(this.options||{},this.defaults,e),this.modal=null,this.rowViews={},this.collection=new s.Folder,this.listenTo(this.collection,"add",this.renderOne),this.listenTo(this.collection,"remove",this.removeOne),this.listenTo(this.collection,"sort",this.rePaint),this.listenTo(this.collection,"reset",this.rePaint),this.fetchFolder()},fetchFolder:function(e){var e=e||{};this.options.include_deleted=e.include_deleted;var t=this;this.folderContainer=new s.FolderContainer({id:this.options.id}),this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents",this.options.include_deleted&&(this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"),this.folderContainer.fetch({success:function(e){t.folder_container=e,t.render()},error:function(e,t){void 0!==t.responseJSON?i.error(t.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}}):i.error("An error occurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}})},render:function(e){this.options=_.extend(this.options,e);var t=this.templateFolder();$(".tooltip").hide();var s,o=this.folderContainer.attributes.metadata.full_path;if(s=1===o.length?0:o[o.length-2][0],this.$el.html(t({path:this.folderContainer.attributes.metadata.full_path,parent_library_id:this.folderContainer.attributes.metadata.parent_library_id,id:this.options.id,upper_folder_id:s,order:this.sort})),this.options.dataset_id){var r=_.findWhere(that.rowViews,{id:this.options.dataset_id});r?r.showDatasetDetails():i.error("Requested dataset not found. Showing folder instead.")}else(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.paginate();$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},paginate:function(e){this.options=_.extend(this.options,e),(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.options.total_items_count=this.folder_container.get("folder").models.length,this.options.page_count=Math.ceil(this.options.total_items_count/Galaxy.libraries.preferences.get("folder_page_size"));var t=Galaxy.libraries.preferences.get("folder_page_size")*(this.options.show_page-1),i=null;i=this.folder_container.get("folder").models.slice(t,t+Galaxy.libraries.preferences.get("folder_page_size")),this.options.items_shown=i.length,Galaxy.libraries.preferences.get("folder_page_size")*this.options.show_page>this.options.total_items_count+Galaxy.libraries.preferences.get("folder_page_size")&&(i=[]),Galaxy.libraries.folderToolbarView.renderPaginator(this.options),this.collection.reset(i)},rePaint:function(e){this.options=_.extend(this.options,e),this.removeAllRows(),this.renderAll(),this.checkEmptiness()},addAll:function(e){_.each(e,function(e){Galaxy.libraries.folderListView.collection.add(e,{sort:!1})}),$("#center [data-toggle]").tooltip(),this.checkEmptiness(),this.postRender()},postRender:function(){var e=this.folderContainer.attributes.metadata;e.contains_file_or_folder=void 0!==this.collection.findWhere({type:"file"})||void 0!==this.collection.findWhere({type:"folder"}),Galaxy.libraries.folderToolbarView.configureElements(e)},renderAll:function(){var e=this;_.each(this.collection.models.reverse(),function(t){e.renderOne(t)}),this.postRender()},renderOne:function(e){this.options.contains_file_or_folder=!0,e.set("folder_id",this.id);var t=new o.FolderRowView({model:e});this.rowViews[e.get("id")]=t,this.$el.find("#first_folder_item").after(t.el)},removeOne:function(e){this.$el.find("tr").filter(function(){return $(this).data("id")&&$(this).data("id")===e.id}).remove()},removeAllRows:function(){$(".library-row").remove()},checkEmptiness:function(){0===this.$el.find(".dataset_row").length&&0===this.$el.find(".folder_row").length?this.$el.find(".empty-folder-message").show():this.$el.find(".empty-folder-message").hide()},sortColumnClicked:function(e){e.preventDefault(),"asc"===this.sort?(this.sortFolder("name","desc"),this.sort="desc"):(this.sortFolder("name","asc"),this.sort="asc"),this.renderSortIcon()},sortFolder:function(e,t){if("undefined"===e&&"undefined"===t)return this.collection.sortByNameAsc();if("name"===e){if("asc"===t)return this.collection.sortByNameAsc();if("desc"===t)return this.collection.sortByNameDesc()}},selectAll:function(e){var t=e.target.checked;that=this,$(":checkbox","#folder_list_body").each(function(){this.checked=t;var e=$(this).closest("tr");t?that.makeDarkRow(e):that.makeWhiteRow(e)})},selectClickedRow:function(e){var t,i,s="";t=$(e.target).closest("tr"),"input"===e.target.localName?(s=e.target,i="input"):"td"===e.target.localName&&(s=t.find(":checkbox")[0],i="td"),s.checked?"td"===i?(s.checked="",this.makeWhiteRow(t)):"input"===i&&this.makeDarkRow(t):"td"===i?(s.checked="selected",this.makeDarkRow(t)):"input"===i&&this.makeWhiteRow(t)},makeDarkRow:function(e){e.removeClass("light").addClass("dark"),e.find("a").removeClass("light").addClass("dark"),e.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file"),e.find(".fa-folder-o").removeClass("fa-folder-o").addClass("fa-folder")},makeWhiteRow:function(e){e.removeClass("dark").addClass("light"),e.find("a").removeClass("dark").addClass("light"),e.find(".fa-file").removeClass("fa-file").addClass("fa-file-o"),e.find(".fa-folder").removeClass("fa-folder").addClass("fa-folder-o")},renderSortIcon:function(){"asc"===this.sort?$(".sort-icon").removeClass("fa-sort-alpha-desc").addClass("fa-sort-alpha-asc"):$(".sort-icon").removeClass("fa-sort-alpha-asc").addClass("fa-sort-alpha-desc")},templateFolder:function(){return _.template(['
      ','
    1. Libraries
      2. ',"<% _.each(path, function(path_item) { %>","<% if (path_item[0] != id) { %>",'
    2. <%- path_item[1] %>
      3. ',"<% } else { %>",'
    3. <%- path_item[1] %>
      4. ',"<% } %>","<% }); %>","
    ",'',"",'','','','','','','',' ',' ',"",'','',"","","","","","","","","","","","
    name descriptiondata typesizetime updated (UTC)state
    ",'" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..',"
    ",'"].join(""))}})}}); //# sourceMappingURL=../../../maps/mvc/library/library-folderlist-view.js.map diff --git a/static/scripts/mvc/library/library-folderrow-view.js b/static/scripts/mvc/library/library-folderrow-view.js index 8736c389c9a..bb466b796e8 100644 --- a/static/scripts/mvc/library/library-folderrow-view.js +++ b/static/scripts/mvc/library/library-folderrow-view.js @@ -1,2 +1,2 @@ -"use strict";define(["libs/toastr","mvc/library/library-model","mvc/library/library-dataset-view"],function(t,e,i){return{FolderRowView:Backbone.View.extend({events:{"click .undelete_dataset_btn":"undeleteDataset","click .undelete_folder_btn":"undeleteFolder","click .edit_folder_btn":"startModifications","click .cancel_folder_btn":"cancelModifications","click .save_folder_btn":"saveModifications"},defaults:{type:null,visibility_config:{edit_folder_btn:!0,save_folder_btn:!1,cancel_folder_btn:!1,permission_folder_btn:!0},edit_mode:!1},initialize:function(t){this.options=_.defaults(t||{},this.defaults),this.render(this.options)},render:function(t){this.options=_.extend(this.options,t);var e=this.options.model,i=null;return"folder"===e.get("type")||"LibraryFolder"===e.get("model_class")?(this.options.type="folder",this.prepareButtons(e),i=e.get("deleted")?this.templateRowDeletedFolder():this.templateRowFolder()):"file"===e.get("type")||"LibraryDatasetDatasetAssociation"===e.get("model_class")||"LibraryDataset"===e.get("model_class")?(this.options.type="file",i=e.get("deleted")?this.templateRowDeletedFile():this.templateRowFile()):(Galaxy.emit.error("Unknown library item type found."),Galaxy.emit.error(e.get("type")||e.get("model_class"))),this.setElement(i({content_item:e,edit_mode:this.options.edit_mode,button_config:this.options.visibility_config})),this.$el.show(),this},prepareButtons:function(t){var e=this.options.visibility_config;!1===this.options.edit_mode?(e.save_folder_btn=!1,e.cancel_folder_btn=!1,!0===t.get("deleted")?