01 Mar 2017 22:51:54,728 INFO : Study reload was initiated by a configured automatic reload timer
01 Mar 2017 22:51:54,730 INFO : User "Bernard" is configured as the reload user for this study. This can be changed by visiting the "Manage Reloading" page.
01 Mar 2017 22:51:54,788 INFO : Starting to run task 'org.labkey.study.importer.StudyImportInitialTask' at location 'webserver'
01 Mar 2017 22:51:54,791 INFO : Reloading study from study.xml
01 Mar 2017 22:51:54,792 INFO : Loading top-level study properties (label, start/end date, description, etc.)
01 Mar 2017 22:51:54,868 INFO : Done importing top-level study properties (label, start/end date, description, etc.)
01 Mar 2017 22:51:54,872 INFO : Loading datasets manifest from datasets_manifest.xml
01 Mar 2017 22:51:54,875 INFO : Loading dataset schema from datasets_metadata.xml
01 Mar 2017 22:51:56,430 INFO : Successfully completed task 'org.labkey.study.importer.StudyImportInitialTask'
01 Mar 2017 22:51:56,449 INFO : Starting to run task 'org.labkey.study.pipeline.StudyImportDatasetTask' at location 'webserver'
01 Mar 2017 22:51:56,451 INFO : Start batch RedCap Integration.dataset
01 Mar 2017 22:51:56,469 INFO : demographics: Starting delete
01 Mar 2017 22:51:56,470 INFO : demographics: Deleted 5 rows
01 Mar 2017 22:51:56,471 INFO : demographics: Starting import from dataset001.tsv
01 Mar 2017 22:51:56,505 DEBUG: commit complete
01 Mar 2017 22:51:56,524 INFO : demographics: Successfully imported 5 rows from dataset001.tsv
01 Mar 2017 22:51:56,540 INFO : emergency_contact_info: Starting delete
01 Mar 2017 22:51:56,541 INFO : emergency_contact_info: Deleted 5 rows
01 Mar 2017 22:51:56,542 INFO : emergency_contact_info: Starting import from dataset002.tsv
01 Mar 2017 22:51:56,562 DEBUG: commit complete
01 Mar 2017 22:51:56,575 INFO : emergency_contact_info: Successfully imported 5 rows from dataset002.tsv
01 Mar 2017 22:51:56,592 INFO : baseline_lab_data: Starting delete
01 Mar 2017 22:51:56,593 INFO : baseline_lab_data: Deleted 5 rows
01 Mar 2017 22:51:56,594 INFO : baseline_lab_data: Starting import from dataset003.tsv
01 Mar 2017 22:51:56,612 DEBUG: commit complete
01 Mar 2017 22:51:56,627 INFO : baseline_lab_data: Successfully imported 5 rows from dataset003.tsv
01 Mar 2017 22:51:56,644 INFO : visit_blood_workup: Starting delete
01 Mar 2017 22:51:56,645 INFO : visit_blood_workup: Deleted 0 rows
01 Mar 2017 22:51:56,645 INFO : visit_blood_workup: Starting import from dataset004.tsv
01 Mar 2017 22:51:56,653 DEBUG: commit complete
01 Mar 2017 22:51:56,666 INFO : visit_blood_workup: Successfully imported 0 rows from dataset004.tsv
01 Mar 2017 22:51:56,682 INFO : completion_data: Starting delete
01 Mar 2017 22:51:56,683 INFO : completion_data: Deleted 0 rows
01 Mar 2017 22:51:56,683 INFO : completion_data: Starting import from dataset005.tsv
01 Mar 2017 22:51:56,692 DEBUG: commit complete
01 Mar 2017 22:51:56,704 INFO : completion_data: Successfully imported 0 rows from dataset005.tsv
01 Mar 2017 22:51:56,722 INFO : completion_project_questionnaire: Starting delete
01 Mar 2017 22:51:56,723 INFO : completion_project_questionnaire: Deleted 0 rows
01 Mar 2017 22:51:56,723 INFO : completion_project_questionnaire: Starting import from dataset006.tsv
01 Mar 2017 22:51:56,732 DEBUG: commit complete
01 Mar 2017 22:51:56,744 INFO : completion_project_questionnaire: Successfully imported 0 rows from dataset006.tsv
01 Mar 2017 22:51:56,744 INFO : Finish batch RedCap Integration.dataset
01 Mar 2017 22:51:56,750 INFO : Updating participant visits
01 Mar 2017 22:51:56,750 INFO : Updating participants
01 Mar 2017 22:51:56,765 INFO : Updating participant visit table
01 Mar 2017 22:51:56,816 INFO : Updating visit table
01 Mar 2017 22:51:56,818 INFO : Updating cohorts
01 Mar 2017 22:51:56,818 INFO : Clearing participant visit caches
01 Mar 2017 22:51:56,822 INFO : Finished updating participants
01 Mar 2017 22:51:56,822 INFO : Successfully completed task 'org.labkey.study.pipeline.StudyImportDatasetTask'
01 Mar 2017 22:51:56,850 INFO : Starting to run task 'org.labkey.study.pipeline.StudyImportSpecimenTask' at location 'webserver'
01 Mar 2017 22:51:56,853 INFO : Successfully completed task 'org.labkey.study.pipeline.StudyImportSpecimenTask'
01 Mar 2017 22:51:56,875 INFO : Starting to run task 'org.labkey.study.importer.StudyImportFinalTask' at location 'webserver'
01 Mar 2017 22:51:56,892 INFO : Loading dataset cohort assignments
01 Mar 2017 22:51:56,892 INFO : Done importing dataset cohort assignments
01 Mar 2017 22:51:56,937 INFO : Loading lists
01 Mar 2017 22:52:00,800 INFO : Failed to complete task 'org.labkey.study.importer.StudyImportFinalTask'
01 Mar 2017 22:52:00,800 ERROR: org.springframework.jdbc.UncategorizedSQLException: ExecutingSelector; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; This connection has already been closed, and may have been left in a bad state. See nested exception for potentially suspect code.; nested exception is java.sql.SQLException: This connection has already been closed, and may have been left in a bad state. See nested exception for potentially suspect code.
