INFO ModuleLoader 2016-04-04 15:02:46,253 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2016-04-04 15:02:47,552 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource Server URL: jdbc:postgresql://localhost:5432/labkey Database Product Name: PostgreSQL Database Product Version: 9.4.6 JDBC Driver Name: PostgreSQL Native Driver JDBC Driver Version: PostgreSQL 9.4.1207 SQL Dialect: PostgreSql94Dialect ERROR DebugInfoDumper 2016-04-04 15:02:47,644 localhost-startStop-1 : Failed to create file /usr/share/labkey/threadDumpRequest java.io.FileNotFoundException: /usr/share/labkey/threadDumpRequest (Permission denied) at java.io.FileOutputStream.open0(Native Method) at java.io.FileOutputStream.open(FileOutputStream.java:270) at java.io.FileOutputStream.(FileOutputStream.java:213) at java.io.FileOutputStream.(FileOutputStream.java:162) at java.io.PrintWriter.(PrintWriter.java:192) at java.io.PrintWriter.(PrintWriter.java:303) at org.labkey.api.util.DebugInfoDumper.(DebugInfoDumper.java:65) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:337) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:238) at org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279) at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260) at org.apache.catalina.core.ApplicationFilterConfig.(ApplicationFilterConfig.java:105) at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4640) at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5247) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:724) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:700) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:714) at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:581) at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1685) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) ERROR DebugInfoDumper 2016-04-04 15:02:47,646 localhost-startStop-1 : Failed to create file /usr/share/labkey/heapDumpRequest java.io.FileNotFoundException: /usr/share/labkey/heapDumpRequest (Permission denied) at java.io.FileOutputStream.open0(Native Method) at java.io.FileOutputStream.open(FileOutputStream.java:270) at java.io.FileOutputStream.(FileOutputStream.java:213) at java.io.FileOutputStream.(FileOutputStream.java:162) at java.io.PrintWriter.(PrintWriter.java:192) at java.io.PrintWriter.(PrintWriter.java:303) at org.labkey.api.util.DebugInfoDumper.(DebugInfoDumper.java:81) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:337) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:238) at org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279) at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260) at org.apache.catalina.core.ApplicationFilterConfig.(ApplicationFilterConfig.java:105) at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4640) at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5247) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:724) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:700) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:714) at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:581) at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1685) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) INFO DbScope 2016-04-04 15:02:47,653 localhost-startStop-1 : Loading DbSchema "labkey.core" (Module) INFO DbScope 2016-04-04 15:02:49,839 localhost-startStop-1 : Loading DbSchema "labkey.prop" (Module) INFO DbScope 2016-04-04 15:02:49,917 localhost-startStop-1 : Loading DbSchema "labkey.test" (Module) INFO DbScope 2016-04-04 15:02:49,922 localhost-startStop-1 : Loading DbSchema "labkey.temp" (Provisioned) INFO DbScope 2016-04-04 15:02:49,925 localhost-startStop-1 : Loading DbSchema "labkey.query" (Module) INFO DbScope 2016-04-04 15:02:49,930 localhost-startStop-1 : Loading DbSchema "labkey.junit" (Module) INFO DbScope 2016-04-04 15:02:49,932 localhost-startStop-1 : no schema metadata xml file found for schema "junit" INFO DbScope 2016-04-04 15:02:49,932 localhost-startStop-1 : Loading DbSchema "labkey.search" (Module) INFO DbScope 2016-04-04 15:02:49,938 localhost-startStop-1 : Loading DbSchema "labkey.umls" (Module) INFO DbScope 2016-04-04 15:02:49,941 localhost-startStop-1 : no schema metadata xml file found for schema "umls" INFO DbScope 2016-04-04 15:02:49,941 localhost-startStop-1 : Loading DbSchema "labkey.issues" (Module) INFO DbScope 2016-04-04 15:02:49,947 localhost-startStop-1 : Loading DbSchema "labkey.comm" (Module) INFO DbScope 2016-04-04 15:02:49,959 localhost-startStop-1 : Loading DbSchema "labkey.pipeline" (Module) INFO DbScope 2016-04-04 15:02:49,963 localhost-startStop-1 : Loading DbSchema "labkey.exp" (Module) INFO DbScope 2016-04-04 15:02:49,970 localhost-startStop-1 : Loading DbSchema "labkey.flow" (Module) INFO DbScope 2016-04-04 15:02:49,975 localhost-startStop-1 : Loading DbSchema "labkey.microarray" (Module) INFO DbScope 2016-04-04 15:02:49,979 localhost-startStop-1 : Loading DbSchema "labkey.filecontent" (Module) INFO DbScope 2016-04-04 15:02:49,987 localhost-startStop-1 : Loading DbSchema "labkey.list" (Provisioned) INFO DbScope 2016-04-04 15:02:49,987 localhost-startStop-1 : Loading DbSchema "labkey.ms2" (Module) INFO DbScope 2016-04-04 15:02:49,999 localhost-startStop-1 : Loading DbSchema "labkey.prot" (Module) INFO DbScope 2016-04-04 15:02:50,004 localhost-startStop-1 : Loading DbSchema "labkey.ms1" (Module) INFO DbScope 2016-04-04 15:02:50,009 localhost-startStop-1 : Loading DbSchema "labkey.survey" (Module) INFO DbScope 2016-04-04 15:02:50,013 localhost-startStop-1 : Loading DbSchema "labkey.dataintegration" (Module) INFO DbScope 2016-04-04 15:02:50,018 localhost-startStop-1 : Loading DbSchema "labkey.study" (Module) INFO DbScope 2016-04-04 15:02:50,032 localhost-startStop-1 : Loading DbSchema "labkey.studydataset" (Provisioned) INFO DbScope 2016-04-04 15:02:50,032 localhost-startStop-1 : Loading DbSchema "labkey.assayresult" (Provisioned) INFO DbScope 2016-04-04 15:02:50,032 localhost-startStop-1 : Loading DbSchema "labkey.studydesign" (Provisioned) INFO DbScope 2016-04-04 15:02:50,032 localhost-startStop-1 : Loading DbSchema "labkey.specimentables" (Provisioned) INFO DbScope 2016-04-04 15:02:50,033 localhost-startStop-1 : Loading DbSchema "labkey.luminex" (Module) INFO DbScope 2016-04-04 15:02:50,038 localhost-startStop-1 : Loading DbSchema "labkey.nab" (Module) INFO DbScope 2016-04-04 15:02:50,042 localhost-startStop-1 : Loading DbSchema "labkey.nabvirus" (Provisioned) INFO DbScope 2016-04-04 15:02:50,042 localhost-startStop-1 : Loading DbSchema "labkey.targetedms" (Module) INFO DbScope 2016-04-04 15:02:50,050 localhost-startStop-1 : Loading DbSchema "labkey.audit" (Provisioned) INFO DbScope 2016-04-04 15:02:50,050 localhost-startStop-1 : Loading DbSchema "labkey.elispotlk" (Module) INFO ModuleLoader 2016-04-04 15:02:50,125 localhost-startStop-1 : LabKey Server startup is complete; modules are being upgraded and initialized in the background INFO ViewServlet 2016-04-04 15:02:50,128 localhost-startStop-1 : ViewServlet initialized INFO ViewServlet 2016-04-04 15:02:50,128 localhost-startStop-1 : WEBAPP: /usr/share/labkey/labkeywebapp INFO ViewServlet 2016-04-04 15:02:50,129 localhost-startStop-1 : PATH: /usr/local/tpp/bin:/bin:/usr/bin:/sbin:/usr/sbin INFO ModuleLoader 2016-04-04 15:02:50,125 Module Upgrade : Starting up modules INFO ModuleLoader 2016-04-04 15:02:50,130 Module Upgrade : Starting module 'Core' INFO ModuleLoader 2016-04-04 15:02:51,056 Module Upgrade : Starting module 'Query' INFO ModuleLoader 2016-04-04 15:02:51,101 Module Upgrade : Starting module 'FCSExpress' INFO ModuleLoader 2016-04-04 15:02:51,118 Module Upgrade : Starting module 'Search' INFO ModuleLoader 2016-04-04 15:02:51,126 Module Upgrade : Starting module 'Wiki' INFO ModuleLoader 2016-04-04 15:02:51,132 Module Upgrade : Starting module 'Issues' INFO ModuleLoader 2016-04-04 15:02:51,142 Module Upgrade : Starting module 'Announcements' INFO ModuleLoader 2016-04-04 15:02:51,220 Module Upgrade : Starting module 'BigIron' INFO ModuleLoader 2016-04-04 15:02:51,221 Module Upgrade : Starting module 'Pipeline' INFO SpringModule 2016-04-04 15:02:51,221 Module Upgrade : Loading Spring configuration for the Pipeline module from [/WEB-INF/pipelineContext.xml] INFO SpringModule$1 2016-04-04 15:02:51,229 Module Upgrade : Refreshing Pipeline WebApplicationContext: startup date [Mon Apr 04 15:02:51 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:02:51,350 Module Upgrade : Starting module 'Experiment' INFO SpringModule 2016-04-04 15:02:51,350 Module Upgrade : Loading Spring configuration for the Experiment module from [/WEB-INF/experimentContext.xml] INFO SpringModule$1 2016-04-04 15:02:51,351 Module Upgrade : Refreshing Experiment WebApplicationContext: startup date [Mon Apr 04 15:02:51 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:02:51,560 Module Upgrade : Starting module 'Flow' INFO ModuleLoader 2016-04-04 15:02:51,598 Module Upgrade : Starting module 'Microarray' INFO SpringModule 2016-04-04 15:02:51,598 Module Upgrade : Loading Spring configuration for the Microarray module from [/WEB-INF/microarrayContext.xml] INFO SpringModule$1 2016-04-04 15:02:51,599 Module Upgrade : Refreshing Microarray WebApplicationContext: startup date [Mon Apr 04 15:02:51 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:02:51,642 Module Upgrade : Starting module 'FileContent' INFO ModuleLoader 2016-04-04 15:02:51,645 Module Upgrade : Starting module 'List' INFO ModuleLoader 2016-04-04 15:02:51,665 Module Upgrade : Starting module 'MS2' INFO SpringModule 2016-04-04 15:02:51,665 Module Upgrade : Loading Spring configuration for the MS2 module from [/WEB-INF/ms2Context.xml] INFO SpringModule$1 2016-04-04 15:02:51,666 Module Upgrade : Refreshing MS2 WebApplicationContext: startup date [Mon Apr 04 15:02:51 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:02:52,068 Module Upgrade : Starting module 'MS1' INFO SpringModule 2016-04-04 15:02:52,070 Module Upgrade : Loading Spring configuration for the MS1 module from [/WEB-INF/ms1Context.xml] INFO SpringModule$1 2016-04-04 15:02:52,071 Module Upgrade : Refreshing MS1 WebApplicationContext: startup date [Mon Apr 04 15:02:52 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:02:52,148 Module Upgrade : Starting module 'Survey' INFO ModuleLoader 2016-04-04 15:02:52,149 Module Upgrade : Starting module 'DataIntegration' INFO ModuleLoader 2016-04-04 15:02:52,159 Module Upgrade : Starting module 'Study' INFO SpringModule 2016-04-04 15:02:52,160 Module Upgrade : Loading Spring configuration for the Study module from [/WEB-INF/studyContext.xml] INFO SpringModule$1 2016-04-04 15:02:52,161 Module Upgrade : Refreshing Study WebApplicationContext: startup date [Mon Apr 04 15:02:52 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:02:52,359 Module Upgrade : Starting module 'Luminex' INFO ModuleLoader 2016-04-04 15:02:52,371 Module Upgrade : Starting module 'Visualization' INFO ModuleLoader 2016-04-04 15:02:52,372 Module Upgrade : Starting module 'Nab' INFO ModuleLoader 2016-04-04 15:02:52,391 Module Upgrade : Starting module 'Elisa' INFO ModuleLoader 2016-04-04 15:02:52,394 Module Upgrade : Starting module 'TargetedMS' INFO SpringModule 2016-04-04 15:02:52,394 Module Upgrade : Loading Spring configuration for the TargetedMS module from [/WEB-INF/targetedmsContext.xml] INFO SpringModule$1 2016-04-04 15:02:52,395 Module Upgrade : Refreshing TargetedMS WebApplicationContext: startup date [Mon Apr 04 15:02:52 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:02:52,421 Module Upgrade : Starting module 'Audit' INFO ModuleLoader 2016-04-04 15:02:52,429 Module Upgrade : Starting module 'ELISpotAssay' INFO ModuleLoader 2016-04-04 15:02:52,434 Module Upgrade : Running startup listener: Audit Log INFO ModuleLoader 2016-04-04 15:02:52,435 Module Upgrade : Running startup listener: Search Service INFO ModuleLoader 2016-04-04 15:02:52,435 Module Upgrade : Running startup listener: PipelineJobRestarter INFO ModuleLoader 2016-04-04 15:02:52,438 Module Upgrade : Running startup listener: DataIntegration INFO ModuleLoader 2016-04-04 15:02:52,443 Module Upgrade : Module startup complete INFO ContextListener 2016-04-04 15:18:03,677 localhost-startStop-2 : Calling HeartBeatThread shutdownPre() INFO ContextListener 2016-04-04 15:18:03,677 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownPre() INFO ContextListener 2016-04-04 15:18:03,677 localhost-startStop-2 : Calling QueryProfilerThread shutdownPre() INFO ContextListener 2016-04-04 15:18:03,677 localhost-startStop-2 : Calling BreakpointThread shutdownPre() INFO ContextListener 2016-04-04 15:18:03,677 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownPre() INFO FileSystemWatcherImpl 2016-04-04 15:18:03,677 FileSystemWatcherThread : FileSystemWatcherThread is terminating INFO ContextListener 2016-04-04 15:18:03,678 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownPre() INFO DatasetSnapshotProvider 2016-04-04 15:18:03,678 SnapshotDependencyThread : QuerySnapshotDependencyThread is terminating due to interruption INFO ContextListener 2016-04-04 15:18:03,678 localhost-startStop-2 : Calling Job Runner (Default) shutdownPre() INFO ContextListener 2016-04-04 15:18:03,678 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownPre() INFO ContextListener 2016-04-04 15:18:03,678 localhost-startStop-2 : Calling Temp table cleanup shutdownPre() INFO ContextListener 2016-04-04 15:18:03,678 localhost-startStop-2 : Calling Temp file deletion shutdownPre() INFO ContextListener 2016-04-04 15:18:03,678 localhost-startStop-2 : Calling Action stats export shutdownPre() INFO CoreModule 2016-04-04 15:18:03,678 localhost-startStop-2 : Starting to log statistics for actions prior to web application shut down INFO CoreModule 2016-04-04 15:18:03,692 localhost-startStop-2 : Completed logging statistics for actions prior to web application shut down INFO ContextListener 2016-04-04 15:18:03,692 localhost-startStop-2 : Calling DataIntegration shutdownPre() INFO ContextListener 2016-04-04 15:18:03,710 localhost-startStop-2 : Calling DAV crawler shutdownPre() INFO ContextListener 2016-04-04 15:18:03,710 localhost-startStop-2 : Calling Search service shutdownPre() INFO ContextListener 2016-04-04 15:18:03,711 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownPre() INFO ContextListener 2016-04-04 15:18:03,711 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownPre() INFO ContextListener 2016-04-04 15:18:03,711 localhost-startStop-2 : Calling Study Reload Handler shutdownPre() INFO ContextListener 2016-04-04 15:18:03,711 localhost-startStop-2 : Calling HeartBeatThread shutdownStarted() INFO ContextListener 2016-04-04 15:18:03,711 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownStarted() INFO ContextListener 2016-04-04 15:18:03,711 localhost-startStop-2 : Calling QueryProfilerThread shutdownStarted() INFO QueryProfiler 2016-04-04 15:18:03,711 localhost-startStop-2 : Starting to log statistics for queries prior to web application shut down INFO QueryProfiler 2016-04-04 15:18:03,728 localhost-startStop-2 : Completed logging statistics for queries prior to web application shut down INFO ContextListener 2016-04-04 15:18:03,728 localhost-startStop-2 : Calling BreakpointThread shutdownStarted() INFO ContextListener 2016-04-04 15:18:03,728 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownStarted() INFO ContextListener 2016-04-04 15:18:03,728 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownStarted() INFO ContextListener 2016-04-04 15:18:03,728 localhost-startStop-2 : Calling Job Runner (Default) shutdownStarted() INFO ContextListener 2016-04-04 15:18:03,728 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownStarted() INFO ContextListener 2016-04-04 15:18:03,728 localhost-startStop-2 : Calling Temp table cleanup shutdownStarted() INFO ContextListener 2016-04-04 15:18:03,728 localhost-startStop-2 : Calling Temp file deletion shutdownStarted() INFO ContextListener 2016-04-04 15:18:03,729 localhost-startStop-2 : Calling Action stats export shutdownStarted() INFO ContextListener 2016-04-04 15:18:03,729 localhost-startStop-2 : Calling DataIntegration shutdownStarted() INFO ContextListener 2016-04-04 15:18:04,210 localhost-startStop-2 : Calling DAV crawler shutdownStarted() INFO ContextListener 2016-04-04 15:18:04,211 localhost-startStop-2 : Calling Search service shutdownStarted() INFO ContextListener 2016-04-04 15:18:04,213 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownStarted() INFO ContextListener 2016-04-04 15:18:04,213 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownStarted() INFO ContextListener 2016-04-04 15:18:04,213 localhost-startStop-2 : Calling Study Reload Handler shutdownStarted() INFO EhCacheProvider 2016-04-04 15:18:04,215 localhost-startStop-2 : Shutting down Ehcache INFO ModuleLoader 2016-04-04 15:18:09,845 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2016-04-04 15:18:11,321 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource Server URL: jdbc:postgresql://localhost:5432/labkey Database Product Name: PostgreSQL Database Product Version: 9.4.6 JDBC Driver Name: PostgreSQL Native Driver JDBC Driver Version: PostgreSQL 9.4.1207 SQL Dialect: PostgreSql94Dialect ERROR DebugInfoDumper 2016-04-04 15:18:11,416 localhost-startStop-1 : Failed to create file /usr/share/labkey/threadDumpRequest java.io.FileNotFoundException: /usr/share/labkey/threadDumpRequest (Permission denied) at java.io.FileOutputStream.open0(Native Method) at java.io.FileOutputStream.open(FileOutputStream.java:270) at java.io.FileOutputStream.(FileOutputStream.java:213) at java.io.FileOutputStream.(FileOutputStream.java:162) at java.io.PrintWriter.(PrintWriter.java:192) at java.io.PrintWriter.(PrintWriter.java:303) at org.labkey.api.util.DebugInfoDumper.(DebugInfoDumper.java:65) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:337) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:238) at org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279) at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260) at org.apache.catalina.core.ApplicationFilterConfig.(ApplicationFilterConfig.java:105) at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4640) at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5247) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:724) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:700) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:714) at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:581) at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1685) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) ERROR DebugInfoDumper 2016-04-04 15:18:11,418 localhost-startStop-1 : Failed to create file /usr/share/labkey/heapDumpRequest java.io.FileNotFoundException: /usr/share/labkey/heapDumpRequest (Permission denied) at java.io.FileOutputStream.open0(Native Method) at java.io.FileOutputStream.open(FileOutputStream.java:270) at java.io.FileOutputStream.(FileOutputStream.java:213) at java.io.FileOutputStream.(FileOutputStream.java:162) at java.io.PrintWriter.(PrintWriter.java:192) at java.io.PrintWriter.(PrintWriter.java:303) at org.labkey.api.util.DebugInfoDumper.(DebugInfoDumper.java:81) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:337) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:238) at org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279) at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260) at org.apache.catalina.core.ApplicationFilterConfig.