(e.edit_folder_btn=!1,e.permission_folder_btn=!1):!1===t.get("deleted")&&(e.save_folder_btn=!1,e.cancel_folder_btn=!1,!0===t.get("can_modify")&&(e.edit_folder_btn=!0),!0===t.get("can_manage")&&(e.permission_folder_btn=!0))):!0===this.options.edit_mode&&(e.edit_folder_btn=!1,e.permission_folder_btn=!1,e.save_folder_btn=!0,e.cancel_folder_btn=!0),this.options.visibility_config=e},showDatasetDetails:function(){Galaxy.libraries.datasetView=new i.LibraryDatasetView({id:this.id})},undeleteDataset:function(i){$(".tooltip").hide();var o=this,a=$(i.target).closest("tr").data("id"),n=Galaxy.libraries.folderListView.collection.get(a);n.url=n.urlRoot+n.id+"?undelete=true",n.destroy({success:function(i,n){Galaxy.libraries.folderListView.collection.remove(a);var l=new e.Item(n);Galaxy.libraries.folderListView.collection.add(l),Galaxy.libraries.folderListView.collection.sortByNameAsc(),t.success("Dataset undeleted. Click this to see it.","",{onclick:function(){var t=o.model.get("folder_id");window.location=Galaxy.root+"library/list#folders/"+t+"/datasets/"+o.id}})},error:function(e,i){void 0!==i.responseJSON?t.error("Dataset was not undeleted. "+i.responseJSON.err_msg):t.error("An error occured! Dataset was not undeleted. Please try again.")}})},undeleteFolder:function(i){$(".tooltip").hide();var o=$(i.target).closest("tr").data("id"),a=Galaxy.libraries.folderListView.collection.get(o);a.url=a.urlRoot+a.id+"?undelete=true",a.destroy({success:function(i,a){Galaxy.libraries.folderListView.collection.remove(o);var n=new e.FolderAsModel(a);Galaxy.libraries.folderListView.collection.add(n),Galaxy.libraries.folderListView.collection.sortByNameAsc(),t.success("Folder undeleted.")},error:function(e,i){void 0!==i.responseJSON?t.error("Folder was not undeleted. "+i.responseJSON.err_msg):t.error("An error occured! Folder was not undeleted. Please try again.")}})},startModifications:function(){this.options.edit_mode=!0,this.repaint()},cancelModifications:function(){this.options.edit_mode=!1,this.repaint()},saveModifications:function(){var e=Galaxy.libraries.folderListView.collection.get(this.$el.data("id")),i=!1,o=this.$el.find(".input_folder_name").val();if(void 0!==o&&o!==e.get("name")){if(!(o.length>2))return void t.warning("Folder name has to be at least 3 characters long.");e.set("name",o),i=!0}var a=this.$el.find(".input_folder_description").val();if(void 0!==a&&a!==e.get("description")&&(e.set("description",a),i=!0),i){var n=this;e.save(null,{patch:!0,success:function(e){n.options.edit_mode=!1,n.repaint(e),t.success("Changes to folder saved.")},error:function(e,i){void 0!==i.responseJSON?t.error(i.responseJSON.err_msg):t.error("An error occured while attempting to update the folder.")}})}else this.options.edit_mode=!1,this.repaint(e),t.info("Nothing has changed.")},repaint:function(){$(".tooltip").hide();var t=this.$el;this.render(),t.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},templateRowFolder:function(){return _.template(['',"",'',"",'',"<% if(!edit_mode) { %>","",'<%- content_item.get("name") %>',"","",'<%- content_item.get("description") %>',"","<% } else if(edit_mode){ %>",'','',"<% } %>","folder","","",'<%= _.escape(content_item.get("update_time")) %>',"","","<% if(edit_mode) { %>",'",'","<% } else if (!edit_mode){%>",'",'','","","<% } %>","",""].join(""))},templateRowFile:function(){return _.template(['',"",'',"",'','',"","",'/datasets/<%- content_item.id %>" class="library-dataset">','<%- content_item.get("name") %>',"","",'<%- content_item.get("message") %>','<%= _.escape(content_item.get("file_ext")) %>','<%= _.escape(content_item.get("file_size")) %>','<%= _.escape(content_item.get("update_time")) %>',"",'<% if (content_item.get("is_unrestricted")) { %>','',"<% } %>",'<% if (content_item.get("is_private")) { %>','',"<% } %>",'<% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %>','',"<% } %>",'<% if (content_item.get("can_manage")) { %>','/datasets/<%- content_item.id %>/permissions">','","","<% } %>","",""].join(""))},templateRowDeletedFile:function(){return _.template(['',"",'',"","",'','<%- content_item.get("name") %>',"","",'<%- content_item.get("message") %>',"","",'<%= _.escape(content_item.get("file_ext")) %>',"","",'<%= _.escape(content_item.get("file_size")) %>',"","",'<%= _.escape(content_item.get("update_time")) %>',"","",'','","",""].join(""))},templateRowDeletedFolder:function(){return _.template(['',"",'',"","",'','<%- content_item.get("name") %>',"","",'<%- content_item.get("description") %>',"","","folder","","","",'<%= _.escape(content_item.get("update_time")) %>',"","",'','","",""].join(""))}})}}); +"use strict";define(["libs/toastr","mvc/library/library-model","mvc/library/library-dataset-view"],function(t,e,i){return{FolderRowView:Backbone.View.extend({events:{"click .undelete_dataset_btn":"undeleteDataset","click .undelete_folder_btn":"undeleteFolder","click .edit_folder_btn":"startModifications","click .cancel_folder_btn":"cancelModifications","click .save_folder_btn":"saveModifications"},defaults:{type:null,visibility_config:{edit_folder_btn:!1,save_folder_btn:!1,cancel_folder_btn:!1,permission_folder_btn:!1},edit_mode:!1},initialize:function(t){this.options=_.defaults(t||{},this.defaults),this.render(this.options)},render:function(t){this.options=_.extend(this.options,t);var e=this.options.model,i=null;return"folder"===e.get("type")||"LibraryFolder"===e.get("model_class")?(this.options.type="folder",this.prepareButtons(e),i=e.get("deleted")?this.templateRowDeletedFolder():this.templateRowFolder()):"file"===e.get("type")||"LibraryDatasetDatasetAssociation"===e.get("model_class")||"LibraryDataset"===e.get("model_class")?(this.options.type="file",i=e.get("deleted")?this.templateRowDeletedFile():this.templateRowFile()):(Galaxy.emit.error("Unknown library item type found."),Galaxy.emit.error(e.get("type")||e.get("model_class"))),this.setElement(i({content_item:e,edit_mode:this.options.edit_mode,button_config:this.options.visibility_config})),this.$el.show(),this},prepareButtons:function(t){var e=this.options.visibility_config;!1===this.options.edit_mode?(e.save_folder_btn=!1,e.cancel_folder_btn=!1,!0===t.get("deleted")?(e.edit_folder_btn=!1,e.permission_folder_btn=!1):!1===t.get("deleted")&&(e.save_folder_btn=!1,e.cancel_folder_btn=!1,!0===t.get("can_modify")&&(e.edit_folder_btn=!0),!0===t.get("can_manage")&&(e.permission_folder_btn=!0))):!0===this.options.edit_mode&&(e.edit_folder_btn=!1,e.permission_folder_btn=!1,e.save_folder_btn=!0,e.cancel_folder_btn=!0),this.options.visibility_config=e},showDatasetDetails:function(){Galaxy.libraries.datasetView=new i.LibraryDatasetView({id:this.id})},undeleteDataset:function(i){$(".tooltip").hide();var o=this,a=$(i.target).closest("tr").data("id"),n=Galaxy.libraries.folderListView.collection.get(a);n.url=n.urlRoot+n.id+"?undelete=true",n.destroy({success:function(i,n){Galaxy.libraries.folderListView.collection.remove(a);var l=new e.Item(n);Galaxy.libraries.folderListView.collection.add(l),Galaxy.libraries.folderListView.collection.sortByNameAsc(),t.success("Dataset undeleted. Click this to see it.","",{onclick:function(){var t=o.model.get("folder_id");window.location=Galaxy.root+"library/list#folders/"+t+"/datasets/"+o.id}})},error:function(e,i){void 0!==i.responseJSON?t.error("Dataset was not undeleted. "+i.responseJSON.err_msg):t.error("An error occured! Dataset was not undeleted. Please try again.")}})},undeleteFolder:function(i){$(".tooltip").hide();var o=$(i.target).closest("tr").data("id"),a=Galaxy.libraries.folderListView.collection.get(o);a.url=a.urlRoot+a.id+"?undelete=true",a.destroy({success:function(i,a){Galaxy.libraries.folderListView.collection.remove(o);var n=new e.FolderAsModel(a);Galaxy.libraries.folderListView.collection.add(n),Galaxy.libraries.folderListView.collection.sortByNameAsc(),t.success("Folder undeleted.")},error:function(e,i){void 0!==i.responseJSON?t.error("Folder was not undeleted. "+i.responseJSON.err_msg):t.error("An error occured! Folder was not undeleted. Please try again.")}})},startModifications:function(){this.options.edit_mode=!0,this.repaint()},cancelModifications:function(){this.options.edit_mode=!1,this.repaint()},saveModifications:function(){var e=Galaxy.libraries.folderListView.collection.get(this.$el.data("id")),i=!1,o=this.$el.find(".input_folder_name").val();if(void 0!==o&&o!==e.get("name")){if(!(o.length>2))return void t.warning("Folder name has to be at least 3 characters long.");e.set("name",o),i=!0}var a=this.$el.find(".input_folder_description").val();if(void 0!==a&&a!==e.get("description")&&(e.set("description",a),i=!0),i){var n=this;e.save(null,{patch:!0,success:function(e){n.options.edit_mode=!1,n.repaint(e),t.success("Changes to folder saved.")},error:function(e,i){void 0!