On Wed, Aug 25, 2010 at 11:30:33AM -0400, Nate Coraor wrote:
The job_to_output_library_dataset is empty.
Okay, so job records were never created for these datasets. I am not sure why, though, it should have been done when the dataset objects themselves were created. Although your situation below may have been related.
Is there a chance that whatever dequeues import jobs is still trying to chew through those 12,000 entries despite the library having been deleted (the datasets aren't showing up as deleted)? There are no errors in the logs and zero system load, but 12K is a lot of imports to wait in line behind...
If you just deleted the library, there actually isn't anything that dequeues them. Are any jobs in a non-terminal state? That'd be 'new', 'upload' (although this state is only used for uploads through the browser), 'queued', 'running' or 'setting_metadata' (only used when 'Auto-Detect' is clicked).
All 24 jobs are in either ok, error, or deleted.
Could I safely clear out those queued datasets or am I playing with internal-referential-integrity fire at that point?
I'd update them all to 'discarded' and set the deleted column to True.
Done. I bounced the galaxy instance after doing so for good measure.
I tried importing a new single (big) fasta file and it's in a similar state. It shows up as queued in the admin interface, but isn't actually running - system load is zero.
I did get this error after clicking submit when importing, but since it looked 'view-level' I discounted it. The 'message' field was empty.
Error Traceback: View as: Interactive | Text | XML (full) ⇝ TypeError: 'NoneType' object is not iterable URL: http://galaxy.msi.umn.edu/library_common/upload_library_dataset Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view >> environ, self.app) Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:107 in __call__ view >> return self.app( environ, start_response ) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:145 in __call__ view >> body = method( trans, **kwargs ) Module galaxy.web.controllers.library_common:978 in upload_library_dataset view >> **kwd ) Module galaxy.web.controllers.library_common:1158 in upload_dataset view >> message=util.sanitize_text( message ), Module galaxy.util:138 in sanitize_text view >> for c in text: TypeError: 'NoneType' object is not iterable
could that be resulting in the stuff half-imported?
Thanks,