Webpack: move data.js into dataset/data.js; pack scripts

client/galaxy/scripts/layout/scratchbook.js

@@ -77,7 +77,7 @@ var GalaxyFrame = Backbone.View.extend({
      */
     add_dataset: function(dataset_id) {
         var self = this;
-        require(['mvc/data'], function(DATA) {
+        require(['mvc/dataset/data'], function(DATA) {
             var dataset = new DATA.Dataset({ id: dataset_id });
             $.when( dataset.fetch() ).then( function() {
                 // Construct frame config based on dataset's type.

client/galaxy/scripts/mvc/tools/tools.js

@@ -5,7 +5,7 @@
  define([
     "libs/underscore",
     "viz/trackster/util",
-    "mvc/data",
+    "mvc/dataset/data",
     "mvc/tools/tools-form",
     "templates/tool_form.handlebars",
     "templates/tool_link.handlebars",

client/galaxy/scripts/viz/phyloviz.js

@@ -1,7 +1,7 @@
 define([
     'libs/d3',
     'viz/visualization',
-    'mvc/data',
+    'mvc/dataset/data',
     'mvc/ui/icon-button'
 ], function(d3, visualization_mod, data_mod, mod_icon_btn) {
 
@@ -204,7 +204,7 @@ var PhyloTree = visualization_mod.Visualization.extend({
         this.set("dataset", new data_mod.Dataset({
             id: options.dataset_id
         }));
-        
+
     },
 
     root : {}, // Root has to be its own independent object because it is not part of the viz_config

client/galaxy/scripts/viz/sweepster.js

@@ -10,7 +10,7 @@ define([
     "viz/visualization",
     "viz/trackster/tracks",
     "mvc/tools/tools",
-    "mvc/data",
+    "mvc/dataset/data",
     "utils/config",
     "mvc/ui/icon-button"
 ], function(_, d3, util, visualization, tracks, tools, data, config, mod_icon_btn) {

client/galaxy/scripts/viz/trackster/tracks.js

@@ -6,7 +6,7 @@ define([
     "viz/trackster/slotting",
     "viz/trackster/painters",
     "viz/trackster/filters",
-    "mvc/data",
+    "mvc/dataset/data",
     "mvc/tools/tools",
     "utils/config",
     "ui/editable-text",

client/galaxy/scripts/viz/visualization.js

@@ -1,7 +1,7 @@
-define( ["libs/underscore", "mvc/data", "viz/trackster/util", "utils/config"], function(_, data_mod, util_mod, config_mod) {
+define( ["libs/underscore", "mvc/dataset/data", "viz/trackster/util", "utils/config"], function(_, data_mod, util_mod, config_mod) {
 
 /**
- * Mixin for returning custom JSON representation from toJSON. Class attribute to_json_keys defines a set of attributes 
+ * Mixin for returning custom JSON representation from toJSON. Class attribute to_json_keys defines a set of attributes
  * to include in the representation; to_json_mappers defines mappers for returned objects.
  */
 var CustomToJSON = {
@@ -25,8 +25,8 @@ var CustomToJSON = {
 /**
  * Model, view, and controller objects for Galaxy visualization framework.
  *
- * Models have no references to views, instead using events to indicate state 
- * changes; this is advantageous because multiple views can use the same object 
+ * Models have no references to views, instead using events to indicate state
+ * changes; this is advantageous because multiple views can use the same object
  * and models can be used without views.
  */
 
@@ -66,13 +66,13 @@ var select_datasets = function(dataset_url, add_track_async_url, filters, succes
                                     dataType: "json"
                                 });
                         });
-                        // To preserve order, wait until there are definitions for all tracks and then add 
+                        // To preserve order, wait until there are definitions for all tracks and then add
                         // them sequentially.
                         $.when.apply($, requests).then(function() {
                             // jQuery always returns an Array for arguments, so need to look at first element
-                            // to determine whether multiple requests were made and consequently how to 
+                            // to determine whether multiple requests were made and consequently how to
                             // map arguments to track definitions.
-                            var track_defs = (arguments[0] instanceof Array ?  
+                            var track_defs = (arguments[0] instanceof Array ?
                                                $.map(arguments, function(arg) { return arg[0]; }) :
                                                [ arguments[0] ]
                                                );
@@ -94,13 +94,13 @@ var select_datasets = function(dataset_url, add_track_async_url, filters, succes
  */
 var CanvasManager = function(default_font) {
     this.default_font = default_font !== undefined ? default_font : "9px Monaco, Lucida Console, monospace";
-    
+
     this.dummy_canvas = this.new_canvas();
     this.dummy_context = this.dummy_canvas.getContext('2d');
     this.dummy_context.font = this.default_font;
-    
+
     this.char_width_px = this.dummy_context.measureText("A").width;
-    
+
     this.patterns = {};
 
     // FIXME: move somewhere to make this more general
@@ -135,13 +135,13 @@ _.extend( CanvasManager.prototype, {
 });
 
 /**
- * Generic cache that handles key/value pairs. Keys can be any object that can be 
+ * Generic cache that handles key/value pairs. Keys can be any object that can be
  * converted to a String and compared.
- */ 
+ */
 var Cache = Backbone.Model.extend({
     defaults: {
         num_elements: 20,
-        // Objects in cache; indexes into cache are strings of keys. 
+        // Objects in cache; indexes into cache are strings of keys.
         obj_cache: null,
         // key_ary contains keys for objects in cache.
         key_ary: null
@@ -153,7 +153,7 @@ var Cache = Backbone.Model.extend({
 
     /**
      * Get an element from the cache using its key.
-     */    
+     */
     get_elt: function(key) {
         var obj_cache = this.attributes.obj_cache,
             key_ary = this.attributes.key_ary,
@@ -178,7 +178,7 @@ var Cache = Backbone.Model.extend({
 
         return obj_cache[key_str];
     },
-    
+
     /**
      * Put an element into the cache.
      */
@@ -206,16 +206,16 @@ var Cache = Backbone.Model.extend({
         obj_cache[key_str] = value;
         return value;
     },
-    
-    /** 
-     * Move key to end of cache. Keys are removed from the front, so moving a key to the end 
+
+    /**
+     * Move key to end of cache. Keys are removed from the front, so moving a key to the end
      * delays the key's removal.
      */
     move_key_to_end: function(key, index) {
         this.attributes.key_ary.splice(index, 1);
         this.attributes.key_ary.push(key);
     },
-    
+
     /**
      * Clear all elements from the cache.
      */
@@ -223,7 +223,7 @@ var Cache = Backbone.Model.extend({
         this.attributes.obj_cache = {};
         this.attributes.key_ary = [];
     },
-    
+
     /** Returns the number of elements in the cache. */
     size: function() {
         return this.attributes.key_ary.length;
@@ -231,8 +231,8 @@ var Cache = Backbone.Model.extend({
 
