Fix for issue #129

longbow/apps/namd.py

@@ -39,9 +39,10 @@
 
 import os
 import re
-
+import logging
 import longbow.exceptions as exceptions
 
+LOG = logging.getLogger("longbow.apps.namd")
 
 EXECDATA = {
     "namd2": {
@@ -88,39 +89,44 @@ def file_parser(filename, path, files, substitutions=None):
 
         fil = _fileopen(path, addfile)
 
-        # Search every line for possible input files.
-        for line in fil:
+        try:
+
+            # Search every line for possible input files.
+            for line in fil:
+
+                # Remove comments.
+                if '#' in line:
 
-            # Remove comments.
-            if '#' in line:
+                    words = line[:line.index('#')].split()
 
-                words = line[:line.index('#')].split()
+                else:
 
-            else:
+                    words = line[:len(line)].split()
 
-                words = line[:len(line)].split()
+                if len(words) > 0:
 
-            if len(words) > 0:
+                    # Pick up substitutions from within file
+                    _internalsubstitutions(variables, words)
 
-                # Pick up substitutions from within file
-                _internalsubstitutions(variables, words)
+                    # If this line is reading in an input file.
+                    if words[0].lower() in keywords:
 
-                # If this line is reading in an input file.
-                if words[0].lower() in keywords:
+                        newfile = words[-1]
 
-                    newfile = words[-1]
+                        # Do variable substitutons
+                        newfile = _variablesubstitutions(newfile, variables)
 
-                    # Do variable substitutons
-                    newfile = _variablesubstitutions(newfile, variables)
+                        # Check newfile.
+                        newfile = _newfilechecks(addfile, newfile, path)
 
-                    # Deduce the location of newfile.
-                    newpath = path
+                        # Recursive function
+                        file_parser(newfile, path, files, substitutions)
 
-                    # Check newfile.
-                    newfile = _newfilechecks(addfile, newfile, path)
+        except UnicodeDecodeError:
 
-                    # Recursive function.
-                    file_parser(newfile, newpath, files, substitutions)
+            LOG.debug("Couldn't read file '{0}' - this is probably because "
+                      "it is a binary format or unknown encoding"
+                      .format(addfile))
 
         fil.close()
 

longbow/entrypoints.py

@@ -70,7 +70,7 @@
 import longbow.staging as staging
 
 PYTHONVERSION = "{0}.{1}".format(sys.version_info[0], sys.version_info[1])
-LONGBOWVERSION = "1.5.2"
+LONGBOWVERSION = "1.5.3-dev"
 
 LOG = logging.getLogger("longbow")
 

setup.py

@@ -56,7 +56,7 @@
 
 # Setup
 setup(name='Longbow',
-      version='1.5.2',
+      version='1.5.3-dev',
       description='Biomolecular simulation remote job submission tool.',
       long_description=open('README.rst').read(),
       author='James T Gebbie-Rayet, Gareth B Shannon',

tests/unit/apps_namd/test_namd_fileparser.py

@@ -98,3 +98,42 @@ def test_fileparser_test3():
     file_parser(filename, path, files, substitutions)
 
     assert files == ["apps_fileparsernamd.txt", "apps_recursivetest.txt"]
+
+
+def test_fileparser_test4():
+
+    """
+    Test with a binary file.
+    """
+
+    filename = "namdcoordfile.coor"
+    path = os.path.join(os.getcwd(), "tests/standards/")
+    files = []
+    substitutions = {}
+
+    file_parser(filename, path, files, substitutions)
+
+    assert files == ["namdcoordfile.coor"]
+
+
+@mock.patch('longbow.apps.namd._internalsubstitutions')
+def test_fileparser_test5(subs):
+
+    """
+    Test with a binary file check file still added for upload on mocked except.
+
+    This is test is really a bit of a fake, since it is difficult to mock the
+    exception in the way it is thrown organically. But this test does do the
+    trick!
+    """
+
+    filename = "namdcoordfile.coor"
+    path = os.path.join(os.getcwd(), "tests/standards/")
+    files = []
+    substitutions = {}
+
+    subs.side_effect = UnicodeDecodeError('blah', b'', 80, 0, '')
+
+    file_parser(filename, path, files, substitutions)
+
+    assert files == ["namdcoordfile.coor"]