def test_query_uniprot(self):
mock = MagicMock()
mock.query = MagicMock(return_value={'total': 0,
'hits': []})
searcher = GeneSymbolSearcher(bclient=mock)
with requests_mock.Mocker() as m:
m.register_uri('GET', 'https://www.uniprot.org/uniprot/HAHA.txt',
status_code='200', text="""ID BXA1_CLOBO Reviewed; 1296 AA.
AC P0DPI0; A5HZZ9; A7G1U9; P01561; P10845; P18639;
DT 18-JUL-2018, integrated into UniProtKB/Swiss-Prot.
DT 18-JUL-2018, sequence version 1.
DT 08-MAY-2019, entry version 9.
DE RecName: Full=Botulinum neurotoxin type A;
DE Short=BoNT/A;
DE AltName: Full=Bontoxilysin-A;
DE Short=BOTOX;
DE AltName: Full=Botulinum neurotoxin type A1;
DE Contains:
DE RecName: Full=Botulinum neurotoxin A light chain;
DE Short=LC;
DE EC=3.4.24.69 {ECO:0000269|PubMed:8243676};
DE Contains:
DE RecName: Full=Botulinum neurotoxin A heavy chain;
DE Short=HC;
DE Flags: Precursor;
GN Name=botA {ECO:0000303|PubMed:2185020};
GN Synonyms=atx {ECO:0000303|PubMed:8521962},
GN bonT {ECO:0000303|PubMed:8863443};
OS Clostridium botulinum.""")
self.assertEqual('botA', searcher.get_symbol('haha'))
def test_symbol_not_in_cache_no_but_got_hit_with_cache_check(self):
mock = MagicMock()
mock.query = MagicMock(return_value={'max_score': 437.58682, 'took': 62,
'total': 5031,
'hits': [{'_id': '7157',
'_score': 437.58682,
'entrezgene': '7157',
'name': 'tumor protein p53',
'symbol': 'TP53',
'taxid': 9606},
{'_id': '24842',
'_score': 306.22318,
'entrezgene': '24842',
'name': 'tumor protein p53',
'symbol': 'Tp53',
'taxid': 10116},
{'_id': '109394672',
'_score': 296.02454,
'entrezgene': '109394672',
'name': 'tumor protein p53',
'symbol': 'TP53',
'taxid': 186990},
{'_id': '113633022',
'_score': 296.02454,
'entrezgene': '113633022',
'name': 'tumor protein p53',
'symbol': 'TP53',
'taxid': 90247},
{'_id': '102169621', '_score': 296.02454, 'entrezgene': '102169621', 'name': 'tumor protein p53', 'symbol': 'TP53', 'taxid': 9925}, {'_id': '113878373', '_score': 296.02454, 'entrezgene': '113878373', 'name': 'tumor protein p53', 'symbol': 'TP53', 'taxid': 30522}, {'_id': '101285670', '_score': 296.02454, 'entrezgene': '101285670', 'name': 'tumor protein p53', 'symbol': 'TP53', 'taxid': 9733}, {'_id': '105819395', '_score': 296.02454, 'entrezgene': '105819395', 'name': 'tumor protein p53', 'symbol': 'TP53', 'taxid': 379532}, {'_id': 'ENSMMMG00000019747', '_score': 296.02454, 'name': 'tumor protein p53', 'symbol': 'TP53', 'taxid': 9994}, {'_id': '100583326', '_score': 296.02454, 'entrezgene': '100583326', 'name': 'tumor protein p53', 'symbol': 'TP53', 'taxid': 61853}]})
searcher = GeneSymbolSearcher(bclient=mock)
self.assertEqual('TP53', searcher.get_symbol('tp53'))
self.assertEqual('TP53', searcher.get_symbol('tp53'))
mock.query.assert_called_once_with('tp53')
def test_symbol_not_in_cache_no_hit_and_none_returned(self):
mock = MagicMock()
mock.query = MagicMock(return_value=None)
searcher = GeneSymbolSearcher(bclient=mock)
with requests_mock.Mocker() as m:
m.register_uri('GET', 'https://www.uniprot.org/uniprot/HAHA.txt',
status_code='404', text=None)
self.assertEqual('', searcher.get_symbol('haha'))
mock.query.assert_called_with('haha')
def test_symbol_not_in_cache_no_hit_and_httperror_raised(self):
mock = MagicMock()
mock.query = MagicMock(side_effect=HTTPError('some error'))
searcher = GeneSymbolSearcher(bclient=mock)
with requests_mock.Mocker() as m:
m.register_uri('GET', 'https://www.uniprot.org/uniprot/HAHA.txt',
status_code='404', text=None)
self.assertEqual('', searcher.get_symbol('haha'))
mock.query.assert_called_with('haha')
def test_get_symbol_cache_hit_is_empty_str(self):
searcher = GeneSymbolSearcher()
searcher._cache['haha'] = ''
self.assertEqual(None, searcher.get_symbol('haha'))
def test_get_symbol_cache_hit(self):
searcher = GeneSymbolSearcher()
searcher._cache['haha'] = 'gee'
self.assertEqual('gee', searcher.get_symbol('haha'))
def test_get_symbol_none_passed_in(self):
searcher = GeneSymbolSearcher()
self.assertEqual(None, searcher.get_symbol(None))