Hi Hans,
OK, thanks: diving into the job table. Your question: "why you consider
the job as being finished, and Galaxy thinks the job is still running"
is the core issue that I need to find out. None of those jobs have
entries in the ps list.
Currently, I think that those jobs are still listed because they were
not nicely shut down by Galaxy, but because of a crash (e.g. of the
virtual machine). Upon restarting Galaxy, Galaxy seems not to check
whether those jobs are currently running, but seems to depend entirely
on the job table to fill the 'unfinished jobs' table.
Cheers,
Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 03/07/2013 11:21 AM, Hans-Rudolf Hotz wrote:
Hi Joachim
I make increasingly use of the Galaxy Reports tool. Until recently I
started it and shut it down again. Now I run it continuously. I have
noticed that a lot of the jobs listed in 'unfinished jobs' are actually
finished.
Any hint on how to clean up the database? Which table? Perhaps I can
make a Trello card: 'Provide a button to remove the jobs from the
unfinished jobs page' ?
Well, you can modify the entries in the 'job' table.....As always, be
very careful when you directly access the MySQL or PostgreSQL database.
In your case I would set the state to 'error', eg:
update job set state='error' where id=123456789;
Once again be careful. I would examine each job individually. And try
to figure out, why you consider the job as being finished, and Galaxy
thinks the job is still running
Regards, Hans-Rudolf
Thanks for taking me further,
Joachim
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