Unit testing around the compounds lib

core/tests/CMakeLists.txt

 set(CORE_UNIT_TESTS
+  test_setcompoundschemlib.py
   test_argcheck.py
 )
 
 set(CORE_TEST_DATA
   test_argcheck.py
+  data/broken_on_purpose.chemlib
 )
 
 promod3_unittest(MODULE core

core/tests/test_setcompoundschemlib.py

+import unittest
+import os
+from ost import conop
+from ost import io
+
+class SetCompoundsChemlibTests(unittest.TestCase):
+    def testNoCompoundsLibOverwrite(self):
+        # Checking that we DO NOT automatically load a compounds library if we
+        # already got one. This is for the case that somebody loads her own lib
+        # for whatever purpose so promod3 should not overwrite it on import.
+        # For the test, we load a library here with a modified aa and check that
+        # its still modified after importing promod3.
+
+        # load compounds lib like in __init__.py.in
+        compound_lib_path = os.path.join('data', 'broken_on_purpose.chemlib')
+        clib = conop.CompoundLib.Load(compound_lib_path)
+        self.assertIsNotNone(clib)
+        conop.SetDefaultLib(clib)
+        io.profiles['DEFAULT'].processor = conop.RuleBasedProcessor(clib)
+        clib = conop.GetDefaultLib()
+
+        # check amino acid
+        fake_gly = ('GLY', 'IOU a formula')
+        cmpd = clib.FindCompound(fake_gly[0])
+        self.assertIsNotNone(cmpd)
+        self.assertEqual(cmpd.formula, fake_gly[1])
+
+        # import promod3, fetch default lib again, rerun test
+        import promod3# pylint: disable=unused-variable
+        clib = conop.GetDefaultLib()
+        cmpd = clib.FindCompound(fake_gly[0])
+        self.assertIsNotNone(cmpd)
+        self.assertEqual(cmpd.formula, fake_gly[1])
+
+    def testCompoundsLibLoadedOnImport(self):
+        # Check that importing promod3 loads the compounds library. First we
+        # test that we do not have a lib before importing, afterwards we import
+        # and check for Glycine. This test reads the systems/ installed lib
+        # which means an external data dependency. Lets assume this is OK: if
+        # we do not have a chemical components dictionary, we do not know amino
+        # acids, so ProMod3 would not work... We also check for essential
+        # compounds in the library. Of course, those are amino acids and... if
+        # there is something you really cannot live without, add it here. One
+        # drawback of going by the systems lib, which should be updated every
+        # week, is that things may change and then our compounds list here will
+        # have to be updated, too.
+
+        # before importing, we do not want to see a lib
+        clib = conop.GetDefaultLib()
+        self.assertIsNone(clib)
+
+        # now there should be one
+        import promod3# pylint: disable=unused-variable
+        clib = conop.GetDefaultLib()
+        self.assertIsNotNone(clib)
+
+        # and it should feature Glycine
+        gly = ('GLY', 'C2 H5 N O2')
+        cmpd = clib.FindCompound(gly[0])
+        self.assertIsNotNone(cmpd)
+        self.assertEqual(cmpd.formula, gly[1])
+
+        # checking selected compounds
+        cmpnds = [('ALA', 'C3 H7 N O2'), ('ASX', 'C4 H6 N O2 X2'),
+                  ('CYS', 'C3 H7 N O2 S'), ('ASP', 'C4 H7 N O4'),
+                  ('GLU', 'C5 H9 N O4'), ('PHE', 'C9 H11 N O2'),
+                  ('GLY', 'C2 H5 N O2'), ('HIS', 'C6 H10 N3 O2'),
+                  ('ILE', 'C6 H13 N O2'), ('LYS', 'C6 H15 N2 O2'),
+                  ('LEU', 'C6 H13 N O2'), ('MET', 'C5 H11 N O2 S'),
+                  ('ASN', 'C4 H8 N2 O3'), ('PRO', 'C5 H9 N O2'),
+                  ('GLN', 'C5 H10 N2 O3'), ('ARG', 'C6 H15 N4 O2'),
+                  ('SER', 'C3 H7 N O3'), ('THR', 'C4 H9 N O3'),
+                  ('VAL', 'C5 H11 N O2'), ('TRP', 'C11 H12 N2 O2'),
+                  ('TYR', 'C9 H11 N O3'), ('GLX', 'C5 H8 N O2 X2'),
+                  ('ADE', 'C5 H5 N5'), ('GUN', 'C5 H5 N5 O'),
+                  ('CYT', 'C4 H5 N3 O'), ('THM', 'C10 H14 N2 O5'),
+                  ('URA', 'C4 H4 N2 O2')]
+        for cmpnd in cmpnds:
+            entry = clib.FindCompound(cmpnd[0])
+            self.assertIsNotNone(entry, msg="Compound '%s' not " % cmpnd[0]+
+                                 "found in default compounds library.")
+            self.assertEqual(entry.formula, cmpnd[1])
+
+if __name__ == "__main__":
+    from ost import testutils
+    testutils.RunTests()
+
+#  LocalWords:  unittest sys os ost conop io clib SetCompoundsChemlibTests aa
+#  LocalWords:  TestCase testNoCompoundsLibOverwrite promod chemlib gly GLY
+#  LocalWords:  assertIsNotNone SetDefaultLib RuleBasedProcessor cmpd ProMod
+#  LocalWords:  GetDefaultLib FindCompound testCompoundsLibLoadedOnImport ASX
+#  LocalWords:  assertIsNone cmpnds CYS GLU PHE ILE LYS LEU ASN GLN ARG SER
+#  LocalWords:  THR TRP TYR GLX CYT THM URA cmpnd msg testutils RunTests