Hey, Getting a fresh copy of the distribution worked! Whatever you did thanks! No more file path error. Things are working good. Victor sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini [sudo] password for victor: Adding standard forms and requests for sequencing Creating potential sample states Adding standard sequencing controls Creating form for sequencing results On Oct 8, 2010, at 9:23 AM, Nate Coraor wrote:
Victor Ruotti wrote:
Thanks Brad. Did an hq pull and hq update.
Looks like its looking for the file_path. Do I set this in the universe_wsgi.ini and what should I set to? thanks Victor
galaxy-central > sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 367, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 62, in main app = SimpleApp(db_con, config['file_path']) KeyError: 'file_path'
Just a heads up to Brad,
I recently changed galaxy.config so that almost everything that was "set" in universe_wsgi.ini was correctly defined as a default in the config, and then I commented out all of those values. The hope is that it makes it easier to maintain your config file against the sample as the sample changes over time. However, it means that a lot of the things your script expects to be defined aren't defined, so you may need to load galaxy.config yourself to access the defaults.
--nate
On Oct 8, 2010, at 6:55 AM, Brad Chapman wrote:
Victor;
Using the central repository with a newer version of python and the virtual env Peter suggested all worked out great.
I was able to create a request form and sample form from the admin section. Now I can create a new sequencing request and use it to add samples etc. All this looked very good!
Awesome. Great to hear it.
Now when I do this 3. Add configured request types, forms and sample states to the database:
$ python scripts/nglims/add_ng_defaults.py universe_wsgi.ini I get,
galaxy-central > sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 363, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 57, in main db_con = "sqlite:///%s?isolation_level=IMMEDIATE" % config["database_file"] KeyError: 'database_file'
It looks like database_connection isn't set in your universe_wsgi.ini. If you update the repository (hg pull; hg update) or grab the latest script I added a fix for this case:
http://bitbucket.org/chapmanb/galaxy-central/src/tip/scripts/nglims/add_ng_d...
You may also want to explicitly set the connection in the configuration file as a more general solution.
Let us know if you run into any other problems. Thanks much, Brad _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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