Hello, Nate Coraor wrote, On 01/27/2009 01:22 PM:
Assaf Gordon wrote:
What I currently do is stop the server, Manually reset the jobs, with the following SQL command: UPDATE job set state='error' where state='new' ; There are some side-effects to this operation, as there are no running/waiting jobs but the history-list pane still shows running/waiting jobs.
These should go away if you refresh the history pane? If not, there is something Very Wrong here.
Well, my Galaxy database is definitely a mess. It had endured many crashes and exceptions, some of them happening in the middle of long workflows which left some jobs waiting on other non-existing jobs and datasets... So I'm guessing that most of what I'm seeing wouldn't really happen in a stable galaxy installation. However, there are two issues I've found which affect the perceived stability... First, the 'state' column in the DATASET table, regardless of the 'state' column in the JOB table. Stopping and Re-Starting Galaxy while there are DATASET marked as 'running' somehow affect the jobs (or maybe I just imagined it?). It might also affect the number of datasets as reported in the history pane - That is - in the DATASET table has datasets marked as 'new' / 'running' they will appear as new (grey) / running (yellow) even if there are no jobs running/waiting. Second, The 'visible' and 'deleted' columns in the HISTORY_DATASET_ASSOCIATION table. I somehow got into a situation where I had a row in that table with: INFO field = "Unable to Finish Job", DELETED field = FALSE, VISIBLE field = FALSE. That dataset appeared as an error (red box) in the history list, but when the user switched to that history, he (obviously) didn't see any red boxes (I guess because of VISIBLE=FALSE). very confusing indeed. I've removed all the 'running' things (datasets / jobs) and re-started Galaxy - I hope things will calm down now. Thanks for all your help. Gordon.