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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_combine_output_simple(self):
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14 '''
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15 comment me
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16 '''
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17 # Create out folder
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18 outdir = "output/metexp/"
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19 if not os.path.exists(outdir):
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20 os.makedirs(outdir)
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21
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22 #Build up arguments and run
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23
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24 rankfilter_and_caslookup_combined_file = resource_filename(__name__, "data/dummy1_produced_combine_output_single.txt")
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25 msclust_quantification_and_spectra_file = resource_filename(__name__, "data/dummy1_sim.txt")
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26 output_csv = resource_filename(__name__, outdir + "metexp_tabular.txt")
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27
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28 sys.argv = ['test',
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29 rankfilter_and_caslookup_combined_file,
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30 msclust_quantification_and_spectra_file,
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31 output_csv]
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32 # Execute main function with arguments provided through sys.argv
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33 export_to_metexp_tabular.main()
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34
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35 '''
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36 # Asserts are based on reading in with process_data and comparing values of
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37 # certain columns
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38
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39 # Check 3: library_lookup RI column, centrotype column, ri_svr column are correct:
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40 caslookup_items = combine_output._process_data(input_caslookup)
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41 rankfilter_items = combine_output._process_data(input_rankfilter)
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42
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43 # check that the caslookup RI column is correctly maintained in its original order in
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44 # the combined file:
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45 ri_caslookup = caslookup_items['RI']
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46 ri_combine_single = combine_result_single_items['RI']
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47 self.assertListEqual(ri_caslookup, ri_combine_single)
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48
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49 # check the centrotype column's integrity:
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50 centrotype_caslookup = caslookup_items['Centrotype']
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51 centrotype_combine_single = combine_result_single_items['Centrotype']
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52 centrotype_rankfilter = _get_centrotype_rankfilter(rankfilter_items['ID'])
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53 self.assertListEqual(centrotype_caslookup, centrotype_combine_single)
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54 self.assertListEqual(centrotype_caslookup, centrotype_rankfilter)
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55
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56 # integration and integrity checks:
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57 file_NIST = resource_filename(__name__, "data/integration/NIST_identification_results_tabular.txt")
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58 file_NIST_items = combine_output._process_data(file_NIST)
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59 # check that rank filter output has exactly the same ID items as the original NIST input file:
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60 self.assertListEqual(file_NIST_items['ID'], rankfilter_items['ID'])
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61 # check the same for the CAS column:
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62 self.assertListEqual(_get_strippedcas(file_NIST_items['CAS']), rankfilter_items['CAS'])
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63 # now check the NIST CAS column against the cas lookup results:
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64 cas_NIST = _get_processedcas(file_NIST_items['CAS'])
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65 self.assertListEqual(cas_NIST, caslookup_items['CAS'])
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66 # now check the CAS of the combined result. If all checks are OK, it means the CAS column's order
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67 # and values remained stable throughout all steps:
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68 self.assertListEqual(rankfilter_items['CAS'], combine_result_single_items['CAS'])
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69
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70 # check that the rankfilter RIsvr column is correctly maintained in its original order in
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71 # the combined file:
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72 risvr_rankfilter = rankfilter_items['RIsvr']
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73 risvr_combine_single = combine_result_single_items['RIsvr']
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74 self.assertListEqual(risvr_rankfilter, risvr_combine_single)
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75 '''
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76
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77
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78
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79 def _read_file(filename):
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80 '''
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81 Helper method to quickly read a file
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82 @param filename:
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83 '''
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84 with open(filename) as handle:
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85 return handle.read()
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