java.lang.RuntimeException: org.springframework.jdbc.UncategorizedSQLException: ConnectionCallback; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; liquibase.exception.DatabaseException: Duplicate entry 'ccc-Drugs-CLASS-Human' for key 'PRIMARY' [Failed SQL: INSERT INTO `opal_tabular`.`categories` (`datasource`, `value_table`, `variable`, `name`, `missing`) VALUES ('ccc', 'Drugs', 'CLASS', 'Human', 0)]; nested exception is java.sql.SQLException: liquibase.exception.DatabaseException: Duplicate entry 'ccc-Drugs-CLASS-Human' for key 'PRIMARY' [Failed SQL: INSERT INTO `opal_tabular`.`categories` (`datasource`, `value_table`, `variable`, `name`, `missing`) VALUES ('ccc', 'Drugs', 'CLASS', 'Human', 0)]

JIRA | Yannick Marcon | 6 months ago
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  1. 0

    When re-importing data or when updating directly a variable, categories (and possibly attributes) are not deleted as expected before being re-inserted. {code} 2016-09-27 22:36:21,459 [pool-4-thread-8] ERROR org.obiba.opal.shell.commands.ImportCommand - Runtime error while importing data java.lang.RuntimeException: org.springframework.jdbc.UncategorizedSQLException: ConnectionCallback; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; liquibase.exception.DatabaseException: Duplicate entry 'ccc-Drugs-CLASS-Human' for key 'PRIMARY' [Failed SQL: INSERT INTO `opal_tabular`.`categories` (`datasource`, `value_table`, `variable`, `name`, `missing`) VALUES ('ccc', 'Drugs', 'CLASS', 'Human', 0)]; nested exception is java.sql.SQLException: liquibase.exception.DatabaseException: Duplicate entry 'ccc-Drugs-CLASS-Human' for key 'PRIMARY' [Failed SQL: INSERT INTO `opal_tabular`.`categories` (`datasource`, `value_table`, `variable`, `name`, `missing`) VALUES ('ccc', 'Drugs', 'CLASS', 'Human', 0)] at org.obiba.opal.core.service.DataImportServiceImpl.copyValueTables(DataImportServiceImpl.java:142) ~[opal-core-2.6-SNAPSHOT.jar:na] at org.obiba.opal.core.service.DataImportServiceImpl.importData(DataImportServiceImpl.java:105) ~[opal-core-2.6-SNAPSHOT.jar:na] at org.obiba.opal.core.service.DataImportServiceImpl.importData(DataImportServiceImpl.java:87) ~[opal-core-2.6-SNAPSHOT.jar:na] at org.obiba.opal.shell.commands.ImportCommand.importFromTables(ImportCommand.java:155) [opal-shell-2.6-SNAPSHOT.jar:na] at org.obiba.opal.shell.commands.ImportCommand.executeImports(ImportCommand.java:89) [opal-shell-2.6-SNAPSHOT.jar:na] at org.obiba.opal.shell.commands.ImportCommand.execute(ImportCommand.java:68) [opal-shell-2.6-SNAPSHOT.jar:na] at org.obiba.opal.shell.CommandJob.run(CommandJob.java:153) [opal-shell-2.6-SNAPSHOT.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$RunnableAdapter.call(Executors.java:511) [na:1.8.0_101] at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_101] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_101] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_101] at java.lang.Thread.run(Thread.java:745) [na:1.8.0_101] Caused by: org.springframework.jdbc.UncategorizedSQLException: ConnectionCallback; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; liquibase.exception.DatabaseException: Duplicate entry 'ccc-Drugs-CLASS-Human' for key 'PRIMARY' [Failed SQL: INSERT INTO `opal_tabular`.`categories` (`datasource`, `value_table`, `variable`, `name`, `missing`) VALUES ('ccc', 'Drugs', 'CLASS', 'Human', 0)]; nested exception is java.sql.SQLException: liquibase.exception.DatabaseException: Duplicate entry 'ccc-Drugs-CLASS-Human' for key 'PRIMARY' [Failed SQL: INSERT INTO `opal_tabular`.