diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py index 156553c6cf9..e8f1b91caff 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -280,9 +280,9 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ): def browse_tool_dependencies( self, trans, **kwd ): if 'operation' in kwd: operation = kwd[ 'operation' ].lower() - if operation == "browse_repository": + if operation == "view_or_manage_repository": return trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repository', + action='view_or_manage_repository', **kwd ) ) return self.tool_dependencies_grid( trans, **kwd ) diff --git a/lib/tool_shed/grids/repository_grids.py b/lib/tool_shed/grids/repository_grids.py index 7f30816ddba..9f664185aee 100644 --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -643,7 +643,10 @@ class RepositoryMetadataGrid( grids.Grid ): class ChangesetRevisionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - return escape_html( repository_metadata.changeset_revision ) + repository = repository_metadata.repository + changeset_revision = repository_metadata.changeset_revision + changeset_revision_label = suc.get_revision_label( trans, repository, changeset_revision ) + return escape_html( changeset_revision_label ) class MaliciousColumn( grids.BooleanColumn ): @@ -719,6 +722,7 @@ class RepositoryMetadataGrid( grids.Grid ): default_sort_key = "Repository.name" columns = [ RepositoryNameColumn( "Repository name", + key="Repository.name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False ), RepositoryOwnerColumn( "Owner", @@ -743,8 +747,7 @@ class RepositoryMetadataGrid( grids.Grid ): .join( model.Repository ) \ .filter( and_( model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) + .join( model.User.table ) class RepositoryDependenciesGrid( RepositoryMetadataGrid ): @@ -767,22 +770,24 @@ class RepositoryDependenciesGrid( RepositoryMetadataGrid ): for index, rd_tup in enumerate( sorted_rd_tups ): name = rd_tup[ 1 ] owner = rd_tup[ 2 ] + changeset_revision = rd_tup[ 3 ] required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) if required_repository: required_repository_id = trans.security.encode_id( required_repository.id ) - rd_str += '' % required_repository_id - rd_str += 'name: %s | owner: %s | revision: %s' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 2 ] ), escape_html( rd_tup[ 3 ] ) ) + rd_str += '' % ( required_repository_id, changeset_revision ) + rd_str += 'Repository %s revision %s owned by %s' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 3 ] ), escape_html( rd_tup[ 2 ] ) ) if required_repository: rd_str += '' if index < num_tups - 1: rd_str += '
' return rd_str - title = "Repository dependency definitions in this tool shed" + title = "Valid repository dependency definitions in this tool shed" + default_sort_key = "Repository.name" columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -806,8 +811,7 @@ class RepositoryDependenciesGrid( RepositoryMetadataGrid ): .filter( and_( model.RepositoryMetadata.table.c.has_repository_dependencies == True, model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) + .join( model.User.table ) class ToolDependenciesGrid( RepositoryMetadataGrid ): @@ -850,10 +854,11 @@ class ToolDependenciesGrid( RepositoryMetadataGrid ): return td_str title = "Tool dependency definitions in this tool shed" + default_sort_key = "Repository.name" columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -877,8 +882,7 @@ class ToolDependenciesGrid( RepositoryMetadataGrid ): .filter( and_( model.RepositoryMetadata.table.c.includes_tool_dependencies == True, model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) + .join( model.User.table ) class ToolsGrid( RepositoryMetadataGrid ): @@ -893,21 +897,30 @@ class ToolsGrid( RepositoryMetadataGrid ): if metadata: tool_dicts = metadata.get( 'tools', [] ) if tool_dicts: - num_tool_dicts = len( tool_dicts ) - for index, tool_dict in enumerate( tool_dicts ): - tool_id = tool_dict[ 'id' ] - name = tool_dict[ 'name' ] - version = tool_dict[ 'version' ] - tool_str += '%s | %s | %s' % ( escape_html( tool_id ), escape_html( name ), escape_html( version ) ) - if index < num_tool_dicts - 1: + # Create tuples of the attributes we want so we can sort them by extension. + tool_tups = [] + for tool_dict in tool_dicts: + tool_id = tool_dict.get( 'id', '' ) + version = tool_dict.get( 'version', '' ) + # For now we'll just display tool id and version. + if tool_id and version: + tool_tups.append( ( tool_id, version ) ) + sorted_tool_tups = sorted( tool_tups, key=lambda tool_tup: tool_tup[ 0 ] ) + num_tool_tups = len( sorted_tool_tups ) + for index, tool_tup in enumerate( sorted_tool_tups ): + tool_id = tool_tup[ 0 ] + version = tool_tup[ 1 ] + tool_str += '%s: %s' % ( escape_html( tool_id ), escape_html( version ) ) + if index < num_tool_tups - 1: tool_str += '
' return tool_str title = "Valid tools in this tool shed" + default_sort_key = "Repository.name" columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -916,7 +929,7 @@ class ToolsGrid( RepositoryMetadataGrid ): key="User.username" ), RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", attach_popup=False ), - ToolsColumn( "Tool id | name | version", + ToolsColumn( "Tool id and version", attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, owner", @@ -931,8 +944,7 @@ class ToolsGrid( RepositoryMetadataGrid ): .filter( and_( model.RepositoryMetadata.table.c.includes_tools == True, model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) + .join( model.User.table ) class DatatypesGrid( RepositoryMetadataGrid ): @@ -947,23 +959,33 @@ class DatatypesGrid( RepositoryMetadataGrid ): if metadata: datatype_dicts = metadata.get( 'datatypes', [] ) if datatype_dicts: - num_datatype_dicts = len( datatype_dicts ) - for index, datatype_dict in enumerate( datatype_dicts ): + # Create tuples of the attributes we want so we can sort them by extension. + datatype_tups = [] + for datatype_dict in datatype_dicts: # Example: {"display_in_upload": "true", "dtype": "galaxy.datatypes.blast:BlastXml", "extension": "blastxml", "mimetype": "application/xml"} extension = datatype_dict.get( 'extension', '' ) dtype = datatype_dict.get( 'dtype', '' ) mimetype = datatype_dict.get( 'mimetype', '' ) display_in_upload = datatype_dict.get( 'display_in_upload', False ) - datatype_str += '%s | %s | %s' % ( escape_html( extension ), escape_html( dtype ), escape_html( mimetype ) ) - if index < num_datatype_dicts - 1: + # For now we'll just display extension and dtype. + if extension and dtype: + datatype_tups.append( ( extension, dtype ) ) + sorted_datatype_tups = sorted( datatype_tups, key=lambda datatype_tup: datatype_tup[ 0 ] ) + num_datatype_tups = len( sorted_datatype_tups ) + for index, datatype_tup in enumerate( sorted_datatype_tups ): + extension = datatype_tup[ 0 ] + dtype = datatype_tup[ 1 ] + datatype_str += '%s: %s' % ( escape_html( extension ), escape_html( dtype ) ) + if index < num_datatype_tups - 1: datatype_str += '
' return datatype_str title = "Custom datatypes in this tool shed" + default_sort_key = "Repository.name" columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -972,7 +994,7 @@ class DatatypesGrid( RepositoryMetadataGrid ): key="User.username" ), RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", attach_popup=False ), - DatatypesColumn( "Datatype extension | Type | Mimetype", + DatatypesColumn( "Datatype extension and class", attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, owner", @@ -987,5 +1009,4 @@ class DatatypesGrid( RepositoryMetadataGrid ): .filter( and_( model.RepositoryMetadata.table.c.includes_datatypes == True, model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) + .join( model.User.table )