"); + } + container.addClass("editable-text"); + + if (on_finish) { + on_finish(new_text); + } + }; + + // Create input element(s) for editing. + var cur_text = ("cur_text" in config_dict ? config_dict.cur_text : container.text() ), + input_elt, button_elt; + + if (use_textarea) { + input_elt = $("") + .attr({ rows: num_rows, cols: num_cols }).text($.trim(cur_text)) + .keyup(function(e) { + if (e.keyCode === 27) { + // Escape key. + set_text(cur_text); + } + }); + button_elt = $("").text("Done").click(function() { + set_text(input_elt.val()); + // Return false so that click does not propogate to container. + return false; + }); + } + else { + input_elt = $("").attr({ value: $.trim(cur_text), size: num_cols }) + .blur(function() { + set_text(cur_text); + }).keyup(function(e) { + if (e.keyCode === 27) { + // Escape key. + $(this).trigger("blur"); + } else if (e.keyCode === 13) { + // Enter key. + set_text($(this).val()); + } + + // Do not propogate event to avoid unwanted side effects. + e.stopPropagation(); + }); + } + + // Replace text with input object(s) and focus & select. + container.text(""); + container.append(input_elt); + if (button_elt) { + container.append(button_elt); + } + input_elt.focus(); + input_elt.select(); + + // Do not propogate to elements below b/c that blurs input and prevents it from being used. + e.stopPropagation(); + }); + + // Add help text if there some. + if (help_text) { + container.attr("title", help_text).tooltip(); + } + + return container; +}; + +/** + * Edit and save text asynchronously. + */ +function async_save_text( click_to_edit_elt, text_elt_id, save_url, + text_parm_name, num_cols, use_textarea, num_rows, on_start, on_finish ) { + // Set defaults if necessary. + if (num_cols === undefined) { + num_cols = 30; + } + if (num_rows === undefined) { + num_rows = 4; + } + + // Set up input element. + $("#" + click_to_edit_elt).click(function() { + // Check if this is already active + if ( $("#renaming-active").length > 0) { + return; + } + var text_elt = $("#" + text_elt_id), + old_text = text_elt.text(), + t; + + if (use_textarea) { + t = $("").attr({ rows: num_rows, cols: num_cols }).text( $.trim(old_text) ); + } else { + t = $("").attr({ value: $.trim(old_text), size: num_cols }); + } + t.attr("id", "renaming-active"); + t.blur( function() { + $(this).remove(); + text_elt.show(); + if (on_finish) { + on_finish(t); + } + }); + t.keyup( function( e ) { + if ( e.keyCode === 27 ) { + // Escape key + $(this).trigger( "blur" ); + } else if ( e.keyCode === 13 ) { + // Enter key submits + var ajax_data = {}; + ajax_data[text_parm_name] = $(this).val(); + $(this).trigger( "blur" ); + $.ajax({ + url: save_url, + data: ajax_data, + error: function() { + alert( "Text editing for elt " + text_elt_id + " failed" ); + // TODO: call finish or no? For now, let's not because error occurred. + }, + success: function(processed_text) { + // Set new text and call finish method. + if (processed_text !== "") { + text_elt.text(processed_text); + } else { + text_elt.html("None"); + } + if (on_finish) { + on_finish(t); + } + } + }); + } + }); + + if (on_start) { + on_start(t); + } + // Replace text with input object and focus & select. + text_elt.hide(); + t.insertAfter(text_elt); + t.focus(); + t.select(); + + return; + }); +} + +function commatize( number ) { + number += ''; // Convert to string + var rgx = /(\d+)(\d{3})/; + while (rgx.test(number)) { + number = number.replace(rgx, '$1' + ',' + '$2'); + } + return number; +} + +// Reset tool search to start state. +function reset_tool_search( initValue ) { + // Function may be called in top frame or in tool_menu_frame; + // in either case, get the tool menu frame. + var tool_menu_frame = $("#galaxy_tools").contents(); + if (tool_menu_frame.length === 0) { + tool_menu_frame = $(document); + } + + // Remove classes that indicate searching is active. + $(this).removeClass("search_active"); + tool_menu_frame.find(".toolTitle").removeClass("search_match"); + + // Reset visibility of tools and labels. + tool_menu_frame.find(".toolSectionBody").hide(); + tool_menu_frame.find(".toolTitle").show(); + tool_menu_frame.find(".toolPanelLabel").show(); + tool_menu_frame.find(".toolSectionWrapper").each( function() { + if ($(this).attr('id') !== 'recently_used_wrapper') { + // Default action. + $(this).show(); + } else if ($(this).hasClass("user_pref_visible")) { + $(this).show(); + } + }); + tool_menu_frame.find("#search-no-results").hide(); + + // Reset search input. + tool_menu_frame.find("#search-spinner").hide(); + if (initValue) { + var search_input = tool_menu_frame.find("#tool-search-query"); + search_input.val("search tools"); + } +} + +// Create GalaxyAsync object. +var GalaxyAsync = function(log_action) { + this.url_dict = {}; + this.log_action = (log_action === undefined ? false : log_action); +}; + +GalaxyAsync.prototype.set_func_url = function( func_name, url ) { + this.url_dict[func_name] = url; +}; + +// Set user preference asynchronously. +GalaxyAsync.prototype.set_user_pref = function( pref_name, pref_value ) { + // Get URL. + var url = this.url_dict[arguments.callee]; + if (url === undefined) { return false; } + $.ajax({ + url: url, + data: { "pref_name" : pref_name, "pref_value" : pref_value }, + error: function() { return false; }, + success: function() { return true; } + }); +}; + +// Log user action asynchronously. +GalaxyAsync.prototype.log_user_action = function( action, context, params ) { + if (!this.log_action) { return; } + + // Get URL. + var url = this.url_dict[arguments.callee]; + if (url === undefined) { return false; } + $.ajax({ + url: url, + data: { "action" : action, "context" : context, "params" : params }, + error: function() { return false; }, + success: function() { return true; } + }); +}; + +// Initialize refresh events. +function init_refresh_on_change () { + $("select[refresh_on_change='true']") + .off('change') + .change(function() { + var select_field = $(this), + select_val = select_field.val(), + refresh = false, + ref_on_change_vals = select_field.attr("refresh_on_change_values"); + if (ref_on_change_vals) { + ref_on_change_vals = ref_on_change_vals.split(','); + var last_selected_value = select_field.attr("last_selected_value"); + if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; + } + } + $(window).trigger("refresh_on_change"); + $(document).trigger("convert_to_values"); // Convert autocomplete text to values + select_field.get(0).form.submit(); + }); + + // checkboxes refresh on change + $(":checkbox[refresh_on_change='true']") + .off('click') + .click( function() { + var select_field = $(this), + select_val = select_field.val(), + refresh = false, + ref_on_change_vals = select_field.attr("refresh_on_change_values"); + if (ref_on_change_vals) { + ref_on_change_vals = ref_on_change_vals.split(','); + var last_selected_value = select_field.attr("last_selected_value"); + if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; + } + } + $(window).trigger("refresh_on_change"); + select_field.get(0).form.submit(); + }); + + // Links with confirmation + $( "a[confirm]" ) + .off('click') + .click( function() { + return confirm( $(this).attr("confirm") ); + }); +}; + +$(document).ready( function() { + + // Refresh events for form fields. + init_refresh_on_change(); + + // Tooltips + if ( $.fn.tooltip ) { + // Put tooltips below items in panel header so that they do not overlap masthead. + $(".unified-panel-header [title]").tooltip( { placement: 'bottom' } ); + + // default tooltip initialization, it will follow the data-placement tag for tooltip location + // and fallback to 'top' if not present + $("[title]").tooltip(); + } + // Make popup menus. + make_popup_menus(); + + // Replace big selects. + replace_big_select_inputs(20, 1500); + + // If galaxy_main frame does not exist and link targets galaxy_main, + // add use_panels=True and set target to self. + $("a").click( function() { + var anchor = $(this); + var galaxy_main_exists = (parent.frames && parent.frames.galaxy_main); + if ( ( anchor.attr( "target" ) == "galaxy_main" ) && ( !galaxy_main_exists ) ) { + var href = anchor.attr("href"); + if (href.indexOf("?") == -1) { + href += "?"; + } + else { + href += "&"; + } + href += "use_panels=True"; + anchor.attr("href", href); + anchor.attr("target", "_self"); + } + return anchor; + }); + +}); diff --git a/client/scripts/galaxy.frame.js b/client/scripts/galaxy.frame.js new file mode 100644 index 00000000000..f6b0db9bfd7 --- /dev/null +++ b/client/scripts/galaxy.frame.js @@ -0,0 +1,173 @@ +// dependencies +define(["galaxy.masthead", "mvc/ui/ui-frames"], function(mod_masthead, Frames) { + +// frame manager +var GalaxyFrame = Backbone.View.extend( +{ + // base element + el_main: 'body', + + // frame active/disabled + active: false, + + // button active + button_active: null, + + // button load + button_load : null, + + // initialize + initialize : function(options) + { + // add to masthead menu + var self = this; + + // create frames + this.frames = new Frames.View({ + visible: false, + }); + + // add activate icon + this.button_active = new mod_masthead.GalaxyMastheadIcon ( + { + icon : 'fa-th', + tooltip : 'Enable/Disable Scratchbook', + onclick : function() { self._activate(); }, + onunload : function() { + if (self.frames.length() > 0) { + return "You opened " + self.frames.length() + " frame(s) which will be lost."; + } + } + }); + + // add to masthead + Galaxy.masthead.append(this.button_active); + + // add load icon + this.button_load = new mod_masthead.GalaxyMastheadIcon ( + { + icon : 'fa-eye', + tooltip : 'Show/Hide Scratchbook', + onclick : function(e) { + if (self.frames.visible) { + self.frames.hide(); + } else { + self.frames.show(); + } + }, + with_number : true + }); + + // add to masthead + Galaxy.masthead.append(this.button_load); + + // create + this.setElement(this.frames.$el); + + // append to main + $(this.el_main).append(this.$el); + + // refresh menu + this.frames.setOnChange(function() { + self._refresh(); + }); + this._refresh(); + }, + + // adds and displays a new frame/window + add: function(options) + { + // open new tab + if (options.target == '_blank') + { + window.open(options.content); + return; + } + + // reload entire window + if (options.target == '_top' || options.target == '_parent' || options.target == '_self') + { + window.location = options.content; + return; + } + + // validate + if (!this.active) + { + // fix url if main frame is unavailable + var $galaxy_main = $(window.parent.document).find('#galaxy_main'); + if (options.target == 'galaxy_main' || options.target == 'center') + { + if ($galaxy_main.length === 0) + { + var href = options.content; + if (href.indexOf('?') == -1) + href += '?'; + else + href += '&'; + href += 'use_panels=True'; + window.location = href; + } else { + $galaxy_main.attr('src', options.content); + } + } else + window.location = options.content; + + // stop + return; + } + + // add to frames view + this.frames.add(options); + }, + + // activate/disable panel + _activate: function () + { + // check + if (this.active) + { + // disable + this.active = false; + + // toggle + this.button_active.untoggle(); + + // hide panel + this.frames.hide(); + } else { + // activate + this.active = true; + + // untoggle + this.button_active.toggle(); + } + }, + + // update frame counter + _refresh: function() + { + // update on screen counter + this.button_load.number(this.frames.length()); + + // check + if(this.frames.length() === 0) + this.button_load.hide(); + else + this.button_load.show(); + + // check + if (this.frames.visible) { + this.button_load.toggle(); + } else { + this.button_load.untoggle(); + } + } +}); + +// return +return { + GalaxyFrame: GalaxyFrame +}; + +}); diff --git a/client/scripts/galaxy.library.js b/client/scripts/galaxy.library.js new file mode 100644 index 00000000000..770550c418f --- /dev/null +++ b/client/scripts/galaxy.library.js @@ -0,0 +1,159 @@ +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +// === MAIN GALAXY LIBRARY MODULE ==== +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM + +define([ + "galaxy.masthead", + "utils/utils", + "libs/toastr", + "mvc/base-mvc", + "mvc/library/library-model", + "mvc/library/library-folderlist-view", + "mvc/library/library-librarylist-view", + "mvc/library/library-librarytoolbar-view", + "mvc/library/library-foldertoolbar-view", + "mvc/library/library-dataset-view", + "mvc/library/library-library-view", + "mvc/library/library-folder-view" + ], +function(mod_masthead, + mod_utils, + mod_toastr, + mod_baseMVC, + mod_library_model, + mod_folderlist_view, + mod_librarylist_view, + mod_librarytoolbar_view, + mod_foldertoolbar_view, + mod_library_dataset_view, + mod_library_library_view, + mod_library_folder_view + ) { + +// ============================================================================ +// ROUTER +var LibraryRouter = Backbone.Router.extend({ + initialize: function() { + this.routesHit = 0; + //keep count of number of routes handled by the application + Backbone.history.on('route', function() { this.routesHit++; }, this); + }, + + routes: { + "" : "libraries", + "library/:library_id/permissions" : "library_permissions", + "folders/:folder_id/permissions" : "folder_permissions", + "folders/:id" : "folder_content", + "folders/:folder_id/datasets/:dataset_id" : "dataset_detail", + "folders/:folder_id/datasets/:dataset_id/permissions" : "dataset_permissions", + "folders/:folder_id/datasets/:dataset_id/versions/:ldda_id" : "dataset_version", + "folders/:folder_id/download/:format" : "download" + }, + + back: function() { + if(this.routesHit > 1) { + //more than one route hit -> user did not land to current page directly + window.history.back(); + } else { + //otherwise go to the home page. Use replaceState if available so + //the navigation doesn't create an extra history entry + this.navigate('#', {trigger:true, replace:true}); + } + } +}); + +// ============================================================================ +/** session storage for library preferences */ +var LibraryPrefs = mod_baseMVC.SessionStorageModel.extend({ + defaults : { + with_deleted : false, + sort_order : 'asc', + sort_by : 'name' + } +}); + +// ============================================================================ +// Main controller of Galaxy Library +var GalaxyLibrary = Backbone.View.extend({ + + libraryToolbarView: null, + libraryListView: null, + library_router: null, + libraryView: null, + folderToolbarView: null, + folderListView: null, + datasetView: null, + + initialize : function(){ + Galaxy.libraries = this; + + this.preferences = new LibraryPrefs( {id: 'global-lib-prefs'} ); + + this.library_router = new LibraryRouter(); + + this.library_router.on('route:libraries', function() { + Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView(); + Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView(); + }); + + this.library_router.on('route:folder_content', function(id) { + if (Galaxy.libraries.folderToolbarView){ + Galaxy.libraries.folderToolbarView.$el.unbind('click'); + } + Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: id}); + Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: id}); + }); + + this.library_router.on('route:download', function(folder_id, format) { + if ($('#folder_list_body').find(':checked').length === 0) { + mod_toastr.info('You have to select some datasets to download'); + Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); + } else { + Galaxy.libraries.folderToolbarView.download(folder_id, format); + Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); + } + }); + + this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){ + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id}); + }); + this.library_router.on('route:dataset_version', function(folder_id, dataset_id, ldda_id){ + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true}); + }); + + this.library_router.on('route:dataset_permissions', function(folder_id, dataset_id){ + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true}); + }); + + this.library_router.on('route:library_permissions', function(library_id){ + if (Galaxy.libraries.libraryView){ + Galaxy.libraries.libraryView.