Upload via FTP - Assertion Error on Change ownership of working dictory

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Upload via FTP - Assertion Error on Change ownership of working dictory

Adam Brenner
Howdy,

I am having trouble uploading data on our local instance of Galaxy
here. The method is via FTP and here is the error I am seeing in the
logs:


galaxy.jobs.runners DEBUG 2014-01-30 14:29:31,987 execution of
external set_meta for job 1367 finished
galaxy.jobs DEBUG 2014-01-30 14:29:32,016 (1367) Changing ownership of
working directory with: /usr/bin/sudo -E
scripts/external_chown_script.py
/som/galaxy/database/job_working_directory/001/1367 root 0
galaxy.jobs ERROR 2014-01-30 14:29:32,058 (1367) Failed to change
ownership of /som/galaxy/database/job_working_directory/001/1367,
failing
Traceback (most recent call last):
  File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line 870, in finish
    self.reclaim_ownership()
  File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line
1316, in reclaim_ownership
    self._change_ownership( self.galaxy_system_pwent[0], str(
self.galaxy_system_pwent[3] ) )
  File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line
1302, in _change_ownership
    assert p.returncode == 0
AssertionError


Any idea on how to fix the issue?
Thanks,
-Adam

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

System Administrator, HPC Cluster
Office of Information Technology
http://hpc.oit.uci.edu/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
[hidden email]
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Re: Upload via FTP - Assertion Error on Change ownership of working dictory

Adam Brenner
Anyone have any ideas on this?

Thanks,
-Adam


--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

System Administrator, HPC Cluster
Office of Information Technology
http://hpc.oit.uci.edu/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
[hidden email]


On Thu, Jan 30, 2014 at 2:33 PM, Adam Brenner <[hidden email]> wrote:

> Howdy,
>
> I am having trouble uploading data on our local instance of Galaxy
> here. The method is via FTP and here is the error I am seeing in the
> logs:
>
>
> galaxy.jobs.runners DEBUG 2014-01-30 14:29:31,987 execution of
> external set_meta for job 1367 finished
> galaxy.jobs DEBUG 2014-01-30 14:29:32,016 (1367) Changing ownership of
> working directory with: /usr/bin/sudo -E
> scripts/external_chown_script.py
> /som/galaxy/database/job_working_directory/001/1367 root 0
> galaxy.jobs ERROR 2014-01-30 14:29:32,058 (1367) Failed to change
> ownership of /som/galaxy/database/job_working_directory/001/1367,
> failing
> Traceback (most recent call last):
>   File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line 870, in finish
>     self.reclaim_ownership()
>   File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line
> 1316, in reclaim_ownership
>     self._change_ownership( self.galaxy_system_pwent[0], str(
> self.galaxy_system_pwent[3] ) )
>   File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line
> 1302, in _change_ownership
>     assert p.returncode == 0
> AssertionError
>
>
> Any idea on how to fix the issue?
> Thanks,
> -Adam
>
> --
> Adam Brenner
> Computer Science, Undergraduate Student
> Donald Bren School of Information and Computer Sciences
>
> System Administrator, HPC Cluster
> Office of Information Technology
> http://hpc.oit.uci.edu/
>
> University of California, Irvine
> www.ics.uci.edu/~aebrenne/
> [hidden email]
___________________________________________________________
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/

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Re: Upload via FTP - Assertion Error on Change ownership of working dictory

Eric Rasche
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Looks like a permission issue. Is your FTP server set to use the same
user/group as galaxy?

For reference: my proftpd is configured to use LDAP user information,
but then it forces the user/group id of uploaded files to be that of galaxy

        # Force those numbers even if LDAP finds a valid UID/GID
        LDAPDefaultUID          {galaxy's UID}
        LDAPDefaultGID          {galaxy group GID}


Hope that helps



On 02/03/2014 11:23 AM, Adam Brenner wrote:

> Anyone have any ideas on this?
>
> Thanks,
> -Adam
>
>
> --
> Adam Brenner
> Computer Science, Undergraduate Student
> Donald Bren School of Information and Computer Sciences
>
> System Administrator, HPC Cluster
> Office of Information Technology
> http://hpc.oit.uci.edu/
>
> University of California, Irvine
> www.ics.uci.edu/~aebrenne/
> [hidden email]
>
>
> On Thu, Jan 30, 2014 at 2:33 PM, Adam Brenner <[hidden email]> wrote:
>> Howdy,
>>
>> I am having trouble uploading data on our local instance of Galaxy
>> here. The method is via FTP and here is the error I am seeing in the
>> logs:
>>
>>
>> galaxy.jobs.runners DEBUG 2014-01-30 14:29:31,987 execution of
>> external set_meta for job 1367 finished
>> galaxy.jobs DEBUG 2014-01-30 14:29:32,016 (1367) Changing ownership of
>> working directory with: /usr/bin/sudo -E
>> scripts/external_chown_script.py
>> /som/galaxy/database/job_working_directory/001/1367 root 0
>> galaxy.jobs ERROR 2014-01-30 14:29:32,058 (1367) Failed to change
>> ownership of /som/galaxy/database/job_working_directory/001/1367,
>> failing
>> Traceback (most recent call last):
>>   File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line 870, in finish
>>     self.reclaim_ownership()
>>   File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line
>> 1316, in reclaim_ownership
>>     self._change_ownership( self.galaxy_system_pwent[0], str(
>> self.galaxy_system_pwent[3] ) )
>>   File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line
>> 1302, in _change_ownership
>>     assert p.returncode == 0
>> AssertionError
>>
>>
>> Any idea on how to fix the issue?
>> Thanks,
>> -Adam
>>
>> --
>> Adam Brenner
>> Computer Science, Undergraduate Student
>> Donald Bren School of Information and Computer Sciences
>>
>> System Administrator, HPC Cluster
>> Office of Information Technology
>> http://hpc.oit.uci.edu/
>>
>> University of California, Irvine
>> www.ics.uci.edu/~aebrenne/
>> [hidden email]
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>

