Merge pull request #1821 from davebx/toolshed_decouple_api

Cherry-picked changes from pull request #1392.
2026-09-24 16:30:27 +08:00 · 2016-03-03 12:17:14 -05:00
parent 779793810d b15a7ff06d
commit 02ed07ca82
13 changed files with 262 additions and 104 deletions
@@ -288,8 +288,9 @@ class SelectField(BaseField):
    <div><input type="checkbox" name="bar" value="3" id="bar|3"><label class="inline" for="bar|3">automatic</label></div>
    <div><input type="checkbox" name="bar" value="4" id="bar|4" checked='checked'><label class="inline" for="bar|4">bazooty</label></div>
    """
-    def __init__( self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=None, size=None ):
+    def __init__( self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=None, size=None, field_id=None ):
        self.name = name
+        self.field_id = field_id
        self.multiple = multiple or False
        self.size = size
        self.options = list()
@@ -312,7 +313,11 @@ class SelectField(BaseField):
    def add_option( self, text, value, selected=False ):
        self.options.append( ( text, value, selected ) )

-    def get_html( self, prefix="", disabled=False ):
+    def get_html( self, prefix="", disabled=False, extra_attr=None ):
+        if extra_attr is not None:
+            self.extra_attributes = ' %s' % ' '.join( [ '%s="%s"' % ( k, escape( v ) ) for k, v in extra_attr.items() ] )
+        else:
+            self.extra_attributes = ''
        if self.display == "checkboxes":
            return self.get_html_checkboxes( prefix, disabled )
        elif self.display == "radio":
@@ -335,8 +340,8 @@ class SelectField(BaseField):
            selected_text = ""
            if selected:
                selected_text = " checked='checked'"
-            rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s" id="%s"%s%s><label class="inline" for="%s">%s</label></div>'
-                         % ( style, prefix, self.name, escaped_value, uniq_id, selected_text, self.get_disabled_str( disabled ), uniq_id, escape( text, quote=True ) ) )
+            rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s" id="%s"%s%s%s><label class="inline" for="%s">%s</label></div>'
+                         % ( style, prefix, self.name, escaped_value, uniq_id, selected_text, self.get_disabled_str( disabled ), self.extra_attributes, uniq_id, escape( text, quote=True ) ) )
            ctr += 1
        return unicodify( "\n".join( rval ) )

@@ -352,7 +357,7 @@ class SelectField(BaseField):
            selected_text = ""
            if selected:
                selected_text = " checked='checked'"
-            rval.append( '<div%s><input type="radio" name="%s%s"%s value="%s" id="%s"%s%s><label class="inline" for="%s">%s</label></div>'
+            rval.append( '<div%s><input type="radio" name="%s%s"%s value="%s" id="%s"%s%s%s><label class="inline" for="%s">%s</label></div>'
                         % ( style,
                             prefix,
                             self.name,
@@ -361,6 +366,7 @@ class SelectField(BaseField):
                             uniq_id,
                             selected_text,
                             self.get_disabled_str( disabled ),
+                             self.extra_attributes,
                             uniq_id,
                             text ) )
            ctr += 1
@@ -388,8 +394,12 @@ class SelectField(BaseField):
            rval.append( '<option value="%s"%s>%s</option>' % ( escape( unicodify( value ), quote=True ), selected_text, escape( unicodify( text ), quote=True ) ) )
        if last_selected_value:
            last_selected_value = ' last_selected_value="%s"' % escape( unicodify( last_selected_value ), quote=True )
-        rval.insert( 0, '<select name="%s%s"%s%s%s%s%s>'
-                     % ( prefix, self.name, multiple, size, self.refresh_on_change_text, last_selected_value, self.get_disabled_str( disabled ) ) )
+        if self.field_id is not None:
+            id_string = ' id="%s"' % self.field_id
+        else:
+            id_string = ''
+        rval.insert( 0, '<select name="%s%s"%s%s%s%s%s%s%s>'
+                     % ( prefix, self.name, multiple, size, self.refresh_on_change_text, last_selected_value, self.get_disabled_str( disabled ), id_string, self.extra_attributes ) )
        rval.append( '</select>' )
        return unicodify( "\n".join( rval ) )

@@ -15,8 +15,11 @@ log = logging.getLogger( __name__ )
 class CategoriesController( BaseAPIController ):
    """RESTful controller for interactions with categories in the Tool Shed."""

