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Created January 27, 2016 17:06
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labkey upgrade error log
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gistfile1.txt
INFO DbScope 2016-01-27 17:18:37,040 Module Upgrade : Loading DbSchema "labkey.ms1" (Module)
INFO DbScope 2016-01-27 17:18:37,061 Module Upgrade : Loading DbSchema "labkey.targetedms" (Module)
INFO DbScope 2016-01-27 17:18:37,096 Module Upgrade : Loading DbSchema "labkey.ms2" (Module)
INFO DbScope 2016-01-27 17:18:37,119 Module Upgrade : Loading DbSchema "labkey.prot" (Module)
INFO SqlScriptRunner 2016-01-27 17:18:37,129 Module Upgrade : Running [ms2-drop.sql]
INFO SqlScriptManager 2016-01-27 17:18:37,130 Module Upgrade : start running script : ms2-drop.sql
INFO SqlScriptManager 2016-01-27 17:18:37,228 Module Upgrade : finished running script : ms2-drop.sql
INFO ScriptService$Console 2016-01-27 17:18:37,235 Module Upgrade : Purging RhinoService caches
INFO DbScope 2016-01-27 17:18:37,250 Module Upgrade : Loading DbSchema "labkey.issues" (Module)
INFO DbScope 2016-01-27 17:18:37,251 http-bio-8080-exec-12 : Loading DbSchema "labkey.core" (Module)
INFO DbScope 2016-01-27 17:18:37,267 Module Upgrade : Loading DbSchema "labkey.luminex" (Module)
INFO DbScope 2016-01-27 17:18:37,290 Module Upgrade : Loading DbSchema "labkey.nab" (Module)
INFO DbScope 2016-01-27 17:18:37,298 Module Upgrade : Loading DbSchema "labkey.nabvirus" (Provisioned)
INFO DbScope 2016-01-27 17:18:37,305 Module Upgrade : Loading DbSchema "labkey.study" (Module)
INFO DbScope 2016-01-27 17:18:37,361 Module Upgrade : Loading DbSchema "labkey.studydataset" (Provisioned)
INFO DbScope 2016-01-27 17:18:37,362 Module Upgrade : Loading DbSchema "labkey.assayresult" (Provisioned)
INFO DbScope 2016-01-27 17:18:37,362 Module Upgrade : Loading DbSchema "labkey.studydesign" (Provisioned)
INFO DbScope 2016-01-27 17:18:37,362 Module Upgrade : Loading DbSchema "labkey.specimentables" (Provisioned)
INFO SqlScriptRunner 2016-01-27 17:18:37,375 Module Upgrade : Running [study-drop.sql]
INFO SqlScriptManager 2016-01-27 17:18:37,377 Module Upgrade : start running script : study-drop.sql
INFO DbScope 2016-01-27 17:18:37,377 http-bio-8080-exec-12 : Loading DbSchema "labkey.prop" (Module)
INFO SqlScriptManager 2016-01-27 17:18:37,399 Module Upgrade : finished running script : study-drop.sql
INFO ScriptService$Console 2016-01-27 17:18:37,402 Module Upgrade : Purging RhinoService caches
INFO DbScope 2016-01-27 17:18:37,402 Module Upgrade : Loading DbSchema "labkey.filecontent" (Module)
INFO DbScope 2016-01-27 17:18:37,417 Module Upgrade : Loading DbSchema "labkey.comm" (Module)
INFO DbScope 2016-01-27 17:18:37,432 http-bio-8080-exec-5 : Loading DbSchema "labkey.core" (Module)
INFO SqlScriptRunner 2016-01-27 17:18:37,441 Module Upgrade : Running [comm-drop.sql]
INFO SqlScriptManager 2016-01-27 17:18:37,441 Module Upgrade : start running script : comm-drop.sql
INFO DbScope 2016-01-27 17:18:37,491 http-bio-8080-exec-12 : Loading DbSchema "labkey.prop" (Module)
INFO SqlScriptManager 2016-01-27 17:18:37,521 Module Upgrade : finished running script : comm-drop.sql
INFO ScriptService$Console 2016-01-27 17:18:37,522 Module Upgrade : Purging RhinoService caches
INFO DbScope 2016-01-27 17:18:37,523 Module Upgrade : Loading DbSchema "labkey.search" (Module)
INFO DbScope 2016-01-27 17:18:37,536 Module Upgrade : Loading DbSchema "labkey.umls" (Module)
INFO DbScope 2016-01-27 17:18:37,541 Module Upgrade : no schema metadata xml file found for schema "umls"
INFO DbScope 2016-01-27 17:18:37,545 Module Upgrade : Loading DbSchema "labkey.flow" (Module)
INFO DbScope 2016-01-27 17:18:37,559 http-bio-8080-exec-20 : Loading DbSchema "labkey.core" (Module)
INFO DbScope 2016-01-27 17:18:37,562 http-bio-8080-exec-5 : Loading DbSchema "labkey.prop" (Module)
INFO DbScope 2016-01-27 17:18:37,568 Module Upgrade : Loading DbSchema "labkey.query" (Module)
INFO DbScope 2016-01-27 17:18:37,600 Module Upgrade : Loading DbSchema "labkey.junit" (Module)
INFO DbScope 2016-01-27 17:18:37,609 Module Upgrade : no schema metadata xml file found for schema "junit"
INFO DbScope 2016-01-27 17:18:37,616 Module Upgrade : Loading DbSchema "labkey.elispotlk" (Module)
INFO DbScope 2016-01-27 17:18:37,642 Module Upgrade : Loading DbSchema "labkey.list" (Provisioned)
INFO DbScope 2016-01-27 17:18:37,646 Module Upgrade : Loading DbSchema "labkey.microarray" (Module)
INFO DbScope 2016-01-27 17:18:37,706 Module Upgrade : Loading DbSchema "labkey.dataintegration" (Module)
