Extra debugging during staging.

lwr_staging.patch

diff -r c80947795972 lib/galaxy/jobs/runners/lwr_client/staging/up.py
--- a/lib/galaxy/jobs/runners/lwr_client/staging/up.py  Fri Feb 21 16:57:59 2014 -0500
+++ b/lib/galaxy/jobs/runners/lwr_client/staging/up.py  Wed Feb 26 08:52:07 2014 -0600
@@ -149,7 +149,9 @@
 
     def __upload_input_extra_files(self, input_file):
         files_path = "%s_files" % input_file[0:-len(".dat")]
+        log.info( "Extra files path guess is %s, exists? %s" % ( files_path, exists( files_path ) ) )
         if exists(files_path) and self.__stage_input(files_path):
+            log.info( "Going to stage extra files - %s" % str(directory_files(files_path)) )
             for extra_file_name in directory_files(files_path):
                 extra_file_path = join(files_path, extra_file_name)
                 remote_name = self.path_helper.remote_name(relpath(extra_file_path, dirname(files_path)))
@@ -283,9 +285,12 @@
         pattern = r"%s" % path
         found = False
         for input_contents in self.__items():
+            log.info("Checking for path %s in %s" % ( path, input_contents ) )
             if findall(pattern, input_contents):
+                log.info("FOUND!")
                 found = True
                 break
+            log.info("NOT FOUND!")
         return found
 
     def rewrite_paths(self, local_path, remote_path):