From 5df51d99bb711ebef7e063830e7289fb8ace20c9 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Fri, 7 Jul 2017 09:51:27 +0200
Subject: [PATCH] Unified handling for compound lib dependent python unittests.
This also enabled test_cleanup, test_nonstandard and test_aligntoseqres which
were previously skipped with 'make check' indep. of compound lib availability
(simply because unittests are launched with 'python' and not with 'ost').
---
modules/base/doc/testutils.rst | 4 +-
modules/base/pymod/testutils.py | 55 ++++++++++++++++++++-
modules/conop/doc/compoundlib.rst | 2 +-
modules/conop/tests/CMakeLists.txt | 6 +--
modules/conop/tests/test_cleanup.py | 15 +++---
modules/conop/tests/test_compound.py | 19 ++-----
modules/conop/tests/test_nonstandard.py | 12 ++---
modules/mol/alg/tests/test_qsscoring.py | 25 +++-------
modules/seq/alg/tests/CMakeLists.txt | 5 +-
modules/seq/alg/tests/test_aligntoseqres.py | 15 +++---
10 files changed, 98 insertions(+), 60 deletions(-)
diff --git a/modules/base/doc/testutils.rst b/modules/base/doc/testutils.rst
index 649a0b3b3..df61f56e7 100644
--- a/modules/base/doc/testutils.rst
+++ b/modules/base/doc/testutils.rst
@@ -4,4 +4,6 @@
.. module:: ost.testutils
:synopsis: Helper Functions to Run Python Unittests
-.. autofunction:: ost.testutils.RunTests
\ No newline at end of file
+.. autofunction:: ost.testutils.RunTests
+
+.. autofunction:: ost.testutils.SetDefaultCompoundLib
diff --git a/modules/base/pymod/testutils.py b/modules/base/pymod/testutils.py
index fe3e7a024..5dd8762e2 100644
--- a/modules/base/pymod/testutils.py
+++ b/modules/base/pymod/testutils.py
@@ -51,4 +51,57 @@ def RunTests():
else:
unittest.main()
except Exception, e:
- print e
\ No newline at end of file
+ print e
+
+
+def SetDefaultCompoundLib():
+ '''
+ This function tries to ensure that a default compound library is set.
+ When calling scripts with ``ost`` this is not needed, but since unit tests are
+ called with ``python`` we need to ensure that it is set. The function is only
+ expected to succeed (and return True) if ``COMPOUND_LIB`` was set when
+ :ref:`configuring the compilation <cmake-flags>`.
+
+ It tries the following:
+
+ - get it with :func:`ost.conop.GetDefaultLib`
+ - look for ``compounds.chemlib`` in ``$OST_ROOT/share/openstructure``
+ - if ``OST_ROOT`` not set in the above, try to guess it based on the path of
+ the ``conop`` module
+
+ To use this check modify the :func:`RunTests` call to read:
+
+ .. code-block:: python
+
+ if __name__ == "__main__":
+ from ost import testutils
+ if testutils.SetDefaultCompoundLib():
+ testutils.RunTests()
+ else:
+ print 'No compound library available. Ignoring test_XXX.py tests.'
+
+ :return: True, if a compound library was found and set to be accessed with
+ :func:`ost.conop.GetDefaultLib`. False otherwise.
+ '''
+ import os
+ from ost import conop, GetSharedDataPath, SetPrefixPath
+ # check if already there
+ if conop.GetDefaultLib():
+ return True
+ else:
+ # try to get the shared data path?
+ try:
+ shared_data_path = GetSharedDataPath()
+ except Exception, e:
+ SetPrefixPath(os.path.abspath(os.path.join(conop.__path__[0], os.pardir,
+ os.pardir, os.pardir,
+ os.pardir, os.pardir)))
+ shared_data_path = GetSharedDataPath()
+ # look for compounds.chemlib in there
+ compound_lib_path = os.path.join(shared_data_path, 'compounds.chemlib')
+ if os.path.exists(compound_lib_path):
+ compound_lib = conop.CompoundLib.Load(compound_lib_path)
+ conop.SetDefaultLib(compound_lib)
+ return True
+ else:
+ return False
diff --git a/modules/conop/doc/compoundlib.rst b/modules/conop/doc/compoundlib.rst
index f88f04709..caca8445b 100644
--- a/modules/conop/doc/compoundlib.rst
+++ b/modules/conop/doc/compoundlib.rst
@@ -25,7 +25,7 @@ build the compound library manually.