+    def __get_repository_count( self, trans, category_name ):
+        return self.app.repository_registry.viewable_repositories_and_suites_by_category.get( category_name, 0 )
+
    def __get_value_mapper( self, trans ):
-        value_mapper = { 'id' : trans.security.encode_id }
+        value_mapper = { 'id': trans.security.encode_id }
        return value_mapper

    @expose_api
@@ -41,11 +44,11 @@ class CategoriesController( BaseAPIController ):
            if not description:
                # Default the description to the name.
                description = name
-            if suc.get_category_by_name( trans.app, name ):
+            if suc.get_category_by_name( self.app, name ):
                raise exceptions.Conflict( 'A category with that name already exists.' )
            else:
                # Create the category
-                category = trans.app.model.Category( name=name, description=description )
+                category = self.app.model.Category( name=name, description=description )
                trans.sa_session.add( category )
                trans.sa_session.flush()
                category_dict = category.to_dict( view='element',
@@ -58,6 +61,30 @@ class CategoriesController( BaseAPIController ):
            raise exceptions.RequestParameterMissingException( 'Missing required parameter "name".' )
        return category_dict

+    @expose_api_anonymous_and_sessionless
+    def get_repositories( self, trans, category_id, **kwd ):
+        """
+        GET /api/categories/{encoded_category_id}/repositories
+        Return information about the provided category and the repositories in that category.
+
+        :param id: the encoded id of the Category object
+
+        Example: GET localhost:9009/api/categories/f9cad7b01a472135/repositories
+        """
+        category = suc.get_category( self.app, category_id )
+        if category is None:
+            category_dict = dict( message='Unable to locate category record for id %s.' % ( str( id ) ),
+                                  status='error' )
+            return category_dict
+        category_dict = category.to_dict( view='element',
+                                          value_mapper=self.__get_value_mapper( trans ) )
+        category_dict[ 'url' ] = web.url_for( controller='categories',
+                                              action='show',
+                                              id=trans.security.encode_id( category.id ) )
+        repositories = suc.get_repositories_by_category( self.app, category.id )
+        category_dict[ 'repositories' ] = repositories
+        return category_dict
+
    @expose_api_anonymous_and_sessionless
    def index( self, trans, deleted=False, **kwd ):
        """
@@ -72,14 +99,15 @@ class CategoriesController( BaseAPIController ):
        deleted = util.asbool( deleted )
        if deleted and not trans.user_is_admin():
            raise exceptions.AdminRequiredException( 'Only administrators can query deleted categories.' )
-        for category in trans.sa_session.query( trans.app.model.Category ) \
-                                        .filter( trans.app.model.Category.table.c.deleted == deleted ) \
-                                        .order_by( trans.app.model.Category.table.c.name ):
+        for category in trans.sa_session.query( self.app.model.Category ) \
+                                        .filter( self.app.model.Category.table.c.deleted == deleted ) \
+                                        .order_by( self.app.model.Category.table.c.name ):
            category_dict = category.to_dict( view='collection',
                                              value_mapper=self.__get_value_mapper( trans ) )
            category_dict[ 'url' ] = web.url_for( controller='categories',
                                                  action='show',
                                                  id=trans.security.encode_id( category.id ) )
+            category_dict[ 'repositories' ] = self.app.repository_registry.viewable_repositories_and_suites_by_category.get( category.name, 0 )
            category_dicts.append( category_dict )
        return category_dicts

@@ -93,7 +121,7 @@ class CategoriesController( BaseAPIController ):

        Example: GET localhost:9009/api/categories/f9cad7b01a472135
        """
-        category = suc.get_category( trans.app, id )
+        category = suc.get_category( self.app, id )
        if category is None:
            category_dict = dict( message='Unable to locate category record for id %s.' % ( str( id ) ),
                                  status='error' )
@@ -73,7 +73,7 @@ class RepositoriesController( BaseAPIController ):
        owner = payload.get( 'owner', '' )
        if not owner:
            raise HTTPBadRequest( detail="Missing required parameter 'owner'." )
-        repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
+        repository = suc.get_repository_by_name_and_owner( self.app, name, owner )
        if repository is None:
            error_message = 'Cannot locate repository with name %s and owner %s,' % ( str( name ), str( owner ) )
            log.debug( error_message )
@@ -81,14 +81,14 @@ class RepositoriesController( BaseAPIController ):
            response_dict[ 'message' ] = error_message
            return response_dict
        # Update the repository registry.
-        trans.app.repository_registry.add_entry( repository )
+        self.app.repository_registry.add_entry( repository )
        response_dict[ 'status' ] = 'ok'
        response_dict[ 'message' ] = 'Entries for repository %s owned by %s have been added to the Tool Shed repository registry.' \
            % ( name, owner )
        return response_dict

    @web.expose_api_anonymous
-    def get_ordered_installable_revisions( self, trans, name, owner, **kwd ):
+    def get_ordered_installable_revisions( self, trans, **kwd ):
        """
        GET /api/repositories/get_ordered_installable_revisions