==i.responseJSON?t.error(i.responseJSON.err_msg):t.error("An error occured while attempting to update the folder.")}})}else this.options.edit_mode=!1,this.repaint(e),t.info("Nothing has changed.")},repaint:function(){$(".tooltip").hide();var t=this.$el;this.render(),t.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},templateRowFolder:function(){return _.template(['',"",'',"",'',"<% if(!edit_mode) { %>","",'<%- content_item.get("name") %>',"","",'<%- content_item.get("description") %>',"","","<% } else if(edit_mode){ %>",'','',"<% } %>","folder","",'<%= _.escape(content_item.get("update_time")) %>',"","","","<% if(edit_mode) { %>",'",'","<% } else if (!edit_mode){%>",'",'','","","<% } %>","",""].join(""))},templateRowFile:function(){return _.template(['',"",'',"",'','',"","",'/datasets/<%- content_item.id %>" class="library-dataset">','<%- content_item.get("name") %>',"","",'<%- content_item.get("message") %>','<%= _.escape(content_item.get("file_ext")) %>','<%= _.escape(content_item.get("file_size")) %>','<%= _.escape(content_item.get("update_time")) %>',"",'<% if ( content_item.get("state") !== "ok" ) { %>','<%= _.escape(content_item.get("state")) %>',"<% } %>","","",'<% if (content_item.get("is_unrestricted")) { %>','',"<% } %>",'<% if (content_item.get("is_private")) { %>','',"<% } %>",'<% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %>','',"<% } %>",'<% if (content_item.get("can_manage")) { %>','/datasets/<%- content_item.id %>/permissions">','","","<% } %>","",""].join(""))},templateRowDeletedFile:function(){return _.template(['',"",'',"","",'','<%- content_item.get("name") %>',"","",'<%- content_item.get("message") %>',"","",'<%= _.escape(content_item.get("file_ext")) %>',"","",'<%= _.escape(content_item.get("file_size")) %>',"","",'<%= _.escape(content_item.get("update_time")) %>',"","",'<% if ( content_item.get("state") !== "ok" ) { %>','<%= _.escape(content_item.get("state")) %>',"<% } %>","","",'','","",""].join(""))},templateRowDeletedFolder:function(){return _.template(['',"",'',"","",'','<%- content_item.get("name") %>',"","",'<%- content_item.get("description") %>',"","","folder","","","",'<%= _.escape(content_item.get("update_time")) %>',"","","",'','","",""].join(""))}})}}); //# sourceMappingURL=../../../maps/mvc/library/library-folderrow-view.js.map diff --git a/static/scripts/mvc/library/library-foldertoolbar-view.js b/static/scripts/mvc/library/library-foldertoolbar-view.js index f2e3887f72d..a97cc2078d2 100644 --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -1,2 +1,2 @@ -"use strict";define(["layout/masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(e,t,i,o,s){return{FolderToolbarView:Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_bulk_delete":"deleteSelectedItems","click .toolbtn-show-locinfo":"showLocInfo","click .page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file_or_folder:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"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."},list_genomes:[],initialize:function(e){this.options=_.defaults(e||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(e){this.options=_.extend(this.options,e);var t=this.templateToolBar(),i={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.user&&(i.is_admin=Galaxy.user.isAdmin(),i.is_anonym=Galaxy.user.isAnonymous(),null===Galaxy.config.user_library_import_dir&&!1===Galaxy.config.allow_library_path_paste&&null===Galaxy.config.library_import_dir||(i.mutiple_add_dataset_options=!0)),this.$el.html(t(i))},renderPaginator:function(e){this.options=_.extend(this.options,e);var t=this.templatePaginator();$("body").find(".folder-paginator").html(t({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown}))},configureElements:function(e){this.options=_.extend(this.options,e),!0===this.options.can_add_library_item?$(".add-library-items").show():$(".add-library-items").hide(),!0===this.options.contains_file_or_folder&&Galaxy.user?Galaxy.user.isAnonymous()?($(".dataset-manipulation").show(),$(".logged-dataset-manipulation").hide()):($(".logged-dataset-manipulation").show(),$(".dataset-manipulation").show()):($(".logged-dataset-manipulation").hide(),$(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(e){e.preventDefault(),e.stopPropagation();var t=this,i=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:i(),buttons:{Create:function(){t.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var e=this.serialize_new_folder();if(this.validate_new_folder(e)){var t,s=new o.FolderAsModel,a=Backbone.history.fragment.split("/");t=a.indexOf("page")>-1?a[a.length-3]:a[a.length-1],s.url=s.urlRoot+t,s.save(e,{success:function(e){Galaxy.modal.hide(),i.success("Folder created."),e.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(e)},error:function(e,t){Galaxy.modal.hide(),void 0!==t.responseJSON?i.error(t.responseJSON.err_msg):i.error("An error occurred.")}})}else i.error("Folder's name is missing.");return!1},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(e){return""!==e.name},modalBulkImport:function(){if(0===this.findCheckedRows().length)i.info("You must select some datasets first.");else{var e=this;this.histories=new o.GalaxyHistories,this.histories.fetch().done(function(){var t=e.templateBulkImportInModal();e.modal=Galaxy.modal,e.modal.show({closing_events:!0,title:"Import into History",body:t({histories:e.histories.models}),buttons:{Import:function(){e.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})}).fail(function(e,t){void 0!==t.responseJSON?i.error(t.responseJSON.err_msg):i.error("An error occurred.")})}},importAllIntoHistory:function(){this.modal.disableButton("Import");var e=this.modal.$("input[name=history_name]").val(),t=this;if(""!==e)$.post(Galaxy.root+"api/histories",{name:e}).done(function(e){t.options.last_used_history_id=e.id,t.processImportToHistory(e.id,e.name)}).fail(function(e,t,o){i.error("An error occurred.")}).always(function(){t.modal.enableButton("Import")});else{var o=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=o;var s=$("select[name=dataset_import_bulk] option:selected").text();this.processImportToHistory(o,s),this.modal.enableButton("Import")}},processImportToHistory:function(e,t){var i=[],s=[];this.findCheckedRows().each(function(){var e=$(this).closest("tr").data("id");"F"==e.substring(0,1)?s.push(e):i.push(e)});for(var a=[],l=i.length-1;l>=0;l--){var r=i[l];(d=new o.HistoryItem).url=d.urlRoot+e+"/contents",d.content=r,d.source="library",a.push(d)}for(l=s.length-1;l>=0;l--){var n=s[l],d=new o.HistoryItem;d.url=d.urlRoot+e+"/contents",d.content=n,d.source="library_folder",a.push(d)}this.initChainCallControl({length:a.length,action:"to_history",history_name:t}),jQuery.getJSON(Galaxy.root+"history/set_as_current?id="+e),this.chainCallImportingIntoHistory(a,t)},updateProgress:function(){this.progress+=this.progressStep,$(".progress-bar-import").width(Math.round(this.progress)+"%");var e=Math.round(this.progress)+"% Complete";$(".completion_span").text(e)},download:function(e,t){var i=[],o=[];this.findCheckedRows().each(function(){var e=$(this).closest("tr").data("id");"F"==e.substring(0,1)?o.push(e):i.push(e)});var s=Galaxy.root+"api/libraries/datasets/download/"+t,a={ld_ids:i,folder_ids:o};this.processDownload(s,a,"get")},processDownload:function(e,t,o){if(e&&t){t="string"==typeof t?t:$.param(t);var s="";$.each(t.split("&"),function(){var e=this.split("=");s+=''}),$('
    '+s+"
