def agent_from_obs(obs_name, model):
db_refs = {}
ag_name = None
for ann in model.annotations:
if ann.subject == obs_name:
if ann.predicate == 'from_indra_agent':
ag_name = ann.object
break
if ag_name:
mon_name = _n(ag_name)
for ann in model.annotations:
if isinstance(ann.subject, Monomer) and \
ann.subject.name == mon_name and ann.predicate == 'is':
db_name, db_ref = parse_identifiers_url(ann.object)
db_refs[db_name] = db_ref
ag = Agent(ag_name, db_refs=db_refs)
return ag
def test_parse_identifiers_url():
url1 = 'http://identifiers.org/foo/bar'
url2 = 'http://identifiers.org/hgnc/12345'
url3 = 'http://identifiers.org/hgnc/HGNC:12345'
url4 = 'http://identifiers.org/uniprot/12345'
url5 = 'http://identifiers.org/chebi/12345'
url6 = 'http://identifiers.org/interpro/12345'
url7 = 'http://identifiers.org/pfam/12345'
(ns, id) = pa.parse_identifiers_url(url1)
assert ns is None and id is None
(ns, id) = pa.parse_identifiers_url(url2)
assert ns is None and id is None
(ns, id) = pa.parse_identifiers_url(url3)
assert ns == 'HGNC' and id == '12345'
(ns, id) = pa.parse_identifiers_url(url4)
assert ns == 'UP' and id == '12345'
(ns, id) = pa.parse_identifiers_url(url5)
assert ns == 'CHEBI' and id == '12345'
(ns, id) = pa.parse_identifiers_url(url6)
assert ns == 'IP' and id == '12345'
(ns, id) = pa.parse_identifiers_url(url7)
assert ns == 'XFAM' and id == '12345'
def test_parse_identifiers_url():
url1 = 'http://identifiers.org/foo/bar'
url2 = 'http://identifiers.org/hgnc/12345'
url3 = 'http://identifiers.org/hgnc/HGNC:12345'
url4 = 'http://identifiers.org/uniprot/12345'
url5 = 'http://identifiers.org/chebi/12345'
url6 = 'http://identifiers.org/interpro/12345'
url7 = 'http://identifiers.org/pfam/12345'
(ns, id) = pa.parse_identifiers_url(url1)
assert ns is None and id is None
(ns, id) = pa.parse_identifiers_url(url2)
assert ns is None and id is None
(ns, id) = pa.parse_identifiers_url(url3)
assert ns == 'HGNC' and id == '12345'
(ns, id) = pa.parse_identifiers_url(url4)
assert ns == 'UP' and id == '12345'
(ns, id) = pa.parse_identifiers_url(url5)
assert ns == 'CHEBI' and id == '12345'
(ns, id) = pa.parse_identifiers_url(url6)
assert ns == 'IP' and id == '12345'
(ns, id) = pa.parse_identifiers_url(url7)
assert ns == 'XFAM' and id == '12345'