     /** Returns key most recently added to cache. */
     most_recently_added: function() {
-        return this.size() === 0 ? null : 
-               // Most recent key is at the end of key array. 
+        return this.size() === 0 ? null :
+               // Most recent key is at the end of key array.
                this.attributes.key_ary[this.attributes.key_ary.length - 1];
     }
 });
@@ -289,9 +289,9 @@ var GenomeDataManager = Cache.extend({
     data_is_ready: function() {
         var dataset = this.get('dataset'),
             ready_deferred = $.Deferred(),
-            // If requesting raw data, query dataset state; if requesting (converted) data, 
+            // If requesting raw data, query dataset state; if requesting (converted) data,
             // need to query converted datasets state.
-            query_type = (this.get('data_type') === 'raw_data' ? 'state' : 
+            query_type = (this.get('data_type') === 'raw_data' ? 'state' :
                           this.get('data_type') === 'data' ? 'converted_datasets_state' : "error" ),
             ss_deferred = new util_mod.ServerStateDeferred({
                 ajax_settings: {
@@ -324,7 +324,7 @@ var GenomeDataManager = Cache.extend({
             };
         return $.getJSON(dataset.url(), params);
     },
-    
+
     /**
      * Load data from server and manages data entries. Adds a Deferred to manager
      * for region; when data becomes available, replaces Deferred with data.
@@ -335,16 +335,16 @@ var GenomeDataManager = Cache.extend({
         var dataset = this.get('dataset'),
             params = {
                         "data_type": this.get('data_type'),
-                        "chrom": region.get('chrom'), 
-                        "low": region.get('start'), 
-                        "high": region.get('end'), 
+                        "chrom": region.get('chrom'),
+                        "low": region.get('start'),
+                        "high": region.get('end'),
                         "mode": mode,
                         "resolution": resolution,
                         "hda_ldda": dataset.get('hda_ldda')
                      };
 
         $.extend(params, extra_params);
-        
+
         // Add track filters to params.
         var filters_manager = this.get('filters_manager');
         if (filters_manager) {
@@ -355,7 +355,7 @@ var GenomeDataManager = Cache.extend({
             }
             params.filter_cols = JSON.stringify(filter_names);
         }
-                        
+
         // Do request.
         var manager = this,
             entry = $.getJSON(dataset.url(), params, function (result) {
@@ -367,14 +367,14 @@ var GenomeDataManager = Cache.extend({
         this.set_data(region, entry);
         return entry;
     },
-    
+
     /**
      * Get data from dataset.
      */
     get_data: function(region, mode, resolution, extra_params) {
         // Look for entry and return if it's a deferred or if data available is compatible with mode.
         var entry = this.get_elt(region);
-        if ( entry && 
+        if ( entry &&
              ( util_mod.is_deferred(entry) || this.get('data_mode_compatible')(entry, mode) ) ) {
             return entry;
         }
@@ -389,14 +389,14 @@ var GenomeDataManager = Cache.extend({
             entry_region, is_subregion;
         for (var i = 0; i < key_ary.length; i++) {
             entry_region = key_ary[i];
-            
+
             if (entry_region.contains(region)) {
                 is_subregion = true;
 
                 // This entry has data in the requested range. Return if data
                 // is compatible and can be subsetted.
                 entry = obj_cache[entry_region.toString()];
-                if ( util_mod.is_deferred(entry) || 
+                if ( util_mod.is_deferred(entry) ||
                     ( this.get('data_mode_compatible')(entry, mode) && this.get('can_subset')(entry) ) ) {
                     this.move_key_to_end(entry_region, i);
 
@@ -412,7 +412,7 @@ var GenomeDataManager = Cache.extend({
             }
         }
 
-        // FIXME: There _may_ be instances where region is a subregion of another entry but cannot be 
+        // FIXME: There _may_ be instances where region is a subregion of another entry but cannot be
         // subsetted. For these cases, do not increase length because region will never be found (and
         // an infinite loop will occur.)
         // If needed, extend region to make it minimum size.
@@ -442,20 +442,20 @@ var GenomeDataManager = Cache.extend({
 
         return this.load_data(region, mode, resolution, extra_params);
     },
-    
+
     /**
      * Alias for set_elt for readbility.
      */
     set_data: function(region, entry) {
-        this.set_elt(region, entry);  
+        this.set_elt(region, entry);
     },
-    
+
     /** "Deep" data request; used as a parameter for DataManager.get_more_data() */
     DEEP_DATA_REQ: "deep",
-    
+
     /** "Broad" data request; used as a parameter for DataManager.get_more_data() */
     BROAD_DATA_REQ: "breadth",
-    
+
     /**
      * Gets more data for a region using either a depth-first or a breadth-first approach.
      */
@@ -465,7 +465,7 @@ var GenomeDataManager = Cache.extend({
             console.log('ERROR: problem with getting more data: current data is not compatible');
             return;
         }
-        
+
         //
         // Set parameters based on request type.
         //
@@ -480,7 +480,7 @@ var GenomeDataManager = Cache.extend({
             query_low = (cur_data.max_high ? cur_data.max_high : cur_data.data[cur_data.data.length - 1][2]) + 1;
         }
         var query_region = region.copy().set('start', query_low);
-        
+
         //
         // Get additional data, append to current data, and set new data. Use a custom deferred object
         // to signal when new data is available.
@@ -605,7 +605,7 @@ var GenomeDataManager = Cache.extend({
         var subset_fns = {
             bigwig: function(data, subregion) {
                 return _.filter(data, function(data_point) {
-                    return data_point[0] >= subregion.get('start') && 
+                    return data_point[0] >= subregion.get('start') &&
                            data_point[0] <= subregion.get('end');
                 });
             },
@@ -640,12 +640,12 @@ var GenomeReferenceDataManager = GenomeDataManager.extend({
 
     load_data: function(region, mode, resolution, extra_params) {
         // Fetch data if region is not too large.
-        return ( region.length() <= 100000 ? 
+        return ( region.length() <= 100000 ?
                  GenomeDataManager.prototype.load_data.call(this, region, mode, resolution, extra_params) :
                  { data: null, region: region } );
     }
 });
- 
+
 /**
  * A genome build.
  */
@@ -659,20 +659,20 @@ var Genome = Backbone.Model.extend({
     initialize: function(options) {
         this.id = options.dbkey;
     },
-    
+
     /**
      * Shorthand for getting to chromosome information.
      */
     get_chroms_info: function() {
-        return this.attributes.chroms_info.chrom_info;  
+        return this.attributes.chroms_info.chrom_info;
     },
 
