Getting synonyms for pubchem id with no synonyms crashes.

[ianlongden]

Here is some test code:-

import pubchempy
import json

pubchem_id = '171839766'  # '102200539'

description = pubchempy.request(pubchem_id, operation='description')
print(description)
raw_data = description.read()
encoding = description.info().get_content_charset('utf8')  # JSON default
description_data = json.loads(raw_data.decode(encoding))
print(description_data)
string_to_add_for_description = ""
for description_item in description_data['InformationList']['Information']:
    if 'Description' in description_item.keys() and 'DescriptionSourceName' in description_item.keys():
        formatted_string = '{}: {}'.format(description_item['DescriptionSourceName'],
                                           description_item['Description'])
        string_to_add_for_description += formatted_string
    elif 'Title' in description_item.keys():
        name = description_item['Title']
        print(name)
    print(string_to_add_for_description)

syn = pubchempy.request(pubchem_id, operation='synonyms')
raw_data = syn.read()
encoding = syn.info().get_content_charset('utf8')  # JSON default
syn_data = json.loads(raw_data.decode(encoding))
print(syn_data)

results = pubchempy.Compound.from_cid(pubchem_id)
inchikey = results.to_dict(properties=['inchikey'])
if 'inchikey' in inchikey:
    print(inchikey['inchikey'])

which when ran produces:-

python pubchem_api_test.py

<http.client.HTTPResponse object at 0x1029e50c0> {'InformationList': {'Information': [{'CID': 171839766, 'Title': '2-methyl-7-(2-methyloctan-2-yl)-2H-chromen-5-ol'}]}} 2-methyl-7-(2-methyloctan-2-yl)-2H-chromen-5-ol

Traceback (most recent call last): File "/usr/dir/harv-py-3.11/lib/python3.11/site-packages/pubchempy.py", line 271, in request response = urlopen(apiurl, postdata) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/Cellar/[email protected]/3.11.9/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/Cellar/[email protected]/3.11.9/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 525, in open response = meth(req, response) ^^^^^^^^^^^^^^^^^^^ File "/usr/local/Cellar/[email protected]/3.11.9/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 634, in http_response response = self.parent.error( ^^^^^^^^^^^^^^^^^^ File "/usr/local/Cellar/[email protected]/3.11.9/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 563, in error return self._call_chain(*args) ^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/Cellar/[email protected]/3.11.9/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/local/Cellar/[email protected]/3.11.9/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 643, in http_error_default raise HTTPError(req.full_url, code, msg, hdrs, fp) urllib.error.HTTPError: HTTP Error 404: PUGREST.NotFound

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/usr/dir/pubchem_api_test.py", line 23, in syn = pubchempy.request(pubchem_id, operation='synonyms') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/dir/harv-py-3.11/lib/python3.11/site-packages/pubchempy.py", line 274, in request raise PubChemHTTPError(e) ^^^^^^^^^^^^^^^^^^^ File "/usr/dir/harv-py-3.11/lib/python3.11/site-packages/pubchempy.py", line 1299, in init raise NotFoundError(self.msg) pubchempy.NotFoundError: 'PUGREST.NotFound'

Would it be possible to put a try/except in the code and return the equivalent of an empty list.

Thanks.