trackster: Add new dbkey column to viz tables, finish "Visualize in Trackster" button functionality

- Dbkey now shown in "Saved Visualizations" grid
- "Visualize in Trackster" icon in history pane for supported dataset now works, letting you add that dataset to an existing browser or to a new browser. Dbkey for existing browsers is also shown.

lib/galaxy/model/mapping.py

@@ -641,6 +641,7 @@ Visualization.table = Table( "visualization", metadata,
             ForeignKey( "visualization_revision.id", use_alter=True, name='visualization_latest_revision_id_fk' ), index=True ),
     Column( "title", TEXT ),
     Column( "type", TEXT ),
+    Column( "dbkey", TEXT, index=True ),
     Column( "deleted", Boolean, default=False, index=True ),
     Column( "importable", Boolean, default=False, index=True ),
     Column( "slug", TEXT, index=True ),
@@ -653,6 +654,7 @@ VisualizationRevision.table = Table( "visualization_revision", metadata,
     Column( "update_time", DateTime, default=now, onupdate=now ),
     Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True, nullable=False ),
     Column( "title", TEXT ),
+    Column( "dbkey", TEXT, index=True ),
     Column( "config", JSONType )
     )
     

lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py

@@ -0,0 +1,58 @@
+"""
+Migration script to add dbkey column for visualization.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+from galaxy.util.json import from_json_string
+
+import logging
+log = logging.getLogger( __name__ )
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+Visualization_table = Table( "visualization", metadata, autoload=True )
+Visualization_revision_table = Table( "visualization_revision", metadata, autoload=True )
+
+def upgrade():
+    
+    print __doc__
+    metadata.reflect()
+
+    # Create dbkey columns.
+    x = Column( "dbkey", TEXT, index=True )
+    y = Column( "dbkey", TEXT, index=True )
+    x.create( Visualization_table )
+    y.create( Visualization_revision_table )
+    assert x is Visualization_table.c.dbkey
+    assert y is Visualization_revision_table.c.dbkey
+    
+    try:
+        i = Index( "ix_visualization_dbkey", Visualization_table.c.dbkey )
+        i.create()
+    except:
+        pass
+    
+    try:
+        i = Index( "ix_visualization_revision_dbkey", Visualization_revision_table.c.dbkey )
+        i.create()
+    except:
+        pass
+    
+    all_viz = db_session.execute( "SELECT visualization.id as viz_id, visualization_revision.id as viz_rev_id, visualization_revision.config FROM visualization_revision \
+                    LEFT JOIN visualization ON visualization.id=visualization_revision.visualization_id" )
+    for viz in all_viz:
+        viz_id = viz['viz_id']
+        viz_rev_id = viz['viz_rev_id']
+        dbkey = from_json_string(viz[Visualization_revision_table.c.config]).get('dbkey', "").replace("'", "\\'")
+        db_session.execute("UPDATE visualization_revision SET dbkey='%s' WHERE id=%s" % (dbkey, viz_rev_id))
+        db_session.execute("UPDATE visualization SET dbkey='%s' WHERE id=%s" % (dbkey, viz_id))
+
+def downgrade():
+    metadata.reflect()
+
+    Visualization_table.c.dbkey.drop()
+    Visualization_revision_table.c.dbkey.drop()

lib/galaxy/web/controllers/tracks.py

@@ -7,10 +7,6 @@ of datasets associated with the same dbkey to display. Once selected, jobs
 are started to create any necessary indexes in the background, and the user
 is redirected to the browser interface, which loads the appropriate datasets.
 
-Problems
---------
- - Must have a LEN file, not currently able to infer from data (not sure we
-   need to support that, but need to make user defined build support better)
 """
 
 import math, re, logging, glob, pkg_resources
@@ -88,12 +84,6 @@ class DatasetSelectionGrid( grids.Grid ):
                     .filter( model.HistoryDatasetAssociation.deleted == False )
                     
 class TracksterSelectionGrid( grids.Grid ):
-#    class DbKeyColumn( grids.GridColumn ):
-#        def filter( self, trans, user, query, dbkey ):
-#            """ Filter by dbkey. """
-#            # use raw SQL b/c metadata is a BLOB
-#            dbkey = dbkey.replace("'", "\\'")
-#            return query.filter( or_( "metadata like '%%\"dbkey\": [\"%s\"]%%'" % dbkey, "metadata like '%%\"dbkey\": \"%s\"%%'" % dbkey ) )
 