-    /** 
+    /**
      * Returns a GenomeRegion object denoting a complete chromosome.
      */
     get_chrom_region: function(chr_name) {
         // FIXME: use findWhere in underscore 1.4
-        var chrom_info = _.find(this.get_chroms_info(), function(chrom_info) { 
+        var chrom_info = _.find(this.get_chroms_info(), function(chrom_info) {
             return chrom_info.chrom === chr_name;
         });
         return new GenomeRegion({
@@ -684,7 +684,7 @@ var Genome = Backbone.Model.extend({
     /** Returns the length of a chromosome. */
     get_chrom_len: function(chr_name) {
         // FIXME: use findWhere in underscore 1.4
-        return _.find(this.get_chroms_info(), function(chrom_info) { 
+        return _.find(this.get_chroms_info(), function(chrom_info) {
             return chrom_info.chrom === chr_name;
         }).len;
     }
@@ -711,7 +711,7 @@ var GenomeRegion = Backbone.Model.extend({
                this.attributes.start === region.get('start') &&
                this.attributes.end === region.get('end');
     },
-    
+
     /**
      * If from_str specified, use it to initialize attributes.
      */
@@ -732,27 +732,27 @@ var GenomeRegion = Backbone.Model.extend({
 
         // Set str_val on attribute change.
         this.on('change', function() {
-            this.attributes.str_val = this.get('chrom') + ":" + this.get('start') + "-" + this.get('end');            
+            this.attributes.str_val = this.get('chrom') + ":" + this.get('start') + "-" + this.get('end');
         }, this);
     },
-    
+
     copy: function() {
         return new GenomeRegion({
             chrom: this.get('chrom'),
             start: this.get('start'),
-            end: this.get('end') 
+            end: this.get('end')
         });
     },
 
     length: function() {
         return this.get('end') - this.get('start');
     },
-    
+
     /** Returns region in canonical form chrom:start-end */
     toString: function() {
         return this.attributes.str_val;
     },
-    
+
     toJSON: function() {
         return {
             chrom: this.get('chrom'),
@@ -760,9 +760,9 @@ var GenomeRegion = Backbone.Model.extend({
             end: this.get('end')
         };
     },
-    
+
     /**
-     * Compute the type of overlap between this region and another region. The overlap is computed relative to the given/second region; 
+     * Compute the type of overlap between this region and another region. The overlap is computed relative to the given/second region;
      * hence, OVERLAP_START indicates that the first region overlaps the start (but not the end) of the second region.
      */
     compute_overlap: function(a_region) {
@@ -770,12 +770,12 @@ var GenomeRegion = Backbone.Model.extend({
             first_start = this.get('start'), second_start = a_region.get('start'),
             first_end = this.get('end'), second_end = a_region.get('end'),
             overlap;
-            
+
         // Compare chroms.
         if (first_chrom && second_chrom && first_chrom !== second_chrom) {
             return GenomeRegion.overlap_results.DIF_CHROMS;
         }
-        
+
         // Compare regions.
         if (first_start < second_start) {
             if (first_end < second_start) {
@@ -800,8 +800,8 @@ var GenomeRegion = Backbone.Model.extend({
             }
         }
         else { // first_start === second_start
-            overlap = (first_end >= second_end ? 
-                       GenomeRegion.overlap_results.CONTAINS : 
+            overlap = (first_end >= second_end ?
+                       GenomeRegion.overlap_results.CONTAINS :
                        GenomeRegion.overlap_results.CONTAINED_BY);
         }
 
@@ -827,7 +827,7 @@ var GenomeRegion = Backbone.Model.extend({
 
         return this;
     },
-    
+
     /**
      * Returns true if this region contains a given region.
      */
@@ -839,18 +839,18 @@ var GenomeRegion = Backbone.Model.extend({
      * Returns true if regions overlap.
      */
     overlaps: function(a_region) {
-        return _.intersection( [this.compute_overlap(a_region)], 
-                               [GenomeRegion.overlap_results.DIF_CHROMS, GenomeRegion.overlap_results.BEFORE, GenomeRegion.overlap_results.AFTER] ).length === 0;  
+        return _.intersection( [this.compute_overlap(a_region)],
+                               [GenomeRegion.overlap_results.DIF_CHROMS, GenomeRegion.overlap_results.BEFORE, GenomeRegion.overlap_results.AFTER] ).length === 0;
     }
 },
 {
     overlap_results: {
         DIF_CHROMS: 1000,
-        BEFORE: 1001, 
-        CONTAINS: 1002, 
-        OVERLAP_START: 1003, 
-        OVERLAP_END: 1004, 
-        CONTAINED_BY: 1005, 
+        BEFORE: 1001,
+        CONTAINS: 1002,
+        OVERLAP_START: 1003,
+        OVERLAP_END: 1004,
+        CONTAINED_BY: 1005,
         AFTER: 1006
     }
 });
@@ -892,7 +892,7 @@ var BackboneTrack = Backbone.Model.extend(CustomToJSON).extend({
     initialize: function(options) {
         this.set('dataset', new data_mod.Dataset(options.dataset));
 
-        // -- Set up config settings. -- 
+        // -- Set up config settings. --
         var models =  [
             { key: 'name', default_value: this.get('dataset').get('name') },
             { key: 'color' },
@@ -959,10 +959,10 @@ var Visualization = Backbone.Model.extend({
     },
 
     urlRoot: galaxy_config.root + "api/visualizations",
-    
+
     /**
      * POSTs visualization's JSON to its URL using the parameter 'vis_json'
-     * Note: This is necessary because (a) Galaxy requires keyword args and 
+     * Note: This is necessary because (a) Galaxy requires keyword args and
      * (b) Galaxy does not handle PUT now.
      */
     save: function() {
@@ -970,7 +970,7 @@ var Visualization = Backbone.Model.extend({
             url: this.url(),
             type: "POST",
             dataType: "json",
-            data: { 
+            data: {
                 vis_json: JSON.stringify(this)
             }
         });
@@ -994,7 +994,7 @@ var GenomeVisualization = Visualization.extend(CustomToJSON).extend({
 
         var models = [];
         this.set('config', config_mod.ConfigSettingCollection.from_models_and_saved_values(models, options.prefs));
-        
+
         // Clear track and data definitions to avoid storing large objects.
         this.unset('tracks');
         this.get('drawables').each(function(d) {
@@ -1039,22 +1039,22 @@ var GenomeVisualization = Visualization.extend(CustomToJSON).extend({
 /**
  * Router for track browser.
  */
-var TrackBrowserRouter = Backbone.Router.extend({    
+var TrackBrowserRouter = Backbone.Router.extend({
     initialize: function(options) {
         this.view = options.view;
-        
+
         // Can't put regular expression in routes dictionary.
         // NOTE: parentheses are used to denote parameters returned to callback.
         this.route(/([\w]+)$/, 'change_location');
         this.route(/([\w\+]+\:[\d,]+-[\d,]+)$/, 'change_location');
-        
+
         // Handle navigate events from view.
         var self = this;
         self.view.on("navigate", function(new_loc) {
             self.navigate(new_loc);
         });
     },
-    
+
     change_location: function(new_loc) {
         this.view.go_to(new_loc);
     }

static/maps/galaxy.tools.js.map

@@ -1 +1 @@
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static/maps/layout/scratchbook.js.map