    ").appendTo("body").submit().remove(),i.info("Your download will begin soon.")}else i.error("An error occurred.")},addFilesFromHistoryModal:function(){this.histories=new o.GalaxyHistories;var e=this;this.histories.fetch().done(function(){e.modal=Galaxy.modal;var t=e.templateAddFilesFromHistory();e.modal.show({closing_events:!0,title:"Adding datasets from your history",body:t({histories:e.histories.models}),buttons:{Add:function(){e.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+e.id,{trigger:!0})}}),e.fetchAndDisplayHistoryContents(e.histories.models[0].id),$("#dataset_add_bulk").change(function(t){e.fetchAndDisplayHistoryContents(t.target.value)})}).fail(function(e,t){void 0!==t.responseJSON?i.error(t.responseJSON.err_msg):i.error("An error occurred.")})},importFilesFromPathModal:function(){var e=this;this.modal=Galaxy.modal;var t=this.templateImportPathModal();this.modal.show({closing_events:!0,title:"Please enter paths to import",body:t({}),buttons:{Import:function(){e.importFromPathsClicked(e)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+e.id,{trigger:!0})}}),this.renderSelectBoxes()},fetchExtAndGenomes:function(){var e=this;t.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(t){e.list_extensions=[];for(var i in t)e.list_extensions.push({id:t[i].extension,text:t[i].extension,description:t[i].description,description_url:t[i].description_url});e.list_extensions.sort(function(e,t){return e.id>t.id?1:e.idt.id?1:e.id=0;c--){var p=n[c].trim();0!==p.length&&d.push(p)}this.initChainCallControl({length:d.length,action:"adding_datasets"}),this.chainCallImportingFolders({paths:d,preserve_dirs:e,link_data:t,space_to_tab:o,to_posix_lines:s,source:"admin_path",file_type:l,tag_using_filenames:a,dbkey:r})}else i.info("Please enter a path relative to Galaxy root.")},initChainCallControl:function(e){var t;switch(e.action){case"adding_datasets":t=this.templateAddingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(t({folder_name:this.options.folder_name}));break;case"deleting_datasets":t=this.templateDeletingItemsProgressBar(),this.modal.$el.find(".modal-body").html(t());break;case"to_history":t=this.templateImportIntoHistoryProgressBar(),this.modal.$el.find(".modal-body").html(t({history_name:e.history_name}));break;default:Galaxy.emit.error("Wrong action specified.","datalibs")}this.progress=0,this.progressStep=100/e.length,this.options.chain_call_control.total_number=e.length,this.options.chain_call_control.failed_number=0},importFromJstreePath:function(e,t){var o=$("#jstree_browser").jstree().get_selected(!0),s=_.filter(o,function(e){return 0==e.state.disabled}),a=this.modal.$el.find(".preserve-checkbox").is(":checked"),l=this.modal.$el.find(".link-checkbox").is(":checked"),r=this.modal.$el.find(".spacetab-checkbox").is(":checked"),n=this.modal.$el.find(".posix-checkbox").is(":checked"),d=this.select_extension.value(),c=this.select_genome.value(),p=this.modal.$el.find(".tag-files").is(":checked"),h=s[0].type,m=[];if(s.length<1)i.info("Please select some items first.");else{this.modal.disableButton("Import");for(var u=s.length-1;u>=0;u--)void 0!==s[u].li_attr.full_path&&m.push(s[u].li_attr.full_path);if(this.initChainCallControl({length:m.length,action:"adding_datasets"}),"folder"===h){f=t.source+"_folder";this.chainCallImportingFolders({paths:m,preserve_dirs:a,link_data:l,space_to_tab:r,to_posix_lines:n,source:f,file_type:d,dbkey:c,tag_using_filenames:p})}else if("file"===h){var f=t.source+"_file";this.chainCallImportingUserdirFiles({paths:m,file_type:d,dbkey:c,link_data:l,space_to_tab:r,to_posix_lines:n,source:f,tag_using_filenames:p})}}},fetchAndDisplayHistoryContents:function(e){var t=this;new o.HistoryContents({id:e}).fetch({success:function(i){var o=t.templateHistoryContents();t.histories.get(e).set({contents:i}),t.modal.$el.find("#selected_history_content").html(o({history_contents:i.models.reverse()})),t.modal.$el.find(".history-import-select-all").bind("click",function(){$("#selected_history_content [type=checkbox]").prop("checked",!0)}),t.modal.$el.find(".history-import-unselect-all").bind("click",function(){$("#selected_history_content [type=checkbox]").prop("checked",!1)})},error:function(e,t){void 0!==t.responseJSON?i.error(t.responseJSON.err_msg):i.error("An error occurred.")}})},addAllDatasetsFromHistory:function(){var e=this.modal.$el.find("#selected_history_content").find(":checked"),t=[],s=[],a=[];if(e.length<1)i.info("You must select some datasets first.");else{this.modal.disableButton("Add"),e.each(function(){var e=$(this).closest("li").data("id");if(e){var i=$(this).closest("li").data("name");t.push(e),s.push(i)}});for(var l=t.length-1;l>=0;l--){var r=t[l],n=new o.Item;n.url=Galaxy.root+"api/folders/"+this.options.id+"/contents","collection"===s[l]?n.set({from_hdca_id:r}):n.set({from_hda_id:r}),a.push(n)}this.initChainCallControl({length:a.length,action:"adding_datasets"}),this.chainCallAddingHdas(a)}},chainCallImportingIntoHistory:function(e,t){var o=this,s=e.pop();if(void 0===s)return 0===this.options.chain_call_control.failed_number?i.success("Selected datasets imported into history. Click this to start analyzing it.","",{onclick:function(){window.location=Galaxy.root}}):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?i.error("There was an error and no datasets were imported into history."):this.options.chain_call_control.failed_number=0;n--){var d=new o.Item({id:e[n]});r.push(d)}for(n=t.length-1;n>=0;n--){var c=new o.FolderAsModel({id:t[n]});r.push(c)}this.options.chain_call_control.total_number=l,this.chainCallDeletingItems(r)}},showLocInfo:function(){var e=null,t=this;null!==Galaxy.libraries.libraryListView?(e=Galaxy.libraries.libraryListView.collection.get(this.options.parent_library_id),this.showLocInfoModal(e)):(e=new o.Library({id:this.options.parent_library_id})).fetch({success:function(){t.showLocInfoModal(e)},error:function(e,t){void 0!==t.responseJSON?i.error(t.responseJSON.err_msg):i.error("An error occurred.")}})},showLocInfoModal:function(e){var t=this,i=this.templateLocInfoInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Location Details",body:i({library:e,options:t.options}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(e){switch(e.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back(),i.error("Invalid import source.")}},showPageSizePrompt:function(){var e=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));null!=e&&e==parseInt(e)&&(Galaxy.libraries.preferences.set({folder_page_size:parseInt(e)}),Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1}))},findCheckedRows:function(){return $("#folder_list_body").find(":checked")},templateToolBar:function(){return _.template(['
    ','
    ','
    ',"DATA LIBRARIES",'','",'","<% if(mutiple_add_dataset_options) { %>",'","<% } else { %>",'","<% } %>",'",'",'','",'','','","","","
    ","",'
    ',"
    ",'
    ',"
    "].join(""))},templateLocInfoInModal:function(){return _.template(["
    ",'',"",'',"","","","","",'',"",'<% if(library.get("description") !== "") { %>',"","",'',"","<% } %>",'<% if(library.get("synopsis") !== "") { %>',"","",'',"","<% } %>",'<% if(library.get("create_time_pretty") !== "") { %>',"","",'',"","<% } %>","","",'',"","","
    library
    name<%- library.get("name") %>
    description<%- library.get("description") %>
    synopsis<%- library.get("synopsis") %>
    created"><%- library.get("create_time_pretty") %>
    id<%- library.get("id") %>
    ",'',"",'',"","","","","","","",'<% if(options.folder_description !== "") { %>',"","","","","<% } %>","","","","","","
    folder
    name<%- options.folder_name %>
    description<%- options.folder_description %>
    id<%- options.id %>
    ","
    "].join(""))},templateNewFolderInModal:function(){return _.template(['
    ',"
    ",'','',"
    ","
    "].join(""))},templateBulkImportInModal:function(){return _.template(["
    ",'
    ',"Select history: ",'","
    ",'
    ',"or create new: ",'',"","
    ","
    "].join(""))},templateImportIntoHistoryProgressBar:function(){return _.template(['
    ',"Importing selected items to history <%= _.escape(history_name) %>","
    ",'
    ','
    ','0% Complete',"
    ","
    "].join(""))},templateAddingDatasetsProgressBar:function(){return _.template(['
    ',"Adding selected datasets to library folder <%= _.escape(folder_name) %>","
    ",'
    ','
    ','0% Complete',"
    ","
    "].join(""))},templateDeletingItemsProgressBar:function(){return _.template(['
    ',"
    ",'
    ','
    ','0% Complete',"
    ","
    "].join(""))},templateBrowserModal:function(){return _.template(['
    ','
    All files you select will be imported into the current folder ignoring their folder structure.
    ','','
    ','",'","
    ",'
    ','",'",'",'","
    ",'",'","
    ",'
    ',"
    ","
    ","

    You can set extension type and genome for all imported datasets at once:

    ","
    ",'Type: ','Genome: ',"
    ","
    ","
    ",'","
    ","
    "].join(""))},templateImportPathModal:function(){return _.template(['
    ','
    All files within the given folders and their subfolders will be imported into the current folder.
