exception while emptying trash (experiment and raw bioassays)

[base]

Just got this error while emptying the trash.

The trash contained a mix of items (including an Experiment and its Raw BioAssays). I will try deleting from "top down" to see if I can empty the trash.

Experiment first, then raw bioassays works fine, although the 57 bioassays take some time.

I tagged it "major" because this would throw a novice user.

cheers, Bob (again!)

Experiment   
Options…   
Unexpected error
BaseException on page /base2dev/views/trashcan/index.jsp
	
Version 	BASE 2.2.2 (build #3172; schema #30)
Web server 	Apache Tomcat/5.5.20
Database Dialect 	org.hibernate.dialect.MySQLInnoDBDialect
JDBC Driver 	com.mysql.jdbc.Driver (version 5.0)
Java runtime 	Java(TM) SE Runtime Environment (1.6.0-b105), Sun Microsystems Inc.
Operating system 	Linux amd64 2.6.16.27-0.9-smp
Memory 	Total: 483.3 MB
Free: 244.0 MB
Max: 910.3 MB
Browser 	Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; en-US; rv:1.8.0.11) Gecko/20070312 Firefox/1.5.0.11
Error message 	Row was updated or deleted by another transaction (or unsaved-value mapping was incorrect): [net.sf.basedb.core.data.BioAssayData#205]
Stack trace 	

...at HibernateUtil.flush(HibernateUtil.java:936)
...at DbControl.commit(DbControl.java:378)
...at org.apache.jsp.views.trashcan.index_jsp.removeItems(index_jsp.java:74)
...at org.apache.jsp.views.trashcan.index_jsp._jspService(index_jsp.java:314)
...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:334)
...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)

...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:71)
...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
...at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
...at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
...at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
...at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
...at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
...at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664)
...at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
...at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
...at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
...at java.lang.Thread.run(Thread.java:619)

Caused by: org.hibernate.StaleObjectStateException
...at org.hibernate.persister.entity.AbstractEntityPersister.check(AbstractEntityPersister.java:1761)
...at org.hibernate.persister.entity.AbstractEntityPersister.delete(AbstractEntityPersister.java:2519)
...at org.hibernate.persister.entity.AbstractEntityPersister.delete(AbstractEntityPersister.java:2693)
...at org.hibernate.action.EntityDeleteAction.execute(EntityDeleteAction.java:74)
...at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:248)
...at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:232)
...at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:144)
...at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298)
...at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
...at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
...at HibernateUtil.flush(HibernateUtil.java:932)
...at DbControl.commit(DbControl.java:378)
...at org.apache.jsp.views.trashcan.index_jsp.removeItems(index_jsp.java:74)
...at org.apache.jsp.views.trashcan.index_jsp._jspService(index_jsp.java:314)
...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:334)
...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)
...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:71)
...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
...at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
...at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
...at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
...at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
...at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
...at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664)
...at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
...at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
...at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
...at java.lang.Thread.run(Thread.java:619)