$el.unbind('click'); + } + Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true}); + }); + + this.library_router.on('route:folder_permissions', function(folder_id){ + if (Galaxy.libraries.folderView){ + Galaxy.libraries.folderView.$el.unbind('click'); + } + Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true}); + }); + + Backbone.history.start({pushState: false}); + } +}); + +return { + GalaxyApp: GalaxyLibrary +}; + +}); diff --git a/client/scripts/galaxy.masthead.js b/client/scripts/galaxy.masthead.js new file mode 100644 index 00000000000..99243410c01 --- /dev/null +++ b/client/scripts/galaxy.masthead.js @@ -0,0 +1,445 @@ +// dependencies +define([], function() { + +// masthead +var GalaxyMasthead = Backbone.View.extend( +{ + // base element + el_masthead: '#everything', + + // options + options : null, + + // background + $background: null, + + // list + list: [], + + // initialize + initialize : function(options) + { + // update options + this.options = options; + + // HACK: due to body events defined in galaxy.panels.js + $("body").off(); + + // define this element + this.setElement($(this._template(options))); + + // append to masthead + $(this.el_masthead).append($(this.el)); + + // assign background + this.$background = $(this.el).find('#masthead-background'); + + // loop through unload functions if the user attempts to unload the page + var self = this; + $(window).on('beforeunload', function() { + var text = ""; + for (key in self.list) { + if (self.list[key].options.onunload) { + var q = self.list[key].options.onunload(); + if (q) text += q + " "; + } + } + if (text != "") { + return text; + } + }); + }, + + // configure events + events: + { + 'click' : '_click', + 'mousedown' : function(e) { e.preventDefault() } + }, + + // adds a new item to the masthead + append : function(item) + { + return this._add(item, true); + }, + + // adds a new item to the masthead + prepend : function(item) + { + return this._add(item, false); + }, + + // activate + highlight: function(id) + { + var current = $(this.el).find('#' + id + '> li'); + if (current) { + current.addClass('active'); + } + }, + + // adds a new item to the masthead + _add : function(item, append) + { + var $loc = $(this.el).find('#' + item.location); + if ($loc) + { + // create frame for new item + var $current = $(item.el); + + // configure class in order to mark new items + $current.addClass('masthead-item'); + + // append to masthead + if (append) { + $loc.append($current); + } else { + $loc.prepend($current); + } + + // add to list + this.list.push(item); + } + + // location not found + return null; + }, + + // handle click event + _click: function(e) + { + // close all popups + var $all = $(this.el).find('.popup'); + if ($all) { + $all.hide(); + } + + // open current item + var $current = $(e.target).closest('.masthead-item').find('.popup'); + if ($(e.target).hasClass('head')) { + $current.show(); + this.$background.show(); + } else { + this.$background.hide(); + } + }, + + /* + HTML TEMPLATES + */ + + // fill template + _template: function(options) + { + var brand_text = options.brand ? ("/ " + options.brand) : "" ; + return '
' +
+ '
' +
+ '' +
+ '' +
+ '' +
+ '
' +
+ '' +
+ '' +
+ '
' +
+ ' Galaxy ' + brand_text + '' +
+ '' +
+ '
' +
+ '' +
+ '' +
+ '' +
+ ' Galaxy ' + brand_text + '' +
+ '' +
+ '' +
+ '';
+ if (options.with_number)
+ tmpl+= '';
+ tmpl += '
';
+
+ // return template
+ return tmpl;
+ }
+});
+
+// tab
+var GalaxyMastheadTab = Backbone.View.extend(
+{
+ // main options
+ options:
+ {
+ id : '',
+ title : '',
+ target : '_parent',
+ content : '',
+ type : 'url',
+ scratchbook : false,
+ onunload : null,
+ visible : true,
+ disabled : false,
+ title_attribute : ''
+ },
+
+ // location
+ location: 'navbar',
+
+ // optional sub menu
+ $menu: null,
+
+ // events
+ events:
+ {
+ 'click .head' : '_head'
+ },
+
+ // initialize
+ initialize: function (options)
+ {
+ // read in defaults
+ if (options)
+ this.options = _.defaults(options, this.options);
+
+ // update url
+ if (this.options.content && this.options.content.indexOf('//') === -1)
+ this.options.content = galaxy_config.root + this.options.content;
+
+ // add template for tab
+ this.setElement($(this._template(this.options)));
+
+ // disable menu items that are not available to anonymous user
+ // also show title to explain why they are disabled
+ if (this.options.disabled){
+ $(this.el).find('.root').addClass('disabled');
+ this._attachPopover();
+ }
+
+ // visiblity
+ if (!this.options.visible)
+ this.hide();
+ },
+
+ // show
+ show: function()
+ {
+ $(this.el).css({visibility : 'visible'});
+ },
+
+ // show
+ hide: function()
+ {
+ $(this.el).css({visibility : 'hidden'});
+ },
+
+ // add menu item
+ add: function (options)
+ {
+ // menu option defaults
+ var menuOptions = {
+ title : 'Title',
+ content : '',
+ type : 'url',
+ target : '_parent',
+ scratchbook : false,
+ divider : false
+ }
+
+ // read in defaults
+ if (options)
+ menuOptions = _.defaults(options, menuOptions);
+
+ // update url
+ if (menuOptions.content && menuOptions.content.indexOf('//') === -1)
+ menuOptions.content = galaxy_config.root + menuOptions.content;
+
+ // check if submenu element is available
+ if (!this.$menu)
+ {
+ // insert submenu element into root
+ $(this.el).find('.root').append(this._templateMenu());
+
+ // show caret
+ $(this.el).find('.symbol').addClass('caret');
+
+ // update element link
+ this.$menu = $(this.el).find('.popup');
+ }
+
+ // create
+ var $item = $(this._templateMenuItem(menuOptions));
+
+ // append menu
+ this.$menu.append($item);
+
+ // add events
+ var self = this;
+ $item.on('click', function(e)
+ {
+ // prevent default
+ e.preventDefault();
+
+ // no modifications if new tab is requested
+ if (self.options.target === '_blank')
+ return true;
+
+ // load into frame
+ Galaxy.frame.add(options);
+ });
+
+ // append divider
+ if (menuOptions.divider)
+ this.$menu.append($(this._templateDivider()));
+ },
+
+ // show menu on header click
+ _head: function(e)
+ {
+ // prevent default
+ e.preventDefault();
+
+ if (this.options.disabled){
+ return // prevent link following if menu item is disabled
+ }
+
+ // check for menu options
+ if (!this.$menu) {
+ Galaxy.frame.add(this.options);
+ }
+ },
+
+ _attachPopover : function()
+ {
+ var $popover_element = $(this.el).find('.head');
+ $popover_element.popover({
+ html: true,
+ content: 'Please log in or register to use this feature.',
+ placement: 'bottom'
+ }).on('shown.bs.popover', function() { // hooking on bootstrap event to automatically hide popovers after delay
+ setTimeout(function() {
+ $popover_element.popover('hide');
+ }, 5000);
+ });
+ },
+
+ // fill template header
+ _templateMenuItem: function (options)
+ {
+ return '",
+ {
+ "Make link": function() {
+ // Get URL, name/title.
+ var sUrl = $(wym._options.hrefSelector).val() || '',
+ sId = $(".wym_id").val() || '',
+ sName = $(wym._options.titleSelector).val() || '';
+
+ if (sUrl || sId) {
+ // Create link.
+ wym._exec(WYMeditor.CREATE_LINK, sStamp);
+
+ // Set link attributes.
+ var link = $("a[href=" + sStamp + "]", wym._doc.body);
+ link.attr(WYMeditor.HREF, sUrl)
+ .attr(WYMeditor.TITLE, sName)
+ .attr("id", sId);
+
+ // If link's text is default (wym-...), change it to the title.
+ if (link.text().indexOf('wym-') === 0) {
+ link.text(sName);
+ }
+ }
+ hide_modal();
+ },
+ "Cancel": function() {
+ hide_modal();
+ }
+ },
+ {},
+ set_link_id
+ );
+ }
+
+ // IMAGE DIALOG
+ if ( dialogType == WYMeditor.DIALOG_IMAGE ) {
+ if(wym._selected_image) {
+ $(wym._options.dialogImageSelector + " " + wym._options.srcSelector)
+ .val($(wym._selected_image).attr(WYMeditor.SRC));
+ $(wym._options.dialogImageSelector + " " + wym._options.titleSelector)
+ .val($(wym._selected_image).attr(WYMeditor.TITLE));
+ $(wym._options.dialogImageSelector + " " + wym._options.altSelector)
+ .val($(wym._selected_image).attr(WYMeditor.ALT));
+ }
+ show_modal(
+ "Image",
+ "" +
+ "Make the selected " + item_info.plural.toLowerCase() + " accessible so that they can viewed by everyone.
"
+ ,
+ {
+ "Insert": function()
+ {
+ // Make selected items accessible (importable) ?
+ var make_importable = false;
+ if ( $('#make-importable:checked').val() !== null )
+ make_importable = true;
+
+ // Insert links to history for each checked item.
+ var item_ids = new Array();
+ $('input[name=id]:checked').each(function() {
+ var item_id = $(this).val();
+
+ // Make item importable?
+ if (make_importable)
+ make_item_importable(item_info.controller, item_id, item_info.singular);
+
+ // Insert link(s) to item(s). This is done by getting item info and then manipulating wym.
+ url_template = get_name_and_link_url + item_id;
+ ajax_url = url_template.replace( "ITEM_CONTROLLER", item_info.controller);
+ $.getJSON( ajax_url, function( returned_item_info ) {
+ // Get link text.
+ wym._exec(WYMeditor.CREATE_LINK, sStamp);
+ var link_text = $("a[href=" + sStamp + "]", wym._doc.body).text();
+
+ // Insert link: need to do different actions depending on link text.
+ if (
+ link_text == "" // Firefox.
+ ||
+ link_text == sStamp // Safari
+ )
+ {
+ // User selected no text; create link from scratch and use default text.
+ wym.insert("" + item_info.singular + " '" + returned_item_info.name + "'");
+ }
+ else
+ {
+ // Link created from selected text; add href and title.
+ $("a[href=" + sStamp + "]", wym._doc.body).attr(WYMeditor.HREF, returned_item_info.link).attr(WYMeditor.TITLE, item_info.singular + item_id);
+ }
+ });
+ });
+
+ hide_modal();
+ },
+ "Cancel": function()
+ {
+ hide_modal();
+ }
+ }
+ );
+ }
+ });
+ }
+ // EMBED GALAXY OBJECT DIALOGS
+ if ( dialogType == Galaxy.DIALOG_EMBED_HISTORY || dialogType == Galaxy.DIALOG_EMBED_DATASET || dialogType == Galaxy.DIALOG_EMBED_WORKFLOW || dialogType == Galaxy.DIALOG_EMBED_PAGE || dialogType == Galaxy.DIALOG_EMBED_VISUALIZATION ) {
+ // Based on item type, set useful vars.
+ var item_info;
+ switch(dialogType)
+ {
+ case(Galaxy.DIALOG_EMBED_HISTORY):
+ item_info = get_item_info(Galaxy.ITEM_HISTORY);
+ break;
+ case(Galaxy.DIALOG_EMBED_DATASET):
+ item_info = get_item_info(Galaxy.ITEM_DATASET);
+ break;
+ case(Galaxy.DIALOG_EMBED_WORKFLOW):
+ item_info = get_item_info(Galaxy.ITEM_WORKFLOW);
+ break;
+ case(Galaxy.DIALOG_EMBED_PAGE):
+ item_info = get_item_info(Galaxy.ITEM_PAGE);
+ break;
+ case(Galaxy.DIALOG_EMBED_VISUALIZATION):
+ item_info = get_item_info(Galaxy.ITEM_VISUALIZATION);
+ break;
+ }
+
+ $.ajax(
+ {
+ url: item_info.list_ajax_url,
+ data: {},
+ error: function() { alert( "Failed to list " + item_info.plural.toLowerCase() + " for selection"); },
+ success: function(list_html)
+ {
+ // Can make histories, workflows importable; cannot make datasets importable.
+ if (dialogType == Galaxy.DIALOG_EMBED_HISTORY || dialogType == Galaxy.DIALOG_EMBED_WORKFLOW
+ || dialogType == Galaxy.DIALOG_EMBED_VISUALIZATION)
+ list_html = list_html + ""
+ + "
" + + "" + + "
"
+ + "" + + "" + + "
"
+ + "
" + + "" + + "
"
+ + "" + + "" + + "
"
+ + "
" + + "" + + "
",
+ {
+ "Insert": function() {
+ var sUrl = $(wym._options.srcSelector).val();
+ if(sUrl.length > 0) {
+ wym._exec(WYMeditor.INSERT_IMAGE, sStamp);
+ $("img[src$=" + sStamp + "]", wym._doc.body)
+ .attr(WYMeditor.SRC, sUrl)
+ .attr(WYMeditor.TITLE, $(wym._options.titleSelector).val())
+ .attr(WYMeditor.ALT, $(wym._options.altSelector).val());
+ }
+ hide_modal();
+ },
+ "Cancel": function() {
+ hide_modal();
+ }
+ }
+ );
+ return;
+ }
+
+ // TABLE DIALOG
+ if ( dialogType == WYMeditor.DIALOG_TABLE ) {
+ show_modal(
+ "Table",
+ "" + + "" + + "
"
+ + "
" + + "" + + "
"
+ + "" + + "" + + "
"
+ + "
" + + "" + + "
"
+ + "" + + "" + + "
"
+ + ""
+ + ""
+ + "
"
+ + ""
+ + ""
+ + ""
+ + "
",
+ {
+ "Insert": function() {
+ var iRows = $(wym._options.rowsSelector).val();
+ var iCols = $(wym._options.colsSelector).val();
+
+ if(iRows > 0 && iCols > 0) {
+
+ var table = wym._doc.createElement(WYMeditor.TABLE);
+ var newRow = null;
+ var newCol = null;
+
+ var sCaption = $(wym._options.captionSelector).val();
+
+ //we create the caption
+ var newCaption = table.createCaption();
+ newCaption.innerHTML = sCaption;
+
+ //we create the rows and cells
+ for(x=0; x" +
+ "Make the selected " + item_info.plural.toLowerCase() + " accessible so that they can viewed by everyone.
";
+ show_modal(
+ "Embed " + item_info.plural,
+ list_html,
+ {
+ "Embed": function()
+ {
+ // Make selected items accessible (importable) ?
+ var make_importable = false;
+ if ( $('#make-importable:checked').val() != null )
+ make_importable = true;
+
+ $('input[name=id]:checked').each(function() {
+ // Get item ID and name.
+ var item_id = $(this).val();
+ // Use ':first' because there are many labels in table; the first one is the item name.
+ var item_name = $("label[for='" + item_id + "']:first").text();
+
+ if (make_importable)
+ make_item_importable(item_info.controller, item_id, item_info.singular);
+
+ // Embedded item HTML; item class is embedded in div container classes; this is necessary because the editor strips
+ // all non-standard attributes when it returns its content (e.g. it will not return an element attribute of the form
+ // item_class='History').
+ var item_elt_id = item_info.iclass + "-" + item_id;
+ var item_embed_html = [
+ "" ].join( '' );
+
+ // Insert embedded item into document.
+ wym.insert(item_embed_html);
+
+ });
+ hide_modal();
+ },
+ "Cancel": function()
+ {
+ hide_modal();
+ }
+ }
+ );
+ }
+ });
+ }
+};
+
+$(function(){
+ // Generic error handling
+ $(document).ajaxError( function ( e, x ) {
+ // console.log( e, x );
+ var message = x.responseText || x.statusText || "Could not connect to server";
+ show_modal( "Server error", message, { "Ignore error" : hide_modal } );
+ return false;
+ });
+ // Create editor
+ $("[name=page_content]").wymeditor( {
+ skin: 'galaxy',
+ basePath: editor_base_path,
+ iframeBasePath: iframe_base_path,
+ boxHtml: ""
+ + WYMeditor.TOOLS
+ + " |
| "
+ + " "
+ // + WYMeditor.HTML
+ + WYMeditor.IFRAME
+ + WYMeditor.STATUS
+ + " "
+ + ""
+ + " |
");
+ }
+ this.$body.html( body );
+ },
+ show: function( options, callback ) {
+ if ( ! this.$dialog.is( ":visible" ) ) {
+ if ( options.backdrop) {
+ this.$backdrop.addClass( "in" );
+ } else {
+ this.$backdrop.removeClass( "in" );
+ }
+ this.$overlay.show();
+ this.$dialog.show();
+ this.$overlay.addClass("in");
+ // Fix min-width so that modal cannot shrink considerably if new content is loaded.
+ this.$body.css( "min-width", this.$body.width() );
+ // Set max-height so that modal does not exceed window size and is in middle of page.
+ // TODO: this could perhaps be handled better using CSS.
+ this.$body.css( "max-height",
+ $(window).height() -
+ this.$footer.outerHeight() -
+ this.$header.outerHeight() -
+ parseInt( this.$dialog.css( "padding-top" ), 10 ) -
+ parseInt( this.$dialog.css( "padding-bottom" ), 10 )
+ );
+ }
+ // Callback on init
+ if ( callback ) {
+ callback();
+ }
+ },
+ hide: function() {
+ var modal = this;
+ modal.$dialog.fadeOut( function() {
+ modal.$overlay.hide();
+ modal.$backdrop.removeClass( "in" );
+ modal.$body.children().remove();
+ // Clear min-width to allow for modal to take size of new body.
