Add API endpoint to check for updates to installed repositories.

lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py

@@ -19,6 +19,7 @@
 from tool_shed.util import hg_util
 from tool_shed.util import workflow_util
 from tool_shed.util import tool_util
+from tool_shed.util import repository_util
 
 import tool_shed.util.shed_util_common as suc
 
@@ -49,6 +50,21 @@ def __ensure_can_install_repos( self, trans ):
         if not trans.user_is_admin():
             raise exceptions.AdminRequiredException( 'You are not authorized to request the latest installable revision for a repository in this Galaxy instance.' )
 
+    @expose_api
+    def check_for_updates( self, trans, repository_id ):
+        '''
+        POST /api/tool_shed_repositories/check_for_updates/{id}
+        Check for updates to the specified repository, or all installed repositories.
+
+        :param key: the current Galaxy admin user's API key
+
+        The following parameters are included in the payload.
+        :param repository_id: the galaxy-side encoded repository ID
+        '''
+        message, status = repository_util.check_for_updates( trans.app, trans.install_model, repository_id )
+        return { 'status': status, 'message': message }
+        # Get the information about the repository to be updated from the payload.
+
     @expose_api
     def exported_workflows( self, trans, id, **kwd ):
         """
@@ -378,20 +394,20 @@ def repair_repository_revision( self, trans, payload, **kwd ):
 
     def __parse_repository_from_payload( self, payload, include_changeset=False ):
         # Get the information about the repository to be installed from the payload.
-        tool_shed_url = payload.get( 'tool_shed_url', '' )
-        if not tool_shed_url:
+        tool_shed_url = payload.get( 'tool_shed_url', None )
+        name = payload.get( 'name', None )
+        owner = payload.get( 'owner', None )
+        if tool_shed_url is None:
             raise exceptions.RequestParameterMissingException( "Missing required parameter 'tool_shed_url'." )
-        name = payload.get( 'name', '' )
-        if not name:
+        if name is None:
             raise exceptions.RequestParameterMissingException( "Missing required parameter 'name'." )
-        owner = payload.get( 'owner', '' )
-        if not owner:
+        if owner is None:
             raise exceptions.RequestParameterMissingException( "Missing required parameter 'owner'." )
         if not include_changeset:
             return tool_shed_url, name, owner
 
-        changeset_revision = payload.get( 'changeset_revision', '' )
-        if not changeset_revision:
+        changeset_revision = payload.get( 'changeset_revision', None )
+        if changeset_revision is None:
             raise HTTPBadRequest( detail="Missing required parameter 'changeset_revision'." )
 
         return tool_shed_url, name, owner, changeset_revision

lib/galaxy/webapps/galaxy/buildapp.py

@@ -567,6 +567,12 @@ def populate_api_routes( webapp, app ):
                             new={ 'install_repository_revision': 'POST' },
                             parent_resources=dict( member_name='tool_shed_repository', collection_name='tool_shed_repositories' ) )
 
+    webapp.mapper.connect( 'repository_update',
+                           '/api/tool_shed_repositories/check_for_updates/{repository_id}',
+                           controller='tool_shed_repositories',
+                           action='check_for_updates',
+                           repository_id=None )
+
     # ==== Trace/Metrics Logger
     # Connect logger from app
     if app.trace_logger:

lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

@@ -2006,41 +2006,8 @@ def update_to_changeset_revision( self, trans, **kwd ):
 