(ApplicationFilterConfig.java:105) at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4640) at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5247) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:724) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:700) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:714) at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:581) at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1685) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) INFO DbScope 2016-04-04 15:18:11,424 localhost-startStop-1 : Loading DbSchema "labkey.core" (Module) INFO DbScope 2016-04-04 15:18:13,851 localhost-startStop-1 : Loading DbSchema "labkey.prop" (Module) INFO DbScope 2016-04-04 15:18:13,936 localhost-startStop-1 : Loading DbSchema "labkey.test" (Module) INFO DbScope 2016-04-04 15:18:13,942 localhost-startStop-1 : Loading DbSchema "labkey.temp" (Provisioned) INFO DbScope 2016-04-04 15:18:13,946 localhost-startStop-1 : Loading DbSchema "labkey.query" (Module) INFO DbScope 2016-04-04 15:18:13,952 localhost-startStop-1 : Loading DbSchema "labkey.junit" (Module) INFO DbScope 2016-04-04 15:18:13,954 localhost-startStop-1 : no schema metadata xml file found for schema "junit" INFO DbScope 2016-04-04 15:18:13,955 localhost-startStop-1 : Loading DbSchema "labkey.search" (Module) INFO DbScope 2016-04-04 15:18:13,960 localhost-startStop-1 : Loading DbSchema "labkey.umls" (Module) INFO DbScope 2016-04-04 15:18:13,964 localhost-startStop-1 : no schema metadata xml file found for schema "umls" INFO DbScope 2016-04-04 15:18:13,964 localhost-startStop-1 : Loading DbSchema "labkey.issues" (Module) INFO DbScope 2016-04-04 15:18:13,970 localhost-startStop-1 : Loading DbSchema "labkey.comm" (Module) INFO DbScope 2016-04-04 15:18:13,979 localhost-startStop-1 : Loading DbSchema "labkey.pipeline" (Module) INFO DbScope 2016-04-04 15:18:13,984 localhost-startStop-1 : Loading DbSchema "labkey.exp" (Module) INFO DbScope 2016-04-04 15:18:13,992 localhost-startStop-1 : Loading DbSchema "labkey.flow" (Module) INFO DbScope 2016-04-04 15:18:13,997 localhost-startStop-1 : Loading DbSchema "labkey.microarray" (Module) INFO DbScope 2016-04-04 15:18:14,001 localhost-startStop-1 : Loading DbSchema "labkey.filecontent" (Module) INFO DbScope 2016-04-04 15:18:14,005 localhost-startStop-1 : Loading DbSchema "labkey.list" (Provisioned) INFO DbScope 2016-04-04 15:18:14,006 localhost-startStop-1 : Loading DbSchema "labkey.ms2" (Module) INFO DbScope 2016-04-04 15:18:14,017 localhost-startStop-1 : Loading DbSchema "labkey.prot" (Module) INFO DbScope 2016-04-04 15:18:14,023 localhost-startStop-1 : Loading DbSchema "labkey.ms1" (Module) INFO DbScope 2016-04-04 15:18:14,028 localhost-startStop-1 : Loading DbSchema "labkey.survey" (Module) INFO DbScope 2016-04-04 15:18:14,033 localhost-startStop-1 : Loading DbSchema "labkey.dataintegration" (Module) INFO DbScope 2016-04-04 15:18:14,037 localhost-startStop-1 : Loading DbSchema "labkey.study" (Module) INFO DbScope 2016-04-04 15:18:14,051 localhost-startStop-1 : Loading DbSchema "labkey.studydataset" (Provisioned) INFO DbScope 2016-04-04 15:18:14,051 localhost-startStop-1 : Loading DbSchema "labkey.assayresult" (Provisioned) INFO DbScope 2016-04-04 15:18:14,052 localhost-startStop-1 : Loading DbSchema "labkey.studydesign" (Provisioned) INFO DbScope 2016-04-04 15:18:14,052 localhost-startStop-1 : Loading DbSchema "labkey.specimentables" (Provisioned) INFO DbScope 2016-04-04 15:18:14,052 localhost-startStop-1 : Loading DbSchema "labkey.luminex" (Module) INFO DbScope 2016-04-04 15:18:14,069 localhost-startStop-1 : Loading DbSchema "labkey.nab" (Module) INFO DbScope 2016-04-04 15:18:14,079 localhost-startStop-1 : Loading DbSchema "labkey.nabvirus" (Provisioned) INFO DbScope 2016-04-04 15:18:14,080 localhost-startStop-1 : Loading DbSchema "labkey.targetedms" (Module) INFO DbScope 2016-04-04 15:18:14,087 localhost-startStop-1 : Loading DbSchema "labkey.audit" (Provisioned) INFO DbScope 2016-04-04 15:18:14,087 localhost-startStop-1 : Loading DbSchema "labkey.elispotlk" (Module) INFO ModuleLoader 2016-04-04 15:18:14,162 localhost-startStop-1 : LabKey Server startup is complete; modules are being upgraded and initialized in the background INFO ModuleLoader 2016-04-04 15:18:14,162 Module Upgrade : Starting up modules INFO ModuleLoader 2016-04-04 15:18:14,163 Module Upgrade : Starting module 'Core' INFO ViewServlet 2016-04-04 15:18:14,166 localhost-startStop-1 : ViewServlet initialized INFO ViewServlet 2016-04-04 15:18:14,166 localhost-startStop-1 : WEBAPP: /usr/share/labkey/labkeywebapp INFO ViewServlet 2016-04-04 15:18:14,167 localhost-startStop-1 : PATH: /usr/local/tpp/bin:/bin:/usr/bin:/sbin:/usr/sbin INFO ModuleLoader 2016-04-04 15:18:15,200 Module Upgrade : Starting module 'Query' INFO ModuleLoader 2016-04-04 15:18:15,250 Module Upgrade : Starting module 'FCSExpress' INFO ModuleLoader 2016-04-04 15:18:15,267 Module Upgrade : Starting module 'Search' INFO ModuleLoader 2016-04-04 15:18:15,275 Module Upgrade : Starting module 'Wiki' INFO ModuleLoader 2016-04-04 15:18:15,282 Module Upgrade : Starting module 'Issues' INFO ModuleLoader 2016-04-04 15:18:15,304 Module Upgrade : Starting module 'Announcements' INFO ModuleLoader 2016-04-04 15:18:15,379 Module Upgrade : Starting module 'BigIron' INFO ModuleLoader 2016-04-04 15:18:15,380 Module Upgrade : Starting module 'Pipeline' INFO SpringModule 2016-04-04 15:18:15,380 Module Upgrade : Loading Spring configuration for the Pipeline module from [/WEB-INF/pipelineContext.xml] INFO SpringModule$1 2016-04-04 15:18:15,382 Module Upgrade : Refreshing Pipeline WebApplicationContext: startup date [Mon Apr 04 15:18:15 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:18:15,518 Module Upgrade : Starting module 'Experiment' INFO SpringModule 2016-04-04 15:18:15,518 Module Upgrade : Loading Spring configuration for the Experiment module from [/WEB-INF/experimentContext.xml] INFO SpringModule$1 2016-04-04 15:18:15,520 Module Upgrade : Refreshing Experiment WebApplicationContext: startup date [Mon Apr 04 15:18:15 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:18:15,745 Module Upgrade : Starting module 'Flow' INFO ModuleLoader 2016-04-04 15:18:15,780 Module Upgrade : Starting module 'Microarray' INFO SpringModule 2016-04-04 15:18:15,781 Module Upgrade : Loading Spring configuration for the Microarray module from [/WEB-INF/microarrayContext.xml] INFO SpringModule$1 2016-04-04 15:18:15,782 Module Upgrade : Refreshing Microarray WebApplicationContext: startup date [Mon Apr 04 15:18:15 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:18:15,830 Module Upgrade : Starting module 'FileContent' INFO ModuleLoader 2016-04-04 15:18:15,834 Module Upgrade : Starting module 'List' INFO ModuleLoader 2016-04-04 15:18:15,856 Module Upgrade : Starting module 'MS2' INFO SpringModule 2016-04-04 15:18:15,856 Module Upgrade : Loading Spring configuration for the MS2 module from [/WEB-INF/ms2Context.xml] INFO SpringModule$1 2016-04-04 15:18:15,857 Module Upgrade : Refreshing MS2 WebApplicationContext: startup date [Mon Apr 04 15:18:15 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:18:16,265 Module Upgrade : Starting module 'MS1' INFO SpringModule 2016-04-04 15:18:16,265 Module Upgrade : Loading Spring configuration for the MS1 module from [/WEB-INF/ms1Context.xml] INFO SpringModule$1 2016-04-04 15:18:16,267 Module Upgrade : Refreshing MS1 WebApplicationContext: startup date [Mon Apr 04 15:18:16 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:18:16,365 Module Upgrade : Starting module 'Survey' INFO ModuleLoader 2016-04-04 15:18:16,366 Module Upgrade : Starting module 'DataIntegration' INFO ModuleLoader 2016-04-04 15:18:16,377 Module Upgrade : Starting module 'Study' INFO SpringModule 2016-04-04 15:18:16,377 Module Upgrade : Loading Spring configuration for the Study module from [/WEB-INF/studyContext.xml] INFO SpringModule$1 2016-04-04 15:18:16,379 Module Upgrade : Refreshing Study WebApplicationContext: startup date [Mon Apr 04 15:18:16 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:18:16,581 Module Upgrade : Starting module 'Luminex' INFO ModuleLoader 2016-04-04 15:18:16,594 Module Upgrade : Starting module 'Visualization' INFO ModuleLoader 2016-04-04 15:18:16,595 Module Upgrade : Starting module 'Nab' INFO ModuleLoader 2016-04-04 15:18:16,614 Module Upgrade : Starting module 'Elisa' INFO ModuleLoader 2016-04-04 15:18:16,618 Module Upgrade : Starting module 'TargetedMS' INFO SpringModule 2016-04-04 15:18:16,618 Module Upgrade : Loading Spring configuration for the TargetedMS module from [/WEB-INF/targetedmsContext.xml] INFO SpringModule$1 2016-04-04 15:18:16,619 Module Upgrade : Refreshing TargetedMS WebApplicationContext: startup date [Mon Apr 04 15:18:16 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:18:16,645 Module Upgrade : Starting module 'Audit' INFO ModuleLoader 2016-04-04 15:18:16,653 Module Upgrade : Starting module 'ELISpotAssay' INFO ModuleLoader 2016-04-04 15:18:16,658 Module Upgrade : Running startup listener: Audit Log INFO ModuleLoader 2016-04-04 15:18:16,658 Module Upgrade : Running startup listener: Search Service INFO ModuleLoader 2016-04-04 15:18:16,658 Module Upgrade : Running startup listener: PipelineJobRestarter INFO ModuleLoader 2016-04-04 15:18:16,660 Module Upgrade : Running startup listener: DataIntegration INFO ModuleLoader 2016-04-04 15:18:16,668 Module Upgrade : Module startup complete INFO ContextListener 2016-04-04 15:28:39,712 localhost-startStop-2 : Calling HeartBeatThread shutdownPre() INFO ContextListener 2016-04-04 15:28:39,712 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownPre() INFO ContextListener 2016-04-04 15:28:39,712 localhost-startStop-2 : Calling QueryProfilerThread shutdownPre() INFO FileSystemWatcherImpl 2016-04-04 15:28:39,713 FileSystemWatcherThread : FileSystemWatcherThread is terminating INFO ContextListener 2016-04-04 15:28:39,713 localhost-startStop-2 : Calling BreakpointThread shutdownPre() INFO ContextListener 2016-04-04 15:28:39,713 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownPre() INFO ContextListener 2016-04-04 15:28:39,713 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownPre() INFO ContextListener 2016-04-04 15:28:39,713 localhost-startStop-2 : Calling Job Runner (Default) shutdownPre() INFO DatasetSnapshotProvider 2016-04-04 15:28:39,714 SnapshotDependencyThread : QuerySnapshotDependencyThread is terminating due to interruption INFO ContextListener 2016-04-04 15:28:39,714 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownPre() INFO ContextListener 2016-04-04 15:28:39,714 localhost-startStop-2 : Calling Temp table cleanup shutdownPre() INFO ContextListener 2016-04-04 15:28:39,714 localhost-startStop-2 : Calling Temp file deletion shutdownPre() INFO ContextListener 2016-04-04 15:28:39,714 localhost-startStop-2 : Calling Action stats export shutdownPre() INFO CoreModule 2016-04-04 15:28:39,714 localhost-startStop-2 : Starting to log statistics for actions prior to web application shut down INFO CoreModule 2016-04-04 15:28:39,737 localhost-startStop-2 : Completed logging statistics for actions prior to web application shut down INFO ContextListener 2016-04-04 15:28:39,737 localhost-startStop-2 : Calling DataIntegration shutdownPre() INFO ContextListener 2016-04-04 15:28:39,754 localhost-startStop-2 : Calling DAV crawler shutdownPre() INFO ContextListener 2016-04-04 15:28:39,754 localhost-startStop-2 : Calling Search service shutdownPre() INFO ContextListener 2016-04-04 15:28:39,754 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownPre() INFO ContextListener 2016-04-04 15:28:39,754 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownPre() INFO ContextListener 2016-04-04 15:28:39,755 localhost-startStop-2 : Calling Study Reload Handler shutdownPre() INFO ContextListener 2016-04-04 15:28:39,755 localhost-startStop-2 : Calling HeartBeatThread shutdownStarted() INFO ContextListener 2016-04-04 15:28:39,755 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownStarted() INFO ContextListener 2016-04-04 15:28:39,755 localhost-startStop-2 : Calling QueryProfilerThread shutdownStarted() INFO QueryProfiler 2016-04-04 15:28:39,755 localhost-startStop-2 : Starting to log statistics for queries prior to web application shut down INFO QueryProfiler 2016-04-04 15:28:39,786 localhost-startStop-2 : Completed logging statistics for queries prior to web application shut down INFO ContextListener 2016-04-04 15:28:39,786 localhost-startStop-2 : Calling BreakpointThread shutdownStarted() INFO ContextListener 2016-04-04 15:28:39,786 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownStarted() INFO ContextListener 2016-04-04 15:28:39,786 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownStarted() INFO ContextListener 2016-04-04 15:28:39,786 localhost-startStop-2 : Calling Job Runner (Default) shutdownStarted() INFO ContextListener 2016-04-04 15:28:39,786 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownStarted() INFO ContextListener 2016-04-04 15:28:39,786 localhost-startStop-2 : Calling Temp table cleanup shutdownStarted() INFO ContextListener 2016-04-04 15:28:39,787 localhost-startStop-2 : Calling Temp file deletion shutdownStarted() INFO ContextListener 2016-04-04 15:28:39,787 localhost-startStop-2 : Calling Action stats export shutdownStarted() INFO ContextListener 2016-04-04 15:28:39,787 localhost-startStop-2 : Calling DataIntegration shutdownStarted() INFO ContextListener 2016-04-04 15:28:40,254 localhost-startStop-2 : Calling DAV crawler shutdownStarted() INFO ContextListener 2016-04-04 15:28:40,255 localhost-startStop-2 : Calling Search service shutdownStarted() INFO ContextListener 2016-04-04 15:28:40,258 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownStarted() INFO ContextListener 2016-04-04 15:28:40,258 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownStarted() INFO ContextListener 2016-04-04 15:28:40,258 localhost-startStop-2 : Calling Study Reload Handler shutdownStarted() INFO EhCacheProvider 2016-04-04 15:28:40,262 localhost-startStop-2 : Shutting down Ehcache INFO ModuleLoader 2016-04-04 15:28:45,816 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2016-04-04 15:28:47,181 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource Server URL: jdbc:postgresql://localhost:5432/labkey Database Product Name: PostgreSQL Database Product Version: 9.4.6 JDBC Driver Name: PostgreSQL Native Driver JDBC Driver Version: PostgreSQL 9.4.1207 SQL Dialect: PostgreSql94Dialect ERROR DebugInfoDumper 2016-04-04 15:28:47,271 localhost-startStop-1 : Failed to create file /usr/share/labkey/threadDumpRequest java.io.FileNotFoundException: /usr/share/labkey/threadDumpRequest (Permission denied) at java.io.FileOutputStream.open0(Native Method) at java.io.FileOutputStream.open(FileOutputStream.java:270) at java.io.FileOutputStream.(FileOutputStream.java:213) at java.io.FileOutputStream.(FileOutputStream.java:162) at java.io.PrintWriter.(PrintWriter.java:192) at java.io.PrintWriter.(PrintWriter.java:303) at org.labkey.api.util.DebugInfoDumper.(DebugInfoDumper.java:65) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:337) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:238) at org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279) at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260) at org.apache.catalina.core.ApplicationFilterConfig.(ApplicationFilterConfig.java:105) at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4640) at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5247) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:724) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:700) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:714) at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:581) at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1685) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) ERROR DebugInfoDumper 2016-04-04 15:28:47,272 localhost-startStop-1 : Failed to create file /usr/share/labkey/heapDumpRequest java.io.FileNotFoundException: /usr/share/labkey/heapDumpRequest (Permission denied) at java.io.FileOutputStream.open0(Native Method) at java.io.FileOutputStream.open(FileOutputStream.java:270) at java.io.FileOutputStream.(FileOutputStream.java:213) at java.io.FileOutputStream.(FileOutputStream.java:162) at java.io.PrintWriter.(PrintWriter.java:192) at java.io.PrintWriter.(PrintWriter.java:303) at org.labkey.api.util.DebugInfoDumper.(DebugInfoDumper.java:81) at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:337) at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:238) at org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279) at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260) at org.apache.catalina.core.ApplicationFilterConfig.(ApplicationFilterConfig.java:105) at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4640) at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5247) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:724) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:700) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:714) at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:581) at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1685) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) INFO DbScope 2016-04-04 15:28:47,279 localhost-startStop-1 : Loading DbSchema "labkey.core" (Module) INFO DbScope 2016-04-04 15:28:49,535 localhost-startStop-1 : Loading DbSchema "labkey.prop" (Module) INFO DbScope 2016-04-04 15:28:49,611 localhost-startStop-1 : Loading DbSchema "labkey.test" (Module) INFO DbScope 2016-04-04 15:28:49,617 localhost-startStop-1 : Loading DbSchema "labkey.temp" (Provisioned) INFO DbScope 2016-04-04 15:28:49,619 localhost-startStop-1 : Loading DbSchema "labkey.query" (Module) INFO DbScope 2016-04-04 15:28:49,624 localhost-startStop-1 : Loading DbSchema "labkey.junit" (Module) INFO DbScope 2016-04-04 15:28:49,626 localhost-startStop-1 : no schema metadata xml file found for schema "junit" INFO DbScope 2016-04-04 15:28:49,626 localhost-startStop-1 : Loading DbSchema "labkey.search" (Module) INFO DbScope 2016-04-04 15:28:49,630 localhost-startStop-1 : Loading DbSchema "labkey.umls" (Module) INFO DbScope 2016-04-04 15:28:49,633 localhost-startStop-1 : no schema metadata xml file found for schema "umls" INFO DbScope 2016-04-04 15:28:49,633 localhost-startStop-1 : Loading DbSchema "labkey.issues" (Module) INFO DbScope 2016-04-04 15:28:49,639 localhost-startStop-1 : Loading DbSchema "labkey.comm" (Module) INFO DbScope 2016-04-04 15:28:49,654 localhost-startStop-1 : Loading DbSchema "labkey.pipeline" (Module) INFO DbScope 2016-04-04 15:28:49,658 localhost-startStop-1 : Loading DbSchema "labkey.exp" (Module) INFO DbScope 2016-04-04 15:28:49,666 localhost-startStop-1 : Loading DbSchema "labkey.flow" (Module) INFO DbScope 2016-04-04 15:28:49,670 localhost-startStop-1 : Loading DbSchema "labkey.microarray" (Module) INFO DbScope 2016-04-04 15:28:49,674 localhost-startStop-1 : Loading DbSchema "labkey.filecontent" (Module) INFO DbScope 2016-04-04 15:28:49,683 localhost-startStop-1 : Loading DbSchema "labkey.list" (Provisioned) INFO DbScope 2016-04-04 15:28:49,683 localhost-startStop-1 : Loading DbSchema "labkey.ms2" (Module) INFO DbScope 2016-04-04 15:28:49,692 localhost-startStop-1 : Loading DbSchema "labkey.prot" (Module) INFO DbScope 2016-04-04 15:28:49,697 localhost-startStop-1 : Loading DbSchema "labkey.ms1" (Module) INFO DbScope 2016-04-04 15:28:49,702 localhost-startStop-1 : Loading DbSchema "labkey.survey" (Module) INFO DbScope 2016-04-04 15:28:49,707 localhost-startStop-1 : Loading DbSchema "labkey.dataintegration" (Module) INFO DbScope 2016-04-04 15:28:49,711 localhost-startStop-1 : Loading DbSchema "labkey.study" (Module) INFO DbScope 2016-04-04 15:28:49,726 localhost-startStop-1 : Loading DbSchema "labkey.studydataset" (Provisioned) INFO DbScope 2016-04-04 15:28:49,726 localhost-startStop-1 : Loading DbSchema "labkey.assayresult" (Provisioned) INFO DbScope 2016-04-04 15:28:49,726 localhost-startStop-1 : Loading DbSchema "labkey.studydesign" (Provisioned) INFO DbScope 2016-04-04 15:28:49,726 localhost-startStop-1 : Loading DbSchema "labkey.specimentables" (Provisioned) INFO DbScope 2016-04-04 15:28:49,726 localhost-startStop-1 : Loading DbSchema "labkey.luminex" (Module) INFO DbScope 2016-04-04 15:28:49,731 localhost-startStop-1 : Loading DbSchema "labkey.nab" (Module) INFO DbScope 2016-04-04 15:28:49,736 localhost-startStop-1 : Loading DbSchema "labkey.nabvirus" (Provisioned) INFO DbScope 2016-04-04 15:28:49,736 localhost-startStop-1 : Loading DbSchema "labkey.targetedms" (Module) INFO DbScope 2016-04-04 15:28:49,744 localhost-startStop-1 : Loading DbSchema "labkey.audit" (Provisioned) INFO DbScope 2016-04-04 15:28:49,745 localhost-startStop-1 : Loading DbSchema "labkey.elispotlk" (Module) INFO ModuleLoader 2016-04-04 15:28:49,815 localhost-startStop-1 : LabKey Server startup is complete; modules are being upgraded and initialized in the background INFO ModuleLoader 2016-04-04 15:28:49,815 Module Upgrade : Starting up modules INFO ModuleLoader 2016-04-04 15:28:49,815 Module Upgrade : Starting module 'Core' INFO ViewServlet 2016-04-04 15:28:49,818 localhost-startStop-1 : ViewServlet initialized INFO ViewServlet 2016-04-04 15:28:49,822 localhost-startStop-1 : WEBAPP: /usr/share/labkey/labkeywebapp INFO ViewServlet 2016-04-04 15:28:49,823 localhost-startStop-1 : PATH: /usr/local/tpp/bin:/bin:/usr/bin:/sbin:/usr/sbin INFO ModuleLoader 2016-04-04 15:28:50,683 Module Upgrade : Starting module 'Query' INFO ModuleLoader 2016-04-04 15:28:50,722 Module Upgrade : Starting module 'FCSExpress' INFO ModuleLoader 2016-04-04 15:28:50,739 Module Upgrade : Starting module 'Search' INFO ModuleLoader 2016-04-04 15:28:50,750 Module Upgrade : Starting module 'Wiki' INFO ModuleLoader 2016-04-04 15:28:50,757 Module Upgrade : Starting module 'Issues' INFO ModuleLoader 2016-04-04 15:28:50,767 Module Upgrade : Starting module 'Announcements' INFO ModuleLoader 2016-04-04 15:28:50,843 Module Upgrade : Starting module 'BigIron' INFO ModuleLoader 2016-04-04 15:28:50,843 Module Upgrade : Starting module 'Pipeline' INFO SpringModule 2016-04-04 15:28:50,844 Module Upgrade : Loading Spring configuration for the Pipeline module from [/WEB-INF/pipelineContext.xml] INFO SpringModule$1 2016-04-04 15:28:50,846 Module Upgrade : Refreshing Pipeline WebApplicationContext: startup date [Mon Apr 04 15:28:50 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:28:50,969 Module Upgrade : Starting module 'Experiment' INFO SpringModule 2016-04-04 15:28:50,970 Module Upgrade : Loading Spring configuration for the Experiment module from [/WEB-INF/experimentContext.xml] INFO SpringModule$1 2016-04-04 15:28:50,972 Module Upgrade : Refreshing Experiment WebApplicationContext: startup date [Mon Apr 04 15:28:50 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:28:51,192 Module Upgrade : Starting module 'Flow' INFO ModuleLoader 2016-04-04 15:28:51,230 Module Upgrade : Starting module 'Microarray' INFO SpringModule 2016-04-04 15:28:51,230 Module Upgrade : Loading Spring configuration for the Microarray module from [/WEB-INF/microarrayContext.xml] INFO SpringModule$1 2016-04-04 15:28:51,231 Module Upgrade : Refreshing Microarray WebApplicationContext: startup date [Mon Apr 04 15:28:51 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:28:51,272 Module Upgrade : Starting module 'FileContent' INFO ModuleLoader 2016-04-04 15:28:51,275 Module Upgrade : Starting module 'List' INFO ModuleLoader 2016-04-04 15:28:51,294 Module Upgrade : Starting module 'MS2' INFO SpringModule 2016-04-04 15:28:51,294 Module Upgrade : Loading Spring configuration for the MS2 module from [/WEB-INF/ms2Context.xml] INFO SpringModule$1 2016-04-04 15:28:51,295 Module Upgrade : Refreshing MS2 WebApplicationContext: startup date [Mon Apr 04 15:28:51 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:28:51,684 Module Upgrade : Starting module 'MS1' INFO SpringModule 2016-04-04 15:28:51,684 Module Upgrade : Loading Spring configuration for the MS1 module from [/WEB-INF/ms1Context.xml] INFO SpringModule$1 2016-04-04 15:28:51,685 Module Upgrade : Refreshing MS1 WebApplicationContext: startup date [Mon Apr 04 15:28:51 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:28:51,764 Module Upgrade : Starting module 'Survey' INFO ModuleLoader 2016-04-04 15:28:51,765 Module Upgrade : Starting module 'DataIntegration' INFO ModuleLoader 2016-04-04 15:28:51,775 Module Upgrade : Starting module 'Study' INFO SpringModule 2016-04-04 15:28:51,776 Module Upgrade : Loading Spring configuration for the Study module from [/WEB-INF/studyContext.xml] INFO SpringModule$1 2016-04-04 15:28:51,777 Module Upgrade : Refreshing Study WebApplicationContext: startup date [Mon Apr 04 15:28:51 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:28:51,968 Module Upgrade : Starting module 'Luminex' INFO ModuleLoader 2016-04-04 15:28:51,980 Module Upgrade : Starting module 'Visualization' INFO ModuleLoader 2016-04-04 15:28:51,981 Module Upgrade : Starting module 'Nab' INFO ModuleLoader 2016-04-04 15:28:51,999 Module Upgrade : Starting module 'Elisa' INFO ModuleLoader 2016-04-04 15:28:52,003 Module Upgrade : Starting module 'TargetedMS' INFO SpringModule 2016-04-04 15:28:52,003 Module Upgrade : Loading Spring configuration for the TargetedMS module from [/WEB-INF/targetedmsContext.xml] INFO SpringModule$1 2016-04-04 15:28:52,004 Module Upgrade : Refreshing TargetedMS WebApplicationContext: startup date [Mon Apr 04 15:28:52 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:28:52,030 Module Upgrade : Starting module 'Audit' INFO ModuleLoader 2016-04-04 15:28:52,038 Module Upgrade : Starting module 'ELISpotAssay' INFO ModuleLoader 2016-04-04 15:28:52,044 Module Upgrade : Running startup listener: Audit Log INFO ModuleLoader 2016-04-04 15:28:52,044 Module Upgrade : Running startup listener: Search Service INFO ModuleLoader 2016-04-04 15:28:52,044 Module Upgrade : Running startup listener: PipelineJobRestarter INFO ModuleLoader 2016-04-04 15:28:52,046 Module Upgrade : Running startup listener: DataIntegration INFO ModuleLoader 2016-04-04 15:28:52,051 Module Upgrade : Module startup complete INFO ContextListener 2016-04-04 15:33:56,072 localhost-startStop-2 : Calling HeartBeatThread shutdownPre() INFO ContextListener 2016-04-04 15:33:56,072 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownPre() INFO ContextListener 2016-04-04 15:33:56,072 localhost-startStop-2 : Calling QueryProfilerThread shutdownPre() INFO ContextListener 2016-04-04 15:33:56,072 localhost-startStop-2 : Calling BreakpointThread shutdownPre() INFO ContextListener 2016-04-04 15:33:56,072 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownPre() INFO ContextListener 2016-04-04 15:33:56,072 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownPre() INFO FileSystemWatcherImpl 2016-04-04 15:33:56,073 FileSystemWatcherThread : FileSystemWatcherThread is terminating INFO ContextListener 2016-04-04 15:33:56,073 localhost-startStop-2 : Calling Job Runner (Default) shutdownPre() INFO DatasetSnapshotProvider 2016-04-04 15:33:56,073 SnapshotDependencyThread : QuerySnapshotDependencyThread is terminating due to interruption INFO ContextListener 2016-04-04 15:33:56,073 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownPre() INFO ContextListener 2016-04-04 15:33:56,073 localhost-startStop-2 : Calling Temp table cleanup shutdownPre() INFO ContextListener 2016-04-04 15:33:56,073 localhost-startStop-2 : Calling Temp file deletion shutdownPre() INFO ContextListener 2016-04-04 15:33:56,073 localhost-startStop-2 : Calling Action stats export shutdownPre() INFO CoreModule 2016-04-04 15:33:56,074 localhost-startStop-2 : Starting to log statistics for actions prior to web application shut down INFO CoreModule 2016-04-04 15:33:56,094 localhost-startStop-2 : Completed logging statistics for actions prior to web application shut down INFO ContextListener 2016-04-04 15:33:56,095 localhost-startStop-2 : Calling DataIntegration shutdownPre() INFO ContextListener 2016-04-04 15:33:56,115 localhost-startStop-2 : Calling DAV crawler shutdownPre() INFO ContextListener 2016-04-04 15:33:56,115 localhost-startStop-2 : Calling Search service shutdownPre() INFO ContextListener 2016-04-04 15:33:56,116 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownPre() INFO ContextListener 2016-04-04 15:33:56,116 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownPre() INFO ContextListener 2016-04-04 15:33:56,122 localhost-startStop-2 : Calling Study Reload Handler shutdownPre() INFO ContextListener 2016-04-04 15:33:56,122 localhost-startStop-2 : Calling HeartBeatThread shutdownStarted() INFO ContextListener 2016-04-04 15:33:56,122 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownStarted() INFO ContextListener 2016-04-04 15:33:56,122 localhost-startStop-2 : Calling QueryProfilerThread shutdownStarted() INFO QueryProfiler 2016-04-04 15:33:56,122 localhost-startStop-2 : Starting to log statistics for queries prior to web application shut down INFO QueryProfiler 2016-04-04 15:33:56,150 localhost-startStop-2 : Completed logging statistics for queries prior to web application shut down INFO ContextListener 2016-04-04 15:33:56,150 localhost-startStop-2 : Calling BreakpointThread shutdownStarted() INFO ContextListener 2016-04-04 15:33:56,150 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownStarted() INFO ContextListener 2016-04-04 15:33:56,150 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownStarted() INFO ContextListener 2016-04-04 15:33:56,150 localhost-startStop-2 : Calling Job Runner (Default) shutdownStarted() INFO ContextListener 2016-04-04 15:33:56,150 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownStarted() INFO ContextListener 2016-04-04 15:33:56,150 localhost-startStop-2 : Calling Temp table cleanup shutdownStarted() INFO ContextListener 2016-04-04 15:33:56,150 localhost-startStop-2 : Calling Temp file deletion shutdownStarted() INFO ContextListener 2016-04-04 15:33:56,151 localhost-startStop-2 : Calling Action stats export shutdownStarted() INFO ContextListener 2016-04-04 15:33:56,151 localhost-startStop-2 : Calling DataIntegration shutdownStarted() INFO ContextListener 2016-04-04 15:33:56,624 localhost-startStop-2 : Calling DAV crawler shutdownStarted() INFO ContextListener 2016-04-04 15:33:56,624 localhost-startStop-2 : Calling Search service shutdownStarted() INFO ContextListener 2016-04-04 15:33:56,628 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownStarted() INFO ContextListener 2016-04-04 15:33:56,628 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownStarted() INFO ContextListener 2016-04-04 15:33:56,628 localhost-startStop-2 : Calling Study Reload Handler shutdownStarted() INFO EhCacheProvider 2016-04-04 15:33:56,631 localhost-startStop-2 : Shutting down Ehcache INFO ModuleLoader 2016-04-04 15:34:02,445 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2016-04-04 15:34:03,727 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource Server URL: jdbc:postgresql://localhost:5432/labkey Database Product Name: PostgreSQL Database Product Version: 9.4.6 JDBC Driver Name: PostgreSQL Native Driver JDBC Driver Version: PostgreSQL 9.4.1207 SQL Dialect: PostgreSql94Dialect INFO DbScope 2016-04-04 15:34:03,827 localhost-startStop-1 : Loading DbSchema "labkey.core" (Module) INFO DbScope 2016-04-04 15:34:06,063 localhost-startStop-1 : Loading DbSchema "labkey.prop" (Module) INFO DbScope 2016-04-04 15:34:06,141 localhost-startStop-1 : Loading DbSchema "labkey.test" (Module) INFO DbScope 2016-04-04 15:34:06,147 localhost-startStop-1 : Loading DbSchema "labkey.temp" (Provisioned) INFO DbScope 2016-04-04 15:34:06,149 localhost-startStop-1 : Loading DbSchema "labkey.query" (Module) INFO DbScope 2016-04-04 15:34:06,154 localhost-startStop-1 : Loading DbSchema "labkey.junit" (Module) INFO DbScope 2016-04-04 15:34:06,157 localhost-startStop-1 : no schema metadata xml file found for schema "junit" INFO DbScope 2016-04-04 15:34:06,157 localhost-startStop-1 : Loading DbSchema "labkey.search" (Module) INFO DbScope 2016-04-04 15:34:06,163 localhost-startStop-1 : Loading DbSchema "labkey.umls" (Module) INFO DbScope 2016-04-04 15:34:06,166 localhost-startStop-1 : no schema metadata xml file found for schema "umls" INFO DbScope 2016-04-04 15:34:06,166 localhost-startStop-1 : Loading DbSchema "labkey.issues" (Module) INFO DbScope 2016-04-04 15:34:06,174 localhost-startStop-1 : Loading DbSchema "labkey.comm" (Module) INFO DbScope 2016-04-04 15:34:06,186 localhost-startStop-1 : Loading DbSchema "labkey.pipeline" (Module) INFO DbScope 2016-04-04 15:34:06,190 localhost-startStop-1 : Loading DbSchema "labkey.exp" (Module) INFO DbScope 2016-04-04 15:34:06,198 localhost-startStop-1 : Loading DbSchema "labkey.flow" (Module) INFO DbScope 2016-04-04 15:34:06,202 localhost-startStop-1 : Loading DbSchema "labkey.microarray" (Module) INFO DbScope 2016-04-04 15:34:06,206 localhost-startStop-1 : Loading DbSchema "labkey.filecontent" (Module) INFO DbScope 2016-04-04 15:34:06,210 localhost-startStop-1 : Loading DbSchema "labkey.list" (Provisioned) INFO DbScope 2016-04-04 15:34:06,210 localhost-startStop-1 : Loading DbSchema "labkey.ms2" (Module) INFO DbScope 2016-04-04 15:34:06,225 localhost-startStop-1 : Loading DbSchema "labkey.prot" (Module) INFO DbScope 2016-04-04 15:34:06,230 localhost-startStop-1 : Loading DbSchema "labkey.ms1" (Module) INFO DbScope 2016-04-04 15:34:06,236 localhost-startStop-1 : Loading DbSchema "labkey.survey" (Module) INFO DbScope 2016-04-04 15:34:06,240 localhost-startStop-1 : Loading DbSchema "labkey.dataintegration" (Module) INFO DbScope 2016-04-04 15:34:06,245 localhost-startStop-1 : Loading DbSchema "labkey.study" (Module) INFO DbScope 2016-04-04 15:34:06,260 localhost-startStop-1 : Loading DbSchema "labkey.studydataset" (Provisioned) INFO DbScope 2016-04-04 15:34:06,260 localhost-startStop-1 : Loading DbSchema "labkey.assayresult" (Provisioned) INFO DbScope 2016-04-04 15:34:06,260 localhost-startStop-1 : Loading DbSchema "labkey.studydesign" (Provisioned) INFO DbScope 2016-04-04 15:34:06,260 localhost-startStop-1 : Loading DbSchema "labkey.specimentables" (Provisioned) INFO DbScope 2016-04-04 15:34:06,260 localhost-startStop-1 : Loading DbSchema "labkey.luminex" (Module) INFO DbScope 2016-04-04 15:34:06,267 localhost-startStop-1 : Loading DbSchema "labkey.nab" (Module) INFO DbScope 2016-04-04 15:34:06,271 localhost-startStop-1 : Loading DbSchema "labkey.nabvirus" (Provisioned) INFO DbScope 2016-04-04 15:34:06,271 localhost-startStop-1 : Loading DbSchema "labkey.targetedms" (Module) INFO DbScope 2016-04-04 15:34:06,279 localhost-startStop-1 : Loading DbSchema "labkey.audit" (Provisioned) INFO DbScope 2016-04-04 15:34:06,279 localhost-startStop-1 : Loading DbSchema "labkey.elispotlk" (Module) INFO ModuleLoader 2016-04-04 15:34:06,358 localhost-startStop-1 : LabKey Server startup is complete; modules are being upgraded and initialized in the background INFO ModuleLoader 2016-04-04 15:34:06,358 Module Upgrade : Starting up modules INFO ModuleLoader 2016-04-04 15:34:06,359 Module Upgrade : Starting module 'Core' INFO ViewServlet 2016-04-04 15:34:06,362 localhost-startStop-1 : ViewServlet initialized INFO ViewServlet 2016-04-04 15:34:06,362 localhost-startStop-1 : WEBAPP: /usr/share/labkey/labkeywebapp INFO ViewServlet 2016-04-04 15:34:06,362 localhost-startStop-1 : PATH: /usr/local/tpp/bin:/bin:/usr/bin:/sbin:/usr/sbin INFO ModuleLoader 2016-04-04 15:34:07,176 Module Upgrade : Starting module 'Query' INFO ModuleLoader 2016-04-04 15:34:07,244 Module Upgrade : Starting module 'FCSExpress' INFO ModuleLoader 2016-04-04 15:34:07,260 Module Upgrade : Starting module 'Search' INFO ModuleLoader 2016-04-04 15:34:07,277 Module Upgrade : Starting module 'Wiki' INFO ModuleLoader 2016-04-04 15:34:07,285 Module Upgrade : Starting module 'Issues' INFO ModuleLoader 2016-04-04 15:34:07,296 Module Upgrade : Starting module 'Announcements' INFO ModuleLoader 2016-04-04 15:34:07,373 Module Upgrade : Starting module 'BigIron' INFO ModuleLoader 2016-04-04 15:34:07,374 Module Upgrade : Starting module 'Pipeline' INFO SpringModule 2016-04-04 15:34:07,374 Module Upgrade : Loading Spring configuration for the Pipeline module from [/WEB-INF/pipelineContext.xml] INFO SpringModule$1 2016-04-04 15:34:07,376 Module Upgrade : Refreshing Pipeline WebApplicationContext: startup date [Mon Apr 04 15:34:07 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:34:07,500 Module Upgrade : Starting module 'Experiment' INFO SpringModule 2016-04-04 15:34:07,500 Module Upgrade : Loading Spring configuration for the Experiment module from [/WEB-INF/experimentContext.xml] INFO SpringModule$1 2016-04-04 15:34:07,501 Module Upgrade : Refreshing Experiment WebApplicationContext: startup date [Mon Apr 04 15:34:07 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:34:07,718 Module Upgrade : Starting module 'Flow' INFO ModuleLoader 2016-04-04 15:34:07,753 Module Upgrade : Starting module 'Microarray' INFO SpringModule 2016-04-04 15:34:07,753 Module Upgrade : Loading Spring configuration for the Microarray module from [/WEB-INF/microarrayContext.xml] INFO SpringModule$1 2016-04-04 15:34:07,754 Module Upgrade : Refreshing Microarray WebApplicationContext: startup date [Mon Apr 04 15:34:07 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:34:07,796 Module Upgrade : Starting module 'FileContent' INFO ModuleLoader 2016-04-04 15:34:07,800 Module Upgrade : Starting module 'List' INFO ModuleLoader 2016-04-04 15:34:07,820 Module Upgrade : Starting module 'MS2' INFO SpringModule 2016-04-04 15:34:07,821 Module Upgrade : Loading Spring configuration for the MS2 module from [/WEB-INF/ms2Context.xml] INFO SpringModule$1 2016-04-04 15:34:07,822 Module Upgrade : Refreshing MS2 WebApplicationContext: startup date [Mon Apr 04 15:34:07 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:34:08,196 Module Upgrade : Starting module 'MS1' INFO SpringModule 2016-04-04 15:34:08,197 Module Upgrade : Loading Spring configuration for the MS1 module from [/WEB-INF/ms1Context.xml] INFO SpringModule$1 2016-04-04 15:34:08,198 Module Upgrade : Refreshing MS1 WebApplicationContext: startup date [Mon Apr 04 15:34:08 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:34:08,283 Module Upgrade : Starting module 'Survey' INFO ModuleLoader 2016-04-04 15:34:08,284 Module Upgrade : Starting module 'DataIntegration' INFO ModuleLoader 2016-04-04 15:34:08,292 Module Upgrade : Starting module 'Study' INFO SpringModule 2016-04-04 15:34:08,292 Module Upgrade : Loading Spring configuration for the Study module from [/WEB-INF/studyContext.xml] INFO SpringModule$1 2016-04-04 15:34:08,293 Module Upgrade : Refreshing Study WebApplicationContext: startup date [Mon Apr 04 15:34:08 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:34:08,466 Module Upgrade : Starting module 'Luminex' INFO ModuleLoader 2016-04-04 15:34:08,489 Module Upgrade : Starting module 'Visualization' INFO ModuleLoader 2016-04-04 15:34:08,490 Module Upgrade : Starting module 'Nab' INFO ModuleLoader 2016-04-04 15:34:08,509 Module Upgrade : Starting module 'Elisa' INFO ModuleLoader 2016-04-04 15:34:08,513 Module Upgrade : Starting module 'TargetedMS' INFO SpringModule 2016-04-04 15:34:08,513 Module Upgrade : Loading Spring configuration for the TargetedMS module from [/WEB-INF/targetedmsContext.xml] INFO SpringModule$1 2016-04-04 15:34:08,514 Module Upgrade : Refreshing TargetedMS WebApplicationContext: startup date [Mon Apr 04 15:34:08 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:34:08,542 Module Upgrade : Starting module 'Audit' INFO ModuleLoader 2016-04-04 15:34:08,551 Module Upgrade : Starting module 'ELISpotAssay' INFO ModuleLoader 2016-04-04 15:34:08,557 Module Upgrade : Running startup listener: Audit Log INFO ModuleLoader 2016-04-04 15:34:08,557 Module Upgrade : Running startup listener: Search Service INFO ModuleLoader 2016-04-04 15:34:08,557 Module Upgrade : Running startup listener: PipelineJobRestarter INFO ModuleLoader 2016-04-04 15:34:08,559 Module Upgrade : Running startup listener: DataIntegration INFO ModuleLoader 2016-04-04 15:34:08,566 Module Upgrade : Module startup complete INFO ContextListener 2016-04-04 15:50:12,885 localhost-startStop-2 : Calling HeartBeatThread shutdownPre() INFO ContextListener 2016-04-04 15:50:12,885 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownPre() INFO ContextListener 2016-04-04 15:50:12,885 localhost-startStop-2 : Calling QueryProfilerThread shutdownPre() INFO ContextListener 2016-04-04 15:50:12,885 localhost-startStop-2 : Calling BreakpointThread shutdownPre() INFO ContextListener 2016-04-04 15:50:12,885 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownPre() INFO ContextListener 2016-04-04 15:50:12,885 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownPre() INFO ContextListener 2016-04-04 15:50:12,885 localhost-startStop-2 : Calling Job Runner (Default) shutdownPre() INFO DatasetSnapshotProvider 2016-04-04 15:50:12,885 SnapshotDependencyThread : QuerySnapshotDependencyThread is terminating due to interruption INFO ContextListener 2016-04-04 15:50:12,885 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownPre() INFO FileSystemWatcherImpl 2016-04-04 15:50:12,885 FileSystemWatcherThread : FileSystemWatcherThread is terminating INFO ContextListener 2016-04-04 15:50:12,885 localhost-startStop-2 : Calling Temp table cleanup shutdownPre() INFO ContextListener 2016-04-04 15:50:12,885 localhost-startStop-2 : Calling Temp file deletion shutdownPre() INFO ContextListener 2016-04-04 15:50:12,885 localhost-startStop-2 : Calling Action stats export shutdownPre() INFO CoreModule 2016-04-04 15:50:12,885 localhost-startStop-2 : Starting to log statistics for actions prior to web application shut down INFO CoreModule 2016-04-04 15:50:12,898 localhost-startStop-2 : Completed logging statistics for actions prior to web application shut down INFO ContextListener 2016-04-04 15:50:12,898 localhost-startStop-2 : Calling DataIntegration shutdownPre() INFO ContextListener 2016-04-04 15:50:12,918 localhost-startStop-2 : Calling DAV crawler shutdownPre() INFO ContextListener 2016-04-04 15:50:12,918 localhost-startStop-2 : Calling Search service shutdownPre() INFO ContextListener 2016-04-04 15:50:12,918 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownPre() INFO ContextListener 2016-04-04 15:50:12,918 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownPre() INFO ContextListener 2016-04-04 15:50:12,918 localhost-startStop-2 : Calling Study Reload Handler shutdownPre() INFO ContextListener 2016-04-04 15:50:12,918 localhost-startStop-2 : Calling HeartBeatThread shutdownStarted() INFO ContextListener 2016-04-04 15:50:12,919 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownStarted() INFO ContextListener 2016-04-04 15:50:12,919 localhost-startStop-2 : Calling QueryProfilerThread shutdownStarted() INFO QueryProfiler 2016-04-04 15:50:12,919 localhost-startStop-2 : Starting to log statistics for queries prior to web application shut down INFO QueryProfiler 2016-04-04 15:50:12,936 localhost-startStop-2 : Completed logging statistics for queries