+ modal.$body.css( "min-width", undefined );
+ });
+ }
+});
+
+var modal;
+
+$(function(){
+ modal = new Modal( { overlay: $("#top-modal"), dialog: $("#top-modal-dialog"), backdrop: $("#top-modal-backdrop") } );
+});
+
+// Backward compatibility
+function hide_modal() {
+ modal.hide();
+}
+function show_modal( title, body, buttons, extra_buttons, init_fn ) {
+ modal.setContent( { title: title, body: body, buttons: buttons, extra_buttons: extra_buttons } );
+ modal.show( { backdrop: true }, init_fn );
+}
+function show_message( title, body, buttons, extra_buttons, init_fn ) {
+ modal.setContent( { title: title, body: body, buttons: buttons, extra_buttons: extra_buttons } );
+ modal.show( { backdrop: false }, init_fn );
+}
+function show_in_overlay( options ) {
+ var width = options.width || '600';
+ var height = options.height || '400';
+ var scroll = options.scroll || 'auto';
+ $("#overlay-background").bind( "click.overlay", function() {
+ hide_modal();
+ $("#overlay-background").unbind( "click.overlay" );
+ });
+ modal.setContent( { closeButton: true, title: " ", body: $( "" ) } );
+ modal.show( { backdrop: true } );
+}
+
+function user_changed( user_email, is_admin ) {
+ if ( user_email ) {
+ $(".loggedin-only").show();
+ $(".loggedout-only").hide();
+ $("#user-email").text( user_email );
+ if ( is_admin ) {
+ $(".admin-only").show();
+ }
+ } else {
+ $(".loggedin-only").hide();
+ $(".loggedout-only").show();
+ $(".admin-only").hide();
+ }
+}
+
+// Masthead dropdown menus
+$(function() {
+ var $dropdowns = $("#masthead ul.nav > li.dropdown > .dropdown-menu");
+ $("body").on( "click.nav_popups", function( e ) {
+ $dropdowns.hide();
+ $("#DD-helper").hide();
+ // If the target is in the menu, treat normally
+ if ( $(e.target).closest( "#masthead ul.nav > li.dropdown > .dropdown-menu" ).length ) {
+ return;
+ }
+ // Otherwise, was the click in a tab
+ var $clicked = $(e.target).closest( "#masthead ul.nav > li.dropdown" );
+ if ( $clicked.length ) {
+ $("#DD-helper").show();
+ $clicked.children( ".dropdown-menu" ).show();
+ e.preventDefault();
+ }
+ });
+});
+
+// Exports
+exports.ensure_dd_helper = ensure_dd_helper;
+exports.Panel = Panel;
+exports.Modal = Modal;
+exports.hide_modal = hide_modal;
+exports.show_modal = show_modal;
+exports.show_message = show_message;
+exports.show_in_overlay = show_in_overlay;
+exports.user_changed = user_changed;
+
+}( window, window.jQuery );
diff --git a/client/scripts/galaxy.tools.js b/client/scripts/galaxy.tools.js
new file mode 100644
index 00000000000..da57624c31f
--- /dev/null
+++ b/client/scripts/galaxy.tools.js
@@ -0,0 +1,158 @@
+// dependencies
+define([ "libs/underscore", "mvc/tools" ], function( _, Tools ) {
+
+ var checkUncheckAll = function( name, check ) {
+ $("input[name='" + name + "'][type='checkbox']").attr('checked', !!check);
+ }
+
+ $(".tool-share-link").each( function() {
+ var href = $(this).attr("href");
+ var href = $(this).attr("data-link");
+ $(this).click(function() {
+ window.prompt("Copy to clipboard: Ctrl+C, Enter", href);
+ });
+ });
+
+ // Inserts the Select All / Unselect All buttons for checkboxes
+ $("div.checkUncheckAllPlaceholder").each( function() {
+ var check_name = $(this).attr("checkbox_name");
+ select_link = $("").text("Select All").click(function() {
+ checkUncheckAll(check_name, true);
+ });
+ unselect_link = $("").text("Unselect All").click(function() {
+ checkUncheckAll(check_name, false);
+ });
+ $(this).append(select_link).append(" ").append(unselect_link);
+ });
+
+ var SELECTION_TYPE = {
+ 'select_single': {
+ 'icon_class': 'fa-file-o',
+ 'select_by': 'Run tool on single input',
+ 'allow_remap': true
+ },
+ 'select_multiple': {
+ 'icon_class': 'fa-files-o',
+ 'select_by': 'Run tool in parallel across multiple datasets',
+ 'allow_remap': false,
+ 'min_option_count': 2 // Don't show multiple select switch if only
+ // one dataset available.
+ },
+ 'select_collection': {
+ 'icon_class': 'fa-folder-o',
+ 'select_by': 'Run tool in parallel across dataset collection',
+ 'allow_remap': false
+ },
+ 'multiselect_single': {
+ 'icon_class': 'fa-list-alt',
+ 'select_by': 'Run tool over multiple datasets',
+ 'allow_remap': true
+ },
+ 'multiselect_collection': {
+ 'icon_class': 'fa-folder-o',
+ 'select_by': 'Run tool over dataset collection',
+ 'allow_remap': false,
+ },
+ 'select_single_collection': {
+ 'icon_class': 'fa-file-o',
+ 'select_by': 'Run tool on single collection',
+ 'allow_remap': true
+ },
+ 'select_map_over_collections': {
+ 'icon_class': 'fa-folder-o',
+ 'select_by': 'Map tool over compontents of nested collection',
+ 'allow_remap': false,
+ }
+ };
+
+ var SwitchSelectView = Backbone.View.extend({
+ initialize: function( data ) {
+ var defaultOption = data.default_option;
+ var defaultIndex = null;
+ var switchOptions = data.switch_options;
+ this.switchOptions = switchOptions;
+ this.prefix = data.prefix;
+ var el = this.$el;
+ var view = this;
+
+ var index = 0;
+ var visibleCount = 0;
+ _.each( this.switchOptions, function( option, onValue ) {
+ var numValues = _.size( option.options );
+ var selectionType = SELECTION_TYPE[ onValue ];
+ var iIndex = index++;
+ var hidden = false;
+ if( defaultOption == onValue ) {
+ defaultIndex = iIndex;
+ } else if( numValues < ( selectionType.min_option_count || 1 ) ) {
+ hidden = true;
+ }
+ if( ! hidden ) {
+ visibleCount++;
+ var button = $('').click(function() {
+ view.enableSelectBy( iIndex, onValue );
+ }).attr(
+ 'title',
+ selectionType['select_by']
+ ).data( "index", iIndex );
+ view.formRow().find( "label" ).append( button );
+ }
+ });
+ if( visibleCount < 2 ) {
+ // Don't show buttons to switch options...
+ view.formRow().find("i.runOptionIcon").hide();
+ }
+
+ if( defaultIndex != null) {
+ view.enableSelectBy( defaultIndex, defaultOption );
+ }
+ },
+
+ formRow: function() {
+ return this.$el.closest( ".form-row" );
+ },
+
+ render: function() {
+ },
+
+ enableSelectBy: function( enableIndex, onValue ) {
+ var selectionType = SELECTION_TYPE[onValue];
+ if(selectionType["allow_remap"]) {
+ $("div#remap-row").css("display", "inherit");
+ } else {
+ $("div#remap-row").css("display", "none");
+ }
+ this.formRow().find( "i" ).each(function(_, iElement) {
+ var $iElement = $(iElement);
+ var index = $iElement.data("index");
+ if(index == enableIndex) {
+ $iElement.css('color', 'black');
+ } else {
+ $iElement.css('color', 'Gray');
+ }
+ });
+ var $select = this.$( "select" );
+ var options = this.switchOptions[ onValue ];
+ $select.attr( "name", this.prefix + options.name );
+ $select.attr( "multiple", options.multiple );
+ // Replace options regardless.
+ var select2ed = this.$(".select2-container").length > 0;
+ $select.html(""); // clear out select list
+ _.each( options.options, function( option ) {
+ var text = option[0];
+ var value = option[1];
+ var selected = option[2];
+ $select.append($("", {text: text, val: value, selected: selected}));
+ });
+ if( select2ed ) {
+ // Without this select2 does not update options.
+ $select.select2();
+ }
+ }
+ });
+
+ return {
+ SwitchSelectView: SwitchSelectView
+ };
+
+});
diff --git a/client/scripts/galaxy.ui.scrollPanel.js b/client/scripts/galaxy.ui.scrollPanel.js
new file mode 100644
index 00000000000..3b9aafd0bf1
--- /dev/null
+++ b/client/scripts/galaxy.ui.scrollPanel.js
@@ -0,0 +1,88 @@
+// This is an extension to jQuery UI draggable
+// When dragging move the parent element ("panel") relative to its parent
+// ("viewport") so that the draggable is always visible.
+
+$.ui.plugin.add("draggable", "scrollPanel", {
+ drag: function(e, ui) {
+ var instance = $(this).data("draggable");
+ clearTimeout( instance.timeout );
+ var o = ui.options,
+ element = instance.element,
+ panel = o.panel,
+ panel_pos = panel.position(),
+ panel_w = panel.width(),
+ panel_h = panel.height()
+ viewport = panel.parent();
+ viewport_w = viewport.width(),
+ viewport_h = viewport.height(),
+ element_w = element.width(),
+ element_h = element.height(),
+ moved = false,
+ close_dist = 5,
+ nudge = 23,
+ // Legal panel range
+ p_min_x = - ( panel_w - viewport_w ),
+ p_min_y = - ( panel_h - viewport_h ),
+ p_max_x = 0,
+ p_max_y = 0,
+ // Visible
+ min_vis_x = - panel_pos.left,
+ max_vis_x = min_vis_x + viewport_w,
+ min_vis_y = - panel_pos.top,
+ max_vis_y = min_vis_y + viewport_h,
+ // Mouse
+ mouse_x = ui.position.left + instance.offset.click.left;
+ mouse_y = ui.position.top + instance.offset.click.top;
+ // Move it
+ if ( ( panel_pos.left < p_max_x ) && ( mouse_x - close_dist < min_vis_x ) ) {
+ var t = Math.min( nudge, p_max_x - panel_pos.left );
+ panel.css( "left", panel_pos.left + t );
+ moved = true;
+ instance.offset.parent.left += t;
+ ui.position.left -= t
+ }
+ if ( ( ! moved ) && ( panel_pos.left > p_min_x ) && ( mouse_x + close_dist > max_vis_x ) ) {
+ var t = Math.min( nudge, panel_pos.left - p_min_x );
+ panel.css( "left", panel_pos.left - t );
+ moved = true;
+ instance.offset.parent.left -= t;
+ ui.position.left += t;
+ }
+ if ( ( ! moved ) && ( panel_pos.top < p_max_y ) && ( mouse_y - close_dist < min_vis_y ) ) {
+ var t = Math.min( nudge, p_max_y - panel_pos.top );
+ panel.css( "top", panel_pos.top + t );
+ // Firefox sometimes moves by less, so we need to check. Yuck.
+ var amount_moved = panel.position().top - panel_pos.top;
+ instance.offset.parent.top += amount_moved;
+ ui.position.top -= amount_moved;
+ moved = true;
+ }
+ if ( ( ! moved ) && ( panel_pos.top > p_min_y ) && ( mouse_y + close_dist > max_vis_y ) ) {
+ var t = Math.min( nudge, panel_pos.top - p_min_x );
+ panel.css( "top", ( panel_pos.top - t ) + "px" );
+ // Firefox sometimes moves by less, so we need to check. Yuck.
+ var amount_moved = panel_pos.top - panel.position().top;
+ instance.offset.parent.top -= amount_moved;
+ ui.position.top += amount_moved;
+ moved = true;
+ }
+ // Still contain in panel
+ ui.position.left = Math.max( ui.position.left, 0 );
+ ui.position.top = Math.max( ui.position.top, 0 );
+ ui.position.left = Math.min( ui.position.left, panel_w - element_w );
+ ui.position.top = Math.min( ui.position.top, panel_h - element_h );
+ // Update offsets
+ if ( moved ) {
+ $.ui.ddmanager.prepareOffsets( instance, e );
+ }
+ // Keep moving even if mouse doesn't move
+ if ( moved ) {
+ instance.old_e = e;
+ instance.timeout = setTimeout( function() { instance.mouseMove( e ) }, 50 );
+ }
+ },
+ stop: function( e, ui ) {
+ var instance = $(this).data("draggable");
+ clearTimeout( instance.timeout );
+ }
+});
\ No newline at end of file
diff --git a/client/scripts/galaxy.workflow_editor.canvas.js b/client/scripts/galaxy.workflow_editor.canvas.js
new file mode 100644
index 00000000000..9414eb090af
--- /dev/null
+++ b/client/scripts/galaxy.workflow_editor.canvas.js
@@ -0,0 +1,1991 @@
+function CollectionTypeDescription( collectionType ) {
+ this.collectionType = collectionType;
+ this.isCollection = true;
+ this.rank = collectionType.split(":").length;
+}
+
+$.extend( CollectionTypeDescription.prototype, {
+ append: function( otherCollectionTypeDescription ) {
+ if( otherCollectionTypeDescription === NULL_COLLECTION_TYPE_DESCRIPTION ) {
+ return this;
+ }
+ if( otherCollectionTypeDescription === ANY_COLLECTION_TYPE_DESCRIPTION ) {
+ return otherCollectionType;
+ }
+ return new CollectionTypeDescription( this.collectionType + ":" + otherCollectionTypeDescription.collectionType );
+ },
+ canMatch: function( otherCollectionTypeDescription ) {
+ if( otherCollectionTypeDescription === NULL_COLLECTION_TYPE_DESCRIPTION ) {
+ return false;
+ }
+ if( otherCollectionTypeDescription === ANY_COLLECTION_TYPE_DESCRIPTION ) {
+ return true;
+ }
+ return otherCollectionTypeDescription.collectionType == this.collectionType;
+ },
+ canMapOver: function( otherCollectionTypeDescription ) {
+ if( otherCollectionTypeDescription === NULL_COLLECTION_TYPE_DESCRIPTION ) {
+ return false;
+ }
+ if( otherCollectionTypeDescription === ANY_COLLECTION_TYPE_DESCRIPTION ) {
+ return false;
+ }
+ if( this.rank <= otherCollectionTypeDescription.rank ) {
+ // Cannot map over self...
+ return false;
+ }
+ var requiredSuffix = otherCollectionTypeDescription.collectionType
+ return this._endsWith( this.collectionType, requiredSuffix );
+ },
+ effectiveMapOver: function( otherCollectionTypeDescription ) {
+ var otherCollectionType = otherCollectionTypeDescription.collectionType;
+ var effectiveCollectionType = this.collectionType.substring( 0, this.collectionType.length - otherCollectionType.length - 1 );
+ return new CollectionTypeDescription( effectiveCollectionType );
+ },
+ equal: function( otherCollectionTypeDescription ) {
+ return otherCollectionTypeDescription.collectionType == this.collectionType;
+ },
+ toString: function() {
+ return "CollectionType[" + this.collectionType + "]";
+ },
+ _endsWith: function( str, suffix ) {
+ return str.indexOf(suffix, str.length - suffix.length) !== -1;
+ }
+} );
+
+NULL_COLLECTION_TYPE_DESCRIPTION = {
+ isCollection: false,
+ canMatch: function( other ) { return false; },
+ canMapOver: function( other ) {
+ return false;
+ },
+ toString: function() {
+ return "NullCollectionType[]";
+ },
+ append: function( otherCollectionType ) {
+ return otherCollectionType;
+ },
+ equal: function( other ) {
+ return other === this;
+ }
+};
+
+ANY_COLLECTION_TYPE_DESCRIPTION = {
+ isCollection: true,
+ canMatch: function( other ) { return NULL_COLLECTION_TYPE_DESCRIPTION !== other; },
+ canMapOver: function( other ) {
+ return false;
+ },
+ toString: function() {
+ return "AnyCollectionType[]";
+ },
+ append: function( otherCollectionType ) {
+ throw "Cannot append to ANY_COLLECTION_TYPE_DESCRIPTION";
+ },
+ equal: function( other ) {
+ return other === this;
+ }
+};
+
+var TerminalMapping = Backbone.Model.extend( {
+ initialize: function( attr ) {
+ this.mapOver = attr.mapOver || NULL_COLLECTION_TYPE_DESCRIPTION;
+ this.terminal = attr.terminal;
+ this.terminal.terminalMapping = this;
+ },
+ disableMapOver: function() {
+ this.setMapOver( NULL_COLLECTION_TYPE_DESCRIPTION );
+ },
+ setMapOver: function( collectionTypeDescription ) {
+ // TODO: Can I use "attributes" or something to auto trigger "change"
+ // event?
