From 6f8935f4f947e3de5ad56d21c20d32184a348319 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 12 Feb 2015 15:57:06 +0100
Subject: [PATCH] Unit testing around the compounds lib
---
core/tests/CMakeLists.txt | 2 +
core/tests/data/broken_on_purpose.chemlib | Bin 0 -> 13312 bytes
core/tests/test_setcompoundschemlib.py | 93 ++++++++++++++++++++++
3 files changed, 95 insertions(+)
create mode 100644 core/tests/data/broken_on_purpose.chemlib
create mode 100644 core/tests/test_setcompoundschemlib.py
diff --git a/core/tests/CMakeLists.txt b/core/tests/CMakeLists.txt
index 89e63b57..51736e2f 100644
--- a/core/tests/CMakeLists.txt
+++ b/core/tests/CMakeLists.txt
@@ -1,9 +1,11 @@
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
diff --git a/core/tests/data/broken_on_purpose.chemlib b/core/tests/data/broken_on_purpose.chemlib
new file mode 100644
index 0000000000000000000000000000000000000000..740c0e2c799a885d23a02f5be36cb76f92fb9b04
GIT binary patch
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diff --git a/core/tests/test_setcompoundschemlib.py b/core/tests/test_setcompoundschemlib.py
new file mode 100644
index 00000000..8f90d569
--- /dev/null
+++ b/core/tests/test_setcompoundschemlib.py
@@ -0,0 +1,93 @@
+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
--
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