Problem with unichem.structure

[sbgsbc]

I'm enabled to get an answer to :

  from chembl_webresource_client.unichem import unichem_client as unichem

  ret = unichem.structure('AAOVKJBEBIDNHE-UHFFFAOYSA-N', 1)

Answer is :

MaxRetryError: HTTPSConnectionPool(host='www.ebi.ac.uk', port=443): Max retries exceeded with url: /unichem/legacy/rest/structure/AAOVKJBEBIDNHE-UHFFFAOYSA-N/1 (Caused by ResponseError('too many 404 error responses'))

But

  ret = unichem.get('AAOVKJBEBIDNHE-UHFFFAOYSA-N', all=True)

is fine.

Is there a problem with the structure() method ?

I'm using chembl_webresource_client 0.10.8 installalled from conda-forge.

Many thanks.

Stephane

[eloyfelix]

Hi Stephane,

The unichem.structure function reutrns the structure for a given pair of source compound id and source id:

from chembl_webresource_client.unichem import unichem_client as unichem
ret = unichem.structure('CHEMBL12', 1)
print(ret)

[{'standardinchikey': 'AAOVKJBEBIDNHE-UHFFFAOYSA-N',
  'standardinchi': 'InChI=1S/C16H13ClN2O/c1-19-14-8-7-12(17)9-13(14)16(18-10-15(19)20)11-5-3-2-4-6-11/h2-9H,10H2,1H3'}]

@ricardoaat

[sbgsbc]

Hi,

Thanks to answer so quick :

I tried from chembl_webresource_client.unichem import unichem_client as unichem ret = unichem.inchiFromKey('AAOVKJBEBIDNHE-UHFFFAOYSA-N') print(ret)

The result is :

[{'standardinchi': 'InChI=1S/C25H23F3N4O2/c26-25(27,28)21-9-4-20(5-10-21)8-13-24-30-22(18-34-24)17-33-23-11-6-19(7-12-23)3-1-2-15-32-16-14-29-31-32/h4-14,16,18H,1-3,15,17H2/b13-8+'}]

So the connexion seems to be ok.

If I try your code from chembl_webresource_client.unichem import unichem_client as unichem ret = unichem.structure('CHEMBL12', 1) print(ret)

After 12 s I obtain the following error :

--------------------------------------------------------------------------- MaxRetryError Traceback (most recent call last) ~/miniconda3/envs/pkidb/lib/python3.9/site-packages/requests/adapters.py in send(self, request, stream, timeout, verify, cert, proxies) 438 if not chunked: --> 439 resp = conn.urlopen( 440 method=request.method, ~/miniconda3/envs/pkidb/lib/python3.9/site-packages/urllib3/connectionpool.py in urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, response_kw) 845 log.debug("Retry: %s", url) --> 846 return self.urlopen( 847 method, ~/miniconda3/envs/pkidb/lib/python3.9/site-packages/urllib3/connectionpool.py in urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, response_kw) 845 log.debug("Retry: %s", url) --> 846 return self.urlopen( 847 method, ~/miniconda3/envs/pkidb/lib/python3.9/site-packages/urllib3/connectionpool.py in urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, response_kw) 845 log.debug("Retry: %s", url) --> 846 return self.urlopen( 847 method, ~/miniconda3/envs/pkidb/lib/python3.9/site-packages/urllib3/connectionpool.py in urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, response_kw) 835 try: --> 836 retries = retries.increment(method, url, response=response, _pool=self) 837 except MaxRetryError: ~/miniconda3/envs/pkidb/lib/python3.9/site-packages/urllib3/util/retry.py in increment(self, method, url, response, error, _pool, _stacktrace) 573 if new_retry.is_exhausted(): --> 574 raise MaxRetryError(_pool, url, error or ResponseError(cause)) 575 MaxRetryError: HTTPSConnectionPool(host='www.ebi.ac.uk', port=443): Max retries exceeded with url: /unichem/rest/structure/CHEMBL12/1 (Caused by ResponseError('too many 404 error responses')) During handling of the above exception, another exception occurred: RetryError Traceback (most recent call last) /tmp/ipykernel_18210/1044002230.py in 1 from chembl_webresource_client.unichem import unichem_client as unichem ----> 2 ret = unichem.structure('CHEMBL12', 1) 3 print(ret) ~/miniconda3/envs/pkidb/lib/python3.9/site-packages/chembl_webresource_client/unichem.py in structure(self, pk, src, all) 128 else: 129 url = '{0}/structure/{1}/{2}'.format(self.base_url,pk,src) --> 130 return self._get_results(url) 131 132 #----------------------------------------------------------------------------------------------------------------------- ~/miniconda3/envs/pkidb/lib/python3.9/site-packages/chembl_webresource_client/unichem.py in _get_results(self, url) 60 def _get_results(self, url): 61 with self._get_session() as session: ---> 62 res = session.get(url, timeout=self.timeout) 63 self.logger.info(res.url) 64 self.logger.info('From cache: {0}'.format(res.from_cache if hasattr(res, 'from_cache') else False)) ~/miniconda3/envs/pkidb/lib/python3.9/site-packages/requests/sessions.py in get(self, url, kwargs) 553 554 kwargs.setdefault('allow_redirects', True) --> 555 return self.request('GET', url, kwargs) 556 557 def options(self, url, kwargs): ~/miniconda3/envs/pkidb/lib/python3.9/site-packages/requests_cache/core.py in request(self, method, url, params, data, kwargs) 120 121 def request(self, method, url, params=None, data=None, kwargs): --> 122 response = super(CachedSession, self).request( 123 method, url, 124 _normalize_parameters(params), ~/miniconda3/envs/pkidb/lib/python3.9/site-packages/requests/sessions.py in request(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json) 540 } 541 send_kwargs.update(settings) --> 542 resp = self.send(prep, send_kwargs) 543 544 return resp ~/miniconda3/envs/pkidb/lib/python3.9/site-packages/requests_cache/core.py in send(self, request, kwargs) 97 response, timestamp = self.cache.get_response_and_time(cache_key) 98 if response is None: ---> 99 return send_request_and_cache_response() 100 101 if self._cache_expire_after is not None: ~/miniconda3/envs/pkidb/lib/python3.9/site-packages/requests_cache/core.py in send_request_and_cache_response() 89 90 def send_request_and_cache_response(): ---> 91 response = super(CachedSession, self).send(request, kwargs) 92 if response.status_code in self._cache_allowable_codes: 93 self.cache.save_response(cache_key, response) ~/miniconda3/envs/pkidb/lib/python3.9/site-packages/requests/sessions.py in send(self, request, kwargs) 653 654 # Send the request --> 655 r = adapter.send(request, kwargs) 656 657 # Total elapsed time of the request (approximately) ~/miniconda3/envs/pkidb/lib/python3.9/site-packages/requests/adapters.py in send(self, request, stream, timeout, verify, cert, proxies) 505 506 if isinstance(e.reason, ResponseError): --> 507 raise RetryError(e, request=request) 508 509 if isinstance(e.reason, _ProxyError):