prior to web application shut down INFO ContextListener 2016-04-04 15:50:12,936 localhost-startStop-2 : Calling BreakpointThread shutdownStarted() INFO ContextListener 2016-04-04 15:50:12,936 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownStarted() INFO ContextListener 2016-04-04 15:50:12,936 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownStarted() INFO ContextListener 2016-04-04 15:50:12,936 localhost-startStop-2 : Calling Job Runner (Default) shutdownStarted() INFO ContextListener 2016-04-04 15:50:12,936 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownStarted() INFO ContextListener 2016-04-04 15:50:12,936 localhost-startStop-2 : Calling Temp table cleanup shutdownStarted() INFO ContextListener 2016-04-04 15:50:12,937 localhost-startStop-2 : Calling Temp file deletion shutdownStarted() INFO ContextListener 2016-04-04 15:50:12,937 localhost-startStop-2 : Calling Action stats export shutdownStarted() INFO ContextListener 2016-04-04 15:50:12,937 localhost-startStop-2 : Calling DataIntegration shutdownStarted() INFO ContextListener 2016-04-04 15:50:13,418 localhost-startStop-2 : Calling DAV crawler shutdownStarted() INFO ContextListener 2016-04-04 15:50:13,419 localhost-startStop-2 : Calling Search service shutdownStarted() INFO ContextListener 2016-04-04 15:50:13,422 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownStarted() INFO ContextListener 2016-04-04 15:50:13,422 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownStarted() INFO ContextListener 2016-04-04 15:50:13,422 localhost-startStop-2 : Calling Study Reload Handler shutdownStarted() INFO EhCacheProvider 2016-04-04 15:50:13,426 localhost-startStop-2 : Shutting down Ehcache INFO ModuleLoader 2016-04-04 15:50:18,896 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2016-04-04 15:50:20,193 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource Server URL: jdbc:postgresql://localhost:5432/labkey Database Product Name: PostgreSQL Database Product Version: 9.4.6 JDBC Driver Name: PostgreSQL Native Driver JDBC Driver Version: PostgreSQL 9.4.1207 SQL Dialect: PostgreSql94Dialect INFO DbScope 2016-04-04 15:50:20,277 localhost-startStop-1 : Loading DbSchema "labkey.core" (Module) INFO DbScope 2016-04-04 15:50:22,478 localhost-startStop-1 : Loading DbSchema "labkey.prop" (Module) INFO DbScope 2016-04-04 15:50:22,556 localhost-startStop-1 : Loading DbSchema "labkey.test" (Module) INFO DbScope 2016-04-04 15:50:22,561 localhost-startStop-1 : Loading DbSchema "labkey.temp" (Provisioned) INFO DbScope 2016-04-04 15:50:22,564 localhost-startStop-1 : Loading DbSchema "labkey.query" (Module) INFO DbScope 2016-04-04 15:50:22,569 localhost-startStop-1 : Loading DbSchema "labkey.junit" (Module) INFO DbScope 2016-04-04 15:50:22,572 localhost-startStop-1 : no schema metadata xml file found for schema "junit" INFO DbScope 2016-04-04 15:50:22,572 localhost-startStop-1 : Loading DbSchema "labkey.search" (Module) INFO DbScope 2016-04-04 15:50:22,577 localhost-startStop-1 : Loading DbSchema "labkey.umls" (Module) INFO DbScope 2016-04-04 15:50:22,580 localhost-startStop-1 : no schema metadata xml file found for schema "umls" INFO DbScope 2016-04-04 15:50:22,580 localhost-startStop-1 : Loading DbSchema "labkey.issues" (Module) INFO DbScope 2016-04-04 15:50:22,586 localhost-startStop-1 : Loading DbSchema "labkey.comm" (Module) INFO DbScope 2016-04-04 15:50:22,598 localhost-startStop-1 : Loading DbSchema "labkey.pipeline" (Module) INFO DbScope 2016-04-04 15:50:22,602 localhost-startStop-1 : Loading DbSchema "labkey.exp" (Module) INFO DbScope 2016-04-04 15:50:22,610 localhost-startStop-1 : Loading DbSchema "labkey.flow" (Module) INFO DbScope 2016-04-04 15:50:22,614 localhost-startStop-1 : Loading DbSchema "labkey.microarray" (Module) INFO DbScope 2016-04-04 15:50:22,618 localhost-startStop-1 : Loading DbSchema "labkey.filecontent" (Module) INFO DbScope 2016-04-04 15:50:22,622 localhost-startStop-1 : Loading DbSchema "labkey.list" (Provisioned) INFO DbScope 2016-04-04 15:50:22,622 localhost-startStop-1 : Loading DbSchema "labkey.ms2" (Module) INFO DbScope 2016-04-04 15:50:22,632 localhost-startStop-1 : Loading DbSchema "labkey.prot" (Module) INFO DbScope 2016-04-04 15:50:22,637 localhost-startStop-1 : Loading DbSchema "labkey.ms1" (Module) INFO DbScope 2016-04-04 15:50:22,642 localhost-startStop-1 : Loading DbSchema "labkey.survey" (Module) INFO DbScope 2016-04-04 15:50:22,647 localhost-startStop-1 : Loading DbSchema "labkey.dataintegration" (Module) INFO DbScope 2016-04-04 15:50:22,651 localhost-startStop-1 : Loading DbSchema "labkey.study" (Module) INFO DbScope 2016-04-04 15:50:22,666 localhost-startStop-1 : Loading DbSchema "labkey.studydataset" (Provisioned) INFO DbScope 2016-04-04 15:50:22,666 localhost-startStop-1 : Loading DbSchema "labkey.assayresult" (Provisioned) INFO DbScope 2016-04-04 15:50:22,666 localhost-startStop-1 : Loading DbSchema "labkey.studydesign" (Provisioned) INFO DbScope 2016-04-04 15:50:22,666 localhost-startStop-1 : Loading DbSchema "labkey.specimentables" (Provisioned) INFO DbScope 2016-04-04 15:50:22,666 localhost-startStop-1 : Loading DbSchema "labkey.luminex" (Module) INFO DbScope 2016-04-04 15:50:22,676 localhost-startStop-1 : Loading DbSchema "labkey.nab" (Module) INFO DbScope 2016-04-04 15:50:22,681 localhost-startStop-1 : Loading DbSchema "labkey.nabvirus" (Provisioned) INFO DbScope 2016-04-04 15:50:22,681 localhost-startStop-1 : Loading DbSchema "labkey.targetedms" (Module) INFO DbScope 2016-04-04 15:50:22,688 localhost-startStop-1 : Loading DbSchema "labkey.audit" (Provisioned) INFO DbScope 2016-04-04 15:50:22,689 localhost-startStop-1 : Loading DbSchema "labkey.elispotlk" (Module) INFO ModuleLoader 2016-04-04 15:50:22,755 localhost-startStop-1 : LabKey Server startup is complete; modules are being upgraded and initialized in the background INFO ModuleLoader 2016-04-04 15:50:22,755 Module Upgrade : Starting up modules INFO ModuleLoader 2016-04-04 15:50:22,756 Module Upgrade : Starting module 'Core' INFO ViewServlet 2016-04-04 15:50:22,758 localhost-startStop-1 : ViewServlet initialized INFO ViewServlet 2016-04-04 15:50:22,758 localhost-startStop-1 : WEBAPP: /usr/share/labkey/labkeywebapp INFO ViewServlet 2016-04-04 15:50:22,758 localhost-startStop-1 : PATH: /usr/local/tpp/bin:/bin:/usr/bin:/sbin:/usr/sbin INFO ModuleLoader 2016-04-04 15:50:23,720 Module Upgrade : Starting module 'Query' INFO ModuleLoader 2016-04-04 15:50:23,768 Module Upgrade : Starting module 'FCSExpress' INFO ModuleLoader 2016-04-04 15:50:23,783 Module Upgrade : Starting module 'Search' INFO ModuleLoader 2016-04-04 15:50:23,791 Module Upgrade : Starting module 'Wiki' INFO ModuleLoader 2016-04-04 15:50:23,797 Module Upgrade : Starting module 'Issues' INFO ModuleLoader 2016-04-04 15:50:23,813 Module Upgrade : Starting module 'Announcements' INFO ModuleLoader 2016-04-04 15:50:23,889 Module Upgrade : Starting module 'BigIron' INFO ModuleLoader 2016-04-04 15:50:23,890 Module Upgrade : Starting module 'Pipeline' INFO SpringModule 2016-04-04 15:50:23,890 Module Upgrade : Loading Spring configuration for the Pipeline module from [/WEB-INF/pipelineContext.xml] INFO SpringModule$1 2016-04-04 15:50:23,892 Module Upgrade : Refreshing Pipeline WebApplicationContext: startup date [Mon Apr 04 15:50:23 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:50:24,018 Module Upgrade : Starting module 'Experiment' INFO SpringModule 2016-04-04 15:50:24,019 Module Upgrade : Loading Spring configuration for the Experiment module from [/WEB-INF/experimentContext.xml] INFO SpringModule$1 2016-04-04 15:50:24,020 Module Upgrade : Refreshing Experiment WebApplicationContext: startup date [Mon Apr 04 15:50:24 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:50:24,244 Module Upgrade : Starting module 'Flow' INFO ModuleLoader 2016-04-04 15:50:24,284 Module Upgrade : Starting module 'Microarray' INFO SpringModule 2016-04-04 15:50:24,284 Module Upgrade : Loading Spring configuration for the Microarray module from [/WEB-INF/microarrayContext.xml] INFO SpringModule$1 2016-04-04 15:50:24,286 Module Upgrade : Refreshing Microarray WebApplicationContext: startup date [Mon Apr 04 15:50:24 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:50:24,327 Module Upgrade : Starting module 'FileContent' INFO ModuleLoader 2016-04-04 15:50:24,330 Module Upgrade : Starting module 'List' INFO ModuleLoader 2016-04-04 15:50:24,350 Module Upgrade : Starting module 'MS2' INFO SpringModule 2016-04-04 15:50:24,350 Module Upgrade : Loading Spring configuration for the MS2 module from [/WEB-INF/ms2Context.xml] INFO SpringModule$1 2016-04-04 15:50:24,351 Module Upgrade : Refreshing MS2 WebApplicationContext: startup date [Mon Apr 04 15:50:24 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:50:24,764 Module Upgrade : Starting module 'MS1' INFO SpringModule 2016-04-04 15:50:24,765 Module Upgrade : Loading Spring configuration for the MS1 module from [/WEB-INF/ms1Context.xml] INFO SpringModule$1 2016-04-04 15:50:24,766 Module Upgrade : Refreshing MS1 WebApplicationContext: startup date [Mon Apr 04 15:50:24 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:50:24,843 Module Upgrade : Starting module 'Survey' INFO ModuleLoader 2016-04-04 15:50:24,844 Module Upgrade : Starting module 'DataIntegration' INFO ModuleLoader 2016-04-04 15:50:24,853 Module Upgrade : Starting module 'Study' INFO SpringModule 2016-04-04 15:50:24,853 Module Upgrade : Loading Spring configuration for the Study module from [/WEB-INF/studyContext.xml] INFO SpringModule$1 2016-04-04 15:50:24,854 Module Upgrade : Refreshing Study WebApplicationContext: startup date [Mon Apr 04 15:50:24 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:50:25,047 Module Upgrade : Starting module 'Luminex' INFO ModuleLoader 2016-04-04 15:50:25,059 Module Upgrade : Starting module 'Visualization' INFO ModuleLoader 2016-04-04 15:50:25,060 Module Upgrade : Starting module 'Nab' INFO ModuleLoader 2016-04-04 15:50:25,079 Module Upgrade : Starting module 'Elisa' INFO ModuleLoader 2016-04-04 15:50:25,082 Module Upgrade : Starting module 'TargetedMS' INFO SpringModule 2016-04-04 15:50:25,083 Module Upgrade : Loading Spring configuration for the TargetedMS module from [/WEB-INF/targetedmsContext.xml] INFO SpringModule$1 2016-04-04 15:50:25,084 Module Upgrade : Refreshing TargetedMS WebApplicationContext: startup date [Mon Apr 04 15:50:25 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 15:50:25,111 Module Upgrade : Starting module 'Audit' INFO ModuleLoader 2016-04-04 15:50:25,124 Module Upgrade : Starting module 'ELISpotAssay' INFO ModuleLoader 2016-04-04 15:50:25,130 Module Upgrade : Running startup listener: Audit Log INFO ModuleLoader 2016-04-04 15:50:25,130 Module Upgrade : Running startup listener: Search Service INFO ModuleLoader 2016-04-04 15:50:25,130 Module Upgrade : Running startup listener: PipelineJobRestarter INFO ModuleLoader 2016-04-04 15:50:25,132 Module Upgrade : Running startup listener: DataIntegration INFO ModuleLoader 2016-04-04 15:50:25,137 Module Upgrade : Module startup complete INFO ContextListener 2016-04-04 16:09:58,101 localhost-startStop-2 : Calling HeartBeatThread shutdownPre() INFO ContextListener 2016-04-04 16:09:58,101 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownPre() INFO ContextListener 2016-04-04 16:09:58,101 localhost-startStop-2 : Calling QueryProfilerThread shutdownPre() INFO ContextListener 2016-04-04 16:09:58,101 localhost-startStop-2 : Calling BreakpointThread shutdownPre() INFO ContextListener 2016-04-04 16:09:58,101 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownPre() INFO ContextListener 2016-04-04 16:09:58,102 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownPre() INFO FileSystemWatcherImpl 2016-04-04 16:09:58,102 FileSystemWatcherThread : FileSystemWatcherThread is terminating INFO DatasetSnapshotProvider 2016-04-04 16:09:58,102 SnapshotDependencyThread : QuerySnapshotDependencyThread is terminating due to interruption INFO ContextListener 2016-04-04 16:09:58,102 localhost-startStop-2 : Calling Job Runner (Default) shutdownPre() INFO ContextListener 2016-04-04 16:09:58,102 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownPre() INFO ContextListener 2016-04-04 16:09:58,103 localhost-startStop-2 : Calling Temp table cleanup shutdownPre() INFO ContextListener 2016-04-04 16:09:58,103 localhost-startStop-2 : Calling Temp file deletion shutdownPre() INFO ContextListener 2016-04-04 16:09:58,103 localhost-startStop-2 : Calling Action stats export shutdownPre() INFO CoreModule 2016-04-04 16:09:58,103 localhost-startStop-2 : Starting to log statistics for actions prior to web application shut down INFO CoreModule 2016-04-04 16:09:58,125 localhost-startStop-2 : Completed logging statistics for actions prior to web application shut down INFO ContextListener 2016-04-04 16:09:58,125 localhost-startStop-2 : Calling DataIntegration shutdownPre() INFO ContextListener 2016-04-04 16:09:58,154 localhost-startStop-2 : Calling DAV crawler shutdownPre() INFO ContextListener 2016-04-04 16:09:58,154 localhost-startStop-2 : Calling Search service shutdownPre() INFO ContextListener 2016-04-04 16:09:58,155 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownPre() INFO ContextListener 2016-04-04 16:09:58,155 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownPre() INFO ContextListener 2016-04-04 16:09:58,155 localhost-startStop-2 : Calling Study Reload Handler shutdownPre() INFO ContextListener 2016-04-04 16:09:58,155 localhost-startStop-2 : Calling Job Runner (Mothership Reporting) shutdownPre() INFO ContextListener 2016-04-04 16:09:58,155 localhost-startStop-2 : Calling HeartBeatThread shutdownStarted() INFO ContextListener 2016-04-04 16:09:58,155 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownStarted() INFO ContextListener 2016-04-04 16:09:58,155 localhost-startStop-2 : Calling QueryProfilerThread shutdownStarted() INFO QueryProfiler 2016-04-04 16:09:58,156 localhost-startStop-2 : Starting to log statistics for queries prior to web application shut down INFO QueryProfiler 2016-04-04 16:09:58,180 localhost-startStop-2 : Completed logging statistics for queries prior to web application shut down INFO ContextListener 2016-04-04 16:09:58,180 localhost-startStop-2 : Calling BreakpointThread shutdownStarted() INFO ContextListener 2016-04-04 16:09:58,180 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownStarted() INFO ContextListener 2016-04-04 16:09:58,180 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownStarted() INFO ContextListener 2016-04-04 16:09:58,180 localhost-startStop-2 : Calling Job Runner (Default) shutdownStarted() INFO ContextListener 2016-04-04 16:09:58,180 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownStarted() INFO ContextListener 2016-04-04 16:09:58,180 localhost-startStop-2 : Calling Temp table cleanup shutdownStarted() INFO ContextListener 2016-04-04 16:09:58,180 localhost-startStop-2 : Calling Temp file deletion shutdownStarted() INFO ContextListener 2016-04-04 16:09:58,181 localhost-startStop-2 : Calling Action stats export shutdownStarted() INFO ContextListener 2016-04-04 16:09:58,181 localhost-startStop-2 : Calling DataIntegration shutdownStarted() INFO ContextListener 2016-04-04 16:09:58,654 localhost-startStop-2 : Calling DAV crawler shutdownStarted() INFO ContextListener 2016-04-04 16:09:58,655 localhost-startStop-2 : Calling Search service shutdownStarted() INFO ContextListener 2016-04-04 16:09:58,659 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownStarted() INFO ContextListener 2016-04-04 16:09:58,659 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownStarted() INFO ContextListener 2016-04-04 16:09:58,659 localhost-startStop-2 : Calling Study Reload Handler shutdownStarted() INFO ContextListener 2016-04-04 16:09:58,659 localhost-startStop-2 : Calling Job Runner (Mothership Reporting) shutdownStarted() INFO EhCacheProvider 2016-04-04 16:09:58,662 localhost-startStop-2 : Shutting down Ehcache INFO ModuleLoader 2016-04-04 16:10:04,721 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2016-04-04 16:10:06,022 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource Server URL: jdbc:postgresql://localhost:5432/labkey Database Product Name: PostgreSQL Database Product Version: 9.4.6 JDBC Driver Name: PostgreSQL Native Driver JDBC Driver Version: PostgreSQL 9.4.1207 SQL Dialect: PostgreSql94Dialect INFO DbScope 2016-04-04 16:10:06,118 localhost-startStop-1 : Loading DbSchema "labkey.core" (Module) INFO DbScope 2016-04-04 16:10:08,324 localhost-startStop-1 : Loading DbSchema "labkey.prop" (Module) INFO DbScope 2016-04-04 16:10:08,399 localhost-startStop-1 : Loading DbSchema "labkey.test" (Module) INFO DbScope 2016-04-04 16:10:08,405 localhost-startStop-1 : Loading DbSchema "labkey.temp" (Provisioned) INFO DbScope 2016-04-04 16:10:08,407 localhost-startStop-1 : Loading DbSchema "labkey.query" (Module) INFO DbScope 2016-04-04 16:10:08,412 localhost-startStop-1 : Loading DbSchema "labkey.junit" (Module) INFO DbScope 2016-04-04 16:10:08,415 localhost-startStop-1 : no schema metadata xml file found for schema "junit" INFO DbScope 2016-04-04 16:10:08,415 localhost-startStop-1 : Loading DbSchema "labkey.search" (Module) INFO DbScope 2016-04-04 16:10:08,419 localhost-startStop-1 : Loading DbSchema "labkey.umls" (Module) INFO DbScope 2016-04-04 16:10:08,423 localhost-startStop-1 : no schema metadata xml file found for schema "umls" INFO DbScope 2016-04-04 16:10:08,423 localhost-startStop-1 : Loading DbSchema "labkey.issues" (Module) INFO DbScope 2016-04-04 16:10:08,437 localhost-startStop-1 : Loading DbSchema "labkey.comm" (Module) INFO DbScope 2016-04-04 16:10:08,448 localhost-startStop-1 : Loading DbSchema "labkey.pipeline" (Module) INFO DbScope 2016-04-04 16:10:08,452 localhost-startStop-1 : Loading DbSchema "labkey.exp" (Module) INFO DbScope 2016-04-04 16:10:08,461 localhost-startStop-1 : Loading DbSchema "labkey.flow" (Module) INFO DbScope 2016-04-04 16:10:08,466 localhost-startStop-1 : Loading DbSchema "labkey.microarray" (Module) INFO DbScope 2016-04-04 16:10:08,470 localhost-startStop-1 : Loading DbSchema "labkey.filecontent" (Module) INFO DbScope 2016-04-04 16:10:08,474 localhost-startStop-1 : Loading DbSchema "labkey.list" (Provisioned) INFO DbScope 2016-04-04 16:10:08,474 localhost-startStop-1 : Loading DbSchema "labkey.ms2" (Module) INFO DbScope 2016-04-04 16:10:08,484 localhost-startStop-1 : Loading DbSchema "labkey.prot" (Module) INFO DbScope 2016-04-04 16:10:08,489 localhost-startStop-1 : Loading DbSchema "labkey.ms1" (Module) INFO DbScope 2016-04-04 16:10:08,494 localhost-startStop-1 : Loading DbSchema "labkey.survey" (Module) INFO DbScope 2016-04-04 16:10:08,499 localhost-startStop-1 : Loading DbSchema "labkey.dataintegration" (Module) INFO DbScope 2016-04-04 16:10:08,504 localhost-startStop-1 : Loading DbSchema "labkey.study" (Module) INFO DbScope 2016-04-04 16:10:08,519 localhost-startStop-1 : Loading DbSchema "labkey.studydataset" (Provisioned) INFO DbScope 2016-04-04 16:10:08,519 localhost-startStop-1 : Loading DbSchema "labkey.assayresult" (Provisioned) INFO DbScope 2016-04-04 16:10:08,519 localhost-startStop-1 : Loading DbSchema "labkey.studydesign" (Provisioned) INFO DbScope 2016-04-04 16:10:08,519 localhost-startStop-1 : Loading DbSchema "labkey.specimentables" (Provisioned) INFO DbScope 2016-04-04 16:10:08,519 localhost-startStop-1 : Loading DbSchema "labkey.luminex" (Module) INFO DbScope 2016-04-04 16:10:08,524 localhost-startStop-1 : Loading DbSchema "labkey.nab" (Module) INFO DbScope 2016-04-04 16:10:08,528 localhost-startStop-1 : Loading DbSchema "labkey.nabvirus" (Provisioned) INFO DbScope 2016-04-04 16:10:08,529 localhost-startStop-1 : Loading DbSchema "labkey.targetedms" (Module) INFO DbScope 2016-04-04 16:10:08,537 localhost-startStop-1 : Loading DbSchema "labkey.audit" (Provisioned) INFO DbScope 2016-04-04 16:10:08,537 localhost-startStop-1 : Loading DbSchema "labkey.elispotlk" (Module) INFO ModuleLoader 2016-04-04 16:10:08,612 localhost-startStop-1 : LabKey Server startup is complete; modules are being upgraded and initialized in the background INFO ModuleLoader 2016-04-04 16:10:08,612 Module Upgrade : Starting up modules INFO ModuleLoader 2016-04-04 16:10:08,613 Module Upgrade : Starting module 'Core' INFO ViewServlet 2016-04-04 16:10:08,615 localhost-startStop-1 : ViewServlet initialized INFO ViewServlet 2016-04-04 16:10:08,615 localhost-startStop-1 : WEBAPP: /usr/share/labkey/labkeywebapp INFO ViewServlet 2016-04-04 16:10:08,616 localhost-startStop-1 : PATH: /usr/local/tpp/bin:/bin:/usr/bin:/sbin:/usr/sbin INFO ModuleLoader 2016-04-04 16:10:09,414 Module Upgrade : Starting module 'Query' INFO ModuleLoader 2016-04-04 16:10:09,462 Module Upgrade : Starting module 'FCSExpress' INFO ModuleLoader 2016-04-04 16:10:09,480 Module Upgrade : Starting module 'Search' INFO ModuleLoader 2016-04-04 16:10:09,491 Module Upgrade : Starting module 'Wiki' INFO ModuleLoader 2016-04-04 16:10:09,498 Module Upgrade : Starting module 'Issues' INFO ModuleLoader 2016-04-04 16:10:09,508 Module Upgrade : Starting module 'Announcements' INFO ModuleLoader 2016-04-04 16:10:09,592 Module Upgrade : Starting module 'BigIron' INFO ModuleLoader 2016-04-04 16:10:09,592 Module Upgrade : Starting module 'Pipeline' INFO SpringModule 2016-04-04 16:10:09,593 Module Upgrade : Loading Spring configuration for the Pipeline module from [/WEB-INF/pipelineContext.xml] INFO SpringModule$1 2016-04-04 16:10:09,595 Module Upgrade : Refreshing Pipeline WebApplicationContext: startup date [Mon Apr 04 16:10:09 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 16:10:09,714 Module Upgrade : Starting module 'Experiment' INFO SpringModule 2016-04-04 16:10:09,714 Module Upgrade : Loading Spring configuration for the Experiment module from [/WEB-INF/experimentContext.xml] INFO SpringModule$1 2016-04-04 16:10:09,715 Module Upgrade : Refreshing Experiment WebApplicationContext: startup date [Mon Apr 04 16:10:09 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 16:10:09,927 Module Upgrade : Starting module 'Flow' INFO ModuleLoader 2016-04-04 16:10:09,961 Module Upgrade : Starting module 'Microarray' INFO SpringModule 2016-04-04 16:10:09,961 Module Upgrade : Loading Spring configuration for the Microarray module from [/WEB-INF/microarrayContext.xml] INFO SpringModule$1 2016-04-04 16:10:09,966 Module Upgrade : Refreshing Microarray WebApplicationContext: startup date [Mon Apr 04 16:10:09 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 16:10:10,008 Module Upgrade : Starting module 'FileContent' INFO ModuleLoader 2016-04-04 16:10:10,011 Module Upgrade : Starting module 'List' INFO ModuleLoader 2016-04-04 16:10:10,031 Module Upgrade : Starting module 'MS2' INFO SpringModule 2016-04-04 16:10:10,031 Module Upgrade : Loading Spring configuration for the MS2 module from [/WEB-INF/ms2Context.xml] INFO SpringModule$1 2016-04-04 16:10:10,032 Module Upgrade : Refreshing MS2 WebApplicationContext: startup date [Mon Apr 04 16:10:10 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 16:10:10,440 Module Upgrade : Starting module 'MS1' INFO SpringModule 2016-04-04 16:10:10,440 Module Upgrade : Loading Spring configuration for the MS1 module from [/WEB-INF/ms1Context.xml] INFO SpringModule$1 2016-04-04 16:10:10,441 Module Upgrade : Refreshing MS1 WebApplicationContext: startup date [Mon Apr 04 16:10:10 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 16:10:10,518 Module Upgrade : Starting module 'Survey' INFO ModuleLoader 2016-04-04 16:10:10,519 Module Upgrade : Starting module 'DataIntegration' INFO ModuleLoader 2016-04-04 16:10:10,529 Module Upgrade : Starting module 'Study' INFO SpringModule 2016-04-04 16:10:10,529 Module Upgrade : Loading Spring configuration for the Study module from [/WEB-INF/studyContext.xml] INFO SpringModule$1 2016-04-04 16:10:10,530 Module Upgrade : Refreshing Study WebApplicationContext: startup date [Mon Apr 04 16:10:10 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 16:10:10,719 Module Upgrade : Starting module 'Luminex' INFO ModuleLoader 2016-04-04 16:10:10,730 Module Upgrade : Starting module 'Visualization' INFO ModuleLoader 2016-04-04 16:10:10,731 Module Upgrade : Starting module 'Nab' INFO ModuleLoader 2016-04-04 16:10:10,747 Module Upgrade : Starting module 'Elisa' INFO ModuleLoader 2016-04-04 16:10:10,753 Module Upgrade : Starting module 'TargetedMS' INFO SpringModule 2016-04-04 16:10:10,753 Module Upgrade : Loading Spring configuration for the TargetedMS module from [/WEB-INF/targetedmsContext.xml] INFO SpringModule$1 2016-04-04 16:10:10,755 Module Upgrade : Refreshing TargetedMS WebApplicationContext: startup date [Mon Apr 04 16:10:10 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-04 16:10:10,779 Module Upgrade : Starting module 'Audit' INFO ModuleLoader 2016-04-04 16:10:10,786 Module Upgrade : Starting module 'ELISpotAssay' INFO ModuleLoader 2016-04-04 16:10:10,791 Module Upgrade : Running startup listener: Audit Log INFO ModuleLoader 2016-04-04 16:10:10,791 Module Upgrade : Running startup listener: Search Service INFO ModuleLoader 2016-04-04 16:10:10,791 Module Upgrade : Running startup listener: PipelineJobRestarter INFO ModuleLoader 2016-04-04 16:10:10,793 Module Upgrade : Running startup listener: DataIntegration INFO ModuleLoader 2016-04-04 16:10:10,798 Module Upgrade : Module startup complete INFO DatabaseMaintenanceTask 2016-04-05 02:00:00,200 JobThread-2.1 : Database maintenance on jdbc:postgresql://localhost:5432/labkey started INFO DatabaseMaintenanceTask 2016-04-05 02:00:00,200 JobThread-2.1 : Database maintenance on jdbc:postgresql://localhost:5432/labkey complete INFO PurgeTask 2016-04-05 02:00:00,211 JobThread-2.1 : MS1 Purge Task starting cycle... INFO PurgeTask 2016-04-05 02:00:00,212 JobThread-2.1 : MS1 Purge Task finished cycle in 0 seconds. INFO ContextListener 2016-04-05 10:47:38,257 localhost-startStop-2 : Calling HeartBeatThread shutdownPre() INFO ContextListener 2016-04-05 10:47:38,257 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownPre() INFO ContextListener 2016-04-05 10:47:38,257 localhost-startStop-2 : Calling QueryProfilerThread shutdownPre() INFO ContextListener 2016-04-05 10:47:38,257 localhost-startStop-2 : Calling BreakpointThread shutdownPre() INFO FileSystemWatcherImpl 2016-04-05 10:47:38,258 FileSystemWatcherThread : FileSystemWatcherThread is terminating INFO ContextListener 2016-04-05 10:47:38,259 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownPre() INFO ContextListener 2016-04-05 10:47:38,260 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownPre() INFO ContextListener 2016-04-05 10:47:38,260 localhost-startStop-2 : Calling Job Runner (Default) shutdownPre() INFO DatasetSnapshotProvider 2016-04-05 10:47:38,260 SnapshotDependencyThread : QuerySnapshotDependencyThread is terminating due to interruption INFO ContextListener 2016-04-05 10:47:38,260 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownPre() INFO ContextListener 2016-04-05 10:47:38,260 localhost-startStop-2 : Calling Temp table cleanup shutdownPre() INFO ContextListener 2016-04-05 10:47:38,260 localhost-startStop-2 : Calling Temp file deletion shutdownPre() INFO ContextListener 2016-04-05 10:47:38,260 localhost-startStop-2 : Calling Action stats export shutdownPre() INFO CoreModule 2016-04-05 10:47:38,261 localhost-startStop-2 : Starting to log statistics for actions prior to web application shut down INFO CoreModule 2016-04-05 10:47:38,282 localhost-startStop-2 : Completed logging statistics for actions prior to web application shut down INFO ContextListener 2016-04-05 10:47:38,282 localhost-startStop-2 : Calling DataIntegration shutdownPre() INFO ContextListener 2016-04-05 10:47:38,307 localhost-startStop-2 : Calling DAV crawler shutdownPre() INFO ContextListener 2016-04-05 10:47:38,307 localhost-startStop-2 : Calling Search service shutdownPre() INFO ContextListener 2016-04-05 10:47:38,307 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownPre() INFO ContextListener 2016-04-05 10:47:38,307 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownPre() INFO ContextListener 2016-04-05 10:47:38,307 localhost-startStop-2 : Calling Study Reload Handler shutdownPre() INFO ContextListener 2016-04-05 10:47:38,307 localhost-startStop-2 : Calling HeartBeatThread shutdownStarted() INFO ContextListener 2016-04-05 10:47:38,308 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownStarted() INFO ContextListener 2016-04-05 10:47:38,308 localhost-startStop-2 : Calling QueryProfilerThread shutdownStarted() INFO QueryProfiler 2016-04-05 10:47:38,308 localhost-startStop-2 : Starting to log statistics for queries prior to web application shut down INFO QueryProfiler 2016-04-05 10:47:38,334 localhost-startStop-2 : Completed logging statistics for queries prior to web application shut down INFO ContextListener 2016-04-05 10:47:38,334 localhost-startStop-2 : Calling BreakpointThread shutdownStarted() INFO ContextListener 2016-04-05 10:47:38,334 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownStarted() INFO ContextListener 2016-04-05 10:47:38,334 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownStarted() INFO ContextListener 2016-04-05 10:47:38,334 localhost-startStop-2 : Calling Job Runner (Default) shutdownStarted() INFO ContextListener 2016-04-05 10:47:38,334 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownStarted() INFO ContextListener 2016-04-05 10:47:38,334 localhost-startStop-2 : Calling Temp table cleanup shutdownStarted() INFO ContextListener 2016-04-05 10:47:38,335 localhost-startStop-2 : Calling Temp file deletion shutdownStarted() INFO ContextListener 2016-04-05 10:47:38,335 localhost-startStop-2 : Calling Action stats export shutdownStarted() INFO ContextListener 2016-04-05 10:47:38,335 localhost-startStop-2 : Calling DataIntegration shutdownStarted() INFO ContextListener 2016-04-05 10:47:38,807 localhost-startStop-2 : Calling DAV crawler shutdownStarted() INFO ContextListener 2016-04-05 10:47:38,807 localhost-startStop-2 : Calling Search service shutdownStarted() INFO ContextListener 2016-04-05 10:47:38,811 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownStarted() INFO ContextListener 2016-04-05 10:47:38,811 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownStarted() INFO ContextListener 2016-04-05 10:47:38,812 localhost-startStop-2 : Calling Study Reload Handler shutdownStarted() INFO EhCacheProvider 2016-04-05 10:47:38,815 localhost-startStop-2 : Shutting down Ehcache INFO ModuleLoader 2016-04-05 10:47:44,173 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2016-04-05 10:47:45,422 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource Server URL: jdbc:postgresql://localhost:5432/labkey Database Product Name: PostgreSQL Database Product Version: 9.4.6 JDBC Driver Name: PostgreSQL Native Driver JDBC Driver Version: PostgreSQL 9.4.1207 SQL Dialect: PostgreSql94Dialect INFO DbScope 2016-04-05 10:47:45,514 localhost-startStop-1 : Loading DbSchema "labkey.core" (Module) INFO DbScope 2016-04-05 10:47:47,719 localhost-startStop-1 : Loading DbSchema "labkey.prop" (Module) INFO DbScope 2016-04-05 10:47:47,793 localhost-startStop-1 : Loading DbSchema "labkey.test" (Module) INFO DbScope 2016-04-05 10:47:47,798 localhost-startStop-1 : Loading DbSchema "labkey.temp" (Provisioned) INFO DbScope 2016-04-05 10:47:47,801 localhost-startStop-1 : Loading DbSchema "labkey.query" (Module) INFO DbScope 2016-04-05 10:47:47,805 localhost-startStop-1 : Loading DbSchema "labkey.junit" (Module) INFO DbScope 2016-04-05 10:47:47,808 localhost-startStop-1 : no schema metadata xml file found for schema "junit" INFO DbScope 2016-04-05 10:47:47,808 localhost-startStop-1 : Loading DbSchema "labkey.search" (Module) INFO DbScope 2016-04-05 10:47:47,812 localhost-startStop-1 : Loading DbSchema "labkey.umls" (Module) INFO DbScope 2016-04-05 10:47:47,815 localhost-startStop-1 : no schema metadata xml file found for schema "umls" INFO DbScope 2016-04-05 10:47:47,815 localhost-startStop-1 : Loading DbSchema "labkey.issues" (Module) INFO DbScope 2016-04-05 10:47:47,821 localhost-startStop-1 : Loading DbSchema "labkey.comm" (Module) INFO DbScope 2016-04-05 10:47:47,829 localhost-startStop-1 : Loading DbSchema "labkey.pipeline" (Module) INFO DbScope 2016-04-05 10:47:47,833 localhost-startStop-1 : Loading DbSchema "labkey.exp" (Module) INFO DbScope 2016-04-05 10:47:47,842 localhost-startStop-1 : Loading DbSchema "labkey.flow" (Module) INFO DbScope 2016-04-05 10:47:47,846 localhost-startStop-1 : Loading DbSchema "labkey.microarray" (Module) INFO DbScope 2016-04-05 10:47:47,850 localhost-startStop-1 : Loading DbSchema "labkey.filecontent" (Module) INFO DbScope 2016-04-05 10:47:47,854 localhost-startStop-1 : Loading DbSchema "labkey.list" (Provisioned) INFO DbScope 2016-04-05 10:47:47,854 localhost-startStop-1 : Loading DbSchema "labkey.ms2" (Module) INFO DbScope 2016-04-05 10:47:47,864 localhost-startStop-1 : Loading DbSchema "labkey.prot" (Module) INFO DbScope 2016-04-05 10:47:47,870 localhost-startStop-1 : Loading DbSchema "labkey.ms1" (Module) INFO DbScope 2016-04-05 10:47:47,874 localhost-startStop-1 : Loading DbSchema "labkey.survey" (Module) INFO DbScope 2016-04-05 10:47:47,879 localhost-startStop-1 : Loading DbSchema "labkey.dataintegration" (Module) INFO DbScope 2016-04-05 10:47:47,889 localhost-startStop-1 : Loading DbSchema "labkey.study" (Module) INFO DbScope 2016-04-05 10:47:47,903 localhost-startStop-1 : Loading DbSchema "labkey.studydataset" (Provisioned) INFO DbScope 2016-04-05 10:47:47,903 localhost-startStop-1 : Loading DbSchema "labkey.assayresult" (Provisioned) INFO DbScope 2016-04-05 10:47:47,903 localhost-startStop-1 : Loading DbSchema "labkey.studydesign" (Provisioned) INFO DbScope 2016-04-05 10:47:47,903 localhost-startStop-1 : Loading DbSchema "labkey.specimentables" (Provisioned) INFO DbScope 2016-04-05 10:47:47,903 localhost-startStop-1 : Loading DbSchema "labkey.luminex" (Module) INFO DbScope 2016-04-05 10:47:47,908 localhost-startStop-1 : Loading DbSchema "labkey.nab" (Module) INFO DbScope 2016-04-05 10:47:47,913 localhost-startStop-1 : Loading DbSchema "labkey.nabvirus" (Provisioned) INFO DbScope 2016-04-05 10:47:47,913 localhost-startStop-1 : Loading DbSchema "labkey.targetedms" (Module) INFO DbScope 2016-04-05 10:47:47,921 localhost-startStop-1 : Loading DbSchema "labkey.audit" (Provisioned) INFO DbScope 2016-04-05 10:47:47,921 localhost-startStop-1 : Loading DbSchema "labkey.elispotlk" (Module) INFO ModuleLoader 2016-04-05 10:47:47,997 localhost-startStop-1 : LabKey Server startup is complete; modules are being upgraded and initialized in the background INFO ModuleLoader 2016-04-05 10:47:47,997 Module Upgrade : Starting up modules INFO ModuleLoader 2016-04-05 10:47:48,000 Module Upgrade : Starting module 'Core' INFO ViewServlet 2016-04-05 10:47:48,000 localhost-startStop-1 : ViewServlet initialized INFO ViewServlet 2016-04-05 10:47:48,002 localhost-startStop-1 : WEBAPP: /usr/share/labkey/labkeywebapp INFO ViewServlet 2016-04-05 10:47:48,002 localhost-startStop-1 : PATH: /usr/local/tpp/bin:/bin:/usr/bin:/sbin:/usr/sbin INFO ModuleLoader 2016-04-05 10:47:48,908 Module Upgrade : Starting module 'Query' INFO ModuleLoader 2016-04-05 10:47:48,947 Module Upgrade : Starting module 'FCSExpress' INFO ModuleLoader 2016-04-05 10:47:48,963 Module Upgrade : Starting module 'Search' INFO ModuleLoader 2016-04-05 10:47:48,971 Module Upgrade : Starting module 'Wiki' INFO ModuleLoader 2016-04-05 10:47:48,978 Module Upgrade : Starting module 'Issues' INFO ModuleLoader 2016-04-05 10:47:48,987 Module Upgrade : Starting module 'Announcements' INFO ModuleLoader 2016-04-05 10:47:49,063 Module Upgrade : Starting module 'BigIron' INFO ModuleLoader 2016-04-05 10:47:49,063 Module Upgrade : Starting module 'Pipeline' INFO SpringModule 2016-04-05 10:47:49,064 Module Upgrade : Loading Spring configuration for the Pipeline module from [/WEB-INF/pipelineContext.xml] INFO SpringModule$1 2016-04-05 10:47:49,066 Module Upgrade : Refreshing Pipeline WebApplicationContext: startup date [Tue Apr 05 10:47:49 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 10:47:49,188 Module Upgrade : Starting module 'Experiment' INFO SpringModule 2016-04-05 10:47:49,189 Module Upgrade : Loading Spring configuration for the Experiment module from [/WEB-INF/experimentContext.xml] INFO SpringModule$1 2016-04-05 10:47:49,190 Module Upgrade : Refreshing Experiment WebApplicationContext: startup date [Tue Apr 05 10:47:49 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 10:47:49,402 Module Upgrade : Starting module 'Flow' INFO ModuleLoader 2016-04-05 10:47:49,438 Module Upgrade : Starting module 'Microarray' INFO SpringModule 2016-04-05 10:47:49,439 Module Upgrade : Loading Spring configuration for the Microarray module from [/WEB-INF/microarrayContext.xml] INFO SpringModule$1 2016-04-05 10:47:49,440 Module Upgrade : Refreshing Microarray WebApplicationContext: startup date [Tue Apr 05 10:47:49 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 10:47:49,489 Module Upgrade : Starting module 'FileContent' INFO ModuleLoader 2016-04-05 10:47:49,492 Module Upgrade : Starting module 'List' INFO ModuleLoader 2016-04-05 10:47:49,511 Module Upgrade : Starting module 'MS2' INFO SpringModule 2016-04-05 10:47:49,512 Module Upgrade : Loading Spring configuration for the MS2 module from [/WEB-INF/ms2Context.xml] INFO SpringModule$1 2016-04-05 10:47:49,512 Module Upgrade : Refreshing MS2 WebApplicationContext: startup date [Tue Apr 05 10:47:49 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 10:47:49,924 Module Upgrade : Starting module 'MS1' INFO SpringModule 2016-04-05 10:47:49,924 Module Upgrade : Loading Spring configuration for the MS1 module from [/WEB-INF/ms1Context.xml] INFO SpringModule$1 2016-04-05 10:47:49,925 Module Upgrade : Refreshing MS1 WebApplicationContext: startup date [Tue Apr 05 10:47:49 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 10:47:50,003 Module Upgrade : Starting module 'Survey' INFO ModuleLoader 2016-04-05 10:47:50,004 Module Upgrade : Starting module 'DataIntegration' INFO ModuleLoader 2016-04-05 10:47:50,013 Module Upgrade : Starting module 'Study' INFO SpringModule 2016-04-05 10:47:50,014 Module Upgrade : Loading Spring configuration for the Study module from [/WEB-INF/studyContext.xml] INFO SpringModule$1 2016-04-05 10:47:50,015 Module Upgrade : Refreshing Study WebApplicationContext: startup date [Tue Apr 05 10:47:50 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 10:47:50,202 Module Upgrade : Starting module 'Luminex' INFO ModuleLoader 2016-04-05 10:47:50,215 Module Upgrade : Starting module 'Visualization' INFO ModuleLoader 2016-04-05 10:47:50,215 Module Upgrade : Starting module 'Nab' INFO ModuleLoader 2016-04-05 10:47:50,234 Module Upgrade : Starting module 'Elisa' INFO ModuleLoader 2016-04-05 10:47:50,237 Module Upgrade : Starting module 'TargetedMS' INFO SpringModule 2016-04-05 10:47:50,238 Module Upgrade : Loading Spring configuration for the TargetedMS module from [/WEB-INF/targetedmsContext.xml] INFO SpringModule$1 2016-04-05 10:47:50,239 Module Upgrade : Refreshing TargetedMS WebApplicationContext: startup date [Tue Apr 05 10:47:50 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 10:47:50,265 Module Upgrade : Starting module 'Audit' INFO ModuleLoader 2016-04-05 10:47:50,273 Module Upgrade : Starting module 'ELISpotAssay' INFO ModuleLoader 2016-04-05 10:47:50,278 Module Upgrade : Running startup listener: Audit Log INFO ModuleLoader 2016-04-05 10:47:50,278 Module Upgrade : Running startup listener: Search Service INFO ModuleLoader 2016-04-05 10:47:50,278 Module Upgrade : Running startup listener: PipelineJobRestarter INFO ModuleLoader 2016-04-05 10:47:50,280 Module Upgrade : Running startup listener: DataIntegration INFO ModuleLoader 2016-04-05 10:47:50,292 Module Upgrade : Module startup complete INFO ContextListener 2016-04-05 10:49:57,264 localhost-startStop-2 : Calling HeartBeatThread shutdownPre() INFO ContextListener 2016-04-05 10:49:57,264 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownPre() INFO ContextListener 2016-04-05 10:49:57,264 localhost-startStop-2 : Calling QueryProfilerThread shutdownPre() INFO ContextListener 2016-04-05 10:49:57,264 localhost-startStop-2 : Calling BreakpointThread shutdownPre() INFO ContextListener 2016-04-05 10:49:57,264 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownPre() INFO ContextListener 2016-04-05 10:49:57,264 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownPre() INFO ContextListener 2016-04-05 10:49:57,265 localhost-startStop-2 : Calling Job Runner (Default) shutdownPre() INFO DatasetSnapshotProvider 2016-04-05 10:49:57,265 SnapshotDependencyThread : QuerySnapshotDependencyThread is terminating due to interruption INFO FileSystemWatcherImpl 2016-04-05 10:49:57,265 FileSystemWatcherThread : FileSystemWatcherThread is terminating INFO ContextListener 2016-04-05 10:49:57,265 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownPre() INFO ContextListener 2016-04-05 10:49:57,267 localhost-startStop-2 : Calling Temp table cleanup shutdownPre() INFO ContextListener 2016-04-05 10:49:57,267 localhost-startStop-2 : Calling Temp file deletion shutdownPre() INFO ContextListener 2016-04-05 10:49:57,267 localhost-startStop-2 : Calling Action stats export shutdownPre() INFO CoreModule 2016-04-05 10:49:57,267 localhost-startStop-2 : Starting to log statistics for actions prior to web application shut down INFO CoreModule 2016-04-05 10:49:57,286 localhost-startStop-2 : Completed logging statistics for actions prior to web application shut down INFO ContextListener 2016-04-05 10:49:57,286 localhost-startStop-2 : Calling DataIntegration shutdownPre() INFO ContextListener 2016-04-05 10:49:57,309 localhost-startStop-2 : Calling DAV crawler