[2025-08-01T11:26:46.860+0000] [Payara 6.2023.8] [SEVERE] [] [javax.enterprise.system.tools.deployment.common] [tid: _ThreadID=98 _ThreadName=admin-thread-pool::admin-listener(1)] [timeMillis: 1754047606860] [levelValue: 1000] [[ Exception while invoking class org.glassfish.ejb.startup.EjbApplication start method jakarta.ejb.EJBException: jakarta.ejb.CreateException: Initialization failed for Singleton StartupFlywayMigrator at com.sun.ejb.containers.AbstractSingletonContainer$SingletonContextFactory.create(AbstractSingletonContainer.java:745) at com.sun.ejb.containers.AbstractSingletonContainer.instantiateSingletonInstance(AbstractSingletonContainer.java:477) at org.glassfish.ejb.startup.SingletonLifeCycleManager.initializeSingleton(SingletonLifeCycleManager.java:219) at org.glassfish.ejb.startup.SingletonLifeCycleManager.initializeSingleton(SingletonLifeCycleManager.java:180) at org.glassfish.ejb.startup.SingletonLifeCycleManager.doStartup(SingletonLifeCycleManager.java:159) at org.glassfish.ejb.startup.EjbApplication.start(EjbApplication.java:171) at org.glassfish.internal.data.EngineRef.start(EngineRef.java:123) at org.glassfish.internal.data.ModuleInfo.start(ModuleInfo.java:292) at org.glassfish.internal.data.ApplicationInfo.start(ApplicationInfo.java:361) at com.sun.enterprise.v3.server.ApplicationLifecycle.initialize(ApplicationLifecycle.java:633) at org.glassfish.deployment.admin.DeployCommand.execute(DeployCommand.java:574) at com.sun.enterprise.v3.admin.CommandRunnerImpl$2$1.run(CommandRunnerImpl.java:556) at com.sun.enterprise.v3.admin.CommandRunnerImpl$2$1.run(CommandRunnerImpl.java:552) at java.base/java.security.AccessController.doPrivileged(AccessController.java:399) at java.base/javax.security.auth.Subject.doAs(Subject.java:376) at com.sun.enterprise.v3.admin.CommandRunnerImpl$2.execute(CommandRunnerImpl.java:551) at com.sun.enterprise.v3.admin.CommandRunnerImpl$3.run(CommandRunnerImpl.java:582) at com.sun.enterprise.v3.admin.CommandRunnerImpl$3.run(CommandRunnerImpl.java:574) at java.base/java.security.AccessController.doPrivileged(AccessController.java:399) at java.base/javax.security.auth.Subject.doAs(Subject.java:376) at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:573) at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:1497) at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1879) at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1755) at org.glassfish.admin.rest.resources.admin.CommandResource.executeCommand(CommandResource.java:409) at org.glassfish.admin.rest.resources.admin.CommandResource.execCommandSimpInMultOut(CommandResource.java:236) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:569) at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory.lambda$static$0(ResourceMethodInvocationHandlerFactory.java:52) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:134) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:177) at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:176) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:81) at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:478) at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:400) at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:81) at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:261) at org.glassfish.jersey.internal.Errors$1.call(Errors.java:248) at org.glassfish.jersey.internal.Errors$1.call(Errors.java:244) at org.glassfish.jersey.internal.Errors.process(Errors.java:292) at org.glassfish.jersey.internal.Errors.process(Errors.java:274) at org.glassfish.jersey.internal.Errors.process(Errors.java:244) at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:265) at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:240) at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:697) at org.glassfish.jersey.grizzly2.httpserver.GrizzlyHttpContainer.service(GrizzlyHttpContainer.java:367) at org.glassfish.admin.rest.adapter.JerseyContainerCommandService$3.service(JerseyContainerCommandService.java:179) at