OpenStructure as a bundle or you :ref:`compiled <cmake-flags>` it
with a specified ``COMPOUND_LIB`` flag, this will return a compound
library when executing scripts with ``ost``.
- :rtype: :class:`CompoundLib`
+ :rtype: :class:`CompoundLib` or None if no library set
.. function:: SetDefaultLib(lib)
diff --git a/modules/conop/tests/CMakeLists.txt b/modules/conop/tests/CMakeLists.txt
index 58a605268..964006509 100644
--- a/modules/conop/tests/CMakeLists.txt
+++ b/modules/conop/tests/CMakeLists.txt
@@ -4,13 +4,13 @@ set(OST_CONOP_UNIT_TESTS
tests.cc
test_rule_based_conop.cc
helper.cc
- test_cleanup.py
test_processor.py
- test_nonstandard.py
)
if (COMPOUND_LIB)
- list(APPEND OST_CONOP_UNIT_TESTS test_compound.py)
+ list(APPEND OST_CONOP_UNIT_TESTS test_compound.py
+ test_cleanup.py
+ test_nonstandard.py)
endif()
ost_unittest(MODULE conop
diff --git a/modules/conop/tests/test_cleanup.py b/modules/conop/tests/test_cleanup.py
index 9c5f0cf27..b0579127a 100644
--- a/modules/conop/tests/test_cleanup.py
+++ b/modules/conop/tests/test_cleanup.py
@@ -1,12 +1,13 @@
import sys
import unittest
-from ost import geom, conop
+from ost import geom, conop, io
from ost.conop import cleanup
class TestCleanUp(unittest.TestCase):
def setUp(self):
- self.comp_lib=conop.GetDefaultLib()
+ self.comp_lib = conop.GetDefaultLib()
+ io.profiles['DEFAULT'].processor = conop.RuleBasedProcessor(self.comp_lib)
self.ent = io.LoadPDB("sample_test_cleanup.pdb")
self.ent_no_wat = io.LoadPDB("sample_nowater.pdb")
self.ent_no_lig = io.LoadPDB("sample_noligands.pdb")
@@ -156,10 +157,10 @@ class TestCleanUp(unittest.TestCase):
self.assertFalse(self.new_ent.residues[6].IsPeptideLinking()) # here assertFalse instead of assertTrue
self.assertTrue(self.new_ent.residues[6].atoms[0].is_hetatom)
-if not conop.GetDefaultLib():
- print 'No compound library available. Ignoring test_cleanup.py tests'
- sys.exit()
-if __name__== '__main__':
+if __name__ == "__main__":
from ost import testutils
- testutils.RunTests()
+ if testutils.SetDefaultCompoundLib():
+ testutils.RunTests()
+ else:
+ print 'No compound library available. Ignoring test_cleanup.py tests.'
diff --git a/modules/conop/tests/test_compound.py b/modules/conop/tests/test_compound.py
index fd480a54b..bd54b7dfa 100644
--- a/modules/conop/tests/test_compound.py
+++ b/modules/conop/tests/test_compound.py
@@ -1,17 +1,6 @@
import unittest
-import os
-from ost import GetSharedDataPath, SetPrefixPath
-from ost import mol
-from ost import conop
+from ost import mol, conop
-def setUpModule():
- SetPrefixPath(os.path.abspath(os.path.join(conop.__path__[0], os.pardir,
- os.pardir, os.pardir,
- os.pardir, os.pardir)))
- compound_lib_path = os.path.join(GetSharedDataPath(),
- 'compounds.chemlib')
- compound_lib = conop.CompoundLib.Load(compound_lib_path)
- conop.SetDefaultLib(compound_lib)
class TestCompound(unittest.TestCase):
def setUp(self):
@@ -36,5 +25,7 @@ class TestCompound(unittest.TestCase):
if __name__=='__main__':
from ost import testutils
- testutils.RunTests()
-
+ if testutils.SetDefaultCompoundLib():
+ testutils.RunTests()
+ else:
+ print 'No compound library available. Ignoring test_compound.py tests.'
