Allow reloading External Display applications without restarting Galaxy.

lib/galaxy/datatypes/display_applications/application.py

@@ -167,23 +167,21 @@ class PopulatedDisplayApplicationLink( object ):
 class DisplayApplication( object ):
     @classmethod
     def from_file( cls, filename, datatypes_registry ):
-        return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry )
+        return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry, filename=filename )
     @classmethod
-    def from_elem( cls, elem, datatypes_registry ):
+    def from_elem( cls, elem, datatypes_registry, filename=None ):
+        att_dict = cls._get_attributes_from_elem( elem )
+        rval = DisplayApplication( att_dict['id'], att_dict['name'], datatypes_registry, att_dict['version'], filename=filename, elem=elem )
+        rval._load_links_from_elem( elem )
+        return rval
+    @classmethod
+    def _get_attributes_from_elem( cls, elem ):
         display_id = elem.get( 'id', None )
         assert display_id, "ID tag is required for a Display Application"
         name = elem.get( 'name', display_id )
         version = elem.get( 'version', None )
-        rval = DisplayApplication( display_id, name, datatypes_registry, version )
-        for link_elem in elem.findall( 'link' ):
-            link = DisplayApplicationLink.from_elem( link_elem, rval )
-            if link:
-                rval.links[ link.id ] = link
-        for dynamic_links in elem.findall( 'dynamic_links' ):
-            for link in DynamicDisplayApplicationBuilder( dynamic_links, rval, datatypes_registry.build_sites ):
-                rval.links[ link.id ] = link
-        return rval
-    def __init__( self, display_id, name, datatypes_registry, version = None ):
+        return dict( id=display_id, name=name, version=version )
+    def __init__( self, display_id, name, datatypes_registry, version = None, filename=None, elem=None ):
         self.id = display_id
         self.name = name
         self.datatypes_registry = datatypes_registry
@@ -191,6 +189,16 @@ class DisplayApplication( object ):
             version = "1.0.0"
         self.version = version
         self.links = odict()
+        self._filename = filename
+        self._elem = elem
+    def _load_links_from_elem( self, elem ):
+        for link_elem in elem.findall( 'link' ):
+            link = DisplayApplicationLink.from_elem( link_elem, self )
+            if link:
+                self.links[ link.id ] = link
+        for dynamic_links in elem.findall( 'dynamic_links' ):
+            for link in DynamicDisplayApplicationBuilder( dynamic_links, self, self.datatypes_registry.build_sites ):
+                self.links[ link.id ] = link
     def get_link( self, link_name, data, dataset_hash, user_hash, trans, app_kwds ):
         #returns a link object with data knowledge to generate links
         return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans, app_kwds )
@@ -200,3 +208,23 @@ class DisplayApplication( object ):
             if link_value.filter_by_dataset( data, trans ):
                 filtered.links[link_name] = link_value
         return filtered
+    def reload( self ):
+        if self._filename:
+            elem = parse_xml( self._filename ).getroot()
+        elif self._elem:
+            elem = self._elem
+        else:
+            raise Exception( "Unable to reload DisplayApplication %s." % ( self.name ) )
+        # All toolshed-specific attributes added by e.g the registry will remain
+        attr_dict = self._get_attributes_from_elem( elem )
+        # We will not allow changing the id at this time (we'll need to fix several mappings upstream to handle this case)
+        assert attr_dict.get( 'id' ) == self.id, ValueError( "You cannot reload a Display application where the ID has changed. You will need to restart the server instead." )
+        # clear old links
+        for key in self.links.keys():
+            del self.links[key]
+        # Set new attributes
+        for key, value in attr_dict.iteritems():
+            setattr( self, key, value )
+        # Load new links
+        self._load_links_from_elem( elem )
+        return self

lib/galaxy/datatypes/registry.py

@@ -621,6 +621,26 @@ class Registry( object ):
                     self.log.debug( "Adding inherited display application '%s' to datatype '%s'" % ( display_app.id, extension ) )
                     d_type1.add_display_application( display_app )
 
