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comparison test/test_query_metexp_LARGE.py @ 0:dffc38727496

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author pieter.lukasse@wur.nl
date Sat, 07 Feb 2015 22:02:00 +0100
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-1:000000000000 0:dffc38727496
1 '''Integration tests for the GCMS project'''
2
3 from pkg_resources import resource_filename # @UnresolvedImport # pylint: disable=E0611
4 from GCMS import query_metexp
5 import os.path
6 import sys
7 import unittest
8
9
10 class IntegrationTest(unittest.TestCase):
11
12
13 # def test_MM_calculations(self):
14 # '''
15 # test the implemented method for MM calculations for
16 # given chemical formulas
17 # '''
18 # export_to_metexp_tabular.init_elements_and_masses_map()
19 #
20 # formula = "C8H18O3"
21 # # should be = 12.01*8 + 1.01*18 + 16*3 = 162.26
22 # result = export_to_metexp_tabular.get_molecular_mass(formula)
23 # self.assertEqual(162.26, result)
24 #
25 # formula = "CH2O3Fe2Ni"
26 # # should be = 12.01*1 + 1.01*2 + 16*3 + 55.85*2 + 58.71 = 232.44
27 # result = export_to_metexp_tabular.get_molecular_mass(formula)
28 # self.assertAlmostEqual(232.44, result, 2)
29 #
30 #
31 #
32
33
34 def test_large(self):
35 '''
36 Simple test, but on larger set, last test executed in 28s
37 '''
38 # Create out folder
39 outdir = "output/metexp_query/"
40 if not os.path.exists(outdir):
41 os.makedirs(outdir)
42
43 #Build up arguments and run
44
45 # input_file = sys.argv[1]
46 # molecular_mass_col = sys.argv[2]
47 # formula_col = sys.argv[3]
48 # metexp_dblink_file = sys.argv[4]
49 # output_result = sys.argv[5]
50
51 input_file = resource_filename(__name__, "data/metexp_query_tabular_large.txt")
52 casid_col = "CAS"
53 formula_col = "FORMULA"
54 molecular_mass_col = "MM"
55 metexp_dblink_file = resource_filename(__name__, "data/METEXP Test DB.txt")
56 output_result = resource_filename(__name__, outdir + "metexp_query_results_added_LARGE.txt")
57
58 sys.argv = ['test',
59 input_file,
60 casid_col,
61 formula_col,
62 molecular_mass_col,
63 metexp_dblink_file,
64 'GC',
65 output_result]
66
67 # Execute main function with arguments provided through sys.argv
68 query_metexp.main()
69
70
71
72
73 def _read_file(filename):
74 '''
75 Helper method to quickly read a file
76 @param filename:
77 '''
78 with open(filename) as handle:
79 return handle.read()