[galaxy-commits] commit/galaxy-central: jgoecks: Trackster: (1) save and restore track groups; (2) support nested groups; (3) make View a DrawableCollection.

24 Sep 2011

1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/61b82db00101/
changeset:   61b82db00101
user:        jgoecks
date:        2011-09-24 16:45:34
summary:     Trackster: (1) save and restore track groups; (2) support nested groups; (3) make View a DrawableCollection.
affected #:  5 files (-1 bytes)

--- a/lib/galaxy/web/base/controller.py	Fri Sep 23 14:27:29 2011 -0400
+++ b/lib/galaxy/web/base/controller.py	Sat Sep 24 10:45:34 2011 -0400
@@ -310,40 +310,62 @@
config = None
         if visualization.type == 'trackster':
-            # Trackster config; taken from tracks/browser
+            # Unpack Trackster config.
             latest_revision = visualization.latest_revision
             bookmarks = latest_revision.config.get( 'bookmarks', [] )
-            tracks = []
+            
+            def pack_track( track_dict ):
+                dataset_id = track_dict['dataset_id']
+                hda_ldda = track_dict.get('hda_ldda', 'hda')
+                if hda_ldda == "hda":
+                    dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True )
+                else:
+                    dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id(dataset_id) )
+
+                try:
+                    prefs = track_dict['prefs']
+                except KeyError:
+                    prefs = {}
+
+                track_type, _ = dataset.datatype.get_track_type()
+                track_data_provider_class = get_data_provider( original_dataset=dataset )
+                track_data_provider = track_data_provider_class( original_dataset=dataset )
+                
+                return {
+                    "track_type": track_type,
+                    "name": track_dict['name'],
+                    "hda_ldda": track_dict.get("hda_ldda", "hda"),
+                    "dataset_id": trans.security.encode_id( dataset.id ),
+                    "prefs": prefs,
+                    "filters": track_data_provider.get_filters(),
+                    "tool": get_tool_def( trans, dataset )
+                }
+            
+            def pack_collection( collection_dict ):
+                drawables = []
+                for drawable_dict in collection_dict[ 'drawables' ]:
+                    if 'track_type' in drawable_dict:
+                        drawables.append( pack_track( drawable_dict ) )
+                    else:
+                        drawables.append( pack_collection( drawable_dict ) )
+                return {
+                    'obj_type': collection_dict[ 'obj_type' ],
+                    'drawables': drawables
+                }
# Set tracks.
+            tracks = []
             if 'tracks' in latest_revision.config:
-                for t in visualization.latest_revision.config['tracks']:
-                    dataset_id = t['dataset_id']
-                    hda_ldda = t.get('hda_ldda', 'hda')
-                    if hda_ldda == "hda":
-                        dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True )
+                # Legacy code.
+                for track_dict in visualization.latest_revision.config[ 'tracks' ]:
+                    tracks.append( pack_track( track_dict ) )
+            elif 'view' in latest_revision.config:
+                for drawable_dict in visualization.latest_revision.config[ 'view' ][ 'drawables' ]:
+                    if 'track_type' in drawable_dict:
+                        tracks.append( pack_track( drawable_dict ) )
                     else:
-                        dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id(dataset_id) )
-
-                    try:
-                        prefs = t['prefs']
-                    except KeyError:
-                        prefs = {}
-
-                    track_type, _ = dataset.datatype.get_track_type()
-                    track_data_provider_class = get_data_provider( original_dataset=dataset )
-                    track_data_provider = track_data_provider_class( original_dataset=dataset )
-
-                    tracks.append( {
-                        "track_type": track_type,
-                        "name": t['name'],
-                        "hda_ldda": t.get("hda_ldda", "hda"),
-                        "dataset_id": trans.security.encode_id( dataset.id ),
-                        "prefs": prefs,
-                        "filters": track_data_provider.get_filters(),
-                        "tool": get_tool_def( trans, dataset )
-                    } )
-
+                        tracks.append( pack_collection( drawable_dict ) )
+                
             config = { "title": visualization.title, "vis_id": trans.security.encode_id( visualization.id ),
                         "tracks": tracks, "bookmarks": bookmarks, "chrom": "", "dbkey": visualization.dbkey }
--- a/lib/galaxy/web/controllers/tracks.py	Fri Sep 23 14:27:29 2011 -0400
+++ b/lib/galaxy/web/controllers/tracks.py	Sat Sep 24 10:45:34 2011 -0400
@@ -615,19 +615,40 @@
         vis_rev.visualization = vis
         vis_rev.title = vis.title
         vis_rev.dbkey = dbkey
-        # Tracks from payload
-        tracks = []
-        # TODO: why go through the trouble of unpacking config only to repack and
-        # put in database? How about sticking JSON directly into database?