    ','
    ','",'","
    ",'",'","
    ",'',"
    ","

    You can set extension type and genome for all imported datasets at once:

    ","
    ",'Type: ','Genome: ',"
    ","
    ",'","
    ","
    "].join(""))},templateAddFilesFromHistory:function(){return _.template(['
    ',"
    ","1. Select history: ",'","
    ","
    ",'
    ',"
    ","
    "].join(""))},templateHistoryContents:function(){return _.template(["

    2. Choose the datasets to import:

    ","
    ",'",'","
    ","
    ","
      ","<% _.each(history_contents, function(history_item) { %>",'<% if (history_item.get("deleted") != true ) { %>','<% var item_name = history_item.get("name") %>','<% if (history_item.get("type") === "collection") { %>','<% var collection_type = history_item.get("collection_type") %>','<% if (collection_type === "list") { %>','
    • " data-name="<%= _.escape(history_item.get("type")) %>">',"
      • ","<% } else { %>",'
    • ','','<%= _.escape(history_item.get("hid")) %>: ','<%= item_name.length > 75 ? _.escape("...".concat(item_name.substr(-75))) : _.escape(item_name) %> (Dataset Collection of type <%= _.escape(collection_type) %> not supported.)',"","
      • ","<% } %>",'<% } else if (history_item.get("visible") === true && history_item.get("state") === "ok") { %>','
    • " data-name="<%= _.escape(history_item.get("type")) %>">','","
      • ","<% } %>","<% } %>","<% }); %>","
    "].join(""))},templatePaginator:function(){return _.template(['",""," showing ",'',"<%- items_shown %>",""," of <%- total_items_count %> items",""].join(""))}})}}); +"use strict";define(["layout/masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(e,t,i,o,s){return{FolderToolbarView:Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_bulk_delete":"deleteSelectedItems","click .toolbtn-show-locinfo":"showLocInfo","click .page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file_or_folder:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"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."},list_genomes:[],initialize:function(e){this.options=_.defaults(e||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(e){this.options=_.extend(this.options,e);var t=this.templateToolBar(),i={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.user&&(i.is_admin=Galaxy.user.isAdmin(),i.is_anonym=Galaxy.user.isAnonymous(),null===Galaxy.config.user_library_import_dir&&!1===Galaxy.config.allow_library_path_paste&&null===Galaxy.config.library_import_dir||(i.mutiple_add_dataset_options=!0)),this.$el.html(t(i))},renderPaginator:function(e){this.options=_.extend(this.options,e);var t=this.templatePaginator();$("body").find(".folder-paginator").html(t({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown,folder_page_size:Galaxy.libraries.preferences.get("folder_page_size")}))},configureElements:function(e){this.options=_.extend(this.options,e),!0===this.options.can_add_library_item?$(".add-library-items").show():$(".add-library-items").hide(),!0===this.options.contains_file_or_folder&&Galaxy.user?Galaxy.user.isAnonymous()?($(".dataset-manipulation").show(),$(".logged-dataset-manipulation").hide()):($(".logged-dataset-manipulation").show(),$(".dataset-manipulation").show()):($(".logged-dataset-manipulation").hide(),$(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(e){e.preventDefault(),e.stopPropagation();var t=this,i=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:i(),buttons:{Create:function(){t.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var e=this.serialize_new_folder();if(this.validate_new_folder(e)){var t,s=new o.FolderAsModel,a=Backbone.history.fragment.split("/");t=a.indexOf("page")>-1?a[a.length-3]:a[a.length-1],s.url=s.urlRoot+t,s.save(e,{success:function(e){Galaxy.modal.hide(),i.success("Folder created."),e.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(e)},error:function(e,t){Galaxy.modal.hide(),void 0!==t.responseJSON?i.error(t.responseJSON.err_msg):i.error("An error occurred.")}})}else i.error("Folder's name is missing.");return!1},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(e){return""!==e.name},modalBulkImport:function(){if(0===this.findCheckedRows().length)i.info("You must select some datasets first.");else{var e=this;this.histories=new o.GalaxyHistories,this.histories.fetch().done(function(){var t=e.templateBulkImportInModal();e.modal=Galaxy.modal,e.modal.show({closing_events:!0,title:"Import into History",body:t({histories:e.histories.models}),buttons:{Import:function(){e.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})}).fail(function(e,t){void 0!==t.responseJSON?i.error(t.responseJSON.err_msg):i.error("An error occurred.")})}},importAllIntoHistory:function(){this.modal.disableButton("Import");var e=this.modal.$("input[name=history_name]").val(),t=this;if(""!==e)$.post(Galaxy.root+"api/histories",{name:e}).done(function(e){t.options.last_used_history_id=e.id,t.processImportToHistory(e.id,e.name)}).fail(function(e,t,o){i.error("An error occurred.")}).always(function(){t.modal.enableButton("Import")});else{var o=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=o;var s=$("select[name=dataset_import_bulk] option:selected").text();this.processImportToHistory(o,s),this.modal.enableButton("Import")}},processImportToHistory:function(e,t){var i=[],s=[];this.findCheckedRows().each(function(){var e=$(this).closest("tr").data("id");"F"==e.substring(0,1)?s.push(e):i.push(e)});for(var a=[],l=i.length-1;l>=0;l--){var r=i[l];(d=new o.HistoryItem).url=d.urlRoot+e+"/contents",d.content=r,d.source="library",a.push(d)}for(l=s.length-1;l>=0;l--){var n=s[l],d=new o.HistoryItem;d.url=d.urlRoot+e+"/contents",d.content=n,d.source="library_folder",a.push(d)}this.initChainCallControl({length:a.length,action:"to_history",history_name:t}),jQuery.getJSON(Galaxy.root+"history/set_as_current?id="+e),this.chainCallImportingIntoHistory(a,t)},updateProgress:function(){this.progress+=this.progressStep,$(".progress-bar-import").width(Math.round(this.progress)+"%");var e=Math.round(this.progress)+"% Complete";$(".completion_span").text(e)},download:function(e,t){var i=[],o=[];this.findCheckedRows().each(function(){var e=$(this).closest("tr").data("id");"F"==e.substring(0,1)?o.push(e):i.push(e)});var s=Galaxy.root+"api/libraries/datasets/download/"+t,a={ld_ids:i,folder_ids:o};this.processDownload(s,a,"get")},processDownload:function(e,t,o){if(e&&t){t="string"==typeof t?t:$.param(t);var s="";$.each(t.split("&"),function(){var e=this.split("=");s+=''}),$('
    '+s+"
    ").appendTo("body").submit().remove(),i.info("Your download will begin soon.")}else i.error("An error occurred.")},addFilesFromHistoryModal:function(){this.histories=new o.GalaxyHistories;var e=this;this.histories.fetch().done(function(){e.modal=Galaxy.modal;var t=e.templateAddFilesFromHistory();e.modal.show({closing_events:!0,title:"Adding datasets from your history",body:t({histories:e.histories.models}),buttons:{Add:function(){e.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+e.id,{trigger:!0})}}),e.fetchAndDisplayHistoryContents(e.histories.models[0].id),$("#dataset_add_bulk").change(function(t){e.fetchAndDisplayHistoryContents(t.target.value)})}).fail(function(e,t){void 0!==t.responseJSON?i.error(t.responseJSON.err_msg):i.error("An error occurred.")})},importFilesFromPathModal:function(){var e=this;this.modal=Galaxy.modal;var t=this.templateImportPathModal();this.modal.show({closing_events:!0,title:"Please enter paths to import",body:t({}),buttons:{Import:function(){e.importFromPathsClicked(e)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+e.id,{trigger:!0})}}),this.renderSelectBoxes()},fetchExtAndGenomes:function(){var e=this;t.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(t){e.list_extensions=[];for(var i in t)e.list_extensions.push({id:t[i].extension,text:t[i].extension,description:t[i].description,description_url:t[i].description_url});e.list_extensions.sort(function(e,t){return e.id>t.id?1:e.idt.id?1:e.id=0;c--){var p=n[c].trim();0!==p.length&&d.push(p)}this.initChainCallControl({length:d.length,action:"adding_datasets"}),this.chainCallImportingFolders({paths:d,preserve_dirs:e,link_data:t,space_to_tab:o,to_posix_lines:s,source:"admin_path",file_type:l,tag_using_filenames:a,dbkey:r})}else i.info("Please enter a path relative to Galaxy root.")},initChainCallControl:function(e){var t;switch(e.action){case"adding_datasets":t=this.templateAddingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(t({folder_name:this.options.folder_name}));break;case"deleting_datasets":t=this.templateDeletingItemsProgressBar(),this.modal.$el.find(".modal-body").html(t());break;case"to_history":t=this.templateImportIntoHistoryProgressBar(),this.modal.$el.find(".modal-body").html(t({history_name:e.history_name}));break;default:Galaxy.emit.error("Wrong action specified.","datalibs")}this.progress=0,this.progressStep=100/e.length,this.options.chain_call_control.total_number=e.length,this.options.chain_call_control.failed_number=0},importFromJstreePath:function(e,t){var o=$("#jstree_browser").jstree().get_selected(!0),s=_.filter(o,function(e){return 0==e.state.disabled}),a=this.modal.$el.find(".preserve-checkbox").is(":checked"),l=this.modal.$el.find(".link-checkbox").is(":checked"),r=this.modal.$el.find(".spacetab-checkbox").is(":checked"),n=this.modal.$el.find(".posix-checkbox").is(":checked"),d=this.select_extension.value(),c=this.select_genome.value(),p=this.modal.$el.find(".tag-files").is(":checked"),h=s[0].type,m=[];if(s.length<1)i.info("Please select some items first.");else{this.modal.disableButton("Import");for(var u=s.length-1;u>=0;u--)void 0!