def test_get_runfolders_does_not_return_none_runfolder(self):
# Adding a directory which does not conform to the runfolder pattern
with_non_runfolder_dir = fake_directories + ["bar"]
file_system_service = mock_file_system_service(with_non_runfolder_dir,
fake_projects)
repo = FileSystemBasedRunfolderRepository(base_path="/foo",
file_system_service=file_system_service)
actual_runfolders = list(repo.get_runfolders())
self.assertListEqual(self.expected_runfolders, actual_runfolders)
class TestRunfolderRepository(unittest.TestCase):
expected_runfolders = FAKE_RUNFOLDERS
file_system_service = mock_file_system_service(fake_directories,
fake_projects)
repo = FileSystemBasedRunfolderRepository(
base_path="/foo", file_system_service=file_system_service)
def test_get_runfolders(self):
actual_runfolders = list(self.repo.get_runfolders())
self.assertListEqual(self.expected_runfolders, actual_runfolders)
for actual_runfolder in actual_runfolders:
for expected_runfolder in self.expected_runfolders:
if actual_runfolder == expected_runfolder:
self.assertListEqual(actual_runfolder.projects,
expected_runfolder.projects)
def test_get_runfolders_does_not_return_none_runfolder(self):
# Adding a directory which does not conform to the runfolder pattern
with_non_runfolder_dir = fake_directories + ["bar"]
file_system_service = mock_file_system_service(with_non_runfolder_dir,
fake_projects)
repo = FileSystemBasedRunfolderRepository(
base_path="/foo", file_system_service=file_system_service)
actual_runfolders = list(repo.get_runfolders())
self.assertListEqual(self.expected_runfolders, actual_runfolders)
def test_get_runfolder(self):
runfolder_name = "160930_ST-E00216_0111_BH37CWALXX"
actual_runfolder = self.repo.get_runfolder(runfolder_name)
self.assertIsInstance(actual_runfolder, Runfolder)
self.assertEqual(actual_runfolder.name, runfolder_name)
def compose_application(config):
"""
Instantiates all service, repos, etc which are then used by the application.
The resulting dictionary can then be passed on to routes which instantiates the
http handlers.
:param config: a configuration instance
:return: a dictionary with references to any relevant resources
"""
runfolder_repo = FileSystemBasedRunfolderRepository(
config["monitored_directory"])
external_program_service = ExternalProgramService()
db_connection_string = config["db_connection_string"]
engine = create_engine(db_connection_string, echo=False)
create_and_migrate_db(engine, db_connection_string)
session_factory = scoped_session(sessionmaker())
session_factory.configure(bind=engine)
staging_repo = DatabaseBasedStagingRepository(
session_factory=session_factory)
staging_service = StagingService(
external_program_service=external_program_service,
runfolder_repo=runfolder_repo,
staging_repo=staging_repo,
staging_dir=config["staging_directory"],
session_factory=session_factory)
delivery_repo = DatabaseBasedDeliveriesRepository(
session_factory=session_factory)
delivery_service = MoverDeliveryService(
external_program_service=external_program_service,
staging_service=staging_service,
delivery_repo=delivery_repo)
return dict(config=config,
runfolder_repo=runfolder_repo,
external_program_service=external_program_service,
staging_service=staging_service,
delivery_service=delivery_service)
def compose_application(config):
"""
Instantiates all service, repos, etc which are then used by the application.
The resulting dictionary can then be passed on to routes which instantiates the
http handlers.
