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comparison test/test_query_metexp.py @ 0:dffc38727496

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initial commit
author pieter.lukasse@wur.nl
date Sat, 07 Feb 2015 22:02:00 +0100
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children 223d1167de58
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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 # copied from test_export_to_metexp_tabular.py
14 # def test_MM_calculations(self):
15 # '''
16 # test the implemented method for MM calculations for
17 # given chemical formulas
18 # '''
19 # export_to_metexp_tabular.init_elements_and_masses_map()
20 #
21 # formula = "C8H18O3"
22 # # should be = 12.01*8 + 1.01*18 + 16*3 = 162.26
23 # result = export_to_metexp_tabular.get_molecular_mass(formula)
24 # self.assertEqual(162.26, result)
25 #
26 # formula = "CH2O3Fe2Ni"
27 # # should be = 12.01*1 + 1.01*2 + 16*3 + 55.85*2 + 58.71 = 232.44
28 # result = export_to_metexp_tabular.get_molecular_mass(formula)
29 # self.assertAlmostEqual(232.44, result, 2)
30 #
31 #
32 #
33
34
35 def test_simple(self):
36 '''
37 Simple initial test
38 '''
39 # Create out folder
40 outdir = "output/metexp_query/"
41 if not os.path.exists(outdir):
42 os.makedirs(outdir)
43
44 #Build up arguments and run
45
46 # input_file = sys.argv[1]
47 # molecular_mass_col = sys.argv[2]
48 # formula_col = sys.argv[3]
49 # metexp_dblink_file = sys.argv[4]
50 # output_result = sys.argv[5]
51
52 input_file = resource_filename(__name__, "data/metexp_query_tabular.txt")
53 casid_col = "CAS"
54 formula_col = "FORMULA"
55 molecular_mass_col = "MM"
56 metexp_dblink_file = resource_filename(__name__, "data/METEXP Test DB.txt")
57 output_result = resource_filename(__name__, outdir + "metexp_query_results_added.txt")
58
59 sys.argv = ['test',
60 input_file,
61 casid_col,
62 formula_col,
63 molecular_mass_col,
64 metexp_dblink_file,
65 'GC',
66 output_result]
67
68 # Execute main function with arguments provided through sys.argv
69 query_metexp.main()
70
71 # TODO - asserts (base them on DB being filled with test data form metexp unit test for upload method)
72 # PA
73
74
75
76
77 def _read_file(filename):
78 '''
79 Helper method to quickly read a file
80 @param filename:
81 '''
82 with open(filename) as handle:
83 return handle.read()