@@ -98,23 +98,21 @@ class RepositoriesController( BaseAPIController ):
        Returns the ordered list of changeset revision hash strings that are associated with installable revisions.
        As in the changelog, the list is ordered oldest to newest.
        """
-        # Example URL: http://localhost:9009/api/repositories/get_installable_revisions?name=add_column&owner=test
-        if name and owner:
+        # Example URL: http://localhost:9009/api/repositories/get_ordered_installable_revisions?name=add_column&owner=test
+        name = kwd.get( 'name', None )
+        owner = kwd.get( 'owner', None )
+        tsr_id = kwd.get( 'tsr_id', None )
+        if None not in [ name, owner ]:
            # Get the repository information.
-            repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
-            if repository is None:
-                error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
-                error_message += "cannot locate repository %s owned by %s." % ( str( name ), str( owner ) )
-                log.debug( error_message )
-                return []
-            repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
-            ordered_installable_revisions = suc.get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True )
-            return ordered_installable_revisions
+            repository = suc.get_repository_by_name_and_owner( self.app, name, owner )
+        elif tsr_id is not None:
+            repository = suc.get_repository_in_tool_shed( self.app, tsr_id )
        else:
            error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
-            error_message += "invalid name %s or owner %s received." % ( str( name ), str( owner ) )
+            error_message += "invalid parameters received." % ( str( name ), str( owner ) )
            log.debug( error_message )
            return []
+        return repository.ordered_installable_revisions( self.app )

    @web.expose_api_anonymous
    def get_repository_revision_install_info( self, trans, name, owner, changeset_revision, **kwd ):
@@ -187,7 +185,7 @@ class RepositoriesController( BaseAPIController ):
        # http://<xyz>/api/repositories/get_repository_revision_install_info?name=<n>&owner=<o>&changeset_revision=<cr>
        if name and owner and changeset_revision:
            # Get the repository information.
-            repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
+            repository = suc.get_repository_by_name_and_owner( self.app, name, owner )
            if repository is None:
                log.debug( 'Cannot locate repository %s owned by %s' % ( str( name ), str( owner ) ) )
                return {}, {}, {}
@@ -198,15 +196,15 @@ class RepositoriesController( BaseAPIController ):
                                                    action='show',
                                                    id=encoded_repository_id )
            # Get the repository_metadata information.
-            repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app,
+            repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app,
                                                                                     encoded_repository_id,
                                                                                     changeset_revision )
            if repository_metadata is None:
                # The changeset_revision column in the repository_metadata table has been updated with a new
                # value value, so find the changeset_revision to which we need to update.
-                repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
+                repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False )
                new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
-                repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app,
+                repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app,
                                                                                         encoded_repository_id,
                                                                                         new_changeset_revision )
                changeset_revision = new_changeset_revision
@@ -226,7 +224,7 @@ class RepositoriesController( BaseAPIController ):
                    includes_tools_for_display_in_tool_panel, \
                    has_repository_dependencies, \
                    has_repository_dependencies_only_if_compiling_contained_td = \
-                    repository_util.get_repo_info_dict( trans.app,
+                    repository_util.get_repo_info_dict( self.app,
                                                        trans.user,
                                                        encoded_repository_id,
                                                        changeset_revision )
@@ -242,10 +240,30 @@ class RepositoriesController( BaseAPIController ):
            log.debug( debug_msg )
            return {}, {}, {}

+    @web.expose_api_anonymous
+    def get_installable_revisions( self, trans, **kwd ):
+        """
+        GET /api/repositories/get_installable_revisions
+
+        :param tsr_id: the encoded toolshed ID of the repository
+
+        Returns a list of lists of changesets, in the format [ [ 0, fbb391dc803c ], [ 1, 9d9ec4d9c03e ], [ 2, 9b5b20673b89 ], [ 3, e8c99ce51292 ] ].
+        """
+        # Example URL: http://localhost:9009/api/repositories/get_installable_revisions?tsr_id=9d37e53072ff9fa4
+        tsr_id = kwd.get( 'tsr_id', None )
+        if tsr_id is not None:
+            repository = suc.get_repository_in_tool_shed( self.app, tsr_id )
+        else:
+            error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
+            error_message += "missing or invalid parameter received."
+            log.debug( error_message )
+            return []
+        return repository.installable_revisions( self.app )
+
    def __get_value_mapper( self, trans ):
-        value_mapper = { 'id' : trans.security.encode_id,
-                         'repository_id' : trans.security.encode_id,
-                         'user_id' : trans.security.encode_id }
+        value_mapper = { 'id': trans.security.encode_id,
+                         'repository_id': trans.security.encode_id,
+                         'user_id': trans.security.encode_id }
        return value_mapper

    @web.expose_api
@@ -283,7 +301,7 @@ class RepositoriesController( BaseAPIController ):
        except tarfile.ReadError, e:
            log.debug( 'Error opening capsule file %s: %s' % ( str( capsule_file_name ), str( e ) ) )
            return {}
-        irm = capsule_manager.ImportRepositoryManager( trans.app,
+        irm = capsule_manager.ImportRepositoryManager( self.app,
                                                       trans.request.host,
                                                       trans.user,
                                                       trans.user_is_admin() )
@@ -386,16 +404,16 @@ class RepositoriesController( BaseAPIController ):
                response = json.dumps( search_results )
            return response

