java.lang.ClassCastException: org.obiba.magma.views.ValueSetWrapper cannot be cast to org.obiba.magma.datasource.hibernate.HibernateValueTable$HibernateValueSet

JIRA | Martin Boulanger | 7 years ago
  1. 0

    1) Import some Onyx data (attached file) into Opal 2) Define the following view in opal-config.xml : <org.obiba.magma.views.View> <name>testJoin3</name> <from class="org.obiba.magma.views.JoinTable"> <tables> <org.obiba.magma.support.ValueTableReference> <reference>a-datasource-with-views.Consent</reference> </org.obiba.magma.support.ValueTableReference> <org.obiba.magma.support.ValueTableReference> <reference>opal-data.Participants</reference> </org.obiba.magma.support.ValueTableReference> </tables> </from> </org.obiba.magma.views.View> 3) copy -o testmerge.xls a-datasource-with-views.testJoin The following Exception is thrown by Opal : java.lang.ClassCastException: org.obiba.magma.views.ValueSetWrapper cannot be cast to org.obiba.magma.datasource.hibernate.HibernateValueTable$HibernateValueSet at org.obiba.magma.datasource.hibernate.HibernateVariableValueSourceFactory$HibernateVariableValueSource.getValue(HibernateVariableValueSourceFactory.java:82) at org.obiba.magma.support.AbstractValueTable.getValue(AbstractValueTable.java:86) at org.obiba.magma.support.AbstractValueTableWrapper.getValue(AbstractValueTableWrapper.java:30) at org.obiba.magma.views.JoinTable.getValue(JoinTable.java:96) at org.obiba.magma.support.AbstractValueTableWrapper.getValue(AbstractValueTableWrapper.java:30) at org.obiba.magma.views.View.getValue(View.java:205) at org.obiba.magma.support.AbstractValueTableWrapper.getValue(AbstractValueTableWrapper.java:30) at org.obiba.magma.views.View.getValue(View.java:205) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:186) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:164) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:144) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:130) at org.obiba.opal.core.service.impl.DefaultExportServiceImpl.exportTablesToDatasource(DefaultExportServiceImpl.java:71) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy38.exportTablesToDatasource(Unknown Source) at org.obiba.opal.shell.commands.CopyCommand.execute(CopyCommand.java:58) at org.obiba.opal.shell.AbstractOpalShell.executeCommand(AbstractOpalShell.java:94) at org.obiba.opal.shell.AbstractOpalShell.run(AbstractOpalShell.java:49) at java.lang.Thread.run(Thread.java:619)

    JIRA | 7 years ago | Martin Boulanger
    java.lang.ClassCastException: org.obiba.magma.views.ValueSetWrapper cannot be cast to org.obiba.magma.datasource.hibernate.HibernateValueTable$HibernateValueSet
  2. 0

    1) Import some Onyx data (attached file) into Opal 2) Define the following view in opal-config.xml : <org.obiba.magma.views.View> <name>testJoin3</name> <from class="org.obiba.magma.views.JoinTable"> <tables> <org.obiba.magma.support.ValueTableReference> <reference>a-datasource-with-views.Consent</reference> </org.obiba.magma.support.ValueTableReference> <org.obiba.magma.support.ValueTableReference> <reference>opal-data.Participants</reference> </org.obiba.magma.support.ValueTableReference> </tables> </from> </org.obiba.magma.views.View> 3) copy -o testmerge.xls a-datasource-with-views.testJoin The following Exception is thrown by Opal : java.lang.ClassCastException: org.obiba.magma.views.ValueSetWrapper cannot be cast to org.obiba.magma.datasource.hibernate.HibernateValueTable$HibernateValueSet at org.obiba.magma.datasource.hibernate.HibernateVariableValueSourceFactory$HibernateVariableValueSource.getValue(HibernateVariableValueSourceFactory.java:82) at org.obiba.magma.support.AbstractValueTable.getValue(AbstractValueTable.java:86) at org.obiba.magma.support.AbstractValueTableWrapper.getValue(AbstractValueTableWrapper.java:30) at org.obiba.magma.views.JoinTable.getValue(JoinTable.java:96) at org.obiba.magma.support.AbstractValueTableWrapper.getValue(AbstractValueTableWrapper.java:30) at org.obiba.magma.views.View.getValue(View.java:205) at org.obiba.magma.support.AbstractValueTableWrapper.getValue(AbstractValueTableWrapper.java:30) at org.obiba.magma.views.View.getValue(View.java:205) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:186) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:164) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:144) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:130) at org.obiba.opal.core.service.impl.DefaultExportServiceImpl.exportTablesToDatasource(DefaultExportServiceImpl.java:71) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy38.exportTablesToDatasource(Unknown Source) at org.obiba.opal.shell.commands.CopyCommand.execute(CopyCommand.java:58) at org.obiba.opal.shell.AbstractOpalShell.executeCommand(AbstractOpalShell.java:94) at org.obiba.opal.shell.AbstractOpalShell.run(AbstractOpalShell.java:49) at java.lang.Thread.run(Thread.java:619)

