Looks like the mv is something I added and forgot about. I changed it to 
shutil.copyfile and it works fine. This also has something to do with the 
isilon. I pushed it to the actual user repository  so you can check it out.

Have a good weekend. 

Thanks,

Ilya


-----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 4:50 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 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>
> > > > 
> > > > 
> > > 
> > 
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this and other 
> Galaxy lists, please use the interface at:
> 
>   http://lists.bx.psu.edu/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this and other Galaxy 
lists, please use the interface at:

  http://lists.bx.psu.edu/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this and other Galaxy 
lists, please use the interface at:

  http://lists.bx.psu.edu/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this and other Galaxy 
lists, please use the interface at:

  http://lists.bx.psu.edu/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this and other Galaxy 
lists, please use the interface at:

  http://lists.bx.psu.edu/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to