     @web.expose
     @web.require_admin
-    def update_tool_shed_status_for_installed_repository( self, trans, all_installed_repositories=False, **kwd ):
-        message = escape( kwd.get( 'message', '' ) )
-        status = kwd.get( 'status', 'done' )
-        if all_installed_repositories:
-            success_count = 0
-            repository_names_not_updated = []
-            updated_count = 0
-            for repository in trans.install_model.context.query( trans.install_model.ToolShedRepository ) \
-                                                         .filter( trans.install_model.ToolShedRepository.table.c.deleted == false() ):
-                ok, updated = \
-                    repository_util.check_or_update_tool_shed_status_for_installed_repository( trans.app, repository )
-                if ok:
-                    success_count += 1
-                else:
-                    repository_names_not_updated.append( '<b>%s</b>' % escape( str( repository.name ) ) )
-                if updated:
-                    updated_count += 1
-            message = "Checked the status in the tool shed for %d repositories.  " % success_count
-            message += "Updated the tool shed status for %d repositories.  " % updated_count
-            if repository_names_not_updated:
-                message += "Unable to retrieve status from the tool shed for the following repositories:\n"
-                message += ", ".join( repository_names_not_updated )
-        else:
-            repository_id = kwd.get( 'id', None )
-            repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id )
-            ok, updated = \
-                repository_util.check_or_update_tool_shed_status_for_installed_repository( trans.app, repository )
-            if ok:
-                if updated:
-                    message = "The tool shed status for repository <b>%s</b> has been updated." % escape( str( repository.name ) )
-                else:
-                    message = "The status has not changed in the tool shed for repository <b>%s</b>." % escape( str( repository.name ) )
-            else:
-                message = "Unable to retrieve status from the tool shed for repository <b>%s</b>." % escape( str( repository.name ) )
-                status = 'error'
+    def update_tool_shed_status_for_installed_repository( self, trans, **kwd ):
+        message, status = repository_util.check_for_updates( trans.app, trans.install_model, kwd.get( 'id', None ) )
         return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
                                                           action='browse_repositories',
                                                           message=message,

lib/tool_shed/util/repository_util.py

@@ -408,6 +408,43 @@ def handle_role_associations( app, role, repository, **kwd ):
     return associations_dict
 
 
+def check_for_updates( app, model, repository_id=None ):
+    message = ''
+    status = 'ok'
+    if repository_id is None:
+        success_count = 0
+        repository_names_not_updated = []
+        updated_count = 0
+        for repository in model.context.query( model.ToolShedRepository ) \
+                                       .filter( model.ToolShedRepository.table.c.deleted == false() ):
+            ok, updated = \
+                check_or_update_tool_shed_status_for_installed_repository( app, repository )
+            if ok:
+                success_count += 1
+            else:
+                repository_names_not_updated.append( '<b>%s</b>' % escape( str( repository.name ) ) )
+            if updated:
+                updated_count += 1
+        message = "Checked the status in the tool shed for %d repositories.  " % success_count
+        message += "Updated the tool shed status for %d repositories.  " % updated_count
+        if repository_names_not_updated:
+            message += "Unable to retrieve status from the tool shed for the following repositories:\n"
+            message += ", ".join( repository_names_not_updated )
+    else:
+        repository = suc.get_tool_shed_repository_by_id( app, repository_id )
+        ok, updated = \
+            check_or_update_tool_shed_status_for_installed_repository( app, repository )
+        if ok:
+            if updated:
+                message = "The tool shed status for repository <b>%s</b> has been updated." % escape( str( repository.name ) )
+            else:
+                message = "The status has not changed in the tool shed for repository <b>%s</b>." % escape( str( repository.name ) )
+        else:
+            message = "Unable to retrieve status from the tool shed for repository <b>%s</b>." % escape( str( repository.name ) )
+            status = 'error'
+    return message, status
+
+
 def validate_repository_name( app, name, user ):
     """
     Validate whether the given name qualifies as a new TS repo name.

lib/tool_shed/util/shed_util_common.py

@@ -414,8 +414,8 @@ def get_repo_info_tuple_contents( repo_info_tuple ):
 
 def get_repositories_by_category( app, category_id ):
     sa_session = app.model.context.current
-    repositories = sa_session.query( app.model.Category ).get( category_id )
-    return [ repo.repository.to_dict() for repo in foo.repositories ]
+    resultset = sa_session.query( app.model.Category ).get( category_id )
+    return [ repo.repository.to_dict() for repo in resultset.repositories ]
 
 
 def get_repository_and_repository_dependencies_from_repo_info_dict( app, repo_info_dict ):