def test_this():
ret = unichem.get('AAOVKJBEBIDNHE-UHFFFAOYSA-N')
filename = 'test.json'
with open(filename, 'w') as f:
json.dump(ret, f, indent=4)
def test_search_compound_in_unichem(self):
ret = unichem.get('AIN')
self.assertEqual(len(ret), 1)
self.assertTrue(set(['aspirin', 'CHEMBL25', 'SCHEMBL1353']).issubset(
set([x['src_compound_id'] for x in ret[list(ret.keys())[0]]])))
from chembl_webresource_client.unichem import unichem_client as unichem
import requests
def test_this():
ret = unichem.get('AAOVKJBEBIDNHE-UHFFFAOYSA-N')
filename = 'test.json'
with open(filename, 'w') as f:
json.dump(ret, f, indent=4)
if __name__ == '__main__':
infile = sys.argv[1]
outfile = sys.argv[2]
# import ipdb; ipdb.set_trace()
with open(infile) as data_file:
data = json.load(data_file)
inputkey = data['inchi-key']
try:
ret = unichem.get(inputkey)
except requests.exceptions.RetryError:
ret = {}
with open(outfile, 'w') as f:
json.dump(ret, f, indent=4)
# If all the data is the same it is repeat data
# If the data is different is an update
if not drug_id in PV_PK_drug_table:
if not drug_id in NEW_drug_list:
NEW_drug_list.append(drug_id)
NEW_complete_drug_list.append(
drug) # Provisional list with the new complete data
count_drug += 1
n_ins_drug += 1
# For each new drug id get the DrugBank id
if not (drug_id, DB_RESOURCEID, DRUG_ENTITYID) in NEW_code_list:
# Get the DrugBank code
from chembl_webresource_client.unichem import unichem_client as unichem
response = unichem.get(drug_id, 1,
2) #1 --> CHEMBL, 2 --> DrugBank
# With the DrugBank code will be fill the table code and has_code
if response:
db_code = response[0]['src_compound_id']
code = (db_code, DB_RESOURCEID, DRUG_ENTITYID)
has_code = (ID_RESOURCE_ID, drug_id, db_code, DB_RESOURCEID,
DRUG_ENTITYID)
chembl_cr = (drug_id, DB_RESOURCEID, DRUG_ENTITYID)
NEW_code_list.append(chembl_cr)
NEW_complete_code_list.append(code)
NEW_complete_has_code_list.append(has_code)
count_code += 1
n_ins_code += 1
else:
with open(names[0]) as csvfile2:
csvreader2 = csv.reader(csvfile2, delimiter=",")