`categories` (`datasource`, `value_table`, `variable`, `name`, `missing`) VALUES ('ccc', 'Drugs', 'CLASS', 'Human', 0)] at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:84) ~[spring-jdbc-4.2.1.RELEASE.jar:4.2.1.RELEASE] at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:81) ~[spring-jdbc-4.2.1.RELEASE.jar:4.2.1.RELEASE] at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:81) ~[spring-jdbc-4.2.1.RELEASE.jar:4.2.1.RELEASE] at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:356) ~[spring-jdbc-4.2.1.RELEASE.jar:4.2.1.RELEASE] at org.obiba.magma.datasource.jdbc.JdbcDatasource.doWithDatabase(JdbcDatasource.java:480) ~[magma-datasource-jdbc-1.12-20160926.114307-99.jar:1.12-SNAPSHOT] at org.obiba.magma.datasource.jdbc.JdbcValueTableWriter$JdbcVariableWriter.close(JdbcValueTableWriter.java:265) ~[magma-datasource-jdbc-1.12-20160926.114307-99.jar:1.12-SNAPSHOT] at org.obiba.magma.support.DatasourceCopier.copyMetadata(DatasourceCopier.java:266) ~[magma-api-1.12-20160926.114307-99.jar:1.12-SNAPSHOT] at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:227) ~[magma-api-1.12-20160926.114307-99.jar:1.12-SNAPSHOT] at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:217) ~[magma-api-1.12-20160926.114307-99.jar:1.12-SNAPSHOT] at org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:200) ~[magma-api-1.12-20160926.114307-99.jar:1.12-SNAPSHOT] at org.obiba.opal.core.service.CopyValueTablesLockingAction$CopyAction.execute(CopyValueTablesLockingAction.java:150) ~[opal-core-2.6-SNAPSHOT.jar:na] at org.obiba.opal.core.magma.concurrent.LockingActionTemplate$1.doInTransactionWithoutResult(LockingActionTemplate.java:47) ~[opal-core-2.6-SNAPSHOT.jar:na] at org.springframework.transaction.support.TransactionCallbackWithoutResult.doInTransaction(TransactionCallbackWithoutResult.java:34) ~[spring-tx-4.2.1.RELEASE.jar:4.2.1.RELEASE] at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:133) ~[spring-tx-4.2.1.RELEASE.jar:4.2.1.RELEASE] at org.obiba.opal.core.magma.concurrent.LockingActionTemplate.doInTransaction(LockingActionTemplate.java:42) ~[opal-core-2.6-SNAPSHOT.jar:na] at org.obiba.opal.core.magma.concurrent.LockingActionTemplate.execute(LockingActionTemplate.java:31) ~[opal-core-2.6-SNAPSHOT.jar:na] at org.obiba.opal.core.service.DataImportServiceImpl.copyValueTables(DataImportServiceImpl.java:134) ~[opal-core-2.6-SNAPSHOT.jar:na] ... 13 common frames omitted Caused by: java.sql.SQLException: liquibase.exception.DatabaseException: Duplicate entry 'ccc-Drugs-CLASS-Human' for key 'PRIMARY' [Failed SQL: INSERT INTO `opal_tabular`.`categories` (`datasource`, `value_table`, `variable`, `name`, `missing`) VALUES ('ccc', 'Drugs', 'CLASS', 'Human', 0)] at org.obiba.magma.datasource.jdbc.JdbcDatasource$6.doInConnection(JdbcDatasource.java:491) ~[magma-datasource-jdbc-1.12-20160926.114307-99.jar:1.12-SNAPSHOT] at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:349) ~[spring-jdbc-4.2.1.RELEASE.jar:4.2.1.RELEASE] ... 26 common frames omitted Caused by: liquibase.exception.DatabaseException: Duplicate entry 'ccc-Drugs-CLASS-Human' for key 'PRIMARY' [Failed SQL: INSERT INTO `opal_tabular`.