def build_galaxy_app(simple_kwargs):
"""Build a Galaxy app object from a simple keyword arguments.
Construct paste style complex dictionary and use load_app_properties so
Galaxy override variables are respected. Also setup "global" references
to sqlalchemy database context for Galaxy and install databases.
"""
log.info("Galaxy database connection: %s",
simple_kwargs["database_connection"])
simple_kwargs['global_conf'] = get_webapp_global_conf()
simple_kwargs['global_conf'][
'__file__'] = "lib/galaxy/config/sample/galaxy.yml.sample"
simple_kwargs = load_app_properties(kwds=simple_kwargs)
# Build the Universe Application
app = GalaxyUniverseApplication(**simple_kwargs)
rebind_container_to_task(app)
log.info("Embedded Galaxy application started")
global galaxy_context
global install_context
galaxy_context = app.model.context
install_context = app.install_model.context
# Toolbox indexing happens via the work queue out of band recently, and,
# beyond potentially running async after tests execute doesn't execute
# without building a uwsgi app (app.is_webapp = False for this test kit).
# We need to ensure to build an index for the test galaxy app -- this is
# pretty fast with the limited toolset
app.reindex_tool_search()
return app
def __init__(self, config=None, **kwargs):
super().__init__()
self[BasicApp] = self
self[MinimalManagerApp] = self
self[StructuredApp] = self
self.config = config or MockAppConfig(**kwargs)
self.security = self.config.security
self[idencoding.IdEncodingHelper] = self.security
self.name = kwargs.get('name', 'galaxy')
self.object_store = objectstore.build_object_store_from_config(
self.config)
self.model = mapping.init("/tmp",
self.config.database_connection,
create_tables=True,
object_store=self.object_store)
self[SharedModelMapping] = self.model
self[GalaxyModelMapping] = self.model
self[scoped_session] = self.model.context
self.security_agent = self.model.security_agent
self.visualizations_registry = MockVisualizationsRegistry()
self.tag_handler = tags.GalaxyTagHandler(self.model.context)
self[tags.GalaxyTagHandler] = self.tag_handler
self.quota_agent = quota.DatabaseQuotaAgent(self.model)
self.init_datatypes()
self.job_config = Bunch(dynamic_params=None,
destinations={},
use_messaging=False,
assign_handler=lambda *args, **kwargs: None)
self.tool_data_tables = {}
self.dataset_collections_service = None
self.container_finder = NullContainerFinder()
self._toolbox_lock = MockLock()
self.tool_shed_registry = Bunch(tool_sheds={})
self.genome_builds = GenomeBuilds(self)
self.job_manager = NoopManager()
self.application_stack = ApplicationStack()
self.auth_manager = AuthManager(self.config)
self.user_manager = UserManager(self)
self.execution_timer_factory = Bunch(
get_timer=StructuredExecutionTimer)
self.is_job_handler = False
rebind_container_to_task(self)
def url_for(*args, **kwds):
return "/mock/url"
self.url_for = url_for