def test_notify_file_archiver(self, expand_curie): archive_submission = MagicMock(ArchiveSubmission) archive_submission.get_url = MagicMock(return_value='url') mock_manifest = self._mock_manifest(self.base_manifest) mock_manifest.get_library_preparation_protocol = MagicMock( return_value=self.base_manifest.get( 'library_preparation_protocol_10x')) seq_files = self.base_manifest.get('files') seq_file = copy.deepcopy(seq_files[0]) seq_file['content']['file_core']['file_name'] = "R2.fastq.gz" seq_files.append(seq_file) mock_manifest.get_files = MagicMock(return_value=seq_files) ingest_api = copy.deepcopy(self.ingest_api) ingest_api.get_manifest_by_id = MagicMock( return_value={'bundleUuid': 'dcp_uuid'}) archiver = IngestArchiver(ingest_api=ingest_api, dsp_api=self.dsp_api, ontology_api=self.ontology_api) archiver.get_manifest = MagicMock(return_value=mock_manifest) entity_map = archiver.convert(['bundle_uuid']) archive_submission.converted_entities = list( entity_map.get_converted_entities()) archive_submission.entity_map = entity_map messages = archiver.notify_file_archiver(archive_submission) expected = { "dsp_api_url": 'dsp_url', "dcp_bundle_uuid": 'dcp_uuid', 'submission_url': 'url', 'files': [{ 'name': 'dummy_manifest_id.bam' }], 'conversion': { 'output_name': 'dummy_manifest_id.bam', 'schema': '10xV2', 'inputs': [{ 'name': 'R1.fastq.gz', 'read_index': 'read1', 'cloud_url': 's3://org-humancellatlas-upload-dev/8cd91cfd-0374-454f-ac83-8db6581d2706/R1.fastq.gz' }, { 'name': 'R2.fastq.gz', 'read_index': 'read1', 'cloud_url': 's3://org-humancellatlas-upload-dev/8cd91cfd-0374-454f-ac83-8db6581d2706/R1.fastq.gz' }] }, 'manifest_id': 'dummy_manifest_id' } self.assertTrue(messages) self.assertEqual(expected, messages[0])
def test_get_archivable_entities(self, expand_curie): mock_manifest = self._mock_manifest(self.base_manifest) archiver = IngestArchiver(ontology_api=self.ontology_api, ingest_api=self.ingest_api, dsp_api=self.dsp_api, exclude_types=['sequencingRun']) archiver.get_manifest = MagicMock(return_value=mock_manifest) entity_map = archiver.convert(['manifest_id']) entities_by_type = entity_map.entities_dict_type self.assertTrue(entities_by_type.get('project')) self.assertTrue(entities_by_type.get('study')) self.assertTrue(entities_by_type.get('sample')) self.assertTrue(entities_by_type.get('sequencingExperiment'))
def test_archive(self): mock_manifest = self._mock_manifest(self.base_manifest) archiver = IngestArchiver(ontology_api=self.ontology_api, ingest_api=self.ingest_api, dsp_api=self.dsp_api, exclude_types=['sequencingRun']) archiver.get_manifest = MagicMock(return_value=mock_manifest) entity_map = archiver.convert(['bundle_uuid']) archive_submission = archiver.archive(entity_map) self.assertTrue(archive_submission.is_completed) for entity in archive_submission.entity_map.get_entities(): self.assertTrue(archive_submission.accession_map.get(entity.id), f"{entity.id} has no accession.")
def test_validate_and_complete_submission(self): mock_manifest = self._mock_manifest(self.base_manifest) archiver = IngestArchiver(ontology_api=self.ontology_api, ingest_api=self.ingest_api, dsp_api=self.dsp_api, exclude_types=['sequencingRun']) archiver.get_manifest = MagicMock(return_value=mock_manifest) entity_map = archiver.convert(['bundle_uuid']) archive_submission, _ = archiver.archive_metadata(entity_map) url = archive_submission.get_url() archive_submission = archiver.complete_submission( dsp_submission_url=url) self.assertTrue(archive_submission.is_completed) self.assertTrue(archive_submission.accession_map)
def test_archive_skip_metadata_with_accessions(self): with open(config.JSON_DIR + 'hca/biomaterial_with_accessions.json', encoding=config.ENCODING) as data_file: biomaterials = json.loads(data_file.read()) biomaterial_manifest = {'biomaterials': biomaterials} mock_manifest = self._mock_manifest(biomaterial_manifest) archiver = IngestArchiver(ontology_api=self.ontology_api, ingest_api=self.ingest_api, dsp_api=self.dsp_api, exclude_types=['sequencingRun']) archiver.get_manifest = MagicMock(return_value=mock_manifest) entity_map = archiver.convert('') archive_submission = archiver.archive(entity_map) self.assertTrue(archive_submission.is_completed) self.assertTrue(archive_submission.errors) self.assertFalse(archive_submission.processing_result)