[galaxy-commits] commit/galaxy-central: greg: Handle invalid complex repository dependency definitions.

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e378b9511acc/ changeset: e378b9511acc user: greg date: 2013-02-01 15:40:22 summary: Handle invalid complex repository dependency definitions. affected #: 3 files diff -r 2a34f751c32cb9b4ab271d1f14c99406b9d04a54 -r e378b9511acccd47642db3bcc6519f0a74dfbb92 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -495,6 +495,13 @@ if repository_metadata: return repository_metadata.malicious return False +def changeset_is_valid( app, repository, changeset_revision ): + repo = hg.repository( get_configured_ui(), repository.repo_path( app ) ) + for changeset in repo.changelog: + changeset_hash = str( repo.changectx( changeset ) ) + if changeset_revision == changeset_hash: + return True + return False def changeset_revision_reviewed_by_user( trans, user, repository, changeset_revision ): """Determine if the current changeset revision has been reviewed by the current user.""" for review in repository.reviews: @@ -871,7 +878,7 @@ but tool_dependencies and repository_dependencies will be None. """ repo_info_dict = {} - repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner ) + repository = get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) if trans.webapp.name == 'community': # We're in the tool shed. repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) @@ -1208,7 +1215,6 @@ """ repository_dependency_tup = [] requirements_dict = {} - error_message = '' package_name = elem.get( 'name', None ) package_version = elem.get( 'version', None ) if package_name and package_version: @@ -1220,15 +1226,15 @@ requirements_dict[ 'readme' ] = sub_elem.text elif sub_elem.tag == 'repository': # We have a complex repository dependency. - current_rd_tups, error_message = handle_repository_elem( app=app, - repository_elem=sub_elem, - repository_dependencies_tups=None ) + current_rd_tups = handle_repository_elem( app=app, + repository_elem=sub_elem, + repository_dependencies_tups=None ) if current_rd_tups: repository_dependency_tup = current_rd_tups[ 0 ] if requirements_dict: dependency_key = '%s/%s' % ( package_name, package_version ) tool_dependencies_dict[ dependency_key ] = requirements_dict - return tool_dependencies_dict, repository_dependency_tup, error_message + return tool_dependencies_dict, repository_dependency_tup def generate_repository_dependency_metadata_for_installed_repository( app, repository_dependencies_config, metadata_dict ): """ Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config. This method @@ -1278,10 +1284,7 @@ is_valid = False if is_valid: for repository_elem in root.findall( 'repository' ): - current_rd_tups, error_message = handle_repository_elem( app, repository_elem, repository_dependencies_tups ) - if error_message: - log.debug( error_message ) - return metadata_dict, error_message + current_rd_tups = handle_repository_elem( app, repository_elem, repository_dependencies_tups ) for crdt in current_rd_tups: repository_dependencies_tups.append( crdt ) if repository_dependencies_tups: @@ -1312,12 +1315,9 @@ repository_dependency_tups = [] for elem in root: if elem.tag == 'package': - tool_dependencies_dict, repository_dependency_tup, message = generate_package_dependency_metadata( app, elem, tool_dependencies_dict ) + tool_dependencies_dict, repository_dependency_tup = generate_package_dependency_metadata( app, elem, tool_dependencies_dict ) if repository_dependency_tup and repository_dependency_tup not in repository_dependency_tups: repository_dependency_tups.append( repository_dependency_tup ) - if message: - log.debug( message ) - error_message = '%s %s' % ( error_message, message ) elif elem.tag == 'set_environment': tool_dependencies_dict = generate_environment_dependency_metadata( elem, tool_dependencies_dict ) if tool_dependencies_dict: @@ -1327,30 +1327,66 @@ handle_existing_tool_dependencies_that_changed_in_update( app, repository, original_tool_dependencies_dict, tool_dependencies_dict ) metadata_dict[ 'tool_dependencies' ] = tool_dependencies_dict if repository_dependency_tups: - tool_shed = get_tool_shed_from_clone_url( repository_clone_url ) - if app.name == 'community': - repository_owner = repository.user.username - else: - repository_owner = repository.owner - rd_key = container_util.generate_repository_dependencies_key_for_repository( toolshed_base_url=tool_shed, - repository_name=repository.name, - repository_owner=repository_owner, - changeset_revision=changeset_revision ) repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', None ) + for repository_dependency_tup in repository_dependency_tups: + rd_tool_shed, rd_name, rd_owner, rd_changeset_revision = repository_dependency_tup + if app.name == 'community': + if tool_shed_is_this_tool_shed( rd_tool_shed ): + # Make sure the repository name id valid. + valid_named_repository = get_repository_by_name( app, rd_name ) + if valid_named_repository: + # See if the owner is valid. + valid_owned_repository = get_repository_by_name_and_owner( app, rd_name, rd_owner ) + if valid_owned_repository: + # See if the defined changeset revision is valid. + if not changeset_is_valid( app, valid_owned_repository, rd_changeset_revision ): + err_msg = "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, changeset revision %s "% \ + ( rd_tool_shed, rd_name, rd_owner, rd_changeset_revision ) + err_msg += "because the changeset revision is invalid. " + log.debug( err_msg ) + error_message += err_msg + continue + else: + err_msg = "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, changeset revision %s "% \ + ( rd_tool_shed, rd_name, rd_owner, rd_changeset_revision ) + err_msg += "because the owner is invalid. " + log.debug( err_msg ) + error_message += err_msg + continue + else: + err_msg = "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, changeset revision %s "% \ + ( rd_tool_shed, rd_name, rd_owner, rd_changeset_revision ) + err_msg += "because the name is invalid. " + log.debug( err_msg ) + error_message += err_msg + continue + else: + err_msg = "Repository dependencies are currently supported only within the same tool shed. Ignoring repository dependency definition " + err_msg += "for tool shed %s, name %s, owner %s, changeset revision %s. " % ( rd_tool_shed, rd_name, rd_owner, rd_changeset_revision ) + log.debug( err_msg ) + error_message += err_msg + continue + else: + repository_owner = repository.owner + rd_key = container_util.generate_repository_dependencies_key_for_repository( toolshed_base_url=rd_tool_shed, + repository_name=rd_name, + repository_owner=rd_owner, + changeset_revision=rd_changeset_revision ) + if repository_dependencies_dict: + if rd_key in repository_dependencies_dict: + repository_dependencies = repository_dependencies_dict[ rd_key ] + for repository_dependency_tup in repository_dependency_tups: + if repository_dependency_tup not in repository_dependencies: + repository_dependencies.append( repository_dependency_tup ) + repository_dependencies_dict[ rd_key ] = repository_dependencies + else: + repository_dependencies_dict[ rd_key ] = repository_dependency_tups + else: + repository_dependencies_dict = dict( root_key=rd_key, + description=root.get( 'description' ), + repository_dependencies=repository_dependency_tups ) if repository_dependencies_dict: - if rd_key in repository_dependencies_dict: - repository_dependencies = repository_dependencies_dict[ rd_key ] - for repository_dependency_tup in repository_dependency_tups: - if repository_dependency_tup not in repository_dependencies: - repository_dependencies.append( repository_dependency_tup ) - repository_dependencies_dict[ rd_key ] = repository_dependencies - else: - repository_dependencies_dict[ rd_key ] = repository_dependency_tups - else: - repository_dependencies_dict = dict( root_key=rd_key, - description=root.get( 'description' ), - repository_dependencies=repository_dependency_tups ) - metadata_dict[ 'repository_dependencies' ] = repository_dependencies_dict + metadata_dict[ 'repository_dependencies' ] = repository_dependencies_dict return metadata_dict, error_message def generate_tool_elem( tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, tool_section ): if tool_section is not None: @@ -1800,22 +1836,27 @@ elif len( repo_info_tuple ) == 7: description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple return description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies -def get_repository_by_name( trans, name ): +def get_repository_by_name( app, name ): """Get a repository from the database via name.""" - return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one() -def get_repository_by_name_and_owner( trans, name, owner ): + sa_session = app.model.context.current + if app.name == 'galaxy': + return sa_session.query( app.model.ToolShedRepository ).filter_by( name=name ).first() + else: + return sa_session.query( app.model.Repository ).filter_by( name=name ).first() +def get_repository_by_name_and_owner( app, name, owner ): """Get a repository from the database via name and owner""" - if trans.webapp.name == 'galaxy': - return trans.sa_session.query( trans.model.ToolShedRepository ) \ - .filter( and_( trans.model.ToolShedRepository.table.c.name == name, - trans.model.ToolShedRepository.table.c.owner == owner ) ) \ - .first() + sa_session = app.model.context.current + if app.name == 'galaxy': + return sa_session.query( app.model.ToolShedRepository ) \ + .filter( and_( app.model.ToolShedRepository.table.c.name == name, + app.model.ToolShedRepository.table.c.owner == owner ) ) \ + .first() # We're in the tool shed. - user = get_user_by_username( trans, owner ) - return trans.sa_session.query( trans.model.Repository ) \ - .filter( and_( trans.model.Repository.table.c.name == name, - trans.model.Repository.table.c.user_id == user.id ) ) \ - .first() + user = get_user_by_username( app, owner ) + return sa_session.query( app.model.Repository ) \ + .filter( and_( app.model.Repository.table.c.name == name, + app.model.Repository.table.c.user_id == user.id ) ) \ + .first() def get_repository_dependencies_for_changeset_revision( trans, repository, repository_metadata, toolshed_base_url, key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None, circular_repository_dependencies=None ): @@ -1929,7 +1970,7 @@ contents.sort() return contents def get_repository_in_tool_shed( trans, id ): - """Get a repository on the tool shed side from the database via id""" + """Get a repository on the tool shed side from the database via id.""" return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) ) def get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ): """Get metadata for a specified repository change set from the database.""" @@ -2166,33 +2207,39 @@ repository_dependency = key_rd_dict[ key ] rd_toolshed, rd_name, rd_owner, rd_changeset_revision = repository_dependency if tool_shed_is_this_tool_shed( rd_toolshed ): - repository = get_repository_by_name_and_owner( trans, rd_name, rd_owner ) - repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, - trans.security.encode_id( repository.id ), - rd_changeset_revision ) - if repository_metadata: - # The repository changeset_revision is installable, so no updates are available. - new_key_rd_dict = {} - new_key_rd_dict[ key ] = repository_dependency - updated_key_rd_dicts.append( key_rd_dict ) - else: - # The repository changeset_revision is no longer installable, so see if there's been an update. - repo_dir = repository.repo_path( trans.app ) - repo = hg.repository( get_configured_ui(), repo_dir ) - changeset_revision = get_next_downloadable_changeset_revision( repository, repo, rd_changeset_revision ) + repository = get_repository_by_name_and_owner( trans.app, rd_name, rd_owner ) + if repository: repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, trans.security.encode_id( repository.id ), - changeset_revision ) + rd_changeset_revision ) if repository_metadata: + # The repository changeset_revision is installable, so no updates are available. new_key_rd_dict = {} - new_key_rd_dict[ key ] = [ rd_toolshed, rd_name, rd_owner, repository_metadata.changeset_revision ] - # We have the updated changset revision. - updated_key_rd_dicts.append( new_key_rd_dict ) + new_key_rd_dict[ key ] = repository_dependency + updated_key_rd_dicts.append( key_rd_dict ) else: - toolshed, repository_name, repository_owner, repository_changeset_revision = container_util.get_components_from_key( key ) - message = "The revision %s defined for repository %s owned by %s is invalid, so repository dependencies defined for repository %s will be ignored." % \ - ( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ), str( repository_name ) ) - log.debug( message ) + # The repository changeset_revision is no longer installable, so see if there's been an update. + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( get_configured_ui(), repo_dir ) + changeset_revision = get_next_downloadable_changeset_revision( repository, repo, rd_changeset_revision ) + repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_revision ) + if repository_metadata: + new_key_rd_dict = {} + new_key_rd_dict[ key ] = [ rd_toolshed, rd_name, rd_owner, repository_metadata.changeset_revision ] + # We have the updated changset revision. + updated_key_rd_dicts.append( new_key_rd_dict ) + else: + toolshed, repository_name, repository_owner, repository_changeset_revision = container_util.get_components_from_key( key ) + message = "The revision %s defined for repository %s owned by %s is invalid, so repository dependencies defined for repository %s will be ignored." % \ + ( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ), str( repository_name ) ) + log.debug( message ) + else: + toolshed, repository_name, repository_owner, repository_changeset_revision = container_util.get_components_from_key( key ) + message = "The revision %s defined for repository %s owned by %s is invalid, so repository dependencies defined for repository %s will be ignored." % \ + ( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ), str( repository_name ) ) + log.debug( message ) return updated_key_rd_dicts def get_url_from_repository_tool_shed( app, repository ): """ @@ -2219,11 +2266,12 @@ def get_user( trans, id ): """Get a user from the database by id.""" return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) -def get_user_by_username( trans, username ): +def get_user_by_username( app, username ): """Get a user from the database by username.""" - return trans.sa_session.query( trans.model.User ) \ - .filter( trans.model.User.table.c.username == username ) \ - .one() + sa_session = app.model.context.current + return sa_session.query( app.model.User ) \ + .filter( app.model.User.table.c.username == username ) \ + .one() def handle_circular_repository_dependency( repository_key, repository_dependency, circular_repository_dependencies, handled_key_rd_dicts, all_repository_dependencies ): all_repository_dependencies_root_key = all_repository_dependencies[ 'root_key' ] repository_dependency_as_key = get_repository_dependency_as_key( repository_dependency ) @@ -2370,7 +2418,7 @@ repository_dependency = key_rd_dict[ current_repository_key ] toolshed, name, owner, changeset_revision = repository_dependency if tool_shed_is_this_tool_shed( toolshed ): - required_repository = get_repository_by_name_and_owner( trans, name, owner ) + required_repository = get_repository_by_name_and_owner( trans.app, name, owner ) required_repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, trans.security.encode_id( required_repository.id ), changeset_revision ) @@ -2422,7 +2470,6 @@ new_rd_tups = [] else: new_rd_tups = [ rdt for rdt in repository_dependencies_tups ] - error_message = '' sa_session = app.model.context.current toolshed = repository_elem.attrib[ 'toolshed' ] name = repository_elem.attrib[ 'name' ] @@ -2438,9 +2485,8 @@ app.model.ToolShedRepository.table.c.owner == owner ) ) \ .first() except: - error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) - log.debug( error_message ) - return new_rd_tups, error_message + log.debug( "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) ) + return new_rd_tups repository_dependencies_tup = ( toolshed, name, owner, changeset_revision ) if repository_dependencies_tup not in new_rd_tups: new_rd_tups.append( repository_dependencies_tup ) @@ -2452,18 +2498,16 @@ .filter( app.model.User.table.c.username == owner ) \ .one() except Exception, e: - error_message = "Invalid owner %s defined for repository %s. Repository dependencies will be ignored." % ( owner, name ) - log.debug( error_message ) - return new_rd_tups, error_message + log.debug( "Invalid owner %s defined for repository %s. Repository dependencies will be ignored." % ( owner, name ) ) + return new_rd_tups try: repository = sa_session.query( app.model.Repository ) \ .filter( and_( app.model.Repository.table.c.name == name, app.model.Repository.table.c.user_id == user.id ) ) \ .first() except: - error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) - log.debug( error_message ) - return new_rd_tups, error_message + log.debug( "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) ) + return new_rd_tups repository_dependencies_tup = ( toolshed, name, owner, changeset_revision ) if repository_dependencies_tup not in new_rd_tups: new_rd_tups.append( repository_dependencies_tup ) @@ -2472,7 +2516,7 @@ error_message = "Invalid tool shed %s defined for repository %s. " % ( toolshed, name ) error_message += "Repository dependencies are currently supported within a single tool shed, so your definition will be ignored." log.debug( error_message ) - return new_rd_tups, error_message + return new_rd_tups def handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, tool_config_filepath, work_dir ): # Copy all sample files from disk to a temporary directory since the sample files may be in multiple directories. message = '' @@ -2981,7 +3025,7 @@ rd_tup = container_util.get_components_from_key( key ) if rd_tup not in rd_tups_processed: toolshed, name, owner, changeset_revision = rd_tup - repository = get_repository_by_name_and_owner( trans, name, owner ) + repository = get_repository_by_name_and_owner( trans.app, name, owner ) repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) @@ -2994,7 +3038,7 @@ for rd_tup in rd_tups: if rd_tup not in rd_tups_processed: toolshed, name, owner, changeset_revision = rd_tup - repository = get_repository_by_name_and_owner( trans, name, owner ) + repository = get_repository_by_name_and_owner( trans.app, name, owner ) repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) diff -r 2a34f751c32cb9b4ab271d1f14c99406b9d04a54 -r e378b9511acccd47642db3bcc6519f0a74dfbb92 lib/galaxy/webapps/community/controllers/hg.py --- a/lib/galaxy/webapps/community/controllers/hg.py +++ b/lib/galaxy/webapps/community/controllers/hg.py @@ -32,7 +32,7 @@ path_info = kwd.get( 'path_info', None ) if path_info: owner, name = path_info.split( '/' ) - repository = get_repository_by_name_and_owner( trans, name, owner ) + repository = get_repository_by_name_and_owner( trans.app, name, owner ) if repository: if hg_version >= '2.2.3': # Set metadata using the repository files on disk. diff -r 2a34f751c32cb9b4ab271d1f14c99406b9d04a54 -r e378b9511acccd47642db3bcc6519f0a74dfbb92 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -542,7 +542,8 @@ # The value of 'id' has been set to the search string, which is a repository name. We'll try to get the desired encoded repository # id to pass on. try: - repository = suc.get_repository_by_name( trans, kwd[ 'id' ] ) + repository_name = kwd[ 'id' ] + repository = suc.get_repository_by_name( trans.app, repository_name ) kwd[ 'id' ] = trans.security.encode_id( repository.id ) except: pass @@ -724,7 +725,7 @@ # We'll try to get the desired encoded repository id to pass on. try: name = kwd[ 'id' ] - repository = suc.get_repository_by_name( trans, name ) + repository = suc.get_repository_by_name( trans.app, name ) kwd[ 'id' ] = trans.security.encode_id( repository.id ) except: pass @@ -825,7 +826,7 @@ name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) - repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) # Default to the current changeset revision. @@ -1282,7 +1283,7 @@ name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) - repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) @@ -1342,7 +1343,7 @@ repository_name = kwd[ 'name' ] repository_owner = kwd[ 'owner' ] changeset_revision = kwd[ 'changeset_revision' ] - repository = suc.get_repository_by_name_and_owner( trans, repository_name, repository_owner ) + repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) @@ -1376,7 +1377,7 @@ repository_name = kwd[ 'name' ] repository_owner = kwd[ 'owner' ] changeset_revision = kwd[ 'changeset_revision' ] - repository = suc.get_repository_by_name_and_owner( trans, repository_name, repository_owner ) + repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) return suc.build_readme_files_dict( repository_metadata.metadata ) @web.json @@ -1386,7 +1387,7 @@ name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) - repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repository_id = trans.security.encode_id( repository.id ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: @@ -1458,7 +1459,7 @@ changeset_revisions = [] for required_repository_tup in decoded_required_repository_tups: tool_shed, name, owner, changeset_revision = required_repository_tup - repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) encoded_repository_ids.append( trans.security.encode_id( repository.id ) ) changeset_revisions.append( changeset_revision ) if encoded_repository_ids and changeset_revisions: @@ -1473,7 +1474,7 @@ name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) - repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + 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 @@ -1489,7 +1490,7 @@ name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) - repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) # TODO: We're currently returning the tool_dependencies.xml file that is available on disk. We need to enhance this process # to retrieve older versions of the tool-dependencies.xml file from the repository manafest. repo_dir = repository.repo_path( trans.app ) @@ -1511,7 +1512,7 @@ name = kwd[ 'name' ] owner = kwd[ 'owner' ] changeset_revision = kwd[ 'changeset_revision' ] - repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) tool_version_dicts = [] @@ -1528,7 +1529,7 @@ @web.json def get_updated_repository_information( self, trans, name, owner, changeset_revision, **kwd ): """Generate a dictionary that contains the information about a repository that is necessary for installing it into a local Galaxy instance.""" - repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repository_id = trans.security.encode_id( repository.id ) repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) @@ -1692,7 +1693,7 @@ owner = kwd.get( 'owner', None ) galaxy_url = kwd.get( 'galaxy_url', None ) if not repository_ids: - repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repository_ids = trans.security.encode_id( repository.id ) if not galaxy_url: # If galaxy_url is not in the request, it had to have been stored in a cookie by the tool shed. @@ -2098,7 +2099,7 @@ name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) - repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) # Get the lower bound changeset revision. @@ -2440,7 +2441,7 @@ name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) - repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) # Get the upper bound changeset revision. 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