org.glassfish.admin.rest.adapter.RestAdapter.service(RestAdapter.java:189) at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:520) at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:217) at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:174) at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:153) at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:196) at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:88) at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:246) at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:178) at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:118) at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:96) at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:51) at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:510) at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:82) at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:83) at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:101) at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:535) at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:515) at java.base/java.lang.Thread.run(Thread.java:840) Caused by: jakarta.ejb.CreateException: Initialization failed for Singleton StartupFlywayMigrator at com.sun.ejb.containers.AbstractSingletonContainer.createSingletonEJB(AbstractSingletonContainer.java:598) at com.sun.ejb.containers.AbstractSingletonContainer$SingletonContextFactory.create(AbstractSingletonContainer.java:743) ... 67 more Caused by: org.flywaydb.core.internal.command.DbMigrate$FlywayMigrateException: Migration V6.1.0.4__5645-geospatial-fieldname-fix.sql failed ------------------------------------------------------------ SQL State : 23505 Error Code : 0 Message : ERROR: duplicate key value violates unique constraint "datasetfieldtype_name_key" Detail: Key (name)=(northLatitude) already exists. Location : db/migration/V6.1.0.4__5645-geospatial-fieldname-fix.sql (/usr/local/payara6/glassfish/domains/domain1/applications/dataverse/WEB-INF/classes/db/migration/V6.1.0.4__5645-geospatial-fieldname-fix.sql) Line : 1 Statement : UPDATE datasetfieldtype SET name = 'northLatitude' WHERE name = 'northLongitude' at org.flywaydb.core.internal.command.DbMigrate.doMigrateGroup(DbMigrate.java:382) at org.flywaydb.core.internal.command.DbMigrate.lambda$applyMigrations$1(DbMigrate.java:272) at org.flywaydb.core.internal.jdbc.TransactionalExecutionTemplate.execute(TransactionalExecutionTemplate.java:55) at org.flywaydb.core.internal.command.DbMigrate.applyMigrations(DbMigrate.java:271) at org.flywaydb.core.internal.command.DbMigrate.migrateGroup(DbMigrate.java:244) at org.flywaydb.core.internal.command.DbMigrate.lambda$migrateAll$0(DbMigrate.java:139) at org.flywaydb.core.internal.database.postgresql.PostgreSQLAdvisoryLockTemplate.execute(PostgreSQLAdvisoryLockTemplate.java:73) at org.flywaydb.core.internal.database.postgresql.PostgreSQLAdvisoryLockTemplate.lambda$execute$0(PostgreSQLAdvisoryLockTemplate.java:56) at org.flywaydb.core.internal.jdbc.TransactionalExecutionTemplate.execute(TransactionalExecutionTemplate.java:55) at org.flywaydb.core.internal.database.postgresql.PostgreSQLAdvisoryLockTemplate.execute(PostgreSQLAdvisoryLockTemplate.java:56) at org.flywaydb.core.internal.database.postgresql.PostgreSQLConnection.lock(PostgreSQLConnection.java:96) at org.flywaydb.core.internal.schemahistory.JdbcTableSchemaHistory.lock(JdbcTableSchemaHistory.java:144) at org.flywaydb.core.internal.command.DbMigrate.migrateAll(DbMigrate.java:139) at org.flywaydb.core.internal.command.DbMigrate.migrate(DbMigrate.java:97) at org.flywaydb.core.Flyway.lambda$migrate$0(Flyway.java:188) at org.flywaydb.core.FlywayExecutor.execute(FlywayExecutor.java:213) at org.flywaydb.core.Flyway.migrate(Flyway.java:140) at edu.harvard.iq.dataverse.flyway.StartupFlywayMigrator.migrateDatabase(StartupFlywayMigrator.java:33) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:569) at com.sun.ejb.containers.interceptors.BeanCallbackInterceptor.intercept(InterceptorManager.java:1022) at com.sun.ejb.containers.interceptors.CallbackChainImpl.invokeNext(CallbackChainImpl.java:72) at com.sun.ejb.containers.interceptors.CallbackInvocationContext.proceed(CallbackInvocationContext.java:204) at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163) at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.init(SystemInterceptorProxy.java:125) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:569) at com.sun.ejb.containers.interceptors.CallbackInterceptor.intercept(InterceptorManager.java:978) at com.sun.ejb.containers.interceptors.CallbackChainImpl.invokeNext(CallbackChainImpl.java:72) at com.sun.ejb.containers.interceptors.CallbackInvocationContext.proceed(CallbackInvocationContext.java:204) at org.jboss.weld.module.