\ No newline at end of file
diff --git a/modules/conop/tests/test_nonstandard.py b/modules/conop/tests/test_nonstandard.py
index f10b7d9d0..566db9a2b 100644
--- a/modules/conop/tests/test_nonstandard.py
+++ b/modules/conop/tests/test_nonstandard.py
@@ -1,5 +1,5 @@
import unittest
-from ost import conop
+from ost import conop, io, mol
class TestNonStandard(unittest.TestCase):
@@ -117,10 +117,8 @@ class TestNonStandard(unittest.TestCase):
if __name__ == "__main__":
- if not conop.GetDefaultLib():
- print 'No compound library available. Ignoring unit tests'
- else:
- from ost import testutils
+ from ost import testutils
+ if testutils.SetDefaultCompoundLib():
testutils.RunTests()
-
-
+ else:
+ print 'No compound library available. Ignoring test_nonstandard.py tests.'
diff --git a/modules/mol/alg/tests/test_qsscoring.py b/modules/mol/alg/tests/test_qsscoring.py
index b883f2f34..a860a0528 100644
--- a/modules/mol/alg/tests/test_qsscoring.py
+++ b/modules/mol/alg/tests/test_qsscoring.py
@@ -1,24 +1,12 @@
-import unittest
-import ost, os
-from ost import io, conop
-from ost import GetSharedDataPath, SetPrefixPath
+import unittest, os
+from ost import io
from ost.mol.alg.qsscoring import *
+
def _LoadFile(file_name):
"""Helper to avoid repeating input path over and over."""
return io.LoadPDB(os.path.join('testfiles', file_name))
-def setUpModule():
- """Called once by unittest: ensures that we have a compound library."""
- if not conop.GetDefaultLib():
- SetPrefixPath(os.path.abspath(os.path.join(conop.__path__[0], os.pardir,
- os.pardir, os.pardir,
- os.pardir, os.pardir)))
- compound_lib_path = os.path.join(GetSharedDataPath(),
- 'compounds.chemlib')
- compound_lib = conop.CompoundLib.Load(compound_lib_path)
- conop.SetDefaultLib(compound_lib)
-
class TestQSscore(unittest.TestCase):
@@ -192,6 +180,9 @@ class TestQSscore(unittest.TestCase):
self.assertAlmostEqual(qs_scorer.best_score, 0.975, 2)
-if __name__== '__main__':
+if __name__ == "__main__":
from ost import testutils
- testutils.RunTests()
+ if testutils.SetDefaultCompoundLib():
+ testutils.RunTests()
+ else:
+ print 'No compound library available. Ignoring test_qsscoring.py tests.'
diff --git a/modules/seq/alg/tests/CMakeLists.txt b/modules/seq/alg/tests/CMakeLists.txt
index 529a3eb62..81b69d15f 100644
--- a/modules/seq/alg/tests/CMakeLists.txt
+++ b/modules/seq/alg/tests/CMakeLists.txt
@@ -8,9 +8,12 @@ set(OST_SEQ_ALG_UNIT_TESTS
test_global_align.py
test_semiglobal_align.py
test_weight_matrix.py
- test_aligntoseqres.py
)
+if (COMPOUND_LIB)
+ list(APPEND OST_SEQ_ALG_UNIT_TESTS test_aligntoseqres.py)
+endif()
+
ost_unittest(MODULE seq_alg SOURCES "${OST_SEQ_ALG_UNIT_TESTS}"
LINK ost_mol ost_io)
diff --git a/modules/seq/alg/tests/test_aligntoseqres.py b/modules/seq/alg/tests/test_aligntoseqres.py
index 126c7f047..2aa1bb4fe 100644
--- a/modules/seq/alg/tests/test_aligntoseqres.py
+++ b/modules/seq/alg/tests/test_aligntoseqres.py
@@ -1,8 +1,6 @@
import unittest
-from ost import *
-from ost import settings
-from ost import seq
-from ost import io
+import ost
+from ost import seq, io, mol
class TestAlignToSeqRes(unittest.TestCase):
def testAlignWorking(self):
@@ -67,9 +65,10 @@ class TestAlignToSeqRes(unittest.TestCase):
validate = False)
self.assertEqual(seq.alg.ValidateSEQRESAlignment(seqres_aln, chain), False)
+
if __name__ == "__main__":
- if not conop.GetDefaultLib():
- print 'No compound library available. Ignoring unit tests'
- else:
- from ost import testutils
+ from ost import testutils
+ if testutils.SetDefaultCompoundLib():
testutils.RunTests()
+ else:
+ print 'No compound library available. Ignoring test_aligntoseqres.py tests.'
--
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