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: )
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
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>
Error: 500
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