[galaxy-commits] commit/galaxy-central: jgoecks: Make it simpler to save/restore visualizations and enable saving/restoring of paramamonster visualizations.

28 Jun 2012

1 new commit in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/603e4ed98fa7/
changeset:   603e4ed98fa7
user:        jgoecks
date:        2012-06-28 21:48:50
summary:     Make it simpler to save/restore visualizations and enable saving/restoring of paramamonster visualizations.
affected #:  9 files

diff -r 063a1d690724b3485f41c620f664f11c7390ceef -r 603e4ed98fa7cb3b3c47f71b3b77bedd67f50fea lib/galaxy/web/base/controller.py

--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -353,8 +353,6 @@
     
     viz_types = [ "trackster", "circster" ]
 
-    len_files = None
-            
     def create_visualization( self, trans, title, slug, type, dbkey, annotation=None, config={} ):
         """ Create visualiation and first revision. """
         visualization = self._create_visualization( trans, title, type, dbkey, slug, annotation )
@@ -434,9 +432,9 @@
                 end = config['viewport']['end']
                 overview = config['viewport']['overview']
                 vis_rev.config[ "viewport" ] = { 'chrom': chrom, 'start': start, 'end': end, 'overview': overview }
-        elif type == 'circster':
-            # TODO.
-            pass
+        else:
+            # Default action is to save the config as is with no validation.
+            vis_rev.config = config
 
         vis.latest_revision = vis_rev
         session.add( vis_rev )
@@ -543,6 +541,10 @@
 
             if 'viewport' in latest_revision.config:
                 config['viewport'] = latest_revision.config['viewport']
+        else:
+            # Default action is to return config unaltered.
+            latest_revision = visualization.latest_revision
+            config = latest_revision.config
 
         return config
         


diff -r 063a1d690724b3485f41c620f664f11c7390ceef -r 603e4ed98fa7cb3b3c47f71b3b77bedd67f50fea lib/galaxy/web/controllers/tracks.py
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -16,7 +16,7 @@
 from galaxy.model import NoConverterException, ConverterDependencyException
 from galaxy.visualization.tracks.data_providers import *
 from galaxy.visualization.genomes import decode_dbkey, Genomes
-from galaxy.visualization.tracks.visual_analytics import get_tool_def, get_dataset_job
+from galaxy.visualization.tracks.visual_analytics import get_dataset_job
 
 
 class NameColumn( grids.TextColumn ):
@@ -471,12 +471,42 @@
                     
     @web.expose
     @web.require_login( "use Galaxy visualizations", use_panels=True )
-    def paramamonster( self, trans, hda_ldda, dataset_id ):
-        # Get dataset.
-        dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id )
+    def paramamonster( self, trans, id=None, hda_ldda=None, dataset_id=None, regions=None ):
+        if id:
+            # Loading a shared visualization.
+            viz = self.get_visualization( trans, id )
+            viz_config = self.get_visualization_config( trans, viz )
+            dataset = self.get_dataset( trans, viz_config[ 'dataset_id' ] )
+        else:
+            # Loading new visualization.
+            dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id )
+            job = get_dataset_job( dataset )
+            viz_config = {
+                'dataset_id': dataset_id,
+                'tool_id': job.tool_id,
+                'regions': regions
+            }
+
+        viz_config[ 'regions' ] = [
+            {
+                'chrom': 'chr19',
+                'start': '10000',
+                'end': '26000'
+            },
+            {
+                'chrom': 'chr19',
+                'start': '150000',
+                'end': '175000'
+            }
+
+        ]
                 
-        return trans.fill_template_mako( "visualization/paramamonster.mako", dataset=dataset,
-                                          tool=self.app.toolbox.tools_by_id[ 'cufflinks' ].to_dict( trans, for_display=True ) )
+        # Add tool, dataset attributes to config based on id.
+        tool = trans.app.toolbox.get_tool( viz_config[ 'tool_id' ] )
+        viz_config[ 'tool' ] = tool.to_dict( trans, for_display=True )
+        viz_config[ 'dataset' ] = dataset.get_api_value()
+
+        return trans.fill_template_mako( "visualization/paramamonster.mako", config=viz_config )
     
