def test_proxy():
proxy = TrsProxy()
assert 'dockstore' == proxy.get_servers()[0]["id"]
tool_id = "#workflow/github.com/jmchilton/galaxy-workflow-dockstore-example-1/mycoolworkflow"
tool = proxy.get_tool("dockstore", tool_id)
assert "description" in tool
b64_tool_id = base64.b64encode(tool_id.encode("UTF-8"))
tool = proxy.get_tool("dockstore", b64_tool_id, tool_id_b64_encoded=True)
assert "description" in tool
versions = proxy.get_versions("dockstore", tool_id)
assert isinstance(versions, list)
assert len(versions) >= 1
version_id = versions[0]["name"]
version = proxy.get_version("dockstore", tool_id, version_id)
assert "descriptor_type" in version
assert GA4GH_GALAXY_DESCRIPTOR in version["descriptor_type"]
descriptor = proxy.get_version_descriptor("dockstore", tool_id, version_id)
content = yaml.safe_load(descriptor)
assert "inputs" in content
def test_search():
proxy = TrsProxy()
search_kwd = parse_search_kwds("documentation")
response = proxy.get_tools("dockstore", **search_kwd)
assert len(response) == 1
search_kwd = parse_search_kwds("n:example")
response = proxy.get_tools("dockstore", **search_kwd)
assert len(response) == 2
search_kwd = parse_search_kwds("organization:jmchilton")
response = proxy.get_tools("dockstore", **search_kwd)
assert len(response) == 2
search_kwd = parse_search_kwds("organization:jmchiltonx")
response = proxy.get_tools("dockstore", **search_kwd)
assert len(response) == 0
response = proxy.get_tools("dockstore", descriptorType="GALAXY")
assert len(response) == 2
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_allowlist(
explicit='sanitize_allowlist_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.workflow_contents_manager = WorkflowContentsManager(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.role_manager = RoleManager(self)
self.dynamic_tool_manager = DynamicToolManager(self)
# ConfiguredFileSources
self.file_sources = ConfiguredFileSources.from_app_config(self.config)
# 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 = 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)
self.toolbox.persist_cache(register_postfork=True)
# 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 = build_tours_registry(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.
self.quota_agent = get_quota_agent(self.config, 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_file,
self.config.oidc_backends_config_file)
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)
self.trs_proxy = TrsProxy(self.config)
# 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 __init__(self, **kwargs) -> None:
startup_timer = ExecutionTimer()
super().__init__(fsmon=True, **kwargs)
self.haltables = [
("queue worker", self._shutdown_queue_worker),
("file watcher", self._shutdown_watcher),
("database heartbeat", self._shutdown_database_heartbeat),
("workflow scheduler", self._shutdown_scheduling_manager),
("object store", self._shutdown_object_store),
("job manager", self._shutdown_job_manager),
("application heartbeat", self._shutdown_heartbeat),
("repository manager", self._shutdown_repo_manager),
("database connection", self._shutdown_model),
("application stack", self._shutdown_application_stack),
]
self._register_singleton(StructuredApp, self)
# A lot of postfork initialization depends on the server name, ensure it is set immediately after forking before other postfork functions
self.application_stack.register_postfork_function(
self.application_stack.set_postfork_server_name, self)
self.config.reload_sanitize_allowlist(
explicit='sanitize_allowlist_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 = self._register_singleton(GalaxyQueueWorker,
GalaxyQueueWorker(self))
self._configure_tool_shed_registry()
self.dependency_resolvers_view = self._register_singleton(
DependencyResolversView, DependencyResolversView(self))
self.test_data_resolver = self._register_singleton(
TestDataResolver,
TestDataResolver(file_dirs=self.config.tool_test_data_directories))
self.dynamic_tool_manager = self._register_singleton(
DynamicToolManager)
self.api_keys_manager = self._register_singleton(ApiKeyManager)
# 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 = self._register_singleton(Genomes)
# Data providers registry.
self.data_provider_registry = self._register_singleton(
DataProviderRegistry)
# Initialize error report plugins.
self.error_reports = self._register_singleton(
ErrorReports, ErrorReports(self.config.error_report_file,
app=self))
# Setup a Tool Cache
self.tool_cache = self._register_singleton(ToolCache)
self.tool_shed_repository_cache = self._register_singleton(
ToolShedRepositoryCache)
# Watch various config files for immediate reload
self.watchers = self._register_singleton(ConfigWatchers)
self._configure_toolbox()
# Load Data Manager
self.data_managers = self._register_singleton(DataManagers)
# Load the update repository manager.
self.update_repository_manager = self._register_singleton(
UpdateRepositoryManager, 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)
self.toolbox.persist_cache(register_postfork=True)
# visualizations registry: associates resources with visualizations, controls how to render
self.visualizations_registry = self._register_singleton(
VisualizationsRegistry,
VisualizationsRegistry(
self,
directories_setting=self.config.
visualization_plugins_directory,
template_cache_dir=self.config.template_cache_path))
# Tours registry
tour_registry = build_tours_registry(self.config.tour_config_dir)
self.tour_registry = tour_registry
self[ToursRegistry] = tour_registry # type: ignore[misc]
# Webhooks registry
self.webhooks_registry = self._register_singleton(
WebhooksRegistry, 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.
self.quota_agent = self._register_singleton(
QuotaAgent, get_quota_agent(self.config, self.model))
# Heartbeat for thread profiling
self.heartbeat = None
self.auth_manager = self._register_singleton(
auth.AuthManager, auth.AuthManager(self.config))
# 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_file,
self.config.oidc_backends_config_file)
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)
if not self.config.enable_celery_tasks and self.config.history_audit_table_prune_interval > 0:
self.prune_history_audit_task = IntervalTask(
func=lambda: galaxy.model.HistoryAudit.prune(self.model.session
),
name="HistoryAuditTablePruneTask",
interval=self.config.history_audit_table_prune_interval,
immediate_start=False,
time_execution=True)
self.application_stack.register_postfork_function(
self.prune_history_audit_task.start)
self.haltables.append(("HistoryAuditTablePruneTask",
self.prune_history_audit_task.shutdown))
# Start the job manager
self.application_stack.register_postfork_function(
self.job_manager.start)
# If app is not job handler but uses mule messaging.
# Can be removed when removing mule support.
self.job_manager._check_jobs_at_startup()
self.proxy_manager = ProxyManager(self.config)
# Must be initialized after job_config.
self.workflow_scheduling_manager = scheduling_manager.WorkflowSchedulingManager(
self)
self.trs_proxy = self._register_singleton(TrsProxy,
TrsProxy(self.config))
# 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.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'))
# 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
# Limit lifetime of tool shed repository cache to app startup
self.tool_shed_repository_cache = None
log.info(f"Galaxy app startup finished {startup_timer}")