fixed unit test for file_path

mdagent/tools/base_tools/preprocess_tools/pdb_tools.py

@@ -1406,6 +1406,15 @@ def molname2smiles(
                 "One possible cause is that the input is incorrect, "
                 "input one molecule at a time."
             )
+        except IndexError:
+            print("The smiles property was not found for this molecule.")
+        except TypeError:
+            print(
+                "The information from the PubChem database is "
+                "not in the expected format."
+            )
+        except ValueError:
+            print("The requested value is not in the expected format.")
         # remove salts
         return Chem.CanonSmiles(self.largest_mol(smi))
 

mdagent/utils/general_utils.py

@@ -17,6 +17,8 @@ def find_file_path(file_name: str, exact_match: bool = True):
             if (exact_match and filename == file_name) or (
                 not exact_match and file_name in filename
             ):
-                return os.path.join(dirpath, filename)
+                path_full = os.path.join(dirpath, filename)
+                # make sure its absolute
+                return os.path.abspath(path_full)
 
     return None

tests/test_utils.py

@@ -159,11 +159,12 @@ def test_init_path_registry(path_registry_with_mocked_fs):
 
 def test_find_file_path():
     file_name = "test_utils.py"
-    file_path_current = os.path.abspath(file_name)
+    # current directory won't include folders
+    cwd = os.getcwd()
+    file_path_current = os.path.join(cwd, "tests", file_name)
     file_path_test = find_file_path(file_name, exact_match=True)
     assert file_path_current == file_path_test
 
-    file_name_short = file_name[-4]
-    file_path_current_short = os.path.abspath(file_name_short)
+    file_name_short = "test_util"
     file_path_test_short = find_file_path(file_name_short, exact_match=False)
-    assert file_path_current_short == file_path_test_short
+    assert file_path_current == file_path_test_short