     @web.expose
     @web.require_login( "use Galaxy visualizations", use_panels=True )


diff -r 063a1d690724b3485f41c620f664f11c7390ceef -r 603e4ed98fa7cb3b3c47f71b3b77bedd67f50fea lib/galaxy/web/controllers/visualization.py
--- a/lib/galaxy/web/controllers/visualization.py
+++ b/lib/galaxy/web/controllers/visualization.py
@@ -5,14 +5,26 @@
 from galaxy.util.sanitize_html import sanitize_html
 
 class VisualizationListGrid( grids.Grid ):
+    def get_link( item ):
+        """
+        Returns dictionary used to create item link.
+        """
+        controller = "tracks"
+        if item.type == "trackster":
+            action = "browser"
+        elif item.type == "paramamonster":
+            action = "paramamonster"
+        elif item.type == "circster":
+            action = "circster"
+        return dict( controller=controller, action=action, id=item.id )
+
     # Grid definition
     title = "Saved Visualizations"
     model_class = model.Visualization
     default_sort_key = "-update_time"
     default_filter = dict( title="All", deleted="False", tags="All", sharing="All" )
     columns = [
-        grids.TextColumn( "Title", key="title", attach_popup=True,
-                         link=( lambda item: dict( controller="tracks", action="browser", id=item.id ) ) ),
+        grids.TextColumn( "Title", key="title", attach_popup=True, link=get_link ),
         grids.TextColumn( "Type", key="type" ),
         grids.TextColumn( "Dbkey", key="dbkey" ),
         grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ),
@@ -383,12 +395,20 @@
                 template="visualization/create.mako" )
                 
     @web.json
-    def save( self, trans, config, type, id=None, title=None, dbkey=None, annotation=None ):
+    def save( self, trans, vis_json=None, type=None, id=None, title=None, dbkey=None, annotation=None ):
         """
         Save a visualization; if visualization does not have an ID, a new 
         visualization is created. Returns JSON of visualization.
         """
-        return self.save_visualization( trans, from_json_string( config ), type, id, title, dbkey, annotation )
+
+        # Get visualization attributes from kwargs or from config.
+        vis_config = from_json_string( vis_json )
+        vis_type = type or vis_config[ 'type' ]
+        vis_id = id or vis_config.get( 'id', None )
+        vis_title = title or vis_config.get( 'title', None )
+        vis_dbkey = dbkey or vis_config.get( 'dbkey', None )
+        vis_annotation = annotation or vis_config.get( 'annotation', None )
+        return self.save_visualization( trans, vis_config, vis_type, vis_id, vis_title, vis_dbkey, vis_annotation )
         
     @web.expose
     @web.require_login( "edit visualizations" )


diff -r 063a1d690724b3485f41c620f664f11c7390ceef -r 603e4ed98fa7cb3b3c47f71b3b77bedd67f50fea static/scripts/mvc/data.js
--- a/static/scripts/mvc/data.js
+++ b/static/scripts/mvc/data.js
@@ -2,7 +2,7 @@
  * A dataset. In Galaxy, datasets are associated with a history, so
  * this object is also known as a HistoryDatasetAssociation.
  */
-var Dataset = Backbone.Model.extend({
+var Dataset = Backbone.RelationalModel.extend({
     defaults: {
         id: "",
         type: "",


diff -r 063a1d690724b3485f41c620f664f11c7390ceef -r 603e4ed98fa7cb3b3c47f71b3b77bedd67f50fea static/scripts/mvc/tools.js
--- a/static/scripts/mvc/tools.js
+++ b/static/scripts/mvc/tools.js
@@ -46,7 +46,8 @@
             key: 'inputs',
             relatedModel: 'ToolInput',
             reverseRelation: {
-                key: 'tool'
+                key: 'tool',
+                includeInJSON: false
             }
         }
     ],


diff -r 063a1d690724b3485f41c620f664f11c7390ceef -r 603e4ed98fa7cb3b3c47f71b3b77bedd67f50fea static/scripts/viz/paramamonster.js
--- a/static/scripts/viz/paramamonster.js
+++ b/static/scripts/viz/paramamonster.js
@@ -6,7 +6,7 @@
 /**
  * Tree for a tool's parameters.
  */
-var ToolParameterTree = Backbone.Model.extend({
+var ToolParameterTree = Backbone.RelationalModel.extend({
     defaults: {
         tool: null,
         tree_data: null
@@ -18,9 +18,6 @@
         this.get('tool').get('inputs').each(function(input) {
             if (!input.get_samples()) { return; }
 