RetryError: HTTPSConnectionPool(host='www.ebi.ac.uk', port=443): Max retries exceeded with url: /unichem/rest/structure/CHEMBL12/1 (Caused by ResponseError('too many 404 error responses'))

Could you explain it ?

Stéphane

De : Eloy Félix @.> Répondre à : chembl/chembl_webresource_client @.> Date : lundi 16 mai 2022 à 15:13 À : chembl/chembl_webresource_client @.> Cc : bourg @.>, Author @.***> Objet : Re: [chembl/chembl_webresource_client] Problem with unichem.structure (Issue #119)

Hi Stephane,

The unichem.structure function reutrns the structure for a given pair of source compound id and source id:

from chembl_webresource_client.unichem import unichem_client as unichem

ret = unichem.structure('CHEMBL12', 1)

print(ret)

[{'standardinchikey': 'AAOVKJBEBIDNHE-UHFFFAOYSA-N',

'standardinchi': 'InChI=1S/C16H13ClN2O/c1-19-14-8-7-12(17)9-13(14)16(18-10-15(19)20)11-5-3-2-4-6-11/h2-9H,10H2,1H3'}]

@ricardoaathttps://github.com/ricardoaat

— Reply to this email directly, view it on GitHubhttps://github.com/chembl/chembl_webresource_client/issues/119#issuecomment-1127655268, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AMEXTHS4D6372JG6AHS2IN3VKJCR7ANCNFSM5WBMYYBA. You are receiving this because you authored the thread.Message ID: @.***>

[eloyfelix]

which version of the library are you using? could you please try with the latest one? 0.10.8

[sbgsbc]

I’m using 0.10.1.

I’ve switched to 0.10.8 and some tests are conclusive. It seems OK.

Many thanks.

Stephane

De : Eloy Félix @.> Répondre à : chembl/chembl_webresource_client @.> Date : lundi 16 mai 2022 à 17:11 À : chembl/chembl_webresource_client @.> Cc : bourg @.>, Author @.***> Objet : Re: [chembl/chembl_webresource_client] Problem with unichem.structure (Issue #119)

which version of the library are you using? could you please try with the latest one? 0.10.8

— Reply to this email directly, view it on GitHubhttps://github.com/chembl/chembl_webresource_client/issues/119#issuecomment-1127796691, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AMEXTHV4ETFHKUMCNFBILR3VKJQPHANCNFSM5WBMYYBA. You are receiving this because you authored the thread.Message ID: @.***>