`categories` (`datasource`, `value_table`, `variable`, `name`, `missing`) VALUES ('ccc', 'Drugs', 'CLASS', 'Human', 0)] at liquibase.executor.jvm.JdbcExecutor$ExecuteStatementCallback.doInStatement(JdbcExecutor.java:316) ~[liquibase-core-3.4.1.jar:na] at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55) ~[liquibase-core-3.4.1.jar:na] at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:122) ~[liquibase-core-3.4.1.jar:na] at liquibase.database.AbstractJdbcDatabase.execute(AbstractJdbcDatabase.java:1247) ~[liquibase-core-3.4.1.jar:na] at org.obiba.magma.datasource.jdbc.JdbcDatasource$ChangeDatabaseCallback.doInDatabase(JdbcDatasource.java:641) ~[magma-datasource-jdbc-1.12-20160926.114307-99.jar:1.12-SNAPSHOT] at org.obiba.magma.datasource.jdbc.JdbcDatasource$6.doInConnection(JdbcDatasource.java:489) ~[magma-datasource-jdbc-1.12-20160926.114307-99.jar:1.12-SNAPSHOT] ... 27 common frames omitted Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException: Duplicate entry 'ccc-Drugs-CLASS-Human' for key 'PRIMARY' at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.8.0_101] at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[na:1.8.0_101] at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.8.0_101] at java.lang.reflect.Constructor.newInstance(Constructor.java:423) ~[na:1.8.0_101] at com.mysql.jdbc.Util.handleNewInstance(Util.java:400) ~[mysql-connector-java-5.1.36.jar:5.1.36] at com.mysql.jdbc.Util.getInstance(Util.java:383) ~[mysql-connector-java-5.1.36.jar:5.1.36] at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:973) ~[mysql-connector-java-5.1.36.jar:5.1.36] at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3847) ~[mysql-connector-java-5.1.36.jar:5.1.36] at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3783) ~[mysql-connector-java-5.1.36.jar:5.1.36] at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2447) ~[mysql-connector-java-5.1.36.jar:5.1.36] at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2594) ~[mysql-connector-java-5.1.36.jar:5.1.36] at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2541) ~[mysql-connector-java-5.1.36.jar:5.1.36] at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2499) ~[mysql-connector-java-5.1.36.jar:5.1.36] at com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:844) ~[mysql-connector-java-5.1.36.jar:5.1.36] at com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:748) ~[mysql-connector-java-5.1.36.jar:5.1.36] at org.apache.commons.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264) ~[commons-dbcp-1.4.jar:1.4] at org.apache.commons.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264) ~[commons-dbcp-1.4.jar:1.4] at liquibase.executor.jvm.JdbcExecutor$ExecuteStatementCallback.doInStatement(JdbcExecutor.java:314) ~[liquibase-core-3.4.1.jar:na] ... 32 common frames omitted {code}

    JIRA | 6 months ago | Yannick Marcon
    java.lang.RuntimeException: org.springframework.jdbc.UncategorizedSQLException: ConnectionCallback; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; liquibase.exception.DatabaseException: Duplicate entry 'ccc-Drugs-CLASS-Human' for key 'PRIMARY' [Failed SQL: INSERT INTO `opal_tabular`.`categories` (`datasource`, `value_table`, `variable`, `name`, `missing`) VALUES ('ccc', 'Drugs', 'CLASS', 'Human', 0)]; nested exception is java.sql.SQLException: liquibase.exception.DatabaseException: Duplicate entry 'ccc-Drugs-CLASS-Human' for key 'PRIMARY' [Failed SQL: INSERT INTO `opal_tabular`.`categories` (`datasource`, `value_table`, `variable`, `name`, `missing`) VALUES ('ccc', 'Drugs', 'CLASS', 'Human', 0)]