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:81) at org.jboss.weld.module.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:569) at com.sun.ejb.containers.interceptors.CallbackInterceptor.intercept(InterceptorManager.java:978) at com.sun.ejb.containers.interceptors.CallbackChainImpl.invokeNext(CallbackChainImpl.java:72) at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:418) at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:381) at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:2071) at com.sun.ejb.containers.AbstractSingletonContainer.createSingletonEJB(AbstractSingletonContainer.java:585) ... 68 more Caused by: org.flywaydb.core.internal.sqlscript.FlywaySqlScriptException: Migration V6.1.0.4__5645-geospatial-fieldname-fix.sql failed ------------------------------------------------------------ SQL State : 23505 Error Code : 0 Message : ERROR: duplicate key value violates unique constraint "datasetfieldtype_name_key" Detail: Key (name)=(northLatitude) already exists. Location : db/migration/V6.1.0.4__5645-geospatial-fieldname-fix.sql (/usr/local/payara6/glassfish/domains/domain1/applications/dataverse/WEB-INF/classes/db/migration/V6.1.0.4__5645-geospatial-fieldname-fix.sql) Line : 1 Statement : UPDATE datasetfieldtype SET name = 'northLatitude' WHERE name = 'northLongitude' at org.flywaydb.core.internal.sqlscript.DefaultSqlScriptExecutor.handleException(DefaultSqlScriptExecutor.java:267) at org.flywaydb.core.internal.sqlscript.DefaultSqlScriptExecutor.executeStatement(DefaultSqlScriptExecutor.java:222) at org.flywaydb.core.internal.sqlscript.DefaultSqlScriptExecutor.execute(DefaultSqlScriptExecutor.java:126) at org.flywaydb.core.internal.resolver.sql.SqlMigrationExecutor.executeOnce(SqlMigrationExecutor.java:68) at org.flywaydb.core.internal.resolver.sql.SqlMigrationExecutor.lambda$execute$0(SqlMigrationExecutor.java:57) at org.flywaydb.core.internal.database.DefaultExecutionStrategy.execute(DefaultExecutionStrategy.java:27) at org.flywaydb.core.internal.resolver.sql.SqlMigrationExecutor.execute(SqlMigrationExecutor.java:56) at org.flywaydb.core.internal.command.DbMigrate.doMigrateGroup(DbMigrate.java:374) ... 113 more Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "datasetfieldtype_name_key" Detail: Key (name)=(northLatitude) already exists. at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2725) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2412) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:371) at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:502) at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:419) at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:341) at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:326) at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:302) at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:297) at jdk.internal.reflect.GeneratedMethodAccessor135.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:569) at org.postgresql.ds.PGPooledConnection$StatementHandler.invoke(PGPooledConnection.java:447) at jdk.proxy96/jdk.proxy96.$Proxy572.execute(Unknown Source) at com.sun.gjc.spi.base.StatementWrapper.execute(StatementWrapper.java:375) at org.flywaydb.core.internal.jdbc.JdbcTemplate.executeStatement(JdbcTemplate.java:201) at org.flywaydb.core.internal.sqlscript.ParsedSqlStatement.execute(ParsedSqlStatement.java:95) at org.flywaydb.core.internal.sqlscript.DefaultSqlScriptExecutor.executeStatement(DefaultSqlScriptExecutor.java:210) ... 