Update PubChem crawler (#163)

* feat: additional error logging in pubchem crawler

* test: enable pubchem tests

* ci: isort

pytoda/__init__.py

@@ -1,2 +1,2 @@
 name = 'pytoda'
-__version__ = '1.1.2'
+__version__ = '1.1.3'

pytoda/preprocessing/crawlers.py

@@ -3,7 +3,7 @@
 import urllib.request as urllib_request
 from itertools import filterfalse
 from typing import Iterable, List, Tuple, Union
-from urllib.error import HTTPError
+from urllib.error import HTTPError, URLError
 
 import pubchempy as pcp
 from pubchempy import BadRequestError, PubChemHTTPError
@@ -180,23 +180,20 @@ def query_pubchem(smiles: str) -> Tuple[bool, int]:
         raise TypeError(f'Please pass str, not {type(smiles)}')
     try:
         result = pcp.get_compounds(smiles, 'smiles')[0]
+        return (False, -1) if result.cid is None else (True, result.cid)
     except BadRequestError:
         logger.warning(f'Skipping SMILES. BadRequestError with: {smiles}')
-        return (False, -2)
     except HTTPError:
         logger.warning(f'Skipping SMILES. HTTPError with: {smiles}')
-        return (False, -2)
     except TimeoutError:
         logger.warning(f'Skipping SMILES. TimeoutError with: {smiles}')
-        return (False, -2)
     except ConnectionResetError:
         logger.warning(f'Skipping SMILES. ConnectionResetError with: {smiles}')
-        return (False, -2)
     except PubChemHTTPError:
         logger.warning(f'Skipping SMILES, server busy. with: {smiles}')
-        return (False, -2)
-
-    return (False, -1) if result.cid is None else (True, result.cid)
+    except URLError:
+        logger.error(f"Skipping SMILES, Network unreachable {smiles}")
+    return (False, -2)
 
 
 def is_pubchem(smiles: str) -> bool:

pytoda/preprocessing/tests/test_crawlers.py

@@ -4,6 +4,8 @@
 from pytoda.preprocessing.crawlers import (  # query_pubchem,; remove_pubchem_smiles,
     get_smiles_from_pubchem,
     get_smiles_from_zinc,
+    query_pubchem,
+    remove_pubchem_smiles,
 )
 
 
@@ -83,29 +85,29 @@ def test_get_smiles_from_pubchem(self) -> None:
 
     def test_query_pubchem(self) -> None:
         """Test query_pubchem"""
-        pass
+        # pass
         # Disabled due to bug in pubchem api
-        # smiles_list = [
-        #     'O1C=CC=NC(=O)C1=O',
-        #     'CC(N)S(O)(=O)C(C)CC(C(C)C)c1cc(F)cc(F)c1',
-        #     'Clc1ccccc2ccnc12',
-        # ]
-        # ground_truths = [(True, 67945516), (False, -2), (False, -1)]
-        # for gt, smiles in zip(ground_truths, smiles_list):
-        #     self.assertTupleEqual(query_pubchem(smiles), gt)
+        smiles_list = [
+            'O1C=CC=NC(=O)C1=O',
+            'CC(N)S(O)(=O)C(C)CC(C(C)C)c1cc(F)cc(F)c1',
+            'Clc1ccccc2ccnc12',
+        ]
+        ground_truths = [(True, 67945516), (False, -2), (False, -1)]
+        for gt, smiles in zip(ground_truths, smiles_list):
+            self.assertTupleEqual(query_pubchem(smiles), gt)
 
     def test_remove_pubchem_smiles(self) -> None:
         """Test remove_pubchem_smiles"""
-        pass
+        # pass
 
         # Disabled due to bug in pubchem api
-        # smiles_list = [
-        #     'O1C=CC=NC(=O)C1=O',
-        #     'CC(N)S(O)(=O)C(C)CC(C(C)C)c1cc(F)cc(F)c1',
-        #     'Clc1ccccc2ccnc12',
-        # ]
-        # ground_truth = ['CC(N)S(O)(=O)C(C)CC(C(C)C)c1cc(F)cc(F)c1', 'Clc1ccccc2ccnc12']
-        # self.assertListEqual(remove_pubchem_smiles(smiles_list), ground_truth)
+        smiles_list = [
+            'O1C=CC=NC(=O)C1=O',
+            'CC(N)S(O)(=O)C(C)CC(C(C)C)c1cc(F)cc(F)c1',
+            'Clc1ccccc2ccnc12',
+        ]
+        ground_truth = ['CC(N)S(O)(=O)C(C)CC(C(C)C)c1cc(F)cc(F)c1', 'Clc1ccccc2ccnc12']
+        self.assertListEqual(remove_pubchem_smiles(smiles_list), ground_truth)
 
 
 if __name__ == '__main__':