shutdownPre() INFO ContextListener 2016-04-05 10:49:57,309 localhost-startStop-2 : Calling Search service shutdownPre() INFO ContextListener 2016-04-05 10:49:57,309 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownPre() INFO ContextListener 2016-04-05 10:49:57,309 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownPre() INFO ContextListener 2016-04-05 10:49:57,310 localhost-startStop-2 : Calling Study Reload Handler shutdownPre() INFO ContextListener 2016-04-05 10:49:57,310 localhost-startStop-2 : Calling HeartBeatThread shutdownStarted() INFO ContextListener 2016-04-05 10:49:57,310 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownStarted() INFO ContextListener 2016-04-05 10:49:57,310 localhost-startStop-2 : Calling QueryProfilerThread shutdownStarted() INFO QueryProfiler 2016-04-05 10:49:57,310 localhost-startStop-2 : Starting to log statistics for queries prior to web application shut down INFO QueryProfiler 2016-04-05 10:49:57,339 localhost-startStop-2 : Completed logging statistics for queries prior to web application shut down INFO ContextListener 2016-04-05 10:49:57,339 localhost-startStop-2 : Calling BreakpointThread shutdownStarted() INFO ContextListener 2016-04-05 10:49:57,339 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownStarted() INFO ContextListener 2016-04-05 10:49:57,339 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownStarted() INFO ContextListener 2016-04-05 10:49:57,339 localhost-startStop-2 : Calling Job Runner (Default) shutdownStarted() INFO ContextListener 2016-04-05 10:49:57,339 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownStarted() INFO ContextListener 2016-04-05 10:49:57,339 localhost-startStop-2 : Calling Temp table cleanup shutdownStarted() INFO ContextListener 2016-04-05 10:49:57,340 localhost-startStop-2 : Calling Temp file deletion shutdownStarted() INFO ContextListener 2016-04-05 10:49:57,340 localhost-startStop-2 : Calling Action stats export shutdownStarted() INFO ContextListener 2016-04-05 10:49:57,340 localhost-startStop-2 : Calling DataIntegration shutdownStarted() INFO ContextListener 2016-04-05 10:49:57,809 localhost-startStop-2 : Calling DAV crawler shutdownStarted() INFO ContextListener 2016-04-05 10:49:57,809 localhost-startStop-2 : Calling Search service shutdownStarted() INFO ContextListener 2016-04-05 10:49:57,813 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownStarted() INFO ContextListener 2016-04-05 10:49:57,813 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownStarted() INFO ContextListener 2016-04-05 10:49:57,813 localhost-startStop-2 : Calling Study Reload Handler shutdownStarted() INFO EhCacheProvider 2016-04-05 10:49:57,816 localhost-startStop-2 : Shutting down Ehcache INFO ModuleLoader 2016-04-05 11:02:59,304 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2016-04-05 11:03:00,563 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource Server URL: jdbc:postgresql://localhost:5432/labkey Database Product Name: PostgreSQL Database Product Version: 9.4.6 JDBC Driver Name: PostgreSQL Native Driver JDBC Driver Version: PostgreSQL 9.4.1207 SQL Dialect: PostgreSql94Dialect INFO DbScope 2016-04-05 11:03:00,658 localhost-startStop-1 : Loading DbSchema "labkey.core" (Module) INFO DbScope 2016-04-05 11:03:02,897 localhost-startStop-1 : Loading DbSchema "labkey.prop" (Module) INFO DbScope 2016-04-05 11:03:02,972 localhost-startStop-1 : Loading DbSchema "labkey.test" (Module) INFO DbScope 2016-04-05 11:03:02,977 localhost-startStop-1 : Loading DbSchema "labkey.temp" (Provisioned) INFO DbScope 2016-04-05 11:03:02,979 localhost-startStop-1 : Loading DbSchema "labkey.query" (Module) INFO DbScope 2016-04-05 11:03:02,984 localhost-startStop-1 : Loading DbSchema "labkey.junit" (Module) INFO DbScope 2016-04-05 11:03:02,986 localhost-startStop-1 : no schema metadata xml file found for schema "junit" INFO DbScope 2016-04-05 11:03:02,987 localhost-startStop-1 : Loading DbSchema "labkey.search" (Module) INFO DbScope 2016-04-05 11:03:02,990 localhost-startStop-1 : Loading DbSchema "labkey.umls" (Module) INFO DbScope 2016-04-05 11:03:02,993 localhost-startStop-1 : no schema metadata xml file found for schema "umls" INFO DbScope 2016-04-05 11:03:02,994 localhost-startStop-1 : Loading DbSchema "labkey.issues" (Module) INFO DbScope 2016-04-05 11:03:02,999 localhost-startStop-1 : Loading DbSchema "labkey.comm" (Module) INFO DbScope 2016-04-05 11:03:03,008 localhost-startStop-1 : Loading DbSchema "labkey.pipeline" (Module) INFO DbScope 2016-04-05 11:03:03,013 localhost-startStop-1 : Loading DbSchema "labkey.exp" (Module) INFO DbScope 2016-04-05 11:03:03,021 localhost-startStop-1 : Loading DbSchema "labkey.flow" (Module) INFO DbScope 2016-04-05 11:03:03,025 localhost-startStop-1 : Loading DbSchema "labkey.microarray" (Module) INFO DbScope 2016-04-05 11:03:03,029 localhost-startStop-1 : Loading DbSchema "labkey.filecontent" (Module) INFO DbScope 2016-04-05 11:03:03,033 localhost-startStop-1 : Loading DbSchema "labkey.list" (Provisioned) INFO DbScope 2016-04-05 11:03:03,033 localhost-startStop-1 : Loading DbSchema "labkey.ms2" (Module) INFO DbScope 2016-04-05 11:03:03,043 localhost-startStop-1 : Loading DbSchema "labkey.prot" (Module) INFO DbScope 2016-04-05 11:03:03,048 localhost-startStop-1 : Loading DbSchema "labkey.ms1" (Module) INFO DbScope 2016-04-05 11:03:03,053 localhost-startStop-1 : Loading DbSchema "labkey.survey" (Module) INFO DbScope 2016-04-05 11:03:03,057 localhost-startStop-1 : Loading DbSchema "labkey.dataintegration" (Module) INFO DbScope 2016-04-05 11:03:03,062 localhost-startStop-1 : Loading DbSchema "labkey.study" (Module) INFO DbScope 2016-04-05 11:03:03,077 localhost-startStop-1 : Loading DbSchema "labkey.studydataset" (Provisioned) INFO DbScope 2016-04-05 11:03:03,077 localhost-startStop-1 : Loading DbSchema "labkey.assayresult" (Provisioned) INFO DbScope 2016-04-05 11:03:03,077 localhost-startStop-1 : Loading DbSchema "labkey.studydesign" (Provisioned) INFO DbScope 2016-04-05 11:03:03,077 localhost-startStop-1 : Loading DbSchema "labkey.specimentables" (Provisioned) INFO DbScope 2016-04-05 11:03:03,077 localhost-startStop-1 : Loading DbSchema "labkey.luminex" (Module) INFO DbScope 2016-04-05 11:03:03,090 localhost-startStop-1 : Loading DbSchema "labkey.nab" (Module) INFO DbScope 2016-04-05 11:03:03,094 localhost-startStop-1 : Loading DbSchema "labkey.nabvirus" (Provisioned) INFO DbScope 2016-04-05 11:03:03,094 localhost-startStop-1 : Loading DbSchema "labkey.targetedms" (Module) INFO DbScope 2016-04-05 11:03:03,101 localhost-startStop-1 : Loading DbSchema "labkey.audit" (Provisioned) INFO DbScope 2016-04-05 11:03:03,102 localhost-startStop-1 : Loading DbSchema "labkey.elispotlk" (Module) INFO ModuleLoader 2016-04-05 11:03:03,167 localhost-startStop-1 : LabKey Server startup is complete; modules are being upgraded and initialized in the background INFO ModuleLoader 2016-04-05 11:03:03,167 Module Upgrade : Starting up modules INFO ModuleLoader 2016-04-05 11:03:03,168 Module Upgrade : Starting module 'Core' INFO ViewServlet 2016-04-05 11:03:03,170 localhost-startStop-1 : ViewServlet initialized INFO ViewServlet 2016-04-05 11:03:03,170 localhost-startStop-1 : WEBAPP: /usr/share/labkey/labkeywebapp INFO ViewServlet 2016-04-05 11:03:03,170 localhost-startStop-1 : PATH: /usr/local/tpp/bin:/bin:/usr/bin:/sbin:/usr/sbin INFO ModuleLoader 2016-04-05 11:03:04,055 Module Upgrade : Starting module 'Query' INFO ModuleLoader 2016-04-05 11:03:04,096 Module Upgrade : Starting module 'FCSExpress' INFO ModuleLoader 2016-04-05 11:03:04,117 Module Upgrade : Starting module 'Search' INFO ModuleLoader 2016-04-05 11:03:04,129 Module Upgrade : Starting module 'Wiki' INFO ModuleLoader 2016-04-05 11:03:04,136 Module Upgrade : Starting module 'Issues' INFO ModuleLoader 2016-04-05 11:03:04,156 Module Upgrade : Starting module 'Announcements' INFO ModuleLoader 2016-04-05 11:03:04,233 Module Upgrade : Starting module 'BigIron' INFO ModuleLoader 2016-04-05 11:03:04,233 Module Upgrade : Starting module 'Pipeline' INFO SpringModule 2016-04-05 11:03:04,234 Module Upgrade : Loading Spring configuration for the Pipeline module from [/WEB-INF/pipelineContext.xml] INFO SpringModule$1 2016-04-05 11:03:04,236 Module Upgrade : Refreshing Pipeline WebApplicationContext: startup date [Tue Apr 05 11:03:04 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 11:03:04,358 Module Upgrade : Starting module 'Experiment' INFO SpringModule 2016-04-05 11:03:04,358 Module Upgrade : Loading Spring configuration for the Experiment module from [/WEB-INF/experimentContext.xml] INFO SpringModule$1 2016-04-05 11:03:04,359 Module Upgrade : Refreshing Experiment WebApplicationContext: startup date [Tue Apr 05 11:03:04 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 11:03:04,573 Module Upgrade : Starting module 'Flow' INFO ModuleLoader 2016-04-05 11:03:04,608 Module Upgrade : Starting module 'Microarray' INFO SpringModule 2016-04-05 11:03:04,609 Module Upgrade : Loading Spring configuration for the Microarray module from [/WEB-INF/microarrayContext.xml] INFO SpringModule$1 2016-04-05 11:03:04,610 Module Upgrade : Refreshing Microarray WebApplicationContext: startup date [Tue Apr 05 11:03:04 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 11:03:04,654 Module Upgrade : Starting module 'FileContent' INFO ModuleLoader 2016-04-05 11:03:04,657 Module Upgrade : Starting module 'List' INFO ModuleLoader 2016-04-05 11:03:04,676 Module Upgrade : Starting module 'MS2' INFO SpringModule 2016-04-05 11:03:04,677 Module Upgrade : Loading Spring configuration for the MS2 module from [/WEB-INF/ms2Context.xml] INFO SpringModule$1 2016-04-05 11:03:04,678 Module Upgrade : Refreshing MS2 WebApplicationContext: startup date [Tue Apr 05 11:03:04 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 11:03:05,066 Module Upgrade : Starting module 'MS1' INFO SpringModule 2016-04-05 11:03:05,066 Module Upgrade : Loading Spring configuration for the MS1 module from [/WEB-INF/ms1Context.xml] INFO SpringModule$1 2016-04-05 11:03:05,067 Module Upgrade : Refreshing MS1 WebApplicationContext: startup date [Tue Apr 05 11:03:05 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 11:03:05,148 Module Upgrade : Starting module 'Survey' INFO ModuleLoader 2016-04-05 11:03:05,148 Module Upgrade : Starting module 'DataIntegration' INFO ModuleLoader 2016-04-05 11:03:05,157 Module Upgrade : Starting module 'Study' INFO SpringModule 2016-04-05 11:03:05,158 Module Upgrade : Loading Spring configuration for the Study module from [/WEB-INF/studyContext.xml] INFO SpringModule$1 2016-04-05 11:03:05,159 Module Upgrade : Refreshing Study WebApplicationContext: startup date [Tue Apr 05 11:03:05 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 11:03:05,336 Module Upgrade : Starting module 'Luminex' INFO ModuleLoader 2016-04-05 11:03:05,348 Module Upgrade : Starting module 'Visualization' INFO ModuleLoader 2016-04-05 11:03:05,349 Module Upgrade : Starting module 'Nab' INFO ModuleLoader 2016-04-05 11:03:05,368 Module Upgrade : Starting module 'Elisa' INFO ModuleLoader 2016-04-05 11:03:05,371 Module Upgrade : Starting module 'TargetedMS' INFO SpringModule 2016-04-05 11:03:05,372 Module Upgrade : Loading Spring configuration for the TargetedMS module from [/WEB-INF/targetedmsContext.xml] INFO SpringModule$1 2016-04-05 11:03:05,373 Module Upgrade : Refreshing TargetedMS WebApplicationContext: startup date [Tue Apr 05 11:03:05 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 11:03:05,396 Module Upgrade : Starting module 'Audit' INFO ModuleLoader 2016-04-05 11:03:05,404 Module Upgrade : Starting module 'ELISpotAssay' INFO ModuleLoader 2016-04-05 11:03:05,408 Module Upgrade : Running startup listener: Audit Log INFO ModuleLoader 2016-04-05 11:03:05,408 Module Upgrade : Running startup listener: Search Service INFO ModuleLoader 2016-04-05 11:03:05,408 Module Upgrade : Running startup listener: PipelineJobRestarter INFO ModuleLoader 2016-04-05 11:03:05,410 Module Upgrade : Running startup listener: DataIntegration INFO ModuleLoader 2016-04-05 11:03:05,415 Module Upgrade : Module startup complete INFO ContextListener 2016-04-05 11:10:14,665 localhost-startStop-2 : Calling HeartBeatThread shutdownPre() INFO ContextListener 2016-04-05 11:10:14,666 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownPre() INFO ContextListener 2016-04-05 11:10:14,666 localhost-startStop-2 : Calling QueryProfilerThread shutdownPre() INFO ContextListener 2016-04-05 11:10:14,666 localhost-startStop-2 : Calling BreakpointThread shutdownPre() INFO ContextListener 2016-04-05 11:10:14,666 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownPre() INFO ContextListener 2016-04-05 11:10:14,666 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownPre() INFO ContextListener 2016-04-05 11:10:14,666 localhost-startStop-2 : Calling Job Runner (Default) shutdownPre() INFO DatasetSnapshotProvider 2016-04-05 11:10:14,666 SnapshotDependencyThread : QuerySnapshotDependencyThread is terminating due to interruption INFO FileSystemWatcherImpl 2016-04-05 11:10:14,666 FileSystemWatcherThread : FileSystemWatcherThread is terminating INFO ContextListener 2016-04-05 11:10:14,666 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownPre() INFO ContextListener 2016-04-05 11:10:14,667 localhost-startStop-2 : Calling Temp table cleanup shutdownPre() INFO ContextListener 2016-04-05 11:10:14,667 localhost-startStop-2 : Calling Temp file deletion shutdownPre() INFO ContextListener 2016-04-05 11:10:14,667 localhost-startStop-2 : Calling Action stats export shutdownPre() INFO CoreModule 2016-04-05 11:10:14,667 localhost-startStop-2 : Starting to log statistics for actions prior to web application shut down INFO CoreModule 2016-04-05 11:10:14,685 localhost-startStop-2 : Completed logging statistics for actions prior to web application shut down INFO ContextListener 2016-04-05 11:10:14,686 localhost-startStop-2 : Calling DataIntegration shutdownPre() INFO ContextListener 2016-04-05 11:10:14,710 localhost-startStop-2 : Calling DAV crawler shutdownPre() INFO ContextListener 2016-04-05 11:10:14,710 localhost-startStop-2 : Calling Search service shutdownPre() INFO ContextListener 2016-04-05 11:10:14,711 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownPre() INFO ContextListener 2016-04-05 11:10:14,711 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownPre() INFO ContextListener 2016-04-05 11:10:14,715 localhost-startStop-2 : Calling Study Reload Handler shutdownPre() INFO ContextListener 2016-04-05 11:10:14,715 localhost-startStop-2 : Calling HeartBeatThread shutdownStarted() INFO ContextListener 2016-04-05 11:10:14,716 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownStarted() INFO ContextListener 2016-04-05 11:10:14,716 localhost-startStop-2 : Calling QueryProfilerThread shutdownStarted() INFO QueryProfiler 2016-04-05 11:10:14,716 localhost-startStop-2 : Starting to log statistics for queries prior to web application shut down INFO QueryProfiler 2016-04-05 11:10:14,741 localhost-startStop-2 : Completed logging statistics for queries prior to web application shut down INFO ContextListener 2016-04-05 11:10:14,741 localhost-startStop-2 : Calling BreakpointThread shutdownStarted() INFO ContextListener 2016-04-05 11:10:14,741 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownStarted() INFO ContextListener 2016-04-05 11:10:14,741 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownStarted() INFO ContextListener 2016-04-05 11:10:14,741 localhost-startStop-2 : Calling Job Runner (Default) shutdownStarted() INFO ContextListener 2016-04-05 11:10:14,741 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownStarted() INFO ContextListener 2016-04-05 11:10:14,741 localhost-startStop-2 : Calling Temp table cleanup shutdownStarted() INFO ContextListener 2016-04-05 11:10:14,742 localhost-startStop-2 : Calling Temp file deletion shutdownStarted() INFO ContextListener 2016-04-05 11:10:14,742 localhost-startStop-2 : Calling Action stats export shutdownStarted() INFO ContextListener 2016-04-05 11:10:14,742 localhost-startStop-2 : Calling DataIntegration shutdownStarted() INFO ContextListener 2016-04-05 11:10:15,216 localhost-startStop-2 : Calling DAV crawler shutdownStarted() INFO ContextListener 2016-04-05 11:10:15,217 localhost-startStop-2 : Calling Search service shutdownStarted() INFO ContextListener 2016-04-05 11:10:15,220 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownStarted() INFO ContextListener 2016-04-05 11:10:15,220 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownStarted() INFO ContextListener 2016-04-05 11:10:15,220 localhost-startStop-2 : Calling Study Reload Handler shutdownStarted() INFO EhCacheProvider 2016-04-05 11:10:15,223 localhost-startStop-2 : Shutting down Ehcache INFO ModuleLoader 2016-04-05 11:40:37,463 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2016-04-05 11:40:38,838 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource Server URL: jdbc:postgresql://localhost:5432/labkey Database Product Name: PostgreSQL Database Product Version: 9.4.6 JDBC Driver Name: PostgreSQL Native Driver JDBC Driver Version: PostgreSQL 9.4.1207 SQL Dialect: PostgreSql94Dialect INFO DbScope 2016-04-05 11:40:38,955 localhost-startStop-1 : Loading DbSchema "labkey.core" (Module) WARN ThumbnailServiceImpl 2016-04-05 11:40:39,388 humbnailGeneratingThread : ThumbnailGeneratingThread is terminating because ThumbnailService is null INFO DbScope 2016-04-05 11:40:41,458 localhost-startStop-1 : Loading DbSchema "labkey.prop" (Module) INFO DbScope 2016-04-05 11:40:41,544 localhost-startStop-1 : Loading DbSchema "labkey.test" (Module) INFO DbScope 2016-04-05 11:40:41,552 localhost-startStop-1 : Loading DbSchema "labkey.temp" (Provisioned) INFO DbScope 2016-04-05 11:40:41,555 localhost-startStop-1 : Loading DbSchema "labkey.query" (Module) INFO DbScope 2016-04-05 11:40:41,560 localhost-startStop-1 : Loading DbSchema "labkey.junit" (Module) INFO DbScope 2016-04-05 11:40:41,563 localhost-startStop-1 : no schema metadata xml file found for schema "junit" INFO DbScope 2016-04-05 11:40:41,564 localhost-startStop-1 : Loading DbSchema "labkey.search" (Module) INFO DbScope 2016-04-05 11:40:41,568 localhost-startStop-1 : Loading DbSchema "labkey.umls" (Module) INFO DbScope 2016-04-05 11:40:41,572 localhost-startStop-1 : no schema metadata xml file found for schema "umls" INFO DbScope 2016-04-05 11:40:41,572 localhost-startStop-1 : Loading DbSchema "labkey.issues" (Module) INFO DbScope 2016-04-05 11:40:41,579 localhost-startStop-1 : Loading DbSchema "labkey.comm" (Module) INFO DbScope 2016-04-05 11:40:41,588 localhost-startStop-1 : Loading DbSchema "labkey.pipeline" (Module) INFO DbScope 2016-04-05 11:40:41,592 localhost-startStop-1 : Loading DbSchema "labkey.exp" (Module) INFO DbScope 2016-04-05 11:40:41,600 localhost-startStop-1 : Loading DbSchema "labkey.flow" (Module) INFO DbScope 2016-04-05 11:40:41,605 localhost-startStop-1 : Loading DbSchema "labkey.microarray" (Module) INFO DbScope 2016-04-05 11:40:41,609 localhost-startStop-1 : Loading DbSchema "labkey.filecontent" (Module) INFO DbScope 2016-04-05 11:40:41,617 localhost-startStop-1 : Loading DbSchema "labkey.list" (Provisioned) INFO DbScope 2016-04-05 11:40:41,617 localhost-startStop-1 : Loading DbSchema "labkey.ms2" (Module) INFO DbScope 2016-04-05 11:40:41,629 localhost-startStop-1 : Loading DbSchema "labkey.prot" (Module) INFO DbScope 2016-04-05 11:40:41,634 localhost-startStop-1 : Loading DbSchema "labkey.ms1" (Module) INFO DbScope 2016-04-05 11:40:41,640 localhost-startStop-1 : Loading DbSchema "labkey.survey" (Module) INFO DbScope 2016-04-05 11:40:41,645 localhost-startStop-1 : Loading DbSchema "labkey.dataintegration" (Module) INFO DbScope 2016-04-05 11:40:41,649 localhost-startStop-1 : Loading DbSchema "labkey.study" (Module) INFO DbScope 2016-04-05 11:40:41,663 localhost-startStop-1 : Loading DbSchema "labkey.studydataset" (Provisioned) INFO DbScope 2016-04-05 11:40:41,663 localhost-startStop-1 : Loading DbSchema "labkey.assayresult" (Provisioned) INFO DbScope 2016-04-05 11:40:41,663 localhost-startStop-1 : Loading DbSchema "labkey.studydesign" (Provisioned) INFO DbScope 2016-04-05 11:40:41,663 localhost-startStop-1 : Loading DbSchema "labkey.specimentables" (Provisioned) INFO DbScope 2016-04-05 11:40:41,663 localhost-startStop-1 : Loading DbSchema "labkey.luminex" (Module) INFO DbScope 2016-04-05 11:40:41,668 localhost-startStop-1 : Loading DbSchema "labkey.nab" (Module) INFO DbScope 2016-04-05 11:40:41,673 localhost-startStop-1 : Loading DbSchema "labkey.nabvirus" (Provisioned) INFO DbScope 2016-04-05 11:40:41,673 localhost-startStop-1 : Loading DbSchema "labkey.targetedms" (Module) INFO DbScope 2016-04-05 11:40:41,683 localhost-startStop-1 : Loading DbSchema "labkey.audit" (Provisioned) INFO DbScope 2016-04-05 11:40:41,684 localhost-startStop-1 : Loading DbSchema "labkey.elispotlk" (Module) INFO