119 more ]] [2025-08-01T11:26:46.862+0000] [Payara 6.2023.8] [SEVERE] [NCLS-CORE-00026] [javax.enterprise.system.core] [tid: _ThreadID=98 _ThreadName=admin-thread-pool::admin-listener(1)] [timeMillis: 1754047606862] [levelValue: 1000] [[ Exception during lifecycle processing jakarta.ejb.EJBException: jakarta.ejb.CreateException: Initialization failed for Singleton StartupFlywayMigrator at com.sun.ejb.containers.AbstractSingletonContainer$SingletonContextFactory.create(AbstractSingletonContainer.java:745) at com.sun.ejb.containers.AbstractSingletonContainer.instantiateSingletonInstance(AbstractSingletonContainer.java:477) at org.glassfish.ejb.startup.SingletonLifeCycleManager.initializeSingleton(SingletonLifeCycleManager.java:219) at org.glassfish.ejb.startup.SingletonLifeCycleManager.initializeSingleton(SingletonLifeCycleManager.java:180) at org.glassfish.ejb.startup.SingletonLifeCycleManager.doStartup(SingletonLifeCycleManager.java:159) at org.glassfish.ejb.startup.EjbApplication.start(EjbApplication.java:171) at org.glassfish.internal.data.EngineRef.start(EngineRef.java:123) at org.glassfish.internal.data.ModuleInfo.start(ModuleInfo.java:292) at org.glassfish.internal.data.ApplicationInfo.start(ApplicationInfo.java:361) at com.sun.enterprise.v3.server.ApplicationLifecycle.initialize(ApplicationLifecycle.java:633) at org.glassfish.deployment.admin.DeployCommand.execute(DeployCommand.java:574) at com.sun.enterprise.v3.admin.CommandRunnerImpl$2$1.run(CommandRunnerImpl.java:556) at com.sun.enterprise.v3.admin.CommandRunnerImpl$2$1.run(CommandRunnerImpl.java:552) at java.base/java.security.AccessController.doPrivileged(AccessController.java:399) at java.base/javax.security.auth.Subject.doAs(Subject.java:376) at com.sun.enterprise.v3.admin.CommandRunnerImpl$2.execute(CommandRunnerImpl.java:551) at com.sun.enterprise.v3.admin.CommandRunnerImpl$3.run(CommandRunnerImpl.java:582) at com.sun.enterprise.v3.admin.CommandRunnerImpl$3.run(CommandRunnerImpl.java:574) at java.base/java.security.AccessController.doPrivileged(AccessController.java:399) at java.base/javax.security.auth.Subject.doAs(Subject.java:376) at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:573) at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:1497) at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1879) at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1755) at org.glassfish.admin.rest.resources.admin.CommandResource.executeCommand(CommandResource.java:409) at org.glassfish.admin.rest.resources.admin.CommandResource.execCommandSimpInMultOut(CommandResource.java:236) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:569) at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory.lambda$static$0(ResourceMethodInvocationHandlerFactory.java:52) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:134) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:177) at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:176) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:81) at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:478) at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:400) at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:81) at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:261) at org.glassfish.jersey.internal.Errors$1.call(Errors.java:248) at org.glassfish.jersey.internal.Errors$1.call(Errors.java:244) at org.glassfish.jersey.internal.Errors.process(Errors.java:292) at org.glassfish.jersey.internal.Errors.process(Errors.java:274) at org.glassfish.jersey.internal.Errors.process(Errors.java:244) at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:265) at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:240) at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:697) at org.glassfish.jersey.grizzly2.httpserver.GrizzlyHttpContainer.service(GrizzlyHttpContainer.java:367) at org.glassfish.admin.rest.adapter.JerseyContainerCommandService$3.service(JerseyContainerCommandService.java:179) at