Hello,

I finally managed to solve this issue. To restore the cleanup scripts I had to 'update' my universe_wsgi.ini file. In the old one the use of the database_connection field was disabled in presence of the standard sqlite database and there was a database_file field pointing to database/universe.sqlite. In the new universe_wsgi.ini the database_file field is no longer present and database_connection points to 'sqlite:///./database/universe.sqlite....'. The new cleanup scripts (probably?) identify the database in use by looking at the database_connection field, using the split(':', 1) function to retrieve the name of the database. In absence of the database_connection field the split function fails.

Thanks for pointing me in the right direction!

Regards,
Rocco

On Wed, 28 Mar 2012 09:07:55 -0400
 Emil Bouvier <d...@bx.psu.edu> wrote:
Rocco,

Are you running delete_datasets.sh from the base galaxy directory or scripts/cleanup_datasets?

From what I can tell, it's not finding your database configuration details in universe_wsgi.ini, which it looks for in the current directory.

    Dave B.

On 3/27/12 3:34 AM, rocco.piazza wrote:

Hello Jennifer,

thank you for your support.
The galaxy-dist I'm running is the March 2012 one. 'hg incoming' doesn't
give any further update. Python is 2.6.5.
Please, note that I can still delete datasets from the UI (if I click on the x button the dataset disappears and if I set Options->Show Deleted Datasets it reappears as a deleted dataset, as expected) however, if I try to purge (Options->Purge Deleted Datasets) it reports a '0 datasets have been deleted permanently' message with the deleted dataset happily
sitting in my history (still labeled as 'deleted').
Any help would be appreciated!

Regards,
Rocco


On Mon, 26 Mar 2012 14:25:43 -0700
   Jennifer Jackson <j...@bx.psu.edu> wrote:
Hi Rocco,

To help us get oriented, which galaxy-dist pull did you start from and which did you update to? If you have the release date/hg pull numbers, that would be great. If you need to reference, these are the prior
distributions:
http://wiki.g2.bx.psu.edu/DevNewsBriefs

Ideally, you would be current through the March 12, 2012 distribution, which included some bugs fixes for python 2.5 support. Support for
python 2.4 ended with the Nov 18, 2011 distribution.

If there is anything else customized about your system that you feel would be relevant (other odd behavior?), that would be good to send back. For example, can you delete and purge datasets through the UI?
Histories?

I am going to move your question over the galaxy-...@bx.psu.edu mailing list, which is the best place to reach the development community. The galaxy-user list is intended for data/tool usage
questions, with a focus on Galaxy main.
http://wiki.g2.bx.psu.edu/Support#Mailing_Lists

Please leave the galaxy-dev list in the "cc" for your return email,

Thanks!

Jen
Galaxy team


On 3/26/12 1:57 AM, rocco.piazza wrote:
Hello,

I'm working on a local instance of Galaxy-dist and I just
updated it. Right after the update I tried to run the
cleanup scripts. Unfortunately what I'm getting is the
following error:

# sh delete_datasets.sh -d 0 -r
Traceback (most recent call last):
     File "./scripts/cleanup_datasets/cleanup_datasets.py",
line 524, in <module>
       if __name__ == "__main__": main()
     File "./scripts/cleanup_datasets/cleanup_datasets.py",
line 101, in main
       app = CleanupDatasetsApplication( config )
     File "./scripts/cleanup_datasets/cleanup_datasets.py",
line 512, in __init__
       self.model = galaxy.model.mapping.init(
config.file_path, config.database_connection,
engine_options={}, create_tables=False,
object_store=self.object_store )
     File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1818, in init
       load_egg_for_url( url )
     File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1798, in load_egg_for_url
       dialect = guess_dialect_for_url( url )
     File
"/illumina/Galaxy/galaxy-dist/lib/galaxy/model/mapping.py",
line 1794, in guess_dialect_for_url
       return (url.split(':', 1))[0]
AttributeError: 'bool' object has no attribute 'split'

The same error occurs if I try to run other cleanup
scripts, such as the delete_datasets or purge_datasets.

Any idea to solve this issue?


Best regards,
Rocco
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