Plier fails to import data
Summary from the BASE mailing list. The entire thread is available at: http://email@example.com/msg00778.html
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
net.sf.basedb.core.BaseException: Table 'base2dynamic.D2Spot' doesn't exist at net.sf.basedb.core.AbstractSqlQuery.iterate(AbstractSqlQuery.java:193) at net.sf.basedb.core.BioAssaySet.countSpotsAndReporters(BioAssaySet.java:1096) at net.sf.basedb.core.BioAssaySet.onBeforeCommit(BioAssaySet.java:315) at net.sf.basedb.core.DbControl.commit(DbControl.java:365) at se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(AbstractExternalBinaryPlugin.java:264) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:88) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420)
I think I partly know what is happening. There are two problems, the first causing the second.
- 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.
- 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...