org.glassfish.admin.rest.adapter.RestAdapter.service(RestAdapter.java:189) at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:520) at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:217) at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:174) at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:153) at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:196) at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:88) at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:246) at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:178) at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:118) at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:96) at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:51) at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:510) at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:82) at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:83) at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:101) at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:535) at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:515) at java.base/java.lang.Thread.run(Thread.java:840) Caused by: jakarta.ejb.CreateException: Initialization failed for Singleton StartupFlywayMigrator at com.sun.ejb.containers.AbstractSingletonContainer.createSingletonEJB(AbstractSingletonContainer.java:598) at com.sun.ejb.containers.AbstractSingletonContainer$SingletonContextFactory.create(AbstractSingletonContainer.java:743) ... 67 more Caused by: org.flywaydb.core.internal.command.DbMigrate$FlywayMigrateException: Migration V6.1.0.4__5645-geospatial-fieldname-fix.sql failed ------------------------------------------------------------ SQL State : 23505 Error Code : 0 Message : ERROR: duplicate key value violates unique constraint "datasetfieldtype_name_key" Detail: Key (name)=(northLatitude) already exists. Location : db/migration/V6.1.0.4__5645-geospatial-fieldname-fix.sql (/usr/local/payara6/glassfish/domains/domain1/applications/dataverse/WEB-INF/classes/db/migration/V6.1.0.4__5645-geospatial-fieldname-fix.sql) Line : 1 Statement : UPDATE datasetfieldtype SET name = 'northLatitude' WHERE name = 'northLongitude' at org.flywaydb.core.internal.command.DbMigrate.doMigrateGroup(DbMigrate.java:382) at org.flywaydb.core.internal.command.DbMigrate.lambda$applyMigrations$1(DbMigrate.java:272) at org.flywaydb.core.internal.jdbc.TransactionalExecutionTemplate.execute(TransactionalExecutionTemplate.java:55) at org.flywaydb.core.internal.command.DbMigrate.applyMigrations(DbMigrate.java:271) at org.flywaydb.core.internal.command.DbMigrate.migrateGroup(DbMigrate.java:244) at org.flywaydb.core.internal.command.DbMigrate.lambda$migrateAll$0(DbMigrate.java:139) at org.flywaydb.core.internal.database.postgresql.PostgreSQLAdvisoryLockTemplate.execute(PostgreSQLAdvisoryLockTemplate.java:73) at org.flywaydb.core.internal.database.postgresql.PostgreSQLAdvisoryLockTemplate.lambda$execute$0(PostgreSQLAdvisoryLockTemplate.java:56) at org.flywaydb.core.internal.jdbc.TransactionalExecutionTemplate.execute(TransactionalExecutionTemplate.java:55) at org.flywaydb.core.internal.database.postgresql.PostgreSQLAdvisoryLockTemplate.execute(PostgreSQLAdvisoryLockTemplate.java:56) at org.flywaydb.core.internal.database.postgresql.PostgreSQLConnection.lock(PostgreSQLConnection.java:96) at org.flywaydb.core.internal.schemahistory.JdbcTableSchemaHistory.lock(JdbcTableSchemaHistory.java:144) at org.flywaydb.core.internal.command.DbMigrate.migrateAll(DbMigrate.java:139) at org.flywaydb.core.internal.command.DbMigrate.migrate(DbMigrate.java:97) at org.flywaydb.core.Flyway.lambda$migrate$0(Flyway.java:188) at org.flywaydb.core.FlywayExecutor.execute(FlywayExecutor.java:213) at org.flywaydb.core.Flyway.migrate(Flyway.java:140) at edu.harvard.iq.dataverse.flyway.StartupFlywayMigrator.migrateDatabase(StartupFlywayMigrator.java:33) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:569) at com.sun.ejb.containers.interceptors.BeanCallbackInterceptor.intercept(InterceptorManager.java:1022) at com.sun.ejb.containers.interceptors.CallbackChainImpl.invokeNext(CallbackChainImpl.java:72) at com.sun.ejb.containers.interceptors.CallbackInvocationContext.proceed(CallbackInvocationContext.java:204) at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163) at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.init(SystemInterceptorProxy.java:125) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:569) at com.sun.ejb.containers.interceptors.CallbackInterceptor.intercept(InterceptorManager.java:978) at com.sun.ejb.containers.interceptors.CallbackChainImpl.invokeNext(CallbackChainImpl.java:72) at com.sun.ejb.containers.interceptors.CallbackInvocationContext.proceed(CallbackInvocationContext.java:204) at org.jboss.weld.module.