Mercurial > repos > pieterlukasse > prims_metabolomics

annotate test/test_query_metexp.py @ 41:e67149fbff20

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small changes/improvements; new metams and xcms tools
author pieter.lukasse@wur.nl
date Thu, 06 Nov 2014 16:14:44 +0100
parents 19d8fd10248e
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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 query_metexp
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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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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_simple(self):
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35 '''
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36 Simple initial test
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37 '''
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38 # Create out folder
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39 outdir = "output/metexp_query/"
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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 # input_file = sys.argv[1]
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46 # molecular_mass_col = sys.argv[2]
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47 # formula_col = sys.argv[3]
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48 # metexp_dblink_file = sys.argv[4]
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49 # output_result = sys.argv[5]
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50
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51 input_file = resource_filename(__name__, "data/metexp_query_tabular.txt")
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52 casid_col = "CAS"
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53 formula_col = "FORMULA"
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54 molecular_mass_col = "MM"
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55 metexp_dblink_file = resource_filename(__name__, "data/METEXP Test DB.txt")
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56 output_result = resource_filename(__name__, outdir + "metexp_query_results_added.txt")
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57
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58 sys.argv = ['test',
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59 input_file,
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60 casid_col,
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61 formula_col,
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62 molecular_mass_col,
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63 metexp_dblink_file,
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64 'GC',
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65 output_result]
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66
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67 # Execute main function with arguments provided through sys.argv
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68 query_metexp.main()
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69
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70 # TODO - asserts (base them on DB being filled with test data form metexp unit test for upload method)
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71 # PA
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75
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76 def _read_file(filename):
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77 '''
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78 Helper method to quickly read a file
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79 @param filename:
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80 '''
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81 with open(filename) as handle:
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82 return handle.read()