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Source code for galaxy.model.unittest_utils.data_app

"""Mock GalaxyApp exposing config + functionality required for galaxy-data package.

There is a more expansive MockApp in test/unit/unittest_utils - but it isn't packaged
and it has dependencies from across the app. This mock application and config is
more appropriate for testing galaxy-data functionality and will be included with
import os
import shutil
import tempfile

from galaxy import model, objectstore
from galaxy.datatypes import registry
from galaxy.model.mapping import GalaxyModelMapping, init
from galaxy.model.security import GalaxyRBACAgent
from galaxy.model.tags import GalaxyTagHandler
from galaxy.security.idencoding import IdEncodingHelper
from galaxy.util.bunch import Bunch

GALAXY_TEST_UNITTEST_SECRET = '6e46ed6483a833c100e68cc3f1d0dd76'

[docs]class GalaxyDataTestConfig(Bunch): """Minimal Galaxy mock config object that exposes and uses only what is needed for the galaxy-data package.""" security: IdEncodingHelper database_connection: str root: str data_dir: str _remove_root: bool
[docs] def __init__(self, root=None, **kwd): Bunch.__init__(self, **kwd) if not root: root = tempfile.mkdtemp() self._remove_root = True else: self._remove_root = False self.root = root self.data_dir = os.path.join(root, 'database') self.security = IdEncodingHelper(id_secret=GALAXY_TEST_UNITTEST_SECRET) self.database_connection = kwd.get('database_connection', GALAXY_TEST_IN_MEMORY_DB_CONNECTION) # objectstore config values... self.object_store_config_file = '' self.object_store = 'disk' self.object_store_check_old_style = False self.object_store_cache_path = '/tmp/cache' self.object_store_store_by = "uuid" self.umask = os.umask(0o77) self.gid = os.getgid() # objectstore config directories... self.jobs_directory = os.path.join(self.data_dir, 'jobs_directory') self.new_file_path = os.path.join(self.data_dir, 'tmp') self.file_path = os.path.join(self.data_dir, 'files') self.server_name = "main"
def __del__(self): if self._remove_root: shutil.rmtree(self.root)
[docs]class GalaxyDataTestApp(): """Minimal Galaxy mock app object that exposes and uses only what is needed for the galaxy-data package.""" security: IdEncodingHelper model: GalaxyModelMapping security_agent: GalaxyRBACAgent
[docs] 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()
[docs] def init_datatypes(self): datatypes_registry = registry.Registry() datatypes_registry.load_datatypes() model.set_datatypes_registry(datatypes_registry) datatypes_registry.set_external_metadata_tool = MockSetExternalTool() self.datatypes_registry = datatypes_registry
[docs]class MockSetExternalTool:
[docs] def regenerate_imported_metadata_if_needed(self, *args, **kwds): pass