Hi Sergio, We are looking in to this problem but have difficulty to reproduce the error. We have tested the plier plugin with apt v1.6. Are you using the latest apt release (1.8)? (Do 'apt-probeset-summarize --version' to get the version information.)
Do you get a new (visible) node in the analysis tree in BASE after running the plugin? We would be happy if we could move this discussion to the ticket related to this issue. Add comments to http://baseplugins.thep.lu.se/ticket/73 but remember to login as base/base to add comments. Cheers, Jari Nicklas Nordborg wrote: > Sergio Contrino wrote: >> dear nicklas, >> thank you for the prompt answer and apologies for the lack of info. >> here the info requested. >> thank you >> sergio >> >> i am running a test base 2.3.2 on mysql 5.1.14-beta (i must apologies >> again, i was thinking to be running on the reccomended 5.0) >> >> the stack (as in base report) is > > I think I partly know what is happening. There are two problems, the > first causing the second. > > 1. The Plier plugin is creating a root bioassayset but is never > inserting any data to it. If no data is inserted, then the missing table > isn't created. > > 2. Before everything is committed to the database the root bioassayset > tries to count the number spots that has been inserted. This fails > because the table isn't there and there is no check if it exists at this > place. > > Number 2 is a bug in the BASE core and should be easy to fix. This will > be included in the 2.4 release in about two weeks. > > Why number 1 is happening is hard to tell. The Plier plug-in seems to > execute without errors. Maybe there is something wrong with the output > from the the 'apt-probeset-summarize' program. In that case, the plug-in > will just ignore it and continue without inserting any data. I guess the > developer of the Plier plug-in knows more about this... > > I'll add a ticket to the BASE plug-ins site about #1. > > /Nicklas > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] -- Jari Hakkinen, PhD Complex Systems Division mailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Solvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