     # Grid definition.
     title = "Insert into visualization"
@@ -105,7 +95,8 @@ class TracksterSelectionGrid( grids.Grid ):
     use_async = True
     use_paging = False
     columns = [
-        grids.TextColumn( "Title", key="title", model_class=model.Visualization )
+        grids.TextColumn( "Title", key="title", model_class=model.Visualization ),
+        grids.TextColumn( "Dbkey", key="dbkey", model_class=model.Visualization )
     ]
     columns.append( 
         grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0] ], 
@@ -138,15 +129,16 @@ class TracksController( BaseController, UsesVisualization ):
     
     @web.expose
     @web.require_login()
-    def index( self, trans ):
+    def index( self, trans, **kwargs ):
         config = {}
         
-        return trans.fill_template( "tracks/browser.mako", config=config )
+        return trans.fill_template( "tracks/browser.mako", config=config, add_dataset=kwargs.get("dataset_id", None), \
+                                        default_dbkey=kwargs.get("default_dbkey", None) )
     
     @web.expose
     @web.require_login()
-    def new_browser( self, trans ):
-        return trans.fill_template( "tracks/new_browser.mako", dbkeys=self._get_dbkeys( trans ) )
+    def new_browser( self, trans, **kwargs ):
+        return trans.fill_template( "tracks/new_browser.mako", dbkeys=self._get_dbkeys( trans ), default_dbkey=kwargs.get("default_dbkey", None) )
             
     @web.json
     @web.require_login()
@@ -204,7 +196,7 @@ class TracksController( BaseController, UsesVisualization ):
             visualization = self.get_visualization( trans, vis_id, check_ownership=False, check_accessible=True )
             visualization.config = self.get_visualization_config( trans, visualization )
             vis_user = visualization.user
-            vis_dbkey = visualization.config['dbkey']
+            vis_dbkey = visualization.dbkey
         else:
             # No vis_id, so visualization is new. User is current user, dbkey must be given.
             vis_user = trans.user
@@ -330,6 +322,7 @@ class TracksController( BaseController, UsesVisualization ):
             vis.user = trans.user
             vis.title = kwargs['vis_title']
             vis.type = "trackster"
+            vis.dbkey = dbkey
             session.add( vis )
         else:
             decoded_id = trans.security.decode_id( vis_id )
@@ -339,6 +332,7 @@ class TracksController( BaseController, UsesVisualization ):
         vis_rev = model.VisualizationRevision()
         vis_rev.visualization = vis
         vis_rev.title = vis.title
+        vis_rev.dbkey = dbkey
         tracks = []
         for track in decoded_payload:
             tracks.append( {    "dataset_id": str(track['dataset_id']),
@@ -346,7 +340,7 @@ class TracksController( BaseController, UsesVisualization ):
                                 "track_type": track['track_type'],
                                 "prefs": track['prefs']
             } )
-        vis_rev.config = { "dbkey": dbkey, "tracks": tracks }
+        vis_rev.config = { "tracks": tracks }
         vis.latest_revision = vis_rev
         session.add( vis_rev )
         session.flush()

lib/galaxy/web/controllers/visualization.py

@@ -14,7 +14,7 @@ class VisualizationListGrid( grids.Grid ):
     columns = [
         grids.TextColumn( "Title", key="title", model_class=model.Visualization, attach_popup=True,
                          link=( lambda item: dict( controller="tracks", action="browser", id=item.id ) ) ),
-        grids.TextColumn( "Type", key="type", model_class=model.Visualization ),
+        grids.TextColumn( "Dbkey", key="dbkey", model_class=model.Visualization ),
         grids.IndividualTagsColumn( "Tags", "tags", model.Visualization, model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ),
         grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Visualization, filterable="advanced", sortable=False ),
         grids.GridColumn( "Created", key="create_time", format=time_ago ),

