def __init__(self, config=None, **kwargs):
self.config = config or MockAppConfig(**kwargs)
self.security = self.config.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.security_agent = self.model.security_agent
self.visualizations_registry = MockVisualizationsRegistry()
self.tag_handler = tags.GalaxyTagHandler(self.model.context)
self.quota_agent = quota.QuotaAgent(self.model)
self.init_datatypes()
self.job_config = Bunch(dynamic_params=None, destinations={})
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)
def url_for(*args, **kwds):
return "/mock/url"
self.url_for = url_for
def __init__(self, test_directory, mock_model=True):
# The following line is needed in order to create
# HistoryDatasetAssociations - ideally the model classes would be
# usable without the ORM infrastructure in place.
in_memomry_model = mapping.init("/tmp",
"sqlite:///:memory:",
create_tables=True)
self.datatypes_registry = Bunch(
integrated_datatypes_configs=
'/galaxy/integrated_datatypes_configs.xml',
get_datatype_by_extension=lambda ext: Bunch(),
)
self.config = Bunch(
outputs_to_working_directory=False,
commands_in_new_shell=True,
new_file_path=os.path.join(test_directory, "new_files"),
tool_data_path=os.path.join(test_directory, "tools"),
root=os.path.join(test_directory, "galaxy"),
admin_users="*****@*****.**",
len_file_path=os.path.join('tool-data', 'shared', 'ucsc', 'chrom'),
builds_file_path=os.path.join('tool-data', 'shared', 'ucsc',
'builds.txt.sample'),
migrated_tools_config=os.path.join(test_directory,
"migrated_tools_conf.xml"),
)
# Setup some attributes for downstream extension by specific tests.
self.job_config = Bunch(dynamic_params=None, )
# Two ways to handle model layer, one is to stub out some objects that
# have an interface similar to real model (mock_model) and can keep
# track of 'persisted' objects in a map. The other is to use a real
# sqlalchemy layer but target an in memory database. Depending on what
# is being tested.
if mock_model:
# Create self.model to mimic app.model.
self.model = Bunch(context=MockContext())
for module_member_name in dir(galaxy.model):
module_member = getattr(galaxy.model, module_member_name)
if type(module_member) == type:
self.model[module_member_name] = module_member
else:
self.model = in_memomry_model
self.genome_builds = GenomeBuilds(self)
self.toolbox = None
self.object_store = None
self.security = SecurityHelper(id_secret="testing")
from galaxy.security import GalaxyRBACAgent
self.job_queue = NoopQueue()
self.security_agent = GalaxyRBACAgent(self.model)
self.tool_data_tables = {}
self.dataset_collections_service = None
self.container_finder = NullContainerFinder()
self.name = "galaxy"
def __init__(self, config=None, **kwargs):
self.config = config or MockAppConfig(**kwargs)
self.security = self.config.security
self.name = kwargs.get('name', 'galaxy')
self.object_store = objectstore.build_object_store_from_config(self.config)
self.model = mapping.init("/tmp", "sqlite:///:memory:", create_tables=True, object_store=self.object_store)
self.security_agent = self.model.security_agent
self.visualizations_registry = MockVisualizationsRegistry()
self.tag_handler = tags.GalaxyTagManager(self.model.context)
self.quota_agent = quota.QuotaAgent(self.model)
self.init_datatypes()
self.job_config = Bunch(
dynamic_params=None,
)
self.tool_data_tables = {}
self.dataset_collections_service = None
self.container_finder = NullContainerFinder()
self._toolbox_lock = MockLock()
self.genome_builds = GenomeBuilds(self)
self.job_manager = Bunch(job_queue=NoopQueue())
self.application_stack = ApplicationStack()