-        for track in decoded_payload['tracks']:
-            tracks.append( {    "dataset_id": track['dataset_id'],
-                                "hda_ldda": track.get('hda_ldda', "hda"),
-                                "name": track['name'],
-                                "track_type": track['track_type'],
-                                "prefs": track['prefs']
-            } )
-        bookmarks = decoded_payload[ 'bookmarks' ]
-        vis_rev.config = { "tracks": tracks, "bookmarks": bookmarks }
+        
+        def unpack_track( track_json ):
+            """ Unpack a track from its json. """
+            return {
+                "dataset_id": track_json['dataset_id'],
+                "hda_ldda": track_json.get('hda_ldda', "hda"),
+                "name": track_json['name'],
+                "track_type": track_json['track_type'],
+                "prefs": track_json['prefs']
+            }
+        
+        def unpack_collection( collection_json ):
+            """ Unpack a collection from its json. """
+            unpacked_drawables = []
+            drawables = collection_json[ 'drawables' ]
+            for drawable_json in drawables:
+                if 'track_type' in drawable_json:
+                    drawable = unpack_track( drawable_json )
+                else:
+                    drawable = unpack_collection( drawable_json )
+                unpacked_drawables.append( drawable )
+            return {
+                "obj_type": collection_json[ 'obj_type' ],
+                "drawables": unpacked_drawables
+            }
+
+        # TODO: unpack and validate bookmarks:
+        def unpack_bookmarks( bookmarks_json ):
+            return 
+        
+        # Unpack and validate view content.
+        view_content = unpack_collection( decoded_payload[ 'view' ] )
+        bookmarks = unpack_bookmarks( decoded_payload[ 'bookmarks' ] )
+        vis_rev.config = { "view": view_content, "bookmarks": bookmarks }
         # Viewport from payload
         if 'viewport' in decoded_payload:
             chrom = decoded_payload['viewport']['chrom']
--- a/static/scripts/trackster.js	Fri Sep 23 14:27:29 2011 -0400
+++ b/static/scripts/trackster.js	Sat Sep 24 10:45:34 2011 -0400
@@ -213,7 +213,7 @@
             }            
         }
-        // Handle dragging into container.
+        // Handle dragging into container. Child is appended to container's content_div.
         container = null;
         for ( i = 0; i < children.length; i++ ) {
             child = $(children.get(i));
@@ -229,8 +229,10 @@
                 else {
                     child.find(".content-div").append(this);
                 }
-                // Update containers.
-                this_obj.container.remove_drawable(this_obj);
+                // Update containers. Object may not have container if it is being moved quickly.
+                if (this_obj.container) {
+                    this_obj.container.remove_drawable(this_obj);                    
+                }
                 html_elt_js_obj_dict[child.attr("id")].add_drawable(this_obj);
                 return;
             }
@@ -250,7 +252,6 @@
         if ( i === children.length ) {
             if ( this !== children.get(i - 1) ) {
                 parent.append(this);
-                // Update container.
                 html_elt_js_obj_dict[parent.attr("id")].move_drawable(this_obj, i);
             }
         }
@@ -574,32 +575,58 @@
 /**
  * Base interface for all drawable objects.
  */
-var Drawable = function(name, view, parent_element, container) {
+var Drawable = function(name, view, parent_element, drag_handle_class, container) {
     this.name = name;
     this.view = view;
     this.parent_element = parent_element;
+    this.drag_handle_class = drag_handle_class;
     this.container = container;
 };
+Drawable.prototype.init = function() {};
 Drawable.prototype.request_draw = function() {};
-Drawable.prototype.draw = function() {};
+Drawable.prototype._draw = function() {};
+Drawable.prototype.to_json = function() {};
/**
  * A collection of drawable objects.
  */
-var DrawableCollection = function(name, view, parent_element, container) {
+var DrawableCollection = function(obj_type, name, view, parent_element, container) {
     Drawable.call(this, name, view, parent_element, container);
// Attribute init.
+    this.obj_type = obj_type;
     this.drawables = [];
 };
 extend(DrawableCollection.prototype, Drawable.prototype, {
+    /**
+     * Init each drawable in the collection.