ModuleLoader 2016-04-05 11:40:41,771 localhost-startStop-1 : LabKey Server startup is complete; modules are being upgraded and initialized in the background INFO ModuleLoader 2016-04-05 11:40:41,772 Module Upgrade : Starting up modules INFO ModuleLoader 2016-04-05 11:40:41,772 Module Upgrade : Starting module 'Core' INFO ViewServlet 2016-04-05 11:40:41,776 localhost-startStop-1 : ViewServlet initialized INFO ViewServlet 2016-04-05 11:40:41,777 localhost-startStop-1 : WEBAPP: /usr/share/labkey/labkeywebapp INFO ViewServlet 2016-04-05 11:40:41,777 localhost-startStop-1 : PATH: /usr/local/tpp/bin:/bin:/usr/bin:/sbin:/usr/sbin INFO ModuleLoader 2016-04-05 11:40:42,731 Module Upgrade : Starting module 'Query' INFO ModuleLoader 2016-04-05 11:40:42,796 Module Upgrade : Starting module 'FCSExpress' INFO ModuleLoader 2016-04-05 11:40:42,821 Module Upgrade : Starting module 'Search' INFO ModuleLoader 2016-04-05 11:40:42,830 Module Upgrade : Starting module 'Wiki' INFO ModuleLoader 2016-04-05 11:40:42,841 Module Upgrade : Starting module 'Issues' INFO ModuleLoader 2016-04-05 11:40:42,855 Module Upgrade : Starting module 'Announcements' INFO ModuleLoader 2016-04-05 11:40:42,951 Module Upgrade : Starting module 'BigIron' INFO ModuleLoader 2016-04-05 11:40:42,952 Module Upgrade : Starting module 'Pipeline' INFO SpringModule 2016-04-05 11:40:42,952 Module Upgrade : Loading Spring configuration for the Pipeline module from [/WEB-INF/pipelineContext.xml] INFO SpringModule$1 2016-04-05 11:40:42,954 Module Upgrade : Refreshing Pipeline WebApplicationContext: startup date [Tue Apr 05 11:40:42 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 11:40:43,098 Module Upgrade : Starting module 'Experiment' INFO SpringModule 2016-04-05 11:40:43,099 Module Upgrade : Loading Spring configuration for the Experiment module from [/WEB-INF/experimentContext.xml] INFO SpringModule$1 2016-04-05 11:40:43,100 Module Upgrade : Refreshing Experiment WebApplicationContext: startup date [Tue Apr 05 11:40:43 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 11:40:43,340 Module Upgrade : Starting module 'Flow' INFO ModuleLoader 2016-04-05 11:40:43,385 Module Upgrade : Starting module 'Microarray' INFO SpringModule 2016-04-05 11:40:43,385 Module Upgrade : Loading Spring configuration for the Microarray module from [/WEB-INF/microarrayContext.xml] INFO SpringModule$1 2016-04-05 11:40:43,388 Module Upgrade : Refreshing Microarray WebApplicationContext: startup date [Tue Apr 05 11:40:43 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 11:40:43,431 Module Upgrade : Starting module 'FileContent' INFO ModuleLoader 2016-04-05 11:40:43,434 Module Upgrade : Starting module 'List' INFO ModuleLoader 2016-04-05 11:40:43,455 Module Upgrade : Starting module 'MS2' INFO SpringModule 2016-04-05 11:40:43,456 Module Upgrade : Loading Spring configuration for the MS2 module from [/WEB-INF/ms2Context.xml] INFO SpringModule$1 2016-04-05 11:40:43,457 Module Upgrade : Refreshing MS2 WebApplicationContext: startup date [Tue Apr 05 11:40:43 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 11:40:43,888 Module Upgrade : Starting module 'MS1' INFO SpringModule 2016-04-05 11:40:43,889 Module Upgrade : Loading Spring configuration for the MS1 module from [/WEB-INF/ms1Context.xml] INFO SpringModule$1 2016-04-05 11:40:43,890 Module Upgrade : Refreshing MS1 WebApplicationContext: startup date [Tue Apr 05 11:40:43 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 11:40:43,984 Module Upgrade : Starting module 'Survey' INFO ModuleLoader 2016-04-05 11:40:43,986 Module Upgrade : Starting module 'DataIntegration' INFO ModuleLoader 2016-04-05 11:40:43,996 Module Upgrade : Starting module 'Study' INFO SpringModule 2016-04-05 11:40:43,996 Module Upgrade : Loading Spring configuration for the Study module from [/WEB-INF/studyContext.xml] INFO SpringModule$1 2016-04-05 11:40:43,997 Module Upgrade : Refreshing Study WebApplicationContext: startup date [Tue Apr 05 11:40:43 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 11:40:44,224 Module Upgrade : Starting module 'Luminex' INFO ModuleLoader 2016-04-05 11:40:44,238 Module Upgrade : Starting module 'Visualization' INFO ModuleLoader 2016-04-05 11:40:44,238 Module Upgrade : Starting module 'Nab' INFO ModuleLoader 2016-04-05 11:40:44,260 Module Upgrade : Starting module 'Elisa' INFO ModuleLoader 2016-04-05 11:40:44,264 Module Upgrade : Starting module 'TargetedMS' INFO SpringModule 2016-04-05 11:40:44,265 Module Upgrade : Loading Spring configuration for the TargetedMS module from [/WEB-INF/targetedmsContext.xml] INFO SpringModule$1 2016-04-05 11:40:44,266 Module Upgrade : Refreshing TargetedMS WebApplicationContext: startup date [Tue Apr 05 11:40:44 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 11:40:44,292 Module Upgrade : Starting module 'Audit' INFO ModuleLoader 2016-04-05 11:40:44,301 Module Upgrade : Starting module 'ELISpotAssay' INFO ModuleLoader 2016-04-05 11:40:44,307 Module Upgrade : Running startup listener: Audit Log INFO ModuleLoader 2016-04-05 11:40:44,307 Module Upgrade : Running startup listener: Search Service INFO ModuleLoader 2016-04-05 11:40:44,307 Module Upgrade : Running startup listener: PipelineJobRestarter INFO ModuleLoader 2016-04-05 11:40:44,309 Module Upgrade : Running startup listener: DataIntegration INFO ModuleLoader 2016-04-05 11:40:44,315 Module Upgrade : Module startup complete INFO ContextListener 2016-04-05 12:15:59,225 localhost-startStop-2 : Calling HeartBeatThread shutdownPre() INFO ContextListener 2016-04-05 12:15:59,225 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownPre() INFO ContextListener 2016-04-05 12:15:59,225 localhost-startStop-2 : Calling QueryProfilerThread shutdownPre() INFO ContextListener 2016-04-05 12:15:59,225 localhost-startStop-2 : Calling BreakpointThread shutdownPre() INFO ContextListener 2016-04-05 12:15:59,225 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownPre() INFO ContextListener 2016-04-05 12:15:59,225 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownPre() INFO ContextListener 2016-04-05 12:15:59,225 localhost-startStop-2 : Calling Job Runner (Default) shutdownPre() INFO DatasetSnapshotProvider 2016-04-05 12:15:59,226 SnapshotDependencyThread : QuerySnapshotDependencyThread is terminating due to interruption INFO ContextListener 2016-04-05 12:15:59,226 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownPre() INFO FileSystemWatcherImpl 2016-04-05 12:15:59,226 FileSystemWatcherThread : FileSystemWatcherThread is terminating INFO ContextListener 2016-04-05 12:15:59,226 localhost-startStop-2 : Calling Temp table cleanup shutdownPre() INFO ContextListener 2016-04-05 12:15:59,226 localhost-startStop-2 : Calling Temp file deletion shutdownPre() INFO ContextListener 2016-04-05 12:15:59,226 localhost-startStop-2 : Calling Action stats export shutdownPre() INFO CoreModule 2016-04-05 12:15:59,226 localhost-startStop-2 : Starting to log statistics for actions prior to web application shut down INFO CoreModule 2016-04-05 12:15:59,246 localhost-startStop-2 : Completed logging statistics for actions prior to web application shut down INFO ContextListener 2016-04-05 12:15:59,246 localhost-startStop-2 : Calling DataIntegration shutdownPre() INFO ContextListener 2016-04-05 12:15:59,258 localhost-startStop-2 : Calling DAV crawler shutdownPre() INFO ContextListener 2016-04-05 12:15:59,258 localhost-startStop-2 : Calling Search service shutdownPre() INFO ContextListener 2016-04-05 12:15:59,258 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownPre() INFO ContextListener 2016-04-05 12:15:59,258 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownPre() INFO ContextListener 2016-04-05 12:15:59,258 localhost-startStop-2 : Calling Study Reload Handler shutdownPre() INFO ContextListener 2016-04-05 12:15:59,258 localhost-startStop-2 : Calling Job Runner (Mothership Reporting) shutdownPre() INFO ContextListener 2016-04-05 12:15:59,259 localhost-startStop-2 : Calling HeartBeatThread shutdownStarted() INFO ContextListener 2016-04-05 12:15:59,259 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownStarted() INFO ContextListener 2016-04-05 12:15:59,259 localhost-startStop-2 : Calling QueryProfilerThread shutdownStarted() INFO QueryProfiler 2016-04-05 12:15:59,259 localhost-startStop-2 : Starting to log statistics for queries prior to web application shut down INFO QueryProfiler 2016-04-05 12:15:59,273 localhost-startStop-2 : Completed logging statistics for queries prior to web application shut down INFO ContextListener 2016-04-05 12:15:59,273 localhost-startStop-2 : Calling BreakpointThread shutdownStarted() INFO ContextListener 2016-04-05 12:15:59,273 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownStarted() INFO ContextListener 2016-04-05 12:15:59,273 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownStarted() INFO ContextListener 2016-04-05 12:15:59,273 localhost-startStop-2 : Calling Job Runner (Default) shutdownStarted() INFO ContextListener 2016-04-05 12:15:59,273 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownStarted() INFO ContextListener 2016-04-05 12:15:59,273 localhost-startStop-2 : Calling Temp table cleanup shutdownStarted() INFO ContextListener 2016-04-05 12:15:59,274 localhost-startStop-2 : Calling Temp file deletion shutdownStarted() INFO ContextListener 2016-04-05 12:15:59,274 localhost-startStop-2 : Calling Action stats export shutdownStarted() INFO ContextListener 2016-04-05 12:15:59,274 localhost-startStop-2 : Calling DataIntegration shutdownStarted() INFO ContextListener 2016-04-05 12:15:59,758 localhost-startStop-2 : Calling DAV crawler shutdownStarted() INFO ContextListener 2016-04-05 12:15:59,758 localhost-startStop-2 : Calling Search service shutdownStarted() INFO ContextListener 2016-04-05 12:15:59,760 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownStarted() INFO ContextListener 2016-04-05 12:15:59,761 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownStarted() INFO ContextListener 2016-04-05 12:15:59,761 localhost-startStop-2 : Calling Study Reload Handler shutdownStarted() INFO ContextListener 2016-04-05 12:15:59,761 localhost-startStop-2 : Calling Job Runner (Mothership Reporting) shutdownStarted() INFO EhCacheProvider 2016-04-05 12:15:59,765 localhost-startStop-2 : Shutting down Ehcache INFO ModuleLoader 2016-04-05 12:16:05,380 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2016-04-05 12:16:06,691 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource Server URL: jdbc:postgresql://localhost:5432/labkey Database Product Name: PostgreSQL Database Product Version: 9.4.6 JDBC Driver Name: PostgreSQL Native Driver JDBC Driver Version: PostgreSQL 9.4.1207 SQL Dialect: PostgreSql94Dialect INFO DbScope 2016-04-05 12:16:06,794 localhost-startStop-1 : Loading DbSchema "labkey.core" (Module) INFO DbScope 2016-04-05 12:16:09,116 localhost-startStop-1 : Loading DbSchema "labkey.prop" (Module) INFO DbScope 2016-04-05 12:16:09,192 localhost-startStop-1 : Loading DbSchema "labkey.test" (Module) INFO DbScope 2016-04-05 12:16:09,197 localhost-startStop-1 : Loading DbSchema "labkey.temp" (Provisioned) INFO DbScope 2016-04-05 12:16:09,200 localhost-startStop-1 : Loading DbSchema "labkey.query" (Module) INFO DbScope 2016-04-05 12:16:09,205 localhost-startStop-1 : Loading DbSchema "labkey.junit" (Module) INFO DbScope 2016-04-05 12:16:09,207 localhost-startStop-1 : no schema metadata xml file found for schema "junit" INFO DbScope 2016-04-05 12:16:09,207 localhost-startStop-1 : Loading DbSchema "labkey.search" (Module) INFO DbScope 2016-04-05 12:16:09,212 localhost-startStop-1 : Loading DbSchema "labkey.umls" (Module) INFO DbScope 2016-04-05 12:16:09,215 localhost-startStop-1 : no schema metadata xml file found for schema "umls" INFO DbScope 2016-04-05 12:16:09,215 localhost-startStop-1 : Loading DbSchema "labkey.issues" (Module) INFO DbScope 2016-04-05 12:16:09,221 localhost-startStop-1 : Loading DbSchema "labkey.comm" (Module) INFO DbScope 2016-04-05 12:16:09,229 localhost-startStop-1 : Loading DbSchema "labkey.pipeline" (Module) INFO DbScope 2016-04-05 12:16:09,233 localhost-startStop-1 : Loading DbSchema "labkey.exp" (Module) INFO DbScope 2016-04-05 12:16:09,241 localhost-startStop-1 : Loading DbSchema "labkey.flow" (Module) INFO DbScope 2016-04-05 12:16:09,245 localhost-startStop-1 : Loading DbSchema "labkey.microarray" (Module) INFO DbScope 2016-04-05 12:16:09,250 localhost-startStop-1 : Loading DbSchema "labkey.filecontent" (Module) INFO DbScope 2016-04-05 12:16:09,256 localhost-startStop-1 : Loading DbSchema "labkey.list" (Provisioned) INFO DbScope 2016-04-05 12:16:09,256 localhost-startStop-1 : Loading DbSchema "labkey.ms2" (Module) INFO DbScope 2016-04-05 12:16:09,265 localhost-startStop-1 : Loading DbSchema "labkey.prot" (Module) INFO DbScope 2016-04-05 12:16:09,276 localhost-startStop-1 : Loading DbSchema "labkey.ms1" (Module) INFO DbScope 2016-04-05 12:16:09,281 localhost-startStop-1 : Loading DbSchema "labkey.survey" (Module) INFO DbScope 2016-04-05 12:16:09,288 localhost-startStop-1 : Loading DbSchema "labkey.dataintegration" (Module) INFO DbScope 2016-04-05 12:16:09,292 localhost-startStop-1 : Loading DbSchema "labkey.study" (Module) INFO DbScope 2016-04-05 12:16:09,306 localhost-startStop-1 : Loading DbSchema "labkey.studydataset" (Provisioned) INFO DbScope 2016-04-05 12:16:09,306 localhost-startStop-1 : Loading DbSchema "labkey.assayresult" (Provisioned) INFO DbScope 2016-04-05 12:16:09,306 localhost-startStop-1 : Loading DbSchema "labkey.studydesign" (Provisioned) INFO DbScope 2016-04-05 12:16:09,306 localhost-startStop-1 : Loading DbSchema "labkey.specimentables" (Provisioned) INFO DbScope 2016-04-05 12:16:09,306 localhost-startStop-1 : Loading DbSchema "labkey.luminex" (Module) INFO DbScope 2016-04-05 12:16:09,313 localhost-startStop-1 : Loading DbSchema "labkey.nab" (Module) INFO DbScope 2016-04-05 12:16:09,317 localhost-startStop-1 : Loading DbSchema "labkey.nabvirus" (Provisioned) INFO DbScope 2016-04-05 12:16:09,317 localhost-startStop-1 : Loading DbSchema "labkey.targetedms" (Module) INFO DbScope 2016-04-05 12:16:09,325 localhost-startStop-1 : Loading DbSchema "labkey.audit" (Provisioned) INFO DbScope 2016-04-05 12:16:09,325 localhost-startStop-1 : Loading DbSchema "labkey.elispotlk" (Module) INFO ModuleLoader 2016-04-05 12:16:09,394 localhost-startStop-1 : LabKey Server startup is complete; modules are being upgraded and initialized in the background INFO ViewServlet 2016-04-05 12:16:09,399 localhost-startStop-1 : ViewServlet initialized INFO ViewServlet 2016-04-05 12:16:09,399 localhost-startStop-1 : WEBAPP: /usr/share/labkey/labkeywebapp INFO ViewServlet 2016-04-05 12:16:09,399 localhost-startStop-1 : PATH: /usr/local/tpp/bin:/bin:/usr/bin:/sbin:/usr/sbin INFO ModuleLoader 2016-04-05 12:16:09,395 Module Upgrade : Starting up modules INFO ModuleLoader 2016-04-05 12:16:09,404 Module Upgrade : Starting module 'Core' INFO ModuleLoader 2016-04-05 12:16:10,323 Module Upgrade : Starting module 'Query' INFO ModuleLoader 2016-04-05 12:16:10,374 Module Upgrade : Starting module 'FCSExpress' INFO ModuleLoader 2016-04-05 12:16:10,391 Module Upgrade : Starting module 'Search' INFO ModuleLoader 2016-04-05 12:16:10,411 Module Upgrade : Starting module 'Wiki' INFO ModuleLoader 2016-04-05 12:16:10,421 Module Upgrade : Starting module 'Issues' INFO ModuleLoader 2016-04-05 12:16:10,433 Module Upgrade : Starting module 'Announcements' INFO ModuleLoader 2016-04-05 12:16:10,519 Module Upgrade : Starting module 'BigIron' INFO ModuleLoader 2016-04-05 12:16:10,520 Module Upgrade : Starting module 'Pipeline' INFO SpringModule 2016-04-05 12:16:10,520 Module Upgrade : Loading Spring configuration for the Pipeline module from [/WEB-INF/pipelineContext.xml] INFO SpringModule$1 2016-04-05 12:16:10,522 Module Upgrade : Refreshing Pipeline WebApplicationContext: startup date [Tue Apr 05 12:16:10 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 12:16:10,662 Module Upgrade : Starting module 'Experiment' INFO SpringModule 2016-04-05 12:16:10,663 Module Upgrade : Loading Spring configuration for the Experiment module from [/WEB-INF/experimentContext.xml] INFO SpringModule$1 2016-04-05 12:16:10,664 Module Upgrade : Refreshing Experiment WebApplicationContext: startup date [Tue Apr 05 12:16:10 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 12:16:10,902 Module Upgrade : Starting module 'Flow' INFO ModuleLoader 2016-04-05 12:16:10,939 Module Upgrade : Starting module 'Microarray' INFO SpringModule 2016-04-05 12:16:10,939 Module Upgrade : Loading Spring configuration for the Microarray module from [/WEB-INF/microarrayContext.xml] INFO SpringModule$1 2016-04-05 12:16:10,940 Module Upgrade : Refreshing Microarray WebApplicationContext: startup date [Tue Apr 05 12:16:10 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 12:16:10,987 Module Upgrade : Starting module 'FileContent' INFO ModuleLoader 2016-04-05 12:16:10,990 Module Upgrade : Starting module 'List' INFO ModuleLoader 2016-04-05 12:16:11,009 Module Upgrade : Starting module 'MS2' INFO SpringModule 2016-04-05 12:16:11,010 Module Upgrade : Loading Spring configuration for the MS2 module from [/WEB-INF/ms2Context.xml] INFO SpringModule$1 2016-04-05 12:16:11,011 Module Upgrade : Refreshing MS2 WebApplicationContext: startup date [Tue Apr 05 12:16:11 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 12:16:11,427 Module Upgrade : Starting module 'MS1' INFO SpringModule 2016-04-05 12:16:11,427 Module Upgrade : Loading Spring configuration for the MS1 module from [/WEB-INF/ms1Context.xml] INFO SpringModule$1 2016-04-05 12:16:11,428 Module Upgrade : Refreshing MS1 WebApplicationContext: startup date [Tue Apr 05 12:16:11 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 12:16:11,516 Module Upgrade : Starting module 'Survey' INFO ModuleLoader 2016-04-05 12:16:11,517 Module Upgrade : Starting module 'DataIntegration' INFO ModuleLoader 2016-04-05 12:16:11,526 Module Upgrade : Starting module 'Study' INFO SpringModule 2016-04-05 12:16:11,527 Module Upgrade : Loading Spring configuration for the Study module from [/WEB-INF/studyContext.xml] INFO SpringModule$1 2016-04-05 12:16:11,528 Module Upgrade : Refreshing Study WebApplicationContext: startup date [Tue Apr 05 12:16:11 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 12:16:11,741 Module Upgrade : Starting module 'Luminex' INFO ModuleLoader 2016-04-05 12:16:11,754 Module Upgrade : Starting module 'Visualization' INFO ModuleLoader 2016-04-05 12:16:11,754 Module Upgrade : Starting module 'Nab' INFO ModuleLoader 2016-04-05 12:16:11,774 Module Upgrade : Starting module 'Elisa' INFO ModuleLoader 2016-04-05 12:16:11,778 Module Upgrade : Starting module 'TargetedMS' INFO SpringModule 2016-04-05 12:16:11,779 Module Upgrade : Loading Spring configuration for the TargetedMS module from [/WEB-INF/targetedmsContext.xml] INFO SpringModule$1 2016-04-05 12:16:11,780 Module Upgrade : Refreshing TargetedMS WebApplicationContext: startup date [Tue Apr 05 12:16:11 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 12:16:11,808 Module Upgrade : Starting module 'Audit' INFO ModuleLoader 2016-04-05 12:16:11,820 Module Upgrade : Starting module 'ELISpotAssay' INFO ModuleLoader 2016-04-05 12:16:11,826 Module Upgrade : Running startup listener: Audit Log INFO ModuleLoader 2016-04-05 12:16:11,826 Module Upgrade : Running startup listener: Search Service INFO ModuleLoader 2016-04-05 12:16:11,826 Module Upgrade : Running startup listener: PipelineJobRestarter INFO ModuleLoader 2016-04-05 12:16:11,828 Module Upgrade : Running startup listener: DataIntegration INFO ModuleLoader 2016-04-05 12:16:11,837 Module Upgrade : Module startup complete INFO ContextListener 2016-04-05 12:20:23,896 localhost-startStop-2 : Calling HeartBeatThread shutdownPre() INFO ContextListener 2016-04-05 12:20:23,896 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownPre() INFO ContextListener 2016-04-05 12:20:23,896 localhost-startStop-2 : Calling QueryProfilerThread shutdownPre() INFO ContextListener 2016-04-05 12:20:23,897 localhost-startStop-2 : Calling BreakpointThread shutdownPre() INFO FileSystemWatcherImpl 2016-04-05 12:20:23,897 FileSystemWatcherThread : FileSystemWatcherThread is terminating INFO ContextListener 2016-04-05 12:20:23,897 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownPre() INFO ContextListener 2016-04-05 12:20:23,897 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownPre() INFO ContextListener 2016-04-05 12:20:23,897 localhost-startStop-2 : Calling Job Runner (Default) shutdownPre() INFO DatasetSnapshotProvider 2016-04-05 12:20:23,897 SnapshotDependencyThread : QuerySnapshotDependencyThread is terminating due to interruption INFO ContextListener 2016-04-05 12:20:23,898 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownPre() INFO ContextListener 2016-04-05 12:20:23,898 localhost-startStop-2 : Calling Temp table