INFO DbScope 2016-01-27 17:18:37,863 Module Upgrade : Loading DbSchema "labkey.survey" (Module)
INFO DbScope 2016-01-27 17:18:37,897 Module Upgrade : Loading DbSchema "labkey.audit" (Provisioned)
INFO DbScope 2016-01-27 17:18:37,900 Module Upgrade : Loading DbSchema "labkey.exp" (Module)
INFO SqlScriptRunner 2016-01-27 17:18:37,923 Module Upgrade : Running [exp-drop.sql]
INFO SqlScriptManager 2016-01-27 17:18:37,923 Module Upgrade : start running script : exp-drop.sql
INFO SqlScriptManager 2016-01-27 17:18:38,028 Module Upgrade : finished running script : exp-drop.sql
INFO DbScope 2016-01-27 17:18:38,030 http-bio-8080-exec-12 : Loading DbSchema "labkey.core" (Module)
INFO ScriptService$Console 2016-01-27 17:18:38,030 Module Upgrade : Purging RhinoService caches
INFO DbScope 2016-01-27 17:18:38,030 Module Upgrade : Loading DbSchema "labkey.pipeline" (Module)
INFO DbScope 2016-01-27 17:18:38,142 http-bio-8080-exec-6 : Loading DbSchema "labkey.prop" (Module)
INFO DbScope 2016-01-27 17:18:38,276 Module Upgrade : Loading DbSchema "labkey.exp" (Module)
INFO SqlScriptRunner 2016-01-27 17:18:38,293 Module Upgrade : Running [exp-create.sql]
INFO SqlScriptManager 2016-01-27 17:18:38,298 Module Upgrade : start running script : exp-create.sql
INFO SqlScriptManager 2016-01-27 17:18:38,474 Module Upgrade : finished running script : exp-create.sql
INFO ScriptService$Console 2016-01-27 17:18:38,475 Module Upgrade : Purging RhinoService caches
INFO DbScope 2016-01-27 17:18:38,475 Module Upgrade : Loading DbSchema "labkey.core" (Module)
INFO DbScope 2016-01-27 17:18:38,553 Module Upgrade : Loading DbSchema "labkey.exp" (Module)
INFO DbScope 2016-01-27 17:18:38,564 Module Upgrade : Loading DbSchema "labkey.audit" (Provisioned)
INFO DbScope 2016-01-27 17:18:38,611 Module Upgrade : Loading DbSchema "labkey.survey" (Module)
INFO DbScope 2016-01-27 17:18:38,628 Module Upgrade : Loading DbSchema "labkey.dataintegration" (Module)
INFO SqlScriptRunner 2016-01-27 17:18:38,640 Module Upgrade : Running [dataintegration-15.20-15.30.sql]
INFO SqlScriptManager 2016-01-27 17:18:38,642 Module Upgrade : start running script : dataintegration-15.20-15.30.sql
INFO SqlScriptManager 2016-01-27 17:18:38,668 Module Upgrade : finished running script : dataintegration-15.20-15.30.sql
INFO ScriptService$Console 2016-01-27 17:18:38,686 Module Upgrade : Purging RhinoService caches
INFO DbScope 2016-01-27 17:18:38,689 Module Upgrade : Loading DbSchema "labkey.core" (Module)
INFO DbScope 2016-01-27 17:18:38,745 Module Upgrade : Loading DbSchema "labkey.dataintegration" (Module)
INFO DbScope 2016-01-27 17:18:38,750 Module Upgrade : Loading DbSchema "labkey.microarray" (Module)
INFO DbScope 2016-01-27 17:18:38,823 Module Upgrade : Loading DbSchema "labkey.list" (Provisioned)
INFO DbScope 2016-01-27 17:18:38,837 Module Upgrade : Loading DbSchema "labkey.elispotlk" (Module)
INFO DbScope 2016-01-27 17:18:38,855 Module Upgrade : Loading DbSchema "labkey.query" (Module)
INFO DbScope 2016-01-27 17:18:38,866 Module Upgrade : Loading DbSchema "labkey.junit" (Module)
INFO DbScope 2016-01-27 17:18:38,869 Module Upgrade : no schema metadata xml file found for schema "junit"
INFO DbScope 2016-01-27 17:18:38,885 Module Upgrade : Loading DbSchema "labkey.flow" (Module)
INFO DbScope 2016-01-27 17:18:38,904 Module Upgrade : Loading DbSchema "labkey.search" (Module)
INFO DbScope 2016-01-27 17:18:38,909 Module Upgrade : Loading DbSchema "labkey.umls" (Module)
INFO DbScope 2016-01-27 17:18:38,920 Module Upgrade : no schema metadata xml file found for schema "umls"
INFO DbScope 2016-01-27 17:18:38,939 http-bio-8080-exec-20 : Loading DbSchema "labkey.prop" (Module)
INFO DbScope 2016-01-27 17:18:38,953 Module Upgrade : Loading DbSchema "labkey.comm" (Module)
INFO SqlScriptRunner 2016-01-27 17:18:38,967 Module Upgrade : Running [comm-create.sql]
INFO SqlScriptManager 2016-01-27 17:18:38,967 Module Upgrade : start running script : comm-create.sql
INFO SqlScriptManager 2016-01-27 17:18:39,004 Module Upgrade : finished running script : comm-create.sql
INFO ScriptService$Console 2016-01-27 17:18:39,005 Module Upgrade : Purging RhinoService caches
INFO DbScope 2016-01-27 17:18:39,005 Module Upgrade : Loading DbSchema "labkey.core" (Module)
INFO DbScope 2016-01-27 17:18:39,036 http-bio-8080-exec-20 : Loading DbSchema "labkey.prop" (Module)
INFO DbScope 2016-01-27 17:18:39,091 Module Upgrade : Loading DbSchema "labkey.comm" (Module)
INFO DbScope 2016-01-27 17:18:39,101 Module Upgrade : Loading DbSchema "labkey.filecontent" (Module)
