def setUp(self): self.case = AMRLocationUploader()
class AMRLocationUploaderTestCase(unittest.TestCase): def setUp(self): self.case = AMRLocationUploader() def tearDown(self): del self.case @mock.patch('superphy.upload.gene_location_upload.GeneLocationUploader.create_gene_location') @mock.patch('superphy.upload.metadata_upload.json.load') @mock.patch('superphy.upload.gene_location_upload.open') def test_parse_result(self, mock_open, mock_load, mock_create): mock_open.return_value = mock.MagicMock(spec=file) mock_load.return_value = { "gene_10|GeneMark.hmm|356_aa|+|5964|7034|gi|606959961|gb|JHNV01100083.1|\ Escherichia coli O119:H4 str. 03-3458 contig83, whole genome shotgun sequence": {}, "gene_12|GeneMark.hmm|304_aa|-|7759|8673|gi|606959961|gb|JHNV01100083.1|\ Escherichia coli O119:H4 str. 03-3458 contig83, whole genome shotgun sequence": { "gnl|BL_ORD_ID|796|hsp_num:0": { "SequenceFromBroadStreet": "MRKSTTLLIGFVKAAYRILQALDNKQ", "orf_start": 7759, "ARO_name": "OCH-3", "type_match": "Loose", "query": "TKQPLENILRVGSQGIASYVDGNTSFLGNGIESRILFDQQRPDNIIE", "evalue": 4.07141, "max-identities": 13, "orf_strand": "-", "bit-score": 25.0238, "cvterm_id": "37077", "sequenceFromDB": "TVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFE", "match": "T +PL ++ +A +DG + F G G+ S+ + D I E", "model_id": "201", "orf_From": "gi|606959961|gb|JHNV01100083.1|\ Escherichia coli O119:H4 str. 03-3458 contig83, whole genome shotgun sequence", "pass_evalue": 1E-100, "query_end": 8628, "ARO_category": { "36696": { "category_aro_name": "antibiotic inactivation enzyme", "category_aro_cvterm_id": "36696", "category_aro_accession": "3000557", "category_aro_description": "Enzyme." }, "36268": { "category_aro_name": "beta-lactam resistance gene", "category_aro_cvterm_id": "36268", "category_aro_accession": "3000129", "category_aro_description": "Genes conferring resistance to beta-lactams." } }, "ARO_accession": "3002516", "query_start": 8488, "model_name": "OCH-3", "model_type": "model-blastP", "orf_end": 8673 } } } self.case.parse_result() mock_load.assert_called_with(mock.ANY) mock_create.assert_called_with("OCH-3_JHNV01100083_0", "OCH-3", "JHNV01100083", 8673, 7759, "", False, "Loose")