This thread prompted me to figure out why I couldn't empty my BASE2 trashcan.
Some items involved convoluted procedures:
Deleting a user involved undeleting it ('restore' in BASE2 parlance), logging
in as that user, deleting its home directory and default directories, empty
its trashcan, log out, then delete user again as administrator.
I had an annotation type which wasn't deleting. The "used item" page pointed
just to "Annotation [id=xxxx]" where the link was not functional. I managed
to find which sample was annotated with this annotation type by a similar
process as above - undeleting it, listing all samples matching '%' on this
annotation type in the sample list view.
I'm still stuck with one item which produces a stacktrace (see below). As
with Chad, it could result from some strange/unpredictable user and system
behaviour while installing/using new plugins.
many thanks,
Bob
Here's the problem item:
1. Plugin definition Batch Data Importer
(Note that I'm not bang up to date.)
Version BASE 2.4.2pre (build #3730; schema #40)
Web server Apache Tomcat/5.5.20
Database Server MySQL 5.0.21-max-log
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: 230.8 MB
Free: 67.2 MB
Max: 910.3 MB
Browser Mozilla/5.0 (Macintosh; U; Intel Mac OS X; en-US; rv:1.8.1.7)
Gecko/20070914 Firefox/2.0.0.7
Error message Cannot delete or update a parent row: a foreign key constraint
fails (`base2dev/Jobs`, CONSTRAINT `FK23507617401FCE` FOREIGN KEY
(`plugindefinition_id`) REFERENCES `PluginDefinitions` (`id`))
Stack trace
...at HibernateUtil.commit(HibernateUtil.java:910)
...at DbControl.commit(DbControl.java:393)
...at Trashcan.delete(Trashcan.java:229)
...at org.apache.jsp.views.trashcan.index_jsp._jspService(index_jsp.java:139)
...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:72)
...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.valves.AccessLogValve.invoke(AccessLogValve.java:541)
...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: com.mysql.jdbc.exceptions.MySQLIntegrityConstraintViolationException
...at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:931)
...at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2934)
...at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1616)
...at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1708)
...at com.mysql.jdbc.Connection.execSQL(Connection.java:3255)
...at
com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1293)
...at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1566)
...at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1480)
...at
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1465)
...at
com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:105)
...at
org.hibernate.persister.entity.AbstractEntityPersister.delete(AbstractEntityPersister.java:2523)
...at
org.hibernate.persister.entity.AbstractEntityPersister.delete(AbstractEntityPersister.java:2697)
...at
org.hibernate.action.EntityDeleteAction.execute(EntityDeleteAction.java:74)
...at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:250)
Nicklas Nordborg writes:
> Chad Matsalla wrote:
> > Nicklas wrote:
> >> Are you logged in as the user that is the owner of the experiment?
> >
> > I am logged in as root. Shouldn't root be able to delete anything?
>
> Yes, the root user can delete anything, but this is not a permission
> issue. It's just that the Trashcan can only list items that are owned by
> the logged in user.
>
> /Nicklas
>
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--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]
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