On Tue, Sep 18, 2012 at 2:55 PM, Scott McManus <scottmcma...@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/__init__.py

e.g.

$ curl -s 
https://bitbucket.org/galaxy/galaxy-central/raw/5359d1066d91/lib/galaxy/jobs/__init__.py
| 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
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