def test_send_all_samples_sends_each_samples_with_project_release_date(self):
# Given
self.submitter.send_sample = MagicMock(return_value='UPDATED')
test_date = datetime.now().isoformat()
project_attributes = {
'releaseDate': test_date
}
project_attributes = make_ingest_entity('projects', random_id(), random_uuid(), project_attributes)
self.submission.map_ingest_entity(project_attributes)
biomaterials = self.map_random_biomaterials(self.submission, 5)
calls = []
call_count = 0
expected_result = {'UPDATED': []}
for entity in biomaterials:
call_count += 1
calls.append(call(entity, test_date))
expected_result['UPDATED'].append(entity)
# When
result = self.submitter.send_all_samples(self.submission)
# Then
self.submitter.send_sample.assert_has_calls(calls, any_order=True)
self.assertEqual(call_count, self.submitter.send_sample.call_count)
self.assertDictEqual(expected_result, result)
def test_submit_sample_return_creation(self):
# Given
self.biosamples.send_sample = MagicMock(return_value={'accession': 'SAMEA1234567'})
test_case = self.submission.map_ingest_entity(make_ingest_entity('biomaterials', random_id(), random_uuid()))
# When
result = self.submitter.send_sample(test_case)
# Then
self.assertEqual('CREATED', result)
def setUp(self) -> None:
# Given
self.test_type = random_id()
self.test_id = random_id()
self.test_uuid = random_uuid()
self.test_case = make_ingest_entity(self.test_type, self.test_id, self.test_uuid)
self.submission = HcaSubmission()
# When
self.test_entity = self.submission.map_ingest_entity(self.test_case)
def map_random_biomaterials(submission: HcaSubmission, entity_count: int) -> List[Entity]:
biomaterials = []
for i in range(0, entity_count):
biomaterials.append(
submission.map_ingest_entity(
make_ingest_entity('biomaterials', random_id(), random_uuid())
)
)
return biomaterials
def test_duplication_entity_with_differing_content_is_ignored(self):
# Given
ignored_uuid = random_uuid()
duplicate_test_case = make_ingest_entity(self.test_type, self.test_id, ignored_uuid)
# When
duplicate_entity = self.submission.map_ingest_entity(duplicate_test_case)
# Then
self.assertEqual(self.test_entity, duplicate_entity)
self.assertEqual(self.test_uuid, self.test_entity.attributes['uuid']['uuid'])
self.assertNotEqual(ignored_uuid, self.test_entity.attributes['uuid']['uuid'])
def test_submit_sample_return_error(self):
# Given
error_msg = f'TestCaseError{random_id(3)}'
self.biosamples.send_sample = MagicMock(side_effect=Exception(error_msg))
test_case = self.submission.map_ingest_entity(
make_ingest_entity('biomaterials', random_id(), random_uuid()))
# When
result = self.submitter.send_sample(test_case)
# Then
self.assertEqual('ERRORED', result)
self.assertDictEqual(test_case.get_errors(), {'content.biomaterial_core.biosamples_accession': [f'BioSamples Error: {error_msg}']})
def test_submit_sample_converts_and_sends_sample(self):
# Given
test_case = self.submission.map_ingest_entity(
make_ingest_entity('biomaterials', random_id(), random_uuid())
)
# When
result = self.submitter.send_sample(test_case)
# Then
self.converter.convert.assert_called_once_with(test_case.attributes, release_date=None, accession=None)
self.biosamples.send_sample.assert_called_once_with(self.empty_sample)
self.assertEqual('UPDATED', result)
def map_random_entities(
submission: HcaSubmission,
entity_count: int,
entity_type: str = None
):
entity_list = []
for i in range(0, entity_count):
entity_list.append(
submission.map_ingest_entity(
make_ingest_entity(
entity_type if entity_type else random_id(),
random_id(),
random_uuid()
)
)
)
return entity_list