Changed molecule error and exception logging into debug

They caused unnecessary clutter in the log file

Author: alongd

arc/molecule/molecule.py

@@ -1935,7 +1935,7 @@ def to_inchi(self, backend='rdkit-first'):
         try:
             return translator.to_inchi(self, backend=backend)
         except:
-            logger.exception(f"Error for molecule \n{self.to_adjacency_list()}")
+            logger.debug(f"Identifier generation failed for molecule\n{self.to_adjacency_list()}", exc_info=True)
             raise
 
     def to_augmented_inchi(self, backend='rdkit-first'):
@@ -1952,7 +1952,7 @@ def to_augmented_inchi(self, backend='rdkit-first'):
         try:
             return translator.to_inchi(self, backend=backend, aug_level=2)
         except:
-            logger.exception(f"Error for molecule \n{self.to_adjacency_list()}")
+            logger.debug(f"Identifier generation failed for molecule\n{self.to_adjacency_list()}", exc_info=True)
             raise
 
     def to_inchi_key(self, backend='rdkit-first'):
@@ -1972,7 +1972,7 @@ def to_inchi_key(self, backend='rdkit-first'):
         try:
             return translator.to_inchi_key(self, backend=backend)
         except:
-            logger.exception(f"Error for molecule \n{self.to_adjacency_list()}")
+            logger.debug(f"Identifier generation failed for molecule\n{self.to_adjacency_list()}", exc_info=True)
             raise
 
     def to_augmented_inchi_key(self, backend='rdkit-first'):
@@ -1990,7 +1990,7 @@ def to_augmented_inchi_key(self, backend='rdkit-first'):
         try:
             return translator.to_inchi_key(self, backend=backend, aug_level=2)
         except:
-            logger.exception(f"Error for molecule \n{self.to_adjacency_list()}")
+            logger.debug(f"Identifier generation failed for molecule\n{self.to_adjacency_list()}", exc_info=True)
             raise
 
     def to_smarts(self):

arc/molecule/translator.py

@@ -553,7 +553,11 @@ def _write(mol, identifier_type, backend):
             logger.warning(f"Unexpected error from backend '{option}': {e}")
             continue
 
-    logger.error(f"Unable to generate identifier '{identifier_type}' for this molecule:\n{mol.to_adjacency_list()}")
+    logger.debug(
+        f"Unable to generate identifier '{identifier_type}' for this molecule "
+        f"(structure may be fragmented or carry anomalous formal charges):\n"
+        f"{mol.to_adjacency_list()}"
+    )
     raise ValueError(f"Unable to generate identifier type '{identifier_type}' with backend(s): {backend}")
 
 

arc/molecule/translator_test.py

@@ -706,5 +706,42 @@ def test_read_inchikey_error(self):
         self.assertTrue('InChIKey is a write-only format' in str(cm.exception))
 
 
+class IdentifierFailureLoggingTest(unittest.TestCase):
+    """When neither backend can canonicalize a molecule into InChI / InChIKey
+    (e.g. malformed resonance structures from RMG perception), the translator
+    and the four Molecule wrappers must raise ValueError but emit nothing at
+    WARNING level or above. The caller (resonance dedup, etc.) routinely
+    swallows the ValueError; the previous WARNING + ERROR-with-traceback pair
+    was log spam."""
+
+    def _assert_wrapper_logs_below_warning(self, wrapper_name, translator_func_name):
+        """Patch the underlying translator function to raise, call the
+        Molecule wrapper, and verify the wrapper re-raises while emitting only
+        DEBUG-level (not WARNING/ERROR) log records."""
+        from arc.molecule import translator as t
+        mol = Molecule().from_smiles('C')
+        with patch.object(t, translator_func_name,
+                          side_effect=ValueError('mocked-out backend')):
+            with self.assertLogs('arc', level='DEBUG') as cm:
+                with self.assertRaises(ValueError):
+                    getattr(mol, wrapper_name)()
+        for record in cm.records:
+            self.assertLess(record.levelno, 30,  # WARNING == 30
+                            f"Unexpected {record.levelname} log line from "
+                            f"{wrapper_name}: {record.getMessage()}")
+
+    def test_to_inchi_wrapper_logs_only_at_debug_on_failure(self):
+        self._assert_wrapper_logs_below_warning('to_inchi', 'to_inchi')
+
+    def test_to_inchi_key_wrapper_logs_only_at_debug_on_failure(self):
+        self._assert_wrapper_logs_below_warning('to_inchi_key', 'to_inchi_key')
+
+    def test_to_augmented_inchi_wrapper_logs_only_at_debug_on_failure(self):
+        self._assert_wrapper_logs_below_warning('to_augmented_inchi', 'to_inchi')
+
+    def test_to_augmented_inchi_key_wrapper_logs_only_at_debug_on_failure(self):
+        self._assert_wrapper_logs_below_warning('to_augmented_inchi_key', 'to_inchi_key')
+
+
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))