Command Line Tool for Creating New Users
Hi, I'm trying to use the tool, however, when I run it I get: python create_galaxy_users.py Traceback (most recent call last): File "create_galaxy_users.py", line 2, in <module> from scripts.db_shell import * ImportError: No module named scripts.db_shell I've set my PYTHONPATH to be ~/galaxy-dist/lib. What else do I need to do? I'm running the script from ~/galaxy-dist/ directory, but I get the same error if I copy it into the scripts directory. I've checked and I can see that the scripts.db_shell.py script exists If I comment out the line then the next error I get is: python create_galaxy_users.py Traceback (most recent call last): File "create_galaxy_users.py", line 7, in <module> from galaxy.security import GalaxyRBACAgent File "/home/galaxy/galaxy-dist/lib/galaxy/security/__init__.py", line 9, in <module> from galaxy.model.orm import * File "/home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 15, in <module> from galaxy.security import RBACAgent, get_permitted_actions ImportError: cannot import name RBACAgent Any help much appreciated Neil ---------------------------------------------------------------------- Message: 1 Date: Sat, 27 Apr 2013 14:07:49 -0500 From: John Chilton <chilton@msi.umn.edu> To: Adam Brenner <aebrenne@uci.edu> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Command Line Tool for Creating New Users Message-ID: <CANwbokctvXO-DFmamr77FU6BbDHGR1STG7mpH_LP+fE2nMcnag@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 I put together a script to do this. It is described in the galaxy-dev thread titled: "[galaxy-dev] user creation using API". It doesn't actually use the API, it uses the db_shell.py script. Hope this helps. -John On Thu, Apr 25, 2013 at 7:11 PM, Adam Brenner <aebrenne@uci.edu> wrote:
Howdy All,
I was wondering if anyone has created a command line tool that will add users to the Galaxy user database?
I did look into switching to external user authentication via nginx, however, this will result in us using the campus wide kerberos system and allowing ~30,000 people access to Galaxy... and thus offering us less fine grain control to Galaxy.
Anything anyone has to share would be much appreciated, -Adam
-- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences
Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/
University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne@uci.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/
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Neil, AFAIK, python will not load a module unless the relevant script file is marked as executable by the current user? Try something like: chmod ugo+x scripts/db_shell.py and see if that fixes your problem? On Tue, Apr 30, 2013 at 11:50 AM, <Neil.Burdett@csiro.au> wrote:
Hi, I'm trying to use the tool, however, when I run it I get:
python create_galaxy_users.py
Traceback (most recent call last): File "create_galaxy_users.py", line 2, in <module> from scripts.db_shell import * ImportError: No module named scripts.db_shell
I've set my PYTHONPATH to be ~/galaxy-dist/lib. What else do I need to do? I'm running the script from ~/galaxy-dist/ directory, but I get the same error if I copy it into the scripts directory. I've checked and I can see that the scripts.db_shell.py script exists
If I comment out the line then the next error I get is:
python create_galaxy_users.py Traceback (most recent call last): File "create_galaxy_users.py", line 7, in <module> from galaxy.security import GalaxyRBACAgent File "/home/galaxy/galaxy-dist/lib/galaxy/security/__init__.py", line 9, in <module> from galaxy.model.orm import * File "/home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 15, in <module> from galaxy.security import RBACAgent, get_permitted_actions ImportError: cannot import name RBACAgent
Any help much appreciated
Neil ----------------------------------------------------------------------
Message: 1 Date: Sat, 27 Apr 2013 14:07:49 -0500 From: John Chilton <chilton@msi.umn.edu> To: Adam Brenner <aebrenne@uci.edu> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Command Line Tool for Creating New Users Message-ID: < CANwbokctvXO-DFmamr77FU6BbDHGR1STG7mpH_LP+fE2nMcnag@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1
I put together a script to do this. It is described in the galaxy-dev thread titled: "[galaxy-dev] user creation using API". It doesn't actually use the API, it uses the db_shell.py script.
Hope this helps.
