--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/test_export_to_metexp_tabular.py	Sat Feb 07 22:02:00 2015 +0100
@@ -0,0 +1,112 @@
+'''Integration tests for the GCMS project'''
+
+from pkg_resources import resource_filename  # @UnresolvedImport # pylint: disable=E0611
+from GCMS import export_to_metexp_tabular
+import os.path
+import sys
+import unittest
+
+
+class IntegrationTest(unittest.TestCase):
+
+
+    def test_MM_calculations(self):
+        '''
+        test the implemented method for MM calculations for 
+        given chemical formulas
+        '''
+        export_to_metexp_tabular.init_elements_and_masses_map()
+        
+        formula = "C8H18O3"
+        # should be = 12.01*8 + 1.01*18 + 16*3 = 162.26
+        result = export_to_metexp_tabular.get_molecular_mass(formula)
+        self.assertEqual(162.26, result)
+        
+        formula = "CH2O3Fe2Ni"
+        # should be = 12.01*1 + 1.01*2 + 16*3 + 55.85*2 + 58.71 = 232.44
+        result = export_to_metexp_tabular.get_molecular_mass(formula)
+        self.assertAlmostEqual(232.44, result, 2)
+        
+        
+        
+        
+
+    def test_combine_output_simple(self):
+        '''
+        comment me
+        '''
+        # Create out folder
+        outdir = "output/metexp/"
+        if not os.path.exists(outdir):
+            os.makedirs(outdir)
+
+        #Build up arguments and run
+        
+        rankfilter_and_caslookup_combined_file = resource_filename(__name__, "data/dummy1_produced_combine_output_single.txt")
+        msclust_quantification_and_spectra_file = resource_filename(__name__, "data/dummy1_sim.txt")
+        output_csv = resource_filename(__name__, outdir + "metexp_tabular.txt")
+    
+        sys.argv = ['test',
+                    rankfilter_and_caslookup_combined_file,
+                    msclust_quantification_and_spectra_file,
+                    output_csv, 
+                    'tomato',
+                    'leafs',
+                    'test experiment',
+                    'pieter',
+                    'DB5 column']
+        
+        # Execute main function with arguments provided through sys.argv
+        export_to_metexp_tabular.main()
+
+        '''
+        # Asserts are based on reading in with process_data and comparing values of 
+        # certain columns
+        
+        # Check 3: library_lookup RI column, centrotype column, ri_svr column are correct:
+        caslookup_items = combine_output._process_data(input_caslookup)
+        rankfilter_items = combine_output._process_data(input_rankfilter)
+        
+        # check that the caslookup RI column is correctly maintained in its original order in
+        # the combined file:
+        ri_caslookup = caslookup_items['RI']
+        ri_combine_single = combine_result_single_items['RI']
+        self.assertListEqual(ri_caslookup, ri_combine_single) 
+        
+        # check the centrotype column's integrity:
+        centrotype_caslookup = caslookup_items['Centrotype']
+        centrotype_combine_single = combine_result_single_items['Centrotype']
+        centrotype_rankfilter = _get_centrotype_rankfilter(rankfilter_items['ID'])
+        self.assertListEqual(centrotype_caslookup, centrotype_combine_single)
+        self.assertListEqual(centrotype_caslookup, centrotype_rankfilter)
+                
+        # integration and integrity checks:
+        file_NIST = resource_filename(__name__, "data/integration/NIST_identification_results_tabular.txt")
+        file_NIST_items = combine_output._process_data(file_NIST)
+        # check that rank filter output has exactly the same ID items as the original NIST input file:
+        self.assertListEqual(file_NIST_items['ID'], rankfilter_items['ID']) 
+        # check the same for the CAS column:
+        self.assertListEqual(_get_strippedcas(file_NIST_items['CAS']), rankfilter_items['CAS'])
+        # now check the NIST CAS column against the cas lookup results:  
+        cas_NIST = _get_processedcas(file_NIST_items['CAS'])
+        self.assertListEqual(cas_NIST, caslookup_items['CAS'])
+        # now check the CAS of the combined result. If all checks are OK, it means the CAS column's order
+        # and values remained stable throughout all steps: 
+        self.assertListEqual(rankfilter_items['CAS'], combine_result_single_items['CAS']) 
+        
+        # check that the rankfilter RIsvr column is correctly maintained in its original order in
+        # the combined file:
+        risvr_rankfilter = rankfilter_items['RIsvr']
+        risvr_combine_single = combine_result_single_items['RIsvr']
+        self.assertListEqual(risvr_rankfilter, risvr_combine_single) 
+        '''
+        
+   
+
+def _read_file(filename):
+    '''
+    Helper method to quickly read a file
+    @param filename:
+    '''
+    with open(filename) as handle:
+        return handle.read()