:param config: a configuration instance
:return: a dictionary with references to any relevant resources
"""
def _assert_is_dir(directory):
if not FileSystemService.isdir(directory):
raise AssertionError("{} is not a directory".format(
os.path.abspath(directory)))
staging_dir = config['staging_directory']
_assert_is_dir(staging_dir)
runfolder_dir = config["runfolder_directory"]
_assert_is_dir(runfolder_dir)
project_links_directory = config["project_links_directory"]
_assert_is_dir(project_links_directory)
runfolder_repo = FileSystemBasedRunfolderRepository(runfolder_dir)
project_repository = UnorganisedRunfolderProjectRepository(
sample_repository=RunfolderProjectBasedSampleRepository())
unorganised_runfolder_repo = FileSystemBasedUnorganisedRunfolderRepository(
runfolder_dir, project_repository=project_repository)
general_project_dir = config['general_project_directory']
_assert_is_dir(general_project_dir)
general_project_repo = GeneralProjectRepository(
root_directory=general_project_dir)
external_program_service = ExternalProgramService()
db_connection_string = config["db_connection_string"]
engine = create_engine(db_connection_string, echo=False)
alembic_path = config["alembic_path"]
create_and_migrate_db(engine, alembic_path, db_connection_string)
session_factory = scoped_session(sessionmaker())
session_factory.configure(bind=engine)
staging_repo = DatabaseBasedStagingRepository(
session_factory=session_factory)
staging_service = StagingService(
external_program_service=external_program_service,
runfolder_repo=runfolder_repo,
project_dir_repo=general_project_repo,
staging_repo=staging_repo,
staging_dir=staging_dir,
project_links_directory=project_links_directory,
session_factory=session_factory)
delivery_repo = DatabaseBasedDeliveriesRepository(
session_factory=session_factory)
path_to_mover = config['path_to_mover']
mover_delivery_service = MoverDeliveryService(
external_program_service=external_program_service,
staging_service=staging_service,
delivery_repo=delivery_repo,
session_factory=session_factory,
path_to_mover=path_to_mover)
dds_conf = config['dds_conf']
dds_project_repo = DDSProjectRepository(session_factory=session_factory)
dds_service = DDSService(external_program_service=external_program_service,
staging_service=staging_service,
staging_dir=staging_dir,
delivery_repo=delivery_repo,
dds_project_repo=dds_project_repo,
session_factory=session_factory,
dds_conf=dds_conf)
delivery_sources_repo = DatabaseBasedDeliverySourcesRepository(
session_factory=session_factory)
runfolder_service = RunfolderService(runfolder_repo)
delivery_service = DeliveryService(
mover_service=mover_delivery_service,
staging_service=staging_service,
delivery_sources_repo=delivery_sources_repo,
general_project_repo=general_project_repo,
runfolder_service=runfolder_service,
project_links_directory=project_links_directory)
best_practice_analysis_service = BestPracticeAnalysisService(
general_project_repo)
organise_service = OrganiseService(
runfolder_service=RunfolderService(unorganised_runfolder_repo))
return dict(config=config,
runfolder_repo=runfolder_repo,
external_program_service=external_program_service,
staging_service=staging_service,
mover_delivery_service=mover_delivery_service,
dds_service=dds_service,
delivery_service=delivery_service,
general_project_repo=general_project_repo,
best_practice_analysis_service=best_practice_analysis_service,
organise_service=organise_service)
def compose_application(config):
"""
Instantiates all service, repos, etc which are then used by the application.
The resulting dictionary can then be passed on to routes which instantiates the
http handlers.
:param config: a configuration instance
:return: a dictionary with references to any relevant resources
"""
def _assert_is_dir(directory):
if not FileSystemService.isdir(directory):
raise AssertionError("{} is not a directory".format(directory))
staging_dir = config['staging_directory']
_assert_is_dir(staging_dir)
runfolder_dir = config["runfolder_directory"]
_assert_is_dir(runfolder_dir)
runfolder_repo = FileSystemBasedRunfolderRepository(runfolder_dir)
general_project_dir = config['general_project_directory']
_assert_is_dir(general_project_dir)
general_project_repo = GeneralProjectRepository(
root_directory=general_project_dir)
external_program_service = ExternalProgramService()
db_connection_string = config["db_connection_string"]
engine = create_engine(db_connection_string, echo=False)
alembic_path = config["alembic_path"]
create_and_migrate_db(engine, alembic_path, db_connection_string)
session_factory = scoped_session(sessionmaker())
session_factory.configure(bind=engine)
staging_repo = DatabaseBasedStagingRepository(
session_factory=session_factory)
staging_service = StagingService(
external_program_service=external_program_service,
runfolder_repo=runfolder_repo,
project_dir_repo=general_project_repo,
staging_repo=staging_repo,
staging_dir=staging_dir,
session_factory=session_factory)
delivery_repo = DatabaseBasedDeliveriesRepository(
session_factory=session_factory)
path_to_mover = config['path_to_mover']
delivery_service = MoverDeliveryService(
external_program_service=external_program_service,
staging_service=staging_service,
delivery_repo=delivery_repo,
session_factory=session_factory,
path_to_mover=path_to_mover)
return dict(config=config,
runfolder_repo=runfolder_repo,
external_program_service=external_program_service,
staging_service=staging_service,
delivery_service=delivery_service)