-        clause_list = [ and_( trans.app.model.Repository.table.c.deprecated == false(),
-                              trans.app.model.Repository.table.c.deleted == deleted ) ]
+        clause_list = [ and_( self.app.model.Repository.table.c.deprecated == false(),
+                              self.app.model.Repository.table.c.deleted == deleted ) ]
        if owner is not None:
-            clause_list.append( and_( trans.app.model.User.table.c.username == owner,
-                                      trans.app.model.Repository.table.c.user_id == trans.app.model.User.table.c.id ) )
+            clause_list.append( and_( self.app.model.User.table.c.username == owner,
+                                      self.app.model.Repository.table.c.user_id == self.app.model.User.table.c.id ) )
        if name is not None:
-            clause_list.append( trans.app.model.Repository.table.c.name == name )
-        for repository in trans.sa_session.query( trans.app.model.Repository ) \
+            clause_list.append( self.app.model.Repository.table.c.name == name )
+        for repository in trans.sa_session.query( self.app.model.Repository ) \
                                          .filter( *clause_list ) \
-                                          .order_by( trans.app.model.Repository.table.c.name ):
+                                          .order_by( self.app.model.Repository.table.c.name ):
            repository_dict = repository.to_dict( view='collection',
                                                  value_mapper=self.__get_value_mapper( trans ) )
            repository_dict[ 'category_ids' ] = \
@@ -471,7 +489,7 @@ class RepositoriesController( BaseAPIController ):
        owner = payload.get( 'owner', '' )
        if not owner:
            raise HTTPBadRequest( detail="Missing required parameter 'owner'." )
-        repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
+        repository = suc.get_repository_by_name_and_owner( self.app, name, owner )
        if repository is None:
            error_message = 'Cannot locate repository with name %s and owner %s,' % ( str( name ), str( owner ) )
            log.debug( error_message )
@@ -479,7 +497,7 @@ class RepositoriesController( BaseAPIController ):
            response_dict[ 'message' ] = error_message
            return response_dict
        # Update the repository registry.
-        trans.app.repository_registry.remove_entry( repository )
+        self.app.repository_registry.remove_entry( repository )
        response_dict[ 'status' ] = 'ok'
        response_dict[ 'message' ] = 'Entries for repository %s owned by %s have been removed from the Tool Shed repository registry.' \
            % ( name, owner )
@@ -504,7 +522,7 @@ class RepositoriesController( BaseAPIController ):
            my_writable = True
        handled_repository_ids = []
        repository_ids = []
-        rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user )
+        rmm = repository_metadata_manager.RepositoryMetadataManager( self.app, trans.user )
        query = rmm.get_query_for_setting_metadata_on_repositories( my_writable=my_writable, order=False )
        # Make sure repositories of type tool_dependency_definition are first in the list.
        for repository in query:
@@ -546,7 +564,7 @@ class RepositoriesController( BaseAPIController ):
                rmm.reset_all_metadata_on_repository_in_tool_shed()
                rmm_invalid_file_tups = rmm.get_invalid_file_tups()
                if rmm_invalid_file_tups:
-                    message = tool_util.generate_message_for_invalid_tools( trans.app,
+                    message = tool_util.generate_message_for_invalid_tools( self.app,
                                                                            rmm_invalid_file_tups,
                                                                            repository,
                                                                            None,
@@ -563,7 +581,7 @@ class RepositoriesController( BaseAPIController ):
            status = '%s : %s' % ( str( repository.name ), message )
            results[ 'repository_status' ].append( status )
            return results
-        rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app,
+        rmm = repository_metadata_manager.RepositoryMetadataManager( app=self.app,
                                                                     user=trans.user,
                                                                     resetting_all_metadata_on_repository=True,
                                                                     updating_installed_repository=False,
@@ -627,7 +645,7 @@ class RepositoriesController( BaseAPIController ):
            results = dict( start_time=start_time,
                            repository_status=[] )
            try:
-                rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app,
+                rmm = repository_metadata_manager.RepositoryMetadataManager( app=self.app,
                                                                             user=trans.user,
                                                                             repository=repository,
                                                                             resetting_all_metadata_on_repository=True,
@@ -636,7 +654,7 @@ class RepositoriesController( BaseAPIController ):
                rmm.reset_all_metadata_on_repository_in_tool_shed()
                rmm_invalid_file_tups = rmm.get_invalid_file_tups()
                if rmm_invalid_file_tups:
-                    message = tool_util.generate_message_for_invalid_tools( trans.app,
+                    message = tool_util.generate_message_for_invalid_tools( self.app,
                                                                            rmm_invalid_file_tups,
                                                                            repository,
                                                                            None,
@@ -656,7 +674,7 @@ class RepositoriesController( BaseAPIController ):

        repository_id = payload.get( 'repository_id', None )
        if repository_id is not None:
-            repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
+            repository = suc.get_repository_in_tool_shed( self.app, repository_id )
            start_time = strftime( "%Y-%m-%d %H:%M:%S" )
            log.debug( "%s...resetting metadata on repository %s" % ( start_time, str( repository.name ) ) )
            results = handle_repository( trans, start_time, repository )
@@ -685,7 +703,7 @@ class RepositoriesController( BaseAPIController ):
        except Exception:
            raise MalformedId( 'The given id is invalid.' )