INFO DbScope 2016-01-27 17:18:39,213 Module Upgrade : Loading DbSchema "labkey.study" (Module)
INFO DbScope 2016-01-27 17:18:39,223 Module Upgrade : Loading DbSchema "labkey.studydataset" (Provisioned)
INFO DbScope 2016-01-27 17:18:39,229 Module Upgrade : Loading DbSchema "labkey.assayresult" (Provisioned)
INFO DbScope 2016-01-27 17:18:39,229 Module Upgrade : Loading DbSchema "labkey.studydesign" (Provisioned)
INFO DbScope 2016-01-27 17:18:39,229 Module Upgrade : Loading DbSchema "labkey.specimentables" (Provisioned)
INFO SqlScriptRunner 2016-01-27 17:18:39,233 Module Upgrade : Running [study-create.sql]
INFO SqlScriptManager 2016-01-27 17:18:39,234 Module Upgrade : start running script : study-create.sql
INFO SqlScriptManager 2016-01-27 17:18:39,259 Module Upgrade : finished running script : study-create.sql
INFO ScriptService$Console 2016-01-27 17:18:39,260 Module Upgrade : Purging RhinoService caches
INFO DbScope 2016-01-27 17:18:39,264 Module Upgrade : Loading DbSchema "labkey.core" (Module)
INFO DbScope 2016-01-27 17:18:39,427 Module Upgrade : Loading DbSchema "labkey.study" (Module)
INFO DbScope 2016-01-27 17:18:39,435 Module Upgrade : Loading DbSchema "labkey.studydataset" (Provisioned)
INFO DbScope 2016-01-27 17:18:39,435 Module Upgrade : Loading DbSchema "labkey.assayresult" (Provisioned)
INFO DbScope 2016-01-27 17:18:39,435 Module Upgrade : Loading DbSchema "labkey.studydesign" (Provisioned)
INFO DbScope 2016-01-27 17:18:39,435 Module Upgrade : Loading DbSchema "labkey.specimentables" (Provisioned)
INFO DbScope 2016-01-27 17:18:39,436 Module Upgrade : Loading DbSchema "labkey.nab" (Module)
INFO DbScope 2016-01-27 17:18:39,440 Module Upgrade : Loading DbSchema "labkey.nabvirus" (Provisioned)
INFO SqlScriptRunner 2016-01-27 17:18:39,443 Module Upgrade : Running [nab-15.20-15.30.sql]
INFO SqlScriptManager 2016-01-27 17:18:39,444 Module Upgrade : start running script : nab-15.20-15.30.sql
INFO ScriptService$Console 2016-01-27 17:18:39,863 Module Upgrade : Purging RhinoService caches
INFO SqlScriptExecutor 2016-01-27 17:18:39,867 Module Upgrade : Adding deferred upgrade task to execute NabUpgradeCode.upgradeDilutionAssayWithNewTables(ModuleContext moduleContext)
INFO ScriptService$Console 2016-01-27 17:18:39,868 Module Upgrade : Purging RhinoService caches
INFO DbScope 2016-01-27 17:18:39,983 http-bio-8080-exec-24 : Loading DbSchema "labkey.core" (Module)
INFO DbScope 2016-01-27 17:18:40,040 http-bio-8080-exec-24 : Loading DbSchema "labkey.prop" (Module)
INFO SqlScriptManager 2016-01-27 17:18:40,167 Module Upgrade : finished running script : nab-15.20-15.30.sql
INFO ScriptService$Console 2016-01-27 17:18:40,231 Module Upgrade : Purging RhinoService caches
INFO DbScope 2016-01-27 17:18:40,234 Module Upgrade : Loading DbSchema "labkey.core" (Module)
INFO DbScope 2016-01-27 17:18:40,352 Module Upgrade : Loading DbSchema "labkey.nab" (Module)
INFO DbScope 2016-01-27 17:18:40,357 Module Upgrade : Loading DbSchema "labkey.nabvirus" (Provisioned)
INFO DbScope 2016-01-27 17:18:40,371 Module Upgrade : Loading DbSchema "labkey.luminex" (Module)
INFO DbScope 2016-01-27 17:18:40,387 Module Upgrade : Loading DbSchema "labkey.issues" (Module)
INFO DbScope 2016-01-27 17:18:40,413 Module Upgrade : Loading DbSchema "labkey.ms2" (Module)
INFO DbScope 2016-01-27 17:18:40,423 Module Upgrade : Loading DbSchema "labkey.prot" (Module)
INFO SqlScriptRunner 2016-01-27 17:18:40,435 Module Upgrade : Running [ms2-create.sql]
INFO SqlScriptManager 2016-01-27 17:18:40,436 Module Upgrade : start running script : ms2-create.sql
INFO SqlScriptManager 2016-01-27 17:18:40,482 Module Upgrade : finished running script : ms2-create.sql
INFO ScriptService$Console 2016-01-27 17:18:40,483 Module Upgrade : Purging RhinoService caches
INFO DbScope 2016-01-27 17:18:40,485 Module Upgrade : Loading DbSchema "labkey.core" (Module)
INFO DbScope 2016-01-27 17:18:40,593 Module Upgrade : Loading DbSchema "labkey.ms2" (Module)
INFO DbScope 2016-01-27 17:18:40,600 Module Upgrade : Loading DbSchema "labkey.prot" (Module)
INFO DbScope 2016-01-27 17:18:40,605 Module Upgrade : Loading DbSchema "labkey.targetedms" (Module)
INFO SqlScriptRunner 2016-01-27 17:18:40,615 Module Upgrade : Running [targetedms-15.20-15.30.sql]
INFO SqlScriptManager 2016-01-27 17:18:40,615 Module Upgrade : start running script : targetedms-15.20-15.30.sql
INFO SqlScriptManager 2016-01-27 17:18:40,655 Module Upgrade : finished running script : targetedms-15.20-15.30.sql
INFO ScriptService$Console 2016-01-27 17:18:40,661 Module Upgrade : Purging RhinoService caches
