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Error for url #131
@RicardoMBorges

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@RicardoMBorges
RicardoMBorges
opened on Jul 28, 2023

Hello,
I wrote a small jupyter notebook script that gets lists from chembl. It ran the first couple of times, but now is giving me this error and I don´t know how to go around this: HttpApplicationError: Error for url https://www.ebi.ac.uk/chembl/api/data/molecule.json, server response: <!doctype HTML>
Can someone give a help for these sort of things?

Thanks

My script:

chembl websource

from chembl_webresource_client.new_client import new_client

Filter CHEMBL for compound of interest. Note that this can be modified (see: )

molecules = new_client.molecule

Select Drugs with molecular weight <= 2000

small_molecules = molecules.filter(molecule_properties__mw_freebase__lte=2000)

Consider filtering for Natural Products. Note that this might be faulty.

NPs = small_molecules.filter(natural_product=1)

Select Approved Drugs

approved_drugs_small = NPs.filter(max_phase=4).order_by('molecule_properties__mw_freebase')
Approved_drugs_small_NP = pd.DataFrame(approved_drugs_small)

The error:

HttpApplicationError Traceback (most recent call last)
Input In [6], in <cell line: 12>()
10 # Select Approved Drugs
11 approved_drugs_small = NPs.filter(max_phase=4).order_by('molecule_properties__mw_freebase')
---> 12 Approved_drugs_small_NP = pd.DataFrame(approved_drugs_small)
14 Approved_drugs_small_NP2 = Approved_drugs_small_NP[["molecule_chembl_id","molecule_structures","pref_name","natural_product"]].copy()
15 Approved_drugs_small_NP2["molecule_structures"] = Approved_drugs_small_NP2["molecule_structures"].astype(str).str.split(",").str[0]

File ~/env_rmb_rdkit/lib/python3.8/site-packages/pandas/core/frame.py:710, in DataFrame.init(self, data, index, columns, dtype, copy)
708 data = np.asarray(data)
709 else:
--> 710 data = list(data)
711 if len(data) > 0:
712 if is_dataclass(data[0]):

File ~/env_rmb_rdkit/lib/python3.8/site-packages/chembl_webresource_client/query_set.py:127, in QuerySet.next(self)
126 def next(self):
--> 127 return self.next()

File ~/env_rmb_rdkit/lib/python3.8/site-packages/chembl_webresource_client/query_set.py:115, in QuerySet.next(self)
113 self.chunk = self.query.get_page()
114 if not self.chunk or self.current_index >= len(self.chunk):
--> 115 self.chunk = self.query.next_page()
116 if not self.chunk:
117 raise StopIteration

File ~/env_rmb_rdkit/lib/python3.8/site-packages/chembl_webresource_client/url_query.py:434, in UrlQuery.next_page(self)
432 start = self.start
433 self.current_index = int(start + self.limit * (self.current_page + 1))
--> 434 return self.get_page()

File ~/env_rmb_rdkit/lib/python3.8/site-packages/chembl_webresource_client/url_query.py:394, in UrlQuery.get_page(self)
392 self.logger.info('From cache: {0}'.format(res.from_cache if hasattr(res, 'from_cache') else False))
393 if not res.ok:
--> 394 handle_http_error(res)
395 if self.frmt == 'json':
396 json_data = res.json()

File ~/env_rmb_rdkit/lib/python3.8/site-packages/chembl_webresource_client/http_errors.py:113, in handle_http_error(request)
111 exception_class = status_to_exception.get(request.status_code, BaseHttpException)
112 if request.text:
--> 113 raise exception_class(request.url, request.text)
114 raise exception_class(request.url, request.content)

HttpApplicationError: Error for url https://www.ebi.ac.uk/chembl/api/data/molecule.json, server response: <!doctype html>

<script> // Detect if JS is on and swap vf-no-js for vf-js on the html element (function(H){H.className=H.className.replace(/\bvf-no-js\b/,'vf-js')})(document.documentElement); </script> 
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- <link rel="stylesheet" media="all" href="/css/styles.css?" /> -->
<title>Error: 500 | EMBL�s European Bionformatics Institute</title>



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