==s[u].li_attr.full_path&&m.push(s[u].li_attr.full_path);if(this.initChainCallControl({length:m.length,action:"adding_datasets"}),"folder"===h){f=t.source+"_folder";this.chainCallImportingFolders({paths:m,preserve_dirs:a,link_data:l,space_to_tab:r,to_posix_lines:n,source:f,file_type:d,dbkey:c,tag_using_filenames:p})}else if("file"===h){var f=t.source+"_file";this.chainCallImportingUserdirFiles({paths:m,file_type:d,dbkey:c,link_data:l,space_to_tab:r,to_posix_lines:n,source:f,tag_using_filenames:p})}}},fetchAndDisplayHistoryContents:function(e){var t=this;new o.HistoryContents({id:e}).fetch({success:function(i){var o=t.templateHistoryContents();t.histories.get(e).set({contents:i}),t.modal.$el.find("#selected_history_content").html(o({history_contents:i.models.reverse()})),t.modal.$el.find(".history-import-select-all").bind("click",function(){$("#selected_history_content [type=checkbox]").prop("checked",!0)}),t.modal.$el.find(".history-import-unselect-all").bind("click",function(){$("#selected_history_content [type=checkbox]").prop("checked",!1)})},error:function(e,t){void 0!==t.responseJSON?i.error(t.responseJSON.err_msg):i.error("An error occurred.")}})},addAllDatasetsFromHistory:function(){var e=this.modal.$el.find("#selected_history_content").find(":checked"),t=[],s=[],a=[];if(e.length<1)i.info("You must select some datasets first.");else{this.modal.disableButton("Add"),e.each(function(){var e=$(this).closest("li").data("id");if(e){var i=$(this).closest("li").data("name");t.push(e),s.push(i)}});for(var l=t.length-1;l>=0;l--){var r=t[l],n=new o.Item;n.url=Galaxy.root+"api/folders/"+this.options.id+"/contents","collection"===s[l]?n.set({from_hdca_id:r}):n.set({from_hda_id:r}),a.push(n)}this.initChainCallControl({length:a.length,action:"adding_datasets"}),this.chainCallAddingHdas(a)}},chainCallImportingIntoHistory:function(e,t){var o=this,s=e.pop();if(void 0===s)return 0===this.options.chain_call_control.failed_number?i.success("Selected datasets imported into history. Click this to start analyzing it.","",{onclick:function(){window.location=Galaxy.root}}):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?i.error("There was an error and no datasets were imported into history."):this.options.chain_call_control.failed_number=0;n--){var d=new o.Item({id:e[n]});r.push(d)}for(n=t.length-1;n>=0;n--){var c=new o.FolderAsModel({id:t[n]});r.push(c)}this.options.chain_call_control.total_number=l,this.chainCallDeletingItems(r)}},showLocInfo:function(){var e=null,t=this;null!==Galaxy.libraries.libraryListView?(e=Galaxy.libraries.libraryListView.collection.get(this.options.parent_library_id),this.showLocInfoModal(e)):(e=new o.Library({id:this.options.parent_library_id})).fetch({success:function(){t.showLocInfoModal(e)},error:function(e,t){void 0!==t.responseJSON?i.error(t.responseJSON.err_msg):i.error("An error occurred.")}})},showLocInfoModal:function(e){var t=this,i=this.templateLocInfoInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Location Details",body:i({library:e,options:t.options}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(e){switch(e.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back(),i.error("Invalid import source.")}},showPageSizePrompt:function(e){e.preventDefault();var t=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));null!=t&&t==parseInt(t)&&(Galaxy.libraries.preferences.set({folder_page_size:parseInt(t)}),Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1}))},findCheckedRows:function(){return $("#folder_list_body").find(":checked")},templateToolBar:function(){return _.template(['
    ','
    ','
    ',"DATA LIBRARIES",'','",'","<% if(mutiple_add_dataset_options) { %>",'","<% } else { %>",'","<% } %>",'",'",'','",'','','","","","
    ","",'
    ',"
    ",'
    ',"
    "].join(""))},templateLocInfoInModal:function(){return _.template(["
    ",'',"",'',"","","","","",'',"",'<% if(library.get("description") !== "") { %>',"","",'',"","<% } %>",'<% if(library.get("synopsis") !== "") { %>',"","",'',"","<% } %>",'<% if(library.get("create_time_pretty") !== "") { %>',"","",'',"","<% } %>","","",'',"","","
    library
    name<%- library.get("name") %>
    description<%- library.get("description") %>
    synopsis<%- library.get("synopsis") %>
    created"><%- library.get("create_time_pretty") %>
    id<%- library.get("id") %>
    ",'',"",'',"","","","","","","",'<% if(options.folder_description !== "") { %>',"","","","","<% } %>","","","","","","
    folder
    name<%- options.folder_name %>
    description<%- options.folder_description %>
    id<%- options.id %>
    ","
    "].join(""))},templateNewFolderInModal:function(){return _.template(['
    ',"
    ",'','',"
    ","
    "].join(""))},templateBulkImportInModal:function(){return _.template(["
    ",'
    ',"Select history: ",'","
    ",'
    ',"or create new: ",'',"","
    ","
    "].join(""))},templateImportIntoHistoryProgressBar:function(){return _.template(['
    ',"Importing selected items to history <%= _.escape(history_name) %>","
    ",'
    ','
    ','0% Complete',"
    ","
    "].join(""))},templateAddingDatasetsProgressBar:function(){return _.template(['
    ',"Adding selected datasets to library folder <%= _.escape(folder_name) %>","
    ",'
    ','
    ','0% Complete',"
    ","
    "].join(""))},templateDeletingItemsProgressBar:function(){return _.template(['
    ',"
    ",'
    ','
    ','0% Complete',"
    ","
    "].join(""))},templateBrowserModal:function(){return _.template(['
    ','
    All files you select will be imported into the current folder ignoring their folder structure.
    ','','
    ','",'","
    ",'
    ','",'",'",'","
    ",'",'","
    ",'
    ',"
    ","
    ","

    You can set extension type and genome for all imported datasets at once:

    ","
    ",'Type: ','Genome: ',"
    ","
    ","
    ",'","
    ","
    "].join(""))},templateImportPathModal:function(){return _.template(['
    ','
    All files within the given folders and their subfolders will be imported into the current folder.
    ','
    ','",'","
    ",'",'","
    ",'',"
    ","

    You can set extension type and genome for all imported datasets at once:

    ","
    ",'Type: ','Genome: ',"
    ","
    ",'","
    ","
    "].join(""))},templateAddFilesFromHistory:function(){return _.template(['
    ',"
    ","1. Select history: ",'","
    ","
    ",'
    ',"
    ","
    "].join(""))},templateHistoryContents:function(){return _.template(["

    2. Choose the datasets to import:

    ","
    ",'",'","
    ","
    ","
      ","<% _.each(history_contents, function(history_item) { %>",'<% if (history_item.get("deleted") != true ) { %>','<% var item_name = history_item.get("name") %>','<% if (history_item.get("type") === "collection") { %>','<% var collection_type = history_item.get("collection_type") %>','<% if (collection_type === "list") { %>','
    • " data-name="<%= _.escape(history_item.get("type")) %>">',"
      • ","<% } else { %>",'
    • ','','<%= _.escape(history_item.get("hid")) %>: ','<%= item_name.length > 75 ? _.escape("...".concat(item_name.substr(-75))) : _.escape(item_name) %> (Dataset Collection of type <%= _.escape(collection_type) %> not supported.)',"","
      • ","<% } %>",'<% } else if (history_item.get("visible") === true && history_item.get("state") === "ok") { %>','
    • " data-name="<%= _.escape(history_item.get("type")) %>">','","
      • ","<% } %>","<% } %>","<% }); %>","
    "].join(""))},templatePaginator:function(){return _.template(['","",' <%- items_shown %> items shown (change)',"",""," <%- total_items_count %> total",""].join(""))}})}}); //# sourceMappingURL=../../../maps/mvc/library/library-foldertoolbar-view.js.map diff --git a/static/scripts/mvc/library/library-libraryrow-view.js b/static/scripts/mvc/library/library-libraryrow-view.js index 06a0d1166f7..bc8878bc622 100644 --- a/static/scripts/mvc/library/library-libraryrow-view.js +++ b/static/scripts/mvc/library/library-libraryrow-view.js @@ -1,2 +1,2 @@ -"use strict";define(["layout/masthead","utils/utils","libs/toastr"],function(t,e,i){return{LibraryRowView:Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library"},edit_mode:!1,element_visibility_config:{upload_library_btn:!1,edit_library_btn:!1,permission_library_btn:!1,save_library_btn:!1,cancel_library_btn:!1,delete_library_btn:!1,undelete_library_btn:!1},initialize:function(t){this.render(t)},render:function(t){void 0===t&&(t=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))),this.prepareButtons(t);var e=this.templateRow();return this.setElement(e({library:t,button_config:this.element_visibility_config,edit_mode:this.edit_mode})),this.$el.show(),this},repaint:function(t){$(".tooltip").hide();var e=this.$el;this.render(),e.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(t){var e=this.element_visibility_config;!1===this.edit_mode?(e.save_library_btn=!1,e.cancel_library_btn=!1,e.delete_library_btn=!1,!0===t.get("deleted")?(e.undelete_library_btn=!0,e.upload_library_btn=!1,e.edit_library_btn=!1,e.permission_library_btn=!1):!1===t.get("deleted")&&(e.save_library_btn=!1,e.cancel_library_btn=!1,e.undelete_library_btn=!1,!0===t.get("can_user_add")&&(e.upload_library_btn=!0),!0===t.get("can_user_modify")&&(e.edit_library_btn=!0),!0===t.get("can_user_manage")&&(e.permission_library_btn=!0))):!0===this.edit_mode&&(e.upload_library_btn=!1,e.edit_library_btn=!1,e.permission_library_btn=!1,e.save_library_btn=!0,e.cancel_library_btn=!0,e.delete_library_btn=!0,e.undelete_library_btn=!1),this.element_visibility_config=e},edit_button_clicked:function(){this.edit_mode=!0,this.repaint()},cancel_library_modification:function(){this.edit_mode=!1,this.repaint()},save_library_modification:function(){var t=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),e=!1,r=this.$el.find(".input_library_name").val();if(void 0!==r&&r!==t.get("name")){if(!