bugfixes

Author: MichelDierckx

tests/ingestion/preprocessing/test_intensity_filter.py

@@ -87,10 +87,10 @@ def test_change_all_peaks_removed(self):
         )
         filtered_spectrum = self.processor.transform(self.spectrum)
         quality_stats = QualityStats()
-        filtered_spectrum = self.validator.validate(filtered_spectrum, quality_stats)
+        valid = self.validator.validate(filtered_spectrum, quality_stats)
 
         # Spectrum should be invalid
-        self.assertEqual(filtered_spectrum, None)
+        self.assertEqual(valid, False)
 
 
 if __name__ == "__main__":

tests/ingestion/preprocessing/test_mz_range_filter.py

@@ -131,8 +131,8 @@ def test_all_peaks_removed(self):
 
         # Validate that the ingestion is invalid
         quality_stats = QualityStats()
-        filtered_spectrum = self.validator.validate(filtered_spectrum, quality_stats)
-        self.assertEqual(None, filtered_spectrum, "Spectrum should be invalidated.")
+        valid = self.validator.validate(filtered_spectrum, quality_stats)
+        self.assertEqual(False, valid, "Spectrum should be invalidated.")
 
 
 if __name__ == "__main__":

tests/ingestion/preprocessing/test_precusor_peak_filter.py

@@ -71,10 +71,10 @@ def test_all_peaks_removed(self):
         self.processor.remove_precursor_tolerance = 1000.0  # Very large tolerance
         filtered_spectrum = self.processor.transform(self.spectrum)
         quality_stats = QualityStats()
-        filtered_spectrum = self.validator.validate(filtered_spectrum, quality_stats)
+        valid = self.validator.validate(filtered_spectrum, quality_stats)
 
         # Expected behavior: all peaks removed except those far from precursor
-        self.assertEqual(None, filtered_spectrum, "Spectrum should be invalidated.")
+        self.assertEqual(False, valid, "Spectrum should be invalidated.")
 
 
 if __name__ == "__main__":

tests/ingestion/preprocessing/test_spectrum_normalizer.py

@@ -23,7 +23,7 @@ def setUp(self):
 
     def test_process(self):
         # Apply the normalization
-        normalized_spectrum = self.processor.process(self.spectrum)
+        normalized_spectrum = self.processor.transform(self.spectrum)
 
         # Compute expected normalized intensities
         original_intensity = self.spectrum.intensity
@@ -82,7 +82,7 @@ def test_process_all_zero_intensity(self):
         )
 
         # Apply the processor
-        normalized_spectrum = self.processor.process(self.spectrum)
+        normalized_spectrum = self.processor.transform(self.spectrum)
 
         # Expect zero intensities to remain unchanged
         np.testing.assert_array_equal(
@@ -103,7 +103,7 @@ def test_process_single_peak(self):
         )
 
         # Apply the processor
-        normalized_spectrum = self.processor.process(self.spectrum)
+        normalized_spectrum = self.processor.transform(self.spectrum)
 
         # Expect single peak intensity to remain 1
         np.testing.assert_array_equal(