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1 '''Integration tests for the GCMS project'''
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2
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3 from pkg_resources import resource_filename # @UnresolvedImport # pylint: disable=E0611
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4 from GCMS import export_to_metexp_tabular
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5 import os.path
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6 import sys
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7 import unittest
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8
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9
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10 class IntegrationTest(unittest.TestCase):
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11
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12
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13 def test_MM_calculations(self):
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14 '''
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15 test the implemented method for MM calculations for
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16 given chemical formulas
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17 '''
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18 export_to_metexp_tabular.init_elements_and_masses_map()
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19
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20 formula = "C8H18O3"
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21 # should be = 12.01*8 + 1.01*18 + 16*3 = 162.26
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22 result = export_to_metexp_tabular.get_molecular_mass(formula)
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23 self.assertEqual(162.26, result)
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24
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25 formula = "CH2O3Fe2Ni"
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26 # should be = 12.01*1 + 1.01*2 + 16*3 + 55.85*2 + 58.71 = 232.44
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27 result = export_to_metexp_tabular.get_molecular_mass(formula)
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28 self.assertAlmostEqual(232.44, result, 2)
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29
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30
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31
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32
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33
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34 def test_combine_output_simple(self):
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35 '''
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36 comment me
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37 '''
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38 # Create out folder
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39 outdir = "output/metexp/"
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40 if not os.path.exists(outdir):
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41 os.makedirs(outdir)
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42
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43 #Build up arguments and run
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44
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45 rankfilter_and_caslookup_combined_file = resource_filename(__name__, "data/dummy1_produced_combine_output_single.txt")
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46 msclust_quantification_and_spectra_file = resource_filename(__name__, "data/dummy1_sim.txt")
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47 output_csv = resource_filename(__name__, outdir + "metexp_tabular.txt")
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48
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49 sys.argv = ['test',
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50 rankfilter_and_caslookup_combined_file,
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51 msclust_quantification_and_spectra_file,
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52 output_csv,
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53 'tomato',
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54 'leafs',
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55 'test experiment',
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56 'pieter',
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57 'DB5 column']
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58
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59 # Execute main function with arguments provided through sys.argv
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60 export_to_metexp_tabular.main()
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61
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62 '''
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63 # Asserts are based on reading in with process_data and comparing values of
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64 # certain columns
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65
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66 # Check 3: library_lookup RI column, centrotype column, ri_svr column are correct:
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67 caslookup_items = combine_output._process_data(input_caslookup)
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68 rankfilter_items = combine_output._process_data(input_rankfilter)
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69
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70 # check that the caslookup RI column is correctly maintained in its original order in
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71 # the combined file:
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72 ri_caslookup = caslookup_items['RI']
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73 ri_combine_single = combine_result_single_items['RI']
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74 self.assertListEqual(ri_caslookup, ri_combine_single)
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75
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76 # check the centrotype column's integrity:
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77 centrotype_caslookup = caslookup_items['Centrotype']
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78 centrotype_combine_single = combine_result_single_items['Centrotype']
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79 centrotype_rankfilter = _get_centrotype_rankfilter(rankfilter_items['ID'])
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80 self.assertListEqual(centrotype_caslookup, centrotype_combine_single)
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81 self.assertListEqual(centrotype_caslookup, centrotype_rankfilter)
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82
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83 # integration and integrity checks:
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84 file_NIST = resource_filename(__name__, "data/integration/NIST_identification_results_tabular.txt")
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85 file_NIST_items = combine_output._process_data(file_NIST)
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86 # check that rank filter output has exactly the same ID items as the original NIST input file:
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87 self.assertListEqual(file_NIST_items['ID'], rankfilter_items['ID'])
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88 # check the same for the CAS column:
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89 self.assertListEqual(_get_strippedcas(file_NIST_items['CAS']), rankfilter_items['CAS'])
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90 # now check the NIST CAS column against the cas lookup results:
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91 cas_NIST = _get_processedcas(file_NIST_items['CAS'])
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92 self.assertListEqual(cas_NIST, caslookup_items['CAS'])
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93 # now check the CAS of the combined result. If all checks are OK, it means the CAS column's order
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94 # and values remained stable throughout all steps:
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95 self.assertListEqual(rankfilter_items['CAS'], combine_result_single_items['CAS'])
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96
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97 # check that the rankfilter RIsvr column is correctly maintained in its original order in
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98 # the combined file:
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99 risvr_rankfilter = rankfilter_items['RIsvr']
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100 risvr_combine_single = combine_result_single_items['RIsvr']
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101 self.assertListEqual(risvr_rankfilter, risvr_combine_single)
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102 '''
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103
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104
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105
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106 def _read_file(filename):
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107 '''
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108 Helper method to quickly read a file
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109 @param filename:
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110 '''
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111 with open(filename) as handle:
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112 return handle.read()
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