INFO DbScope 2016-01-27 17:18:40,664 Module Upgrade : Loading DbSchema "labkey.core" (Module)
INFO DbScope 2016-01-27 17:18:40,711 Module Upgrade : Loading DbSchema "labkey.targetedms" (Module)
INFO DbScope 2016-01-27 17:18:40,717 Module Upgrade : Loading DbSchema "labkey.ms1" (Module)
INFO DbScope 2016-01-27 17:18:40,769 Module Upgrade : Loading DbSchema "labkey.vehicle" (Module)
INFO DbScope 2016-01-27 17:18:40,785 Module Upgrade : Loading DbSchema "labkey.genotyping" (Module)
INFO DbScope 2016-01-27 17:18:41,201 http-bio-8080-exec-24 : Loading DbSchema "labkey.prop" (Module)
INFO ModuleLoader 2016-01-27 17:18:41,340 http-bio-8080-exec-24 : Starting up modules
INFO ModuleLoader 2016-01-27 17:18:41,353 Module Starter : Starting module 'Core'
INFO DbScope 2016-01-27 17:18:41,574 Module Starter : Loading DbSchema "labkey.exp" (Module)
INFO DbScope 2016-01-27 17:18:42,136 Module Starter : Loading DbSchema "labkey.audit" (Provisioned)
INFO DbScope 2016-01-27 17:18:42,362 Module Starter : Loading DbSchema "labkey.temp" (Provisioned)
INFO ModuleLoader 2016-01-27 17:18:42,551 Module Starter : Starting module 'BigIron'
INFO ModuleLoader 2016-01-27 17:18:42,552 Module Starter : Starting module 'FCSExpress'
INFO ModuleLoader 2016-01-27 17:18:42,571 Module Starter : Starting module 'Pipeline'
INFO SpringModule 2016-01-27 17:18:42,572 Module Starter : Loading Spring configuration for the Pipeline module from [/WEB-INF/pipelineContext.xml]
INFO SpringModule$1 2016-01-27 17:18:42,574 Module Starter : Refreshing Pipeline WebApplicationContext: startup date [Wed Jan 27 17:18:42 CET 2016]; parent: Root WebApplicationContext
INFO DbScope 2016-01-27 17:18:42,668 Module Starter : Loading DbSchema "labkey.pipeline" (Module)
INFO ModuleLoader 2016-01-27 17:18:42,741 Module Starter : Starting module 'Experiment'
INFO SpringModule 2016-01-27 17:18:42,742 Module Starter : Loading Spring configuration for the Experiment module from [/WEB-INF/experimentContext.xml]
INFO SpringModule$1 2016-01-27 17:18:42,747 Module Starter : Refreshing Experiment WebApplicationContext: startup date [Wed Jan 27 17:18:42 CET 2016]; parent: Root WebApplicationContext
INFO ModuleLoader 2016-01-27 17:18:43,225 Module Starter : Starting module 'Audit'
INFO ModuleLoader 2016-01-27 17:18:43,240 Module Starter : Starting module 'Survey'
INFO ModuleLoader 2016-01-27 17:18:43,241 Module Starter : Starting module 'DataIntegration'
INFO ModuleLoader 2016-01-27 17:18:43,255 Module Starter : Starting module 'Microarray'
INFO SpringModule 2016-01-27 17:18:43,256 Module Starter : Loading Spring configuration for the Microarray module from [/WEB-INF/microarrayContext.xml]
INFO SpringModule$1 2016-01-27 17:18:43,258 Module Starter : Refreshing Microarray WebApplicationContext: startup date [Wed Jan 27 17:18:43 CET 2016]; parent: Root WebApplicationContext
INFO ModuleLoader 2016-01-27 17:18:43,342 Module Starter : Starting module 'List'
INFO ModuleLoader 2016-01-27 17:18:43,376 Module Starter : Starting module 'ELISpotAssay'
INFO ModuleLoader 2016-01-27 17:18:43,384 Module Starter : Starting module 'Query'
INFO DbScope 2016-01-27 17:18:43,545 Module Starter : Loading DbSchema "labkey.study" (Module)
INFO DbScope 2016-01-27 17:18:43,845 Module Starter : Loading DbSchema "labkey.audit" (Provisioned)
INFO ModuleLoader 2016-01-27 17:18:43,853 Module Starter : Starting module 'Flow'
INFO DbScope 2016-01-27 17:18:43,869 Module Starter : Loading DbSchema "labkey.flow" (Module)
INFO ModuleLoader 2016-01-27 17:18:43,920 Module Starter : Starting module 'Search'
INFO DbScope 2016-01-27 17:18:43,932 Module Starter : Loading DbSchema "labkey.audit" (Provisioned)
INFO ModuleLoader 2016-01-27 17:18:43,937 Module Starter : Starting module 'Wiki'
INFO ModuleLoader 2016-01-27 17:18:43,942 Module Starter : Starting module 'Announcements'
INFO DbScope 2016-01-27 17:18:43,975 Module Starter : Loading DbSchema "labkey.comm" (Module)
INFO ModuleLoader 2016-01-27 17:18:44,086 Module Starter : Starting module 'FileContent'
INFO ModuleLoader 2016-01-27 17:18:44,090 Module Starter : Starting module 'Study'
INFO SpringModule 2016-01-27 17:18:44,091 Module Starter : Loading Spring configuration for the Study module from [/WEB-INF/studyContext.xml]
INFO SpringModule$1 2016-01-27 17:18:44,092 Module Starter : Refreshing Study WebApplicationContext: startup date [Wed Jan 27 17:18:44 CET 2016]; parent: Root WebApplicationContext
ERROR Table 2016-01-27 17:18:44,695 Module Starter : SQL Exception
org.postgresql.util.PSQLException: This ResultSet is closed.