+     */
+    init: function() {
+        for (var i = 0; i < this.drawables.length; i++) {
+            this.drawables[i].init();
+        }
+    },    
+    /**
+     * Draw each drawable in the collection.
+     */
+    _draw: function() {
+        for (var i = 0; i < this.drawables.length; i++) {
+            this.drawables[i]._draw();
+        }
+    },
+    /**
+     * Returns jsonified representation of collection.
+     */
     to_json: function() {
-        // For now, just return list of drawables in collection.
-        var json_obj = [];
+        var jsonified_drawables = [];
         for (var i = 0; i < this.drawables.length; i++) {
-            
+            jsonified_drawables.push(this.drawables[i].to_json());
         }
+        return { 
+            obj_type: this.obj_type,
+            drawables: jsonified_drawables
+            };
     },
     /**
      * Add a drawable to the end of the collection.
@@ -652,25 +679,30 @@
  * A group of drawables that are moveable, visible.
  */
 var DrawableGroup = function(name, view, parent_element, container) {
-    DrawableCollection.call(this, name, view, parent_element, container);
-    
-    this.drag_handle_class = "group-handle";
+    DrawableCollection.call(this, "DrawableGroup", name, view, parent_element, "group-handle", container);
// HTML elements.
-    this.container_div = $("<div/>").addClass("group").appendTo(this.parent_element);
+    if (!DrawableGroup.id_counter) { DrawableGroup.id_counter = 0; }
+    var group_id = DrawableGroup.id_counter++
+    this.container_div = $("<div/>").addClass("group").attr("id", "group_" + group_id).appendTo(this.parent_element);
     this.container_div.append($("<div/>").addClass(this.drag_handle_class));
     this.name_div = $("<div/>").addClass("group-name").text(this.name).appendTo(this.container_div);
-    this.content_div = $("<div/>").addClass("content-div").appendTo(this.container_div);
+    this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + group_id + "_content_div").appendTo(this.container_div);
+    
+    // Set up containers/moving for group: register both container and content div as container
+    // because both are used as containers. Group can be moved.
     is_container(this.container_div, this);
+    is_container(this.content_div, this);
+    moveable(this.container_div, this.drag_handle_class, ".group", this);
 };
-extend(DrawableGroup.prototype, DrawableCollection.prototype, Drawable.prototype);
+extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype);
/**
  * View object manages complete viz view, including tracks and user interactions.
  */
 var View = function(container, title, vis_id, dbkey, callback) {
-    DrawableCollection.call(this);
+    DrawableCollection.call(this, "View");
     this.container = container;
     this.chrom = null;
     this.vis_id = vis_id;
@@ -682,8 +714,6 @@
     this.tracks_to_be_redrawn = [];
     this.max_low = 0;
     this.max_high = 0;
-    this.num_tracks = 0;
-    this.track_id_counter = 0;
     this.zoom_factor = 3;
     this.min_separation = 30;
     this.has_changes = false;
@@ -870,22 +900,6 @@
         $(window).trigger("resize");
         this.update_intro_div();
     },
-    /** JSONify view. */
-    to_json: function() {
-        var 
-            view = this,
-            jsonified_drawables = [];
-        this.viewport_container.children(".track,.group").each(function() {
-            // Get object ID.
-            var id = $(this).attr("id");
-            id = parseInt( id.slice(id.lastIndexOf("_") + 1) );
-            
-            // JSONify drawable.
-            jsonified_drawables.push(view.tracks[id].to_json());
-        });
-        
-        return jsonified_drawables;
-    },
     /** Add or remove intro div depending on view state. */
     update_intro_div: function() {
         if (this.num_tracks === 0) {
@@ -1039,17 +1053,11 @@
         view.request_redraw();
     },
     /**
-     * Add a track to the view.
+     * Add a drawable to the view.
      */
-    add_track: function(track) {
-        track.view = this;
-        track.track_id = this.track_id_counter;
-        this.tracks.push(track);
-        if (track.init) { track.init(); }
-        track.container_div.attr('id', 'track_' + track.track_id);
-        moveable(track.container_div, track.drag_handle_class, ".group", track);
-        this.track_id_counter += 1;
-        this.num_tracks += 1;
+    add_drawable: function(drawable) {
+        DrawableCollection.prototype.add_drawable.call(this, drawable);
+        if (drawable.init) { drawable.init(); }
         this.has_changes = true;
         this.update_intro_div();
     },
@@ -1058,17 +1066,18 @@
         this.label_tracks.push(label_track);
     },
     /**
-     * Remove a track from the view.
