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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