def uninstall_repository(self, trans, id=None, **kwd): """ DELETE /api/tool_shed_repositories/id DELETE /api/tool_shed_repositories/ :param id: encoded repository id. Either id or name, owner, changeset_revision and tool_shed_url need to be supplied :param kwd: 'remove_from_disk': Remove repository from disk or deactivate repository. Defaults to `True` (= remove repository from disk). 'name': Repository name 'owner': Repository owner 'changeset_revision': Changeset revision to uninstall 'tool_shed_url': Tool Shed URL """ remove_from_disk = util.asbool(kwd.get('remove_from_disk', True)) if id: try: repository = get_tool_shed_repository_by_id(self.app, id) except ValueError: raise HTTPBadRequest( detail="No repository with id '%s' found" % id) else: tsr_arguments = [ 'name', 'owner', 'changeset_revision', 'tool_shed_url' ] try: tsr_arguments = {key: kwd[key] for key in tsr_arguments} except KeyError as e: raise HTTPBadRequest(detail="Missing required parameter '%s'" % e.args[0]) repository = get_installed_repository( app=self.app, tool_shed=tsr_arguments['tool_shed_url'], name=tsr_arguments['name'], owner=tsr_arguments['owner'], changeset_revision=tsr_arguments['changeset_revision']) if not repository: raise HTTPBadRequest(detail="Repository not found") irm = InstalledRepositoryManager(app=self.app) errors = irm.uninstall_repository(repository=repository, remove_from_disk=remove_from_disk) if not errors: action = 'removed' if remove_from_disk else 'deactivated' return { 'message': f'The repository named {repository.name} has been {action}.' } else: raise Exception( f'Attempting to uninstall tool dependencies for repository named {repository.name} resulted in errors: {errors}' )
def __init__(self, **kwargs): super().__init__(**kwargs) self._register_singleton(MinimalManagerApp, self) self.execution_timer_factory = self._register_singleton( ExecutionTimerFactory, ExecutionTimerFactory(self.config)) self.configure_fluent_log() self.application_stack = self._register_singleton( ApplicationStack, application_stack_instance(app=self)) # Initialize job metrics manager, needs to be in place before # config so per-destination modifications can be made. self.job_metrics = self._register_singleton( JobMetrics, JobMetrics(self.config.job_metrics_config_file, app=self)) # Initialize the job management configuration self.job_config = self._register_singleton(jobs.JobConfiguration) # Tag handler self.tag_handler = self._register_singleton(GalaxyTagHandler) self.user_manager = self._register_singleton(UserManager) self._register_singleton(GalaxySessionManager) self.hda_manager = self._register_singleton(HDAManager) self.history_manager = self._register_singleton(HistoryManager) self.job_search = self._register_singleton(JobSearch) self.dataset_collection_manager = self._register_singleton( DatasetCollectionManager) self.workflow_manager = self._register_singleton(WorkflowsManager) self.workflow_contents_manager = self._register_singleton( WorkflowContentsManager) self.library_folder_manager = self._register_singleton(FolderManager) self.library_manager = self._register_singleton(LibraryManager) self.role_manager = self._register_singleton(RoleManager) from galaxy.jobs.manager import JobManager self.job_manager = self._register_singleton(JobManager) # ConfiguredFileSources self.file_sources = self._register_singleton( ConfiguredFileSources, ConfiguredFileSources.from_app_config(self.config)) # We need the datatype registry for running certain tasks that modify HDAs, and to build the registry we need # to setup the installed repositories ... this is not ideal self._configure_tool_config_files() self.installed_repository_manager = self._register_singleton( InstalledRepositoryManager, InstalledRepositoryManager(self)) self._configure_datatypes_registry(self.installed_repository_manager) self._register_singleton(Registry, self.datatypes_registry) galaxy.model.set_datatypes_registry(self.datatypes_registry) self.sentry_client = None if self.config.sentry_dsn: def postfork_sentry_client(): import raven self.sentry_client = raven.Client( self.config.sentry_dsn, transport=raven.transport.HTTPTransport) self.application_stack.register_postfork_function( postfork_sentry_client)