- --
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
404-692-2048
[hidden email]
[hidden email]
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___________________________________________________________
Please keep all replies on the list by using "reply all"
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Re: Upload via FTP - Assertion Error on Change ownership of working dictory

Adam Brenner
Thanks for the tip Eric. I was able to figure it out. The key to this,
was you suggested was permission issue.

I had to modify sudoers so tty was not required. This will allow
scripts to change ownership to the correct user so SGE can submit
them.

Thanks!
-Adam

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

System Administrator, HPC Cluster
Office of Information Technology
http://hpc.oit.uci.edu/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
[hidden email]


On Mon, Feb 3, 2014 at 9:57 AM, Eric Rasche <[hidden email]> wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Looks like a permission issue. Is your FTP server set to use the same
> user/group as galaxy?
>
> For reference: my proftpd is configured to use LDAP user information,
> but then it forces the user/group id of uploaded files to be that of galaxy
>
>         # Force those numbers even if LDAP finds a valid UID/GID
>         LDAPDefaultUID          {galaxy's UID}
>         LDAPDefaultGID          {galaxy group GID}
>
>
> Hope that helps
>
>
>
> On 02/03/2014 11:23 AM, Adam Brenner wrote:
>> Anyone have any ideas on this?
>>
>> Thanks,
>> -Adam
>>
>>
>> --
>> Adam Brenner
>> Computer Science, Undergraduate Student
>> Donald Bren School of Information and Computer Sciences
>>
>> System Administrator, HPC Cluster
>> Office of Information Technology
>> http://hpc.oit.uci.edu/
>>
>> University of California, Irvine
>> www.ics.uci.edu/~aebrenne/
>> [hidden email]
>>
>>
>> On Thu, Jan 30, 2014 at 2:33 PM, Adam Brenner <[hidden email]> wrote:
>>> Howdy,
>>>
>>> I am having trouble uploading data on our local instance of Galaxy
>>> here. The method is via FTP and here is the error I am seeing in the
>>> logs:
>>>
>>>
>>> galaxy.jobs.runners DEBUG 2014-01-30 14:29:31,987 execution of
>>> external set_meta for job 1367 finished
>>> galaxy.jobs DEBUG 2014-01-30 14:29:32,016 (1367) Changing ownership of
>>> working directory with: /usr/bin/sudo -E
>>> scripts/external_chown_script.py
>>> /som/galaxy/database/job_working_directory/001/1367 root 0
>>> galaxy.jobs ERROR 2014-01-30 14:29:32,058 (1367) Failed to change
>>> ownership of /som/galaxy/database/job_working_directory/001/1367,
>>> failing
>>> Traceback (most recent call last):
>>>   File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line 870, in finish
>>>     self.reclaim_ownership()
>>>   File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line
>>> 1316, in reclaim_ownership
>>>     self._change_ownership( self.galaxy_system_pwent[0], str(
>>> self.galaxy_system_pwent[3] ) )
>>>   File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line
>>> 1302, in _change_ownership
>>>     assert p.returncode == 0
>>> AssertionError
>>>
>>>
>>> Any idea on how to fix the issue?
>>> Thanks,
>>> -Adam
>>>
>>> --
>>> Adam Brenner
>>> Computer Science, Undergraduate Student
>>> Donald Bren School of Information and Computer Sciences
>>>
>>> System Administrator, HPC Cluster
>>> Office of Information Technology
>>> http://hpc.oit.uci.edu/
>>>
>>> University of California, Irvine
>>> www.ics.uci.edu/~aebrenne/
>>> [hidden email]
>> ___________________________________________________________
>> 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/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
> - --
> Eric Rasche
> Programmer II
> Center for Phage Technology
> Texas A&M University
> College Station, TX 77843
> 404-692-2048
> [hidden email]
> [hidden email]
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> -----END PGP SIGNATURE-----
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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:
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To search Galaxy mailing lists use the unified search at:
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