[galaxy-commits] commit/galaxy-central: 3 new changesets

13 Oct 2013

3 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/f938aac3397b/
Changeset:   f938aac3397b
User:        jgoecks
Date:        2013-10-13 22:28:13
Summary:     Trackster: fold content_visible flag into config.
Affected #:  1 file

diff -r 5c10579e88db53ed05013c4314573d3919d72e17 -r f938aac3397bfd12da241b3f60daecf90574d0ec static/scripts/viz/trackster/tracks.js

--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -207,6 +207,11 @@
     this.name = obj_dict.name;
     this.view = view;
     this.container = container;
+    this.drag_handle_class = obj_dict.drag_handle_class;
+    this.is_overview = false;
+    this.action_icons = {};
+    
+    // Set up drawable configuration.
     this.config = new Config({
         params: this.config_params,
         onchange: this.config_onchange,
@@ -216,12 +221,6 @@
         this.config.on('change:values', this.config_onchange, this);
     }
     this.prefs = this.config.get('values');
-    this.drag_handle_class = obj_dict.drag_handle_class;
-    this.is_overview = false;
-    this.action_icons = {};
-    
-    // FIXME: this should be a saved setting
-    this.content_visible = true;
     
     // Build Drawable HTML and behaviors.
     this.container_div = this.build_container_div();
@@ -258,13 +257,14 @@
         title: "Hide/show content",
         css_class: "toggle",
         on_click_fn: function(drawable) {
-            if ( drawable.content_visible ) {
+            if ( drawable.prefs.content_visible ) {
                 drawable.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");
                 drawable.hide_contents();
-                drawable.content_visible = false;
-            } else {
+                drawable.prefs.content_visible = false;
+            } 
+            else {
                 drawable.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");
-                drawable.content_visible = true;
+                drawable.prefs.content_visible = true;
                 drawable.show_contents();
             }
         }
@@ -296,7 +296,8 @@
 
 extend(Drawable.prototype, {
     config_params: [ 
-            { key: 'name', label: 'Name', type: 'text', default_value: this.name }
+            { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+            { key: 'content_visible', type: 'bool', default_value: true, hidden: true }
     ],
 
     config_onchange: function() {
@@ -310,7 +311,7 @@
     },
 
     can_draw: function() {
-        if (this.enabled && this.content_visible) { 
+        if (this.enabled && this.prefs.content_visible) { 
             return true;
         }
         
@@ -2541,7 +2542,7 @@
         var drag_control = $( "<div class='track-resize'>" );
         // Control shows on hover over track, stays while dragging
         $(track.container_div).hover( function() { 
-            if ( track.content_visible ) {
+            if ( track.prefs.content_visible ) {
                 in_handle = true;
                 drag_control.show(); 
             }
@@ -2831,6 +2832,9 @@
     
     // Add tiles_div, overlay_div to content_div.
     this.tiles_div = $("<div/>").addClass("tiles").appendTo(this.content_div);
+    if (!this.prefs.content_visible) {
+        this.tiles_div.hide();
+    }
     this.overlay_div = $("<div/>").addClass("overlay").appendTo(this.content_div);
     
     if (obj_dict.mode) {
@@ -3808,14 +3812,13 @@
 extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     display_modes: CONTINUOUS_DATA_MODES,
 
-    config_params: [
-            { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+    config_params: _.union( Drawable.prototype.config_params, [
             { key: 'color', label: 'Color', type: 'color', default_value: util.get_random_color() },
             { key: 'min_value', label: 'Min Value', type: 'float', default_value: undefined },
             { key: 'max_value', label: 'Max Value', type: 'float', default_value: undefined },
             { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
             { key: 'height', type: 'int', default_value: 30, hidden: true }
-    ],
+    ] ),
     
     config_onchange: function() {
             this.set_name(this.prefs.name);
@@ -3863,15 +3866,14 @@
 extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     display_modes: ["Heatmap"],
 
-    config_params: [
-        { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+    config_params: _.union( Drawable.prototype.config_params, [
         { key: 'pos_color', label: 'Positive Color', type: 'color', default_value: "#FF8C00" },
         { key: 'neg_color', label: 'Negative Color', type: 'color', default_value: "#4169E1" },
         { key: 'min_value', label: 'Min Value', type: 'float', default_value: -1 },
         { key: 'max_value', label: 'Max Value', type: 'float', default_value: 1 },
         { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
         { key: 'height', type: 'int', default_value: 500, hidden: true }
-    ],
+    ] ),
 
     config_onchange: function() {
         this.set_name(this.prefs.name);
@@ -3908,8 +3910,7 @@
 extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     display_modes: ["Auto", "Coverage", "Dense", "Squish", "Pack"],
 