-        repository = suc.get_repository_in_tool_shed( trans.app, id )
+        repository = suc.get_repository_in_tool_shed( self.app, id )
        if repository is None:
            raise ObjectNotFound( 'Unable to locate repository for the given id.' )
        repository_dict = repository.to_dict( view='element',
@@ -695,6 +713,37 @@ class RepositoriesController( BaseAPIController ):
            [ trans.security.encode_id( x.category.id ) for x in repository.categories ]
        return repository_dict

+    @expose_api_anonymous_and_sessionless
+    def show_tools( self, trans, id, changeset, **kwd ):
+        repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app,
+                                                                                 id,
+                                                                                 changeset )
+        if repository_metadata is not None:
+            encoded_repository_metadata_id = trans.security.encode_id( repository_metadata.id )
+            repository_metadata_dict = repository_metadata.to_dict( view='collection',
+                                                                    value_mapper=self.__get_value_mapper( trans ) )
+            repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions',
+                                                             action='show',
+                                                             id=encoded_repository_metadata_id )
+            if 'tools' in repository_metadata.metadata:
+                repository_metadata_dict[ 'valid_tools' ] = repository_metadata.metadata[ 'tools' ]
+            # Get the repo_info_dict for installing the repository.
+            repo_info_dict, \
+                includes_tools, \
+                includes_tool_dependencies, \
+                includes_tools_for_display_in_tool_panel, \
+                has_repository_dependencies, \
+                has_repository_dependencies_only_if_compiling_contained_td = \
+                repository_util.get_repo_info_dict( self.app,
+                                                    trans.user,
+                                                    id,
+                                                    changeset )
+            return repository_metadata_dict
+        else:
+            log.debug( "Unable to locate repository_metadata record for repository id %s and changeset_revision %s" %
+                       ( str( id ), str( changeset ) ) )
+            return {}
+
    @expose_api_anonymous_and_sessionless
    def metadata( self, trans, id, **kwd ):
        """
@@ -714,6 +763,7 @@ class RepositoriesController( BaseAPIController ):
            trans.security.decode_id( id )
        except Exception:
            raise MalformedId( 'The given id is invalid.' )
+        recursive = util.asbool( kwd.get( 'recursive', 'True' ) )
        all_metadata = {}
        repository = suc.get_repository_in_tool_shed( self.app, id )
        for changeset, changehash in repository.installable_revisions( self.app ):
@@ -722,15 +772,15 @@ class RepositoriesController( BaseAPIController ):
                continue
            metadata_dict = metadata.to_dict( value_mapper={ 'id': self.app.security.encode_id, 'repository_id': self.app.security.encode_id } )
            metadata_dict[ 'repository' ] = repository.to_dict( value_mapper={ 'id': self.app.security.encode_id } )
-            if metadata.has_repository_dependencies:
+            if metadata.has_repository_dependencies and recursive:
                metadata_dict[ 'repository_dependencies' ] = metadata_util.get_all_dependencies( self.app, metadata, processed_dependency_links=[] )
            else:
                metadata_dict[ 'repository_dependencies' ] = []
-            if metadata.includes_tool_dependencies:
+            if metadata.includes_tool_dependencies and recursive:
                metadata_dict[ 'tool_dependencies' ] = repository.get_tool_dependencies( changehash )
            else:
                metadata_dict[ 'tool_dependencies' ] = {}
-            all_metadata[ '%s:%s' % ( changeset, changehash ) ] = metadata_dict
+            all_metadata[ '%s:%s' % ( int( changeset ), changehash ) ] = metadata_dict
        return all_metadata

    @expose_api
@@ -779,7 +829,7 @@ class RepositoriesController( BaseAPIController ):
            category_ids=category_ids,
        )

-        repo, message = repository_util.update_repository( app=trans.app, trans=trans, id=id, **update_kwds )
+        repo, message = repository_util.update_repository( app=self.app, trans=trans, id=id, **update_kwds )
        if repo is None:
            if "You are not the owner" in message:
                raise InsufficientPermissionsException( message )
@@ -835,11 +885,11 @@ class RepositoriesController( BaseAPIController ):
        if repo_type not in rt_util.types:
            raise RequestParameterInvalidException( 'This repository type is not valid' )

