Add error handling if import data does not have all expected data

Author: kheal

corems/mass_spectrum/input/massList.py

@@ -173,9 +173,12 @@ def add_molecular_formula(self, mass_spec_obj, dataframe):
                     mfobj.mspeak_index_mono_isotopic = int(dataframe.iloc[df_index]['Mono Isotopic Index'])
 
                 # Add the confidence score and isotopologue similarity and average MZ error score
-                mfobj._mass_error_average_score = float(dataframe.iloc[df_index]['m/z Error Score'])
-                mfobj._confidence_score = float(dataframe.iloc[df_index]['Confidence Score'])
-                mfobj._isotopologue_similarity = float(dataframe.iloc[df_index]['Isotopologue Similarity'])
+                if 'm/z Error Score' in dataframe:
+                    mfobj._mass_error_average_score = float(dataframe.iloc[df_index]['m/z Error Score'])
+                if 'Confidence Score' in dataframe:
+                    mfobj._confidence_score = float(dataframe.iloc[df_index]['Confidence Score'])
+                if 'Isotopologue Similarity' in dataframe:
+                    mfobj._isotopologue_similarity = float(dataframe.iloc[df_index]['Isotopologue Similarity'])
                 mass_spec_obj[ms_peak_index].add_molecular_formula(mfobj)
 
 

tests/test_mass_spectra_export_import.py

@@ -1,56 +1,74 @@
+import shutil
+
 from corems.mass_spectrum.input.numpyArray import ms_from_array_centroid
 from corems.molecular_id.search.molecularFormulaSearch import SearchMolecularFormulas
 from corems.encapsulation.factory.parameters import MSParameters
 from corems.mass_spectrum.output.export import HighResMassSpecExport
 from corems.mass_spectrum.input.coremsHDF5 import ReadCoreMSHDF_MassSpectrum
 
+
 def prep_mass_spec_obj():
     # Test for generating accurate molecular formula from a single mass using the local sql database
     # Now also tests that it is handling isotopes correctly (for non-adducts)
     mz = [760.58156938877, 761.58548]
     abundance = [1000, 400]
-    rp, s2n = [[1, 1],[10, 10]]
-    
-    MSParameters.mass_spectrum.noise_threshold_method = 'relative_abundance'
-    MSParameters.mass_spectrum.noise_threshold_absolute_abundance = 0 
-    
-    MSParameters.molecular_search.url_database = ''
-    MSParameters.molecular_search.error_method = 'None'
-    MSParameters.molecular_search.min_ppm_error  = -5
+    rp, s2n = [[1, 1], [10, 10]]
+
+    MSParameters.mass_spectrum.noise_threshold_method = "relative_abundance"
+    MSParameters.mass_spectrum.noise_threshold_absolute_abundance = 0
+
+    MSParameters.molecular_search.url_database = ""
+    MSParameters.molecular_search.error_method = "None"
+    MSParameters.molecular_search.min_ppm_error = -5
     MSParameters.molecular_search.max_ppm_error = 5
     MSParameters.molecular_search.mz_error_range = 1
-    MSParameters.molecular_search.isProtonated = True 
-    MSParameters.molecular_search.isRadical= False 
-    MSParameters.molecular_search.isAdduct= False 
+    MSParameters.molecular_search.isProtonated = True
+    MSParameters.molecular_search.isRadical = False
+    MSParameters.molecular_search.isAdduct = False
 
-    usedatoms = {'C': (1,57) , 'H': (4,200), 'N': (0,1)}
+    usedatoms = {"C": (1, 57), "H": (4, 200), "N": (0, 1)}
     MSParameters.molecular_search.usedAtoms = usedatoms
-    mass_spectrum_obj = ms_from_array_centroid(mz, abundance, rp, s2n, 'single mf search', polarity=1, auto_process=True)
+    mass_spectrum_obj = ms_from_array_centroid(
+        mz, abundance, rp, s2n, "single mf search", polarity=1, auto_process=True
+    )
     return mass_spectrum_obj
 
+
 def run_molecular_formula_search(mass_spectrum_obj):
     mass_spectrum_obj.molecular_search_settings.use_min_peaks_filter = False
     mass_spectrum_obj.molecular_search_settings.use_isotopologue_filter = False
-    SearchMolecularFormulas(mass_spectrum_obj, find_isotopologues=True).run_worker_ms_peaks([mass_spectrum_obj[0]])
+    SearchMolecularFormulas(
+        mass_spectrum_obj, find_isotopologues=True
+    ).run_worker_ms_peaks([mass_spectrum_obj[0]])
     return mass_spectrum_obj
 
-mass_spectrum_obj = prep_mass_spec_obj()
-mass_spectrum_obj = run_molecular_formula_search(mass_spectrum_obj)
-ms_df1 = mass_spectrum_obj.to_dataframe()
-assert  mass_spectrum_obj[0][0].string == 'C56 H73 N1'
-assert ms_df1.shape == (2, 26)
-assert mass_spectrum_obj[1][0].string == 'C55 H73 N1 13C1'
-
-exportMS = HighResMassSpecExport('my_mass_spec', mass_spectrum_obj)
-exportMS._output_type = 'hdf5'
-exportMS.save()
-
-parser = ReadCoreMSHDF_MassSpectrum('my_mass_spec.hdf5')
-mass_spectrum_obj2 = parser.get_mass_spectrum(auto_process=True, load_settings=True)
-
-# Below errors out:
-ms_df2 = mass_spectrum_obj2.to_dataframe()
-assert  mass_spectrum_obj2[0][0].string == 'C56 H73 N1'
-assert ms_df2.shape == (2, 26)
-assert mass_spectrum_obj2[1][0].string == 'C55 H73 N1 13C1'
-    
+
+def test_mass_spec_export_import_with_annote():
+    mass_spectrum_obj = prep_mass_spec_obj()
+    mass_spectrum_obj = run_molecular_formula_search(mass_spectrum_obj)
+    ms_df1 = mass_spectrum_obj.to_dataframe()
+    assert mass_spectrum_obj[0][0].string == "C56 H73 N1"
+    assert ms_df1.shape == (2, 26)
+    assert mass_spectrum_obj[1][0].string == "C55 H73 N1 13C1"
+
+    exportMS = HighResMassSpecExport("my_mass_spec", mass_spectrum_obj)
+    exportMS._output_type = "hdf5"
+    exportMS.save()
+
+    parser = ReadCoreMSHDF_MassSpectrum("my_mass_spec.hdf5")
+    mass_spectrum_obj2 = parser.get_mass_spectrum(auto_process=True, load_settings=True)
+
+    ms_df2 = mass_spectrum_obj2.to_dataframe()
+    assert mass_spectrum_obj2[0][0].string == "C56 H73 N1"
+    assert ms_df2.shape == (2, 26)
+    assert mass_spectrum_obj2[1][0].string == "C55 H73 N1 13C1"
+
+    # Remove the file
+    shutil.rmtree(
+        "my_mass_spec.hdf5",
+        ignore_errors=True,
+    )
+
+
+if __name__ == "__main__":
+    test_mass_spec_export_import_with_annote()