I am getting a strange error when I am uploading a file
mv: inter-device move failed: `/illumina/scratch/Swim/galaxy/tmpk2sbZl' to
`/home/galaxy/ichorny/galaxy-central/database/tmp/upload_file_data_isAnwO';
unable to remove target: Permission denied
I figured out that the mv is coming from
lib/galaxy/datatypes/sniff.py
if in_place:
fnamemode = stat.S_IMODE( os.stat(fname).st_mode )
os.system('mv %s %s' %(temp_name,fname))
# Return number of lines in file.
return ( i + 1, None )
else:
return ( i + 1, temp_name )
Any thoughts on what might be going on? If I comment out the move the upload
works just fine.
Thanks,
Ilya
-----Original Message-----
From: Chorny, Ilya
Sent: Friday, November 04, 2011 11:11 AM
To: Chorny, Ilya; Nate Coraor (n...@bx.psu.edu); Duddy, John
Cc: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Looks like actual user breaks splitting
Well I think I figured out why we get OSError: [Errno 39] Directory not empty:
'./database/job_working_directory/451'. I changed it to an rm -rf and got the
following error:
`./database/job_working_directory/455/.nfs0000000161e986fc00000068' ': Device
or resource busy
It might have something to do with our mounts being Isilon. Any thought on how
to deal with this?
-----Original Message-----
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
Sent: Friday, November 04, 2011 10:50 AM
To: Nate Coraor (n...@bx.psu.edu)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Looks like actual user breaks splitting
I came up with a fix for User killed running job, but error encountered
removing from DRM queue: 'DRMAAJobRunner' object has no attribute
'job_user_uid' and pushed it.
-----Original Message-----
From: Chorny, Ilya
Sent: Friday, November 04, 2011 10:24 AM
To: Chorny, Ilya; Nate Coraor (n...@bx.psu.edu)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Looks like actual user breaks splitting
I am also getting the following error in the log file which makes no sense
because the directory is empty. I will try to track it down. Thoughts?
Ilya
Traceback (most recent call last):
File "/home/galaxy/ichorny/galaxy-central/lib/galaxy/jobs/__init__.py", line
732, in cleanup
shutil.rmtree( self.working_directory )
File "/usr/lib64/python2.6/shutil.py", line 225, in rmtree
onerror(os.rmdir, path, sys.exc_info())
File "/usr/lib64/python2.6/shutil.py", line 223, in rmtree
os.rmdir(path)
OSError: [Errno 39] Directory not empty: './database/job_working_directory/451'
-----Original Message-----
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
Sent: Friday, November 04, 2011 9:07 AM
To: Duddy, John; Nate Coraor (n...@bx.psu.edu)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Looks like actual user breaks splitting
Nate,
I get the following error when I try to kill a job.
User killed running job, but error encountered removing from DRM queue:
'DRMAAJobRunner' object has no attribute 'job_user_uid'.
Ilya
-----Original Message-----
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Duddy, John
Sent: Thursday, November 03, 2011 3:55 PM
To: Nate Coraor (n...@bx.psu.edu)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Looks like actual user breaks splitting
I just came to that conclusion myself. If you need me to do anything, let me
know - but it sounds like you have a handle on it.
Muchas gracias.
John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.com
-----Original Message-----
From: Nate Coraor (n...@bx.psu.edu) [mailto:n...@bx.psu.edu]
Sent: Thursday, November 03, 2011 3:53 PM
To: Duddy, John
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Looks like actual user breaks splitting
Nate Coraor (n...@bx.psu.edu) wrote:
> Duddy, John wrote:
> > I'm not following you - it's been 6 months since I wrote that code
> > ;-}
>
> I know the feeling!
>
> > IT looks to me like a DatasetPath() object is always placed in that array,
> > and with one exception near then, it looks like the change I made generates
> > those objects the same way.
>
> It's creating a dict in self.output_dataset_paths, and that dict looks
> like this when outputs_to_working_directory = False:
>
> { output_param_name : [ HDA, DatasetPath ], ... }
>
> And this when True:
>
> { output_param_name : [ Dataset, DatasetPath ], ... }
>
> > Do you have a stack trace for the merge problem I can look at?
>
> If you put this in do_merge()'s except block:
>
> log.exception( stdout )
>
> You'll get:
>
> Traceback (most recent call last):
> File
> "/space/nate/galaxy-central-ichorny/lib/galaxy/jobs/splitters/multi.py", line
> 128, in do_merge
> output_type = outputs[output][0].datatype
> AttributeError: 'Dataset' object has no attribute 'datatype'
>
> I could just change both methods to put an HDA in the list inside the
> dict there, but I haven't looked much into what output_dataset_paths
> is used for, so I wasn't sure what that might break.
