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.aumailto: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.commailto: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.edumailto: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.aumailto: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.pyhttp://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.edumailto:chilton@msi.umn.edu> To: Adam Brenner <aebrenne@uci.edumailto:aebrenne@uci.edu> Cc: "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto: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.commailto: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