(r.length>2))return void i.warning("Library name has to be at least 3 characters long.");t.set("name",r),e=!0}var a=this.$el.find(".input_library_description").val();void 0!==a&&a!==t.get("description")&&(t.set("description",a),e=!0);var l=this.$el.find(".input_library_synopsis").val();if(void 0!==l&&l!==t.get("synopsis")&&(t.set("synopsis",l),e=!0),e){var n=this;t.save(null,{patch:!0,success:function(t){n.edit_mode=!1,n.repaint(t),i.success("Changes to library saved.")},error:function(t,e){void 0!==e.responseJSON?i.error(e.responseJSON.err_msg):i.error("An error occured while attempting to update the library.")}})}else this.edit_mode=!1,this.repaint(t),i.info("Nothing has changed.")},delete_library:function(){var t=this;Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")).destroy({success:function(e){e.set("deleted",!0),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,!1===Galaxy.libraries.preferences.get("with_deleted")?($(".tooltip").hide(),t.repaint(e),t.$el.remove()):!0===Galaxy.libraries.preferences.get("with_deleted")&&t.repaint(e),i.success("Library has been marked deleted.")},error:function(t,e){void 0!==e.responseJSON?i.error(e.responseJSON.err_msg):i.error("An error occured during deleting the library.")}})},undelete_library:function(){var t=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),e=this;t.url=t.urlRoot+t.id+"?undelete=true",t.destroy({success:function(t){t.set("deleted",!1),Galaxy.libraries.libraryListView.collection.add(t),e.edit_mode=!1,e.repaint(t),i.success("Library has been undeleted.")},error:function(t,e){void 0!==e.responseJSON?i.error(e.responseJSON.err_msg):i.error("An error occured while undeleting the library.")}})},templateRow:function(){return _.template(['" style="display:none;" data-id="<%- library.get("id") %>">',"<% if(!edit_mode) { %>",'<% if(library.get("deleted")) { %>',' <%- library.get("name") %>',"<% } else { %>",'"><%- library.get("name") %>',"<% } %>",'<% if(library.get("description")) { %>','<% if( (library.get("description")).length> 80 ) { %>','"><%= _.escape(library.get("description")).substring(0, 80) + "..." %>',"<% } else { %>",'<%= _.escape(library.get("description"))%>',"<% } %>","<% } else { %>","","<% } %>",'<% if(library.get("synopsis")) { %>','<% if( (library.get("synopsis")).length> 120 ) { %>','"><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %>',"<% } else { %>",'<%= _.escape(library.get("synopsis"))%>',"<% } %>","<% } else { %>","","<% } %>","<% } else if(edit_mode){ %>",'','','',"<% } %>",'','<% if( (library.get("public")) && (library.get("deleted") === false) ) { %>',' ',"<% }%>",'','/permissions">','','','','',"",""].join(""))}})}}); +"use strict";define(["layout/masthead","utils/utils","libs/toastr"],function(t,e,i){return{LibraryRowView:Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library"},edit_mode:!1,element_visibility_config:{upload_library_btn:!1,edit_library_btn:!1,permission_library_btn:!1,save_library_btn:!1,cancel_library_btn:!1,delete_library_btn:!1,undelete_library_btn:!1},initialize:function(t){this.render(t)},render:function(t){void 0===t&&(t=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))),this.prepareButtons(t);var e=this.templateRow();return this.setElement(e({library:t,button_config:this.element_visibility_config,edit_mode:this.edit_mode})),this.$el.show(),this},repaint:function(t){$(".tooltip").hide();var e=this.$el;this.render(),e.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(t){var e=this.element_visibility_config;!1===this.edit_mode?(e.save_library_btn=!1,e.cancel_library_btn=!1,e.delete_library_btn=!1,!0===t.get("deleted")?(e.undelete_library_btn=!0,e.upload_library_btn=!1,e.edit_library_btn=!1,e.permission_library_btn=!1):!1===t.get("deleted")&&(e.save_library_btn=!1,e.cancel_library_btn=!1,e.undelete_library_btn=!1,!0===t.get("can_user_add")&&(e.upload_library_btn=!0),!0===t.get("can_user_modify")&&(e.edit_library_btn=!0),!0===t.get("can_user_manage")&&(e.permission_library_btn=!0))):!0===this.edit_mode&&(e.upload_library_btn=!1,e.edit_library_btn=!1,e.permission_library_btn=!1,e.save_library_btn=!0,e.cancel_library_btn=!0,e.delete_library_btn=!0,e.undelete_library_btn=!1),this.element_visibility_config=e},edit_button_clicked:function(){this.edit_mode=!0,this.repaint()},cancel_library_modification:function(){this.edit_mode=!1,this.repaint()},save_library_modification:function(){var t=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),e=!1,r=this.$el.find(".input_library_name").val();if(void 0!==r&&r!==t.get("name")){if(!(r.length>2))return void i.warning("Library name has to be at least 3 characters long.");t.set("name",r),e=!0}var a=this.$el.find(".input_library_description").val();void 0!==a&&a!==t.get("description")&&(t.set("description",a),e=!0);var l=this.$el.find(".input_library_synopsis").val();if(void 0!==l&&l!==t.get("synopsis")&&(t.set("synopsis",l),e=!0),e){var n=this;t.save(null,{patch:!0,success:function(t){n.edit_mode=!1,n.repaint(t),i.success("Changes to library saved.")},error:function(t,e){void 0!==e.responseJSON?i.error(e.responseJSON.err_msg):i.error("An error occured while attempting to update the library.")}})}else this.edit_mode=!1,this.repaint(t),i.info("Nothing has changed.")},delete_library:function(){var t=this;Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")).destroy({success:function(e){e.set("deleted",!0),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,!1===Galaxy.libraries.preferences.get("with_deleted")?($(".tooltip").hide(),t.repaint(e),t.$el.remove()):!0===Galaxy.libraries.preferences.get("with_deleted")&&t.repaint(e),i.success("Library has been marked deleted.")},error:function(t,e){void 0!==e.responseJSON?i.error(e.responseJSON.err_msg):i.error("An error occured during deleting the library.")}})},undelete_library:function(){var t=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),e=this;t.url=t.urlRoot+t.id+"?undelete=true",t.destroy({success:function(t){t.set("deleted",!1),Galaxy.libraries.libraryListView.collection.add(t),e.edit_mode=!1,e.repaint(t),i.success("Library has been undeleted.")},error:function(t,e){void 0!==e.responseJSON?i.error(e.responseJSON.err_msg):i.error("An error occured while undeleting the library.")}})},templateRow:function(){return _.template(['" style="display:none;" data-id="<%- library.get("id") %>">',"<% if(!edit_mode) { %>",'<% if(library.get("deleted")) { %>','<%- library.get("name") %>',"<% } else { %>",'"><%- library.get("name") %>',"<% } %>",'<% if(library.get("description")) { %>','<% if( (library.get("description")).length> 80 ) { %>','"><%= _.escape(library.get("description")).substring(0, 80) + "..." %>',"<% } else { %>",'<%= _.escape(library.get("description"))%>',"<% } %>","<% } else { %>","","<% } %>",'<% if(library.get("synopsis")) { %>','<% if( (library.get("synopsis")).length> 120 ) { %>','"><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %>',"<% } else { %>",'<%= _.escape(library.get("synopsis"))%>',"<% } %>","<% } else { %>","","<% } %>","<% } else if(edit_mode){ %>",'','','',"<% } %>",'','<% if( (library.get("public")) && (library.get("deleted") === false) ) { %>',' ',"<% }%>",'','/permissions">','','','','" class="fa fa-ban fa-lg">','',"",""].join(""))}})}}); //# sourceMappingURL=../../../maps/mvc/library/library-libraryrow-view.js.map diff --git a/static/scripts/mvc/library/library-librarytoolbar-view.js b/static/scripts/mvc/library/library-librarytoolbar-view.js index 4d4b4a25bbd..fb6b07d01c3 100644 --- a/static/scripts/mvc/library/library-librarytoolbar-view.js +++ b/static/scripts/mvc/library/library-librarytoolbar-view.js @@ -1,2 +1,2 @@ -"use strict";define(["libs/toastr","mvc/library/library-model"],function(e,a){return{LibraryToolbarView:Backbone.View.extend({el:"#center",defaults:{search_term:""},events:{"click #create_new_library_btn":"createLibraryFromModal","click #include_deleted_chk":"includeDeletedChecked","click #exclude_restricted_chk":"excludeRestrictedChecked","click #lib_page_size_prompt":"showPageSizePrompt","keyup .library-search-input":"searchLibraries"},initialize:function(e){this.options=_.defaults(this.options||{},e,this.defaults),this.render()},render:function(){var e=this.templateToolBar(),a=!1,i=!0;Galaxy.user&&(a=Galaxy.user.isAdmin(),i=Galaxy.user.isAnonymous()),this.$el.html(e({admin_user:a,anon_user:i})),a&&(this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted"),this.$el.find("#exclude_restricted_chk")[0].checked=Galaxy.libraries.preferences.get("without_restricted"))},renderPaginator:function(e){this.options=_.extend(this.options,e);var a=this.templatePaginator();this.$el.find("#library_paginator").html(a({show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_libraries_count:this.options.total_libraries_count,libraries_shown:this.options.libraries_shown}))},createLibraryFromModal:function(e){e.preventDefault(),e.stopPropagation();var a=this;this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){a.createNewLibrary()},Close:function(){a.modal.hide()}}})},createNewLibrary:function(){var i=this.serializeNewLibrary();if(this.validateNewLibrary(i)){var r=this;(new a.Library).save(i,{success:function(a){Galaxy.libraries.libraryListView.collection.add(a),r.modal.hide(),r.clearLibraryModal(),Galaxy.libraries.libraryListView.render(),e.success("Library created.")},error:function(a,i){void 0!==i.responseJSON?e.error(i.responseJSON.err_msg):e.error("An error occured.")}})}else e.error("Library's name is missing.");return!1},showPageSizePrompt:function(){var e=prompt("How many libraries per page do you want to see?",Galaxy.libraries.preferences.get("library_page_size"));null!=e&&e==parseInt(e)&&(Galaxy.libraries.preferences.set({library_page_size:parseInt(e)}),Galaxy.libraries.libraryListView.render({show_page:1}))},clearLibraryModal:function(){$("input[name='Name']").val(""),$("input[name='Description']").val(""),$("input[name='Synopsis']").val("")},serializeNewLibrary:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validateNewLibrary:function(e){return""!==e.name},includeDeletedChecked:function(e){e.target.checked?(Galaxy.libraries.preferences.set({with_deleted:!0}),Galaxy.libraries.libraryListView.fetchDeleted()):(Galaxy.libraries.preferences.set({with_deleted:!1}),Galaxy.libraries.libraryListView.render())},excludeRestrictedChecked:function(e){e.target.checked?Galaxy.libraries.preferences.set({without_restricted:!0}):Galaxy.libraries.preferences.set({without_restricted:!1}),Galaxy.libraries.libraryListView.render()},searchLibraries:function(e){var a=$(".library-search-input").val();this.options.search_term=a,Galaxy.libraries.libraryListView.searchLibraries(a)},templateToolBar:function(){return _.template(['