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:81) at org.jboss.weld.module.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:569) at com.sun.ejb.containers.interceptors.CallbackInterceptor.intercept(InterceptorManager.java:978) at com.sun.ejb.containers.interceptors.CallbackChainImpl.invokeNext(CallbackChainImpl.java:72) at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:418) at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:381) at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:2071) at com.sun.ejb.containers.AbstractSingletonContainer.createSingletonEJB(AbstractSingletonContainer.java:585) ... 68 more Caused by: org.flywaydb.core.internal.sqlscript.FlywaySqlScriptException: Migration V6.1.0.4__5645-geospatial-fieldname-fix.sql failed ------------------------------------------------------------ SQL State : 23505 Error Code : 0 Message : ERROR: duplicate key value violates unique constraint "datasetfieldtype_name_key" Detail: Key (name)=(northLatitude) already exists. Location : db/migration/V6.1.0.4__5645-geospatial-fieldname-fix.sql (/usr/local/payara6/glassfish/domains/domain1/applications/dataverse/WEB-INF/classes/db/migration/V6.1.0.4__5645-geospatial-fieldname-fix.sql) Line : 1 Statement : UPDATE datasetfieldtype SET name = 'northLatitude' WHERE name = 'northLongitude' at org.flywaydb.core.internal.sqlscript.DefaultSqlScriptExecutor.handleException(DefaultSqlScriptExecutor.java:267) at org.flywaydb.core.internal.sqlscript.DefaultSqlScriptExecutor.executeStatement(DefaultSqlScriptExecutor.java:222) at org.flywaydb.core.internal.sqlscript.DefaultSqlScriptExecutor.execute(DefaultSqlScriptExecutor.java:126) at org.flywaydb.core.internal.resolver.sql.SqlMigrationExecutor.executeOnce(SqlMigrationExecutor.java:68) at org.flywaydb.core.internal.resolver.sql.SqlMigrationExecutor.lambda$execute$0(SqlMigrationExecutor.java:57) at org.flywaydb.core.internal.database.DefaultExecutionStrategy.execute(DefaultExecutionStrategy.java:27) at org.flywaydb.core.internal.resolver.sql.SqlMigrationExecutor.execute(SqlMigrationExecutor.java:56) at org.flywaydb.core.internal.command.DbMigrate.doMigrateGroup(DbMigrate.java:374) ... 113 more Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "datasetfieldtype_name_key" Detail: Key (name)=(northLatitude) already exists. at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2725) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2412) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:371) at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:502) at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:419) at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:341) at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:326) at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:302) at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:297) at jdk.internal.reflect.GeneratedMethodAccessor135.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:569) at org.postgresql.ds.PGPooledConnection$StatementHandler.invoke(PGPooledConnection.java:447) at jdk.proxy96/jdk.proxy96.$Proxy572.execute(Unknown Source) at com.sun.gjc.spi.base.StatementWrapper.execute(StatementWrapper.java:375) at org.flywaydb.core.internal.jdbc.JdbcTemplate.executeStatement(JdbcTemplate.java:201) at org.flywaydb.core.internal.sqlscript.ParsedSqlStatement.execute(ParsedSqlStatement.java:95) at org.flywaydb.core.internal.sqlscript.DefaultSqlScriptExecutor.executeStatement(DefaultSqlScriptExecutor.java:210) ... 