-    config_params: [
-        { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+    config_params: _.union( Drawable.prototype.config_params, [
         { key: 'block_color', label: 'Block color', type: 'color', default_value: util.get_random_color() },
         { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: util.get_random_color() },
         { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
@@ -3921,7 +3922,7 @@
             options: [ { label: 'Line with arrows', value: 'fishbone' }, { label: 'Arcs', value: 'arcs' } ] },
         { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
         { key: 'height', type: 'int', default_value: 0, hidden: true}
-    ],
+    ] ),
 
     config_onchange: function() {
         this.set_name(this.prefs.name);
@@ -4207,14 +4208,13 @@
 extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
     display_modes: ["Auto", "Coverage", "Dense", "Squish", "Pack"],
 
-    config_params: [
-        { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+    config_params: _.union( Drawable.prototype.config_params, [
         { key: 'color', label: 'Histogram color', type: 'color', default_value: util.get_random_color() },
         { key: 'show_sample_data', label: 'Show sample data', type: 'bool', default_value: true },
         { key: 'show_labels', label: 'Show summary and sample labels', type: 'bool', default_value: true },
         { key: 'summary_height', label: 'Locus summary height', type: 'float', default_value: 20 },
         { key: 'mode', type: 'string', default_value: this.mode, hidden: true }
-    ],
+    ] ),
     
     config_onchange: function() {
         this.set_name(this.prefs.name);
@@ -4352,8 +4352,7 @@
 };
 
 extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype, {
-    config_params: [
-        { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+    config_params: _.union( Drawable.prototype.config_params, [
         { key: 'block_color', label: 'Block and sense strand color', type: 'color', default_value: util.get_random_color() },
         { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: util.get_random_color() },
         { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
@@ -4364,7 +4363,7 @@
         { key: 'min_value', label: 'Histogram minimum', type: 'float', default_value: null, help: 'clear value to set automatically' },
         { key: 'max_value', label: 'Histogram maximum', type: 'float', default_value: null, help: 'clear value to set automatically' },
         { key: 'height', type: 'int', default_value: 0, hidden: true}
-    ],
+    ] ),
 
     config_onchange: function() {
         this.set_name(this.prefs.name);


https://bitbucket.org/galaxy/galaxy-central/commits/ae23a7b44e3e/
Changeset:   ae23a7b44e3e
User:        jgoecks
Date:        2013-10-13 23:00:27
Summary:     Trackster: fold name attribute into object preferences.
Affected #:  2 files

diff -r f938aac3397bfd12da241b3f60daecf90574d0ec -r ae23a7b44e3eb1679cd4befd5f26a0c514649554 lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -1082,7 +1082,6 @@
                 return {
                     "dataset_id": trans.security.decode_id( dataset_dict['id'] ),
                     "hda_ldda": dataset_dict.get('hda_ldda', 'hda'),
-                    "name": track_dict['name'],
                     "track_type": track_dict['track_type'],
                     "prefs": track_dict['prefs'],
                     "mode": track_dict['mode'],
@@ -1101,7 +1100,6 @@
                         drawable = unpack_collection( drawable_json )
                     unpacked_drawables.append( drawable )
                 return {
-                    "name": collection_json.get( 'name', '' ),
                     "obj_type": collection_json[ 'obj_type' ],
                     "drawables": unpacked_drawables,
                     "prefs": collection_json.get( 'prefs' , [] ),
@@ -1192,7 +1190,6 @@
                 return {
                     "track_type": dataset.datatype.track_type,
                     "dataset": trans.security.encode_dict_ids( dataset.to_dict() ),
-                    "name": track_dict['name'],
                     "prefs": prefs,
                     "mode": track_dict.get( 'mode', 'Auto' ),
                     "filters": track_dict.get( 'filters', { 'filters' : track_data_provider.get_filters() } ),
@@ -1208,7 +1205,6 @@
                     else:
                         drawables.append( pack_collection( drawable_dict ) )
                 return {
-                    'name': collection_dict.get( 'name', 'dummy' ),
                     'obj_type': collection_dict[ 'obj_type' ],
                     'drawables': drawables,
                     'prefs': collection_dict.get( 'prefs', [] ),

diff -r f938aac3397bfd12da241b3f60daecf90574d0ec -r ae23a7b44e3eb1679cd4befd5f26a0c514649554 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -204,23 +204,28 @@
 var Drawable = function(view, container, obj_dict) {
     if (!Drawable.id_counter) { Drawable.id_counter = 0; }
     this.id = Drawable.id_counter++;
-    this.name = obj_dict.name;
     this.view = view;
     this.container = container;
     this.drag_handle_class = obj_dict.drag_handle_class;
     this.is_overview = false;
     this.action_icons = {};
     