    ','
    ','
    ','
    ','DATA LIBRARIES','',"",'
    ','',"
    ","<% if(admin_user === true) { %>",'
    ',"","","
    ",'','',"","<% } %>",'','','',"","","
    ","
    ","
    ",'
    ',"
    ","
    "].join(""))},templatePaginator:function(){return _.template(['",'',' showing <%- libraries_shown %> of <%- total_libraries_count %> libraries',""].join(""))},templateNewLibraryInModal:function(){return _.template(['
    ',"
    ",'','','',"
    ","
    "].join(""))}})}}); +"use strict";define(["libs/toastr","mvc/library/library-model"],function(e,a){return{LibraryToolbarView:Backbone.View.extend({el:"#center",defaults:{search_term:""},events:{"click #create_new_library_btn":"createLibraryFromModal","click #include_deleted_chk":"includeDeletedChecked","click #exclude_restricted_chk":"excludeRestrictedChecked","click .page_size_prompt":"showPageSizePrompt","keyup .library-search-input":"searchLibraries"},initialize:function(e){this.options=_.defaults(this.options||{},e,this.defaults),this.render()},render:function(){var e=this.templateToolBar(),a=!1,i=!0;Galaxy.user&&(a=Galaxy.user.isAdmin(),i=Galaxy.user.isAnonymous()),this.$el.html(e({admin_user:a,anon_user:i})),a&&(this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted"),this.$el.find("#exclude_restricted_chk")[0].checked=Galaxy.libraries.preferences.get("without_restricted"))},renderPaginator:function(e){this.options=_.extend(this.options,e);var a=this.templatePaginator();this.$el.find("#library_paginator").html(a({show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_libraries_count:this.options.total_libraries_count,libraries_shown:this.options.libraries_shown,library_page_size:Galaxy.libraries.preferences.get("library_page_size")}))},createLibraryFromModal:function(e){e.preventDefault(),e.stopPropagation();var a=this;this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){a.createNewLibrary()},Close:function(){a.modal.hide()}}})},createNewLibrary:function(){var i=this.serializeNewLibrary();if(this.validateNewLibrary(i)){var r=this;(new a.Library).save(i,{success:function(a){Galaxy.libraries.libraryListView.collection.add(a),r.modal.hide(),r.clearLibraryModal(),Galaxy.libraries.libraryListView.render(),e.success("Library created.")},error:function(a,i){void 0!==i.responseJSON?e.error(i.responseJSON.err_msg):e.error("An error occured.")}})}else e.error("Library's name is missing.");return!1},showPageSizePrompt:function(e){e.preventDefault();var a=prompt("How many libraries per page do you want to see?",Galaxy.libraries.preferences.get("library_page_size"));null!=a&&a==parseInt(a)&&(Galaxy.libraries.preferences.set({library_page_size:parseInt(a)}),Galaxy.libraries.libraryListView.render({show_page:1}))},clearLibraryModal:function(){$("input[name='Name']").val(""),$("input[name='Description']").val(""),$("input[name='Synopsis']").val("")},serializeNewLibrary:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validateNewLibrary:function(e){return""!==e.name},includeDeletedChecked:function(e){e.target.checked?(Galaxy.libraries.preferences.set({with_deleted:!0}),Galaxy.libraries.libraryListView.fetchDeleted()):(Galaxy.libraries.preferences.set({with_deleted:!1}),Galaxy.libraries.libraryListView.render())},excludeRestrictedChecked:function(e){e.target.checked?Galaxy.libraries.preferences.set({without_restricted:!0}):Galaxy.libraries.preferences.set({without_restricted:!1}),Galaxy.libraries.libraryListView.render()},searchLibraries:function(e){var a=$(".library-search-input").val();this.options.search_term=a,Galaxy.libraries.libraryListView.searchLibraries(a)},templateToolBar:function(){return _.template(['
    ','
    ','
    ','
    ','DATA LIBRARIES','',"",'
    ','',"
    ","<% if(admin_user === true) { %>",'
    ',"","","
    ",'','',"","<% } %>",'','','',"","","
    ","
    ","
    ",'
    ',"
    ","
    "].join(""))},templatePaginator:function(){return _.template(['","",' <%- libraries_shown %> libraries shown (change)',"",""," <%- total_libraries_count %> total",""].join(""))},templateNewLibraryInModal:function(){return _.template(['
    ',"
    ",'','','',"
    ","
    "].join(""))}})}}); //# sourceMappingURL=../../../maps/mvc/library/library-librarytoolbar-view.js.map diff --git a/static/style/blue/base.css b/static/style/blue/base.css index ffd8e51802b..f1d5897f439 100644 --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1,4 +1,4 @@ /*! normalize.css v2.1.0 | MIT License | git.io/normalize */article,aside,details,figcaption,figure,footer,header,hgroup,main,nav,section,summary{display:block}audio,canvas,video{display:inline-block}audio:not([controls]){display:none;height:0}[hidden]{display:none}html{font-family:sans-serif;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%}body{margin:0}a:focus{outline:thin dotted}a:active,a:hover{outline:0}h1{font-size:2em;margin:.67em 0}abbr[title]{border-bottom:1px dotted}b,strong{font-weight:bold}dfn{font-style:italic}hr{-moz-box-sizing:content-box;box-sizing:content-box;height:0}mark{background:#ff0;color:#000}code,kbd,pre,samp{font-family:monospace,serif;font-size:1em}pre{white-space:pre-wrap}q{quotes:"\201C" "\201D" "\2018" "\2019"}small{font-size:80%}sub,sup{font-size:75%;line-height:0;position:relative;vertical-align:baseline}sup{top:-0.5em}sub{bottom:-0.25em}img{border:0}svg:not(:root){overflow:hidden}figure{margin:0}fieldset{border:1px solid #c0c0c0;margin:0 2px;padding:.35em .625em .75em}legend{border:0;padding:0}button,input,select,textarea{font-family:inherit;font-size:100%;margin:0}button,input{line-height:normal}button,select{text-transform:none}button,html input[type="button"],input[type="reset"],input[type="submit"]{-webkit-appearance:button;cursor:pointer}button[disabled],html input[disabled]{cursor:default}input[type="checkbox"],input[type="radio"]{box-sizing:border-box;padding:0}input[type="search"]{-webkit-appearance:textfield;-moz-box-sizing:content-box;-webkit-box-sizing:content-box;box-sizing:content-box}input[type="search"]::-webkit-search-cancel-button,input[type="search"]::-webkit-search-decoration{-webkit-appearance:none}button::-moz-focus-inner,input::-moz-focus-inner{border:0;padding:0}textarea{overflow:auto;vertical-align:top}table{border-collapse:collapse;border-spacing:0}@media print{*{text-shadow:none !important;color:#000 !important;background:transparent !important;box-shadow:none !important}a,a:visited{text-decoration:underline}a[href]:after{content:" (" attr(href) ")"}abbr[title]:after{content:" (" attr(title) ")"}.ir a:after,a[href^="javascript:"]:after,a[href^="#"]:after{content:""}pre,blockquote{border:1px solid #999;page-break-inside:avoid}thead{display:table-header-group}tr,img{page-break-inside:avoid}img{max-width:100% 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.state-icon:before,.has-job-state-mixin.state-setting_metadata .state-icon:before{content:"\f110"}.has-job-state-mixin.state-paused{background:#d9edf7}.has-job-state-mixin.state-paused .state-icon:before{content:"\f04c"}.has-job-state-mixin.state-discarded{background:#eee}.has-job-state-mixin.state-discarded .state-icon:before{content:"\f014"}.has-job-state-mixin.state-noPermission{background:#eee;filter:alpha(opacity=60);-moz-opacity:.6;opacity:.6}.has-job-state-mixin.state-noPermission .state-icon{font-size:20px}.has-job-state-mixin.state-noPermission .state-icon:before{content:"\f023"}.has-job-state-mixin.state-new{background:#eee}.has-job-state-mixin.state-new .state-icon:before{content:"\f017"}.dataset.state-ok,.dataset.state-failed_metadata{background:#b0f1b0}.dataset.state-ok .state-icon,.dataset.state-failed_metadata .state-icon{display:none}.dataset.state-error,.dataset.state-empty{background:#f9c7c5}.dataset.state-error .state-icon,.dataset.state-empty .state-icon{background-color:white;border-radius:8px}.dataset.state-error .state-icon:before,.dataset.state-empty .state-icon:before{font-size:20px;line-height:16px;color:red;content:"\f057"}.dataset.state-upload{background:#a8e5f7}.dataset.state-upload .state-icon{overflow:hidden}.dataset.state-upload .state-icon:before{display:inline-block;-webkit-animation:eclipse 2s infinite linear;-moz-animation:eclipse 2s infinite linear;-o-animation:eclipse 2s infinite linear;animation:eclipse 2s infinite linear;content:"\f062"}@-moz-keyframes eclipse{0%{-moz-transform:translate(0, 16px)}100%{-moz-transform:translate(0, -16px)}}@-webkit-keyframes eclipse{0%{-webkit-transform:translate(0, 16px)}100%{-webkit-transform:translate(0, -16px)}}@-o-keyframes eclipse{0%{-o-transform:translate(0, 16px)}100%{-o-transform:translate(0, -16px)}}@-ms-keyframes eclipse{0%{-ms-transform:translate(0, 16px)}100%{-ms-transform:translate(0, -16px)}}@keyframes eclipse{0%{transform:translate(0, 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