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static/maps/ui/scroll-panel.js.map

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static/scripts/galaxy.tools.js

@@ -1,2 +1,2 @@
-define(["libs/underscore","mvc/tools"],function(a){var b=function(a,b){$("input[name='"+a+"'][type='checkbox']").attr("checked",!!b)};$(".tool-share-link").each(function(){var a=$(this).attr("href"),a=$(this).attr("data-link");$(this).click(function(){window.prompt("Copy to clipboard: Ctrl+C, Enter",a)})}),$("div.checkUncheckAllPlaceholder").each(function(){var a=$(this).attr("checkbox_name");select_link=$("<a class='action-button'></a>").text("Select All").click(function(){b(a,!0)}),unselect_link=$("<a class='action-button'></a>").text("Unselect All").click(function(){b(a,!1)}),$(this).append(select_link).append(" ").append(unselect_link)});var c={select_single:{icon_class:"fa-file-o",select_by:"Run tool on single input",allow_remap:!0},select_multiple:{icon_class:"fa-files-o",select_by:"Run tool in parallel across multiple datasets",allow_remap:!1,min_option_count:2},select_collection:{icon_class:"fa-folder-o",select_by:"Run tool in parallel across dataset collection",allow_remap:!1},multiselect_single:{icon_class:"fa-list-alt",select_by:"Run tool over multiple datasets",allow_remap:!0},multiselect_collection:{icon_class:"fa-folder-o",select_by:"Run tool over dataset collection",allow_remap:!1},select_single_collection:{icon_class:"fa-file-o",select_by:"Run tool on single collection",allow_remap:!0},select_map_over_collections:{icon_class:"fa-folder-o",select_by:"Map tool over compontents of nested collection",allow_remap:!1}},d=Backbone.View.extend({initialize:function(b){var d=b.default_option,e=null,f=b.switch_options;this.switchOptions=f,this.prefix=b.prefix;var g=(this.$el,this),h=0,i=0;a.each(this.switchOptions,function(b,f){var j=a.size(b.options),k=c[f],l=h++,m=!1;if(d==f?e=l:j<(k.min_option_count||1)&&(m=!0),!m){i++;var n=$('<i class="fa '+k.icon_class+' runOptionIcon" style="padding-left: 5px; padding-right: 2px;"></i>').click(function(){g.enableSelectBy(l,f)}).attr("title",k.select_by).data("index",l);g.formRow().find("label").append(n)}}),2>i&&g.formRow().find("i.runOptionIcon").hide(),null!=e&&g.enableSelectBy(e,d)},formRow:function(){return this.$el.closest(".form-row")},render:function(){},enableSelectBy:function(b,d){var e=c[d];e.allow_remap?$("div#remap-row").css("display","inherit"):$("div#remap-row").css("display","none"),this.formRow().find("i").each(function(a,c){var d=$(c),e=d.data("index");e==b?d.css("color","black"):d.css("color","Gray")});var f=this.$("select"),g=this.switchOptions[d];f.attr("name",this.prefix+g.name),f.attr("multiple",g.multiple);var h=this.$(".select2-container").length>0;f.html(""),a.each(g.options,function(a){var b=a[0],c=a[1],d=a[2];f.append($("<option />",{text:b,val:c,selected:d}))}),h&&f.select2()}});return{SwitchSelectView:d}});
+define(["libs/underscore","mvc/tools/tools"],function(a){var b=function(a,b){$("input[name='"+a+"'][type='checkbox']").attr("checked",!!b)};$(".tool-share-link").each(function(){var a=$(this).attr("href"),a=$(this).attr("data-link");$(this).click(function(){window.prompt("Copy to clipboard: Ctrl+C, Enter",a)})}),$("div.checkUncheckAllPlaceholder").each(function(){var a=$(this).attr("checkbox_name");select_link=$("<a class='action-button'></a>").text("Select All").click(function(){b(a,!0)}),unselect_link=$("<a class='action-button'></a>").text("Unselect All").click(function(){b(a,!1)}),$(this).append(select_link).append(" ").append(unselect_link)});var c={select_single:{icon_class:"fa-file-o",select_by:"Run tool on single input",allow_remap:!0},select_multiple:{icon_class:"fa-files-o",select_by:"Run tool in parallel across multiple datasets",allow_remap:!1,min_option_count:2},select_collection:{icon_class:"fa-folder-o",select_by:"Run tool in parallel across dataset collection",allow_remap:!1},multiselect_single:{icon_class:"fa-list-alt",select_by:"Run tool over multiple datasets",allow_remap:!0},multiselect_collection:{icon_class:"fa-folder-o",select_by:"Run tool over dataset collection",allow_remap:!1},select_single_collection:{icon_class:"fa-file-o",select_by:"Run tool on single collection",allow_remap:!0},select_map_over_collections:{icon_class:"fa-folder-o",select_by:"Map tool over compontents of nested collection",allow_remap:!1}},d=Backbone.View.extend({initialize:function(b){var d=b.default_option,e=null,f=b.switch_options;this.switchOptions=f,this.prefix=b.prefix;var g=(this.$el,this),h=0,i=0;a.each(this.switchOptions,function(b,f){var j=a.size(b.options),k=c[f],l=h++,m=!1;if(d==f?e=l:j<(k.min_option_count||1)&&(m=!0),!m){i++;var n=$('<i class="fa '+k.icon_class+' runOptionIcon" style="padding-left: 5px; padding-right: 2px;"></i>').click(function(){g.enableSelectBy(l,f)}).attr("title",k.select_by).data("index",l);g.formRow().find("label").append(n)}}),2>i&&g.formRow().find("i.runOptionIcon").hide(),null!=e&&g.enableSelectBy(e,d)},formRow:function(){return this.$el.closest(".form-row")},render:function(){},enableSelectBy:function(b,d){var e=c[d];e.allow_remap?$("div#remap-row").css("display","inherit"):$("div#remap-row").css("display","none"),this.formRow().find("i").each(function(a,c){var d=$(c),e=d.data("index");e==b?d.css("color","black"):d.css("color","Gray")});var f=this.$("select"),g=this.switchOptions[d];f.attr("name",this.prefix+g.name),f.attr("multiple",g.multiple);var h=this.$(".select2-container").length>0;f.html(""),a.each(g.options,function(a){var b=a[0],c=a[1],d=a[2];f.append($("<option />",{text:b,val:c,selected:d}))}),h&&f.select2()}});return{SwitchSelectView:d}});
 //# sourceMappingURL=../maps/galaxy.tools.js.map

