Problem with cleaning up galaxy datasets
Dear all, I have a problem with the cleanup scripts on my local galaxy instance. I am using the updated cleanup_datasets.py, as per Nate's earlier reply here http://gmod.827538.n3.nabble.com/Problem-running-purge-datasets-sh-cleanup-s.... <http://gmod.827538.n3.nabble.com/Problem-running-purge-datasets-sh-cleanup-scripts-td3688016.html#none> This is the output I get when running cleanup_datasets.py: ~/ngs-bin/galaxy-dist $ scripts/cleanup_datasets/cleanup_datasets.py -d 2 -6 -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 82, in main ini_file = args[0] IndexError: list index out of range ... and this if I call it via the shell script cleanup_datasets.sh ~/ngs-bin/galaxy-dist $ scripts/cleanup_datasets/delete_datasets.sh 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 "/home/klausmetzeler/ngs-bin/galaxy-dist/lib/galaxy/model/mapping.py", line 1818, in init load_egg_for_url( url ) File "/home/klausmetzeler/ngs-bin/galaxy-dist/lib/galaxy/model/mapping.py", line 1798, in load_egg_for_url dialect = guess_dialect_for_url( url ) File "/home/klausmetzeler/ngs-bin/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' Any idea what might be wrong? Thanks a lot for your support, Klaus
Yes, you do not have a url like http://some_path or ssh://some_path defined in your config file. Look at the command-line options for your routines and figure out how it is finding your config file. It could be looking in the wrong place or you could have an error in the config file (missing piece or undefined variable which would default to False (a boolean). On 4/11/12, Klaus Metzeler <mail@klaus-metzeler.de> wrote:
Dear all,
I have a problem with the cleanup scripts on my local galaxy instance. I am using the updated cleanup_datasets.py, as per Nate's earlier reply here http://gmod.827538.n3.nabble.com/Problem-running-purge-datasets-sh-cleanup-s.... <http://gmod.827538.n3.nabble.com/Problem-running-purge-datasets-sh-cleanup-scripts-td3688016.html#none>
This is the output I get when running cleanup_datasets.py:
~/ngs-bin/galaxy-dist $ scripts/cleanup_datasets/cleanup_datasets.py -d 2 -6 -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 82, in main ini_file = args[0] IndexError: list index out of range
... and this if I call it via the shell script cleanup_datasets.sh
~/ngs-bin/galaxy-dist $ scripts/cleanup_datasets/delete_datasets.sh 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 "/home/klausmetzeler/ngs-bin/galaxy-dist/lib/galaxy/model/mapping.py", line 1818, in init load_egg_for_url( url ) File "/home/klausmetzeler/ngs-bin/galaxy-dist/lib/galaxy/model/mapping.py", line 1798, in load_egg_for_url dialect = guess_dialect_for_url( url ) File "/home/klausmetzeler/ngs-bin/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'
Any idea what might be wrong? Thanks a lot for your support, Klaus
OK, this pointed me to the right direction. The universe_wsgi.ini file has a key that reads: database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE This entry was commented out in my version of the file (ie, had a # in front of it). While Galaxy itself uses this database connection by default, but the cleanup script looks for this config file entry to locate the database. So, if anyone encounters the same problem, just un-comment this entry and all runs fine. Thanks for your help, Michael. Am 04/13/2012 08:43 PM, schrieb Michael Moore:
Yes, you do not have a url like http://some_path or ssh://some_path defined in your config file. Look at the command-line options for your routines and figure out how it is finding your config file. It could be looking in the wrong place or you could have an error in the config file (missing piece or undefined variable which would default to False (a boolean).
On 4/11/12, Klaus Metzeler<mail@klaus-metzeler.de> wrote:
Dear all,
I have a problem with the cleanup scripts on my local galaxy instance. I am using the updated cleanup_datasets.py, as per Nate's earlier reply here http://gmod.827538.n3.nabble.com/Problem-running-purge-datasets-sh-cleanup-s.... <http://gmod.827538.n3.nabble.com/Problem-running-purge-datasets-sh-cleanup-scripts-td3688016.html#none>
This is the output I get when running cleanup_datasets.py:
~/ngs-bin/galaxy-dist $ scripts/cleanup_datasets/cleanup_datasets.py -d 2 -6 -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 82, in main ini_file = args[0] IndexError: list index out of range
... and this if I call it via the shell script cleanup_datasets.sh
~/ngs-bin/galaxy-dist $ scripts/cleanup_datasets/delete_datasets.sh 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 "/home/klausmetzeler/ngs-bin/galaxy-dist/lib/galaxy/model/mapping.py", line 1818, in init load_egg_for_url( url ) File "/home/klausmetzeler/ngs-bin/galaxy-dist/lib/galaxy/model/mapping.py", line 1798, in load_egg_for_url dialect = guess_dialect_for_url( url ) File "/home/klausmetzeler/ngs-bin/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'
Any idea what might be wrong? Thanks a lot for your support, Klaus
Klaus, I'm getting this too. I tried yesterday fro the first time to clean up my local Galaxy data. (I was trying to purge all data and histories, ie. reset the database to as-new). This is in a Galaxy download and install done on 12 March 2012. I'd give you the hg -heads/summary and some other stats but I've deleted the dist. (I downloaded a complete new dist instead). I dodn't use the update mentioned below. Python is 2.6.1 on Mac OSX 10.6.8. Just checked, sh delete_userless_histories.sh produces the same error in the latest dist. Rgds, Greg On Wed, Apr 11, 2012 at 9:26 PM, Klaus Metzeler <mail@klaus-metzeler.de>wrote:
Dear all,
I have a problem with the cleanup scripts on my local galaxy instance. I am using the updated cleanup_datasets.py, as per Nate's earlier reply here
This is the output I get when running cleanup_datasets.py:
~/ngs-bin/galaxy-dist $ scripts/cleanup_datasets/cleanup_datasets.py -d 2 -6 -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 82, in main ini_file = args[0] IndexError: list index out of range
... and this if I call it via the shell script cleanup_datasets.sh
~/ngs-bin/galaxy-dist $ scripts/cleanup_datasets/delete_datasets.sh 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 "/home/klausmetzeler/ngs-bin/galaxy-dist/lib/galaxy/model/mapping.py", line 1818, in init load_egg_for_url( url ) File "/home/klausmetzeler/ngs-bin/galaxy-dist/lib/galaxy/model/mapping.py", line 1798, in load_egg_for_url dialect = guess_dialect_for_url( url ) File "/home/klausmetzeler/ngs-bin/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'
Any idea what might be wrong? Thanks a lot for your support, Klaus
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participants (3)
-
Greg Edwards -
Klaus Metzeler -
Michael Moore