Tables for storing visualizations, visualization tab (if enable_tracks is true)

lib/galaxy/model/__init__.py

@@ -1292,7 +1292,7 @@ class UserAddress( object ):
         if self.phone:
             html = html + '<br/>' + 'Phone: ' + self.phone
         return html
-    
+
 class Page( object ):
     def __init__( self ):
         self.id = None
@@ -1307,6 +1307,22 @@ class PageRevision( object ):
         self.user = None
         self.title = None
         self.content = None
+
+class Visualization( object ):
+    def __init__( self ):
+        self.id = None
+        self.user = None
+        self.type = None
+        self.title = None
+        self.latest_revision = None
+        self.revisions = []
+
+class VisualizationRevision( object ):
+    def __init__( self ):
+        self.id = None
+        self.visualization = None
+        self.title = None
+        self.config = None
         
 class Tag ( object ):
     def __init__( self, id=None, type=None, parent_id=None, name=None ):

lib/galaxy/model/mapping.py

@@ -556,6 +556,26 @@ PageRevision.table = Table( "page_revision", metadata,
     Column( "content", TEXT )
     )
 
+Visualization.table = Table( "visualization", metadata,
+    Column( "id", Integer, primary_key=True ),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ),
+    Column( "latest_revision_id", Integer,
+            ForeignKey( "visualization_revision.id", use_alter=True, name='visualization_latest_revision_id_fk' ), index=True ),
+    Column( "title", TEXT ),
+    Column( "type", TEXT )
+    )
+
+VisualizationRevision.table = Table( "visualization_revision", metadata,
+    Column( "id", Integer, primary_key=True ),
+    Column( "create_time", DateTime, default=now ),
+    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True, nullable=False ),
+    Column( "title", TEXT ),
+    Column( "config", JSONType )
+    )
+
 Tag.table = Table( "tag", metadata,
     Column( "id", Integer, primary_key=True ),
     Column( "type", Integer ),
@@ -1012,6 +1032,18 @@ assign_mapper( context, Page, Page.table,
                      tags=relation(PageTagAssociation, order_by=PageTagAssociation.table.c.id, backref="pages") 
                    ) )
 
+assign_mapper( context, VisualizationRevision, VisualizationRevision.table )
+
+assign_mapper( context, Visualization, Visualization.table,
+    properties=dict( user=relation( User ),
+                     revisions=relation( VisualizationRevision, backref='visualization',
+                                         cascade="all, delete-orphan",
+                                         primaryjoin=( Visualization.table.c.id == VisualizationRevision.table.c.visualization_id ) ),
+                     latest_revision=relation( VisualizationRevision, post_update=True,
+                                               primaryjoin=( Visualization.table.c.latest_revision_id == VisualizationRevision.table.c.id ),
+                                               lazy=False )
+                   ) )
+
 assign_mapper( context, Tag, Tag.table,
     properties=dict( children=relation(Tag, backref=backref( 'parent', remote_side=[Tag.table.c.id] ) )  
                      ) )

lib/galaxy/web/controllers/tracks.py

@@ -63,18 +63,35 @@ class TracksController( BaseController ):
         return trans.fill_template( "tracks/index.mako" )
 
     @web.expose
-    def new_browser( self, trans, dbkey=None, dataset_ids=None, browse=None ):
+    def new_browser( self, trans, dbkey=None, dataset_ids=None, browse=None, title=None ):
         """
         Build a new browser from datasets in the current history. Redirects
-        to 'index' once datasets to browse have been selected.
+        to 'browser' once datasets to browse have been selected.
         """
         session = trans.sa_session
         # If the user clicked the submit button explicitly, try to build the browser
-        if browse and dataset_ids:
+        if title and browse and dataset_ids:
             if not isinstance( dataset_ids, list ):
                 dataset_ids = [ dataset_ids ]
-            dataset_ids = ",".join( map( str, dataset_ids ) )
-            trans.response.send_redirect( web.url_for( controller='tracks', action='browser', chrom="", dataset_ids=dataset_ids ) )
+            # Build config
+            tracks = []
+            for dataset_id in dataset_ids:
+                tracks.append( { "dataset_id": str( dataset_id ) } )
+            config = { "tracks": tracks }
+            # Build visualization object
+            vis = model.Visualization()
+            vis.user = trans.user
+            vis.title = title
+            vis.type = "trackster"
+            vis_rev = model.VisualizationRevision()
+            vis_rev.visualization = vis
+            vis_rev.title = title
+            vis_rev.config = config
+            vis.latest_revision = vis_rev
+            session.add( vis )
+            session.add( vis_rev )
+            session.flush()
+            trans.response.send_redirect( web.url_for( controller='tracks', action='browser', id=trans.security.encode_id( vis.id ) ) )
         else:
             # Determine the set of all dbkeys that are used in the current history
             dbkeys = [ d.metadata.dbkey for d in trans.get_history().datasets if not d.deleted ]
@@ -96,14 +113,18 @@ class TracksController( BaseController ):
             return trans.fill_template( "tracks/new_browser.mako", converters=browsable_types, dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets )
 