org.labkey.api.pipeline.PipelineJobException: org.springframework.jdbc.UncategorizedSQLException: ExecutingSelector; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; This connection has already been closed, and may have been left in a bad state. See nested exception for potentially suspect code.; nested exception is java.sql.SQLException: This connection has already been closed, and may have been left in a bad state. See nested exception for potentially suspect code.
    at org.labkey.study.importer.StudyImportFinalTask.doImport(StudyImportFinalTask.java:125)
    at org.labkey.study.importer.StudyImportFinalTask.run(StudyImportFinalTask.java:56)
    at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:710)
    at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:941)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.RuntimeException: org.springframework.jdbc.UncategorizedSQLException: ExecutingSelector; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; This connection has already been closed, and may have been left in a bad state. See nested exception for potentially suspect code.; nested exception is java.sql.SQLException: This connection has already been closed, and may have been left in a bad state. See nested exception for potentially suspect code.
    at org.labkey.audit.AuditLogImpl._addEvent(AuditLogImpl.java:165)
    at org.labkey.audit.AuditLogImpl.addEvent(AuditLogImpl.java:100)
    at org.labkey.list.model.ListManager.addAuditEvent(ListManager.java:846)
    at org.labkey.list.model.ListQueryUpdateService.insertUsingDataIterator(ListQueryUpdateService.java:227)
    at org.labkey.list.model.ListDefinitionImpl.insertListItems(ListDefinitionImpl.java:568)
    at org.labkey.list.model.ListImporter.process(ListImporter.java:213)
    at org.labkey.list.model.FolderListImporter.process(FolderListImporter.java:65)
    at org.labkey.study.importer.StudyImportFinalTask.doImport(StudyImportFinalTask.java:103)
    ... 10 more
    Suppressed: java.lang.IllegalStateException: SPID=30994 DbScope=labkey No transactions remain, can't decrement!
        at org.labkey.api.data.DbScope.createIllegalStateException(DbScope.java:230)
        at org.labkey.api.data.DbScope.access$1200(DbScope.java:109)
        at org.labkey.api.data.DbScope$TransactionImpl.decrement(DbScope.java:1769)
        at org.labkey.api.data.DbScope$TransactionImpl.close(DbScope.java:1666)
        at org.labkey.list.model.ListImporter.process(ListImporter.java:254)
        ... 12 more
    Caused by: java.lang.Throwable: This connection may have been closed by a codepath that did not intend to leave it in this state
        at org.labkey.api.data.ConnectionWrapper.markAsSuspiciouslyClosed(ConnectionWrapper.java:901)
        at org.labkey.api.data.DbScope$TransactionImpl.close(DbScope.java:1669)
        at org.labkey.api.data.ContainerManager.getForPath(ContainerManager.java:924)
        at org.labkey.api.data.ContainerManager.getForPath(ContainerManager.java:890)
        at org.labkey.api.data.ContainerManager.getRoot(ContainerManager.java:960)
        at org.labkey.api.settings.AbstractSettingsGroup.lookupStringValue(AbstractSettingsGroup.java:61)
        at org.labkey.api.settings.AppPropsImpl.getDefaultLsidAuthority(AppPropsImpl.java:227)
        at org.labkey.api.exp.XarContext.<init>(XarContext.java:90)
        at org.labkey.api.audit.query.AbstractAuditDomainKind.getDomainURI(AbstractAuditDomainKind.java:159)
        at org.labkey.api.audit.query.AbstractAuditDomainKind.getDomainURI(AbstractAuditDomainKind.java:152)
        at org.labkey.api.audit.query.AbstractAuditDomainKind.generatePropertyURI(AbstractAuditDomainKind.java:174)
        at org.labkey.api.audit.query.AbstractAuditDomainKind.createPropertyDescriptor(AbstractAuditDomainKind.java:335)
        at org.labkey.api.audit.query.AbstractAuditDomainKind.createPropertyDescriptor(AbstractAuditDomainKind.java:312)
        at org.labkey.list.model.ListAuditProvider$ListAuditDomainKind.<init>(ListAuditProvider.java:244)
        at org.labkey.list.model.ListAuditProvider.getDomainKind(ListAuditProvider.java:70)
        at org.labkey.api.audit.AbstractAuditTypeProvider.getDomain(AbstractAuditTypeProvider.java:272)