at org.postgresql.jdbc2.AbstractJdbc2ResultSet.checkClosed(AbstractJdbc2ResultSet.java:2859)
at org.postgresql.jdbc2.AbstractJdbc2ResultSet.next(AbstractJdbc2ResultSet.java:1897)
at org.apache.tomcat.dbcp.dbcp.DelegatingResultSet.next(DelegatingResultSet.java:207)
at org.apache.tomcat.dbcp.dbcp.DelegatingResultSet.next(DelegatingResultSet.java:207)
at org.labkey.api.data.BaseSelector.lambda$forEach$6(BaseSelector.java:201)
at org.labkey.api.data.BaseSelector$$Lambda$17/1996795222.handle(Unknown Source)
at org.labkey.api.data.BaseSelector.handleResultSet(BaseSelector.java:247)
at org.labkey.api.data.BaseSelector.forEach(BaseSelector.java:200)
at org.labkey.api.data.BaseSelector.forEach(BaseSelector.java:195)
at org.labkey.study.model.DatasetDefinition.cleanupOrphanedDatasetDomains(DatasetDefinition.java:3294)
at org.labkey.study.StudyModule.startupAfterSpringConfig(StudyModule.java:450)
at org.labkey.api.module.SpringModule.doStartup(SpringModule.java:113)
at org.labkey.api.module.DefaultModule.startup(DefaultModule.java:289)
at org.labkey.api.module.ModuleLoader.completeStartup(ModuleLoader.java:1296)
at org.labkey.api.module.ModuleLoader.access$100(ModuleLoader.java:121)
at org.labkey.api.module.ModuleLoader$1.run(ModuleLoader.java:1259)
ERROR Table 2016-01-27 17:18:44,701 Module Starter : SQL [3641]
SELECT domainid FROM exp.domaindescriptor WHERE domainuri like '%:StudyDataset%Folder-%' and domainuri not in (SELECT typeuri from study.dataset)
org.labkey.api.data.SqlExecutingSelector$ExecutingResultSetFactory.handleSqlException(SqlExecutingSelector.java:445)
org.labkey.api.data.BaseSelector.handleResultSet(BaseSelector.java:259)
org.labkey.api.data.BaseSelector.forEach(BaseSelector.java:200)
org.labkey.api.data.BaseSelector.forEach(BaseSelector.java:195)
org.labkey.study.model.DatasetDefinition.cleanupOrphanedDatasetDomains(DatasetDefinition.java:3294)
ERROR ModuleLoader 2016-01-27 17:18:44,762 Module Starter : Failure starting module: Study
org.springframework.jdbc.UncategorizedSQLException: ExecutingSelector; uncategorized SQLException for SQL []; SQL state [55000]; error code [0]; This ResultSet is closed.; nested exception is org.postgresql.util.PSQLException: This ResultSet is closed.
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:259)
at org.labkey.api.data.BaseSelector.forEach(BaseSelector.java:200)
at org.labkey.api.data.BaseSelector.forEach(BaseSelector.java:195)
at org.labkey.study.model.DatasetDefinition.cleanupOrphanedDatasetDomains(DatasetDefinition.java:3294)
at org.labkey.study.StudyModule.startupAfterSpringConfig(StudyModule.java:450)
at org.labkey.api.module.SpringModule.doStartup(SpringModule.java:113)
at org.labkey.api.module.DefaultModule.startup(DefaultModule.java:289)
at org.labkey.api.module.ModuleLoader.completeStartup(ModuleLoader.java:1296)
at org.labkey.api.module.ModuleLoader.access$100(ModuleLoader.java:121)
at org.labkey.api.module.ModuleLoader$1.run(ModuleLoader.java:1259)
Caused by: org.postgresql.util.PSQLException: This ResultSet is closed.
at org.postgresql.jdbc2.AbstractJdbc2ResultSet.checkClosed(AbstractJdbc2ResultSet.java:2859)
at org.postgresql.jdbc2.AbstractJdbc2ResultSet.next(AbstractJdbc2ResultSet.java:1897)
at org.apache.tomcat.dbcp.dbcp.DelegatingResultSet.next(DelegatingResultSet.java:207)
at org.apache.tomcat.dbcp.dbcp.DelegatingResultSet.next(DelegatingResultSet.java:207)
at org.labkey.api.data.BaseSelector.lambda$forEach$6(BaseSelector.java:201)
at org.labkey.api.data.BaseSelector$$Lambda$17/1996795222.handle(Unknown Source)
at org.labkey.api.data.BaseSelector.handleResultSet(BaseSelector.java:247)
... 9 more
INFO ModuleLoader 2016-01-27 17:18:44,763 Module Starter : Starting module 'Nab'
INFO ModuleLoader 2016-01-27 17:18:44,787 Module Starter : Starting module 'Elisa'
INFO ModuleLoader 2016-01-27 17:18:44,791 Module Starter : Starting module 'Visualization'
INFO ModuleLoader 2016-01-27 17:18:44,792 Module Starter : Starting module 'Luminex'
INFO ModuleLoader 2016-01-27 17:18:44,814 Module Starter : Starting module 'Issues'
INFO DbScope 2016-01-27 17:18:44,819 Module Starter : Loading DbSchema "labkey.issues" (Module)
INFO ModuleLoader 2016-01-27 17:18:44,835 Module Starter : Starting module 'FreezerPro'
INFO ModuleLoader 2016-01-27 17:18:44,837 Module Starter : Starting module 'MS2'
INFO SpringModule 2016-01-27 17:18:44,838 Module Starter : Loading Spring configuration for the MS2 module from [/WEB-INF/ms2Context.xml]
INFO SpringModule$1 2016-01-27 17:18:44,841 Module Starter : Refreshing MS2 WebApplicationContext: startup date [Wed Jan 27 17:18:44 CET 2016]; parent: Root WebApplicationContext
INFO DbScope 2016-01-27 17:18:45,191 Module Starter : Loading DbSchema "labkey.ms2" (Module)
INFO DbScope 2016-01-27 17:18:45,327 Module Starter : Loading DbSchema "labkey.prot" (Module)
ERROR ExceptionUtil 2016-01-27 17:18:45,342 http-bio-8080-exec-7 : Unhandled exception: 500: Unexpected server error
org.springframework.jdbc.UncategorizedSQLException: ExecutingSelector; uncategorized SQLException for SQL []; SQL state [55000]; error code [0]; This ResultSet is closed.; nested exception is org.postgresql.util.PSQLException: This ResultSet is closed.