static/scripts/galaxy.base.js

@@ -559,18 +559,19 @@ $(".trackster-add").live("click", function() {
         dataset_jquery = $(this);
     $.ajax({
         url: dataset_jquery.attr("data-url"),
-        data: { "f-dbkey": "hi" },
         dataType: "html",
         error: function() { alert( "Could not add this dataset to browser." ); },
         success: function(table_html) {
             var parent = window.parent;
             parent.show_modal("Add to Browser:", table_html, {
-                "Insert Dataset Into": function() {
+                "Insert into selected": function() {
                     $(parent.document).find('input[name=id]:checked').each(function() {
                         var vis_id = $(this).val();
                         parent.location = dataset_jquery.attr("action-url") + "&id=" + vis_id;
                     });
-                    parent.hide_modal();
+                },
+                "Insert into new browser": function() {
+                    parent.location = dataset_jquery.attr("new-url");
                 },
                 "Cancel": function() {
                     parent.hide_modal();

templates/root/history_common.mako

@@ -120,7 +120,8 @@
                         <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a>
                         %if app.config.get_bool( 'enable_tracks', False ) and data.ext in app.datatypes_registry.get_available_tracks():
                             <a data-url="${h.url_for( controller='tracks', action='list_tracks' )}" class="icon-button vis-chart tooltip trackster-add"
-                                action-url="${h.url_for( controller='tracks', action='browser', dataset_id=dataset_id)}" title="Visualize in Trackster"></a>
+                                action-url="${h.url_for( controller='tracks', action='browser', dataset_id=dataset_id)}"
+                                new-url="${h.url_for( controller='tracks', action='index', dataset_id=dataset_id, default_dbkey=data.dbkey)}" title="Visualize in Trackster"></a>
                         %endif
                         %if trans.user:
                             <div style="float: right">

templates/tracks/browser.mako

@@ -94,7 +94,7 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jquery.event.drag",
                 hide_modal();
             };
             $.ajax({
-                url: "${h.url_for( action='new_browser' )}",
+                url: "${h.url_for( action='new_browser', default_dbkey=default_dbkey )}",
                 data: {},
                 error: function() { alert( "Couldn't create new browser" ) },
                 success: function(form_html) {
@@ -126,10 +126,6 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jquery.event.drag",
         
         // Execute initializer for EDITOR specific javascript
         function init() {
-            %if add_dataset:
-                console.log("Adding dataset");
-                ## Code for adding new dataset
-            %endif
             
             if (view.num_tracks === 0) {
                 $("#no-tracks").show();
@@ -148,6 +144,27 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jquery.event.drag",
                     return "There are unsaved changes to your visualization which will be lost.";
                 }
             };
+            
+            var add_async_success = function(track_data) {
+                var td = track_data,
+					track_types = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack },
+					new_track = new track_types[track_data.track_type]( track_data.name, view, track_data.dataset_id, track_data.prefs);
+					
+                view.add_track(new_track);
+                view.has_changes = true;
+                $("#no-tracks").hide();
+                sidebar_box(new_track);
+            };
+            
+            %if add_dataset is not None:
+                $.ajax( {
+                    url: "${h.url_for( action='add_track_async' )}",
+                    data: { id: "${add_dataset}" },
+                    dataType: "json",
+                    success: add_async_success
+                });
+                
+            %endif
 
             // Use a popup grid to add more tracks
             $("#add-track").bind( "click", function(e) {
@@ -164,17 +181,7 @@ ${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jquery.event.drag",
                                         url: "${h.url_for( action='add_track_async' )}",
                                         data: { id: item_id },
                                         dataType: "json",
-                                        error: function() {},
-                                        success: function(track_data) {
-                                            var td = track_data,
-												track_types = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack },
-												new_track = new track_types[track_data.track_type]( track_data.name, view, track_data.dataset_id, track_data.prefs);
-												
-                                            view.add_track(new_track);
-                                            view.has_changes = true;
-                                            $("#no-tracks").hide();
-                                            sidebar_box(new_track);
-                                        }
+                                        success: add_async_success
                                     });
 
                                 });

templates/tracks/new_browser.mako

@@ -21,4 +21,10 @@
         Is your build not listed here? 
         <a href="${h.url_for( controller='user', action='dbkeys', panels=True )}">Add a Custom Build</a>
     </div>
+    %if default_dbkey is not None:
+        <script type="text/javascript">
+            console.log("${default_dbkey}");
+            $("#new-dbkey option[value='${default_dbkey}']").attr("selected", true);
+        </script>
+    %endif
 </form>