-            // All inputs are in tree to start.
-            self.add_param(input);
-
             // Listen for changes to input's attributes.
             input.on('change:min change:max change:num_samples', function(input) {
                 if (input.get('in_ptree')) {
@@ -38,7 +35,16 @@
             }, self);
         });
 
-        self.set_tree_data();
+        // If there is a config, use it.
+        if (options.config) {
+            _.each(options.config, function(input_config) {
+                var input = self.get('tool').get('inputs').find(function(input) {
+                    return input.get('name') === input_config.name;
+                });
+                self.add_param(input);
+                input.set(input_config);
+            });
+        }
     },
 
     add_param: function(param) {
@@ -203,16 +209,51 @@
             cur_node = find_child(cur_node.children);
         }
         return cur_node;
+    },
+
+    /**
+     * Returns a list of parameters used in tree.
+     */
+    toJSON: function() {
+        // FIXME: returning and jsonifying complete param causes trouble on the server side, 
+        // so just use essential attributes for now.
+        return this.get_tree_params().map(function(param) {
+            return {
+                name: param.get('name'),
+                min: param.get('min'),
+                max: param.get('max'),
+                num_samples: param.get('num_samples')
+            };
+        });
     }
 });
 
-var ParamaMonsterTrack = Backbone.Model.extend({
+var ParamaMonsterTrack = Backbone.RelationalModel.extend({
     defaults: {
         track: null,
         settings: null,
         regions: null
     },
 
+    relations: [
+        {
+            type: Backbone.HasMany,
+            key: 'regions',
+            relatedModel: 'GenomeRegion'
+        }
+    ],
+
+    initialize: function(options) {
+        // FIXME: find a better way to deal with needed URLs:
+        var track_config = _.extend({
+                                data_url: galaxy_paths.get('raw_data_url'),
+                                converted_datasets_state_url: galaxy_paths.get('dataset_state_url')
+                            }, options.track);
+        // HACK: remove prefs b/c they cause a redraw, which is not supported now.
+        delete track_config.mode;
+        this.set('track', object_from_template(track_config, {}, null));
+    },
+
     same_settings: function(a_track) {
         var this_settings = this.get('settings'),
             other_settings = a_track.get('settings');
@@ -223,6 +264,14 @@
             }
         }
         return true;
+    },
+
+    toJSON: function() {
+        return {
+            track: this.get('track').to_dict(),
+            settings: this.get('settings'),
+            regions: this.get('regions')
+        };
     }
 });
 
@@ -235,18 +284,45 @@
  */
 var ParamaMonsterVisualization = Visualization.extend({
     defaults: _.extend({}, Visualization.prototype.defaults, {
+        dataset: null,
         tool: null,
         parameter_tree: null,
         regions: null,
         tracks: null
     }),
+
+    relations: [
+        {
+            type: Backbone.HasOne,
+            key: 'dataset',
+            relatedModel: 'Dataset'
+        },
+        {
+            type: Backbone.HasOne,
+            key: 'tool',
+            relatedModel: 'Tool'
+        },
+        {
+            type: Backbone.HasMany,
+            key: 'regions',
+            relatedModel: 'GenomeRegion'
+        },
+        {
+            type: Backbone.HasMany,
+            key: 'tracks',
+            relatedModel: 'ParamaMonsterTrack'
+        }
+        // NOTE: cannot use relationship for parameter tree because creating tree is complex.
+    ],
     
     initialize: function(options) {
         var tool_with_samplable_inputs = this.get('tool').copy(true);
         this.set('tool_with_samplable_inputs', tool_with_samplable_inputs);
         
