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/f557b7b05fdd701cbf99ee04f311bcadb1ae29c4#chg-lib/galaxy/jobs/__init__.py
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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