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:259)
at org.labkey.api.data.BaseSelector.forEach(BaseSelector.java:200)
at org.labkey.api.data.BaseSelector.forEach(BaseSelector.java:195)
at org.labkey.study.model.DatasetDefinition.cleanupOrphanedDatasetDomains(DatasetDefinition.java:3294)
at org.labkey.study.StudyModule.startupAfterSpringConfig(StudyModule.java:450)
at org.labkey.api.module.SpringModule.doStartup(SpringModule.java:113)
at org.labkey.api.module.DefaultModule.startup(DefaultModule.java:289)
at org.labkey.api.module.ModuleLoader.completeStartup(ModuleLoader.java:1296)
at org.labkey.api.module.ModuleLoader.access$100(ModuleLoader.java:121)
at org.labkey.api.module.ModuleLoader$1.run(ModuleLoader.java:1259)
Caused by: org.postgresql.util.PSQLException: This ResultSet is closed.
at org.postgresql.jdbc2.AbstractJdbc2ResultSet.checkClosed(AbstractJdbc2ResultSet.java:2859)
at org.postgresql.jdbc2.AbstractJdbc2ResultSet.next(AbstractJdbc2ResultSet.java:1897)
at org.apache.tomcat.dbcp.dbcp.DelegatingResultSet.next(DelegatingResultSet.java:207)
at org.apache.tomcat.dbcp.dbcp.DelegatingResultSet.next(DelegatingResultSet.java:207)
at org.labkey.api.data.BaseSelector.lambda$forEach$6(BaseSelector.java:201)
at org.labkey.api.data.BaseSelector$$Lambda$17/1996795222.handle(Unknown Source)
at org.labkey.api.data.BaseSelector.handleResultSet(BaseSelector.java:247)
... 9 more
INFO ModuleLoader 2016-01-27 17:18:45,418 Module Starter : Starting module 'TargetedMS'
INFO SpringModule 2016-01-27 17:18:45,418 Module Starter : Loading Spring configuration for the TargetedMS module from [/WEB-INF/targetedmsContext.xml]
INFO SpringModule$1 2016-01-27 17:18:45,420 Module Starter : Refreshing TargetedMS WebApplicationContext: startup date [Wed Jan 27 17:18:45 CET 2016]; parent: Root WebApplicationContext
INFO ModuleLoader 2016-01-27 17:18:45,451 Module Starter : Starting module 'MS1'
INFO SpringModule 2016-01-27 17:18:45,451 Module Starter : Loading Spring configuration for the MS1 module from [/WEB-INF/ms1Context.xml]
INFO SpringModule$1 2016-01-27 17:18:45,454 Module Starter : Refreshing MS1 WebApplicationContext: startup date [Wed Jan 27 17:18:45 CET 2016]; parent: Root WebApplicationContext
ERROR ExceptionUtil 2016-01-27 17:18:45,463 http-bio-8080-exec-8 : Unhandled exception: 500: Unexpected server error
org.springframework.jdbc.UncategorizedSQLException: ExecutingSelector; uncategorized SQLException for SQL []; SQL state [55000]; error code [0]; This ResultSet is closed.; nested exception is org.postgresql.util.PSQLException: This ResultSet is closed.
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:259)
at org.labkey.api.data.BaseSelector.forEach(BaseSelector.java:200)
at org.labkey.api.data.BaseSelector.forEach(BaseSelector.java:195)
at org.labkey.study.model.DatasetDefinition.cleanupOrphanedDatasetDomains(DatasetDefinition.java:3294)
at org.labkey.study.StudyModule.startupAfterSpringConfig(StudyModule.java:450)
at org.labkey.api.module.SpringModule.doStartup(SpringModule.java:113)
at org.labkey.api.module.DefaultModule.startup(DefaultModule.java:289)
at org.labkey.api.module.ModuleLoader.completeStartup(ModuleLoader.java:1296)
at org.labkey.api.module.ModuleLoader.access$100(ModuleLoader.java:121)
at org.labkey.api.module.ModuleLoader$1.run(ModuleLoader.java:1259)
Caused by: org.postgresql.util.PSQLException: This ResultSet is closed.
