What script updates the umask of database/files/* and deletes database/job_working_directory
When running as the actual user in drama, I made it so the .dat files are not initially created so that when a tool moves data from the a temp directory to the out .dat file it will not fail. (i.e. unix does not allow moving a file owned by one user to a file owned by another user because mv carries the attributes of the original file). Now I want to change the ownership of the files through a sudo call at the end. Which script is run at the end to clean things up?
Thanks,
Ilya
Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.commailto:ichorny@illumina.com Website: www.illumina.comhttp://www.illumina.com
So I figured out that it is job/runners/__init__.py that does the cleanup. But now I can't figure out how to pass the galaxy username to my script to change the permission back. I thought os.getlogin() would give me the right username but it returns my user name and not the galaxy user. Thoughts?
Thanks,
Ilya
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Tuesday, August 23, 2011 1:46 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] What script updates the umask of database/files/* and deletes database/job_working_directory
When running as the actual user in drama, I made it so the .dat files are not initially created so that when a tool moves data from the a temp directory to the out .dat file it will not fail. (i.e. unix does not allow moving a file owned by one user to a file owned by another user because mv carries the attributes of the original file). Now I want to change the ownership of the files through a sudo call at the end. Which script is run at the end to clean things up?
Thanks,
Ilya
Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.commailto:ichorny@illumina.com Website: www.illumina.comhttp://www.illumina.com
Hi Ilya,
Sorry, I haven't yet had a chance to check out your code. Are you using the username column of the user table to determine the local username? This would then be job.user.username.
--nate
Chorny, Ilya wrote:
So I figured out that it is job/runners/__init__.py that does the cleanup. But now I can't figure out how to pass the galaxy username to my script to change the permission back. I thought os.getlogin() would give me the right username but it returns my user name and not the galaxy user. Thoughts?
Thanks,
Ilya
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Tuesday, August 23, 2011 1:46 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] What script updates the umask of database/files/* and deletes database/job_working_directory
When running as the actual user in drama, I made it so the .dat files are not initially created so that when a tool moves data from the a temp directory to the out .dat file it will not fail. (i.e. unix does not allow moving a file owned by one user to a file owned by another user because mv carries the attributes of the original file). Now I want to change the ownership of the files through a sudo call at the end. Which script is run at the end to clean things up?
Thanks,
Ilya
Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.commailto:ichorny@illumina.com Website: www.illumina.comhttp://www.illumina.com
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Chorny, Ilya -
Nate Coraor