diff test/test_query_metexp.py @ 21:19d8fd10248e

* Added interface to METEXP data store, including tool to fire queries in batch mode * Improved quantification output files of MsClust, a.o. sorting mass list based on intensity (last two columns of quantification files) * Added Molecular Mass calculation method

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/test_query_metexp.py	Wed Mar 05 17:20:11 2014 +0100
@@ -0,0 +1,82 @@
+'''Integration tests for the GCMS project'''
+
+from pkg_resources import resource_filename  # @UnresolvedImport # pylint: disable=E0611
+from GCMS import query_metexp
+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_simple(self):
+        '''
+        Simple initial test
+        '''
+        # Create out folder
+        outdir = "output/metexp_query/"
+        if not os.path.exists(outdir):
+            os.makedirs(outdir)
+
+        #Build up arguments and run
+        
+        #         input_file = sys.argv[1]
+        #         molecular_mass_col = sys.argv[2]
+        #         formula_col = sys.argv[3]
+        #         metexp_dblink_file = sys.argv[4]
+        #         output_result = sys.argv[5]
+        
+        input_file = resource_filename(__name__, "data/metexp_query_tabular.txt")
+        casid_col = "CAS"
+        formula_col = "FORMULA"
+        molecular_mass_col = "MM"
+        metexp_dblink_file = resource_filename(__name__, "data/METEXP Test DB.txt")
+        output_result = resource_filename(__name__, outdir + "metexp_query_results_added.txt")
+    
+        sys.argv = ['test',
+                    input_file,
+                    casid_col,
+                    formula_col, 
+                    molecular_mass_col,
+                    metexp_dblink_file,
+                    'GC',
+                    output_result]
+        
+        # Execute main function with arguments provided through sys.argv
+        query_metexp.main()
+        
+        # TODO - asserts  (base them on DB being filled with test data form metexp unit test for upload method)
+        # PA
+
+        
+   
+
+def _read_file(filename):
+    '''
+    Helper method to quickly read a file
+    @param filename:
+    '''
+    with open(filename) as handle:
+        return handle.read()