Thanks, Jorrit! That was a good catch. Yes, it's a problem with the TaskWrapper. I'll see what I can do about it. -Scott ----- Original Message -----
Is it possible that you are looking at different classes? TaskWrapper's finish method does not use the job variable in my recently merged code either (line ~1045), while JobWrapper's does around line 315.
cheers, jorrit
On 09/18/2012 03:55 PM, Scott McManus 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.)
Thanks again!
-Scott
----- Original Message -----
I'll check it out. Thanks.
----- Original Message -----
Hi all (and in particular, Scott),
I've just updated my development server and found the following error when running jobs on our SGE cluster via DRMMA:
galaxy.jobs.runners.drmaa ERROR 2012-09-18 09:43:20,698 Job wrapper finish method failed Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", line 371, in finish_job drm_job_state.job_wrapper.finish( stdout, stderr, exit_code ) File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py", line 1048, in finish if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): TypeError: check_tool_output() takes exactly 5 arguments (4 given)
This looks to have been introduced in this commit: https://bitbucket.org/galaxy/galaxy-central/changeset/f557b7b05fdd701cbf99ee...
There should be an additional jobs argument, proposed fix:
$ hg diff lib/galaxy/jobs/__init__.py diff -r 4007494e37e1 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Tue Sep 18 09:40:19 2012 +0100 +++ b/lib/galaxy/jobs/__init__.py Tue Sep 18 10:06:44 2012 +0100 @@ -1045,7 +1045,8 @@ # Check what the tool returned. If the stdout or stderr matched # regular expressions that indicate errors, then set an error. # The same goes if the tool's exit code was in a given range. - if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): + job = self.get_job() + if ( self.check_tool_output( stdout, stderr, tool_exit_code, job ) ): task.state = task.states.OK else: task.state = task.states.ERROR
(Let me know if you want this as a pull request - it seems a lot of effort for a tiny change.)
Regards,
Peter
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