def test_from_dict_fail_fast_with_missing_info(self):
# given:
data = {}
# then:
with self.assertRaises(MetadataParseException):
# when
MetadataResource.from_dict(data)
def test_generate_complete_experiment_graph(self):
# given
ingest_client = self.mock_ingest
crawler = GraphCrawler(MetadataService(ingest_client))
test_assay_process = MetadataResource.from_dict(
self.mock_files.get_entity('processes', 'mock-assay-process'))
test_project = MetadataResource.from_dict(
self.mock_files.get_entity('projects', 'mock-project'))
# when
experiment_graph = crawler.generate_complete_experiment_graph(
test_assay_process, test_project)
# then
expected_links = self.mock_files.get_links_json()
nodes = self._get_nodes(expected_links)
self.assertEqual(
set([node.uuid for node in experiment_graph.nodes.get_nodes()]),
nodes)
self.assertEqual(len(experiment_graph.links.get_links()),
len(expected_links.get('links', [])))
self.assertEqual(experiment_graph.links.to_dict(), expected_links)
def test_provenance_from_dict_fail_fast(self):
# given:
uuid_value = '3f3212da-d5d0-4e55-b31d-83243fa02e0d'
data = {'uuid': uuid_value, # unexpected structure structure
'submissionDate': 'a submission date',
'updateDate': 'an update date'}
# then:
with self.assertRaises(MetadataParseException):
# when
MetadataResource.provenance_from_dict(data)
def test_provenance_from_dict_newer_version(self):
# given:
uuid_value = '3f3212da-d5d0-4e55-b31d-83243fa02e0d'
data = self._create_test_data(uuid_value)
data['content']['describedBy'] = 'https://15.1.1/cell_suspension'
# when:
metadata_provenance = MetadataResource.provenance_from_dict(data)
# then:
self.assertEqual(15, metadata_provenance.schema_major_version)
self.assertEqual(1, metadata_provenance.schema_minor_version)
def test_provenance_from_dict_older_version(self):
# given:
uuid_value = '3f3212da-d5d0-4e55-b31d-83243fa02e0d'
data = self._create_test_data(uuid_value)
data['content']['describedBy'] = 'https://13.1.1/cell_suspension'
# when:
metadata_provenance = MetadataResource.provenance_from_dict(data)
# then:
self.assertIsNotNone(metadata_provenance)
self.assertIsNone(metadata_provenance.to_dict().get('schema_major_version'))
self.assertIsNone(metadata_provenance.to_dict().get('schema_minor_version'))
def test_generate_experiment_process_graph(self):
# given
ingest_client = self.mock_ingest
crawler = GraphCrawler(MetadataService(ingest_client))
test_assay_process = MetadataResource.from_dict(
self.mock_files.get_entity('processes', 'mock-assay-process'))
# when
experiment_graph = crawler.generate_experiment_graph(
test_assay_process)
# then
self.assertEqual(len(experiment_graph.nodes.get_nodes()), 15)
self.assertEqual(len(experiment_graph.links.get_links()), 4)
def test_generate_supplementary_files_graph(self):
# given
ingest_client = self.mock_ingest
crawler = GraphCrawler(MetadataService(ingest_client))
test_project = MetadataResource.from_dict(
self.mock_files.get_entity('projects', 'mock-project'))
# when
experiment_graph = crawler.generate_supplementary_files_graph(
test_project)
# then
self.assertEqual(len(experiment_graph.nodes.get_nodes()), 3)
self.assertEqual(len(experiment_graph.links.get_links()),
1) # project, and 2 supplementary files
def write_metadata(self, metadata: MetadataResource, project_uuid: str):
# TODO1: only proceed if lastContentModified > last
dest_object_key = f'{project_uuid}/metadata/{metadata.concrete_type()}/{metadata.uuid}_{metadata.dcp_version}.json'
metadata_json = metadata.get_content(with_provenance=True)
data_stream = DcpStagingClient.dict_to_json_stream(metadata_json)
self.write_to_staging_bucket(dest_object_key, data_stream)
# TODO2: patch dcpVersion
#patch_url = metadata.metadata_json['_links']['self']['href']
#self.ingest_client.patch(patch_url, {"dcpVersion": metadata.dcp_version})
if metadata.metadata_type == "file":
self.write_file_descriptor(metadata, project_uuid)
def test_provenance_from_dict(self):
# given:
uuid_value = '3f3212da-d5d0-4e55-b31d-83243fa02e0d'
data = self._create_test_data(uuid_value)
data['content']['describedBy'] = 'https://some-schema/1.2.3'
# when:
metadata_provenance = MetadataResource.provenance_from_dict(data)
# then:
self.assertIsNotNone(metadata_provenance)
self.assertEqual(data['uuid']['uuid'], metadata_provenance.document_id)
self.assertEqual('a date', metadata_provenance.submission_date)
self.assertEqual('another date', metadata_provenance.update_date)
self.assertEqual(1, metadata_provenance.schema_major_version)
self.assertEqual(2, metadata_provenance.schema_minor_version)
def test_from_dict(self):
# given:
uuid_value = '3f3212da-d5d0-4e55-b31d-83243fa02e0d'
data = self._create_test_data(uuid_value)
# when:
metadata = MetadataResource.from_dict(data)
# then:
self.assertIsNotNone(metadata)
self.assertEqual('biomaterial', metadata.metadata_type)
self.assertEqual(data['content'], metadata.metadata_json)
self.assertEqual(utils.to_dcp_version(data['dcpVersion']), metadata.dcp_version)
# and:
self.assertEqual(uuid_value, metadata.uuid)
def project_for_process(self,
process: MetadataResource) -> MetadataResource:
return MetadataResource.from_dict(
list(
self.ingest_client.get_related_entities(
"projects", process.full_resource, "projects"))[0])
def get_process(self, process_uuid) -> MetadataResource:
return MetadataResource.from_dict(
self.ingest_client.get_entity_by_uuid('processes', process_uuid))
def from_metadata_resource(metadata: MetadataResource) -> 'ProtocolLink':
return ProtocolLink(metadata.concrete_type(), metadata.uuid)