119 more ]] [2025-08-01T11:26:46.863+0000] [Payara 6.2023.8] [SEVERE] [] [javax.enterprise.system.core] [tid: _ThreadID=98 _ThreadName=admin-thread-pool::admin-listener(1)] [timeMillis: 1754047606863] [levelValue: 1000] [[ Exception while loading the app]] [2025-08-01T11:26:47.037+0000] [Payara 6.2023.8] [SEVERE] [AS-WEB-GLUE-00192] [jakarta.enterprise.web] [tid: _ThreadID=98 _ThreadName=admin-thread-pool::admin-listener(1)] [timeMillis: 1754047607037] [levelValue: 1000] [[ Undeployment failed for context ]] [2025-08-01T11:26:47.038+0000] [Payara 6.2023.8] [WARNING] [] [jakarta.enterprise.web.util] [tid: _ThreadID=98 _ThreadName=admin-thread-pool::admin-listener(1)] [timeMillis: 1754047607038] [levelValue: 900] [[ The web application [unknown] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.]] [2025-08-01T11:26:47.047+0000] [Payara 6.2023.8] [INFO] [] [javax.enterprise.system.container.ejb.com.sun.ejb.containers] [tid: _ThreadID=98 _ThreadName=admin-thread-pool::admin-listener(1)] [timeMillis: 1754047607047] [levelValue: 800] [[ No timers to be deleted for id: 114953159021690880]] [2025-08-01T11:26:47.052+0000] [Payara 6.2023.8] [SEVERE] [] [] [tid: _ThreadID=98 _ThreadName=admin-thread-pool::admin-listener(1)] [timeMillis: 1754047607052] [levelValue: 1000] [[ java.util.logging.ErrorManager: 5: Error in formatting Logrecord]] [2025-08-01T11:26:47.053+0000] [Payara 6.2023.8] [SEVERE] [] [] [tid: _ThreadID=98 _ThreadName=admin-thread-pool::admin-listener(1)] [timeMillis: 1754047607053] [levelValue: 1000] [[ org.flywaydb.core.api.FlywayException: Unable to find resource on disk: db/migration/V6.1.0.4__5645-geospatial-fieldname-fix.sql at org.flywaydb.core.internal.resource.classpath.ClassPathResource.getAbsolutePathOnDisk(ClassPathResource.java:80) at org.flywaydb.core.internal.sqlscript.FlywaySqlScriptException.getMessage(FlywaySqlScriptException.java:71) at java.base/java.lang.Throwable.getLocalizedMessage(Throwable.java:397) at java.base/java.lang.Throwable.toString(Throwable.java:496) at java.base/java.lang.String.valueOf(String.java:4220) at java.base/java.lang.StringBuilder.append(StringBuilder.java:173) at java.base/java.lang.Throwable.printEnclosedStackTrace(Throwable.java:710) at java.base/java.lang.Throwable.printEnclosedStackTrace(Throwable.java:724) at java.base/java.lang.Throwable.printStackTrace(Throwable.java:682) at java.base/java.lang.Throwable.printStackTrace(Throwable.java:736) at com.sun.enterprise.server.logging.UniformLogFormatter.uniformLogFormat(UniformLogFormatter.java:391) at com.sun.enterprise.server.logging.UniformLogFormatter.format(UniformLogFormatter.java:164) at java.logging/java.util.logging.StreamHandler.publish(StreamHandler.java:199) at java.logging/java.util.logging.ConsoleHandler.publish(ConsoleHandler.java:95) at java.logging/java.util.logging.Logger.log(Logger.java:980) at java.logging/java.util.logging.Logger.doLog(Logger.java:1007) at java.logging/java.util.logging.Logger.log(Logger.java:1118) at org.glassfish.deployment.admin.DeployCommand.execute(DeployCommand.java:677) at com.sun.enterprise.v3.admin.CommandRunnerImpl$2$1.run(CommandRunnerImpl.java:556) at com.sun.enterprise.v3.admin.CommandRunnerImpl$2$1.run(CommandRunnerImpl.java:552) at java.base/java.security.AccessController.doPrivileged(AccessController.java:399) at java.base/javax.security.auth.Subject.doAs(Subject.java:376) at com.sun.enterprise.v3.admin.CommandRunnerImpl$2.execute(CommandRunnerImpl.java:551) at com.sun.enterprise.v3.admin.CommandRunnerImpl$3.run(CommandRunnerImpl.java:582) at com.sun.enterprise.v3.admin.CommandRunnerImpl$3.run(CommandRunnerImpl.java:574) at java.base/java.security.AccessController.doPrivileged(AccessController.java:399) at java.base/javax.security.auth.Subject.doAs(Subject.java:376) at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:573) at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:1497) at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1879) at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1755) at org.glassfish.admin.rest.resources.admin.CommandResource.executeCommand(CommandResource.java:409) at