+ this.mapOver = collectionTypeDescription;
+ this.trigger("change");
+ }
+} );
+
+var TerminalMappingView = Backbone.View.extend( {
+ tagName: "div",
+ className: "fa-icon-button fa fa-folder-o",
+
+ initialize: function( options ) {
+ var mapText = "Run tool in parallel over collection";
+ this.$el.tooltip( {delay: 500, title: mapText } );
+ this.model.bind( "change", _.bind( this.render, this ) );
+ },
+
+ render: function() {
+ if( this.model.mapOver.isCollection ) {
+ this.$el.show();
+ } else {
+ this.$el.hide();
+ }
+ },
+
+} );
+
+var InputTerminalMappingView = TerminalMappingView.extend( {
+ events: {
+ "click": "onClick",
+ "mouseenter": "onMouseEnter",
+ "mouseleave": "onMouseLeave",
+ },
+ onMouseEnter: function( e ) {
+ var model = this.model;
+ if( ! model.terminal.connected() && model.mapOver.isCollection ) {
+ this.$el.css( "color", "red" );
+ }
+ },
+ onMouseLeave: function( e ) {
+ this.$el.css( "color", "black" );
+ },
+ onClick: function( e ) {
+ var model = this.model;
+ if( ! model.terminal.connected() && model.mapOver.isCollection ) {
+ // TODO: Consider prompting...
+ model.terminal.resetMapping();
+ }
+ },
+} );
+
+var InputTerminalMapping = TerminalMapping;
+var InputCollectionTerminalMapping = TerminalMapping;
+var OutputTerminalMapping = TerminalMapping;
+var OutputTerminalMappingView = TerminalMappingView;
+var InputCollectionTerminalMappingView = InputTerminalMappingView;
+var OutputCollectionTerminalMapping = TerminalMapping;
+var OutputCollectionTerminalMappingView = TerminalMappingView;
+
+var Terminal = Backbone.Model.extend( {
+ initialize: function( attr ) {
+ this.element = attr.element;
+ this.connectors = [];
+ },
+ connect: function ( connector ) {
+ this.connectors.push( connector );
+ if ( this.node ) {
+ this.node.markChanged();
+ }
+ },
+ disconnect: function ( connector ) {
+ this.connectors.splice( $.inArray( connector, this.connectors ), 1 );
+ if ( this.node ) {
+ this.node.markChanged();
+ this.resetMappingIfNeeded();
+ }
+ },
+ redraw: function () {
+ $.each( this.connectors, function( _, c ) {
+ c.redraw();
+ });
+ },
+ destroy: function () {
+ $.each( this.connectors.slice(), function( _, c ) {
+ c.destroy();
+ });
+ },
+ destroyInvalidConnections: function( ) {
+ _.each( this.connectors, function( connector ) {
+ connector.destroyIfInvalid();
+ } );
+ },
+ setMapOver : function( val ) {
+ if( this.multiple ) {
+ return; // Cannot set this to be multirun...
+ }
+
+ if( ! this.mapOver().equal( val ) ) {
+ this.terminalMapping.setMapOver( val );
+ _.each( this.node.output_terminals, function( outputTerminal ) {
+ outputTerminal.setMapOver( val );
+ } );
+ }
+ },
+ mapOver: function( ) {
+ if ( ! this.terminalMapping ) {
+ return NULL_COLLECTION_TYPE_DESCRIPTION;
+ } else {
+ return this.terminalMapping.mapOver;
+ }
+ },
+ isMappedOver: function( ) {
+ return this.terminalMapping && this.terminalMapping.mapOver.isCollection;
+ },
+ resetMapping: function() {
+ this.terminalMapping.disableMapOver();
+ },
+
+ resetMappingIfNeeded: function( ) {}, // Subclasses should override this...
+
+} );
+
+var OutputTerminal = Terminal.extend( {
+ initialize: function( attr ) {
+ Terminal.prototype.initialize.call( this, attr );
+ this.datatypes = attr.datatypes;
+ },
+
+ resetMappingIfNeeded: function( ) {
+ // If inputs were only mapped over to preserve
+ // an output just disconnected reset these...
+ if( ! this.node.hasConnectedOutputTerminals() && ! this.node.hasConnectedMappedInputTerminals()){
+ _.each( this.node.mappedInputTerminals(), function( mappedInput ) {
+ mappedInput.resetMappingIfNeeded();
+ } );
+ }
+
+ var noMappedInputs = ! this.node.hasMappedOverInputTerminals();
+ if( noMappedInputs ) {
+ this.resetMapping();
+ }
+ },
+
+ resetMapping: function() {
+ this.terminalMapping.disableMapOver();
+ _.each( this.connectors, function( connector ) {
+ var connectedInput = connector.handle2;
+ if( connectedInput ) {
+ // Not exactly right because this is still connected.
+ // Either rewrite resetMappingIfNeeded or disconnect
+ // and reconnect if valid.
+ connectedInput.resetMappingIfNeeded();
+ connector.destroyIfInvalid();
+ }
+ } );
+ }
+
+} );
+
+
+var BaseInputTerminal = Terminal.extend( {
+ initialize: function( attr ) {
+ Terminal.prototype.initialize.call( this, attr );
+ this.update( attr.input ); // subclasses should implement this...
+ },
+ canAccept: function ( other ) {
+ if( this._inputFilled() ) {
+ return false;
+ } else {
+ return this.attachable( other );
+ }
+ },
+ resetMappingIfNeeded: function( ) {
+ var mapOver = this.mapOver();
+ if( ! mapOver.isCollection ) {
+ return;
+ }
+ // No output terminals are counting on this being mapped
+ // over if connected inputs are still mapped over or if none
+ // of the outputs are connected...
+ var reset = this.node.hasConnectedMappedInputTerminals() ||
+ ( ! this.node.hasConnectedOutputTerminals() );
+ if( reset ) {
+ this.resetMapping();
+ }
+ },
+ resetMapping: function() {
+ this.terminalMapping.disableMapOver();
+ if( ! this.node.hasMappedOverInputTerminals() ) {
+ _.each( this.node.output_terminals, function( terminal) {
+ // This shouldn't be called if there are mapped over
+ // outputs.
+ terminal.resetMapping();
+ } );
+ }
+ },
+ connected: function() {
+ return this.connectors.length !== 0;
+ },
+ _inputFilled: function() {
+ var inputFilled;
+ if( ! this.connected() ) {
+ inputFilled = false;
+ } else {
+ if( this.multiple ) {
+ if(this._collectionAttached()) {
+ // Can only attach one collection to multiple input
+ // data parameter.
+ inputsFilled = true;
+ } else {
+ inputFilled = false;
+ }
+ } else {
+ inputFilled = true;
+ }
+ }
+ return inputFilled;
+ },
+ _collectionAttached: function( ) {
+ if( ! this.connected() ) {
+ return false;
+ } else {
+ var firstOutput = this.connectors[ 0 ].handle1;
+ if( ! firstOutput ){
+ return false;
+ } else {
+ if( firstOutput.isDataCollectionInput || firstOutput.isMappedOver() || firstOutput.datatypes.indexOf( "input_collection" ) > 0 ) {
+ return true;
+ } else {
+ return false;
+ }
+ }
+ }
+ },
+ _mappingConstraints: function( ) {
+ // If this is a connected terminal, return list of collection types
+ // other terminals connected to node are constraining mapping to.
+ if( ! this.node ) {
+ return []; // No node - completely unconstrained
+ }
+ var mapOver = this.mapOver();
+ if( mapOver.isCollection ) {
+ return [ mapOver ];
+ }
+
+ var constraints = [];
+ if( ! this.node.hasConnectedOutputTerminals() ) {
+ _.each( this.node.connectedMappedInputTerminals(), function( inputTerminal ) {
+ constraints.push( inputTerminal.mapOver() );
+ } );
+ } else {
+ // All outputs should have same mapOver status - least specific.
+ constraints.push( _.first( _.values( this.node.output_terminals ) ).mapOver() );
+ }
+ return constraints;
+ },
+ _producesAcceptableDatatype: function( other ) {
+ // other is a non-collection output...
+ for ( var t in this.datatypes ) {
+ var cat_outputs = new Array();
+ cat_outputs = cat_outputs.concat(other.datatypes);
+ if (other.node.post_job_actions){
+ for (var pja_i in other.node.post_job_actions){
+ var pja = other.node.post_job_actions[pja_i];
+ if (pja.action_type == "ChangeDatatypeAction" && (pja.output_name == '' || pja.output_name == other.name) && pja.action_arguments){
+ cat_outputs.push(pja.action_arguments['newtype']);
+ }
+ }
+ }
+ // FIXME: No idea what to do about case when datatype is 'input'
+ for ( var other_datatype_i in cat_outputs ) {
+ var other_datatype = cat_outputs[other_datatype_i];
+ if ( other_datatype == "input" || other_datatype == "input_collection" || issubtype( cat_outputs[other_datatype_i], this.datatypes[t] ) ) {
+ return true;
+ }
+ }
+ }
+ return false;
+ },
+ _otherCollectionType: function( other ) {
+ var otherCollectionType = NULL_COLLECTION_TYPE_DESCRIPTION;
+ if( other.isDataCollectionInput ) {
+ otherCollectionType = other.collectionType;
+ } else {
+ var otherMapOver = other.mapOver();
+ if( otherMapOver.isCollection ) {
+ otherCollectionType = otherMapOver;
+ }
+ }
+ return otherCollectionType;
+ },
+} );
+
+
+
+
+
+var InputTerminal = BaseInputTerminal.extend( {
+ update: function( input ) {
+ this.datatypes = input.extensions;
+ this.multiple = input.multiple;
+ this.collection = false;
+ },
+ connect: function( connector ) {
+ BaseInputTerminal.prototype.connect.call( this, connector );
+ var other_output = connector.handle1;
+ if( ! other_output ) {
+ return;
+ }
+ var otherCollectionType = this._otherCollectionType( other_output );
+ if( otherCollectionType.isCollection ) {
+ this.setMapOver( otherCollectionType );
+ }
+ },
+ attachable: function( other ) {
+ var otherCollectionType = this._otherCollectionType( other );
+ var thisMapOver = this.mapOver();
+ if( otherCollectionType.isCollection ) {
+ if( this.multiple ) {
+ if( this.connected() && ! this._collectionAttached() ) {
+ // if single inputs attached, cannot also attach a
+ // collection (yet...)
+ return false;
+ }
+ if( otherCollectionType.rank == 1 ) {
+ return this._producesAcceptableDatatype( other );
+ } else {
+ // TODO: Allow subcollection mapping over this as if it were
+ // a list collection input.
+ return false;
+ }
+ }
+ if( thisMapOver.isCollection && thisMapOver.canMatch( otherCollectionType ) ) {
+ return this._producesAcceptableDatatype( other );
+ } else {
+ // Need to check if this would break constraints...
+ var mappingConstraints = this._mappingConstraints();
+ if( mappingConstraints.every( _.bind( otherCollectionType.canMatch, otherCollectionType ) ) ) {
+ return this._producesAcceptableDatatype( other );
+ } else {
+ return false;
+ }
+ }
+ } else if( thisMapOver.isCollection ) {
+ // Attempting to match a non-collection output to an
+ // explicitly collection input.
+ return false;
+ }
+ return this._producesAcceptableDatatype( other );
+ }
+
+});
+
+var InputCollectionTerminal = BaseInputTerminal.extend( {
+ update: function( input ) {
+ this.multiple = false;
+ this.collection = true;
+ this.datatypes = input.extensions;
+ if( input.collection_type ) {
+ this.collectionType = new CollectionTypeDescription( input.collection_type );
+ } else {
+ this.collectionType = ANY_COLLECTION_TYPE_DESCRIPTION;
+ }
+ },
+ connect: function( connector ) {
+ BaseInputTerminal.prototype.connect.call( this, connector );
+ var other = connector.handle1;
+ if( ! other ) {
+ return;
+ }
+
+ var effectiveMapOver = this._effectiveMapOver( other );
+ this.setMapOver( effectiveMapOver );
+ },
+ _effectiveMapOver: function( other ) {
+ var collectionType = this.collectionType;
+ var otherCollectionType = this._otherCollectionType( other );
+ if( ! collectionType.canMatch( otherCollectionType ) ) {
+ return otherCollectionType.effectiveMapOver( collectionType );
+ } else {
+ return NULL_COLLECTION_TYPE_DESCRIPTION;
+ }
+ },
+ _effectiveCollectionType: function( ) {
+ var collectionType = this.collectionType;
+ var thisMapOver = this.mapOver();
+ return thisMapOver.append( collectionType );
+ },
+ attachable: function ( other ) {
+ var otherCollectionType = this._otherCollectionType( other );
+ if( otherCollectionType.isCollection ) {
+ var effectiveCollectionType = this._effectiveCollectionType( );
+ var thisMapOver = this.mapOver();
+ if( effectiveCollectionType.canMatch( otherCollectionType ) ) {
+ // Only way a direct match...
+ return this._producesAcceptableDatatype( other );
+ // Otherwise we need to mapOver
+ } else if( thisMapOver.isCollection ) {
+ // In this case, mapOver already set and we didn't match skipping...
+ return false;
+ } else if( otherCollectionType.canMapOver( this.collectionType ) ) {
+ var effectiveMapOver = this._effectiveMapOver( other );
+ if( ! effectiveMapOver.isCollection ) {
+ return false;
+ }
+ // Need to check if this would break constraints...
+ var mappingConstraints = this._mappingConstraints();
+ if( mappingConstraints.every( effectiveMapOver.canMatch ) ) {
+ return this._producesAcceptableDatatype( other );
+ }
+ }
+ }
+ return false;
+ }
+});
+
+var OutputCollectionTerminal = Terminal.extend( {
+ initialize: function( attr ) {
+ Terminal.prototype.initialize.call( this, attr );
+ this.datatypes = attr.datatypes;
+ this.collectionType = new CollectionTypeDescription( attr.collection_type );
+ this.isDataCollectionInput = true;
+ },
+ update: function( output ) {
+ var newCollectionType = new CollectionTypeDescription( output.collection_type );
+ if( newCollectionType.collectionType != this.collectionType.collectionType ) {
+ _.each( this.connectors, function( connector ) {
+ // TODO: consider checking if connection valid before removing...
