Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-08 Thread Nate Coraor 
This converts line endings to UNIX line endings, so in most cases it wouldn't 
break anything to not happen, however, if the uploaded file had DOS line 
endings, the uploaded file content would be wrong.

The best way to handle this is probably to change the ownership of the uploaded 
temporary file.  The code needs to be very careful not to change ownership of 
anything not uploaded by an actual user (i.e. files for "linking" or even 
copied in from the library side).

--nate

On Nov 7, 2011, at 11:12 AM, Chorny, Ilya wrote:

> I am not sure what the copy is for. I did not add the move/copy I just 
> changed shutil.mv to os.system(mv) because it has less baggage.  In fact if I 
> comment it out the upload still works.
> 
> Ilya
> 
> -Original Message-
> From: Nate Coraor [mailto:n...@bx.psu.edu] 
> Sent: Monday, November 07, 2011 7:57 AM
> To: Chorny, Ilya
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Looks like actual user breaks splitting
> 
> On Nov 4, 2011, at 8:03 PM, Chorny, Ilya wrote:
> 
>> 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.
> 
> Okay, I'll have a look.  What's the copy for?  We try to avoid moving bits as 
> much as possible during upload since it can slow down the entire upload tool 
> run pretty significantly if there are multiple copies taking place.
> 
> --nate
> 
>> 
>> 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_isA
>> nwO'; 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/.nfs0000000161e986fc0068' ': 
>> 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):
&

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-07 Thread Chorny, Ilya 
I am not sure what the copy is for. I did not add the move/copy I just changed 
shutil.mv to os.system(mv) because it has less baggage.  In fact if I comment 
it out the upload still works.

Ilya

-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu] 
Sent: Monday, November 07, 2011 7:57 AM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Looks like actual user breaks splitting

On Nov 4, 2011, at 8:03 PM, Chorny, Ilya wrote:

> 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.

Okay, I'll have a look.  What's the copy for?  We try to avoid moving bits as 
much as possible during upload since it can slow down the entire upload tool 
run pretty significantly if there are multiple copies taking place.

--nate

> 
> 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_isA
> nwO'; 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/.nfs000161e986fc0068' ': 
> 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 re

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-07 Thread Nate Coraor 
On Nov 4, 2011, at 8:03 PM, Chorny, Ilya wrote:

> 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.

Okay, I'll have a look.  What's the copy for?  We try to avoid moving bits as 
much as possible during upload since it can slow down the entire upload tool 
run pretty significantly if there are multiple copies taking place.

--nate

> 
> 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/.nfs000161e986fc0068' ': 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: [gala

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-07 Thread Nate Coraor 
On Nov 4, 2011, at 2:10 PM, Chorny, Ilya wrote:

> 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/.nfs000161e986fc0068' ': Device 
> or resource busy

This is an open file on NFS where the named file on the filesystem has been 
deleted.  Something must be holding the file open, we'd need to figure out what 
the file is.  Checking /proc//fd at the right moment might reveal the 
answer.

--nate

> 
> 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

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-04 Thread Chorny, Ilya 
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/.nfs000161e986fc0068' ': 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 wit

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-04 Thread Chorny, Ilya 
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/.nfs000161e986fc0068' ': 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:
> 
>

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-04 Thread Chorny, Ilya 
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/.nfs000161e986fc0068' ': 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

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-04 Thread Chorny, Ilya 
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 HistoryDatasetAssoc

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-04 Thread Chorny, Ilya 
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. St

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-04 Thread Chorny, Ilya 
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
> > > S

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-03 Thread Duddy, John 
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
> > &g

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-03 Thread Nate Coraor (n...@bx.psu.edu) 
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
> > > > 
> > > > 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
> > > >

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-03 Thread Nate Coraor (n...@bx.psu.edu) 
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.

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
> > > 
> > > 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
> > > Website: 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/

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-03 Thread Duddy, John 
I'm not following you - it's been 6 months since I wrote that code ;-}

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.

Do you have a stack trace for the merge problem I can look at?

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
> > 
> > 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
> > Website: 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/

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-03 Thread Nate Coraor (n...@bx.psu.edu) 
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
> > 
> > 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
> > Website: 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/

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-02 Thread Duddy, John 
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
> 
> 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
> Website: 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/

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-02 Thread Nate Coraor (n...@bx.psu.edu) 
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
> 
> 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
> Website: 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/

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-02 Thread Duddy, John 
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

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
Website: 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/