org.obiba.magma.MagmaRuntimeException: Cannot find identifier for line 1394 in file hopsim3ob.csv

JIRA | Yannick Marcon | 4 years ago
  1. 0

    When first record has null values, corresponding variable headers are unknown. {code} java.lang.RuntimeException: org.obiba.magma.MagmaRuntimeException: Cannot update the CSV ValueTable [Hearing]. The new ValueSet (record) included the following unexpected Variables (fields): RES_RIGHT_8K_ERR at org.obiba.opal.core.service.DataExportServiceImpl.exportTablesToDatasource(DataExportServiceImpl.java:88) at org.obiba.opal.shell.commands.CopyCommand.execute(CopyCommand.java:122) at org.obiba.opal.shell.CommandJob.run(CommandJob.java:153) at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120) at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.obiba.magma.MagmaRuntimeException: Cannot update the CSV ValueTable [Hearing]. The new ValueSet (record) included the following unexpected Variables (fields): RES_RIGHT_8K_ERR at org.obiba.magma.datasource.csv.CsvValueTableWriter$CsvValueSetWriter.writeTableWithData(CsvValueTableWriter.java:172) at org.obiba.magma.datasource.csv.CsvValueTableWriter$CsvValueSetWriter.close(CsvValueTableWriter.java:133) at org.obiba.magma.support.MultithreadedDatasourceCopier$ConcurrentValueSetWriter.copyValue(MultithreadedDatasourceCopier.java:351) at org.obiba.magma.support.MultithreadedDatasourceCopier$ConcurrentValueSetWriter.run(MultithreadedDatasourceCopier.java:339) at org.obiba.magma.support.MultithreadedDatasourceCopier.write(MultithreadedDatasourceCopier.java:185) at org.obiba.magma.support.MultithreadedDatasourceCopier.copy(MultithreadedDatasourceCopier.java:172) at org.obiba.opal.core.service.DataExportServiceImpl$ExportActionTemplate$ExportAction.exportTableToDatasource(DataExportServiceImpl.java:202) at org.obiba.opal.core.service.DataExportServiceImpl$ExportActionTemplate$ExportAction.execute(DataExportServiceImpl.java:171) at org.obiba.opal.core.magma.concurrent.LockingActionTemplate.execute(LockingActionTemplate.java:33) at org.obiba.opal.core.service.DataExportServiceImpl.exportTablesToDatasource(DataExportServiceImpl.java:80) ... 9 more {code}

    JIRA | 1 year ago | Dwain Elson
    java.lang.RuntimeException: org.obiba.magma.MagmaRuntimeException: Cannot update the CSV ValueTable [Hearing]. The new ValueSet (record) included the following unexpected Variables (fields): RES_RIGHT_8K_ERR
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  3. 0

    When first record has null values, corresponding variable headers are unknown. {code} java.lang.RuntimeException: org.obiba.magma.MagmaRuntimeException: Cannot update the CSV ValueTable [Hearing]. The new ValueSet (record) included the following unexpected Variables (fields): RES_RIGHT_8K_ERR at org.obiba.opal.core.service.DataExportServiceImpl.exportTablesToDatasource(DataExportServiceImpl.java:88) at org.obiba.opal.shell.commands.CopyCommand.execute(CopyCommand.java:122) at org.obiba.opal.shell.CommandJob.run(CommandJob.java:153) at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120) at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: org.obiba.magma.MagmaRuntimeException: Cannot update the CSV ValueTable [Hearing]. The new ValueSet (record) included the following unexpected Variables (fields): RES_RIGHT_8K_ERR at org.obiba.magma.datasource.csv.CsvValueTableWriter$CsvValueSetWriter.writeTableWithData(CsvValueTableWriter.java:172) at org.obiba.magma.datasource.csv.CsvValueTableWriter$CsvValueSetWriter.close(CsvValueTableWriter.java:133) at org.obiba.magma.support.MultithreadedDatasourceCopier$ConcurrentValueSetWriter.copyValue(MultithreadedDatasourceCopier.java:351) at org.obiba.magma.support.MultithreadedDatasourceCopier$ConcurrentValueSetWriter.run(MultithreadedDatasourceCopier.java:339) at org.obiba.magma.support.MultithreadedDatasourceCopier.write(MultithreadedDatasourceCopier.java:185) at org.obiba.magma.support.MultithreadedDatasourceCopier.copy(MultithreadedDatasourceCopier.java:172) at org.obiba.opal.core.service.DataExportServiceImpl$ExportActionTemplate$ExportAction.exportTableToDatasource(DataExportServiceImpl.java:202) at org.obiba.opal.core.service.DataExportServiceImpl$ExportActionTemplate$ExportAction.execute(DataExportServiceImpl.java:171) at org.obiba.opal.core.magma.concurrent.LockingActionTemplate.execute(LockingActionTemplate.java:33) at org.obiba.opal.core.service.DataExportServiceImpl.exportTablesToDatasource(DataExportServiceImpl.java:80) ... 9 more {code}

    JIRA | 1 year ago | Dwain Elson
    java.lang.RuntimeException: org.obiba.magma.MagmaRuntimeException: Cannot update the CSV ValueTable [Hearing]. The new ValueSet (record) included the following unexpected Variables (fields): RES_RIGHT_8K_ERR
  4. 0