+ connector.destroy();
+ } );
+ }
+ this.collectionType = newCollectionType;
+ }
+} );
+
+function Connector( handle1, handle2 ) {
+ this.canvas = null;
+ this.dragging = false;
+ this.inner_color = "#FFFFFF";
+ this.outer_color = "#D8B365";
+ if ( handle1 && handle2 ) {
+ this.connect( handle1, handle2 );
+ }
+}
+$.extend( Connector.prototype, {
+ connect: function ( t1, t2 ) {
+ this.handle1 = t1;
+ if ( this.handle1 ) {
+ this.handle1.connect( this );
+ }
+ this.handle2 = t2;
+ if ( this.handle2 ) {
+ this.handle2.connect( this );
+ }
+ },
+ destroy : function () {
+ if ( this.handle1 ) {
+ this.handle1.disconnect( this );
+ }
+ if ( this.handle2 ) {
+ this.handle2.disconnect( this );
+ }
+ $(this.canvas).remove();
+ },
+ destroyIfInvalid: function() {
+ if( this.handle1 && this.handle2 && ! this.handle2.attachable( this.handle1 ) ) {
+ this.destroy();
+ }
+ },
+ redraw : function () {
+ var canvas_container = $("#canvas-container");
+ if ( ! this.canvas ) {
+ this.canvas = document.createElement( "canvas" );
+ // excanvas specific hack
+ if ( window.G_vmlCanvasManager ) {
+ G_vmlCanvasManager.initElement( this.canvas );
+ }
+ canvas_container.append( $(this.canvas) );
+ if ( this.dragging ) {
+ this.canvas.style.zIndex = "300";
+ }
+ }
+ var relativeLeft = function( e ) {
+ return $(e).offset().left - canvas_container.offset().left;
+ };
+ var relativeTop = function( e ) {
+ return $(e).offset().top - canvas_container.offset().top;
+ };
+ if (!this.handle1 || !this.handle2) {
+ return;
+ }
+ // Find the position of each handle
+ var start_x = relativeLeft( this.handle1.element ) + 5;
+ var start_y = relativeTop( this.handle1.element ) + 5;
+ var end_x = relativeLeft( this.handle2.element ) + 5;
+ var end_y = relativeTop( this.handle2.element ) + 5;
+ // Calculate canvas area
+ var canvas_extra = 100;
+ var canvas_min_x = Math.min( start_x, end_x );
+ var canvas_max_x = Math.max( start_x, end_x );
+ var canvas_min_y = Math.min( start_y, end_y );
+ var canvas_max_y = Math.max( start_y, end_y );
+ var cp_shift = Math.min( Math.max( Math.abs( canvas_max_y - canvas_min_y ) / 2, 100 ), 300 );
+ var canvas_left = canvas_min_x - canvas_extra;
+ var canvas_top = canvas_min_y - canvas_extra;
+ var canvas_width = canvas_max_x - canvas_min_x + 2 * canvas_extra;
+ var canvas_height = canvas_max_y - canvas_min_y + 2 * canvas_extra;
+ // Place the canvas
+ this.canvas.style.left = canvas_left + "px";
+ this.canvas.style.top = canvas_top + "px";
+ this.canvas.setAttribute( "width", canvas_width );
+ this.canvas.setAttribute( "height", canvas_height );
+ // Adjust points to be relative to the canvas
+ start_x -= canvas_left;
+ start_y -= canvas_top;
+ end_x -= canvas_left;
+ end_y -= canvas_top;
+ // Draw the line
+
+ var c = this.canvas.getContext("2d"),
+ start_offsets = null,
+ end_offsets = null;
+ var num_offsets = 1;
+ if ( this.handle1 && this.handle1.isMappedOver() ) {
+ var start_offsets = [ -6, -3, 0, 3, 6 ];
+ num_offsets = 5;
+ } else {
+ var start_offsets = [ 0 ];
+ }
+ if ( this.handle2 && this.handle2.isMappedOver() ) {
+ var end_offsets = [ -6, -3, 0, 3, 6 ];
+ num_offsets = 5;
+ } else {
+ var end_offsets = [ 0 ];
+ }
+ var connector = this;
+ for( var i = 0; i < num_offsets; i++ ) {
+ var inner_width = 5,
+ outer_width = 7;
+ if( start_offsets.length > 1 || end_offsets.length > 1 ) {
+ // We have a multi-run, using many lines, make them small.
+ inner_width = 1;
+ outer_width = 3;
+ }
+ connector.draw_outlined_curve( start_x, start_y, end_x, end_y, cp_shift, inner_width, outer_width, start_offsets[ i % start_offsets.length ], end_offsets[ i % end_offsets.length ] );
+ }
+ },
+ draw_outlined_curve : function( start_x, start_y, end_x, end_y, cp_shift, inner_width, outer_width, offset_start, offset_end ) {
+ var offset_start = offset_start || 0;
+ var offset_end = offset_end || 0;
+ var c = this.canvas.getContext("2d");
+ c.lineCap = "round";
+ c.strokeStyle = this.outer_color;
+ c.lineWidth = outer_width;
+ c.beginPath();
+ c.moveTo( start_x, start_y + offset_start );
+ c.bezierCurveTo( start_x + cp_shift, start_y + offset_start, end_x - cp_shift, end_y + offset_end, end_x, end_y + offset_end);
+ c.stroke();
+ // Inner line
+ c.strokeStyle = this.inner_color;
+ c.lineWidth = inner_width;
+ c.beginPath();
+ c.moveTo( start_x, start_y + offset_start );
+ c.bezierCurveTo( start_x + cp_shift, start_y + offset_start, end_x - cp_shift, end_y + offset_end, end_x, end_y + offset_end );
+ c.stroke();
+ }
+} );
+
+var Node = Backbone.Model.extend({
+
+ initialize: function( attr ) {
+ this.element = attr.element;
+ this.input_terminals = {};
+ this.output_terminals = {};
+ this.tool_errors = {};
+ },
+ connectedOutputTerminals: function() {
+ return this._connectedTerminals( this.output_terminals );
+ },
+ _connectedTerminals: function( terminals ) {
+ var connectedTerminals = [];
+ $.each( terminals, function( _, t ) {
+ if( t.connectors.length > 0 ) {
+ connectedTerminals.push( t );
+ }
+ } );
+ return connectedTerminals;
+ },
+ hasConnectedOutputTerminals: function() {
+ // return this.connectedOutputTerminals().length > 0; <- optimized this
+ var outputTerminals = this.output_terminals;
+ for( var outputName in outputTerminals ) {
+ if( outputTerminals[ outputName ].connectors.length > 0 ) {
+ return true;
+ }
+ }
+ return false;
+ },
+ connectedMappedInputTerminals: function() {
+ return this._connectedMappedTerminals( this.input_terminals );
+ },
+ hasConnectedMappedInputTerminals: function() {
+ // return this.connectedMappedInputTerminals().length > 0; <- optimized this
+ var inputTerminals = this.input_terminals;
+ for( var inputName in inputTerminals ) {
+ var inputTerminal = inputTerminals[ inputName ];
+ if( inputTerminal.connectors.length > 0 && inputTerminal.isMappedOver() ) {
+ return true;
+ }
+ }
+ return false;
+ },
+ _connectedMappedTerminals: function( terminals ) {
+ var mapped_outputs = [];
+ $.each( terminals, function( _, t ) {
+ var mapOver = t.mapOver();
+ if( mapOver.isCollection ) {
+ if( t.connectors.length > 0 ) {
+ mapped_outputs.push( t );
+ }
+ }
+ });
+ return mapped_outputs;
+ },
+ mappedInputTerminals: function() {
+ return this._mappedTerminals( this.input_terminals );
+ },
+ _mappedTerminals: function( terminals ) {
+ var mappedTerminals = [];
+ $.each( terminals, function( _, t ) {
+ var mapOver = t.mapOver();
+ if( mapOver.isCollection ) {
+ mappedTerminals.push( t );
+ }
+ } );
+ return mappedTerminals;
+ },
+ hasMappedOverInputTerminals: function() {
+ var found = false;
+ _.each( this.input_terminals, function( t ) {
+ var mapOver = t.mapOver();
+ if( mapOver.isCollection ) {
+ found = true;
+ }
+ } );
+ return found;
+ },
+ redraw : function () {
+ $.each( this.input_terminals, function( _, t ) {
+ t.redraw();
+ });
+ $.each( this.output_terminals, function( _, t ) {
+ t.redraw();
+ });
+ },
+ destroy : function () {
+ $.each( this.input_terminals, function( k, t ) {
+ t.destroy();
+ });
+ $.each( this.output_terminals, function( k, t ) {
+ t.destroy();
+ });
+ workflow.remove_node( this );
+ $(this.element).remove();
+ },
+ make_active : function () {
+ $(this.element).addClass( "toolForm-active" );
+ },
+ make_inactive : function () {
+ // Keep inactive nodes stacked from most to least recently active
+ // by moving element to the end of parent's node list
+ var element = this.element.get(0);
+ (function(p) { p.removeChild( element ); p.appendChild( element ); })(element.parentNode);
+ // Remove active class
+ $(element).removeClass( "toolForm-active" );
+ },
+ init_field_data : function ( data ) {
+ if ( data.type ) {
+ this.type = data.type;
+ }
+ this.name = data.name;
+ this.form_html = data.form_html;
+ this.tool_state = data.tool_state;
+ this.tool_errors = data.tool_errors;
+ this.tooltip = data.tooltip ? data.tooltip : "";
+ this.annotation = data.annotation;
+ this.post_job_actions = data.post_job_actions ? data.post_job_actions : {};
+ this.workflow_outputs = data.workflow_outputs ? data.workflow_outputs : [];
+
+ var node = this;
+ var nodeView = new NodeView({
+ el: this.element[ 0 ],
+ node: node,
+ });
+ node.nodeView = nodeView;
+
+ $.each( data.data_inputs, function( i, input ) {
+ nodeView.addDataInput( input );
+ });
+ if ( ( data.data_inputs.length > 0 ) && ( data.data_outputs.length > 0 ) ) {
+ nodeView.addRule();
+ }
+ $.each( data.data_outputs, function( i, output ) {
+ nodeView.addDataOutput( output );
+ } );
+ nodeView.render();
+ workflow.node_changed( this );
+ },
+ update_field_data : function( data ) {
+ var node = this;
+ nodeView = node.nodeView;
+ this.tool_state = data.tool_state;
+ this.form_html = data.form_html;
+ this.tool_errors = data.tool_errors;
+ this.annotation = data['annotation'];
+ if( "post_job_actions" in data ) {
+ // Won't be present in response for data inputs
+ var pja_in = $.parseJSON(data.post_job_actions);
+ this.post_job_actions = pja_in ? pja_in : {};
+ }
+ node.nodeView.renderToolErrors();
+ // Update input rows
+ var old_body = nodeView.$( "div.inputs" );
+ var new_body = nodeView.newInputsDiv();
+ var newTerminalViews = {};
+ _.each( data.data_inputs, function( input ) {
+ var terminalView = node.nodeView.addDataInput( input, new_body );
+ newTerminalViews[ input.name ] = terminalView;
+ });
+ // Cleanup any leftover terminals
+ _.each( _.difference( _.values( nodeView.terminalViews ), _.values( newTerminalViews ) ), function( unusedView ) {
+ unusedView.el.terminal.destroy();
+ } );
+ nodeView.terminalViews = newTerminalViews;
+ // In general workflow editor assumes tool outputs don't change in # or
+ // type (not really valid right?) but adding special logic here for
+ // data collection input parameters that can have their collection
+ // change.
+ if( data.data_outputs.length == 1 && "collection_type" in data.data_outputs[ 0 ] ) {
+ nodeView.updateDataOutput( data.data_outputs[ 0 ] );
+ }
+
+ old_body.replaceWith( new_body );
+ // If active, reactivate with new form_html
+ this.markChanged();
+ this.redraw();
+ },
+ error : function ( text ) {
+ var b = $(this.element).find( ".toolFormBody" );
+ b.find( "div" ).remove();
+ var tmp = "
" + text + "
";
+ this.form_html = tmp;
+ b.html( tmp );
+ workflow.node_changed( this );
+ },
+ markChanged: function() {
+ workflow.node_changed( this );
+ }
+} );
+
+function Workflow( canvas_container ) {
+ this.canvas_container = canvas_container;
+ this.id_counter = 0;
+ this.nodes = {};
+ this.name = null;
+ this.has_changes = false;
+ this.active_form_has_changes = false;
+}
+$.extend( Workflow.prototype, {
+ add_node : function( node ) {
+ node.id = this.id_counter;
+ node.element.attr( 'id', 'wf-node-step-' + node.id );
+ this.id_counter++;
+ this.nodes[ node.id ] = node;
+ this.has_changes = true;
+ node.workflow = this;
+ },
+ remove_node : function( node ) {
+ if ( this.active_node == node ) {
+ this.clear_active_node();
+ }
+ delete this.nodes[ node.id ] ;
+ this.has_changes = true;
+ },
+ remove_all : function() {
+ wf = this;
+ $.each( this.nodes, function ( k, v ) {
+ v.destroy();
+ wf.remove_node( v );
+ });
+ },
+ rectify_workflow_outputs : function() {
+ // Find out if we're using workflow_outputs or not.
+ var using_workflow_outputs = false;
+ var has_existing_pjas = false;
+ $.each( this.nodes, function ( k, node ) {
+ if (node.workflow_outputs && node.workflow_outputs.length > 0){
+ using_workflow_outputs = true;
+ }
+ $.each(node.post_job_actions, function(pja_id, pja){
+ if (pja.action_type === "HideDatasetAction"){
+ has_existing_pjas = true;
+ }
+ });
+ });
+ if (using_workflow_outputs !== false || has_existing_pjas !== false){
+ // Using workflow outputs, or has existing pjas. Remove all PJAs and recreate based on outputs.
+ $.each(this.nodes, function (k, node ){
+ if (node.type === 'tool'){
+ var node_changed = false;
+ if (node.post_job_actions == null){
+ node.post_job_actions = {};
+ node_changed = true;
+ }
+ var pjas_to_rem = [];
+ $.each(node.post_job_actions, function(pja_id, pja){
+ if (pja.action_type == "HideDatasetAction"){
+ pjas_to_rem.push(pja_id);
+ }
+ });
+ if (pjas_to_rem.length > 0 ) {
+ $.each(pjas_to_rem, function(i, pja_name){
+ node_changed = true;
+ delete node.post_job_actions[pja_name];
+ });
+ }
+ if (using_workflow_outputs){
+ $.each(node.output_terminals, function(ot_id, ot){
+ var create_pja = true;
+ $.each(node.workflow_outputs, function(i, wo_name){
+ if (ot.name === wo_name){
+ create_pja = false;
+ }
+ });
+ if (create_pja === true){
+ node_changed = true;
+ var pja = {
+ action_type : "HideDatasetAction",
+ output_name : ot.name,
+ action_arguments : {}
+ }
+ node.post_job_actions['HideDatasetAction'+ot.name] = null;
+ node.post_job_actions['HideDatasetAction'+ot.name] = pja;
+ }
+ });
+ }
+ // lastly, if this is the active node, and we made changes, reload the display at right.
+ if (workflow.active_node == node && node_changed === true) {
+ workflow.reload_active_node();
+ }
+ }
+ });
+ }
+ },
+ to_simple : function () {
+ var nodes = {};
+ $.each( this.nodes, function ( i, node ) {
+ var input_connections = {};
+ $.each( node.input_terminals, function ( k, t ) {
+ input_connections[ t.name ] = null;
+ // There should only be 0 or 1 connectors, so this is
+ // really a sneaky if statement
+ var cons = []
+ $.each( t.connectors, function ( i, c ) {
+ cons[i] = { id: c.handle1.node.id, output_name: c.handle1.name };
+ input_connections[ t.name ] = cons;
+ });
+ });
+ var post_job_actions = {};
+ if (node.post_job_actions){
+ $.each( node.post_job_actions, function ( i, act ) {
+ var pja = {
+ action_type : act.action_type,
+ output_name : act.output_name,
+ action_arguments : act.action_arguments
+ }
+ post_job_actions[ act.action_type + act.output_name ] = null;
+ post_job_actions[ act.action_type + act.output_name ] = pja;
+ });
+ }
+ if (!node.workflow_outputs){
+ node.workflow_outputs = [];
+ // Just in case.
+ }
+ var node_data = {
+ id : node.id,
+ type : node.type,
+ tool_id : node.tool_id,
+ tool_state : node.tool_state,
+ tool_errors : node.tool_errors,
+ input_connections : input_connections,
+ position : $(node.element).position(),
+ annotation: node.annotation,
+ post_job_actions: node.post_job_actions,
+ workflow_outputs: node.workflow_outputs
+ };
+ nodes[ node.id ] = node_data;
+ });
+ return { steps: nodes };
+ },
+ from_simple : function ( data ) {
+ wf = this;
+ var max_id = 0;
+ wf.name = data.name;
+ // First pass, nodes
+ var using_workflow_outputs = false;
+ $.each( data.steps, function( id, step ) {
+ var node = prebuild_node( step.type, step.name, step.tool_id );
+ node.init_field_data( step );
+ if ( step.position ) {
+ node.element.css( { top: step.position.top, left: step.position.left } );
+ }
+ node.id = step.id;
+ wf.nodes[ node.id ] = node;
+ max_id = Math.max( max_id, parseInt( id ) );
+ // For older workflows, it's possible to have HideDataset PJAs, but not WorkflowOutputs.
+ // Check for either, and then add outputs in the next pass.