    JIRA | 7 years ago | Martin Boulanger
    java.lang.ClassCastException: org.obiba.magma.views.ValueSetWrapper cannot be cast to org.obiba.magma.datasource.hibernate.HibernateValueTable$HibernateValueSet
  3. 0

    Action: test opal-221 -- Implement the export to Excel command Step: 1) create fresh databases 'opal' and 'key' for opal 1.0.1 2) issue an upgrade 3) import a zip file with 1 completed interview exported from onyx1.6.4 cohort ontario (please check the attachment, it's a non-encrypted zip file) 4) show variable table list 5) export tables to an excel file based on the listed tables Result: in step 4), the listed tables shown as follows: opal-keys opal-keys.keys opal-data-ohs opal-data-ohs.Participants opal-data-ohs.CIPreliminaryQuestionnaire opal-data-ohs.BloodSamplesCollection opal-data-ohs.HealthQuestionnaireNurse opal-data-ohs.Weight opal-data-ohs.BoneDensity opal-data-ohs.SalivaSamplesCollection opal-data-ohs.BloodPressure opal-data-ohs.ArmSpan opal-data-ohs.SittingHeight opal-data-ohs.GripStrength opal-data-ohs.AnkleBrachial opal-data-ohs.UrineSamplesCollection opal-data-ohs.HealthQuestionnaireTouchScreen opal-data-ohs.Impedance418 opal-data-ohs.ConclusionQuestionnaire opal-data-ohs.Instruments opal-data-ohs.Consent opal-data-ohs.StandingHeight opal-data-ohs.Hips opal-data-ohs.Spirometry opal-data-ohs.Waist opal-data-ohs.Workstations opal-data in step 5) among the tables, 3 kinds of errors happened when 7 of them being exported (others were exported correctly): --> Error 1: happened in tables: opal-data-ohs.BloodSamplesCollection opal-data-ohs.SalivaSamplesCollection opal-data-ohs.UrineSamplesCollection Error info from opal-error.log java.lang.ClassCastException: java.util.ArrayList cannot be cast to java.lang.Boolean at org.obiba.magma.datasource.excel.support.ExcelUtil.setCellValue(ExcelUtil.java:30) at org.obiba.magma.datasource.excel.ExcelValueTableWriter$ExcelValueSetWriter.writeValue(ExcelValueTableWriter.java:229) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:182) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:158) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:138) at org.obiba.opal.core.service.impl.DefaultExportServiceImpl.exportTablesToDatasource(DefaultExportServiceImpl.java:70) at org.obiba.opal.core.service.impl.DefaultExportServiceImpl.exportTablesToDatasource(DefaultExportServiceImpl.java:52) at org.obiba.opal.core.service.impl.DefaultExportServiceImpl.exportTablesToExcelFile(DefaultExportServiceImpl.java:87) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy47.exportTablesToExcelFile(Unknown Source) at org.obiba.opal.cli.client.command.ExportCommand.execute(ExportCommand.java:35) at org.obiba.opal.cli.client.OpalConsole.prompt(OpalConsole.java:136) at org.obiba.opal.cli.client.OpalConsole.<init>(OpalConsole.java:103) at org.obiba.opal.cli.client.OpalConsole.main(OpalConsole.java:185) --> Error 2: happened in table: opal-data-ohs.Participants Error info from opal-error.log: java.lang.ClassCastException: java.util.ArrayList cannot be cast to java.lang.Long at org.obiba.magma.datasource.excel.support.ExcelUtil.setCellValue(ExcelUtil.java:36) at org.obiba.magma.datasource.excel.ExcelValueTableWriter$ExcelValueSetWriter.writeValue(ExcelValueTableWriter.java:229) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:182) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:158) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:138) at org.obiba.opal.core.service.impl.DefaultExportServiceImpl.exportTablesToDatasource(DefaultExportServiceImpl.java:70) at org.obiba.opal.core.service.impl.DefaultExportServiceImpl.exportTablesToDatasource(DefaultExportServiceImpl.java:52) at org.obiba.opal.core.service.impl.DefaultExportServiceImpl.exportTablesToExcelFile(DefaultExportServiceImpl.java:87) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy39.exportTablesToExcelFile(Unknown Source) at org.obiba.opal.cli.client.command.ExportCommand.execute(ExportCommand.java:35) at org.obiba.opal.cli.client.OpalConsole.prompt(OpalConsole.java:136) at org.obiba.opal.cli.client.OpalConsole.<init>(OpalConsole.java:103) at org.obiba.opal.cli.client.OpalConsole.main(OpalConsole.java:185) --> Error 3: happened in tables: opal-data-ohs.CIPreliminaryQuestionnaire opal-data-ohs.HealthQuestionnaireNurse opal-data-ohs.HealthQuestionnaireTouchScreen Error info from opal-error.log: java.lang.IllegalArgumentException: Invalid column index (256). Allowable column range for BIFF8 is (0..255) or ('A'..'IV') at org.apache.poi.hssf.usermodel.HSSFCell.checkBounds(HSSFCell.java:926) at org.apache.poi.hssf.usermodel.HSSFCell.<init>(HSSFCell.java:162) at org.apache.poi.hssf.usermodel.HSSFRow.createCell(HSSFRow.java:141) at org.apache.poi.hssf.usermodel.HSSFRow.createCell(HSSFRow.java:38) at org.obiba.magma.datasource.excel.ExcelValueTable.getVariableColumn(ExcelValueTable.java:85) at org.obiba.magma.datasource.excel.ExcelValueTableWriter$ExcelVariableWriter.writeVariable(ExcelValueTableWriter.java:68) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:170) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:148) at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:138) at org.obiba.opal.core.service.impl.DefaultExportServiceImpl.exportTablesToDatasource(DefaultExportServiceImpl.java:70) at org.obiba.opal.core.service.impl.DefaultExportServiceImpl.exportTablesToDatasource(DefaultExportServiceImpl.java:52) at org.obiba.opal.core.service.impl.DefaultExportServiceImpl.exportTablesToExcelFile(DefaultExportServiceImpl.java:87) at sun.reflect.GeneratedMethodAccessor6.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy47.exportTablesToExcelFile(Unknown Source) at org.obiba.opal.cli.client.command.ExportCommand.execute(ExportCommand.java:35) at org.obiba.opal.cli.client.OpalConsole.prompt(OpalConsole.java:136) at org.obiba.opal.cli.client.OpalConsole.<init>(OpalConsole.java:103) at org.obiba.opal.cli.client.OpalConsole.main(OpalConsole.java:185)