static/scripts/layout/scratchbook.js

@@ -1,2 +1,2 @@
-define(["mvc/ui/ui-frames"],function(a){var b=Backbone.View.extend({el_main:"body",active:!1,button_active:null,button_load:null,initialize:function(b){b=b||{};var d=this;this.frames=new a.View({visible:!1}),this.button_active=new c({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",onclick:function(){d._activate()},onunload:function(){return d.frames.length()>0?"You opened "+d.frames.length()+" frame(s) which will be lost.":void 0}}),this.button_load=new c({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",onclick:function(){d.frames.visible?d.frames.hide():d.frames.show()},with_number:!0}),b.masthead&&(b.masthead.append(this.button_active),b.masthead.append(this.button_load)),this.setElement(this.frames.$el),$(this.el_main).append(this.$el),this.frames.setOnChange(function(){d._refresh()}),this._refresh()},add_dataset:function(a){var b=this;require(["mvc/data"],function(c){var d=new c.Dataset({id:a});$.when(d.fetch()).then(function(){var a={title:d.get("name")},e=_.find(["tabular","interval"],function(a){return-1!==d.get("data_type").indexOf(a)});if(e){var f=new c.TabularDataset(d.toJSON());_.extend(a,{type:"other",content:function(a){c.createTabularDatasetChunkedView({model:f,parent_elt:a,embedded:!0,height:"100%"})}})}else _.extend(a,{type:"url",content:galaxy_config.root+"datasets/"+d.id+"/display/?preview=True"});b.add(a)})})},add_trackster_viz:function(a){var b=this;require(["viz/visualization","viz/trackster"],function(c,d){var e=new c.Visualization({id:a});$.when(e.fetch()).then(function(){var a=new d.TracksterUI(galaxy_config.root),c={title:e.get("name"),type:"other",content:function(b){var c={container:b,name:e.get("title"),id:e.id,dbkey:e.get("dbkey"),stand_alone:!1},d=e.get("latest_revision"),f=d.config.view.drawables;_.each(f,function(a){a.dataset={hda_ldda:a.hda_ldda,id:a.dataset_id}}),view=a.create_visualization(c,d.config.viewport,d.config.view.drawables,d.config.bookmarks,!1)}};b.add(c)})})},add:function(a){if("_blank"==a.target)return void window.open(a.content);if("_top"==a.target||"_parent"==a.target||"_self"==a.target)return void(window.location=a.content);if(this.active)this.frames.add(a);else{var b=$(window.parent.document).find("#galaxy_main");if("galaxy_main"==a.target||"center"==a.target)if(0===b.length){var c=a.content;c+=-1==c.indexOf("?")?"?":"&",c+="use_panels=True",window.location=c}else b.attr("src",a.content);else window.location=a.content}},_activate:function(){this.active?(this.active=!1,this.button_active.untoggle(),this.frames.hide()):(this.active=!0,this.button_active.toggle())},_refresh:function(){this.button_load.number(this.frames.length()),0===this.frames.length()?this.button_load.hide():this.button_load.show(),this.frames.visible?this.button_load.toggle():this.button_load.untoggle()}}),c=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:!1,onclick:function(){alert("clicked")},onunload:null,visible:!0},location:"iconbar",initialize:function(a){a&&(this.options=_.defaults(a,this.options)),this.setElement($(this._template(this.options)));var b=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",b.options.onclick),this.options.visible||this.hide()},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(a){$(this.el).find(".icon").removeClass(this.options.icon).addClass(a),this.options.icon=a},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(a){$(this.el).find(".number").text(a)},_template:function(a){var b='<div id="'+a.id+'" class="symbol"><div class="icon fa fa-2x '+a.icon+'"></div>';return a.with_number&&(b+='<div class="number"></div>'),b+="</div>"}});return{GalaxyFrame:b,GalaxyMastheadIcon:c}});
+define(["mvc/ui/ui-frames"],function(a){var b=Backbone.View.extend({el_main:"body",active:!1,button_active:null,button_load:null,initialize:function(b){b=b||{};var d=this;this.frames=new a.View({visible:!1}),this.button_active=new c({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",onclick:function(){d._activate()},onunload:function(){return d.frames.length()>0?"You opened "+d.frames.length()+" frame(s) which will be lost.":void 0}}),this.button_load=new c({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",onclick:function(){d.frames.visible?d.frames.hide():d.frames.show()},with_number:!0}),b.masthead&&(b.masthead.append(this.button_active),b.masthead.append(this.button_load)),this.setElement(this.frames.$el),$(this.el_main).append(this.$el),this.frames.setOnChange(function(){d._refresh()}),this._refresh()},add_dataset:function(a){var b=this;require(["mvc/dataset/data"],function(c){var d=new c.Dataset({id:a});$.when(d.fetch()).then(function(){var a={title:d.get("name")},e=_.find(["tabular","interval"],function(a){return-1!==d.get("data_type").indexOf(a)});if(e){var f=new c.TabularDataset(d.toJSON());_.extend(a,{type:"other",content:function(a){c.createTabularDatasetChunkedView({model:f,parent_elt:a,embedded:!0,height:"100%"})}})}else _.extend(a,{type:"url",content:galaxy_config.root+"datasets/"+d.id+"/display/?preview=True"});b.add(a)})})},add_trackster_viz:function(a){var b=this;require(["viz/visualization","viz/trackster"],function(c,d){var e=new c.Visualization({id:a});$.when(e.fetch()).then(function(){var a=new d.TracksterUI(galaxy_config.root),c={title:e.get("name"),type:"other",content:function(b){var c={container:b,name:e.get("title"),id:e.id,dbkey:e.get("dbkey"),stand_alone:!1},d=e.get("latest_revision"),f=d.config.view.drawables;_.each(f,function(a){a.dataset={hda_ldda:a.hda_ldda,id:a.dataset_id}}),view=a.create_visualization(c,d.config.viewport,d.config.view.drawables,d.config.bookmarks,!1)}};b.add(c)})})},add:function(a){if("_blank"==a.target)return void window.open(a.content);if("_top"==a.target||"_parent"==a.target||"_self"==a.target)return void(window.location=a.content);if(this.active)this.frames.add(a);else{var b=$(window.parent.document).find("#galaxy_main");if("galaxy_main"==a.target||"center"==a.target)if(0===b.length){var c=a.content;c+=-1==c.indexOf("?")?"?":"&",c+="use_panels=True",window.location=c}else b.attr("src",a.content);else window.location=a.content}},_activate:function(){this.active?(this.active=!1,this.button_active.untoggle(),this.frames.hide()):(this.active=!0,this.button_active.toggle())},_refresh:function(){this.button_load.number(this.frames.length()),0===this.frames.length()?this.button_load.hide():this.button_load.show(),this.frames.visible?this.button_load.toggle():this.button_load.untoggle()}}),c=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:!1,onclick:function(){alert("clicked")},onunload:null,visible:!0},location:"iconbar",initialize:function(a){a&&(this.options=_.defaults(a,this.options)),this.setElement($(this._template(this.options)));var b=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",b.options.onclick),this.options.visible||this.hide()},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(a){$(this.el).find(".icon").removeClass(this.options.icon).addClass(a),this.options.icon=a},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(a){$(this.el).find(".number").text(a)},_template:function(a){var b='<div id="'+a.id+'" class="symbol"><div class="icon fa fa-2x '+a.icon+'"></div>';return a.with_number&&(b+='<div class="number"></div>'),b+="</div>"}});return{GalaxyFrame:b,GalaxyMastheadIcon:c}});
 //# sourceMappingURL=../../maps/layout/scratchbook.js.map

