Thank you for prompt reply. Yes I have deleted many datasets through history panel but the history itself is exist. Date: Wed, 23 Apr 2014 09:35:19 -0400 Subject: Re: [galaxy-dev] purging deleted datasets From: dannon.baker@gmail.com To: mi.bastami@live.com CC: galaxy-dev@lists.bx.psu.edu Hi Milad, That's just a warning, it should not cause any issues (I've just confirmed this locally on a sqlite instance). So you're sure you have histories with deleted datasets older than 0 days? The commands you have run will not remove datasets that haven't been deleted first by a user (usually through the history panel). -Dannon On Wed, Apr 23, 2014 at 9:21 AM, Milad Bastami <mi.bastami@live.com> wrote: Dear all,I have some unwanted datasets to remove but I need their main histories, so in galaxy I just deleted the unwanted datasets but not the histories. Then I tried to purge the deleted datasets with the following commands: python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 0 -6 -r python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 0 -3 -r and I saw the this error: /galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/types.py:215: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. Purged 0 datasetsFreed disk space: 0Elapsed time: 0.0748069286346 Unfortunately I can't understand the warning and why nothing was deleted. Any help would be most appreciated. ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

On Sat, Apr 26, 2014 at 12:52 AM, Milad Bastami <mi.bastami@live.com> wrote:

Hi all, Using two commands below, I am unable to purge deleted datasets (from a local instance of galaxy installed on ubuntu). I have deleted some datasets from the history panel and I want to purge only datasets not the history itself.

*commands:* *1. python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 0 -6 -r * *2. python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 0 -3 -r * *results:* Purged 0 datasets Freed disk space: 0

I can't figure out what's wrong. Maybe a privilege problem or something else?? Any help would be most appreciated.

Hi Milad, There's a simpler way to selectively purge datasets. If `allow_user_dataset_purge = True` in universe_wsgi.ini, you can use the "Include deleted datasets" history option to make those datasets visible, then use the "immediately remove from disk" link to purge the file. That said, if the process you've used is still not removing any datasets from disk, you may need to ensure that there are no undeleted instances of the datasets in question. Are those dataset shared or copied between histories? --nate

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