Mercurial > repos > pieterlukasse > prims_metabolomics
view rankfilter_GCMS/test/test_pdfread.py @ 26:637830ac8bcd
added validation in metexp to tabular tool; added workaround/fix for L and D compound types
author | pieter.lukasse@wur.nl |
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date | Thu, 24 Apr 2014 11:28:38 +0200 |
parents | 53e1eee93430 |
children | d685210eef3e |
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''' Created on Mar 13, 2012 @author: marcelk ''' from GCMS.rankfilter_GCMS import pdfread # @UnresolvedImport from pkg_resources import resource_filename # @UnresolvedImport # pylint: disable=E0611 import unittest class Test(unittest.TestCase): def setUp(self): self.nist_pdf = resource_filename(__name__, "data/NIST_test_PDF.txt") def test_getPDF(self): ''' Tests the reading and parsing of a NIST PDF file ''' [hitlist, hitlist_missed] = pdfread.getPDF(self.nist_pdf, True) rows = [hitlist[row] for row in hitlist.keys()] data = [set(row) for row in zip(*rows)] expected_element = set(('12.3', ' Sucrose ', '14', 'undef', ' standards 2009', ' 660', 'not_def', '18495-0.142537-21284-2.26544e+07-135', '22.6544', ' 714')) self.failUnless(expected_element in data) self.failUnless(len(hitlist_missed) != 0) ''' Check for last (dummy) hit: Hit 6 : (dummy hit)Sorbopyranose, 1,2,3,4,5-pentakis-O-(trimethylsilyl)-, LC21H52O6Si5;MF: 658; RMF: 658; Prob 15.6%; CAS: 30645-02-4; Lib: mainlib; ID: 37062. ''' expected_element = set(['C21H52O6Si5', ' 30645-02-4', ' mainlib', '15.6', ' (dummy hit)Sorbopyranose, 1,2,3,4,5-pentakis-O-(trimethylsilyl)-, L C21H52O6Si5', '7298-1-9580-1.29014e+07-9', ' 658', '12.9014', '37062']) self.failUnless(expected_element in data) if __name__ == "__main__": #import sys;sys.argv = ['', 'Test.test_getPDF'] unittest.main()