+    def reload_display_applications( self, display_application_ids=None ):
+        """
+        Reloads display applications: by id, or all if no ids provided
+        Returns tuple( [reloaded_ids], [failed_ids] )
+        """
+        if not display_application_ids:
+            display_application_ids = self.display_applications.keys()
+        elif not isinstance( display_application_ids, list ):
+            display_application_ids = [ display_application_ids ]
+        reloaded = []
+        failed = []
+        for display_application_id in display_application_ids:
+            try:
+                self.display_applications[ display_application_id ].reload()
+                reloaded.append( display_application_id )
+            except Exception, e:
+                self.log.debug( 'Requested to reload display application "%s", but failed: %s.', display_application_id, e  )
+                failed.append( display_application_id )
+        return ( reloaded, failed )
+
     def load_external_metadata_tool( self, toolbox ):
         """Adds a tool which is used to set external metadata"""
         # We need to be able to add a job to the queue to set metadata. The queue will currently only accept jobs with an associated

lib/galaxy/webapps/galaxy/controllers/admin.py

@@ -883,3 +883,21 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuotaMixin, QuotaP
         message = escape( galaxy.util.restore_text( kwd.get( 'message', '' ) ) )
         status = galaxy.util.restore_text( kwd.get( 'status', 'done' ) )
         return trans.fill_template( 'admin/view_data_tables_registry.mako', message=message, status=status )
+
+    @web.expose
+    @web.require_admin
+    def display_applications( self, trans, **kwd ):
+        return trans.fill_template( 'admin/view_display_applications.mako', display_applications=trans.app.datatypes_registry.display_applications )
+
+    @web.expose
+    @web.require_admin
+    def reload_display_application( self, trans, **kwd ):
+        reloaded, failed = trans.app.datatypes_registry.reload_display_applications( kwd.get( 'id' ) )
+        if not reloaded and failed:
+            return trans.show_error_message( 'Unable to reload any of the %i requested display applications ("%s").' % ( len( failed ), '", "'.join( failed ) ) )
+        if failed:
+            return trans.show_warn_message( 'Reloaded %i display applications ("%s"), but failed to reload %i display applications ("%s").'
+                                             % ( len( reloaded ), '", "'.join( reloaded ), len( failed ), '", "'.join( failed ) ) )
+        if not reloaded:
+            return trans.show_warn_message( 'You need to request at least one display application to reload.' )
+        return trans.show_ok_message( 'Reloaded %i requested display applications ("%s").' % ( len( reloaded ), '", "'.join( reloaded ) ) )

templates/webapps/galaxy/admin/index.mako

@@ -75,6 +75,7 @@
                     <div class="toolSectionBg">
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='view_datatypes_registry' )}" target="galaxy_main">View data types registry</a></div>
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='view_tool_data_tables' )}" target="galaxy_main">View data tables registry</a></div>
+                        <div class="toolTitle"><a href="${h.url_for( controller='admin', action='display_applications' )}" target="galaxy_main">View display applications</a></div>
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='tool_versions' )}" target="galaxy_main">View tool lineage</a></div>
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='package_tool' )}" target="galaxy_main">Download tool tarball</a></div>
                         <div class="toolTitle"><a href="${h.url_for( controller='admin', action='reload_tool' )}" target="galaxy_main">Reload a tool's configuration</a></div>

templates/webapps/galaxy/admin/view_display_applications.mako

@@ -0,0 +1,48 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">There are currently ${len( display_applications )} <a class="icon-btn" href="${ h.url_for( controller='admin', action='reload_display_application' ) }" title="Reload all display applications" data-placement="bottom">
+                        <span class="fa fa-refresh"></span>
+                    </a> display applications loaded.</div>
+    <div class="toolFormBody">
+        <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
+            <tr>
+                <th bgcolor="#D8D8D8">Reload</th>
+                <th bgcolor="#D8D8D8">Name</th>
+                <th bgcolor="#D8D8D8">ID</th>
+                <th bgcolor="#D8D8D8">Version</th>
+                <th bgcolor="#D8D8D8">Links</th>
+                <th bgcolor="#D8D8D8">Filename</th>
+            </tr>
+            <% ctr = 0 %>
+            %for display_app in display_applications.values():
+                %if ctr % 2 == 1:
+                    <tr class="odd_row">
+                %else:
+                    <tr class="tr">
+                %endif
+                    <td>
+                        <a class="icon-btn" href="${ h.url_for( controller='admin', action='reload_display_application', id=display_app.id ) }" title="Reload ${ display_app.name | h } display application" data-placement="bottom">
+                            <span class="fa fa-refresh"></span>
+                        </a>
+                    </td>
+                    <td>${ display_app.name | h }</td>
+                    <td>${ display_app.id | h }</td>
+                    <td>${ display_app.version | h }</td>
+                    <td><ul>
+                        %for link in display_app.links.values():
+                            <li>${  link.name | h }</li>
+                        %endfor
+                    </ul></td>
+                    <td>${ display_app._filename | h }</td>
+                </tr>
+                <% ctr += 1 %>
+            %endfor
+        </table>
+    </div>
+</div>