Simon McGowan wrote: > Hi, > > We have run into problems after editing the raw-data-types.xml and > extended-properties.xml > files. After each edit the server was stopped, I ran updatedb.sh and > updateindexes.sh and > restarted the server. However we can now no longer see any reporters via the > gui (they are > still accessible in the Reporters table via MySQL) and no new reporters can > be imported. > Has this kind of problem after modifying these xml files together been seen > before?
It is hard to tell exactly what happens. There is a known issue about invalid values in the extended-properties.xml and raw-data-types.xml that aren't detected (http://base.thep.lu.se/ticket/480) and later on they will produces errors. To be able to check if your problem is related to this I have to know what changes you made to the configuration files. Another thing to remember is that the updatedb.sh script can only add new columns, it can't modify or delete existing columns. If you have done such changes you must do the corresponding changes manually in MySQL. /Nicklas > Many thanks, Simon > > The stack trace when you go into Experiment Explorer in a pre existing > analysis, is: > > Experiment > Options… > Unexpected error > BaseException on page /views/experiments/explorer/view/view.jsp > > Version BASE 2.2.1 (build #0; schema #29) > Web server Apache Tomcat/5.5.17 > Database Dialect org.hibernate.dialect.MySQLInnoDBDialect > JDBC Driver com.mysql.jdbc.Driver (version 5.0) > Java runtime Java(TM) 2 Runtime Environment, Standard Edition > (1.5.0_09-b03), Sun > Microsystems Inc. > Operating system Linux amd64 2.6.19-1.2895.fc6 > Memory Total: 157.0 MB > Free: 84.7 MB > Max: 444.5 MB > Browser Mozilla/5.0 (Windows; U; Windows NT 5.1; en-GB; rv:1.8.1.3) > Gecko/20070309 > Firefox/2.0.0.3 > Error message could not load an entity: > [net.sf.basedb.core.data.ReporterData#66625] > Stack trace > > ...at HibernateUtil.loadData(HibernateUtil.java:1085) > ...at Reporter.getById(Reporter.java:82) > ...at > net.sf.basedb.clients.web.ExperimentExplorer.getReporter(ExperimentExplorer.java:564) > ...at > org.apache.jsp.views.experiments.explorer.view.view_jsp._jspService(view_jsp.java:235) > ...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:332) > ...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:595) > > Caused by: org.hibernate.exception.SQLGrammarException > ...at > org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:67) > ...at > org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) > ...at org.hibernate.loader.Loader.loadEntity(Loader.java:1865) > ...at > org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:48) > ...at > org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:42) > ...at > org.hibernate.persister.entity.AbstractEntityPersister.load(AbstractEntityPersister.java:3038) > ...at > org.hibernate.impl.StatelessSessionImpl.get(StatelessSessionImpl.java:158) > ...at > org.hibernate.impl.StatelessSessionImpl.get(StatelessSessionImpl.java:153) > ...at > org.hibernate.impl.StatelessSessionImpl.get(StatelessSessionImpl.java:145) > ...at HibernateUtil.loadData(HibernateUtil.java:1081) > ...at Reporter.getById(Reporter.java:82) > ...at > net.sf.basedb.clients.web.ExperimentExplorer.getReporter(ExperimentExplorer.java:564) > ...at > org.apache.jsp.views.experiments.explorer.view.view_jsp._jspService(view_jsp.java:235) > ...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:332) > ...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:595) > > Caused by: com.mysql.jdbc.exceptions.MySQLSyntaxErrorException > ...at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:936) > ...at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2870) > ...at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1573) > ...at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1665) > ...at com.mysql.jdbc.Connection.execSQL(Connection.java:3176) > ...at > com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1153) > ...at > com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1266) > ...at > com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:76) > ...at > org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:186) > ...at org.hibernate.loader.Loader.getResultSet(Loader.java:1778) > ...at org.hibernate.loader.Loader.doQuery(Loader.java:662) > ...at > org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224) > ...at org.hibernate.loader.Loader.loadEntity(Loader.java:1851) > ...at > org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:48) > ...at > org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:42) > ...at > org.hibernate.persister.entity.AbstractEntityPersister.load(AbstractEntityPersister.java:3038) > ...at > org.hibernate.impl.StatelessSessionImpl.get(StatelessSessionImpl.java:158) > ...at > org.hibernate.impl.StatelessSessionImpl.get(StatelessSessionImpl.java:153) > ...at > org.hibernate.impl.StatelessSessionImpl.get(StatelessSessionImpl.java:145) > ...at HibernateUtil.loadData(HibernateUtil.java:1081) > ...at Reporter.getById(Reporter.java:82) > ...at > net.sf.basedb.clients.web.ExperimentExplorer.getReporter(ExperimentExplorer.java:564) > ...at > org.apache.jsp.views.experiments.explorer.view.view_jsp._jspService(view_jsp.java:235) > ...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:332) > ...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:595) > > > ------------------------------------------------------------------------- > Take Surveys. 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