def test_get_hpo_from_omim(connection, hpo_terms, mim_terms):
"""docstring for test_get_description"""
populate_disease(
connection=connection,
disease_terms=mim_terms,
)
cursor = get_cursor(connection=connection)
cursor.execute("SELECT * FROM disease WHERE mim_nr = '600920'")
hpo_ids = set()
for row in cursor.fetchall():
hpo_ids.add(row['mim_hpo'])
assert hpo_ids == set([767, 3042,5280,1363,772,1195,2987])
def test_get_hpo_from_omim(connection, hpo_terms, mim_terms):
"""docstring for test_get_description"""
populate_disease(
connection=connection,
disease_terms=mim_terms,
)
cursor = get_cursor(connection=connection)
cursor.execute("SELECT * FROM disease WHERE mim_nr = '600920'")
hpo_ids = set()
for row in cursor.fetchall():
hpo_ids.add(row['mim_hpo'])
assert hpo_ids == set([767, 3042, 5280, 1363, 772, 1195, 2987])
def database(request, connection, hpo_terms, mim_terms, genes):
"""Return a populated database"""
populate_hpo(
connection=connection,
hpo_terms=hpo_terms,
)
populate_disease(
connection=connection,
disease_terms=mim_terms
)
populate_genes(
connection=connection,
genes=genes
)
return connection