-John
Thanks for the info Ross But I still get the same error "ImportError: No module named scripts.db_shell" After chmod 777 scripts/db_shell.py When you get "ImportError: No module named galaxy" for example it's because the PYTHONPATH isn't set so I guess there's some variable I need to set for the scripts directory??? Thanks anyway Neil From: Ross [mailto:ross.lazarus@gmail.com] Sent: Tuesday, 30 April 2013 12:00 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Command Line Tool for Creating New Users Neil, AFAIK, python will not load a module unless the relevant script file is marked as executable by the current user? Try something like: chmod ugo+x scripts/db_shell.py and see if that fixes your problem? On Tue, Apr 30, 2013 at 11:50 AM, <Neil.Burdett@csiro.au<mailto:Neil.Burdett@csiro.au>> wrote: Hi, I'm trying to use the tool, however, when I run it I get: python create_galaxy_users.py Traceback (most recent call last): File "create_galaxy_users.py", line 2, in <module> from scripts.db_shell import * ImportError: No module named scripts.db_shell I've set my PYTHONPATH to be ~/galaxy-dist/lib. What else do I need to do? I'm running the script from ~/galaxy-dist/ directory, but I get the same error if I copy it into the scripts directory. I've checked and I can see that the scripts.db_shell.py<http://scripts.db_shell.py> script exists If I comment out the line then the next error I get is: python create_galaxy_users.py Traceback (most recent call last): File "create_galaxy_users.py", line 7, in <module> from galaxy.security import GalaxyRBACAgent File "/home/galaxy/galaxy-dist/lib/galaxy/security/__init__.py", line 9, in <module> from galaxy.model.orm import * File "/home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 15, in <module> from galaxy.security import RBACAgent, get_permitted_actions ImportError: cannot import name RBACAgent Any help much appreciated Neil ---------------------------------------------------------------------- Message: 1 Date: Sat, 27 Apr 2013 14:07:49 -0500 From: John Chilton <chilton@msi.umn.edu<mailto:chilton@msi.umn.edu>> To: Adam Brenner <aebrenne@uci.edu<mailto:aebrenne@uci.edu>> Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" <galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>> Subject: Re: [galaxy-dev] Command Line Tool for Creating New Users Message-ID: <CANwbokctvXO-DFmamr77FU6BbDHGR1STG7mpH_LP+fE2nMcnag@mail.gmail.com<mailto:CANwbokctvXO-DFmamr77FU6BbDHGR1STG7mpH_LP%2BfE2nMcnag@mail.gmail.com>> Content-Type: text/plain; charset=ISO-8859-1 I put together a script to do this. It is described in the galaxy-dev thread titled: "[galaxy-dev] user creation using API". It doesn't actually use the API, it uses the db_shell.py script. Hope this helps. -John
Funny, it works for me. One last thought: You do still have the distributed __init__.py readable by your userid in /scripts so the module loader knows it's a python package directory? On Tue, Apr 30, 2013 at 12:05 PM, <Neil.Burdett@csiro.au> wrote:
Thanks for the info Ross****
** **
But I still get the same error****
** **
“ImportError: No module named scripts.db_shell”****
** **
After chmod 777 scripts/db_shell.py****
** **
When you get “ImportError: No module named galaxy” for example it’s because the PYTHONPATH isn’t set so I guess there’s some variable I need to set for the scripts directory???****
** **
Thanks anyway****
** **
Neil****
** **
*From:* Ross [mailto:ross.lazarus@gmail.com] *Sent:* Tuesday, 30 April 2013 12:00 PM *To:* Burdett, Neil (ICT Centre, Herston - RBWH) *Cc:* galaxy-dev@lists.bx.psu.edu
*Subject:* Re: [galaxy-dev] Command Line Tool for Creating New Users****
** **
Neil, ****
AFAIK, python will not load a module unless the relevant script file is marked as executable by the current user?****
Try something like:****
chmod ugo+x scripts/db_shell.py****
and see if that fixes your problem?****
** **
** **
On Tue, Apr 30, 2013 at 11:50 AM, <Neil.Burdett@csiro.au> wrote:****
Hi, I'm trying to use the tool, however, when I run it I get:
python create_galaxy_users.py
Traceback (most recent call last): File "create_galaxy_users.py", line 2, in <module> from scripts.db_shell import * ImportError: No module named scripts.db_shell
I've set my PYTHONPATH to be ~/galaxy-dist/lib. What else do I need to do? I'm running the script from ~/galaxy-dist/ directory, but I get the same error if I copy it into the scripts directory. I've checked and I can see that the scripts.db_shell.py script exists
If I comment out the line then the next error I get is:
python create_galaxy_users.py Traceback (most recent call last): File "create_galaxy_users.py", line 7, in <module> from galaxy.security import GalaxyRBACAgent File "/home/galaxy/galaxy-dist/lib/galaxy/security/__init__.py", line 9, in <module> from galaxy.model.orm import * File "/home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 15, in <module> from galaxy.security import RBACAgent, get_permitted_actions ImportError: cannot import name RBACAgent
Any help much appreciated
Neil ----------------------------------------------------------------------
Message: 1 Date: Sat, 27 Apr 2013 14:07:49 -0500 From: John Chilton <chilton@msi.umn.edu> To: Adam Brenner <aebrenne@uci.edu> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Command Line Tool for Creating New Users Message-ID: < CANwbokctvXO-DFmamr77FU6BbDHGR1STG7mpH_LP+fE2nMcnag@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1
I put together a script to do this. It is described in the galaxy-dev thread titled: "[galaxy-dev] user creation using API". It doesn't actually use the API, it uses the db_shell.py script.