class InstalledRepositoryManagerTestCase(ToolShedRepoBaseTestCase): def setUp(self): super().setUp() self.irm = InstalledRepositoryManager(self.app) def test_uninstall_repository(self): repository = self._setup_repository() assert repository.uninstalled is False self.irm.uninstall_repository(repository=repository, remove_from_disk=True) assert repository.uninstalled is True def test_deactivate_repository(self): self._deactivate_repository() def test_activate_repository(self): repository = self._deactivate_repository() self.irm.activate_repository(repository) assert repository.status == self.app.install_model.ToolShedRepository.installation_status.INSTALLED def test_create_or_update_tool_shed_repository_update(self): repository = self._setup_repository() self._create_or_update_tool_shed_repository(repository=repository, changeset_revision='2') def test_create_or_update_tool_shed_repository_create(self): self._create_or_update_tool_shed_repository(repository=None, changeset_revision='2') def _create_or_update_tool_shed_repository(self, repository=None, changeset_revision='2'): if repository is None: repository = DEFAULT_TEST_REPO new_repository = repository_util.create_or_update_tool_shed_repository( app=self.app, name=repository.name, description=repository.description, installed_changeset_revision=repository.installed_changeset_revision, ctx_rev=repository.changeset_revision, repository_clone_url='https://github.com/galaxyproject/example/test_tool/0.%s' % repository.installed_changeset_revision, # not needed if owner is given status=repository.status, metadata_dict=None, current_changeset_revision=str(int(repository.changeset_revision) + 1), owner=repository.owner, dist_to_shed=False ) assert new_repository.changeset_revision == changeset_revision def _deactivate_repository(self): repository = self._setup_repository() assert repository.uninstalled is False self.irm.uninstall_repository(repository=repository, remove_from_disk=False) assert repository.uninstalled is False assert repository.status == self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED return repository
def __init__(self, **kwargs): if not log.handlers: # Paste didn't handle it, so we need a temporary basic log # configured. The handler added here gets dumped and replaced with # an appropriately configured logger in configure_logging below. logging.basicConfig(level=logging.DEBUG) log.debug("python path is: %s", ", ".join(sys.path)) self.name = 'galaxy' # is_webapp will be set to true when building WSGI app self.is_webapp = False self.startup_timer = ExecutionTimer() self.new_installation = False # Read config file and check for errors self.config = config.Configuration(**kwargs) self.config.check() config.configure_logging(self.config) self.execution_timer_factory = ExecutionTimerFactory(self.config) self.configure_fluent_log() # A lot of postfork initialization depends on the server name, ensure it is set immediately after forking before other postfork functions self.application_stack = application_stack_instance(app=self) self.application_stack.register_postfork_function( self.application_stack.set_postfork_server_name, self) self.config.reload_sanitize_whitelist( explicit='sanitize_whitelist_file' in kwargs) self.amqp_internal_connection_obj = galaxy.queues.connection_from_config( self.config) # queue_worker *can* be initialized with a queue, but here we don't # want to and we'll allow postfork to bind and start it. self.queue_worker = GalaxyQueueWorker(self) self._configure_tool_shed_registry() self._configure_object_store(fsmon=True) # Setup the database engine and ORM config_file = kwargs.get('global_conf', {}).get('__file__', None) if config_file: log.debug('Using "galaxy.ini" config file: %s', config_file) check_migrate_tools = self.config.check_migrate_tools self._configure_models( check_migrate_databases=self.config.check_migrate_databases, check_migrate_tools=check_migrate_tools, config_file=config_file) # Security helper self._configure_security() # Tag handler self.tag_handler = GalaxyTagHandler(self.model.context) self.dataset_collections_service = DatasetCollectionManager(self) self.history_manager = HistoryManager(self) self.hda_manager = HDAManager(self) self.workflow_manager = WorkflowsManager(self) self.dependency_resolvers_view = DependencyResolversView(self) self.test_data_resolver = test_data.TestDataResolver( file_dirs=self.config.tool_test_data_directories) self.library_folder_manager = FolderManager() self.library_manager = LibraryManager() self.dynamic_tool_manager = DynamicToolManager(self) # Tool Data Tables self._configure_tool_data_tables(from_shed_config=False) # Load dbkey / genome build manager self._configure_genome_builds(data_table_name="__dbkeys__", load_old_style=True) # Genomes self.genomes = Genomes(self) # Data providers registry. self.data_provider_registry = DataProviderRegistry() # Initialize job metrics manager, needs to be in place before # config so per-destination modifications can be made. self.job_metrics = job_metrics.JobMetrics( self.config.job_metrics_config_file, app=self) # Initialize error report plugins. self.error_reports = ErrorReports(self.config.error_report_file, app=self) # Initialize the job management configuration self.job_config = jobs.JobConfiguration(self) # Setup a Tool Cache self.tool_cache = ToolCache() self.tool_shed_repository_cache = ToolShedRepositoryCache(self) # Watch various config files for immediate reload self.watchers = ConfigWatchers(self) self._configure_tool_config_files() self.installed_repository_manager = InstalledRepositoryManager(self) self._configure_datatypes_registry(self.installed_repository_manager) galaxy.model.set_datatypes_registry(self.datatypes_registry) self._configure_toolbox() # Load