-        invalid_message = repository_util.validate_repository_name( trans.app, name, trans.user )
+        invalid_message = repository_util.validate_repository_name( self.app, name, trans.user )
        if invalid_message:
            raise RequestParameterInvalidException( invalid_message )

-        repo, message = repository_util.create_repository( app=trans.app,
+        repo, message = repository_util.create_repository( app=self.app,
                                                           name=name,
                                                           type=repo_type,
                                                           description=synopsis,
@@ -871,24 +921,24 @@ class RepositoriesController( BaseAPIController ):
        """

        # Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135
-        rdah = attribute_handlers.RepositoryDependencyAttributeHandler( trans.app, unpopulate=False )
-        tdah = attribute_handlers.ToolDependencyAttributeHandler( trans.app, unpopulate=False )
+        rdah = attribute_handlers.RepositoryDependencyAttributeHandler( self.app, unpopulate=False )
+        tdah = attribute_handlers.ToolDependencyAttributeHandler( self.app, unpopulate=False )

-        repository = suc.get_repository_in_tool_shed( trans.app, id )
+        repository = suc.get_repository_in_tool_shed( self.app, id )

        if not ( trans.user_is_admin() or
-                 trans.app.security_agent.user_can_administer_repository( trans.user, repository ) or
-                 trans.app.security_agent.can_push( trans.app, trans.user, repository ) ):
+                 self.app.security_agent.user_can_administer_repository( trans.user, repository ) or
+                 self.app.security_agent.can_push( self.app, trans.user, repository ) ):
            trans.response.status = 400
            return {
                "err_msg": "You do not have permission to update this repository.",
            }

-        repo_dir = repository.repo_path( trans.app )
-        repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False )
+        repo_dir = repository.repo_path( self.app )
+        repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False )

        upload_point = commit_util.get_upload_point( repository, **kwd )
-        tip = repository.tip( trans.app )
+        tip = repository.tip( self.app )

        file_data = payload.get('file')
        # Code stolen from gx's upload_common.py
@@ -938,12 +988,12 @@ class RepositoriesController( BaseAPIController ):
            # Update the repository files for browsing.
            hg_util.update_repository( repo )
            # Get the new repository tip.
-            if tip == repository.tip( trans.app ):
+            if tip == repository.tip( self.app ):
                trans.response.status = 400
                message = 'No changes to repository.'
                ok = False
            else:
-                rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app,
+                rmm = repository_metadata_manager.RepositoryMetadataManager( app=self.app,
                                                                             user=trans.user,
                                                                             repository=repository )
                status, error_message = \
@@ -109,12 +109,18 @@ def app_factory( global_conf, **kwargs ):
                            name_prefix='category_',
                            path_prefix='/api',
                            parent_resources=dict( member_name='category', collection_name='categories' ) )
+    webapp.mapper.connect( 'repositories_in_category',
+                           '/api/categories/{category_id}/repositories',
+                           controller='categories',
+                           action='get_repositories',
+                           conditions=dict( method=[ "GET" ] ) )
    webapp.mapper.resource( 'repository',
                            'repositories',
                            controller='repositories',
                            collection={ 'add_repository_registry_entry': 'POST',
                                         'get_repository_revision_install_info': 'GET',
                                         'get_ordered_installable_revisions': 'GET',
+                                         'get_installable_revisions': 'GET',
                                         'remove_repository_registry_entry': 'POST',
                                         'repository_ids_for_setting_metadata': 'GET',
                                         'reset_metadata_on_repositories': 'POST',
@@ -152,6 +158,11 @@ def app_factory( global_conf, **kwargs ):
                           controller='repositories',
                           action='metadata',
                           conditions=dict( method=[ "GET" ] ) )
+    webapp.mapper.connect( 'repository_show_tools',
+                           '/api/repositories/{id}/{changeset}/show_tools',
+                           controller='repositories',
+                           action='show_tools',
+                           conditions=dict( method=[ "GET" ] ) )
    webapp.mapper.connect( 'create_repository',
                           '/api/repositories',
                           controller='repositories',
@@ -1618,22 +1618,10 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
        owner = kwd.get( 'owner', None )
        changeset_revision = kwd.get( 'changeset_revision', None )
        repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
-        # We aren't concerned with repositories of type tool_dependency_definition here if a
-        # repository_metadata record is not returned because repositories of this type will never
-        # have repository dependencies. However, if a readme file is uploaded, or some other change
-        # is made that does not create a new downloadable changeset revision but updates the existing
-        # one, we still want to be able to get repository dependencies.
-        repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( trans.app,
-                                                                                          repository,
-                                                                                          changeset_revision )
-        if repository_metadata:
-            metadata = repository_metadata.metadata
-            if metadata:
-                toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' )
-                rb = relation_builder.RelationBuilder( trans.app, repository, repository_metadata, toolshed_base_url )
-                repository_dependencies = rb.get_repository_dependencies_for_changeset_revision()
-                if repository_dependencies:
-                    return encoding_util.tool_shed_encode( repository_dependencies )
+        # get_repository_dependencies( self, app, changeset, toolshed_url )
+        dependencies = repository.get_repository_dependencies( trans.app, changeset_revision, web.url_for( '/', qualified=True ) )
+        if dependencies:
+            return encoding_util.tool_shed_encode( dependencies )
        return ''

