Error for url https://www.ebi.ac.uk/chembl/api/data/activity.json, server response: <!doctype html>
FelPVic opened this issue · 6 comments
FelPVic commented
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
Hi,
I obtain the same error, any solutions for this?
eloyfelix commented
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.
PARODBE commented
Now, it is working fine.
Thanks!
YojanaGadiya commented
@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
@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
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?