-        this.set('parameter_tree', new ToolParameterTree({ tool: tool_with_samplable_inputs }));
-        this.set('tracks', new TrackCollection());
+        this.set('parameter_tree', new ToolParameterTree({ 
+            tool: tool_with_samplable_inputs,
+            config: options.tree_config
+        }));
     },
 
     add_placeholder: function(settings) {
@@ -255,6 +331,20 @@
 
     add_track: function(track) {
         this.get('tracks').add(track);
+    },
+
+    toJSON: function() {
+        // TODO: could this be easier by using relational models?
+        return {
+            id: this.get('id'),
+            title: 'Parameter exploration for dataset \''  + this.get('dataset').get('name') + '\'',
+            type: 'paramamonster',
+            dataset_id: this.get('dataset').id,
+            tool_id: this.get('tool').id,
+            regions: this.get('regions').toJSON(),
+            tree_config: this.get('parameter_tree').toJSON(),
+            tracks: this.get('tracks').toJSON()
+        };
     }
 });
 
@@ -301,7 +391,7 @@
         settings_td.prepend(icon_menu.$el);
 
         // Render tile placeholders.
-        _.each(this.model.get('regions'), function() {
+        this.model.get('regions').each(function() {
             self.$el.append($('<td/>').addClass('tile').html(
                 $('<img/>').attr('src', galaxy_paths.get('image_path') + '/loading_large_white_bg.gif')
             ));
@@ -322,7 +412,7 @@
         // When data is ready, draw tiles.
         $.when(track.data_manager.data_is_ready()).then(function(data_ok) {
             // Draw tile for each region.
-            _.each(regions, function(region, index) {
+            regions.each(function(region, index) {
                 var resolution = region.length() / 300,
                     w_scale = 1/resolution,
                     mode = 'Pack';
@@ -550,6 +640,12 @@
 
         // Handle node clicks for tree data.
         this.model.get('parameter_tree').on('change:tree_data', this.handle_node_clicks, this);
+
+        // Each track must have a view so it has a canvas manager.
+        var self = this;
+        this.model.get('tracks').each(function(track) {
+            track.get('track').view = self;
+        });
     },
     
     render: function() {
@@ -565,13 +661,17 @@
             regions = self.model.get('regions'),
             tr = $('<tr/>').appendTo(this.track_collection_container);
 
-        _.each(regions, function(region) {
+        regions.each(function(region) {
             tr.append( $('<th>').text(region.toString()) );
         });
         tr.children().first().attr('colspan', 2);
 
         $('#right').append(this.track_collection_container);
 
+        self.model.get('tracks').each(function(track) {
+            self.add_track(track);
+        });
+
         // Render tool parameter tree in center panel.
         this.tool_param_tree_view.render();
         $('#center').append(this.tool_param_tree_view.$el);
@@ -588,6 +688,34 @@
         });
     },
 
+    /**
+     * Add track to model and view.
+     */
+    add_track: function(pm_track) {
+        var self = this;
+        self.model.add_track(pm_track);
+        var track_view = new ParamaMonsterTrackView({
+            model: pm_track,
+            canvas_manager: self.canvas_manager
+        });
+        track_view.on('run_on_dataset', self.run_tool_on_dataset, self);
+        self.track_collection_container.append(track_view.$el);
+        track_view.$el.hover(function() {
+            var settings_leaf = param_tree.get_leaf(settings);
+            var connected_node_ids = _.pluck(param_tree.get_connected_nodes(settings_leaf), 'id');
+
+            // TODO: can do faster with enter?
+            d3.select(self.tool_param_tree_view.$el[0]).selectAll("g.node")
+            .filter(function(d) {
+                return _.find(connected_node_ids, function(id) { return id === d.id; }) !== undefined;
+            }).style('fill', '#f00');
+        },
+        function() {
+            d3.select(self.tool_param_tree_view.$el[0]).selectAll("g.node").style('fill', '#000');
+        });
+        return pm_track;
+    },
+
     handle_node_clicks: function() {
         // When node clicked in tree, run tool and add tracks to model.
         var self = this,


diff -r 063a1d690724b3485f41c620f664f11c7390ceef -r 603e4ed98fa7cb3b3c47f71b3b77bedd67f50fea static/scripts/viz/visualization.js
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -69,7 +69,7 @@
     this.load_pattern( 'left_strand', "/visualization/strand_left.png" );
     this.load_pattern( 'right_strand_inv', "/visualization/strand_right_inv.png" );
     this.load_pattern( 'left_strand_inv', "/visualization/strand_left_inv.png" );
-}
+};
 