static/scripts/mvc/app/app-analysis.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/tools","mvc/upload/upload-view","mvc/ui/ui-misc","mvc/history/options-menu","mvc/history/history-panel-edit-current","mvc/tools/tools-form"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{}),this.setElement(this._template());var c=this;this.$("#galaxy_main").on("load",function(){var a=this.contentWindow&&this.contentWindow.location;a&&a.host&&($(this).show(),c.prev&&c.prev.remove(),c.$("#center-panel").hide(),Galaxy.trigger("galaxy_main:load",{fullpath:a.pathname+a.search+a.hash,pathname:a.pathname,search:a.search,hash:a.hash}))});var d=$.extend({},Galaxy.params);"upload1"!==d.tool_id&&(d.tool_id||d.job_id)?(d.tool_id&&(d.id=d.tool_id),this.display(new g.View(d))):this.$("#galaxy_main").prop("src",Galaxy.root+(d.workflow_id&&"workflow/run?id="+d.workflow_id||d.m_c&&d.m_c+"/"+d.m_a||"root/welcome"))},display:function(a){this.prev&&this.prev.remove(),this.prev=a,this.$("#galaxy_main").hide(),this.$("#center-panel").scrollTop(0).append(a.$el).show()},_template:function(){return'<div style="position: absolute; width: 100%; height: 100%"><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;"/><div id="center-panel" style="position: absolute; width: 100%; height: 100%; padding: 10px; overflow: auto;"/></div>'}}),i=Backbone.View.extend({initialize:function(d){if(this.options=a.merge(d,{}),this.setElement(this._template()),Galaxy.user.id||!Galaxy.config.require_login){var e=new b.ToolSearch({spinner_url:d.spinner_url,search_url:d.search_url,hidden:!1}),f=new b.ToolCollection(d.toolbox),g=new b.ToolPanel({tool_search:e,tools:f,layout:d.toolbox_in_panel});tool_panel_view=new b.ToolPanelView({model:g}),Galaxy.toolPanel=g,g.get("layout").size()>0&&(tool_panel_view.render(),this.$(".toolMenu").show()),this.$el.prepend(tool_panel_view.$el),this.$("#internal-workflows").append(this._templateTool({title:"All workflows",href:"workflow/list_for_run"}));for(var h in d.stored_workflow_menu_entries){var i=d.stored_workflow_menu_entries[h];this.$("#internal-workflows").append(this._templateTool({title:i.stored_workflow.name,href:"workflow/run?id="+i.encoded_stored_workflow_id}))}this.$("a[minsizehint]").click(function(){parent.handle_minwidth_hint&&parent.handle_minwidth_hint($(this).attr("minsizehint"))}),Galaxy.upload=new c(d),this.components={header:{title:"Tools",buttons:[Galaxy.upload]}}}},_templateTool:function(a){return'<div class="toolTitle"><a href="'+Galaxy.root+a.href+'" target="galaxy_main">'+a.title+"</a></div>"},_template:function(){return'<div class="toolMenuContainer"><div class="toolMenu" style="display: none"><div id="search-no-results" style="display: none; padding-top: 5px"><em><strong>Search did not match any tools.</strong></em></div></div><div class="toolSectionPad"/><div class="toolSectionPad"/><div class="toolSectionTitle" id="title_XXinternalXXworkflow"><span>Workflows</span></div><div id="internal-workflows" class="toolSectionBody"><div class="toolSectionBg"/></div></div>'}}),j=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{}),this.setElement(this._template());var c=[],g=new d.ButtonLink({id:"history-refresh-button",title:"Refresh history",cls:"panel-header-button",icon:"fa fa-refresh",onclick:function(){top.Galaxy&&top.Galaxy.currHistoryPanel&&top.Galaxy.currHistoryPanel.loadCurrentHistory()}});c.push(g);var h=new d.ButtonLink({id:"history-options-button",title:"History options",cls:"panel-header-button",target:"galaxy_main",icon:"fa fa-cog",href:Galaxy.root+"root/history_options"});if(c.push(h),!Galaxy.user.isAnonymous()){var i=new d.ButtonLink({id:"history-view-multi-button",title:"View all histories",cls:"panel-header-button",icon:"fa fa-columns",href:Galaxy.root+"history/view_multiple"});c.push(i)}this.components={header:{title:"History",cls:"history-panel-header",buttons:c},body:{cls:"unified-panel-body-background"}},Galaxy.historyOptionsMenu=e(h.$el,{anonymous:Galaxy.user.isAnonymous(),purgeAllowed:Galaxy.config.allow_user_dataset_purge,root:Galaxy.root}),Galaxy.currHistoryPanel=new f.CurrentHistoryPanel({el:this.$el,purgeAllowed:Galaxy.config.allow_user_dataset_purge,linkTarget:"galaxy_main",$scrollContainer:function(){return this.$el.parent()}}),Galaxy.currHistoryPanel.connectToQuotaMeter(Galaxy.quotaMeter),Galaxy.currHistoryPanel.listenToGalaxy(Galaxy),Galaxy.currHistoryPanel.loadCurrentHistory()},_template:function(){return'<div id="current-history-panel" class="history-panel"/>'}});return{left:i,center:h,right:j}});