-    // Set up drawable configuration.
+    // -- Set up drawable configuration. --
+
     this.config = new Config({
         params: this.config_params,
         onchange: this.config_onchange,
         saved_values: obj_dict.prefs
     });
+    this.prefs = this.config.get('values');
+
+    // If there's no saved name, use object name.
+    if (!this.prefs.name) {
+        this.prefs.name = obj_dict.name;
+    }
     if (this.config_onchange) {
         this.config.on('change:values', this.config_onchange, this);
     }
-    this.prefs = this.config.get('values');
     
     // Build Drawable HTML and behaviors.
     this.container_div = this.build_container_div();
@@ -296,7 +301,7 @@
 
 extend(Drawable.prototype, {
     config_params: [ 
-            { key: 'name', label: 'Name', type: 'text', default_value: this.name },
+            { key: 'name', label: 'Name', type: 'text', default_value: '' },
             { key: 'content_visible', type: 'bool', default_value: true, hidden: true }
     ],
 
@@ -332,9 +337,9 @@
      * Set drawable name.
      */ 
     set_name: function(new_name) {
-        this.old_name = this.name;
-        this.name = new_name;
-        this.name_div.text(this.name);
+        this.old_name = this.prefs.name;
+        this.prefs.name = new_name;
+        this.name_div.text(this.prefs.name);
     },
 
     /**
@@ -342,8 +347,8 @@
      */
     revert_name: function() {
         if (this.old_name) {
-            this.name = this.old_name;
-            this.name_div.text(this.name);
+            this.prefs.name = this.old_name;
+            this.name_div.text(this.prefs.name);
         }
     },
 
@@ -473,7 +478,6 @@
             dictified_drawables.push(this.drawables[i].to_dict());
         }
         return {
-            name: this.name,
             prefs: this.prefs,
             obj_type: this.obj_type,
             drawables: dictified_drawables
@@ -669,7 +673,7 @@
     build_header_div: function() {
         var header_div = $("<div/>").addClass("track-header");
         header_div.append($("<div/>").addClass(this.drag_handle_class));
-        this.name_div = $("<div/>").addClass("track-name").text(this.name).appendTo(header_div);
+        this.name_div = $("<div/>").addClass("track-name").text(this.prefs.name).appendTo(header_div);
         return header_div;
     },
 
@@ -830,7 +834,7 @@
      */
     show_composite_track: function() {
         var composite_track = new CompositeTrack(this.view, this.view, {
-            name: this.name,
+            name: this.prefs.name,
             drawables: this.drawables
         });
         var index = this.container.replace_drawable(this, composite_track, true);
@@ -1792,7 +1796,7 @@
         // already in group, add track to group.
         if (current_track.container === view) {
             // Create new group.
-            var group = new DrawableGroup(view, view, { name: this.name });
+            var group = new DrawableGroup(view, view, { name: this.prefs.name });
             
             // Replace track with group.
             var index = current_track.container.replace_drawable(current_track, group, false);
@@ -2512,8 +2516,8 @@
     build_header_div: function() {
         var header_div = $("<div class='track-header'/>");
         if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(header_div); }
-        this.name_div = $("<div/>").addClass("track-name").appendTo(header_div).text(this.name)
-                        .attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() );
+        this.name_div = $("<div/>").addClass("track-name").appendTo(header_div).text(this.prefs.name)
+                        .attr( "id", this.prefs.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() );
         return header_div;
     },
 
@@ -2889,7 +2893,6 @@
     to_dict: function() {
         return {
             track_type: this.get_type(),
-            name: this.name,
             dataset: {
                 id: this.dataset.id,
                 hda_ldda: this.dataset.get('hda_ldda')
@@ -3643,7 +3646,7 @@
     show_group: function() {
         // Create group with individual tracks.
         var group = new DrawableGroup(this.view, this.container, {
-                name: this.name
+                name: this.prefs.name
             }),
             track;
         for (var i = 0; i < this.drawables.length; i++) {


https://bitbucket.org/galaxy/galaxy-central/commits/7781a13a9ba0/
Changeset:   7781a13a9ba0
User:        jgoecks
Date:        2013-10-13 23:09:39
Summary:     Trackster: prevent inadvertent keyboard navigation when configuring track.
Affected #:  1 file

diff -r ae23a7b44e3eb1679cd4befd5f26a0c514649554 -r 7781a13a9ba0adf43cba0b1949fa84fd074c5323 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -1986,7 +1986,11 @@
         //
 
         var track_config = this.model;
-        var container = $("<div />");
+
+        // Prevent propagation of keydown events to viz to avoid inadvertent navigation.
+        var container = $("<div/>").keydown(function(e) {
+            e.stopPropagation();
+        });
         var param;
         // Function to process parameters recursively
         function handle_params( params, container ) {

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: 3 new changesets

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