Merge branch 'dev' of https://github.com/Airistotal/galaxy into Repor…

…ts_homepage

Conflicts:
	client/galaxy/style/less/base.less
	static/style/blue/base.css

client/galaxy/scripts/mvc/form/form-select-content.js

@@ -2,9 +2,6 @@
 define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs', 'mvc/tools/tools-template'],
         function(Utils, Ui, Tabs, ToolTemplate) {
 
-// track current history elements
-history = {};
-
 // hda/hdca content selector ui element
 var View = Backbone.View.extend({
     // initialize
@@ -13,6 +10,10 @@ var View = Backbone.View.extend({
         this.app = app;
         this.options = options;
 
+        // track current history elements
+        this.history = {};
+
+
         // link this
         var self = this;
 
@@ -197,7 +198,7 @@ var View = Backbone.View.extend({
                         value: item.id
                     });
                     // backup to local history
-                    history[item.id + '_' + item.src] = item;
+                    self.history[item.id + '_' + item.src] = item;
                 }
                 // update field
                 field.update(select_options);
@@ -272,7 +273,7 @@ var View = Backbone.View.extend({
 
         // append to dataset ids
         for (var i in id_list) {
-            var details = history[id_list[i] + '_' + this.list[this.current].type];
+            var details = this.history[id_list[i] + '_' + this.list[this.current].type];
             if (details) {
                 result.values.push(details);
             } else {
@@ -315,7 +316,7 @@ var View = Backbone.View.extend({
     /** Assists in identifying the batch mode */
     _batch: function() {
         if (this.current == 'collection') {
-            var hdca = history[this._select().value() + '_hdca'];
+            var hdca = this.history[this._select().value() + '_hdca'];
             if (hdca && hdca.map_over_type) {
                 return true;
             }

client/galaxy/scripts/utils/query-string-parsing.js

@@ -0,0 +1,21 @@
+define([], function(){
+// ============================================================================
+function get( key, queryString ){
+    queryString = queryString || window.location.search.substr( 1 );
+    var keyRegex = new RegExp( key + '=([^&#$]+)' ),
+        matches = queryString.match( keyRegex );
+    if( !matches || !matches.length ){
+        return undefined;
+    }
+    matches = matches.splice( 1 );
+    if( matches.length === 1 ){
+        return matches[0];
+    }
+    return matches;
+}
+
+// ============================================================================
+    return {
+        get : get
+    };
+});

client/galaxy/scripts/viz/trackster.js

@@ -31,8 +31,8 @@ require(
 });
 
 // trackster viewer
-define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization", "mvc/ui/icon-button" ],
-        function(_, base, tracks, visualization, mod_icon_btn) {
+define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization", "mvc/ui/icon-button", "utils/query-string-parsing" ],
+        function(_, base, tracks, visualization, mod_icon_btn, query_string ) {
 /**
  * User interface controls for trackster
  */
@@ -401,11 +401,84 @@ var TracksterView = Backbone.View.extend(
         // hide right panel
         force_right_panel("hide");
 
+
         // check if id is available
-        if (galaxy_config.app.id)
+        if (galaxy_config.app.id){
             this.view_existing();
-        else
+        } else if( query_string.get( 'dataset_id' ) ){
+            this.choose_existing_or_new();
+        } else {
             this.view_new();
+        }
+    },
+
+    choose_existing_or_new : function () {
+        var self = this;
+        var dbkey = query_string.get( 'dbkey' ),
+            listTracksParams = {},
+            dataset_params = {
+                dbkey       : dbkey,
+                dataset_id  : query_string.get( 'dataset_id' ),
+                hda_ldda    : query_string.get( 'hda_ldda' )
+            };
+        if (dbkey){
+            listTracksParams[ 'f-dbkey' ] = dbkey;
+        }
+        $.ajax({
+            url: galaxy_config.root + 'visualization/list_tracks?' + $.param( listTracksParams ),
+            dataType: "html",
+            error: function() { alert( "Could not add this dataset to browser." ); },
+
+            success: function(table_html) {
+                console.debug( 'success' );
+                function view_in_saved(){
+                    // Show new modal with saved visualizations.
+                    Galaxy.modal.show({
+                        title : "Add Data to Saved Visualization",
+                        body : table_html,
+                        buttons : {
+                            "Cancel": function() {
+                                // go back to the first choice
+                                show_choice();
+                            },
+                            "Add to visualization": function() {
+                                $(parent.document).find('input[name=id]:checked').each(function() {
+                                    var vis_id = $(this).val();
+                                    dataset_params.id = vis_id;
+                                    window.location = galaxy_config.root + "visualization/trackster?" + $.param(dataset_params);
+                                });
+                            }
+                        }
+                    });
+                }
+                function show_choice(){
+                    Galaxy.modal.show({
+                        title : "View Data in a New or Saved Visualization?",
+                        // either have text in here or have to remove body and the header/footer margins
+                        body  : (
+                            // TODO: yay. inline styles. thanks, galaxy
+                            '<p><ul style="list-style: disc inside none">You can add this dataset as:' +
+                                "<li>a new track to one of your existing, saved Trackster " +
+                                "sessions if they share the genome build: <b>" + dbkey + "</b></li>" +
+                                "<li>or create a new session with this dataset as the only track</li>" +
+                            "</ul></p>"
+                        ),
+                        buttons : {
+                            "Cancel": function() {
+                                window.location = galaxy_config.root + "visualization/list";
+                            },
+                            "View in saved visualization": function() {
+                                view_in_saved();
+                            },
+                            "View in new visualization": function() {
+                                self.view_new();
+                            }
+                        }
+                    });
+                }
+                show_choice();
+            }
+        });
     },
 
