Add test for importing exporting corems spectrum with annotations and isotopes

Author: kheal

tests/test_mass_spectra_export_import.py

@@ -0,0 +1,52 @@
+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 = [1, 0.4]
+    rp, s2n = [[1, 1],[1, 1]]
+    
+    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 
+
+    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)
+    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]])
+    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)
+
+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()
+