java.lang.RuntimeException: java.lang.NullPointerException

JIRA | Pieter Lukasse | 2 years ago
  1. 0

    I want to create a "mapping" table that contains the key and one extra field with the codes that map to this key. The purpose of this table is to be used as an annotation source of other views using the "join" method. Example: - I have a view with a field Diagnosis, which contains some ICD-10 code - I want to add another field e.g. "General Diagnosis", which should contain the parent ICD-10 codes of the Diagnosis field value. E.g. if the field Diagnosis contains "E10 (Insulin-dependent diabetes mellitus)" then the "General Diagnosis" field should contain the parent group code "E10–E14 (Diabetes mellitus)" The problem is that when I try to create such a mapping table, containing only this field, it fails with the following error when importing data into it (I hope this is the correct one from the log - see also attachment with steps on how to reproduce): 2014-10-01 12:45:31,531 [pool-2-thread-7] INFO org.obiba.magma.support.DatasourceCopier - Copying ValueTable 'ICD_codes_to_parents_mapping' to 'ICD_parent_mapping. ICD_codes_to_parents_mapping' (copyMetadata=true, copyValues=true). 2014-10-01 12:45:31,547 [pool-2-thread-7] ERROR org.obiba.opal.shell.commands.ImportCommand - Runtime error while importing data java.lang.RuntimeException: java.lang.NullPointerException at org.obiba.opal.core.service.DataImportServiceImpl.copyValueTables(DataImportServiceImpl.java:142) ~[opal-core-2.4.jar:na] at org.obiba.opal.core.service.DataImportServiceImpl.importData(DataImportServiceImpl.java:105) ~[opal-core-2.4.jar:na] at org.obiba.opal.core.service.DataImportServiceImpl.importData(DataImportServiceImpl.java:87) ~[opal-core-2.4.jar:na] at org.obiba.opal.shell.commands.ImportCommand.importFromTables(ImportCommand.java:155) [opal-shell-2.4.jar:na] at org.obiba.opal.shell.commands.ImportCommand.executeImports(ImportCommand.java:89) [opal-shell-2.4.jar:na] at org.obiba.opal.shell.commands.ImportCommand.execute(ImportCommand.java:68) [opal-shell-2.4.jar:na] at org.obiba.opal.shell.CommandJob.run(CommandJob.java:149) [opal-shell-2.4.jar:na] at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120) [shiro-core-1.2.3-java8.jar:1.2.3-java8] at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108) [shiro-core-1.2.3-java8.jar:1.2.3-java8] at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) [na:1.7.0_65] at java.util.concurrent.FutureTask.run(FutureTask.java:262) [na:1.7.0_65] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) [na:1.7.0_65] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) [na:1.7.0_65] at java.lang.Thread.run(Thread.java:745) [na:1.7.0_65] Caused by: java.lang.NullPointerException: null at org.obiba.magma.datasource.hibernate.converter.VariableConverter.getStateForVariable(VariableConverter.java:27) ~[magma-datasource-hibernate-1.11-sesi.jar:na] at org.obiba.magma.datasource.hibernate.converter.VariableConverter.marshal(VariableConverter.java:34) ~[magma-datasource-hibernate-1.11-sesi.jar:na] at org.obiba.magma.datasource.hibernate.HibernateValueTableWriter$HibernateVariableWriter.writeVariable(HibernateValueTableWriter.java:115) ~[magma-datasource-hibernate-1.11-sesi.jar:na] at org.obiba.magma.support.DatasourceCopier.copyMetadata(DatasourceCopier.java:270) ~[magma-api-1.11-sesi.jar:na] at org.obiba.magma.support.DatasourceCopier.copyMetadata(DatasourceCopier.java:262) ~[magma-api-1.11-sesi.jar:na] at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:224) ~[magma-api-1.11-sesi.jar:na] at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:214) ~[magma-api-1.11-sesi.jar:na] at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:202) ~[magma-api-1.11-sesi.jar:na] at org.obiba.opal.core.service.CopyValueTablesLockingAction$CopyAction.execute(CopyValueTablesLockingAction.java:132) ~[opal-core-2.4.jar:na] at org.obiba.opal.core.magma.concurrent.LockingActionTemplate$1.doInTransactionWithoutResult(LockingActionTemplate.java:47) ~[opal-core-2.4.jar:na] at org.springframework.transaction.support.TransactionCallbackWithoutResult.doInTransaction(TransactionCallbackWithoutResult.java:34) ~[spring-tx-4.0.3.RELEASE.jar:4.0.3.RELEASE] at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:133) ~[spring-tx-4.0.3.RELEASE.jar:4.0.3.RELEASE] at org.obiba.opal.core.magma.concurrent.LockingActionTemplate.doInTransaction(LockingActionTemplate.java:42) ~[opal-core-2.4.jar:na] at org.obiba.opal.core.magma.concurrent.LockingActionTemplate.execute(LockingActionTemplate.java:31) ~[opal-core-2.4.jar:na] at org.obiba.opal.core.service.DataImportServiceImpl.copyValueTables(DataImportServiceImpl.java:133) ~[opal-core-2.4.jar:na] ... 13 common frames omitted 2014-10-01 12:45:31,547 [pool-2-thread-7] INFO org.obiba.opal.shell.commands.ImportCommand - Import failed in 18.42 ms

