Merge pull request #89 from nsoranzo/fixes_for_py3_planemo

Fixes for Python3 planemo

Author: jmchilton

galaxy/tools/deps/commands.py

@@ -3,17 +3,29 @@
 import subprocess
 import sys as _sys
 
+import six
 from six.moves import shlex_quote
 
-from galaxy.util import which
+from galaxy.util import (
+    unicodify,
+    which
+)
 
 STDOUT_INDICATOR = "-"
 
 
 def redirecting_io(sys=_sys):
-    """Predicate to determine if we are redicting I/O in process."""
+    """Predicate to determine if we are redicting stdout in process."""
     assert sys is not None
-    return not hasattr(sys.stdout, "fileno")
+    try:
+        # Need to explicitly call fileno() because sys.stdout could be a
+        # io.StringIO object, which has a fileno() method but only raises an
+        # io.UnsupportedOperation exception
+        sys.stdout.fileno()
+    except Exception:
+        return True
+    else:
+        return False
 
 
 def redirect_aware_commmunicate(p, sys=_sys):
@@ -22,9 +34,15 @@ def redirect_aware_commmunicate(p, sys=_sys):
     out, err = p.communicate()
     if redirecting_io(sys=sys):
         if out:
+            # We don't unicodify in Python2 because sys.stdout may be a
+            # cStringIO.StringIO object, which does not accept Unicode strings
+            if not six.PY2:
+                out = unicodify(out)
             sys.stdout.write(out)
             out = None
         if err:
+            if not six.PY2:
+                err = unicodify(err)
             sys.stderr.write(err)
             err = None
     return out, err