Hi Bob, Looks like there is a Job item that used the batch importer and therefore you cannot delete the plugin definition while the Job item still exists. Try deleting that job and it should go.
Cheers Micha ================================== Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.ac.uk/staff/michabayer ================================== > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:basedb-users- > [EMAIL PROTECTED] On Behalf Of Bob MacCallum > Sent: 08 October 2007 11:41 > To: BASE ML > Subject: Re: [base] problems with my trashcan > > > 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.j > ava: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(Applic > ationFilterChain.java:252) > ...at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFil > terChain.java:173) > ...at > net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(Char > acterEncodingFilter.java:72) > ...at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applic > ationFilterChain.java:202) > ...at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFil > terChain.java:173) > ...at > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperVal > ve.java:213) > ...at > org.apache.catalina.core.StandardContextValve.invoke(StandardContextVal > ve.java:178) > ...at > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.jav > a:126) > ...at > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.jav > a:105) > ...at > org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:54 > 1) > ...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:8 > 69) > ...at > org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.pro > cessConnection(Http11BaseProtocol.java:664) > ...at > org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoin > t.java:527) > ...at > org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollo > werWorkerThread.java:80) > ...at > org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPoo > l.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:1 > 566) > ...at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1 > 480) > ...at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1 > 465) > ...at > com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewPro > xyPreparedStatement.java:105) > ...at > org.hibernate.persister.entity.AbstractEntityPersister.delete(AbstractE > ntityPersister.java:2523) > ...at > org.hibernate.persister.entity.AbstractEntityPersister.delete(AbstractE > ntityPersister.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 > > > > -------------------------------------------------------------------- > ----- > > 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] > > -- > Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | > Division of Cell and Molecular Biology | Imperial College London | > Phone +442075941945 | Email [EMAIL PROTECTED] > > ----------------------------------------------------------------------- > -- > 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] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ SCRI, Invergowrie, Dundee, DD2 5DA. The Scottish Crop Research Institute is a charitable company limited by guarantee. Registered in Scotland No: SC 29367. Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. 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