Hope this helps.
-John
****
-- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
Thanks Ross. I was missing __init__.py It now works thanks Neil From: Ross [mailto:ross.lazarus@gmail.com] Sent: Tuesday, 30 April 2013 12:14 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Command Line Tool for Creating New Users Funny, it works for me. One last thought: You do still have the distributed __init__.py readable by your userid in /scripts so the module loader knows it's a python package directory? On Tue, Apr 30, 2013 at 12:05 PM, <Neil.Burdett@csiro.au<mailto:Neil.Burdett@csiro.au>> wrote: Thanks for the info Ross But I still get the same error "ImportError: No module named scripts.db_shell" After chmod 777 scripts/db_shell.py When you get "ImportError: No module named galaxy" for example it's because the PYTHONPATH isn't set so I guess there's some variable I need to set for the scripts directory??? Thanks anyway Neil From: Ross [mailto:ross.lazarus@gmail.com<mailto:ross.lazarus@gmail.com>] Sent: Tuesday, 30 April 2013 12:00 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Command Line Tool for Creating New Users Neil, AFAIK, python will not load a module unless the relevant script file is marked as executable by the current user? Try something like: chmod ugo+x scripts/db_shell.py and see if that fixes your problem? On Tue, Apr 30, 2013 at 11:50 AM, <Neil.Burdett@csiro.au<mailto:Neil.Burdett@csiro.au>> wrote: Hi, I'm trying to use the tool, however, when I run it I get: python create_galaxy_users.py Traceback (most recent call last): File "create_galaxy_users.py", line 2, in <module> from scripts.db_shell import * ImportError: No module named scripts.db_shell I've set my PYTHONPATH to be ~/galaxy-dist/lib. What else do I need to do? I'm running the script from ~/galaxy-dist/ directory, but I get the same error if I copy it into the scripts directory. I've checked and I can see that the scripts.db_shell.py<http://scripts.db_shell.py> script exists If I comment out the line then the next error I get is: python create_galaxy_users.py Traceback (most recent call last): File "create_galaxy_users.py", line 7, in <module> from galaxy.security import GalaxyRBACAgent File "/home/galaxy/galaxy-dist/lib/galaxy/security/__init__.py", line 9, in <module> from galaxy.model.orm import * File "/home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 15, in <module> from galaxy.security import RBACAgent, get_permitted_actions ImportError: cannot import name RBACAgent Any help much appreciated Neil ---------------------------------------------------------------------- Message: 1 Date: Sat, 27 Apr 2013 14:07:49 -0500 From: John Chilton <chilton@msi.umn.edu<mailto:chilton@msi.umn.edu>> To: Adam Brenner <aebrenne@uci.edu<mailto:aebrenne@uci.edu>> Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" <galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>> Subject: Re: [galaxy-dev] Command Line Tool for Creating New Users Message-ID: <CANwbokctvXO-DFmamr77FU6BbDHGR1STG7mpH_LP+fE2nMcnag@mail.gmail.com<mailto:CANwbokctvXO-DFmamr77FU6BbDHGR1STG7mpH_LP%2BfE2nMcnag@mail.gmail.com>> Content-Type: text/plain; charset=ISO-8859-1 I put together a script to do this. It is described in the galaxy-dev thread titled: "[galaxy-dev] user creation using API". It doesn't actually use the API, it uses the db_shell.py script. Hope this helps. -John -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
participants (2)
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Neil.Burdett＠csiro.au -
Ross