    @web.expose
@@ -1724,13 +1712,9 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
        owner = kwd.get( 'owner', None )
        changeset_revision = kwd.get( 'changeset_revision', None )
        repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
-        for downloadable_revision in repository.downloadable_revisions:
-            if downloadable_revision.changeset_revision == changeset_revision:
-                break
-        metadata = downloadable_revision.metadata
-        tool_dependencies = metadata.get( 'tool_dependencies', '' )
-        if tool_dependencies:
-            return encoding_util.tool_shed_encode( tool_dependencies )
+        dependencies = repository.get_tool_dependencies( changeset_revision )
+        if dependencies is not None:
+            return encoding_util.tool_shed_encode( dependencies )
        return ''

    @web.expose
@@ -8,8 +8,8 @@ from galaxy.util.bunch import Bunch
 from galaxy.util.hash_util import new_secure_hash
 from galaxy.util.dictifiable import Dictifiable
 import tool_shed.repository_types.util as rt_util
-import tool_shed.util.shed_util_common as suc
 from tool_shed.dependencies.repository import relation_builder
+from tool_shed.util import shed_util_common as suc

 from mercurial import hg
 from mercurial import ui
@@ -253,14 +253,14 @@ class Repository( object, Dictifiable ):
    def installable_revisions( self, app ):
        return suc.get_metadata_revisions( self, hg.repository( ui.ui(), self.repo_path( app ) ), sort_revisions=True )

-    def ordered_installable_revisions( self, app ):
-        return suc.get_ordered_metadata_changeset_revisions( self, hg.repository( ui.ui(), self.repo_path( app ) ), downloadable=True )
-
    def is_new( self, app ):
        repo = hg.repository( ui.ui(), self.repo_path( app ) )
        tip_ctx = repo.changectx( repo.changelog.tip() )
        return tip_ctx.rev() < 0

+    def ordered_installable_revisions( self, app ):
+        return suc.get_ordered_metadata_changeset_revisions( self, hg.repository( ui.ui(), self.repo_path( app ) ), downloadable=True )
+
    def repo_path( self, app ):
        return app.hgweb_config_manager.get_entry( os.path.join( "repos", self.user.username, self.name ) )

@@ -201,7 +201,7 @@ Category.table = Table( "category", metadata,
                        Column( "create_time", DateTime, default=now ),
                        Column( "update_time", DateTime, default=now, onupdate=now ),
                        Column( "name", TrimmedString( 255 ), index=True, unique=True ),
-                        Column( "description" , TEXT ),
+                        Column( "description", TEXT ),
                        Column( "deleted", Boolean, index=True, default=False ) )

 Tag.table = Table( "tag", metadata,
@@ -341,7 +341,7 @@ def remove_protocol_from_tool_shed_url( tool_shed_url ):
    return util.remove_protocol_from_url( tool_shed_url )


-def tool_shed_get( app, base_url, pathspec=[], params={} ):
+def tool_shed_get( app, base_url, pathspec=None, params=None ):
    """Make contact with the tool shed via the uri provided."""
    registry = app.tool_shed_registry
    # urllib2 auto-detects system proxies, when passed a Proxyhandler.
@@ -71,6 +71,11 @@ def get_latest_repository_metadata( app, decoded_repository_id, downloadable=Fal
                                                              changeset_revision )


+def get_metadata_by_id( app, metadata_id ):
+    sa_session = app.model.context.current
+    return sa_session.query( app.model.RepositoryMetadata ).filter( app.model.RepositoryMetadata.table.c.id == metadata_id ).one()
+
+
 def get_previous_metadata_changeset_revision( repository, repo, before_changeset_revision, downloadable=True ):
    """
    Return the changeset_revision in the repository changelog that has associated metadata prior to
@@ -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.
@@ -341,7 +341,9 @@ def get_ids_of_tool_shed_repositories_being_installed( app, as_string=False ):
    return installing_repository_ids


-def get_latest_downloadable_changeset_revision( app, repository, repo ):
+def get_latest_downloadable_changeset_revision( app, repository, repo=None ):
+    if repo is None:
+        repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
    repository_tip = repository.tip( app )
    repository_metadata = get_repository_metadata_by_changeset_revision( app, app.security.encode_id( repository.id ), repository_tip )
    if repository_metadata and repository_metadata.downloadable:
@@ -365,6 +367,21 @@ def get_tool_dependency_definition_metadata_from_tool_shed( app, tool_shed_url,
    return metadata