    JIRA | 7 years ago
    java.lang.ClassCastException: java.util.ArrayList cannot be cast to java.lang.Boolean
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    Root Cause Analysis

    1. java.lang.ClassCastException

      org.obiba.magma.views.ValueSetWrapper cannot be cast to org.obiba.magma.datasource.hibernate.HibernateValueTable$HibernateValueSet

      at org.obiba.magma.datasource.hibernate.HibernateVariableValueSourceFactory$HibernateVariableValueSource.getValue()
    2. org.obiba.magma
      DatasourceCopier.copy
      1. org.obiba.magma.datasource.hibernate.HibernateVariableValueSourceFactory$HibernateVariableValueSource.getValue(HibernateVariableValueSourceFactory.java:82)
      2. org.obiba.magma.support.AbstractValueTable.getValue(AbstractValueTable.java:86)
      3. org.obiba.magma.support.AbstractValueTableWrapper.getValue(AbstractValueTableWrapper.java:30)
      4. org.obiba.magma.views.JoinTable.getValue(JoinTable.java:96)
      5. org.obiba.magma.support.AbstractValueTableWrapper.getValue(AbstractValueTableWrapper.java:30)
      6. org.obiba.magma.views.View.getValue(View.java:205)
      7. org.obiba.magma.support.AbstractValueTableWrapper.getValue(AbstractValueTableWrapper.java:30)
      8. org.obiba.magma.views.View.getValue(View.java:205)
      9. org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:186)
      10. org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:164)
      11. org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:144)
      12. org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:130)
      12 frames
    3. org.obiba.opal
      DefaultExportServiceImpl.exportTablesToDatasource
      1. org.obiba.opal.core.service.impl.DefaultExportServiceImpl.exportTablesToDatasource(DefaultExportServiceImpl.java:71)
      1 frame
    4. Java RT
      Method.invoke
      1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
      3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
      4. java.lang.reflect.Method.invoke(Method.java:597)
      4 frames
    5. Spring AOP
      ReflectiveMethodInvocation.proceed
      1. org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
      2. org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182)
      3. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149)
      3 frames
    6. Spring Tx
      TransactionInterceptor.invoke
      1. org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106)
      1 frame
    7. Spring AOP
      JdkDynamicAopProxy.invoke
      1. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
      2. org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
      2 frames
    8. Unknown
      $Proxy38.exportTablesToDatasource
      1. $Proxy38.exportTablesToDatasource(Unknown Source)
      1 frame
    9. org.obiba.opal
      AbstractOpalShell.run
      1. org.obiba.opal.shell.commands.CopyCommand.execute(CopyCommand.java:58)
      2. org.obiba.opal.shell.AbstractOpalShell.executeCommand(AbstractOpalShell.java:94)
      3. org.obiba.opal.shell.AbstractOpalShell.run(AbstractOpalShell.java:49)
      3 frames
    10. Java RT
      Thread.run
      1. java.lang.Thread.run(Thread.java:619)
      1 frame