+     * Remove drawable from the view.
      */
-    remove_track: function(track) {
-        this.has_changes = true;
-        this.tracks.splice(this.tracks.indexOf(track), 1);
-        this.num_tracks -= 1;
-        var view = this;
-        track.container_div.fadeOut('slow', function() { 
-            $(this).remove();
-            view.update_intro_div(); 
-        });
+    remove_drawable: function(drawable, hide) {
+        DrawableCollection.prototype.remove_drawable.call(this, drawable);
+        if (hide) {
+            var view = this;
+            drawable.container_div.fadeOut('slow', function() { 
+                $(this).remove();
+                view.update_intro_div(); 
+            });
+            this.has_changes = true;
+        }
     },
     reset: function() {
         this.low = this.max_low;
@@ -1161,7 +1170,7 @@
                 track = this.tracks_to_be_redrawn[i][0];
                 force = this.tracks_to_be_redrawn[i][1];
                 clear_after = this.tracks_to_be_redrawn[i][2];
-                if (track && track.enabled) {
+                if (track) {
                     track._draw(force, clear_after);
                 }
             }
@@ -1310,9 +1319,9 @@
     run_on_region_button.click( function() {
         // Create group for track + new tracks and put track in group.
         var 
-            parent_elt = this.track.parent_element,
-            new_group = new DrawableCollection("New Group", parent_elt);
-            //this.track.view.add_track(new_group);
+            parent_elt = this.track.parent_element;
+            //new_group = new DrawableCollection("New Group", parent_elt);
+            //this.track.view.add_drawable(new_group);
// Run tool to create new track.
@@ -1399,7 +1408,7 @@
             new_track = new ToolDataFeatureTrack(track_name, view, current_track.hda_ldda, undefined, {}, {}, current_track);  
             new_track.change_mode(current_track.mode);
         }
-        this.track.view.add_track(new_track);
+        this.track.view.add_drawable(new_track);
         new_track.content_div.text("Starting job.");
// Run tool.
@@ -2007,7 +2016,7 @@
  */
 var Track = function(name, view, parent_element, data_url, data_query_wait) {
     // For now, track's container is always view.
-    Drawable.call(this, name, view, parent_element, view);
+    Drawable.call(this, name, view, parent_element, "draghandle", view);
//
     // Attribute init.
@@ -2016,12 +2025,12 @@
     this.data_url_extra_params = {}
     this.data_query_wait = (data_query_wait ? data_query_wait : DEFAULT_DATA_QUERY_WAIT);
     this.dataset_check_url = converted_datasets_state_url;
-    this.drag_handle_class = "draghandle";
//
     // Create HTML element structure for track.
     //
-    this.container_div = $("<div />").addClass('track').css("position", "relative");
+    if (!Track.id_counter) { Track.id_counter = 0; }
+    this.container_div = $("<div />").addClass('track').attr("id", "track_" + Track.id_counter++).css("position", "relative");
     if (!this.hidden) {
         this.header_div = $("<div class='track-header' />").appendTo(this.container_div);
         if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div); }
@@ -2154,6 +2163,9 @@
 var TiledTrack = function(filters_list, tool_dict, parent_track) {
     var track = this,
         view = track.view;
+        
+    // Make track moveable.
+    moveable(track.container_div, track.drag_handle_class, ".group", track);
// Attribute init.
     this.filters_manager = (filters_list !== undefined ? new FiltersManager(this, filters_list) : undefined);
@@ -2327,8 +2339,8 @@
         // Remove option.
         //
         track_dropdown.Remove = function() {
-            view.remove_track(track);
-            if (parent_obj.num_tracks === 0) {
+            view.remove_drawable(track, true);
+            if (view.num_tracks === 0) {
                 $("#no-tracks").show();
             }
         };
@@ -2401,6 +2413,8 @@
      * can manage drawing.
      */
     _draw: function(force, clear_after) {
+        if (!this.enabled) { return; }
+        
         // HACK: ReferenceTrack can draw without dataset ID, but other tracks cannot.
         if ( !(this instanceof ReferenceTrack) && (!this.dataset_id) ) { return; }
--- a/static/scripts/trackster_ui.js	Fri Sep 23 14:27:29 2011 -0400
+++ b/static/scripts/trackster_ui.js	Sat Sep 24 10:45:34 2011 -0400
@@ -29,20 +29,54 @@
 };
/**
- * Types of tracks that can be added to a view.
+ * Objects that can be added to a view.