+def get_metadata_changeset_revisions( repository, repo ):
+    """
+    Return an unordered list of changeset_revisions and changeset numbers that are defined as installable.
+    """
+    changeset_tups = []
+    for repository_metadata in repository.downloadable_revisions:
+        ctx = hg_util.get_changectx_for_changeset( repo, repository_metadata.changeset_revision )
+        if ctx:
+            rev = ctx.rev()
+        else:
+            rev = -1
+        changeset_tups.append( ( rev, repository_metadata.changeset_revision ) )
+    return sorted( changeset_tups )
+
+
 def get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision ):
    """
    Return the installable changeset_revision in the repository changelog after the changeset to which
@@ -477,6 +494,22 @@ def get_repo_info_tuple_contents( repo_info_tuple ):
    return description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies


+def get_repositories_by_category( app, category_id ):
+    sa_session = app.model.context.current
+    resultset = sa_session.query( app.model.Category ).get( category_id )
+    repositories = []
+    default_value_mapper = { 'id': app.security.encode_id, 'user_id': app.security.encode_id }
+    for row in resultset.repositories:
+        repository_dict = row.repository.to_dict( value_mapper=default_value_mapper )
+        repository_dict[ 'metadata' ] = {}
+        for changeset, changehash in row.repository.installable_revisions( app ):
+            encoded_id = app.security.encode_id( row.repository.id )
+            metadata = get_repository_metadata_by_changeset_revision( app, encoded_id, changehash )
+            repository_dict[ 'metadata' ][ '%s:%s' % ( changeset, changehash ) ] = metadata.to_dict( value_mapper=default_value_mapper )
+        repositories.append( repository_dict )
+    return repositories
+
+
 def get_repository_and_repository_dependencies_from_repo_info_dict( app, repo_info_dict ):
    """Return a tool_shed_repository or repository record defined by the information in the received repo_info_dict."""
    repository_name = repo_info_dict.keys()[ 0 ]
@@ -34,7 +34,7 @@ def build_tool_panel_section_select_field( app ):
    options = []
    for section_id, section_name in app.toolbox.get_sections():
        options.append( ( section_name, section_id ) )
-    select_field = SelectField( name='tool_panel_section_id', display='radio' )
+    select_field = SelectField( name='tool_panel_section_id', field_id='tool_panel_section_select' )
    for option_tup in options:
        select_field.add_option( option_tup[ 0 ], option_tup[ 1 ] )
    return select_field
@@ -108,7 +108,7 @@ class TestInstallingCircularDependencies( ShedTwillTestCase ):
        self.display_installed_repository_manage_page( installed_filtering_repository )
        self.deactivate_repository( installed_filtering_repository )
        self.test_db_util.ga_refresh( installed_filtering_repository )
-        self.check_galaxy_repository_tool_panel_section( installed_filtering_repository, '' )
+        self.check_galaxy_repository_tool_panel_section( installed_filtering_repository, 'Get Data' )
        strings_displayed = [ 'Missing repository', 'filtering', 'freebayes_0040', 'user1', "Galaxy's freebayes tool for test 0040" ]
        self.display_installed_repository_manage_page( installed_freebayes_repository, strings_displayed=strings_displayed )
        self.check_galaxy_repository_db_status( filtering_repository_name,
@@ -133,7 +133,7 @@ class TestInstallingCircularDependencies( ShedTwillTestCase ):
        self.display_installed_repository_manage_page( installed_filtering_repository )
        self.deactivate_repository( installed_freebayes_repository )
        self.test_db_util.ga_refresh( installed_freebayes_repository )
-        self.check_galaxy_repository_tool_panel_section( installed_freebayes_repository, '' )
+        self.check_galaxy_repository_tool_panel_section( installed_freebayes_repository, 'Get Data' )
        strings_displayed = [ 'Missing repository', 'freebayes', 'filtering_0040', 'user1', "Galaxy's filtering tool for test 0040" ]
        self.display_installed_repository_manage_page( installed_filtering_repository, strings_displayed=strings_displayed )
        self.check_galaxy_repository_db_status( 'freebayes_0040',
@@ -148,7 +148,7 @@ class TestInstallingCircularDependencies( ShedTwillTestCase ):
        self.display_installed_repository_manage_page( installed_filtering_repository )
        self.deactivate_repository( installed_filtering_repository )
        self.test_db_util.ga_refresh( installed_filtering_repository )
-        self.check_galaxy_repository_tool_panel_section( installed_filtering_repository, '' )
+        self.check_galaxy_repository_tool_panel_section( installed_filtering_repository, 'Get Data' )
        strings_displayed = [ 'Missing repository', 'filtering', 'freebayes_0040', 'user1', "Galaxy's freebayes tool for test 0040" ]
        self.display_installed_repository_manage_page( installed_freebayes_repository, strings_displayed=strings_displayed )
        self.check_galaxy_repository_db_status( filtering_repository_name,