    JIRA | 2 years ago | Pieter Lukasse
    java.lang.RuntimeException: java.lang.NullPointerException
  2. 0

    I want to create a "mapping" table that contains the key and one extra field with the codes that map to this key. The purpose of this table is to be used as an annotation source of other views using the "join" method. Example: - I have a view with a field Diagnosis, which contains some ICD-10 code - I want to add another field e.g. "General Diagnosis", which should contain the parent ICD-10 codes of the Diagnosis field value. E.g. if the field Diagnosis contains "E10 (Insulin-dependent diabetes mellitus)" then the "General Diagnosis" field should contain the parent group code "E10–E14 (Diabetes mellitus)" The problem is that when I try to create such a mapping table, containing only this field, it fails with the following error when importing data into it (I hope this is the correct one from the log - see also attachment with steps on how to reproduce): 2014-10-01 12:45:31,531 [pool-2-thread-7] INFO org.obiba.magma.support.DatasourceCopier - Copying ValueTable 'ICD_codes_to_parents_mapping' to 'ICD_parent_mapping. ICD_codes_to_parents_mapping' (copyMetadata=true, copyValues=true). 2014-10-01 12:45:31,547 [pool-2-thread-7] ERROR org.obiba.opal.shell.commands.ImportCommand - Runtime error while importing data java.lang.RuntimeException: java.lang.NullPointerException at org.obiba.opal.core.service.DataImportServiceImpl.copyValueTables(DataImportServiceImpl.java:142) ~[opal-core-2.4.jar:na] at org.obiba.opal.core.service.DataImportServiceImpl.importData(DataImportServiceImpl.java:105) ~[opal-core-2.4.jar:na] at org.obiba.opal.core.service.DataImportServiceImpl.importData(DataImportServiceImpl.java:87) ~[opal-core-2.4.jar:na] at org.obiba.opal.shell.commands.ImportCommand.importFromTables(ImportCommand.java:155) [opal-shell-2.4.jar:na] at org.obiba.opal.shell.commands.ImportCommand.executeImports(ImportCommand.java:89) [opal-shell-2.4.jar:na] at org.obiba.opal.shell.commands.ImportCommand.execute(ImportCommand.java:68) [opal-shell-2.4.jar:na] at org.obiba.opal.shell.CommandJob.run(CommandJob.java:149) [opal-shell-2.4.jar:na] at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120) [shiro-core-1.2.3-java8.jar:1.2.3-java8] at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108) [shiro-core-1.2.3-java8.jar:1.2.3-java8] at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) [na:1.7.0_65] at java.util.concurrent.FutureTask.run(FutureTask.java:262) [na:1.7.0_65] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) [na:1.7.0_65] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) [na:1.7.0_65] at java.lang.Thread.run(Thread.java:745) [na:1.7.0_65] Caused by: java.lang.NullPointerException: null at org.obiba.magma.datasource.hibernate.converter.VariableConverter.getStateForVariable(VariableConverter.java:27) ~[magma-datasource-hibernate-1.11-sesi.jar:na] at org.obiba.magma.datasource.hibernate.converter.VariableConverter.marshal(VariableConverter.java:34) ~[magma-datasource-hibernate-1.11-sesi.jar:na] at org.obiba.magma.datasource.hibernate.HibernateValueTableWriter$HibernateVariableWriter.writeVariable(HibernateValueTableWriter.java:115) ~[magma-datasource-hibernate-1.11-sesi.jar:na] at org.obiba.magma.support.DatasourceCopier.copyMetadata(DatasourceCopier.java:270) ~[magma-api-1.11-sesi.jar:na] at org.obiba.magma.support.DatasourceCopier.copyMetadata(DatasourceCopier.java:262) ~[magma-api-1.11-sesi.jar:na] at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:224) ~[magma-api-1.11-sesi.jar:na] at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:214) ~[magma-api-1.11-sesi.jar:na] at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:202) ~[magma-api-1.11-sesi.jar:na] at org.obiba.opal.core.service.CopyValueTablesLockingAction$CopyAction.execute(CopyValueTablesLockingAction.java:132) ~[opal-core-2.4.jar:na] at org.obiba.opal.core.magma.concurrent.LockingActionTemplate$1.doInTransactionWithoutResult(LockingActionTemplate.java:47) ~[opal-core-2.4.jar:na] at org.springframework.transaction.support.TransactionCallbackWithoutResult.doInTransaction(TransactionCallbackWithoutResult.java:34) ~[spring-tx-4.0.3.RELEASE.jar:4.0.3.RELEASE] at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:133) ~[spring-tx-4.0.3.RELEASE.jar:4.0.3.RELEASE] at org.obiba.opal.core.magma.concurrent.LockingActionTemplate.doInTransaction(LockingActionTemplate.java:42) ~[opal-core-2.4.jar:na] at org.obiba.opal.core.magma.concurrent.LockingActionTemplate.execute(LockingActionTemplate.java:31) ~[opal-core-2.4.jar:na] at org.obiba.opal.core.service.DataImportServiceImpl.copyValueTables(DataImportServiceImpl.java:133) ~[opal-core-2.4.jar:na] ... 13 common frames omitted 2014-10-01 12:45:31,547 [pool-2-thread-7] INFO org.obiba.opal.shell.commands.ImportCommand - Import failed in 18.42 ms

