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")