     // view
@@ -459,7 +532,8 @@ var TracksterView = Backbone.View.extend(
                 });
 
                 // select default
-                if (galaxy_config.app.default_dbkey) {
+                var dbkeys_in_genomes = response.map( function( r ){ return r[1]; });
+                if (galaxy_config.app.default_dbkey && _.contains(dbkeys_in_genomes,galaxy_config.app.default_dbkey)) {
                     $("#new-dbkey").val( galaxy_config.app.default_dbkey );
                 }
 

client/galaxy/style/less/base.less

@@ -4,6 +4,9 @@
 // Galaxy specific variables
 @import "galaxy_variables.less";
 
+// Galaxy Report Webapp
+@import "reports";
+
 @white: #fff;
 @black: #000;
 
@@ -134,28 +137,6 @@ body  {
 #left-border  {
     left: 250px;
 }
-.reports-panel-container {
-    position: absolute;
-    top: @panel_header_height;
-    bottom: 10px;
-    overflow: scroll;
-    width: 100%;
-    padding: 10px;
-}
-#reports_home {
-    content: url("../images/reports_webapp/home-icon-hov.png");
-    position: relative;
-    top: -6px;
-    left: 6px;
-    width: 26px;
-    float: right;
-}
-#reports_home:hover {
-    content: url("../images/reports_webapp/home-icon-hov.png");
-}
-#reports_home:active {
-    content: url("../images/reports_webapp/home-icon-active.png");
-}
 #center  {
     left:250 + @border-default-color_padding;
     right: 250 + @border-default-color_padding;
@@ -1716,84 +1697,3 @@ div.toolTitleNoSection
 #for_bears {
     display: none;
 }
-
-// ================================================================Reports Webapp Styles
-.chart {
-    cursor: zoom-in;
-    position: relative;
-    z-index: 2;
-}
-
-.chart rect {
-    fill: steelblue;
-    shape-rendering: preserveAspectRatio;
-}
-
-.chart text {
-    fill: black;
-    font: 7px sans-serif;
-    text-anchor: end;
-}
-
-.tick text {
-    fill: black;
-    font-family: Arial, sans-serif;
-    font-size: 7px;
-    text-anchor: end;
-}
-
-.axis path, .axis line {
-    fill: none;
-    stroke: #000;
-    shape-rendering: preserveAspectRatio;
-}
-
-.x_path {
-    stroke: #000;
-    stroke-width: 1;
-}
-
-.chart .title {
-    fill: black;
-    font-size: 15px;
-    font-family: "Lucida Grande",verdana,arial,helvetica,sans-serif;
-    font-weight: 800;
-    line-height: 1.1;
-}
-
-.chart .ax_title {
-    fill: black;
-}
-
-.hr_container, .dy_container {
-    position: relative;
-    z-index: 2;
-    display: inline-block;
-    vertical-align: top;
-}
-
-.charts {
-    margin-top: 10px;
-    margin-left: 0;
-    margin-right: 0;
-    text-align: center;
-    position: relative;
-    display: block;
-    overflow-x: auto;
-    overflow-y: hidden;
-    white-space: nowrap
-}
-
-.trim {
-    position:relative;
-    height:10px;
-    top: 50px;
-    background: #ebd9b2;
-    color: #000;
-    border-top: solid #d6b161 1px;
-    border-bottom: solid #d6b161 1px;
-}
-
-.tool_tip text {
-    fill: white;
-}