  */
-var addable_track_types = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack };
+var addable_objects = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack, "DrawableGroup": DrawableGroup };
/**
  * Decode a track from a dictionary.
  */
 var track_from_dict = function(track_dict) {
-    return new addable_track_types[track_dict.track_type]( 
+    return new addable_objects[track_dict.track_type]( 
                         track_dict.name, view, track_dict.hda_ldda, track_dict.dataset_id,
                         track_dict.prefs, track_dict.filters, track_dict.tool);
 };
/**
+ * Decode a drawable collection from a dictionary.
+ */
+var drawable_collection_from_dict = function(collection_dict) {
+    var collection = new addable_objects[collection_dict.obj_type]("New Group", view, view.viewport_container, view);
+    for (var i = 0; i < collection_dict.drawables.length; i++) {
+        var 
+            drawable_dict = collection_dict.drawables[i],
+            drawable;
+        if (drawable_dict['track_type']) {
+            drawable = track_from_dict(drawable_dict);
+        }
+        else {
+            drawable = drawable_collection_from_dict(drawable_dict);
+        }
+        collection.add_drawable(drawable);
+        // HACK: move track from view to collection's content_div. 
+        // FIX: Tracks should be able to be be added to arbitrary containers; 
+        // every moveable should have a container_div, and every container should have 
+        // a content_div (though perhaps name changes are needed).
+        collection.content_div.append(drawable.container_div);
+    }
+    return collection;
+};
+
+/**
+ * Decode a drawable from a dict.
+ */
+var drawable_from_dict = function(drawable_dict) {
+    return (drawable_dict['track_type'] ? 
+            track_from_dict(drawable_dict) :
+            drawable_collection_from_dict(drawable_dict));
+};
+
+/**
  * Create a complete Trackster visualization. Returns view.
  */
 var create_visualization = function(parent_elt, title, id, dbkey, callback, tracks_config, bookmarks_config) {
@@ -51,21 +85,12 @@
     view = new View(parent_elt, title, id, dbkey, callback);
     view.editor = true;
-    // Add tracks to view.
+    // Add drawables to view.
     if (tracks_config) {
-        var track_config, track, parent_track, parent_obj;
+        var track_config;
         for (var i = 0; i < tracks_config.length; i++) {
             track_config = tracks_config[i];
-            track = track_from_dict(track_config);
-            parent_obj = view;
-            if (track_config.is_child) {
-                parent_obj = parent_track;
-            }
-            else {
-                // New parent track is this track.
-                parent_track = track;
-            }
-            parent_obj.add_track(track);
+            view.add_drawable( drawable_from_dict(track_config) );
         }
     }
--- a/templates/tracks/browser.mako	Fri Sep 23 14:27:29 2011 -0400
+++ b/templates/tracks/browser.mako	Sat Sep 24 10:45:34 2011 -0400
@@ -101,7 +101,7 @@
                                                    [ arguments[0] ]
                                                    );
                                  for (var i= 0; i < track_defs.length; i++) {
-                                     view.add_track( track_from_dict(track_defs[i]) ); 
+                                     view.add_drawable( track_from_dict(track_defs[i]) ); 
                                  }
                             });
                             hide_modal();
@@ -186,7 +186,7 @@
                     url: "${h.url_for( action='add_track_async' )}",
                     data: { hda_id: "${add_dataset}" },
                     dataType: "json",
-                    success: function(track_data) { view.add_track( track_from_dict(track_data) ) }
+                    success: function(track_data) { view.add_drawable( track_from_dict(track_data) ) }
                 });
%endif
@@ -199,15 +199,12 @@
                 "Add Tracks": add_tracks,
                 "Add Group": function() {
                     var group = new DrawableGroup("New Group", view, view.viewport_container, view);
-                    view.add_track(group);
+                    view.add_drawable(group);
                 },
                 "Save": function() {
                     // Show saving dialog box
                     show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>");
-                    
-                    // Save tracks.
-                    var saved_tracks = view.to_json();
-                    
+                                        
                     // Save bookmarks.
                     var bookmarks = [];
                     $(".bookmark").each(function() { 
@@ -219,7 +216,7 @@
var overview_track_name = (view.overview_track ? view.overview_track.name : null);
                     var payload = { 
-                        'tracks': saved_tracks, 
+                        'view': view.to_json(), 
                         'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name },
                         'bookmarks': bookmarks
                     };
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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[galaxy-commits] commit/galaxy-central: jgoecks: Trackster: (1) save and restore track groups; (2) support nested groups; (3) make View a DrawableCollection.