Sorta answered it myself, it looks like you created this precisely for
do_merge(), so changing it to contain the HDA fixes the problem (and shouldn't
break anything else).
--nate
>
> Thanks,
> --nate
>
> > John Duddy
> > Sr. Staff Software Engineer
> > Illumina, Inc.
> > 9885 Towne Centre Drive
> > San Diego, CA 92121
> > Tel: 858-736-3584
> > E-mail: jdu...@illumina.com
> >
> >
> > -----Original Message-----
> > From: Nate Coraor (n...@bx.psu.edu) [mailto:n...@bx.psu.edu]
> > Sent: Thursday, November 03, 2011 2:22 PM
> > To: Duddy, John
> > Cc: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu
> > Subject: Re: Looks like actual user breaks splitting
> >
> > Hi John,
> >
> > It looks like the first issue is related to the change from
> > get_output_fnames() -> compute_outputs(). When
> > outputs_to_working_directory = False (default) this method
> > stores/returns a HistoryDatasetAssociation, but when True,
> > stores/returns a Dataset (the original method's behavior). Thus,
> > accessing the object's .datatype attribute in the splitter's
> > do_merge() fails.
> >
> > Thanks,
> > --nate
> >
> > Duddy, John wrote:
> > > I'll submit a pull request shortly...
> > >
> > > John Duddy
> > > Sr. Staff Software Engineer
> > > Illumina, Inc.
> > > 9885 Towne Centre Drive
> > > San Diego, CA 92121
> > > Tel: 858-736-3584
> > > E-mail: jdu...@illumina.com
> > >
> > >
> > > -----Original Message-----
> > > From: Nate Coraor (n...@bx.psu.edu) [mailto:n...@bx.psu.edu]
> > > Sent: Wednesday, November 02, 2011 12:24 PM
> > > To: Duddy, John
> > > Cc: Chorny, Ilya; galaxy-dev@lists.bx.psu.edu
> > > Subject: Re: Looks like actual user breaks splitting
> > >
> > > John, Ilya,
> > >
> > > I get further with sequence type inputs but it looks like
> > > JobWrapper.get_output_datasets_and_fnames() is not returning the
> > > right thing when outputs_to_working_directory = True
> > >
> > > BTW, the base Data.split() method is broken after the updates to
> > > Sequence.split() since it wasn't updated to expect
> > > HistoryDatasetAssociations rather than filenames. Could you take
> > > a look at that when you get a chance?
> > >
> > > --nate
> > >
> > > Duddy, John wrote:
> > > > The datatype you are using does not define a split method. Are you
> > > > working with our in-progress gz type or fastqillumina?
> > > >
> > > > John Duddy
> > > > Sr. Staff Software Engineer
> > > > Illumina, Inc.
> > > > 9885 Towne Centre Drive
> > > > San Diego, CA 92121
> > > > Tel: 858-736-3584
> > > > E-mail: jdu...@illumina.com<mailto:jdu...@illumina.com>
> > > >
> > > > From: Chorny, Ilya
> > > > Sent: Wednesday, November 02, 2011 11:50 AM
> > > > To: Duddy, John
> > > > Cc: Nate Coraor (n...@bx.psu.edu); galaxy-dev@lists.bx.psu.edu
> > > > Subject: Looks like actual user breaks splitting
> > > >
> > > > Hey John,
> > > >
> > > > Any thoughts?
> > > >
> > > > Ilya
> > > >
> > > > Traceback (most recent call last):
> > > > File
> > > > "/home/galaxy/ichorny/galaxy-central/lib/galaxy/jobs/runners/tasks.py",
> > > > line 73, in run_job
> > > > tasks = splitter.do_split(job_wrapper)
> > > > File
> > > > "/home/galaxy/ichorny/galaxy-central/lib/galaxy/jobs/splitters/multi.py",
> > > > line 73, in do_split
> > > > input_type.split(input_datasets, get_new_working_directory_name,
> > > > parallel_settings)
> > > > File
> > > > "/home/galaxy/ichorny/galaxy-central/lib/galaxy/datatypes/data.py",
> > > > line 473, in split
> > > > raise Exception("Text file splitting does not support
> > > > multiple files")
> > > > Exception: Text file splitting does not support multiple files
> > > >
> > > > Ilya Chorny Ph.D.
> > > > Bioinformatics Scientist I
> > > > Illumina, Inc.
> > > > 9885 Towne Centre Drive
> > > > San Diego, CA 92121
> > > > Work: 858.202.4582
> > > > Email: icho...@illumina.com<mailto:icho...@illumina.com>
> > > > Website: www.illumina.com<http://www.illumina.com>
> > > >
> > > >
> > >
> >
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