+ if (!using_workflow_outputs && node.type === 'tool'){
+ if (node.workflow_outputs.length > 0){
+ using_workflow_outputs = true;
+ }
+ else{
+ $.each(node.post_job_actions, function(pja_id, pja){
+ if (pja.action_type === "HideDatasetAction"){
+ using_workflow_outputs = true;
+ }
+ });
+ }
+ }
+ });
+ wf.id_counter = max_id + 1;
+ // Second pass, connections
+ $.each( data.steps, function( id, step ) {
+ var node = wf.nodes[id];
+ $.each( step.input_connections, function( k, v ) {
+ if ( v ) {
+ if ( ! $.isArray( v ) ) {
+ v = [ v ];
+ }
+ $.each( v, function( l, x ) {
+ var other_node = wf.nodes[ x.id ];
+ var c = new Connector();
+ c.connect( other_node.output_terminals[ x.output_name ],
+ node.input_terminals[ k ] );
+ c.redraw();
+ });
+ }
+ });
+ if(using_workflow_outputs && node.type === 'tool'){
+ // Ensure that every output terminal has a WorkflowOutput or HideDatasetAction.
+ $.each(node.output_terminals, function(ot_id, ot){
+ if(node.post_job_actions['HideDatasetAction'+ot.name] === undefined){
+ node.workflow_outputs.push(ot.name);
+ callout = $(node.element).find('.callout.'+ot.name);
+ callout.find('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small.png');
+ workflow.has_changes = true;
+ }
+ });
+ }
+ });
+ },
+ check_changes_in_active_form : function() {
+ // If active form has changed, save it
+ if (this.active_form_has_changes) {
+ this.has_changes = true;
+ // Submit form.
+ $("#right-content").find("form").submit();
+ this.active_form_has_changes = false;
+ }
+ },
+ reload_active_node : function() {
+ if (this.active_node){
+ var node = this.active_node;
+ this.clear_active_node();
+ this.activate_node(node);
+ }
+ },
+ clear_active_node : function() {
+ if ( this.active_node ) {
+ this.active_node.make_inactive();
+ this.active_node = null;
+ }
+ parent.show_form_for_tool( "No node selected
" );
+ },
+ activate_node : function( node ) {
+ if ( this.active_node != node ) {
+ this.check_changes_in_active_form();
+ this.clear_active_node();
+ parent.show_form_for_tool( node.form_html + node.tooltip, node );
+ node.make_active();
+ this.active_node = node;
+ }
+ },
+ node_changed : function ( node ) {
+ this.has_changes = true;
+ if ( this.active_node == node ) {
+ // Reactive with new form_html
+ this.check_changes_in_active_form(); //Force changes to be saved even on new connection (previously dumped)
+ parent.show_form_for_tool( node.form_html + node.tooltip, node );
+ }
+ },
+ layout : function () {
+ this.check_changes_in_active_form();
+ this.has_changes = true;
+ // Prepare predecessor / successor tracking
+ var n_pred = {};
+ var successors = {};
+ // First pass to initialize arrays even for nodes with no connections
+ $.each( this.nodes, function( id, node ) {
+ if ( n_pred[id] === undefined ) { n_pred[id] = 0; }
+ if ( successors[id] === undefined ) { successors[id] = []; }
+ });
+ // Second pass to count predecessors and successors
+ $.each( this.nodes, function( id, node ) {
+ $.each( node.input_terminals, function ( j, t ) {
+ $.each( t.connectors, function ( k, c ) {
+ // A connection exists from `other` to `node`
+ var other = c.handle1.node;
+ // node gains a predecessor
+ n_pred[node.id] += 1;
+ // other gains a successor
+ successors[other.id].push( node.id );
+ });
+ });
+ });
+ // Assemble order, tracking levels
+ node_ids_by_level = [];
+ while ( true ) {
+ // Everything without a predecessor
+ level_parents = [];
+ for ( var pred_k in n_pred ) {
+ if ( n_pred[ pred_k ] == 0 ) {
+ level_parents.push( pred_k );
+ }
+ }
+ if ( level_parents.length == 0 ) {
+ break;
+ }
+ node_ids_by_level.push( level_parents );
+ // Remove the parents from this level, and decrement the number
+ // of predecessors for each successor
+ for ( var k in level_parents ) {
+ var v = level_parents[k];
+ delete n_pred[v];
+ for ( var sk in successors[v] ) {
+ n_pred[ successors[v][sk] ] -= 1;
+ }
+ }
+ }
+ if ( n_pred.length ) {
+ // ERROR: CYCLE! Currently we do nothing
+ return;
+ }
+ // Layout each level
+ var all_nodes = this.nodes;
+ var h_pad = 80; v_pad = 30;
+ var left = h_pad;
+ $.each( node_ids_by_level, function( i, ids ) {
+ // We keep nodes in the same order in a level to give the user
+ // some control over ordering
+ ids.sort( function( a, b ) {
+ return $(all_nodes[a].element).position().top - $(all_nodes[b].element).position().top;
+ });
+ // Position each node
+ var max_width = 0;
+ var top = v_pad;
+ $.each( ids, function( j, id ) {
+ var node = all_nodes[id];
+ var element = $(node.element);
+ $(element).css( { top: top, left: left } );
+ max_width = Math.max( max_width, $(element).width() );
+ top += $(element).height() + v_pad;
+ });
+ left += max_width + h_pad;
+ });
+ // Need to redraw all connectors
+ $.each( all_nodes, function( _, node ) { node.redraw(); } );
+ },
+ bounds_for_all_nodes: function() {
+ var xmin = Infinity, xmax = -Infinity,
+ ymin = Infinity, ymax = -Infinity,
+ p;
+ $.each( this.nodes, function( id, node ) {
+ e = $(node.element);
+ p = e.position();
+ xmin = Math.min( xmin, p.left );
+ xmax = Math.max( xmax, p.left + e.width() );
+ ymin = Math.min( ymin, p.top );
+ ymax = Math.max( ymax, p.top + e.width() );
+ });
+ return { xmin: xmin, xmax: xmax, ymin: ymin, ymax: ymax };
+ },
+ fit_canvas_to_nodes: function() {
+ // Span of all elements
+ var bounds = this.bounds_for_all_nodes();
+ var position = this.canvas_container.position();
+ var parent = this.canvas_container.parent();
+ // Determine amount we need to expand on top/left
+ var xmin_delta = fix_delta( bounds.xmin, 100 );
+ var ymin_delta = fix_delta( bounds.ymin, 100 );
+ // May need to expand farther to fill viewport
+ xmin_delta = Math.max( xmin_delta, position.left );
+ ymin_delta = Math.max( ymin_delta, position.top );
+ var left = position.left - xmin_delta;
+ var top = position.top - ymin_delta;
+ // Same for width/height
+ var width = round_up( bounds.xmax + 100, 100 ) + xmin_delta;
+ var height = round_up( bounds.ymax + 100, 100 ) + ymin_delta;
+ width = Math.max( width, - left + parent.width() );
+ height = Math.max( height, - top + parent.height() );
+ // Grow the canvas container
+ this.canvas_container.css( {
+ left: left,
+ top: top,
+ width: width,
+ height: height
+ });
+ // Move elements back if needed
+ this.canvas_container.children().each( function() {
+ var p = $(this).position();
+ $(this).css( "left", p.left + xmin_delta );
+ $(this).css( "top", p.top + ymin_delta );
+ });
+ }
+});
+
+function fix_delta( x, n ) {
+ if ( x < n|| x > 3*n ) {
+ new_pos = ( Math.ceil( ( ( x % n ) ) / n ) + 1 ) * n;
+ return ( - ( x - new_pos ) );
+ }
+ return 0;
+}
+
+function round_up( x, n ) {
+ return Math.ceil( x / n ) * n;
+}
+
+function prebuild_node( type, title_text, tool_id ) {
+ var f = $("");
+ var node = new Node( { element: f } );
+ node.type = type;
+ if ( type == 'tool' ) {
+ node.tool_id = tool_id;
+ }
+ var title = $("" + title_text + "
" );
+ f.append( title );
+ f.css( "left", $(window).scrollLeft() + 20 ); f.css( "top", $(window).scrollTop() + 20 );
+ var b = $("");
+ var tmp = "![](" + galaxy_config.root + "static/images/loading_small_white_bg.gif){kind=small}
loading tool info...").addClass("fa-icon-button fa fa-times").click( function( e ) {
+ node.destroy();
+ }));
+ // Place inside container
+ f.appendTo( "#canvas-container" );
+ // Position in container
+ var o = $("#canvas-container").position();
+ var p = $("#canvas-container").parent();
+ var width = f.width();
+ var height = f.height();
+ f.css( { left: ( - o.left ) + ( p.width() / 2 ) - ( width / 2 ), top: ( - o.top ) + ( p.height() / 2 ) - ( height / 2 ) } );
+ buttons.prependTo( title );
+ width += ( buttons.width() + 10 );
+ f.css( "width", width );
+ $(f).bind( "dragstart", function() {
+ workflow.activate_node( node );
+ }).bind( "dragend", function() {
+ workflow.node_changed( this );
+ workflow.fit_canvas_to_nodes();
+ canvas_manager.draw_overview();
+ }).bind( "dragclickonly", function() {
+ workflow.activate_node( node );
+ }).bind( "drag", function( e, d ) {
+ // Move
+ var po = $(this).offsetParent().offset(),
+ x = d.offsetX - po.left,
+ y = d.offsetY - po.top;
+ $(this).css( { left: x, top: y } );
+ // Redraw
+ $(this).find( ".terminal" ).each( function() {
+ this.terminal.redraw();
+ });
+ });
+ return node;
+}
+
+function add_node( type, title_text, tool_id ) {
+ // Abstraction for use by galaxy.workflow.js to hide
+ // some editor details from workflow code and reduce duplication
+ // between add_node_for_tool and add_node_for_module.
+ var node = prebuild_node( type, title_text, tool_id );
+ workflow.add_node( node );
+ workflow.fit_canvas_to_nodes();
+ canvas_manager.draw_overview();
+ workflow.activate_node( node );
+ return node;
+}
+
+
+var ext_to_type = null;
+var type_to_type = null;
+
+function issubtype( child, parent ) {
+ child = ext_to_type[child];
+ parent = ext_to_type[parent];
+ return ( type_to_type[child] ) && ( parent in type_to_type[child] );
+}
+
+function populate_datatype_info( data ) {
+ ext_to_type = data.ext_to_class_name;
+ type_to_type = data.class_to_classes;
+}
+
+
+//////////////
+// START VIEWS
+//////////////
+
+
+var NodeView = Backbone.View.extend( {
+ initialize: function( options ){
+ this.node = options.node;
+ this.output_width = Math.max(150, this.$el.width());
+ this.tool_body = this.$el.find( ".toolFormBody" );
+ this.tool_body.find( "div" ).remove();
+ this.newInputsDiv().appendTo( this.tool_body );
+ this.terminalViews = {};
+ this.outputTerminlViews = {};
+ },
+
+ render : function() {
+ this.renderToolErrors();
+ this.$el.css( "width", Math.min(250, Math.max(this.$el.width(), this.output_width )));
+ },
+
+ renderToolErrors: function( ) {
+ if ( this.node.tool_errors ) {
+ this.$el.addClass( "tool-node-error" );
+ } else {
+ this.$el.removeClass( "tool-node-error" );
+ }
+ },
+
+ newInputsDiv: function() {
+ return $("");
+ },
+
+ updateMaxWidth: function( newWidth ) {
+ this.output_width = Math.max( this.output_width, newWidth );
+ },
+
+ addRule: function() {
+ this.tool_body.append( $( "" ) );
+ },
+
+ addDataInput: function( input, body ) {
+ var skipResize = true;
+ if( ! body ) {
+ body = this.$( ".inputs" );
+ // initial addition to node - resize input to help calculate node
+ // width.