at org.postgresql.jdbc2.AbstractJdbc2ResultSet.checkClosed(AbstractJdbc2ResultSet.java:2859)
at org.postgresql.jdbc2.AbstractJdbc2ResultSet.next(AbstractJdbc2ResultSet.java:1897)
at org.apache.tomcat.dbcp.dbcp.DelegatingResultSet.next(DelegatingResultSet.java:207)
at org.apache.tomcat.dbcp.dbcp.DelegatingResultSet.next(DelegatingResultSet.java:207)
at org.labkey.api.data.BaseSelector.lambda$forEach$6(BaseSelector.java:201)
at org.labkey.api.data.BaseSelector$$Lambda$17/1996795222.handle(Unknown Source)
at org.labkey.api.data.BaseSelector.handleResultSet(BaseSelector.java:247)
... 9 more
INFO ModuleLoader 2016-01-27 17:18:45,581 Module Starter : Starting module 'pipelinetest'
INFO ModuleLoader 2016-01-27 17:18:45,583 Module Starter : Starting module 'simpletest'
INFO ModuleLoader 2016-01-27 17:18:45,584 Module Starter : Starting module 'R_TestModule'
INFO ModuleLoader 2016-01-27 17:18:45,584 Module Starter : Starting module 'Genotyping'
INFO ModuleLoader 2016-01-27 17:18:45,762 Module Starter : Starting module 'Illumina'
INFO ModuleLoader 2016-01-27 17:18:45,766 Module Starter : Starting module 'testtriggers'
INFO ModuleLoader 2016-01-27 17:18:45,766 Module Starter : Starting module 'RNASeqMatrixDemo'
INFO ModuleLoader 2016-01-27 17:18:45,767 Module Starter : Starting module 'Proteomics'
INFO ModuleLoader 2016-01-27 17:18:45,768 Module Starter : Running deferred upgrade for module 'Nab': upgradeDilutionAssayWithNewTables
INFO DbScope 2016-01-27 17:18:45,907 Module Starter : Loading DbSchema "labkey.filecontent" (Module)
INFO ModuleLoader 2016-01-27 17:18:46,299 Module Starter : Running startup listener: Audit Log
INFO DbScope 2016-01-27 17:18:46,416 Module Starter : Loading DbSchema "labkey.query" (Module)
INFO ModuleLoader 2016-01-27 17:18:46,986 Module Starter : Running startup listener: Search Service: clear indexes
INFO DbScope 2016-01-27 17:18:47,514 Module Starter : Loading DbSchema "labkey.search" (Module)
INFO ModuleLoader 2016-01-27 17:18:47,955 Module Starter : Running startup listener: PipelineJobRestarter
INFO ModuleLoader 2016-01-27 17:18:47,958 Module Starter : Running startup listener: DataIntegration
INFO DbScope 2016-01-27 17:18:47,959 Module Starter : Loading DbSchema "labkey.dataintegration" (Module)
INFO ModuleLoader 2016-01-27 17:18:47,976 Module Starter : Running startup listener: Search Service
INFO ModuleLoader 2016-01-27 17:18:48,640 Module Starter : Running startup listener: Daily Message Digest
INFO ModuleLoader 2016-01-27 17:18:48,641 Module Starter : Running startup listener: Short Message Digest
INFO ModuleLoader 2016-01-27 17:18:48,642 Module Starter : Module startup complete
WARN SimpleFolderType 2016-01-27 17:18:50,835 DavCrawler : Module 'Portal' not available for folder type 'My XML-defined Folder Type'
INFO DbScope 2016-01-27 17:18:51,467 SearchService:runner : Loading DbSchema "labkey.list" (Provisioned)
INFO DbScope 2016-01-27 17:18:56,403 SearchService:runner : Loading DbSchema "labkey.specimentables" (Provisioned)
INFO DbScope 2016-01-27 17:18:56,541 SearchService:runner : Loading DbSchema "labkey.studydataset" (Provisioned)
INFO StorageProvisioner 2016-01-27 17:19:00,704 SearchService:runner : Column not found in storage table: c119d1187_studies.DTI_directions__max_2__removed_before_processing_ja_0__nein_1_
WARN LuceneSearchServiceImpl 2016-01-27 17:19:01,136 SearchService:index : Can't index file "/opt/labkey/files/sciCORE Group/Demos/Assay and Transformation Scripts Demo/@files/LabKeyDemoFiles141/Assays/Microarray/test1.pdf (folder: /sciCORE Group/Demos/Assay and Transformation Scripts Demo)" due to: Can't parse this PDF document [Error: End-of-File, expected line]
WARN LuceneSearchServiceImpl 2016-01-27 17:19:01,827 SearchService:index : Can't index file "/opt/labkey/files/sciCORE Group/Demos/Assay and Transformation Scripts Demo/@files/LabKeyDemoFiles141/Assays/Microarray/test2.pdf (folder: /sciCORE Group/Demos/Assay and Transformation Scripts Demo)" due to: Can't parse this PDF document [Error: End-of-File, expected line]
WARN FileQueryUpdateService 2016-01-27 17:19:11,434 SearchService:index : More than one row returned for data file: WHERE (DataFileUrl = 'file:/opt/labkey/files/Jenö%20Group/@files/assaydata/Circadian_4h_Trial_edited.xlsx') AND (Folder = 'ffd15c5e-f302-1032-a062-5d5c86b27818')
INFO DbScope 2016-01-27 17:19:19,452 SearchService:runner : Loading DbSchema "pg.public" (Bare)
ERROR ListDefinitionImpl 2016-01-27 17:19:25,233 SearchService:runner : Failed to construct list table
java.lang.IllegalStateException: Instruments.Key (primary key) has not been provisioned properly. Ensure the domain is established before constructing.
at org.labkey.list.model.ListTable.<init>(ListTable.java:105)
at org.labkey.list.model.ListDefinitionImpl.getTable(ListDefinitionImpl.java:635)
at org.labkey.list.model.ListDefinitionImpl.getTable(ListDefinitionImpl.java:625)
at org.labkey.list.model.ListManager.indexEntireList(ListManager.java:546)
at org.labkey.list.model.ListManager.indexList(ListManager.java:277)
at org.labkey.list.model.ListManager.lambda$enumerateDocuments$0(ListManager.java:239)
at org.labkey.list.model.ListManager$$Lambda$45/960801965.run(Unknown Source)
at org.labkey.search.model.AbstractSearchService$2.run(AbstractSearchService.java:878)
at java.lang.Thread.run(Thread.java:745)
ERROR ListDefinitionImpl 2016-01-27 17:19:25,273 SearchService:runner : Failed to construct list table
java.lang.IllegalStateException: Countries.CountryName (primary key) has not been provisioned properly. Ensure the domain is established before constructing.