    JIRA | 2 years ago | Pieter Lukasse
    java.lang.RuntimeException: java.lang.NullPointerException
  3. 0

    HQL Exception (org.hibernate.dialect.Dialect$3)

    Stack Overflow | 4 years ago | Hari
    java.lang.NullPointerException: null
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    java.lang.NullPointerException: null

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    Root Cause Analysis

    1. java.lang.NullPointerException

      null

      at org.obiba.magma.datasource.hibernate.converter.VariableConverter.getStateForVariable()
    2. org.obiba.magma
      DatasourceCopier.copy
      1. org.obiba.magma.datasource.hibernate.converter.VariableConverter.getStateForVariable(VariableConverter.java:27)[magma-datasource-hibernate-1.11-sesi.jar:na]
      2. org.obiba.magma.datasource.hibernate.converter.VariableConverter.marshal(VariableConverter.java:34)[magma-datasource-hibernate-1.11-sesi.jar:na]
      3. org.obiba.magma.datasource.hibernate.HibernateValueTableWriter$HibernateVariableWriter.writeVariable(HibernateValueTableWriter.java:115)[magma-datasource-hibernate-1.11-sesi.jar:na]
      4. org.obiba.magma.support.DatasourceCopier.copyMetadata(DatasourceCopier.java:270)[magma-api-1.11-sesi.jar:na]
      5. org.obiba.magma.support.DatasourceCopier.copyMetadata(DatasourceCopier.java:262)[magma-api-1.11-sesi.jar:na]
      6. org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:224)[magma-api-1.11-sesi.jar:na]
      7. org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:214)[magma-api-1.11-sesi.jar:na]
      8. org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:202)[magma-api-1.11-sesi.jar:na]
      8 frames
    3. org.obiba.opal
      LockingActionTemplate$1.doInTransactionWithoutResult
      1. org.obiba.opal.core.service.CopyValueTablesLockingAction$CopyAction.execute(CopyValueTablesLockingAction.java:132)[opal-core-2.4.jar:na]
      2. org.obiba.opal.core.magma.concurrent.LockingActionTemplate$1.doInTransactionWithoutResult(LockingActionTemplate.java:47)[opal-core-2.4.jar:na]
      2 frames
    4. Spring Tx
      TransactionTemplate.execute
      1. org.springframework.transaction.support.TransactionCallbackWithoutResult.doInTransaction(TransactionCallbackWithoutResult.java:34)[spring-tx-4.0.3.RELEASE.jar:4.0.3.RELEASE]
      2. org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:133)[spring-tx-4.0.3.RELEASE.jar:4.0.3.RELEASE]
      2 frames
    5. org.obiba.opal
      CommandJob.run
      1. org.obiba.opal.core.magma.concurrent.LockingActionTemplate.doInTransaction(LockingActionTemplate.java:42)[opal-core-2.4.jar:na]
      2. org.obiba.opal.core.magma.concurrent.LockingActionTemplate.execute(LockingActionTemplate.java:31)[opal-core-2.4.jar:na]
      3. org.obiba.opal.core.service.DataImportServiceImpl.copyValueTables(DataImportServiceImpl.java:133)[opal-core-2.4.jar:na]
      4. org.obiba.opal.core.service.DataImportServiceImpl.importData(DataImportServiceImpl.java:105)[opal-core-2.4.jar:na]
      5. org.obiba.opal.core.service.DataImportServiceImpl.importData(DataImportServiceImpl.java:87)[opal-core-2.4.jar:na]
      6. org.obiba.opal.shell.commands.ImportCommand.importFromTables(ImportCommand.java:155)[opal-shell-2.4.jar:na]
      7. org.obiba.opal.shell.commands.ImportCommand.executeImports(ImportCommand.java:89)[opal-shell-2.4.jar:na]
      8. org.obiba.opal.shell.commands.ImportCommand.execute(ImportCommand.java:68)[opal-shell-2.4.jar:na]
      9. org.obiba.opal.shell.CommandJob.run(CommandJob.java:149)[opal-shell-2.4.jar:na]
      9 frames
    6. Shiro
      SubjectRunnable.run
      1. org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120)[shiro-core-1.2.3-java8.jar:1.2.3-java8]
      2. org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108)[shiro-core-1.2.3-java8.jar:1.2.3-java8]
      2 frames
    7. Java RT
      Thread.run
      1. java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)[na:1.7.0_65]
      2. java.util.concurrent.FutureTask.run(FutureTask.java:262)[na:1.7.0_65]
      3. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)[na:1.7.0_65]
      4. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)[na:1.7.0_65]
      5. java.lang.Thread.run(Thread.java:745)[na:1.7.0_65]
      5 frames