def test_convert_library(self):
model = create_stub_library()
converted_model = convert_to_sqlalchemy_model(model) # type: SQLAlchemyLibrary
self.assertEqual(converted_model.__class__, SQLAlchemyLibrary)
self.assertEqual(converted_model.internal_id, INTERNAL_ID)
self.assertEqual(converted_model.name, NAME)
self.assertEqual(converted_model.library_type, LIBRARY_TYPE)
def test_convert_study(self):
model = create_stub_study()
converted_model = convert_to_sqlalchemy_model(model) # type: SQLAlchemyStudy
self.assertEqual(converted_model.__class__, SQLAlchemyStudy)
self.assertEqual(converted_model.internal_id, INTERNAL_ID)
self.assertEqual(converted_model.name, NAME)
self.assertEqual(converted_model.accession_number, ACCESSION_NUMBER)
self.assertEqual(converted_model.study_type, STUDY_TYPE)
self.assertEqual(converted_model.description, DESCRIPTION)
self.assertEqual(converted_model.study_title, STUDY_TITLE)
self.assertEqual(converted_model.study_visibility, STUDY_VISIBILITY)
self.assertEqual(converted_model.faculty_sponsor, FACULTY_SPONSOR)
def add(self, models: Union[Model, Iterable[MappedType]]):
if models is None:
raise ValueError("Cannot add `None`")
if not isinstance(models, list):
models = [models]
session = self._database_connector.create_session()
for model in models:
sqlalchemy_model = convert_to_sqlalchemy_model(model)
session.add(sqlalchemy_model)
session.commit()
session.close()
def test_convert_sample(self):
model = create_stub_sample()
converted_model = convert_to_sqlalchemy_model(model) # type: SQLAlchemySample
self.assertEqual(converted_model.__class__, SQLAlchemySample)
self.assertEqual(converted_model.internal_id, INTERNAL_ID)
self.assertEqual(converted_model.name, NAME)
self.assertEqual(converted_model.accession_number, ACCESSION_NUMBER)
self.assertEqual(converted_model.organism, ORGANISM)
self.assertEqual(converted_model.common_name, COMMON_NAME)
self.assertEqual(converted_model.taxon_id, TAXON_ID)
self.assertEqual(converted_model.gender, GENDER)
self.assertEqual(converted_model.ethnicity, ETHNICITY)
self.assertEqual(converted_model.cohort, COHORT)
self.assertEqual(converted_model.country_of_origin, COUNTRY_OF_ORIGIN)
self.assertEqual(converted_model.geographical_region, GEOGRAPHICAL_REGION)
def test_convert_multiplexed_library(self):
alchemy_model = convert_to_sqlalchemy_model(create_stub_multiplexed_library())
converted_model = convert_to_popo_model(alchemy_model) # type: MultiplexedLibrary
self.assertEqual(converted_model.__class__, MultiplexedLibrary)
self.assertEqual(converted_model.internal_id, INTERNAL_ID)
self.assertEqual(converted_model.name, NAME)
def test_convert_well(self):
alchemy_model = convert_to_sqlalchemy_model(create_stub_well())
converted_model = convert_to_popo_model(alchemy_model) # type: Well
self.assertEqual(converted_model.__class__, Well)
self.assertEqual(converted_model.internal_id, INTERNAL_ID)
self.assertEqual(converted_model.name, NAME)
