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chembl / chembl_webresource_client

Official Python client for accessing ChEMBL API
https://www.ebi.ac.uk/chembl/api/data/docs
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Error for url https://www.ebi.ac.uk/chembl/api/data/activity.json, server response: <!doctype html> #116

Closed FelPVic closed 2 years ago

FelPVic commented 2 years ago

Grettings I will try to extract some activities and pass to dataframe with this code:

      ` ### Conect with ChEMBL API            
        activity =  new_client.activity
        target = new_client.target
        listOfActivities = activity.filter(target_chembl_id=id).filter(
                standard_type="IC50").filter(standard_units="nM").only(
                    "canonical_smiles", "molecule_chembl_id", "pchembl_value", 
                    "standard_units", "standard_value"
                )
        if not listOfActivities:
            print("Error in ChEMBL ID")
        else:
            targetInfo = target.filter(target_chembl_id=id).only(
                "pref_name", "target_type"
                )
            targetData = pd.DataFrame(targetInfo)
            targetName = targetData["pref_name"][0]
            targetData["activities_founded"] = len(listOfActivities)
          ### Do a dataframe and calculate pIC50
          dfActivities = pd.DataFrame(listOfActivities)`

But the script returns this error in some ocations:

  `File "/nfs/home/dvictori/Documents/chembl/chembl_activites.py", line 50, in <module>
      dfActivities = pd.DataFrame(listOfActivities)
    File "/nfs/home/dvictori/anaconda3/envs/rdkit/lib/python3.9/site-packages/pandas/core/frame.py", line 710, in __init__
      data = list(data)
    File "/nfs/home/dvictori/anaconda3/envs/rdkit/lib/python3.9/site-packages/chembl_webresource_client/query_set.py", line 127, in __next__
      return self.next()
    File "/nfs/home/dvictori/anaconda3/envs/rdkit/lib/python3.9/site-packages/chembl_webresource_client/query_set.py", line 115, in next
      self.chunk = self.query.next_page()
    File "/nfs/home/dvictori/anaconda3/envs/rdkit/lib/python3.9/site-packages/chembl_webresource_client/url_query.py", line 434, in next_page
      return self.get_page()
    File "/nfs/home/dvictori/anaconda3/envs/rdkit/lib/python3.9/site-packages/chembl_webresource_client/url_query.py", line 394, in get_page
      handle_http_error(res)
    File "/nfs/home/dvictori/anaconda3/envs/rdkit/lib/python3.9/site-packages/chembl_webresource_client/http_errors.py", line 113, in handle_http_error
      raise exception_class(request.url, request.text)
  chembl_webresource_client.http_errors.HttpApplicationError: Error for url https://www.ebi.ac.uk/chembl/api/data/activity.json, server response: <!doctype html>
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` I am doing any wrong?

PARODBE commented 2 years ago

Hi,

I obtain the same error, any solutions for this?

eloyfelix commented 2 years ago

Hi,

Are you still having issues with it? Could you please share a minimal reproducible example without using other third libraries (pandas...)?

The web services (this library is working on top of it) seems to be working fine.

@juanfmx2

PARODBE commented 2 years ago

Now, it is working fine.

Thanks!

YojanaGadiya commented 1 year ago

@eloyfelix I get the same error. It looks like the error probably arises due to the results containing truncated data cell no.9 in the example notebook. This causes the breaking of the loop at some point. Please can you suggest a way to extract all the results without any truncation?

Thank You.

khanmf commented 1 year ago

@eloyfelix @PARODBE @FelPVic @YojanaGadiya I am getting the same error. Please help me in resolving the issue if anyone of you guyz know the solution.

Thanks in advance

ailnicka commented 1 year ago

I'm also getting this error (500) now, whenever I have a longer list of targets for which I try to get activities. Is there a problem with EBI server?