AnnotatedSpectrumIndex type error

casanovo/denovo/model_runner.py

@@ -419,7 +419,19 @@ def _get_index(
 
         Index = AnnotatedSpectrumIndex if annotated else SpectrumIndex
         valid_charge = np.arange(1, self.config.max_charge + 1)
-        return Index(index_fname, filenames, valid_charge=valid_charge)
+
+        try:
+            return Index(index_fname, filenames, valid_charge=valid_charge)
+        except TypeError as e:
+            if Index == AnnotatedSpectrumIndex:
+                raise TypeError(
+                    "Error creating annotated spectrum index. "
+                    "This may be the result of having an unannotated MGF file "
+                    "present in the validation peak file path list.\n"
+                    f"Original error message: {e}"
+                )
+
+            raise e
 
     def _get_strategy(self) -> Union[str, DDPStrategy]:
         """Get the strategy for the Trainer.

tests/unit_tests/test_runner.py

@@ -198,20 +198,21 @@ def test_evaluate(
     assert result_file.is_file()
     result_file.unlink()
 
-    # Test evaluation with unannotated peak files
-    # NOTE: Depth Charge raises a TypeError exception when an unannotated
-    #   peak file is in the peak file list when initializing a
-    #   AnnotatedSpectrumIndex
-    # TODO: Reexamine after Depth Charge v0.4 release
+    exception_string = (
+        "Error creating annotated spectrum index. "
+        "This may be the result of having an unannotated MGF file "
+        "present in the validation peak file path list.\n"
+    )
+
     with pytest.raises(FileNotFoundError):
         with ModelRunner(config, model_filename=str(model_file)) as runner:
             runner.predict([mzml_small], result_file, evaluate=True)
 
-    with pytest.raises(TypeError):
+    with pytest.raises(TypeError, match=exception_string):
         with ModelRunner(config, model_filename=str(model_file)) as runner:
             runner.predict([mgf_small_unannotated], result_file, evaluate=True)
 
-    with pytest.raises(TypeError):
+    with pytest.raises(TypeError, match=exception_string):
         with ModelRunner(config, model_filename=str(model_file)) as runner:
             runner.predict(
                 [mgf_small_unannotated, mzml_small], result_file, evaluate=True
@@ -230,7 +231,7 @@ def test_evaluate(
     assert result_file.is_file()
     result_file.unlink()
 
-    with pytest.raises(TypeError):
+    with pytest.raises(TypeError, match=exception_string):
         with ModelRunner(config, model_filename=str(model_file)) as runner:
             runner.predict(
                 [mgf_small, mgf_small_unannotated], result_file, evaluate=True
@@ -239,7 +240,7 @@ def test_evaluate(
     assert result_file.is_file()
     result_file.unlink()
 
-    with pytest.raises(TypeError):
+    with pytest.raises(TypeError, match=exception_string):
         with ModelRunner(config, model_filename=str(model_file)) as runner:
             runner.predict(
                 [mgf_small, mgf_small_unannotated, mzml_small],