 _.extend( CanvasManager.prototype, {
     load_pattern: function( key, path ) {
@@ -79,7 +79,7 @@
         image.src = galaxy_paths.attributes.image_path + path;
         image.onload = function() {
             patterns[key] = dummy_context.createPattern( image, "repeat" );
-        }
+        };
     },
     get_pattern: function( key ) {
         return this.patterns[key];
@@ -215,8 +215,8 @@
                         
         // ReferenceDataManager does not have dataset.
         if (dataset) {
-            params['dataset_id'] = dataset.id;
-            params['hda_ldda'] = dataset.get('hda_ldda');
+            params.dataset_id = dataset.id;
+            params.hda_ldda = dataset.get('hda_ldda');
         }
         
         $.extend(params, extra_params);
@@ -265,17 +265,16 @@
         // TODO: this logic could be improved if the visualization knew whether
         // the data was "index" or "data."
         //
-        var 
-            key_ary = this.get('key_ary'),
+        var key_ary = this.get('key_ary'),
             obj_cache = this.get('obj_cache'),
-            key, region, entry_region, mode, entry;
+            key, entry_region;
         for (var i = 0; i < key_ary.length; i++) {
             entry_region = new GenomeRegion(key_ary[i]);
         
             if (entry_region.contains(region)) {
                 // This entry has data in the requested range. Return if data
                 // is compatible and can be subsetted.
-                var entry = obj_cache[key];
+                entry = obj_cache[key];
                 if ( is_deferred(entry) || 
                     ( this.get('data_mode_compatible')(entry, mode) && this.get('can_subset')(entry) ) ) {
                     this.move_key_to_end(key, i);
@@ -298,8 +297,6 @@
         this.set_elt(region, entry);  
     },
     
-    /**
-    
     /** "Deep" data request; used as a parameter for DataManager.get_more_data() */
     DEEP_DATA_REQ: "deep",
     
@@ -341,7 +338,7 @@
         //
         var 
             data_manager = this,
-            new_data_request = this.load_data(query_region, mode, resolution, extra_params)
+            new_data_request = this.load_data(query_region, mode, resolution, extra_params),
             new_data_available = $.Deferred();
         // load_data sets cache to new_data_request, but use custom deferred object so that signal and data
         // is all data, not just new data.
@@ -408,7 +405,7 @@
 /**
  * A genomic region.
  */
-var GenomeRegion = Backbone.Model.extend({
+var GenomeRegion = Backbone.RelationalModel.extend({
     defaults: {
         chrom: null,
         start: 0,
@@ -431,9 +428,9 @@
             !this.get('end') && 'as_str' in options) {
             var pieces = options.as_str.split(':'),
                 chrom = pieces[0],
-                pieces = pieces.split('-'),
-                start = pieces[0],
-                end = pieces[1];
+                start_end = pieces.split('-'),
+                start = start_end[0],
+                end = start_end[1];
             this.set('chrom', chrom);
             this.set('start', start);
             this.set('end', end);
@@ -462,7 +459,7 @@
             chrom: this.get('chrom'),
             start: this.get('start'),
             end: this.get('end')
-        }
+        };
     },
     
     /**
@@ -556,7 +553,7 @@
         datasets: []
     },
     
-    url: function() { return galaxy_paths.get("visualization_url"); },
+    url: galaxy_paths.get("visualization_url"),
     
