def set_up_managers(self):
super().set_up_managers()
self.hda_manager = hdas.HDAManager(self.app)
self.history_manager = HistoryManager(self.app)
self.dataset_manager = DatasetManager(self.app)
self.tag_handler = GalaxyTagHandler(self.trans.sa_session)
self.user = self.user_manager.create(**user2_data)
def __init__(self, config: GalaxyDataTestConfig = None, **kwd):
config = config or GalaxyDataTestConfig(**kwd)
self.config = config
self.security = config.security
self.object_store = objectstore.build_object_store_from_config(
self.config)
self.model = init("/tmp",
self.config.database_connection,
create_tables=True,
object_store=self.object_store)
self.security_agent = self.model.security_agent
self.tag_handler = GalaxyTagHandler(self.model.context)
self.init_datatypes()
def __init__(
self,
model: GalaxyModelMapping,
security: IdEncodingHelper,
hda_manager: HDAManager,
history_manager: HistoryManager,
tag_handler: GalaxyTagHandler,
ldda_manager: LDDAManager,
):
self.type_registry = DATASET_COLLECTION_TYPES_REGISTRY
self.collection_type_descriptions = COLLECTION_TYPE_DESCRIPTION_FACTORY
self.model = model
self.security = security
self.hda_manager = hda_manager
self.history_manager = history_manager
self.tag_handler = tag_handler.create_tag_handler_session()
self.ldda_manager = ldda_manager
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'
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.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)
# control_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.control_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)
# Manage installed tool shed repositories.
self.installed_repository_manager = installed_repository_manager.InstalledRepositoryManager(
self)
self._configure_datatypes_registry(self.installed_repository_manager)
galaxy.model.set_datatypes_registry(self.datatypes_registry)
# 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.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_toolbox()
# Load Data Manager
self.data_managers = DataManagers(self)
# Load the update repository manager.
self.update_repository_manager = 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)
# Tours registry
self.tour_registry = ToursRegistry(self.config.tour_config_dir)
# Webhooks registry
self.webhooks_registry = WebhooksRegistry(self.config.webhooks_dirs)
# 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)
# 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)
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)
# 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.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.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)
class TagHandlerTestCase(BaseTestCase):
def set_up_managers(self):
super().set_up_managers()
self.hda_manager = hdas.HDAManager(self.app)
self.history_manager = HistoryManager(self.app)
self.dataset_manager = DatasetManager(self.app)
self.tag_handler = GalaxyTagHandler(self.trans.sa_session)
self.user = self.user_manager.create(**user2_data)
def _create_vanilla_hda(self, user=None):
owner = user or self.user
history1 = self.history_manager.create(name='history1', user=owner)
dataset1 = self.dataset_manager.create()
return self.hda_manager.create(history=history1, dataset=dataset1)
def _check_tag_list(self, tags, expected_tags):
self.assertEqual(len(tags), len(expected_tags))
actual_tags = []
for tag in tags:
if tag.user_value:
tag = f"{tag.user_tname}:{tag.user_value}"
else:
tag = tag.user_tname
actual_tags.append(tag)
expected = [unicodify(e) for e in expected_tags]
assert sorted(expected) == sorted(
actual_tags), f"{expected} vs {actual_tags}"
def test_apply_item_tags(self):
tag_strings = [
'tag1',
'tag1:value1',
'tag1:value1:value11',
'\x00tag1',
'tag1:\x00value1',
'tag1,tag2',
'...',
'.test',
'test.a.b',
]
expected_tags = [
['tag1'],
['tag1:value1'],
['tag1:value1:value11'],
['tag1'],
['tag1:value1'],
['tag1', 'tag2'],
[],
['test'],
['test.a.b'],
]
for tag_string, expected_tag in zip(tag_strings, expected_tags):
hda = self._create_vanilla_hda()
self.tag_handler.apply_item_tags(user=self.user,
item=hda,
tags_str=tag_string)
self._check_tag_list(hda.tags, expected_tag)
def test_set_tag_from_list(self):
hda = self._create_vanilla_hda()
tags = ['tag1', 'tag2']
self.tag_handler.set_tags_from_list(self.user, hda, tags)
self._check_tag_list(hda.tags, tags)
# Setting tags should erase previous tags
self.tag_handler.set_tags_from_list(self.user, hda, ['tag1'])
self._check_tag_list(hda.tags, expected_tags=['tag1'])
def test_add_tag_from_list(self):
hda = self._create_vanilla_hda()
tags = ['tag1', 'tag2']
self.tag_handler.add_tags_from_list(self.user, hda, tags)
self._check_tag_list(tags=hda.tags, expected_tags=tags)
# Adding tags should keep previous tags
self.tag_handler.add_tags_from_list(self.user, hda, ['tag3'])
self._check_tag_list(hda.tags, expected_tags=['tag1', 'tag2', 'tag3'])
def test_remove_tag_from_list(self):
hda = self._create_vanilla_hda()
tags = ['tag1', 'tag2', 'tag3']
self.tag_handler.set_tags_from_list(self.user, hda, tags)
self._check_tag_list(hda.tags, tags)
self.tag_handler.remove_tags_from_list(self.user, hda,
['tag1', 'tag3'])
self._check_tag_list(hda.tags, ['tag2'])
def test_delete_item_tags(self):
hda = self._create_vanilla_hda()
tags = ['tag1']
self.tag_handler.set_tags_from_list(self.user, hda, tags)
self.tag_handler.delete_item_tags(user=self.user, item=hda)
self.assertEqual(hda.tags, [])
def test_item_has_tag(self):
hda = self._create_vanilla_hda()
tags = ['tag1']
self.tag_handler.set_tags_from_list(self.user, hda, tags)
self.assertTrue(
self.tag_handler.item_has_tag(self.user, item=hda, tag='tag1'))
# ItemTagAssociation
self.assertTrue(
self.tag_handler.item_has_tag(self.user, item=hda,
tag=hda.tags[0]))
# Tag
self.assertTrue(
self.tag_handler.item_has_tag(self.user,
item=hda,
tag=hda.tags[0].tag))
self.assertFalse(
self.tag_handler.item_has_tag(self.user, item=hda, tag='tag2'))