And as if by magic... that worked! Thanks Micha. Micha Bayer writes: > 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. It may not be disclosed or used by any other than that addressee. > If you are not the intended recipient you are requested to preserve this > confidentiality and you must not use, disclose, copy, print or rely on this > e-mail in any way. Please notify [EMAIL PROTECTED] quoting the > name of the sender and delete the email from your system. > > Although SCRI has taken reasonable precautions to ensure no viruses are > present in this email, neither the Institute nor the sender accepts any > responsibility for any viruses, and it is your responsibility to scan the > email > and the attachments (if any). > > > ------------------------------------------------------------------------- > 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]