at org.labkey.list.model.ListTable.<init>(ListTable.java:105)
at org.labkey.list.model.ListDefinitionImpl.getTable(ListDefinitionImpl.java:635)
at org.labkey.list.model.ListDefinitionImpl.getTable(ListDefinitionImpl.java:625)
at org.labkey.list.model.ListManager.indexEntireList(ListManager.java:546)
at org.labkey.list.model.ListManager.indexList(ListManager.java:277)
at org.labkey.list.model.ListManager.lambda$enumerateDocuments$0(ListManager.java:239)
at org.labkey.list.model.ListManager$$Lambda$45/960801965.run(Unknown Source)
at org.labkey.search.model.AbstractSearchService$2.run(AbstractSearchService.java:878)
at java.lang.Thread.run(Thread.java:745)
ERROR ListDefinitionImpl 2016-01-27 17:19:25,360 SearchService:runner : Failed to construct list table
java.lang.IllegalStateException: ARVType.ARVID (primary key) has not been provisioned properly. Ensure the domain is established before constructing.
at org.labkey.list.model.ListTable.<init>(ListTable.java:105)
at org.labkey.list.model.ListDefinitionImpl.getTable(ListDefinitionImpl.java:635)
at org.labkey.list.model.ListDefinitionImpl.getTable(ListDefinitionImpl.java:625)
at org.labkey.list.model.ListManager.indexEntireList(ListManager.java:546)
at org.labkey.list.model.ListManager.indexList(ListManager.java:277)
at org.labkey.list.model.ListManager.lambda$enumerateDocuments$0(ListManager.java:239)
at org.labkey.list.model.ListManager$$Lambda$45/960801965.run(Unknown Source)
at org.labkey.search.model.AbstractSearchService$2.run(AbstractSearchService.java:878)
at java.lang.Thread.run(Thread.java:745)
WARN FileQueryUpdateService 2016-01-27 17:19:28,994 SearchService:index : More than one row returned for data file: WHERE (DataFileUrl = 'file:/opt/labkey/files/sciCORE%20Group/Demos/Assay%20and%20Transformation%20Scripts%20Demo/@files/LabKeyDemoFiles141/Assays/Generic/GenericAssay_Run2.xls') AND (Folder = '3baaa00b-6440-1032-985c-5d5c86b279ce')
WARN FileQueryUpdateService 2016-01-27 17:19:30,158 SearchService:index : More than one row returned for data file: WHERE (DataFileUrl = 'file:/opt/labkey/files/sciCORE%20Group/Demos/Assay%20and%20Transformation%20Scripts%20Demo/@files/LabKeyDemoFiles141/Assays/Generic/GenericAssay_Run1.xls') AND (Folder = '3baaa00b-6440-1032-985c-5d5c86b279ce')
INFO DbScope 2016-01-27 17:19:55,647 SearchService:runner : Loading DbSchema "labkey.assayresult" (Provisioned)
WARN LuceneSearchServiceImpl 2016-01-27 17:20:33,550 SearchService:index : Can't index file "/opt/labkey/files/sciCORE Group/Demos/Assay and Transformation Scripts Demo/@files/LabKeyDemoFiles141/Assays/Microarray/Old datasets/test1.pdf (folder: /sciCORE Group/Demos/Assay and Transformation Scripts Demo)" due to: Can't parse this PDF document [Error: End-of-File, expected line]
ERROR ListDefinitionImpl 2016-01-27 17:20:35,317 SearchService:runner : Failed to construct list table
java.lang.IllegalStateException: Instruments.Key (primary key) has not been provisioned properly. Ensure the domain is established before constructing.
at org.labkey.list.model.ListTable.<init>(ListTable.java:105)
at org.labkey.list.model.ListDefinitionImpl.getTable(ListDefinitionImpl.java:635)
at org.labkey.list.model.ListDefinitionImpl.getTable(ListDefinitionImpl.java:625)
at org.labkey.list.model.ListManager.hasModifiedItems(ListManager.java:716)
at org.labkey.list.model.ListManager.indexEntireList(ListManager.java:510)
at org.labkey.list.model.ListManager.indexList(ListManager.java:277)
at org.labkey.list.model.ListManager.lambda$enumerateDocuments$0(ListManager.java:239)
at org.labkey.list.model.ListManager$$Lambda$45/960801965.run(Unknown Source)
at org.labkey.search.model.AbstractSearchService$2.run(AbstractSearchService.java:878)
at java.lang.Thread.run(Thread.java:745)
ERROR ListDefinitionImpl 2016-01-27 17:20:35,411 SearchService:runner : Failed to construct list table
java.lang.IllegalStateException: Reagents.Key (primary key) has not been provisioned properly. Ensure the domain is established before constructing.
at org.labkey.list.model.ListTable.<init>(ListTable.java:105)
at org.labkey.list.model.ListDefinitionImpl.getTable(ListDefinitionImpl.java:635)
at org.labkey.list.model.ListDefinitionImpl.getTable(ListDefinitionImpl.java:625)
at org.labkey.list.model.ListManager.hasModifiedItems(ListManager.java:716)
at org.labkey.list.model.ListManager.indexEntireList(ListManager.java:510)
at org.labkey.list.model.ListManager.indexList(ListManager.java:277)
at org.labkey.list.model.ListManager.lambda$enumerateDocuments$0(ListManager.java:239)
at org.labkey.list.model.ListManager$$Lambda$45/960801965.run(Unknown Source)
at org.labkey.search.model.AbstractSearchService$2.run(AbstractSearchService.java:878)
at java.lang.Thread.run(Thread.java:745)
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