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    org.hibernate.JDBCException: Error during import script execution at line 4
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    Moving DataBase HSQLDB to MySQL - Page 2 - Broadleaf Commerce Discussion Forums

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Root Cause Analysis

  1. com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException

    Duplicate entry 'ccc-Drugs-CLASS-Human' for key 'PRIMARY'

    at sun.reflect.NativeConstructorAccessorImpl.newInstance0()
  2. Java RT
    Constructor.newInstance
    1. sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)[na:1.8.0_101]
    2. sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)[na:1.8.0_101]
    3. sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)[na:1.8.0_101]
    4. java.lang.reflect.Constructor.newInstance(Constructor.java:423)[na:1.8.0_101]
    4 frames
  3. MySQL jdbc
    StatementImpl.execute
    1. com.mysql.jdbc.Util.handleNewInstance(Util.java:400)[mysql-connector-java-5.1.36.jar:5.1.36]
    2. com.mysql.jdbc.Util.getInstance(Util.java:383)[mysql-connector-java-5.1.36.jar:5.1.36]
    3. com.mysql.jdbc.SQLError.createSQLException(SQLError.java:973)[mysql-connector-java-5.1.36.jar:5.1.36]
    4. com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3847)[mysql-connector-java-5.1.36.jar:5.1.36]
    5. com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3783)[mysql-connector-java-5.1.36.jar:5.1.36]
    6. com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2447)[mysql-connector-java-5.1.36.jar:5.1.36]
    7. com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2594)[mysql-connector-java-5.1.36.jar:5.1.36]
    8. com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2541)[mysql-connector-java-5.1.36.jar:5.1.36]
    9. com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2499)[mysql-connector-java-5.1.36.jar:5.1.36]
    10. com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:844)[mysql-connector-java-5.1.36.jar:5.1.36]
    11. com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:748)[mysql-connector-java-5.1.36.jar:5.1.36]
    11 frames
  4. Commons DBCP
    DelegatingStatement.execute
    1. org.apache.commons.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)[commons-dbcp-1.4.jar:1.4]
    2. org.apache.commons.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)[commons-dbcp-1.4.jar:1.4]
    2 frames
  5. Liquibase Core
    AbstractJdbcDatabase.execute
    1. liquibase.executor.jvm.JdbcExecutor$ExecuteStatementCallback.doInStatement(JdbcExecutor.java:314)[liquibase-core-3.4.1.jar:na]
    2. liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)[liquibase-core-3.4.1.jar:na]
    3. liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:122)[liquibase-core-3.4.1.jar:na]
    4. liquibase.database.AbstractJdbcDatabase.execute(AbstractJdbcDatabase.java:1247)[liquibase-core-3.4.1.jar:na]
    4 frames
  6. org.obiba.magma
    JdbcDatasource$6.doInConnection
    1. org.obiba.magma.datasource.jdbc.JdbcDatasource$ChangeDatabaseCallback.doInDatabase(JdbcDatasource.java:641)[magma-datasource-jdbc-1.12-20160926.114307-99.jar:1.12-SNAPSHOT]
    2. org.obiba.magma.datasource.jdbc.JdbcDatasource$6.doInConnection(JdbcDatasource.java:489)[magma-datasource-jdbc-1.12-20160926.114307-99.jar:1.12-SNAPSHOT]
    2 frames
  7. Spring Framework
    JdbcTemplate.execute