org.glassfish.admin.rest.resources.admin.CommandResource.execCommandSimpInMultOut(CommandResource.java:236) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:569) at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory.lambda$static$0(ResourceMethodInvocationHandlerFactory.java:52) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:134) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:177) at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:176) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:81) at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:478) at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:400) at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:81) at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:261) at org.glassfish.jersey.internal.Errors$1.call(Errors.java:248) at org.glassfish.jersey.internal.Errors$1.call(Errors.java:244) at org.glassfish.jersey.internal.Errors.process(Errors.java:292) at org.glassfish.jersey.internal.Errors.process(Errors.java:274) at org.glassfish.jersey.internal.Errors.process(Errors.java:244) at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:265) at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:240) at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:697) at org.glassfish.jersey.grizzly2.httpserver.GrizzlyHttpContainer.service(GrizzlyHttpContainer.java:367) at org.glassfish.admin.rest.adapter.JerseyContainerCommandService$3.service(JerseyContainerCommandService.java:179) at org.glassfish.admin.rest.adapter.RestAdapter.service(RestAdapter.java:189) at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:520) at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:217) at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:174) at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:153) at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:196) at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:88) at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:246) at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:178) at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:118) at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:96) at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:51) at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:510) at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:82) at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:83) at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:101) at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:535) at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:515) at java.base/java.lang.Thread.run(Thread.java:840) ]] [2025-08-01T11:26:47.054+0000] [Payara 6.2023.8] [SEVERE] [] [] [tid: _ThreadID=34 _ThreadName=GFFileHandler log pump] [timeMillis: 1754047607054] [levelValue: 1000] [[ java.util.logging.ErrorManager: 5: Error in formatting Logrecord]] [2025-08-01T11:26:47.054+0000] [Payara 6.2023.8] [SEVERE] [] [] [tid: _ThreadID=34 _ThreadName=GFFileHandler log pump] [timeMillis: 1754047607054] [levelValue: 1000] [[ org.flywaydb.core.api.FlywayException: Unable to find resource on disk: db/migration/V6.1.0.4__5645-geospatial-fieldname-fix.sql at org.flywaydb.core.internal.resource.classpath.ClassPathResource.getAbsolutePathOnDisk(ClassPathResource.java:80) at org.flywaydb.core.internal.sqlscript.FlywaySqlScriptException.getMessage(FlywaySqlScriptException.java:71) at java.base/java.lang.Throwable.getLocalizedMessage(Throwable.java:397) at java.base/java.lang.Throwable.toString(Throwable.java:496) at java.base/java.lang.String.valueOf(String.java:4220) at java.base/java.lang.StringBuilder.append(StringBuilder.java:173) at java.base/java.lang.Throwable.printEnclosedStackTrace(Throwable.java:710) at java.base/java.lang.Throwable.printEnclosedStackTrace(Throwable.java:724) at java.base/java.lang.Throwable.printStackTrace(Throwable.java:682) at java.base/java.lang.Throwable.printStackTrace(Throwable.java:736) at com.sun.enterprise.server.logging.ODLLogFormatter.getLogMessage(ODLLogFormatter.java:355) at com.sun.enterprise.server.logging.ODLLogFormatter.odlLogFormat(ODLLogFormatter.java:162) at com.sun.enterprise.server.logging.ODLLogFormatter.format(ODLLogFormatter.java:143) at java.logging/java.util.logging.StreamHandler.publish(StreamHandler.java:199) at com.sun.enterprise.server.logging.GFFileHandler.log(GFFileHandler.java:948) at com.sun.enterprise.server.logging.GFFileHandler$1.run(GFFileHandler.java:581) ]]