+define(["utils/utils","mvc/tools/tools","mvc/upload/upload-view","mvc/ui/ui-misc","mvc/history/options-menu","mvc/history/history-panel-edit-current","mvc/tools/tools-form"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{}),this.setElement(this._template());var c=this;this.$("#galaxy_main").on("load",function(){var a=this.contentWindow&&this.contentWindow.location;a&&a.host&&($(this).show(),c.prev&&c.prev.remove(),c.$("#center-panel").hide(),Galaxy.trigger("galaxy_main:load",{fullpath:a.pathname+a.search+a.hash,pathname:a.pathname,search:a.search,hash:a.hash}))});var d=$.extend({},Galaxy.params);"upload1"!==d.tool_id&&(d.tool_id||d.job_id)?(d.tool_id&&(d.id=d.tool_id),this.display(new g.View(d))):this.$("#galaxy_main").prop("src",Galaxy.root+(d.workflow_id&&"workflow/run?id="+d.workflow_id||d.m_c&&d.m_c+"/"+d.m_a||"root/welcome"))},display:function(a){this.prev&&this.prev.remove(),this.prev=a,this.$("#galaxy_main").hide(),this.$("#center-panel").scrollTop(0).append(a.$el).show()},_template:function(){return'<div style="position: absolute; width: 100%; height: 100%"><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;"/><div id="center-panel" style="position: absolute; width: 100%; height: 100%; padding: 10px; overflow: auto;"/></div>'}}),i=Backbone.View.extend({initialize:function(d){if(this.options=a.merge(d,{}),this.setElement(this._template()),Galaxy.user.id||!Galaxy.config.require_login){var e=new b.ToolSearch({spinner_url:d.spinner_url,search_url:d.search_url,hidden:!1}),f=new b.ToolCollection(d.toolbox),g=new b.ToolPanel({tool_search:e,tools:f,layout:d.toolbox_in_panel});tool_panel_view=new b.ToolPanelView({model:g}),Galaxy.toolPanel=g,g.get("layout").size()>0&&(tool_panel_view.render(),this.$(".toolMenu").show()),this.$el.prepend(tool_panel_view.$el),this.$("#internal-workflows").append(this._templateTool({title:"All workflows",href:"workflow/list_for_run"}));for(var h in d.stored_workflow_menu_entries){var i=d.stored_workflow_menu_entries[h];this.$("#internal-workflows").append(this._templateTool({title:i.stored_workflow.name,href:"workflow/run?id="+i.encoded_stored_workflow_id}))}this.$("a[minsizehint]").click(function(){parent.handle_minwidth_hint&&parent.handle_minwidth_hint($(this).attr("minsizehint"))}),Galaxy.upload=new c(d),this.components={header:{title:"Tools",buttons:[Galaxy.upload]}}}},_templateTool:function(a){return'<div class="toolTitle"><a href="'+Galaxy.root+a.href+'" target="galaxy_main">'+a.title+"</a></div>"},_template:function(){return'<div class="toolMenuContainer"><div class="toolMenu" style="display: none"><div id="search-no-results" style="display: none; padding-top: 5px"><em><strong>Search did not match any tools.</strong></em></div></div><div class="toolSectionPad"/><div class="toolSectionPad"/><div class="toolSectionTitle" id="title_XXinternalXXworkflow"><span>Workflows</span></div><div id="internal-workflows" class="toolSectionBody"><div class="toolSectionBg"/></div></div>'}}),j=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{}),this.setElement(this._template());var c=[],g=new d.ButtonLink({id:"history-refresh-button",title:"Refresh history",cls:"panel-header-button",icon:"fa fa-refresh",onclick:function(){top.Galaxy&&top.Galaxy.currHistoryPanel&&top.Galaxy.currHistoryPanel.loadCurrentHistory()}});c.push(g);var h=new d.ButtonLink({id:"history-options-button",title:"History options",cls:"panel-header-button",target:"galaxy_main",icon:"fa fa-cog",href:Galaxy.root+"root/history_options"});if(c.push(h),!Galaxy.user.isAnonymous()){var i=new d.ButtonLink({id:"history-view-multi-button",title:"View all histories",cls:"panel-header-button",icon:"fa fa-columns",href:Galaxy.root+"history/view_multiple"});c.push(i)}this.components={header:{title:"History",cls:"history-panel-header",buttons:c},body:{cls:"unified-panel-body-background"}},Galaxy.historyOptionsMenu=e(h.$el,{anonymous:Galaxy.user.isAnonymous(),purgeAllowed:Galaxy.config.allow_user_dataset_purge,root:Galaxy.root}),Galaxy.currHistoryPanel=new f.CurrentHistoryPanel({el:this.$el,purgeAllowed:Galaxy.config.allow_user_dataset_purge,linkTarget:"galaxy_main",$scrollContainer:function(){return this.$el.parent()}}),Galaxy.currHistoryPanel.connectToQuotaMeter(Galaxy.quotaMeter),Galaxy.currHistoryPanel.listenToGalaxy(Galaxy),Galaxy.currHistoryPanel.loadCurrentHistory()},_template:function(){return'<div id="current-history-panel" class="history-panel"/>'}});return{left:i,center:h,right:j}});
 //# sourceMappingURL=../../../maps/mvc/app/app-analysis.js.map