    1. org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:349)[spring-jdbc-4.2.1.RELEASE.jar:4.2.1.RELEASE]
    1 frame
  8. org.obiba.magma
    DatasourceCopier.copy
    1. org.obiba.magma.datasource.jdbc.JdbcDatasource.doWithDatabase(JdbcDatasource.java:480)[magma-datasource-jdbc-1.12-20160926.114307-99.jar:1.12-SNAPSHOT]
    2. org.obiba.magma.datasource.jdbc.JdbcValueTableWriter$JdbcVariableWriter.close(JdbcValueTableWriter.java:265)[magma-datasource-jdbc-1.12-20160926.114307-99.jar:1.12-SNAPSHOT]
    3. org.obiba.magma.support.DatasourceCopier.copyMetadata(DatasourceCopier.java:266)[magma-api-1.12-20160926.114307-99.jar:1.12-SNAPSHOT]
    4. org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:227)[magma-api-1.12-20160926.114307-99.jar:1.12-SNAPSHOT]
    5. org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:217)[magma-api-1.12-20160926.114307-99.jar:1.12-SNAPSHOT]
    6. org.obiba.magma.support.DatasourceCopier.copy(DatasourceCopier.java:200)[magma-api-1.12-20160926.114307-99.jar:1.12-SNAPSHOT]
    6 frames
  9. org.obiba.opal
    LockingActionTemplate$1.doInTransactionWithoutResult
    1. org.obiba.opal.core.service.CopyValueTablesLockingAction$CopyAction.execute(CopyValueTablesLockingAction.java:150)[opal-core-2.6-SNAPSHOT.jar:na]
    2. org.obiba.opal.core.magma.concurrent.LockingActionTemplate$1.doInTransactionWithoutResult(LockingActionTemplate.java:47)[opal-core-2.6-SNAPSHOT.jar:na]
    2 frames
  10. Spring Tx
    TransactionTemplate.execute
    1. org.springframework.transaction.support.TransactionCallbackWithoutResult.doInTransaction(TransactionCallbackWithoutResult.java:34)[spring-tx-4.2.1.RELEASE.jar:4.2.1.RELEASE]
    2. org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:133)[spring-tx-4.2.1.RELEASE.jar:4.2.1.RELEASE]
    2 frames
  11. org.obiba.opal
    CommandJob.run
    1. org.obiba.opal.core.magma.concurrent.LockingActionTemplate.doInTransaction(LockingActionTemplate.java:42)[opal-core-2.6-SNAPSHOT.jar:na]
    2. org.obiba.opal.core.magma.concurrent.LockingActionTemplate.execute(LockingActionTemplate.java:31)[opal-core-2.6-SNAPSHOT.jar:na]
    3. org.obiba.opal.core.service.DataImportServiceImpl.copyValueTables(DataImportServiceImpl.java:134)[opal-core-2.6-SNAPSHOT.jar:na]
    4. org.obiba.opal.core.service.DataImportServiceImpl.importData(DataImportServiceImpl.java:105)[opal-core-2.6-SNAPSHOT.jar:na]
    5. org.obiba.opal.core.service.DataImportServiceImpl.importData(DataImportServiceImpl.java:87)[opal-core-2.6-SNAPSHOT.jar:na]
    6. org.obiba.opal.shell.commands.ImportCommand.importFromTables(ImportCommand.java:155)[opal-shell-2.6-SNAPSHOT.jar:na]
    7. org.obiba.opal.shell.commands.ImportCommand.executeImports(ImportCommand.java:89)[opal-shell-2.6-SNAPSHOT.jar:na]
    8. org.obiba.opal.shell.commands.ImportCommand.execute(ImportCommand.java:68)[opal-shell-2.6-SNAPSHOT.jar:na]
    9. org.obiba.opal.shell.CommandJob.run(CommandJob.java:153)[opal-shell-2.6-SNAPSHOT.jar:na]
    9 frames
  12. 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
  13. Java RT
    Thread.run
    1. java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)[na:1.8.0_101]
    2. java.util.concurrent.FutureTask.run(FutureTask.java:266)[na:1.8.0_101]
    3. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)[na:1.8.0_101]
    4. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)[na:1.8.0_101]
    5. java.lang.Thread.run(Thread.java:745)[na:1.8.0_101]
    5 frames