Data Manager self.data_managers = DataManagers(self) # Load the update repository manager. self.update_repository_manager = UpdateRepositoryManager(self) # Load proprietary datatype converters and display applications. self.installed_repository_manager.load_proprietary_converters_and_display_applications( ) # Load datatype display applications defined in local datatypes_conf.xml self.datatypes_registry.load_display_applications(self) # Load datatype converters defined in local datatypes_conf.xml self.datatypes_registry.load_datatype_converters(self.toolbox) # Load external metadata tool self.datatypes_registry.load_external_metadata_tool(self.toolbox) # Load history import/export tools. load_lib_tools(self.toolbox) # visualizations registry: associates resources with visualizations, controls how to render self.visualizations_registry = VisualizationsRegistry( self, directories_setting=self.config.visualization_plugins_directory, template_cache_dir=self.config.template_cache_path) # Tours registry self.tour_registry = ToursRegistry(self.config.tour_config_dir) # Webhooks registry self.webhooks_registry = WebhooksRegistry(self.config.webhooks_dir) # Load security policy. self.security_agent = self.model.security_agent self.host_security_agent = galaxy.model.security.HostAgent( model=self.security_agent.model, permitted_actions=self.security_agent.permitted_actions) # Load quota management. if self.config.enable_quotas: self.quota_agent = galaxy.quota.QuotaAgent(self.model) else: self.quota_agent = galaxy.quota.NoQuotaAgent(self.model) # Heartbeat for thread profiling self.heartbeat = None from galaxy import auth self.auth_manager = auth.AuthManager(self) self.user_manager = UserManager(self) # Start the heartbeat process if configured and available (wait until # postfork if using uWSGI) if self.config.use_heartbeat: if heartbeat.Heartbeat: self.heartbeat = heartbeat.Heartbeat( self.config, period=self.config.heartbeat_interval, fname=self.config.heartbeat_log) self.heartbeat.daemon = True self.application_stack.register_postfork_function( self.heartbeat.start) self.authnz_manager = None if self.config.enable_oidc: from galaxy.authnz import managers self.authnz_manager = managers.AuthnzManager( self, self.config.oidc_config, self.config.oidc_backends_config) self.sentry_client = None if self.config.sentry_dsn: def postfork_sentry_client(): import raven self.sentry_client = raven.Client( self.config.sentry_dsn, transport=raven.transport.HTTPTransport) self.application_stack.register_postfork_function( postfork_sentry_client) # Transfer manager client if self.config.get_bool('enable_beta_job_managers', False): from galaxy.jobs import transfer_manager self.transfer_manager = transfer_manager.TransferManager(self) # Start the job manager from galaxy.jobs import manager self.job_manager = manager.JobManager(self) self.application_stack.register_postfork_function( self.job_manager.start) self.proxy_manager = ProxyManager(self.config) from galaxy.workflow import scheduling_manager # Must be initialized after job_config. self.workflow_scheduling_manager = scheduling_manager.WorkflowSchedulingManager( self) # Must be initialized after any component that might make use of stack messaging is configured. Alternatively if # it becomes more commonly needed we could create a prefork function registration method like we do with # postfork functions. self.application_stack.init_late_prefork() self.containers = {} if self.config.enable_beta_containers_interface: self.containers = build_container_interfaces( self.config.containers_config_file, containers_conf=self.config.containers_conf) self.interactivetool_manager = InteractiveToolManager(self) # Configure handling of signals handlers = {} if self.heartbeat: handlers[signal.SIGUSR1] = self.heartbeat.dump_signal_handler self._configure_signal_handlers(handlers) self.database_heartbeat = DatabaseHeartbeat( application_stack=self.application_stack) self.database_heartbeat.add_change_callback(self.watchers.change_state) self.application_stack.register_postfork_function( self.database_heartbeat.start) # Start web stack message handling self.application_stack.register_postfork_function( self.application_stack.start) self.application_stack.register_postfork_function( self.queue_worker.bind_and_start) # Delay toolbox index until after startup self.application_stack.register_postfork_function( lambda: send_local_control_task(self, 'rebuild_toolbox_search_index')) self.model.engine.dispose() # Inject url_for for components to more easily optionally depend # on url_for. self.url_for = url_for self.server_starttime = int(time.time()) # used for cachebusting log.info("Galaxy app startup finished %s" % self.startup_timer)
def setUp(self): super().setUp() self.irm = InstalledRepositoryManager(self.app)
def setUp(self): super(InstalledRepositoryManagerTestCase, self).setUp() self.irm = InstalledRepositoryManager(self.app)