BIOLOGICAL_ROLE_ID = '24432'
APPLICATION_ROLE_ID = '33232'
BIOCHEMICAL_ROLE_CHEBI_ID = '52206'
PATHWAY_INHIBITOR_CHEBI_ID = '76932'
ENZYME_INHIBITOR_CHEBI_ID = '23924'
AGONIST_CHEBI_ID = '48705'
INVERSE_AGONIST_CHEBI_ID = '90847'
INHIBITOR_CHEBI_ID = '35222'
ANTAGONIST_CHEBI_ID = '48706'
BLACKLIST = [
'48001', # protein synthesis inhibitor
'64106', # protein kinase agonist
]
chebi_obo = pyobo.get('chebi')
chebi_id_to_name = pyobo.get_id_name_mapping('chebi')
XREFS_DF = get_xrefs_df()
CURATED_ROLE_CHEBI_IDS = {
source_id[len('CHEBI:'):]
for source_db, source_id in XREFS_DF[['source_db', 'source_id']].values
if source_db == 'chebi'
}
IRRELEVANT_ROLE_CHEBI_IDS = set(
itt.chain.from_iterable(
chebi_obo.descendants(chebi_id[len('CHEBI'):])
for chebi_id in get_irrelevant_roles_df().identifier
if chebi_id[len('CHEBI'):] in chebi_obo.hierarchy))
def setUp(self) -> None:
"""Set up the test with the mock ChEBI OBO file."""
with chebi_patch:
self.obo = get('chebi')
def setUp(self) -> None:
"""Set up the test with the mock ChEBI OBO file."""
# TODO use mock
self.obo = get('chebi', url=TEST_CHEBI_OBO_PATH, local=True)
def test_get_obo(self):
"""Test getting an OBO document."""
obo = get('chebi', url=TEST_CHEBI_OBO_PATH, local=True)
terms = list(obo)
self.assertEqual(18, len(terms))