Since tempfiles seem to occasionally be left behind, allow logging of

open tempfiles, including a traceback (to determine callers) if
LOG_TEMPFILES is set in the environment when Galaxy starts.  This
should be considered temporary and will be removed when it's determined
where/how this happens.

lib/log_tempfile.py

@@ -0,0 +1,27 @@
+# override tempfile methods for debugging
+
+import tempfile, traceback
+
+import logging
+log = logging.getLogger( __name__ )
+
+class TempFile( object ):
+    def __init__( self ):
+        tempfile._NamedTemporaryFile = tempfile.NamedTemporaryFile
+        tempfile._mkstemp = tempfile.mkstemp
+        tempfile.NamedTemporaryFile = self.NamedTemporaryFile
+        tempfile.mkstemp = self.mkstemp
+    def NamedTemporaryFile( self, *args, **kwargs ):
+        f = tempfile._NamedTemporaryFile( *args, **kwargs )
+        try:
+            log.debug( ( "Opened tempfile %s with NamedTemporaryFile:\n" % f.name ) + "".join( traceback.format_stack() ) )
+        except AttributeError:
+            pass
+        return f
+    def mkstemp( self, *args, **kwargs ):
+        f = tempfile._mkstemp( *args, **kwargs )
+        try:
+            log.debug( ( "Opened tempfile %s with mkstemp:\n" % f[1] ) + "".join( traceback.format_stack() ) )
+        except TypeError:
+            pass
+        return f

scripts/paster.py

@@ -16,6 +16,11 @@ sys.path = new_path
 from galaxy import eggs
 import pkg_resources
 
+if 'LOG_TEMPFILES' in os.environ:
+    from log_tempfile import TempFile
+    _log_tempfile = TempFile()
+    import tempfile
+
 pkg_resources.require( "PasteScript" )
 
 from paste.script import command