+ skipResize = false;
+ }
+ var terminalView = this.terminalViews[ input.name ];
+ var terminalViewClass = ( input.input_type == "dataset_collection" ) ? InputCollectionTerminalView : InputTerminalView;
+ if( terminalView && ! ( terminalView instanceof terminalViewClass ) ) {
+ terminalView.el.terminal.destroy();
+ terminalView = null;
+ }
+ if( ! terminalView ) {
+ terminalView = new terminalViewClass( {
+ node: this.node,
+ input: input
+ } );
+ } else {
+ var terminal = terminalView.el.terminal;
+ terminal.update( input );
+ terminal.destroyInvalidConnections();
+ }
+ this.terminalViews[ input.name ] = terminalView;
+ var terminalElement = terminalView.el;
+ var inputView = new DataInputView( {
+ terminalElement: terminalElement,
+ input: input,
+ nodeView: this,
+ skipResize: skipResize
+ } );
+ var ib = inputView.$el;
+
+ // Append to new body
+ body.append( ib.prepend( terminalView.terminalElements() ) );
+ return terminalView;
+ },
+
+ addDataOutput: function( output ) {
+ var terminalViewClass = ( output.collection_type ) ? OutputCollectionTerminalView : OutputTerminalView;
+ var terminalView = new terminalViewClass( {
+ node: this.node,
+ output: output
+ } );
+ var outputView = new DataOutputView( {
+ "output": output,
+ "terminalElement": terminalView.el,
+ "nodeView": this,
+ } );
+ this.tool_body.append( outputView.$el.append( terminalView.terminalElements() ) );
+ },
+
+ updateDataOutput: function( output ) {
+ var outputTerminal = this.node.output_terminals[ output.name ];
+ outputTerminal.update( output );
+ }
+
+} );
+
+
+
+var DataInputView = Backbone.View.extend( {
+ className: "form-row dataRow input-data-row",
+
+ initialize: function( options ){
+ this.input = options.input;
+ this.nodeView = options.nodeView;
+ this.terminalElement = options.terminalElement;
+
+ this.$el.attr( "name", this.input.name )
+ .html( this.input.label );
+
+ if( ! options.skipResize ) {
+ this.$el.css({ position:'absolute',
+ left: -1000,
+ top: -1000,
+ display:'none'});
+ $('body').append(this.el);
+ this.nodeView.updateMaxWidth( this.$el.outerWidth() );
+ this.$el.css({ position:'',
+ left:'',
+ top:'',
+ display:'' });
+ this.$el.remove();
+ }
+ },
+
+} );
+
+
+
+var OutputCalloutView = Backbone.View.extend( {
+ tagName: "div",
+
+ initialize: function( options ) {
+ this.label = options.label;
+ this.node = options.node;
+ this.output = options.output;
+
+ var view = this;
+ this.$el
+ .attr( "class", 'callout '+this.label )
+ .css( { display: 'none' } )
+ .append(
+ $("").append(
+ $("![]()
").attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small-outline.png').click( function() {
+ if ($.inArray(view.output.name, view.node.workflow_outputs) != -1){
+ view.node.workflow_outputs.splice($.inArray(view.output.name, view.node.workflow_outputs), 1);
+ view.$('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small-outline.png');
+ }else{
+ view.node.workflow_outputs.push(view.output.name);
+ view.$('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small.png');
+ }
+ workflow.has_changes = true;
+ canvas_manager.draw_overview();
+ })))
+ .tooltip({delay:500, title: "Mark dataset as a workflow output. All unmarked datasets will be hidden." });
+
+ this.$el.css({
+ top: '50%',
+ margin:'-8px 0px 0px 0px',
+ right: 8
+ });
+ this.$el.show();
+ this.resetImage();
+ },
+
+ resetImage: function() {
+ if ($.inArray( this.output.name, this.node.workflow_outputs) === -1){
+ this.$('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small-outline.png');
+ } else{
+ this.$('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small.png');
+ }
+ },
+
+ hoverImage: function() {
+ this.$('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small-yellow.png');
+ }
+
+} );
+
+
+
+
+var DataOutputView = Backbone.View.extend( {
+ className: "form-row dataRow",
+
+ initialize: function( options ) {
+ this.output = options.output;
+ this.terminalElement = options.terminalElement;
+ this.nodeView = options.nodeView;
+
+ var output = this.output;
+ var label = output.name;
+ var node = this.nodeView.node;
+
+ var isInput = output.extensions.indexOf( 'input' ) >= 0 || output.extensions.indexOf( 'input_collection' ) >= 0;
+ if ( ! isInput ) {
+ label = label + " (" + output.extensions.join(", ") + ")";
+ }
+ this.$el.html( label )
+
+ if (node.type == 'tool'){
+ var calloutView = new OutputCalloutView( {
+ "label": label,
+ "output": output,
+ "node": node,
+ });
+ this.$el.append( calloutView.el );
+ this.$el.hover( function() { calloutView.hoverImage() }, function() { calloutView.resetImage() } );
+ }
+ this.$el.css({ position:'absolute',
+ left: -1000,
+ top: -1000,
+ display:'none'});
+ $('body').append( this.el );
+ this.nodeView.updateMaxWidth( this.$el.outerWidth() + 17 );
+ this.$el.css({ position:'',
+ left:'',
+ top:'',
+ display:'' })
+ .detach();
+ }
+
+} );
+
+
+var TerminalView = Backbone.View.extend( {
+
+ setupMappingView: function( terminal ) {
+ var terminalMapping = new this.terminalMappingClass( { terminal: terminal } );
+ var terminalMappingView = new this.terminalMappingViewClass( { model: terminalMapping } );
+ terminalMappingView.render();
+ terminal.terminalMappingView = terminalMappingView;
+ this.terminalMappingView = terminalMappingView;
+ },
+
+ terminalElements: function() {
+ if( this.terminalMappingView ) {
+ return [ this.terminalMappingView.el, this.el ];
+ } else{
+ return [ this.el ];
+ }
+ }
+
+} );
+
+
+var BaseInputTerminalView = TerminalView.extend( {
+ className: "terminal input-terminal",
+
+ initialize: function( options ) {
+ var node = options.node;
+ var input = options.input;
+ var name = input.name;
+ var terminal = this.terminalForInput( input );
+ if( ! terminal.multiple ) {
+ this.setupMappingView( terminal );
+ }
+ this.el.terminal = terminal;
+ terminal.node = node;
+ terminal.name = name;
+ node.input_terminals[name] = terminal;
+ },
+
+ events: {
+ "dropinit": "onDropInit",
+ "dropstart": "onDropStart",
+ "dropend": "onDropEnd",
+ "drop": "onDrop",
+ "hover": "onHover",
+ },
+
+ onDropInit: function( e, d ) {
+ var terminal = this.el.terminal;
+ // Accept a dragable if it is an output terminal and has a
+ // compatible type
+ return $(d.drag).hasClass( "output-terminal" ) && terminal.canAccept( d.drag.terminal );
+ },
+
+ onDropStart: function( e, d ) {
+ if (d.proxy.terminal) {
+ d.proxy.terminal.connectors[0].inner_color = "#BBFFBB";
+ }
+ },
+
+ onDropEnd: function ( e, d ) {
+ if (d.proxy.terminal) {
+ d.proxy.terminal.connectors[0].inner_color = "#FFFFFF";
+ }
+ },
+
+ onDrop: function( e, d ) {
+ var terminal = this.el.terminal;
+ new Connector( d.drag.terminal, terminal ).redraw();
+ },
+
+ onHover: function() {
+ var element = this.el;
+ var terminal = element.terminal;
+
+ // If connected, create a popup to allow disconnection
+ if ( terminal.connectors.length > 0 ) {
+ // Create callout
+ var t = $("")
+ .css( { display: 'none' } )
+ .appendTo( "body" )
+ .append(
+ $("").append(
+ $("").addClass("fa-icon-button fa fa-times").click( function() {
+ $.each( terminal.connectors, function( _, x ) {
+ if (x) {
+ x.destroy();
+ }
+ });
+ t.remove();
+ })))
+ .bind( "mouseleave", function() {
+ $(this).remove();
+ });
+ // Position it and show
+ t.css({
+ top: $(element).offset().top - 2,
+ left: $(element).offset().left - t.width(),
+ 'padding-right': $(element).width()
+ }).show();
+ }
+ },
+
+} );
+
+var InputTerminalView = BaseInputTerminalView.extend( {
+ terminalMappingClass: InputTerminalMapping,
+ terminalMappingViewClass: InputTerminalMappingView,
+
+ terminalForInput: function( input ) {
+ return new InputTerminal( { element: this.el, input: input } );
+ },
+
+} );
+
+var InputCollectionTerminalView = BaseInputTerminalView.extend( {
+ terminalMappingClass: InputCollectionTerminalMapping,
+ terminalMappingViewClass: InputCollectionTerminalMappingView,
+
+ terminalForInput: function( input ) {
+ return new InputCollectionTerminal( { element: this.el, input: input } );
+ },
+
+} );
+
+var BaseOutputTerminalView = TerminalView.extend( {
+ className: "terminal output-terminal",
+
+ initialize: function( options ) {
+ var node = options.node;
+ var output = options.output;
+
+ var name = output.name;
+ var terminal = this.terminalForOutput( output );
+ this.setupMappingView( terminal );
+ this.el.terminal = terminal;
+ terminal.node = node;
+ terminal.name = name;
+ node.output_terminals[name] = terminal;
+ },
+
+ events: {
+ "drag": "onDrag",
+ "dragstart": "onDragStart",
+ "dragend": "onDragEnd",
+ },
+
+ onDrag: function ( e, d ) {
+ var onmove = function() {
+ var po = $(d.proxy).offsetParent().offset(),
+ x = d.offsetX - po.left,
+ y = d.offsetY - po.top;
+ $(d.proxy).css( { left: x, top: y } );
+ d.proxy.terminal.redraw();
+ // FIXME: global
+ canvas_manager.update_viewport_overlay();
+ };
+ onmove();
+ $("#canvas-container").get(0).scroll_panel.test( e, onmove );
+ },
+
+ onDragStart: function( e, d ) {
+ $( d.available ).addClass( "input-terminal-active" );
+ // Save PJAs in the case of change datatype actions.
+ workflow.check_changes_in_active_form();
+ // Drag proxy div
+ var h = $( '' )
+ .appendTo( "#canvas-container" ).get(0);
+ // Terminal and connection to display noodle while dragging
+ h.terminal = new OutputTerminal( { element: h } );
+ var c = new Connector();
+ c.dragging = true;
+ c.connect( this.el.terminal, h.terminal );
+ return h;
+ },
+
+ onDragEnd: function ( e, d ) {
+ var connector = d.proxy.terminal.connectors[0];
+ // check_changes_in_active_form may change the state and cause a
+ // the connection to have already been destroyed. There must be better
+ // ways to handle this but the following check fixes some serious GUI
+ // bugs for now.
+ if(connector) {
+ connector.destroy();
+ }
+ $(d.proxy).remove();
+ $( d.available ).removeClass( "input-terminal-active" );
+ $("#canvas-container").get(0).scroll_panel.stop();
+ }
+
+} );
+
+var OutputTerminalView = BaseOutputTerminalView.extend( {
+ terminalMappingClass: OutputTerminalMapping,
+ terminalMappingViewClass: OutputTerminalMappingView,
+
+ terminalForOutput: function( output ) {
+ var type = output.extensions;
+ var terminal = new OutputTerminal( { element: this.el, datatypes: type } );
+ return terminal;
+ },
+
+} );
+
+var OutputCollectionTerminalView = BaseOutputTerminalView.extend( {
+ terminalMappingClass: OutputCollectionTerminalMapping,
+ terminalMappingViewClass: OutputCollectionTerminalMappingView,
+
+ terminalForOutput: function( output ) {
+ var collection_type = output.collection_type;
+ var terminal = new OutputCollectionTerminal( { element: this.el, collection_type: collection_type, datatypes: output.extensions } );
+ return terminal;
+ },
+
+} );
+
+
+////////////
+// END VIEWS
+////////////
+
+
+// FIXME: merge scroll panel into CanvasManager, clean up hardcoded stuff.
+
+function ScrollPanel( panel ) {
+ this.panel = panel;
+}
+$.extend( ScrollPanel.prototype, {
+ test: function( e, onmove ) {
+ clearTimeout( this.timeout );
+ var x = e.pageX,
+ y = e.pageY,
+ // Panel size and position
+ panel = $(this.panel),
+ panel_pos = panel.position(),
+ panel_w = panel.width(),
+ panel_h = panel.height(),
+ // Viewport size and offset
+ viewport = panel.parent(),
+ viewport_w = viewport.width(),
+ viewport_h = viewport.height(),
+ viewport_offset = viewport.offset(),
+ // Edges of viewport (in page coordinates)
+ min_x = viewport_offset.left,
+ min_y = viewport_offset.top,
+ max_x = min_x + viewport.width(),
+ max_y = min_y + viewport.height(),
+ // Legal panel range
+ p_min_x = - ( panel_w - ( viewport_w / 2 ) ),
+ p_min_y = - ( panel_h - ( viewport_h / 2 )),
+ p_max_x = ( viewport_w / 2 ),
+ p_max_y = ( viewport_h / 2 ),
+ // Did the panel move?
+ moved = false,
+ // Constants
+ close_dist = 5,
+ nudge = 23;
+ if ( x - close_dist < min_x ) {
+ if ( panel_pos.left < p_max_x ) {
+ var t = Math.min( nudge, p_max_x - panel_pos.left );
+ panel.css( "left", panel_pos.left + t );
+ moved = true;
+ }
+ } else if ( x + close_dist > max_x ) {
+ if ( panel_pos.left > p_min_x ) {
+ var t = Math.min( nudge, panel_pos.left - p_min_x );
+ panel.css( "left", panel_pos.left - t );
+ moved = true;
+ }
+ } else if ( y - close_dist < min_y ) {
+ if ( panel_pos.top < p_max_y ) {
+ var t = Math.min( nudge, p_max_y - panel_pos.top );
+ panel.css( "top", panel_pos.top + t );
+ moved = true;
+ }
+ } else if ( y + close_dist > max_y ) {
+ if ( panel_pos.top > p_min_y ) {
+ var t = Math.min( nudge, panel_pos.top - p_min_x );
+ panel.css( "top", ( panel_pos.top - t ) + "px" );
+ moved = true;
+ }
+ }
+ if ( moved ) {
+ // Keep moving even if mouse doesn't move
+ onmove();
+ var panel = this;
+ this.timeout = setTimeout( function() { panel.test( e, onmove ); }, 50 );
+ }
+ },
+ stop: function( e, ui ) {
+ clearTimeout( this.timeout );
+ }
+});
+
+function CanvasManager( canvas_viewport, overview ) {
+ this.cv = canvas_viewport;
+ this.cc = this.cv.find( "#canvas-container" );
+ this.oc = overview.find( "#overview-canvas" );
+ this.ov = overview.find( "#overview-viewport" );
+ // Make overview box draggable
+ this.init_drag();
+}
+$.extend( CanvasManager.prototype, {
+ init_drag : function () {
+ var self = this;
+ var move = function( x, y ) {
+ x = Math.min( x, self.cv.width() / 2 );
+ x = Math.max( x, - self.cc.width() + self.cv.width() / 2 );
+ y = Math.min( y, self.cv.height() / 2 );
+ y = Math.max( y, - self.cc.height() + self.cv.height() / 2 );
+ self.cc.css( {
+ left: x,
+ top: y
+ });
+ self.update_viewport_overlay();
+ };
+ // Dragging within canvas background
+ this.cc.each( function() {
+ this.scroll_panel = new ScrollPanel( this );
+ });
+ var x_adjust, y_adjust;
+ this.cv.bind( "dragstart", function() {
+ var o = $(this).offset();
+ var p = self.cc.position();
+ y_adjust = p.top - o.top;
+ x_adjust = p.left - o.left;
+ }).bind( "drag", function( e, d ) {
+ move( d.offsetX + x_adjust, d.offsetY + y_adjust );
+ }).bind( "dragend", function() {
+ workflow.fit_canvas_to_nodes();
+ self.draw_overview();
+ });
+ // Dragging for overview pane
+ this.ov.bind( "drag", function( e, d ) {
+ var in_w = self.cc.width(),
+ in_h = self.cc.height(),
+ o_w = self.oc.width(),
+ o_h = self.oc.height(),
+ p = $(this).offsetParent().offset(),
+ new_x_offset = d.offsetX - p.left,
+ new_y_offset = d.offsetY - p.top;
+ move( - ( new_x_offset / o_w * in_w ),
+ - ( new_y_offset / o_h * in_h ) );
+ }).bind( "dragend", function() {
+ workflow.fit_canvas_to_nodes();
+ self.draw_overview();
+ });
+ // Dragging for overview border (resize)
+ $("#overview-border").bind( "drag", function( e, d ) {
+ var op = $(this).offsetParent();
+ var opo = op.offset();
+ var new_size = Math.max( op.width() - ( d.offsetX - opo.left ),
+ op.height() - ( d.offsetY - opo.top ) );
+ $(this).css( {
+ width: new_size,
+ height: new_size
+ });
+ self.draw_overview();
+ });
+
+ /* Disable dragging for child element of the panel so that resizing can
+ only be done by dragging the borders */
+ $("#overview-border div").bind("drag", function() { });
+
+ },
+ update_viewport_overlay: function() {
+ var cc = this.cc,
+ cv = this.cv,
+ oc = this.oc,
+ ov = this.ov,
+ in_w = cc.width(),
+ in_h = cc.height(),
+ o_w = oc.width(),
+ o_h = oc.height(),
+ cc_pos = cc.position();
+ ov.css( {
+ left: - ( cc_pos.left / in_w * o_w ),
+ top: - ( cc_pos.top / in_h * o_h ),
+ // Subtract 2 to account for borders (maybe just change box sizing style instead?)
+ width: ( cv.width() / in_w * o_w ) - 2,
+ height: ( cv.height() / in_h * o_h ) - 2
+ });
+ },
+ draw_overview: function() {
+ var canvas_el = $("#overview-canvas"),
+ size = canvas_el.parent().parent().width(),
+ c = canvas_el.get(0).getContext("2d"),
+ in_w = $("#canvas-container").width(),
+ in_h = $("#canvas-container").height();
+ var o_h, shift_h, o_w, shift_w;
+ // Fit canvas into overview area
+ var cv_w = this.cv.width();
+ var cv_h = this.cv.height();
+ if ( in_w < cv_w && in_h < cv_h ) {
+ // Canvas is smaller than viewport
+ o_w = in_w / cv_w * size;
+ shift_w = ( size - o_w ) / 2;
+ o_h = in_h / cv_h * size;
+ shift_h = ( size - o_h ) / 2;
+ } else if ( in_w < in_h ) {
+ // Taller than wide
+ shift_h = 0;
+ o_h = size;
+ o_w = Math.ceil( o_h * in_w / in_h );
+ shift_w = ( size - o_w ) / 2;
+ } else {
+ // Wider than tall
+ o_w = size;
+ shift_w = 0;
+ o_h = Math.ceil( o_w * in_h / in_w );
+ shift_h = ( size - o_h ) / 2;
+ }
+ canvas_el.parent().css( {
+ left: shift_w,
+ top: shift_h,
+ width: o_w,
+ height: o_h
+ });
+ canvas_el.attr( "width", o_w );
+ canvas_el.attr( "height", o_h );
+ // Draw overview
+ $.each( workflow.nodes, function( id, node ) {
+ c.fillStyle = "#D2C099";
+ c.strokeStyle = "#D8B365";
+ c.lineWidth = 1;
+ var node_element = $(node.element),
+ position = node_element.position(),
+ x = position.left / in_w * o_w,
+ y = position.top / in_h * o_h,
+ w = node_element.width() / in_w * o_w,
+ h = node_element.height() / in_h * o_h;
+ if (node.tool_errors){
+ c.fillStyle = "#FFCCCC";
+ c.strokeStyle = "#AA6666";
+ } else if (node.workflow_outputs != undefined && node.workflow_outputs.length > 0){
+ c.fillStyle = "#E8A92D";
+ c.strokeStyle = "#E8A92D";
+ }
+ c.fillRect( x, y, w, h );
+ c.strokeRect( x, y, w, h );
+ });
+ this.update_viewport_overlay();
+ }
+});
diff --git a/client/scripts/galaxy.workflows.js b/client/scripts/galaxy.workflows.js
new file mode 100644
index 00000000000..3bbd302ffc2
--- /dev/null
+++ b/client/scripts/galaxy.workflows.js
@@ -0,0 +1,612 @@
+$( function() {
+
+ if ( window.lt_ie_7 ) {
+ show_modal(
+ "Browser not supported",
+ "Sorry, the workflow editor is not supported for IE6 and below."
+ );
+ return;
+ }
+
+ // Init searching.
+ $("#tool-search-query").click( function (){
+ $(this).focus();
+ $(this).select();
+ })
+ .keyup( function () {
+ // Remove italics.
