Mercurial > repos > pieterlukasse > prims_metabolomics

annotate test/test_query_mass_repos.py @ 27:ecd3f6c9e606

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small fix to support spaces in parameters
author pieter.lukasse@wur.nl
date Thu, 01 May 2014 11:19:52 +0200
parents 637830ac8bcd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 '''Integration tests for the GCMS project'''
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3 from pkg_resources import resource_filename # @UnresolvedImport # pylint: disable=E0611
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4 from MS import query_mass_repos
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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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10 class IntegrationTest(unittest.TestCase):
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15 def test_simple(self):
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16 '''
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17 Simple initial test
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18 '''
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19 # Create out folder
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20 outdir = "output/query_mass_repos/"
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21 if not os.path.exists(outdir):
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22 os.makedirs(outdir)
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24 #Build up arguments and run
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26 # input_file = sys.argv[1]
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27 # molecular_mass_col = sys.argv[2]
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28 # repository_file = sys.argv[3]
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29 # mass_tolerance = float(sys.argv[4])
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30 # output_result = sys.argv[5]
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32 input_file = resource_filename(__name__, "data/service_query_tabular.txt")
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34 molecular_mass_col = "mass (Da)"
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35 dblink_file = resource_filename(__name__, "data/MFSearcher ExactMassDB service.txt")
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36 output_result = resource_filename(__name__, outdir + "metexp_query_results_added.txt")
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41 sys.argv = ['test',
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42 input_file,
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43 molecular_mass_col,
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44 dblink_file,
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45 '0.001',
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46 'ms',
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47 output_result]
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48
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49 # Execute main function with arguments provided through sys.argv
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50 query_mass_repos.main()
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56 def _read_file(filename):
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57 '''
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58 Helper method to quickly read a file
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59 @param filename:
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60 '''
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61 with open(filename) as handle:
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62 return handle.read()