Making naccess a bit more secure with dots

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)
 
 

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 

modules/bindings/tests/test_naccess.py

+''' 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()