+ $(this).css("font-style", "normal");
+ // Don't update if same value as last time
+ if ( this.value.length < 3 ) {
+ reset_tool_search(false);
+ } else if ( this.value != this.lastValue ) {
+ // Add class to denote that searching is active.
+ $(this).addClass("search_active");
+ // input.addClass(config.loadingClass);
+ // Add '*' to facilitate partial matching.
+ var q = this.value + '*';
+ // Stop previous ajax-request
+ if (this.timer) {
+ clearTimeout(this.timer);
+ }
+ // Start a new ajax-request in X ms
+ $("#search-spinner").show();
+ this.timer = setTimeout(function () {
+ $.get(tool_search_url, { query: q }, function (data) {
+ // input.removeClass(config.loadingClass);
+ // Show live-search if results and search-term aren't empty
+ $("#search-no-results").hide();
+ // Hide all tool sections.
+ $(".toolSectionWrapper").hide();
+ // This hides all tools but not workflows link (which is in a .toolTitle div).
+ $(".toolSectionWrapper").find(".toolTitle").hide();
+ if ( data.length != 0 ) {
+ // Map tool ids to element ids and join them.
+ var s = $.map( data, function( n, i ) { return "link-" + n; } );
+ // First pass to show matching tools and their parents.
+ $(s).each( function(index,id) {
+ // Add class to denote match.
+ $("[id='"+id+"']").parent().addClass("search_match");
+ $("[id='"+id+"']").parent().show().parent().parent().show().parent().show();
+ });
+ // Hide labels that have no visible children.
+ $(".toolPanelLabel").each( function() {
+ var this_label = $(this);
+ var next = this_label.next();
+ var no_visible_tools = true;
+ // Look through tools following label and, if none are visible, hide label.
+ while (next.length !== 0 && next.hasClass("toolTitle")) {
+ if (next.is(":visible")) {
+ no_visible_tools = false;
+ break;
+ } else {
+ next = next.next();
+ }
+ }
+ if (no_visible_tools) {
+ this_label.hide();
+ }
+ });
+ } else {
+ $("#search-no-results").show();
+ }
+ $("#search-spinner").hide();
+ }, "json" );
+ }, 200 );
+ }
+ this.lastValue = this.value;
+ });
+
+ // Canvas overview management
+ canvas_manager = new CanvasManager( $("#canvas-viewport"), $("#overview") );
+
+ // Initialize workflow state
+ reset();
+ // Load the datatype info
+ $.ajax( {
+ url: get_datatypes_url,
+ dataType: "json",
+ cache: false,
+ success: function( data ) {
+ populate_datatype_info( data );
+ // Load workflow definition
+ $.ajax( {
+ url: load_workflow_url,
+ data: { id: workflow_id, "_": "true" },
+ dataType: 'json',
+ cache: false,
+ success: function( data ) {
+ reset();
+ workflow.from_simple( data );
+ workflow.has_changes = false;
+ workflow.fit_canvas_to_nodes();
+ scroll_to_nodes();
+ canvas_manager.draw_overview();
+ // Determine if any parameters were 'upgraded' and provide message
+ upgrade_message = "";
+ $.each( data.upgrade_messages, function( k, v ) {
+ upgrade_message += ( "Step " + ( parseInt(k, 10) + 1 ) + ": " + workflow.nodes[k].name + " ";
+ });
+ if ( upgrade_message ) {
+ show_modal( "Workflow loaded with changes",
+ "Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.";
+ }
+ }
+ $("#output-fill-area").html(new_content);
+ $("#output-fill-area input").bind('click', function(){
+ var node_id = this.name.split('|')[0];
+ var output_name = this.name.split('|')[1];
+ if (this.checked){
+ if($.inArray(output_name, workflow.nodes[node_id].workflow_outputs) == -1){
+ workflow.nodes[node_id].workflow_outputs.push(output_name);
+ }//else it's already in the array. Shouldn't happen, but forget it.
+ }else{
+ while ($.inArray(output_name, workflow.nodes[node_id].workflow_outputs) != -1){
+ var ia = $.inArray(output_name, workflow.nodes[node_id].workflow_outputs);
+ workflow.nodes[node_id].workflow_outputs = workflow.nodes[node_id].workflow_outputs.slice(0,ia).concat( workflow.nodes[node_id].workflow_outputs.slice(ia+1) );
+ }
+ }
+ workflow.has_changes = true;
+ });
+ $('#workflow-output-area').show();
+ }
+
+ function layout_editor() {
+ workflow.layout();
+ workflow.fit_canvas_to_nodes();
+ scroll_to_nodes();
+ canvas_manager.draw_overview();
+ }
+
+ function edit_workflow_attributes() {
+ workflow.clear_active_node();
+ $('.right-content').hide();
+ $('#edit-attributes').show();
+
+ }
+
+ // On load, set the size to the pref stored in local storage if it exists
+ overview_size = $.jStorage.get("overview-size");
+ if (overview_size !== undefined) {
+ $("#overview-border").css( {
+ width: overview_size,
+ height: overview_size
+ });
+ }
+
+ // Show viewport on load unless pref says it's off
+ if ($.jStorage.get("overview-off")) {
+ hide_overview();
+ } else {
+ show_overview();
+ }
+
+ // Stores the size of the overview into local storage when it's resized
+ $("#overview-border").bind( "dragend", function( e, d ) {
+ var op = $(this).offsetParent();
+ var opo = op.offset();
+ var new_size = Math.max( op.width() - ( d.offsetX - opo.left ),
+ op.height() - ( d.offsetY - opo.top ) );
+ $.jStorage.set("overview-size", new_size + "px");
+ });
+
+ function show_overview() {
+ $.jStorage.set("overview-off", false);
+ $("#overview-border").css("right", "0px");
+ $("#close-viewport").css("background-position", "0px 0px");
+ }
+
+ function hide_overview() {
+ $.jStorage.set("overview-off", true);
+ $("#overview-border").css("right", "20000px");
+ $("#close-viewport").css("background-position", "12px 0px");
+ }
+
+ // Lets the overview be toggled visible and invisible, adjusting the arrows accordingly
+ $("#close-viewport").click( function() {
+ if ( $("#overview-border").css("right") === "0px" ) {
+ hide_overview();
+ } else {
+ show_overview();
+ }
+ });
+
+ // Unload handler
+ window.onbeforeunload = function() {
+ if ( workflow && workflow.has_changes ) {
+ return "There are unsaved changes to your workflow which will be lost.";
+ }
+ };
+
+ // Tool menu
+ $( "div.toolSectionBody" ).hide();
+ $( "div.toolSectionTitle > span" ).wrap( "" );
+ var last_expanded = null;
+ $( "div.toolSectionTitle" ).each( function() {
+ var body = $(this).next( "div.toolSectionBody" );
+ $(this).click( function() {
+ if ( body.is( ":hidden" ) ) {
+ if ( last_expanded ) last_expanded.slideUp( "fast" );
+ last_expanded = body;
+ body.slideDown( "fast" );
+ }
+ else {
+ body.slideUp( "fast" );
+ last_expanded = null;
+ }
+ });
+ });
+
+ // Rename async.
+ async_save_text("workflow-name", "workflow-name", rename_async_url, "new_name");
+
+ // Tag async. Simply have the workflow edit element generate a click on the tag element to activate tagging.
+ $('#workflow-tag').click( function() {
+ $('.tag-area').click();
+ return false;
+ });
+ // Annotate async.
+ async_save_text("workflow-annotation", "workflow-annotation", annotate_async_url, "new_annotation", 25, true, 4);
+});
+
+// Global state for the whole workflow
+function reset() {
+ if ( workflow ) {
+ workflow.remove_all();
+ }
+ workflow = new Workflow( $("#canvas-container") );
+}
+
+function scroll_to_nodes() {
+ var cv = $("#canvas-viewport");
+ var cc = $("#canvas-container");
+ var top, left;
+ if ( cc.width() < cv.width() ) {
+ left = ( cv.width() - cc.width() ) / 2;
+ } else {
+ left = 0;
+ }
+ if ( cc.height() < cv.height() ) {
+ top = ( cv.height() - cc.height() ) / 2;
+ } else {
+ top = 0;
+ }
+ cc.css( { left: left, top: top } );
+}
+
+// Add a new step to the workflow by tool id
+function add_node_for_tool( id, title ) {
+ node = add_node( 'tool', title, id );
+ $.ajax( {
+ url: get_new_module_info_url,
+ data: { type: "tool", tool_id: id, "_": "true" },
+ global: false,
+ dataType: "json",
+ success: function( data ) {
+ node.init_field_data( data );
+ },
+ error: function( x, e ) {
+ var m = "error loading field data";
+ if ( x.status === 0 ) {
+ m += ", server unavailable";
+ }
+ node.error( m );
+ }
+ });
+}
+
+function add_node_for_module( type, title ) {
+ node = add_node( type, title );
+ $.ajax( {
+ url: get_new_module_info_url,
+ data: { type: type, "_": "true" },
+ dataType: "json",
+ success: function( data ) {
+ node.init_field_data( data );
+ },
+ error: function( x, e ) {
+ var m = "error loading field data"
+ if ( x.status == 0 ) {
+ m += ", server unavailable"
+ }
+ node.error( m );
+ }
+ });
+}
+
+// This function preloads how to display known pja's.
+function display_pja(pja, node) {
+ // DBTODO SANITIZE INPUTS.
+ $("#pja_container").append( get_pja_form(pja, node) );
+ $("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function (){
+ action_to_rem = $(this).closest(".toolForm", ".action_tag").children(".action_tag:first").text();
+ $(this).closest(".toolForm").remove();
+ delete workflow.active_node.post_job_actions[action_to_rem];
+ workflow.active_form_has_changes = true;
+ });
+}
+
+function display_pja_list(){
+ return pja_list;
+}
+
+function display_file_list(node){
+ addlist = "";
+ return addlist;
+}
+
+function new_pja(action_type, target, node){
+ if (node.post_job_actions === undefined){
+ //New tool node, set up dict.
+ node.post_job_actions = {};
+ }
+ if (node.post_job_actions[action_type+target] === undefined){
+ var new_pja = {};
+ new_pja.action_type = action_type;
+ new_pja.output_name = target;
+ node.post_job_actions[action_type+target] = null;
+ node.post_job_actions[action_type+target] = new_pja;
+ display_pja(new_pja, node);
+ workflow.active_form_has_changes = true;
+ return true;
+ } else {
+ return false;
+ }
+}
+
+function show_workflow_parameters(){
+ var parameter_re = /\$\{.+?\}/g;
+ var workflow_parameters = [];
+ var wf_parm_container = $("#workflow-parameters-container");
+ var wf_parm_box = $("#workflow-parameters-box");
+ var new_parameter_content = "";
+ var matches = [];
+ $.each(workflow.nodes, function (k, node){
+ var form_matches = node.form_html.match(parameter_re);
+ if (form_matches){
+ matches = matches.concat(form_matches);
+ }
+ if (node.post_job_actions){
+ $.each(node.post_job_actions, function(k, pja){
+ if (pja.action_arguments){
+ $.each(pja.action_arguments, function(k, action_argument){
+ var arg_matches = action_argument.match(parameter_re);
+ if (arg_matches){
+ matches = matches.concat(arg_matches);
+ }
+ });
+ }
+ });
+ if (matches){
+ $.each(matches, function(k, element){
+ if ($.inArray(element, workflow_parameters) === -1){
+ workflow_parameters.push(element);
+ }
+ });
+ }
+ }
+ });
+ if (workflow_parameters && workflow_parameters.length !== 0){
+ $.each(workflow_parameters, function(k, element){
+ new_parameter_content += "%4 ",
+ MATCH: /(.*):(before|after).*/,
+
+ count: 0
+});
+
+// =========================================================================
+// ie8-html.js
+// =========================================================================
+
+var UNSUCCESSFUL = /^(submit|reset|button)$/;
+
+// -----------------------------------------------------------------------
+//
- ");
+ $.each( v, function( i, vv ) {
+ upgrade_message += "
- " + vv +" "; + }); + upgrade_message += "
- " + upgrade_message + "
Step " + node.id + " - " + node.name + "
";
+ for (var ot_key in node.output_terminals){
+ var output = node.output_terminals[ot_key];
+ // if (node.workflow_outputs[node.id + "|" + output.name]){
+ if ($.inArray(output.name, node.workflow_outputs) != -1){
+ new_content += ""+output.name +"
"; + } + else{ + new_content += ""+output.name +"
"; + } + } + new_content += "" + element.substring(2, element.length -1) + "
";
+ });
+ wf_parm_container.html(new_parameter_content);
+ wf_parm_box.show();
+ }else{
+ wf_parm_container.html(new_parameter_content);
+ wf_parm_box.hide();
+ }
+}
+
+function show_form_for_tool( text, node ) {
+ $('.right-content').hide();
+ $("#right-content").show().html( text );
+ // Add metadata form to tool.
+ if (node) {
+ $("#right-content").find(".toolForm:first").after( "" );
+ }
+ // Add step actions.
+ if (node && node.type=='tool'){
+ pjastr = "";
+ $("#right-content").find(".toolForm").after( pjastr );
+ for (var key in node.post_job_actions){
+ if (key != "undefined"){ //To make sure we haven't just deleted it.
+ display_pja(node.post_job_actions[key], node);
+ }
+ }
+ $("#add_pja").click(function (){
+ new_pja($("#new_pja_list").val(),$("#node_data_list").val(), node);
+ });
+ }
+ $("#right-content").find( "form" ).ajaxForm( {
+ type: 'POST',
+ dataType: 'json',
+ success: function( data ) {
+ workflow.active_form_has_changes = false;
+ node.update_field_data( data );
+ show_workflow_parameters();
+ },
+ beforeSubmit: function( data ) {
+ data.push( { name: 'tool_state', value: node.tool_state } );
+ data.push( { name: '_', value: "true" } );
+ }
+ }).each( function() {
+ var form = this;
+ $(this).find( "select[refresh_on_change='true']").change( function() {
+ $(form).submit();
+ });
+ $(this).find( "input[refresh_on_change='true']").change( function() {
+ $(form).submit();
+ });
+ $(this).find( ".popupmenu" ).each( function() {
+ var id = $(this).parents( "div.form-row" ).attr( 'id' );
+ var b = $('▼');
+ var options = {};
+ $(this).find( "button" ).each( function() {
+ var name = $(this).attr( 'name' );
+ var value = $(this).attr( 'value' );
+ options[ $(this).text() ] = function() {
+ $(form).append( "" ).submit();
+ };
+ });
+ b.insertAfter( this );
+ $(this).remove();
+ make_popupmenu( b, options );
+ });
+ // Implements auto-saving based on whether the inputs change. We consider
+ // "changed" to be when a field is accessed and not necessarily modified
+ // because of an issue where "onchange" is not triggered when activating
+ // another node, or saving the workflow.
+ $(this).find("input,textarea,select").each( function() {
+ $(this).bind("focus click", function() {
+ workflow.active_form_has_changes = true;
+ });
+ });
+ });
+}
+
+var close_editor = function() {
+ workflow.check_changes_in_active_form();
+ if ( workflow && workflow.has_changes ) {
+ do_close = function() {
+ window.onbeforeunload = undefined;
+ window.document.location = workflow_index_url;
+ };
+ show_modal( "Close workflow editor",
+ "There are unsaved changes to your workflow which will be lost.",
+ {
+ "Cancel" : hide_modal,
+ "Save Changes" : function() {
+ save_current_workflow( null, do_close );
+ }
+ }, {
+ "Don't Save": do_close
+ } );
+ } else {
+ window.document.location = workflow_index_url;
+ }
+};
+
+var save_current_workflow = function ( eventObj, success_callback ) {
+ show_message( "Saving workflow", "progress" );
+ workflow.check_changes_in_active_form();
+ if (!workflow.has_changes) {
+ hide_modal();
+ if ( success_callback ) {
+ success_callback();
+ }
+ return;
+ }
+ workflow.rectify_workflow_outputs();
+ var savefn = function(callback) {
+ $.ajax( {
+ url: save_workflow_url,
+ type: "POST",
+ data: {
+ id: workflow_id,
+ workflow_data: function() { return JSON.stringify( workflow.to_simple() ); },
+ "_": "true"
+ },
+ dataType: 'json',
+ success: function( data ) {
+ var body = $("").text( data.message );
+ if ( data.errors ) {
+ body.addClass( "warningmark" );
+ var errlist = $( "