        at org.labkey.api.audit.AbstractAuditTypeProvider.createStorageTableInfo(AbstractAuditTypeProvider.java:288)
        at org.labkey.list.model.ListAuditProvider.createTableInfo(ListAuditProvider.java:94)
        at org.labkey.audit.query.AuditQuerySchema.createTable(AuditQuerySchema.java:90)
        at org.labkey.api.query.UserSchema._getTableOrQuery(UserSchema.java:214)
        at org.labkey.api.query.UserSchema.getTable(UserSchema.java:159)
        at org.labkey.api.query.UserSchema.getTable(UserSchema.java:151)
        at org.labkey.api.query.UserSchema.getTable(UserSchema.java:250)
        at org.labkey.audit.model.LogManager._insertEvent(LogManager.java:92)
        at org.labkey.audit.AuditLogImpl._addEvent(AuditLogImpl.java:158)
        at org.labkey.audit.AuditLogImpl.addEvent(AuditLogImpl.java:100)
        at org.labkey.list.model.ListManager.addAuditEvent(ListManager.java:846)
        at org.labkey.list.model.ListQueryUpdateService.insertUsingDataIterator(ListQueryUpdateService.java:227)
        at org.labkey.list.model.ListDefinitionImpl.insertListItems(ListDefinitionImpl.java:568)
        at org.labkey.list.model.ListImporter.process(ListImporter.java:213)
        ... 12 more
Caused by: org.springframework.jdbc.UncategorizedSQLException: ExecutingSelector; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; This connection has already been closed, and may have been left in a bad state. See nested exception for potentially suspect code.; nested exception is java.sql.SQLException: This connection has already been closed, and may have been left in a bad state. See nested exception for potentially suspect code.
    at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:84)
    at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:81)
    at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:81)
    at org.labkey.api.data.ExceptionFramework$1.translate(ExceptionFramework.java:37)
    at org.labkey.api.data.ExceptionFramework$1.translate(ExceptionFramework.java:31)
    at org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.handleSqlException(SqlExecutingSelector.java:450)
    at org.labkey.api.data.BaseSelector.handleResultSet(BaseSelector.java:280)
    at org.labkey.api.data.BaseSelector.getArrayList(BaseSelector.java:102)
    at org.labkey.api.data.BaseSelector.getArrayList(BaseSelector.java:97)
    at org.labkey.api.exp.OntologyManager.getDomainDescriptor(OntologyManager.java:2072)
    at org.labkey.experiment.api.property.PropertyServiceImpl.getDomain(PropertyServiceImpl.java:87)
    at org.labkey.api.audit.AbstractAuditTypeProvider.getDomain(AbstractAuditTypeProvider.java:276)
    at org.labkey.api.audit.AbstractAuditTypeProvider.createStorageTableInfo(AbstractAuditTypeProvider.java:288)
    at org.labkey.list.model.ListAuditProvider.createTableInfo(ListAuditProvider.java:94)
    at org.labkey.audit.query.AuditQuerySchema.createTable(AuditQuerySchema.java:90)
    at org.labkey.api.query.UserSchema._getTableOrQuery(UserSchema.java:214)
    at org.labkey.api.query.UserSchema.getTable(UserSchema.java:159)
    at org.labkey.api.query.UserSchema.getTable(UserSchema.java:151)
    at org.labkey.api.query.UserSchema.getTable(UserSchema.java:250)
    at org.labkey.audit.model.LogManager._insertEvent(LogManager.java:92)
    at org.labkey.audit.AuditLogImpl._addEvent(AuditLogImpl.java:158)
    ... 17 more
Caused by: java.sql.SQLException: This connection has already been closed, and may have been left in a bad state. See nested exception for potentially suspect code.
    at org.labkey.api.data.ConnectionWrapper.checkForSuspiciousClose(ConnectionWrapper.java:895)
    at org.labkey.api.data.ConnectionWrapper.prepareStatement(ConnectionWrapper.java:530)
    at org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.executeQuery(SqlExecutingSelector.java:385)
    at org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.getResultSet(SqlExecutingSelector.java:331)
    at org.labkey.api.data.BaseSelector.handleResultSet(BaseSelector.java:261)
    ... 31 more
    [CIRCULAR REFERENCE:java.lang.Throwable: This connection may have been closed by a codepath that did not intend to leave it in this state]