    I started a new project: - deleted git views (to be certain) - deleted my config files - deleted my DBs (opal_data and opal_key in 'mysql') - created new config files - started OPAL server - setup the identifiers DB - setup the default storage DB - created a new project (always using the same name, think is irrelevant) - selected the Tables section Got the following exception: {code} 2013-10-18 17:31:29:478 INFO Loading configuration from input stream [OServerConfigurationLoaderXml] 2013-10-18 17:31:29:715 INFO Profiler is recording metrics with configuration: 0,0,0 [OJVMProfiler] 2013-10-18 17:31:29:716 INFO OrientDB Server v1.5.1 is starting up... [OServer] 2013-10-18 17:31:29:748 INFO Listening binary connections on 0.0.0.0:2424 (protocol v.17) [OServerNetworkListener] 2013-10-18 17:31:29:748 INFO Listening http connections on 0.0.0.0:2480 (protocol v.10) [OServerNetworkListener] 2013-10-18 17:31:29:758 INFO Mail plugin installed and active. Loaded 1 profile(s): [default] [OMailPlugin] 2013-10-18 17:31:29:760 INFO OrientDB Server v1.5.1 is active. [OServer]Upgrading Opal. Upgrade successful. Starting Opal. Opal Server successfully started. Opal is attached to this console. Press ctrl-c to stop. 2013-10-18 17:36:05,628 - ERROR - dbc.spi.SqlExceptionHelper - Duplicate entry 'opal-keys' for key 'UK_c270jcqlmvthpcasvusahxb7h' 2013-10-18 17:36:05,629 - ERROR - der.RuntimeExceptionMapper - Unhandled exception org.obiba.magma.MagmaRuntimeException: org.hibernate.exception.ConstraintViolationException: could not execute statement at org.obiba.magma.support.Initialisables.initialise(Initialisables.java:18) at org.obiba.opal.core.service.impl.DefaultIdentifiersTableService.getDatasource(DefaultIdentifiersTableService.java:120) at org.obiba.opal.core.service.impl.DefaultIdentifiersTableService.getValueTable(DefaultIdentifiersTableService.java:61) at org.obiba.opal.web.FunctionalUnitsResource.getEntitiesTable(FunctionalUnitsResource.java:215) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at org.jboss.resteasy.core.ResourceLocator.createResource(ResourceLocator.java:65) at org.jboss.resteasy.core.ResourceLocator.createResource(ResourceLocator.java:54) at org.jboss.resteasy.core.ResourceLocator.invoke(ResourceLocator.java:91) at org.jboss.resteasy.core.SynchronousDispatcher.getResponse(SynchronousDispatcher.java:542) at org.jboss.resteasy.core.SynchronousDispatcher.invoke(SynchronousDispatcher.java:524) at org.jboss.resteasy.core.SynchronousDispatcher.invoke(SynchronousDispatcher.java:126) at org.jboss.resteasy.plugins.server.servlet.ServletContainerDispatcher.service(ServletContainerDispatcher.java:208) at org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.service(HttpServletDispatcher.java:55) at org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.service(HttpServletDispatcher.java:50) at javax.servlet.http.HttpServlet.service(HttpServlet.java:820) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:652) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1329) at org.obiba.opal.server.httpd.OpalJettyServer$TransactionFilter$1.doInTransactionWithoutResult(OpalJettyServer.java:325) at org.springframework.transaction.support.TransactionCallbackWithoutResult.doInTransaction(TransactionCallbackWithoutResult.java:33) at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:131) at org.obiba.opal.server.httpd.OpalJettyServer$TransactionFilter.doFilterInternal(OpalJettyServer.java:321) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1300) at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:99) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1300) at org.obiba.opal.server.httpd.security.AuthenticationFilter.doFilterInternal(AuthenticationFilter.java:82) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1300) at org.obiba.opal.server.httpd.OpalJettyServer$OpalVersionFilter.doFilterInternal(OpalJettyServer.java:305) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1300) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:445) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1038) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:374) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:972) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135) at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116) at org.eclipse.jetty.server.Server.handle(Server.java:363) at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:483) at org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:920) at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:982) at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:635) at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235) at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82) at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:628) at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:52) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608) at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543) at java.lang.Thread.run(Thread.java:722) {code}

    JIRA | 3 years ago | Ramin Haeri Azad
    org.obiba.magma.MagmaRuntimeException: org.hibernate.exception.ConstraintViolationException: could not execute statement

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    Root Cause Analysis

    1. org.obiba.magma.MagmaRuntimeException

      Cannot find identifier for line 1394 in file hopsim3ob.csv

      at org.obiba.magma.datasource.csv.CsvValueTable.buildDataLineIndex()
    2. org.obiba.magma
      CsvValueTable.initialise
      1. org.obiba.magma.datasource.csv.CsvValueTable.buildDataLineIndex(CsvValueTable.java:344)
      2. org.obiba.magma.datasource.csv.CsvValueTable.initialiseData(CsvValueTable.java:264)
      3. org.obiba.magma.datasource.csv.CsvValueTable.initialise(CsvValueTable.java:146)
      3 frames