[galaxy-dev] unable to purge deleted datasets
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 datasetsFreed disk space: 0 I can't figure out what's wrong. Maybe a privilege problem or something else?? 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/
[galaxy-dev] purging deleted datasets
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/
Re: [galaxy-dev] purging deleted datasets
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.ba...@gmail.com To: mi.bast...@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.bast...@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/ ___ 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/
[galaxy-dev] error in workflow
Dear Galaxy Developers,I'm running galaxy local on ubuntu and trying to run a workflow on multiple datasets (separately). Occasionally when I try to run workflow on input dataset I get Unable to finish job error in some steps, in most time the problem will be solved when I run the workflow again, but this going to happen more frequently. I attached the error message here. I suspect it may be related to increase in number of datasets of the current history (1757 datasets with ~350GB size).I will appreciate your helpTraceback (most recent call last): File /media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 116, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File /media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/__init__.py, line 1068, in finish self.sa_session.flush() File /media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py, line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File /media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py, line 1718, in flush self._flush(objects) File /media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py, line 1804, in _flush transaction.commit() File /media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py, line 365, in commit t[1].commit() File /media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 2045, in commit self._do_commit() File /media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 2075, in _do_commit self.connection._commit_impl() File /media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1280, in _commit_impl self._handle_dbapi_exception(e, None, None, None, None) File /media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1277, in _commit_impl self.engine.dialect.do_commit(self.connection) File /media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py, line 307, in do_commit connection.commit() OperationalError: (OperationalError) database is locked None None ___ 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/
