On Tue, Sep 18, 2012 at 2:55 PM, Scott McManus <scottmcmanus@gatech.edu> wrote:
I have to admit that I'm a little confused as to why you would be getting this error at all - the "job" variable is introduced at line 298 in the same file, and it's used as the last variable to check_tool_output in the changeset you pointed to. (Also, thanks for pointing to it - that made investigating easier.)
Is it possible that there was a merge problem when you pulled the latest set of code? For my own sanity, would you mind downloading a fresh copy of galaxy-central or galaxy-dist into a separate directory and see if the problem is still there? (I fully admit that there could be a bug that I left in, but all job runners should have stumbled across the same problem - the "finish" method should be called by all job runners.)
I've not done a fresh install, but just browsing on bitbucket there is an inconsistency in the self.check_tool_output(...) call signature: https://bitbucket.org/galaxy/galaxy-central/src/5359d1066d91/lib/galaxy/jobs... e.g. $ curl -s https://bitbucket.org/galaxy/galaxy-central/raw/5359d1066d91/lib/galaxy/jobs... | grep check_tool_output if ( self.check_tool_output( stdout, stderr, tool_exit_code, job )): def check_tool_output( self, stdout, stderr, tool_exit_code, job ): if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): Clearly the last occurrence of self.check_tool_output(...) is not including the job argument (line 1048, in class TaskWrapper). I suspect you need to have use_tasked_jobs = True in universe_wsgi.ini to hit this code branch. Peter