static/scripts/onload.js

@@ -1,2 +1,2 @@
-function replace_big_select_inputs(a,b,c){function d(a){var b=$(a),c={placeholder:"Click to select",closeOnSelect:!b.is("[MULTIPLE]"),dropdownAutoWidth:!0,containerCssClass:"select2-minwidth"};return a.select2(c)}jQuery.fn.select2&&(void 0===a&&(a=20),void 0===b&&(b=3e3),c=c||$("select"),c.each(function(){var c=$(this).not("[multiple]"),e=c.find("option").length;a>e||e>b||c.hasClass("no-autocomplete")||d(c)}))}function init_refresh_on_change(){$("select[refresh_on_change='true']").off("change").change(function(){var a=$(this),b=a.val(),c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var d=a.attr("last_selected_value");if(-1===$.inArray(b,c)&&-1===$.inArray(d,c))return}$(window).trigger("refresh_on_change"),$(document).trigger("convert_to_values"),a.get(0).form.submit()}),$(":checkbox[refresh_on_change='true']").off("click").click(function(){var a=$(this),b=a.val(),c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var d=a.attr("last_selected_value");if(-1===$.inArray(b,c)&&-1===$.inArray(d,c))return}$(window).trigger("refresh_on_change"),a.get(0).form.submit()}),$("a[confirm]").off("click").click(function(){return confirm($(this).attr("confirm"))})}window.jQuery=jQuery,window.$=jQuery,window._=_,window.Backbone=Backbone,window.Handlebars=Handlebars,window.panels=require("layout/panel"),_.extend(window,require("modal")),window.async_save_text=require("utils/async-save-text");var POPUPMENU=require("ui/popupmenu");window.make_popupmenu=POPUPMENU.make_popupmenu,window.make_popup_menus=POPUPMENU.make_popup_menus,window.init_tag_click_function=require("ui/autocom_tagging"),window.init_refresh_on_change=init_refresh_on_change,$(document).ready(function(){var a=$("#masthead ul.nav > li.dropdown > .dropdown-menu");$("body").on("click.nav_popups",function(b){if(a.hide(),$("#dd-helper").hide(),!$(b.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){var c=$(b.target).closest("#masthead ul.nav > li.dropdown");c.length&&($("#dd-helper").show(),c.children(".dropdown-menu").show(),b.preventDefault())}}),init_refresh_on_change(),$.fn.tooltip&&($(".unified-panel-header [title]").tooltip({placement:"bottom"}),$("[title]").tooltip()),make_popup_menus(),replace_big_select_inputs(20,1500),$("a").click(function(){var a=$(this),b=parent.frames&&parent.frames.galaxy_main;if("galaxy_main"==a.attr("target")&&!b){var c=a.attr("href");c+=-1==c.indexOf("?")?"?":"&",c+="use_panels=True",a.attr("href",c),a.attr("target","_self")}return a})});
+function replace_big_select_inputs(a,b,c){function d(a){var b=$(a),c={placeholder:"Click to select",closeOnSelect:!b.is("[MULTIPLE]"),dropdownAutoWidth:!0,containerCssClass:"select2-minwidth"};return a.select2(c)}jQuery.fn.select2&&(void 0===a&&(a=20),void 0===b&&(b=3e3),c=c||$("select"),c.each(function(){var c=$(this).not("[multiple]"),e=c.find("option").length;a>e||e>b||c.hasClass("no-autocomplete")||d(c)}))}function init_refresh_on_change(){$("select[refresh_on_change='true']").off("change").change(function(){var a=$(this),b=a.val(),c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var d=a.attr("last_selected_value");if(-1===$.inArray(b,c)&&-1===$.inArray(d,c))return}$(window).trigger("refresh_on_change"),$(document).trigger("convert_to_values"),a.get(0).form.submit()}),$(":checkbox[refresh_on_change='true']").off("click").click(function(){var a=$(this),b=a.val(),c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var d=a.attr("last_selected_value");if(-1===$.inArray(b,c)&&-1===$.inArray(d,c))return}$(window).trigger("refresh_on_change"),a.get(0).form.submit()}),$("a[confirm]").off("click").click(function(){return confirm($(this).attr("confirm"))})}window.jQuery=jQuery,window.$=jQuery,window._=_,window.Backbone=Backbone,window.Handlebars=Handlebars,window.panels=require("layout/panel"),_.extend(window,require("layout/modal")),window.async_save_text=require("utils/async-save-text");var POPUPMENU=require("ui/popupmenu");window.make_popupmenu=POPUPMENU.make_popupmenu,window.make_popup_menus=POPUPMENU.make_popup_menus,window.init_tag_click_function=require("ui/autocom_tagging"),window.init_refresh_on_change=init_refresh_on_change,$(document).ready(function(){var a=$("#masthead ul.nav > li.dropdown > .dropdown-menu");$("body").on("click.nav_popups",function(b){if(a.hide(),$("#dd-helper").hide(),!$(b.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){var c=$(b.target).closest("#masthead ul.nav > li.dropdown");c.length&&($("#dd-helper").show(),c.children(".dropdown-menu").show(),b.preventDefault())}}),init_refresh_on_change(),$.fn.tooltip&&($(".unified-panel-header [title]").tooltip({placement:"bottom"}),$("[title]").tooltip()),make_popup_menus(),replace_big_select_inputs(20,1500),$("a").click(function(){var a=$(this),b=parent.frames&&parent.frames.galaxy_main;if("galaxy_main"==a.attr("target")&&!b){var c=a.attr("href");c+=-1==c.indexOf("?")?"?":"&",c+="use_panels=True",a.attr("href",c),a.attr("target","_self")}return a})});
 //# sourceMappingURL=../maps/onload.js.map

static/scripts/ui/scroll-panel.js

@@ -1,2 +1,2 @@
 $.ui.plugin.add("draggable","scrollPanel",{drag:function(a,b){var c=$(this).data("draggable");clearTimeout(c.timeout);var d=b.options,e=c.element,f=d.panel,g=f.position(),h=f.width(),i=f.height();if(viewport=f.parent(),viewport_w=viewport.width(),viewport_h=viewport.height(),element_w=e.width(),element_h=e.height(),moved=!1,close_dist=5,nudge=23,p_min_x=-(h-viewport_w),p_min_y=-(i-viewport_h),p_max_x=0,p_max_y=0,min_vis_x=-g.left,max_vis_x=min_vis_x+viewport_w,min_vis_y=-g.top,max_vis_y=min_vis_y+viewport_h,mouse_x=b.position.left+c.offset.click.left,mouse_y=b.position.top+c.offset.click.top,g.left<p_max_x&&mouse_x-close_dist<min_vis_x){var j=Math.min(nudge,p_max_x-g.left);f.css("left",g.left+j),moved=!0,c.offset.parent.left+=j,b.position.left-=j}if(!moved&&g.left>p_min_x&&mouse_x+close_dist>max_vis_x){var j=Math.min(nudge,g.left-p_min_x);f.css("left",g.left-j),moved=!0,c.offset.parent.left-=j,b.position.left+=j}if(!moved&&g.top<p_max_y&&mouse_y-close_dist<min_vis_y){var j=Math.min(nudge,p_max_y-g.top);f.css("top",g.top+j);var k=f.position().top-g.top;c.offset.parent.top+=k,b.position.top-=k,moved=!0}if(!moved&&g.top>p_min_y&&mouse_y+close_dist>max_vis_y){var j=Math.min(nudge,g.top-p_min_x);f.css("top",g.top-j+"px");var k=g.top-f.position().top;c.offset.parent.top-=k,b.position.top+=k,moved=!0}b.position.left=Math.max(b.position.left,0),b.position.top=Math.max(b.position.top,0),b.position.left=Math.min(b.position.left,h-element_w),b.position.top=Math.min(b.position.top,i-element_h),moved&&$.ui.ddmanager.prepareOffsets(c,a),moved&&(c.old_e=a,c.timeout=setTimeout(function(){c.mouseMove(a)},50))},stop:function(){var a=$(this).data("draggable");clearTimeout(a.timeout)}});
-//# sourceMappingURL=../maps/galaxy.ui.scrollPanel.js.map
+//# sourceMappingURL=../../maps/ui/scroll-panel.js.map

templates/webapps/galaxy/dataset/display.mako

@@ -17,7 +17,7 @@
             urlArgs: 'v=${app.server_starttime}'
         });
 
-        require(['mvc/data'], function(data) {
+        require(['mvc/dataset/data'], function(data) {
             //
             // Use tabular data display progressively by deleting data from page body
             // and then showing dataset view.

templates/webapps/galaxy/dataset/tabular_chunked.mako

@@ -16,7 +16,7 @@
             urlArgs: 'v=${app.server_starttime}'
         });
 
-        require([ 'mvc/data' ], function( data ) {
+        require([ 'mvc/dataset/data' ], function( data ) {
             data.createTabularDatasetChunkedView({
                 dataset_config : _.extend( ${ h.dumps( trans.security.encode_dict_ids( dataset.to_dict() ) )}, {
                         first_data_chunk: ${ chunk }