def test_add_member_genes(self):
net = NiceCXNetwork()
aid = net.create_node('a')
net.set_node_attribute(aid, NodeMemberUpdator.TYPE, 'proteinfamily')
notinid = net.create_node('x')
net.set_node_attribute(notinid, NodeMemberUpdator.TYPE,
'proteinfamily')
mock = GeneSymbolSearcher(bclient=None)
mock.get_symbol = MagicMock(side_effect=['', None])
updator = NodeMemberUpdator(None, None, genesearcher=mock)
aidnode = net.get_node(aid)
res = updator._add_member_genes(net, aidnode, [])
self.assertEqual(['No proteins obtained for node: ' + str(aidnode)],
res)
notinidnode = net.get_node(notinid)
res = updator._add_member_genes(net, notinidnode, ['x'])
self.assertTrue('For node ' + str(notinidnode) +
' No gene symbol found for x. Skipping.' in res)
self.assertTrue('Not a single gene symbol found. Skipping insertion '
'of member attribute for node ' +
str(notinidnode) in res)
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_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_update_network_containing_all_types(self):
pfdict = {'a': ['2', '3'], 'SIGNOR-PF10': ['7', '8']}
cdict = {'e': ['5', '6'], 'SIGNOR-C1': ['9', '10']}
net = NiceCXNetwork()
aid = net.create_node('a')
net.set_node_attribute(aid, NodeMemberUpdator.TYPE, 'proteinfamily')
eid = net.create_node('e')
net.set_node_attribute(eid, NodeMemberUpdator.TYPE, 'complex')
oid = net.create_node('c')
o2id = net.create_node('d')
net.set_node_attribute(o2id, NodeMemberUpdator.TYPE, 'protein')
notinid = net.create_node('x')
net.set_node_attribute(notinid, NodeMemberUpdator.TYPE,
'proteinfamily')
notinid2 = net.create_node('y')
net.set_node_attribute(notinid2, NodeMemberUpdator.TYPE, 'complex')
mock = GeneSymbolSearcher(bclient=None)
mock.get_symbol = MagicMock(side_effect=['AA', 'BB', 'CC', 'DD'])
updator = NodeMemberUpdator(pfdict, cdict, genesearcher=mock)
res = updator.update(net)
self.assertTrue(
"No entry in proteinfamily map for node: {'@id': 4, 'n': 'x', 'r': 'x'}"
in res)
self.assertTrue(
"No entry in complexes map for node: {'@id': 5, 'n': 'y', 'r': 'y'}"
in res)
res = net.get_node_attribute(aid, NodeMemberUpdator.MEMBER)
self.assertTrue('hgnc.symbol:AA' in res['v'])
self.assertTrue('hgnc.symbol:BB' in res['v'])
res = net.get_node_attribute(eid, NodeMemberUpdator.MEMBER)
self.assertTrue('hgnc.symbol:CC' in res['v'])
self.assertTrue('hgnc.symbol:DD' in res['v'])
res = net.get_node_attribute(oid, NodeMemberUpdator.MEMBER)
self.assertEqual(None, res)
res = net.get_node_attribute(o2id, NodeMemberUpdator.MEMBER)
self.assertEqual(None, res)
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))
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')