     /**
      * POSTs visualization's JSON to its URL using the parameter 'vis_json'
@@ -565,7 +562,7 @@
      */
     save: function() {
         return $.ajax({
-            url: this.url(),
+            url: this.url,
             type: "POST",
             dataType: "json",
             data: { 
@@ -818,7 +815,7 @@
                                 requests[requests.length] = $.ajax({
                                     url: add_track_async_url,
                                     data: data,
-                                    dataType: "json",
+                                    dataType: "json"
                                 });
                         });
                         // To preserve order, wait until there are definitions for all tracks and then add 


diff -r 063a1d690724b3485f41c620f664f11c7390ceef -r 603e4ed98fa7cb3b3c47f71b3b77bedd67f50fea templates/base_panels.mako
--- a/templates/base_panels.mako
+++ b/templates/base_panels.mako
@@ -57,7 +57,8 @@
             data_url: '${h.url_for( controller="tracks", action="data" )}',
             raw_data_url: '${h.url_for( controller="tracks", action="raw_data" )}',
             converted_datasets_state_url: '${h.url_for( controller="tracks", action="converted_datasets_state" )}',
-            dataset_state_url: '${h.url_for( controller="tracks", action="dataset_state" )}'
+            dataset_state_url: '${h.url_for( controller="tracks", action="dataset_state" )}',
+            visualization_url: '${h.url_for( controller="visualization", action="save" )}'
         });
     </script></%def>


diff -r 063a1d690724b3485f41c620f664f11c7390ceef -r 603e4ed98fa7cb3b3c47f71b3b77bedd67f50fea templates/visualization/paramamonster.mako
--- a/templates/visualization/paramamonster.mako
+++ b/templates/visualization/paramamonster.mako
@@ -90,34 +90,43 @@
     <script type="text/javascript">
         var viz;
         $(function() {            
-            // -- Viz set up. --
-            
-            var tool = new Tool(JSON.parse('${ h.to_json_string( tool ) }')),
-                regions = [
-                    new GenomeRegion({
-                        chrom: 'chr19',
-                        start: '10000',
-                        end: '26000'
-                    }),
-                    new GenomeRegion({
-                        chrom: 'chr19',
-                        start: '150000',
-                        end: '175000'
-                    })
-                ],
-                // HACK: need to replace \ with \\ due to simplejson bug. 
-                dataset = new Dataset(JSON.parse('${ h.to_json_string( dataset.get_api_value() ).replace('\\', '\\\\' ) }'));
-                
-                
-            viz = new ParamaMonsterVisualization({
-                tool: tool,
-                dataset: dataset,
-                regions: regions
-            });
+            // -- Viz set up. --    
+            var viz = new ParamaMonsterVisualization(
+                ${ h.to_json_string( config ).replace('\\', '\\\\' )}
+            );
             var viz_view = new ParamaMonsterVisualizationView({ model: viz });
                 
             viz_view.render();
             $('.unified-panel-body').append(viz_view.$el);
+
+            // -- Menu set up. --
+            var menu = create_icon_buttons_menu([
+            { icon_class: 'disk--arrow', title: 'Save', on_click: function() { 
+                // Show saving dialog box
+                show_modal("Saving...", "progress");
+
+                viz.save().success(function(vis_info) {
+                    hide_modal();
+                    viz.set({
+                        'id': vis_info.vis_id,
+                        'has_changes': false
+                    });
+                })
+                .error(function() { 
+                    show_modal( "Could Not Save", "Could not save visualization. Please try again later.", 
+                                { "Close" : hide_modal } );
+                });
+            } },
+            { icon_class: 'cross-circle', title: 'Close', on_click: function() { 
+                window.location = "${h.url_for( controller='visualization', action='list' )}";
+            } }
+            ], 
+            {
+                tipsy_config: {gravity: 'n'}
+            });
+            
+            menu.$el.attr("style", "float: right");
+            $("#right .unified-panel-header-inner").append(menu.$el);
         });
     </script></%def>
@@ -129,4 +138,8 @@
 </%def><%def name="right_panel()">
+    <div class="unified-panel-header" unselectable="on">
+        <div class="unified-panel-header-inner">
+        </div>
+    </div></%def>
\ No newline at end of file

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

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[galaxy-commits] commit/galaxy-central: jgoecks: Make it simpler to save/restore visualizations and enable saving/restoring of paramamonster visualizations.

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