From 2b7ab33b5e5b1a34e15b7d41db1c7684b3e42977 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Tue, 16 May 2017 18:28:23 +0200
Subject: [PATCH] Making naccess a bit more secure with dots
---
modules/bindings/pymod/naccess.py | 4 +--
modules/bindings/tests/CMakeLists.txt | 1 +
modules/bindings/tests/test_naccess.py | 42 ++++++++++++++++++++++++++
3 files changed, 45 insertions(+), 2 deletions(-)
create mode 100644 modules/bindings/tests/test_naccess.py
diff --git a/modules/bindings/pymod/naccess.py b/modules/bindings/pymod/naccess.py
index 621067e7b..268b72ac1 100644
--- a/modules/bindings/pymod/naccess.py
+++ b/modules/bindings/pymod/naccess.py
@@ -60,9 +60,9 @@ def _SetupFiles(entity, selection, scratch_dir, max_number_of_atoms):
raise RuntimeError, "Could not create view for selection (%s)"%(selection)
# write entity to tmp file
- tmp_file_name=os.path.join(tmp_dir_name,"entity.pdb")
+ tmp_file_name = "entity.pdb"
tmp_file_base = os.path.join(tmp_dir_name,"entity")
- io.SavePDB(entity_view, tmp_file_name)
+ io.SavePDB(entity_view, os.path.join(tmp_dir_name, tmp_file_name))
return (tmp_dir_name, tmp_file_name, tmp_file_base)
diff --git a/modules/bindings/tests/CMakeLists.txt b/modules/bindings/tests/CMakeLists.txt
index c443de132..dd257c1cb 100644
--- a/modules/bindings/tests/CMakeLists.txt
+++ b/modules/bindings/tests/CMakeLists.txt
@@ -4,6 +4,7 @@ set(OST_BINDINGS_UNIT_TESTS
test_hhblits.py
test_blast.py
test_kclust.py
+ test_naccess.py
)
ost_unittest(MODULE bindings
diff --git a/modules/bindings/tests/test_naccess.py b/modules/bindings/tests/test_naccess.py
new file mode 100644
index 000000000..891f01bd7
--- /dev/null
+++ b/modules/bindings/tests/test_naccess.py
@@ -0,0 +1,42 @@
+''' Unit tests for the Naccess wrapper
+'''
+
+import unittest
+import os
+import sys
+import shutil
+import tempfile
+
+from ost.bindings import naccess
+from ost import io
+
+class TestNaccessBindings(unittest.TestCase):
+ def testTempDirWithDot(self):
+ # naccess itself has problems with '.' in the path. So we need to test
+ # that it works when data is used which has a correpsonding path.
+ na_tmp_dir = tempfile.mkdtemp(prefix="ih.")
+ def cleanup():
+ shutil.rmtree(na_tmp_dir)
+ self.addCleanup(cleanup)
+ na_bin = os.path.join(os.getenv('EBROOTNACCESS'), 'naccess')
+ ost_ent = io.LoadPDB('testfiles/testprotein.pdb')
+ excp_raised = False
+ try:
+ sasa = naccess.CalculateSurfaceArea(ost_ent,
+ scratch_dir=na_tmp_dir,
+ naccess_exe=na_bin)
+ except:
+ excp_raised = True
+ raise
+ self.assertEquals(excp_raised, False, msg="Naccess raised an "+
+ "exception on a path containing a '.'. This is not "+
+ "supposed to happen.")
+
+if __name__ == "__main__":
+ naccess_dir = os.getenv('EBROOTNACCESS')
+ if not naccess_dir:
+ print "No environment variable 'EBROOTNACCESS'. To enable the "+\
+ "unit test, this needs to point to your Naccess installation."
+ sys.exit(0)
+ from ost import testutils
+ testutils.RunTests()
--
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