     @web.expose
-    def browser(self, trans, dataset_ids, chrom=""):
+    def browser(self, trans, id, chrom=""):
         """
         Display browser for the datasets listed in `dataset_ids`.
         """
+        decoded_id = trans.security.decode_id( id )
+        session = trans.sa_session
+        vis = session.query( model.Visualization ).get( decoded_id )
         tracks = []
         dbkey = ""
-        for dataset_id in dataset_ids.split( "," ):
-            dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id )
+        for t in vis.latest_revision.config['tracks']:
+            dataset_id = t['dataset_id']
+            dataset = trans.app.model.HistoryDatasetAssociation.get( dataset_id )
             tracks.append( {
                 "type": dataset.datatype.get_track_type(),
                 "name": dataset.name,
@@ -114,7 +135,8 @@ class TracksController( BaseController ):
         if chrom_lengths is None:
             error( "No chromosome lengths file found for '%s'" % dataset.name )
         return trans.fill_template( 'tracks/browser.mako',
-                                    dataset_ids=dataset_ids,
+                                    #dataset_ids=dataset_ids,
+                                    id=id,
                                     tracks=tracks,
                                     chrom=chrom,
                                     dbkey=dbkey,

lib/galaxy/web/controllers/visualization.py

@@ -0,0 +1,47 @@
+from galaxy.web.base.controller import *
+from galaxy.web.framework.helpers import time_ago, grids
+from galaxy.util.sanitize_html import sanitize_html
+
+
+class VisualizationListGrid( grids.Grid ):
+    # Grid definition
+    use_panels = True
+    title = "Visualizations"
+    model_class = model.Visualization
+    default_sort_key = "-create_time"
+    columns = [
+        grids.GridColumn( "Title", key="title", attach_popup=True,
+                         link=( lambda item: dict( controller="tracks", action="browser", id=item.id ) ) ),
+        grids.GridColumn( "Type", key="type" ),
+        grids.GridColumn( "Created", key="create_time", format=time_ago ),
+        grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
+    ]
+    ## global_actions = [
+    ##     grids.GridAction( "Add new page", dict( action='create' ) )
+    ## ]
+    operations = [
+        grids.GridOperation( "View", allow_multiple=False, url_args=dict( controller="tracks", action='browser' ) ),
+    ]
+    def apply_default_filter( self, trans, query, **kwargs ):
+        return query.filter_by( user=trans.user )
+
+class VisualizationController( BaseController ):
+    
+    @web.expose
+    def index( self, trans ):
+        return trans.fill_template( "panels.mako", active_view='visualization', main_url=url_for( action='list' ) )
+    
+    list_grid = VisualizationListGrid()    
+    @web.expose
+    def list( self, trans, *args, **kwargs ):
+        return self.list_grid( trans, *args, **kwargs )
+    
+    #@web.expose
+    #@web.require_admin  
+    #def index( self, trans, *args, **kwargs ):
+    #    # Build grid
+    #    grid = self.list( trans, *args, **kwargs )
+    #    # Render grid wrapped in panels
+    #    return trans.fill_template( "page/index.mako", grid=grid )
+    
+    

templates/base_panels.mako

@@ -173,11 +173,18 @@
     %endif
 
     %if app.config.get_bool( 'enable_tracks', False ):
-    <td class="tab">
+    <%
+    cls = "tab"
+    if self.active_view == 'visualization':
+	cls += " active"
+    %>
+    <td class="${cls}">
         Visualization
         <div class="submenu">
         <ul>
             <li><a href="${h.url_for( controller='tracks', action='index' )}">Build track browser</a></li>
+            <li><hr style="color: inherit; background-color: gray"/></li>
+	    <li><a href="${h.url_for( controller='visualization', action='index' )}">Stored visualizations</a></li>
         </ul>
         </div>
     </td>

templates/panels.mako

@@ -0,0 +1,16 @@
+<%inherit file="/base_panels.mako"/>
+
+<%def name="init()">
+<%
+    self.has_left_panel=False
+    self.has_right_panel=False
+    self.active_view=active_view
+    self.message_box_visible=False
+%>
+</%def>
+
+<%def name="center_panel()">
+
+    <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${main_url}"> </iframe>
+
+</%def>

templates/tracks/browser.mako

@@ -124,7 +124,8 @@ ${h.js( "jquery", "jquery.event.drag", "jquery.mousewheel", "lrucache", "trackst
             <select id="chrom" name="chrom">
                 <option value="">Loading</option>
             </select>
-            <input type="hidden" name="dataset_ids" value="${dataset_ids}" />
+            ## <input type="hidden" name="dataset_ids" value="${dataset_ids}" />
+	    <input type="hidden" name="id" value="${id}" /> 
             <a href="#" onclick="javascript:view.zoom_in();view.redraw();">+</a>
             <a href="#" onclick="javascript:view.zoom_out();view.redraw();">-</a>
         </form>

templates/tracks/new_browser.mako

@@ -19,10 +19,17 @@ $( function() {
 
 % else:
     <div class="form">
-        <div class="form-title">Select datasets to include in browser</div>
+        <div class="form-title">Create new track browser</div>
     
         <div id="dbkey" class="form-body">
             <form id="form" method="POST">
+                <div class="form-row">
+                    <label for="dbkey">Browser name:</label>
+                    <div class="form-row-input">
+                        <input type="text" name="title" id="title" value="Unnamed Browser"></input>
+                    </div>
+                    <div style="clear: both;"></div>
+                </div>
                 <div class="form-row">
                     <label for="dbkey">Reference genome build (dbkey): </label>
                     <div class="form-row-input">