cleanup shutdownPre() INFO ContextListener 2016-04-05 12:20:23,898 localhost-startStop-2 : Calling Temp file deletion shutdownPre() INFO ContextListener 2016-04-05 12:20:23,898 localhost-startStop-2 : Calling Action stats export shutdownPre() INFO CoreModule 2016-04-05 12:20:23,898 localhost-startStop-2 : Starting to log statistics for actions prior to web application shut down INFO CoreModule 2016-04-05 12:20:23,912 localhost-startStop-2 : Completed logging statistics for actions prior to web application shut down INFO ContextListener 2016-04-05 12:20:23,912 localhost-startStop-2 : Calling DataIntegration shutdownPre() INFO ContextListener 2016-04-05 12:20:23,937 localhost-startStop-2 : Calling DAV crawler shutdownPre() INFO ContextListener 2016-04-05 12:20:23,937 localhost-startStop-2 : Calling Search service shutdownPre() INFO ContextListener 2016-04-05 12:20:23,937 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownPre() INFO ContextListener 2016-04-05 12:20:23,937 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownPre() INFO ContextListener 2016-04-05 12:20:23,937 localhost-startStop-2 : Calling Study Reload Handler shutdownPre() INFO ContextListener 2016-04-05 12:20:23,937 localhost-startStop-2 : Calling HeartBeatThread shutdownStarted() INFO ContextListener 2016-04-05 12:20:23,937 localhost-startStop-2 : Calling FileSystemWatcherThread shutdownStarted() INFO ContextListener 2016-04-05 12:20:23,937 localhost-startStop-2 : Calling QueryProfilerThread shutdownStarted() INFO QueryProfiler 2016-04-05 12:20:23,937 localhost-startStop-2 : Starting to log statistics for queries prior to web application shut down INFO QueryProfiler 2016-04-05 12:20:23,956 localhost-startStop-2 : Completed logging statistics for queries prior to web application shut down INFO ContextListener 2016-04-05 12:20:23,956 localhost-startStop-2 : Calling BreakpointThread shutdownStarted() INFO ContextListener 2016-04-05 12:20:23,956 localhost-startStop-2 : Calling ThumbnailGeneratingThread shutdownStarted() INFO ContextListener 2016-04-05 12:20:23,956 localhost-startStop-2 : Calling QuerySnapshotDependencyThread shutdownStarted() INFO ContextListener 2016-04-05 12:20:23,956 localhost-startStop-2 : Calling Job Runner (Default) shutdownStarted() INFO ContextListener 2016-04-05 12:20:23,956 localhost-startStop-2 : Calling Job Runner (Pipeline) shutdownStarted() INFO ContextListener 2016-04-05 12:20:23,956 localhost-startStop-2 : Calling Temp table cleanup shutdownStarted() INFO ContextListener 2016-04-05 12:20:23,956 localhost-startStop-2 : Calling Temp file deletion shutdownStarted() INFO ContextListener 2016-04-05 12:20:23,956 localhost-startStop-2 : Calling Action stats export shutdownStarted() INFO ContextListener 2016-04-05 12:20:23,956 localhost-startStop-2 : Calling DataIntegration shutdownStarted() INFO ContextListener 2016-04-05 12:20:24,438 localhost-startStop-2 : Calling DAV crawler shutdownStarted() INFO ContextListener 2016-04-05 12:20:24,438 localhost-startStop-2 : Calling Search service shutdownStarted() INFO ContextListener 2016-04-05 12:20:24,441 localhost-startStop-2 : Calling Message digest timer task (DailyMessageDigest) shutdownStarted() INFO ContextListener 2016-04-05 12:20:24,441 localhost-startStop-2 : Calling Message digest timer task (ShortMessageDigest) shutdownStarted() INFO ContextListener 2016-04-05 12:20:24,441 localhost-startStop-2 : Calling Study Reload Handler shutdownStarted() INFO EhCacheProvider 2016-04-05 12:20:24,443 localhost-startStop-2 : Shutting down Ehcache INFO ModuleLoader 2016-04-05 12:20:30,189 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2016-04-05 12:20:31,603 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource Server URL: jdbc:postgresql://localhost:5432/labkey Database Product Name: PostgreSQL Database Product Version: 9.4.6 JDBC Driver Name: PostgreSQL Native Driver JDBC Driver Version: PostgreSQL 9.4.1207 SQL Dialect: PostgreSql94Dialect INFO DbScope 2016-04-05 12:20:31,702 localhost-startStop-1 : Loading DbSchema "labkey.core" (Module) INFO DbScope 2016-04-05 12:20:34,160 localhost-startStop-1 : Loading DbSchema "labkey.prop" (Module) INFO DbScope 2016-04-05 12:20:34,239 localhost-startStop-1 : Loading DbSchema "labkey.test" (Module) INFO DbScope 2016-04-05 12:20:34,249 localhost-startStop-1 : Loading DbSchema "labkey.temp" (Provisioned) INFO DbScope 2016-04-05 12:20:34,252 localhost-startStop-1 : Loading DbSchema "labkey.query" (Module) INFO DbScope 2016-04-05 12:20:34,257 localhost-startStop-1 : Loading DbSchema "labkey.junit" (Module) INFO DbScope 2016-04-05 12:20:34,260 localhost-startStop-1 : no schema metadata xml file found for schema "junit" INFO DbScope 2016-04-05 12:20:34,260 localhost-startStop-1 : Loading DbSchema "labkey.search" (Module) INFO DbScope 2016-04-05 12:20:34,264 localhost-startStop-1 : Loading DbSchema "labkey.umls" (Module) INFO DbScope 2016-04-05 12:20:34,267 localhost-startStop-1 : no schema metadata xml file found for schema "umls" INFO DbScope 2016-04-05 12:20:34,267 localhost-startStop-1 : Loading DbSchema "labkey.issues" (Module) INFO DbScope 2016-04-05 12:20:34,273 localhost-startStop-1 : Loading DbSchema "labkey.comm" (Module) INFO DbScope 2016-04-05 12:20:34,283 localhost-startStop-1 : Loading DbSchema "labkey.pipeline" (Module) INFO DbScope 2016-04-05 12:20:34,287 localhost-startStop-1 : Loading DbSchema "labkey.exp" (Module) INFO DbScope 2016-04-05 12:20:34,296 localhost-startStop-1 : Loading DbSchema "labkey.flow" (Module) INFO DbScope 2016-04-05 12:20:34,300 localhost-startStop-1 : Loading DbSchema "labkey.microarray" (Module) INFO DbScope 2016-04-05 12:20:34,307 localhost-startStop-1 : Loading DbSchema "labkey.filecontent" (Module) INFO DbScope 2016-04-05 12:20:34,312 localhost-startStop-1 : Loading DbSchema "labkey.list" (Provisioned) INFO DbScope 2016-04-05 12:20:34,312 localhost-startStop-1 : Loading DbSchema "labkey.ms2" (Module) INFO DbScope 2016-04-05 12:20:34,321 localhost-startStop-1 : Loading DbSchema "labkey.prot" (Module) INFO DbScope 2016-04-05 12:20:34,328 localhost-startStop-1 : Loading DbSchema "labkey.ms1" (Module) INFO DbScope 2016-04-05 12:20:34,333 localhost-startStop-1 : Loading DbSchema "labkey.survey" (Module) INFO DbScope 2016-04-05 12:20:34,337 localhost-startStop-1 : Loading DbSchema "labkey.dataintegration" (Module) INFO DbScope 2016-04-05 12:20:34,342 localhost-startStop-1 : Loading DbSchema "labkey.study" (Module) INFO DbScope 2016-04-05 12:20:34,356 localhost-startStop-1 : Loading DbSchema "labkey.studydataset" (Provisioned) INFO DbScope 2016-04-05 12:20:34,357 localhost-startStop-1 : Loading DbSchema "labkey.assayresult" (Provisioned) INFO DbScope 2016-04-05 12:20:34,357 localhost-startStop-1 : Loading DbSchema "labkey.studydesign" (Provisioned) INFO DbScope 2016-04-05 12:20:34,357 localhost-startStop-1 : Loading DbSchema "labkey.specimentables" (Provisioned) INFO DbScope 2016-04-05 12:20:34,357 localhost-startStop-1 : Loading DbSchema "labkey.luminex" (Module) INFO DbScope 2016-04-05 12:20:34,362 localhost-startStop-1 : Loading DbSchema "labkey.nab" (Module) INFO DbScope 2016-04-05 12:20:34,367 localhost-startStop-1 : Loading DbSchema "labkey.nabvirus" (Provisioned) INFO DbScope 2016-04-05 12:20:34,367 localhost-startStop-1 : Loading DbSchema "labkey.targetedms" (Module) INFO DbScope 2016-04-05 12:20:34,375 localhost-startStop-1 : Loading DbSchema "labkey.audit" (Provisioned) INFO DbScope 2016-04-05 12:20:34,375 localhost-startStop-1 : Loading DbSchema "labkey.elispotlk" (Module) INFO ModuleLoader 2016-04-05 12:20:34,455 localhost-startStop-1 : LabKey Server startup is complete; modules are being upgraded and initialized in the background INFO ModuleLoader 2016-04-05 12:20:34,455 Module Upgrade : Starting up modules INFO ViewServlet 2016-04-05 12:20:34,459 localhost-startStop-1 : ViewServlet initialized INFO ModuleLoader 2016-04-05 12:20:34,462 Module Upgrade : Starting module 'Core' INFO ViewServlet 2016-04-05 12:20:34,462 localhost-startStop-1 : WEBAPP: /usr/share/labkey/labkeywebapp INFO ViewServlet 2016-04-05 12:20:34,462 localhost-startStop-1 : PATH: /usr/local/tpp/bin:/bin:/usr/bin:/sbin:/usr/sbin INFO ModuleLoader 2016-04-05 12:20:35,434 Module Upgrade : Starting module 'Query' INFO ModuleLoader 2016-04-05 12:20:35,487 Module Upgrade : Starting module 'FCSExpress' INFO ModuleLoader 2016-04-05 12:20:35,504 Module Upgrade : Starting module 'Search' INFO ModuleLoader 2016-04-05 12:20:35,525 Module Upgrade : Starting module 'Wiki' INFO ModuleLoader 2016-04-05 12:20:35,532 Module Upgrade : Starting module 'Issues' INFO ModuleLoader 2016-04-05 12:20:35,543 Module Upgrade : Starting module 'Announcements' INFO ModuleLoader 2016-04-05 12:20:35,625 Module Upgrade : Starting module 'BigIron' INFO ModuleLoader 2016-04-05 12:20:35,626 Module Upgrade : Starting module 'Pipeline' INFO SpringModule 2016-04-05 12:20:35,626 Module Upgrade : Loading Spring configuration for the Pipeline module from [/WEB-INF/pipelineContext.xml] INFO SpringModule$1 2016-04-05 12:20:35,628 Module Upgrade : Refreshing Pipeline WebApplicationContext: startup date [Tue Apr 05 12:20:35 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 12:20:35,775 Module Upgrade : Starting module 'Experiment' INFO SpringModule 2016-04-05 12:20:35,775 Module Upgrade : Loading Spring configuration for the Experiment module from [/WEB-INF/experimentContext.xml] INFO SpringModule$1 2016-04-05 12:20:35,776 Module Upgrade : Refreshing Experiment WebApplicationContext: startup date [Tue Apr 05 12:20:35 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 12:20:36,018 Module Upgrade : Starting module 'Flow' INFO ModuleLoader 2016-04-05 12:20:36,055 Module Upgrade : Starting module 'Microarray' INFO SpringModule 2016-04-05 12:20:36,055 Module Upgrade : Loading Spring configuration for the Microarray module from [/WEB-INF/microarrayContext.xml] INFO SpringModule$1 2016-04-05 12:20:36,056 Module Upgrade : Refreshing Microarray WebApplicationContext: startup date [Tue Apr 05 12:20:36 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 12:20:36,107 Module Upgrade : Starting module 'FileContent' INFO ModuleLoader 2016-04-05 12:20:36,110 Module Upgrade : Starting module 'List' INFO ModuleLoader 2016-04-05 12:20:36,138 Module Upgrade : Starting module 'MS2' INFO SpringModule 2016-04-05 12:20:36,138 Module Upgrade : Loading Spring configuration for the MS2 module from [/WEB-INF/ms2Context.xml] INFO SpringModule$1 2016-04-05 12:20:36,139 Module Upgrade : Refreshing MS2 WebApplicationContext: startup date [Tue Apr 05 12:20:36 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 12:20:36,546 Module Upgrade : Starting module 'MS1' INFO SpringModule 2016-04-05 12:20:36,547 Module Upgrade : Loading Spring configuration for the MS1 module from [/WEB-INF/ms1Context.xml] INFO SpringModule$1 2016-04-05 12:20:36,548 Module Upgrade : Refreshing MS1 WebApplicationContext: startup date [Tue Apr 05 12:20:36 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 12:20:36,627 Module Upgrade : Starting module 'Survey' INFO ModuleLoader 2016-04-05 12:20:36,628 Module Upgrade : Starting module 'DataIntegration' INFO ModuleLoader 2016-04-05 12:20:36,639 Module Upgrade : Starting module 'Study' INFO SpringModule 2016-04-05 12:20:36,639 Module Upgrade : Loading Spring configuration for the Study module from [/WEB-INF/studyContext.xml] INFO SpringModule$1 2016-04-05 12:20:36,640 Module Upgrade : Refreshing Study WebApplicationContext: startup date [Tue Apr 05 12:20:36 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 12:20:36,844 Module Upgrade : Starting module 'Luminex' INFO ModuleLoader 2016-04-05 12:20:36,868 Module Upgrade : Starting module 'Visualization' INFO ModuleLoader 2016-04-05 12:20:36,869 Module Upgrade : Starting module 'Nab' INFO ModuleLoader 2016-04-05 12:20:36,888 Module Upgrade : Starting module 'Elisa' INFO ModuleLoader 2016-04-05 12:20:36,892 Module Upgrade : Starting module 'TargetedMS' INFO SpringModule 2016-04-05 12:20:36,892 Module Upgrade : Loading Spring configuration for the TargetedMS module from [/WEB-INF/targetedmsContext.xml] INFO SpringModule$1 2016-04-05 12:20:36,893 Module Upgrade : Refreshing TargetedMS WebApplicationContext: startup date [Tue Apr 05 12:20:36 CEST 2016]; parent: Root WebApplicationContext INFO ModuleLoader 2016-04-05 12:20:36,920 Module Upgrade : Starting module 'Audit' INFO ModuleLoader 2016-04-05 12:20:36,930 Module Upgrade : Starting module 'ELISpotAssay' INFO ModuleLoader 2016-04-05 12:20:36,936 Module Upgrade : Running startup listener: Audit Log INFO ModuleLoader 2016-04-05 12:20:36,936 Module Upgrade : Running startup listener: Search Service INFO ModuleLoader 2016-04-05 12:20:36,936 Module Upgrade : Running startup listener: PipelineJobRestarter INFO ModuleLoader 2016-04-05 12:20:36,939 Module Upgrade : Running startup listener: DataIntegration INFO ModuleLoader 2016-04-05 12:20:36,946 Module Upgrade : Module startup complete WARN AuthenticationManager 2016-04-05 12:28:41,488 http-apr-8443-exec-4 : andrej.studen@ijs.si failed to login: incorrect password WARN MailHelper 2016-04-05 12:30:26,837 http-apr-8443-exec-5 : Exception sending email; check your SMTP configuration in labkey.xml from: LabKey Server to: andrej.studen@ijs.si subject: Reset Password Notification from the LabKey Server Web Site com.sun.mail.util.MailConnectException: Couldn't connect to host, port: @@smtpHost@@, 25; timeout -1; nested exception is: java.net.UnknownHostException: @@smtpHost@@ at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:2053) at com.sun.mail.smtp.SMTPTransport.protocolConnect(SMTPTransport.java:697) at javax.mail.Service.connect(Service.java:364) at javax.mail.Service.connect(Service.java:245) at javax.mail.Service.connect(Service.java:194) at javax.mail.Transport.send0(Transport.java:253) at javax.mail.Transport.send(Transport.java:124) at org.labkey.api.util.MailHelper.send(MailHelper.java:199) at org.labkey.api.security.SecurityManager.sendEmail(SecurityManager.java:835) at org.labkey.core.login.LoginController$ResetPasswordAction.handlePost(LoginController.java:2244) at org.labkey.core.login.LoginController$ResetPasswordAction.handlePost(LoginController.java:2160) at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:101) at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:80) at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:216) at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:412) at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1281) at org.labkey.api.view.ViewServlet._service(ViewServlet.java:190) at org.labkey.api.view.ViewServlet.service(ViewServlet.java:124) at javax.servlet.http.HttpServlet.service(HttpServlet.java:725) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1144) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:180) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:506) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:537) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1081) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:658) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:277) at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2403) at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2392) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:745) Caused by: java.net.UnknownHostException: @@smtpHost@@ at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:589) at java.net.Socket.connect(Socket.java:538) at com.sun.mail.util.SocketFetcher.createSocket(SocketFetcher.java:312) at com.sun.mail.util.SocketFetcher.getSocket(SocketFetcher.java:236) at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:2019) ... 52 more WARN AuthenticationManager 2016-04-05 12:30:55,830 http-apr-8443-exec-5 : andrej.studen@ijs.si failed to login: incorrect password ERROR AuditLogImpl 2016-04-05 12:36:47,934 http-apr-8443-exec-6 : Failed to insert audit log event java.lang.NullPointerException: Could not find domain for AppPropsEvent at org.labkey.api.audit.AbstractAuditTypeProvider.createStorageTableInfo(AbstractAuditTypeProvider.java:227) at org.labkey.api.audit.provider.SiteSettingsAuditProvider.createTableInfo(SiteSettingsAuditProvider.java:90) at org.labkey.audit.query.AuditQuerySchema.createTable(AuditQuerySchema.java:90) at org.labkey.api.query.UserSchema._getTableOrQuery(UserSchema.java:212) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:157) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:149) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:248) at org.labkey.audit.model.LogManager._insertEvent(LogManager.java:92) at org.labkey.audit.AuditLogImpl._addEvent(AuditLogImpl.java:157) at org.labkey.audit.AuditLogImpl.addEvent(AuditLogImpl.java:100) at org.labkey.api.settings.AbstractWriteableSettingsGroup.writeAuditLogEvent(AbstractWriteableSettingsGroup.java:106) at org.labkey.core.admin.AdminController$CustomizeSiteAction.handlePost(AdminController.java:1294) at org.labkey.core.admin.AdminController$CustomizeSiteAction.handlePost(AdminController.java:1159) at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:101) at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:80) at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:216) at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:412) at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1281) at org.labkey.api.view.ViewServlet._service(ViewServlet.java:190) at org.labkey.api.view.ViewServlet.service(ViewServlet.java:124) at javax.servlet.http.HttpServlet.service(HttpServlet.java:725) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1144) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:180) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:506) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:537) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1081) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:658) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:277) at org.apache.tomcat.util.net.AprEndpoint$SocketWithOptionsProcessor.run(AprEndpoint.java:2340) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:745) ERROR ExceptionUtil 2016-04-05 12:36:47,935 http-apr-8443-exec-6 : Exception detected and logged to mothership java.lang.NullPointerException: Could not find domain for AppPropsEvent at org.labkey.api.audit.AbstractAuditTypeProvider.createStorageTableInfo(AbstractAuditTypeProvider.java:227) at org.labkey.api.audit.provider.SiteSettingsAuditProvider.createTableInfo(SiteSettingsAuditProvider.java:90) at org.labkey.audit.query.AuditQuerySchema.createTable(AuditQuerySchema.java:90) at org.labkey.api.query.UserSchema._getTableOrQuery(UserSchema.java:212) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:157) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:149) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:248) at org.labkey.audit.model.LogManager._insertEvent(LogManager.java:92) at org.labkey.audit.AuditLogImpl._addEvent(AuditLogImpl.java:157) at org.labkey.audit.AuditLogImpl.addEvent(AuditLogImpl.java:100) at org.labkey.api.settings.AbstractWriteableSettingsGroup.writeAuditLogEvent(AbstractWriteableSettingsGroup.java:106) at org.labkey.core.admin.AdminController$CustomizeSiteAction.handlePost(AdminController.java:1294) at org.labkey.core.admin.AdminController$CustomizeSiteAction.handlePost(AdminController.java:1159) at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:101) at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:80) at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:216) at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:412) at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1281) at org.labkey.api.view.ViewServlet._service(ViewServlet.java:190) at org.labkey.api.view.ViewServlet.service(ViewServlet.java:124) at javax.servlet.http.HttpServlet.service(HttpServlet.java:725) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1144) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:180) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:506) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:537) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1081) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:658) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:277) at org.apache.tomcat.util.net.AprEndpoint$SocketWithOptionsProcessor.run(AprEndpoint.java:2340) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:745) ERROR ExceptionUtil 2016-04-05 12:36:47,939 http-apr-8443-exec-6 : Unhandled exception: 500: Unexpected server error java.lang.NullPointerException: Could not find domain for AppPropsEvent at org.labkey.api.audit.AbstractAuditTypeProvider.createStorageTableInfo(AbstractAuditTypeProvider.java:227) at org.labkey.api.audit.provider.SiteSettingsAuditProvider.createTableInfo(SiteSettingsAuditProvider.java:90) at org.labkey.audit.query.AuditQuerySchema.createTable(AuditQuerySchema.java:90) at org.labkey.api.query.UserSchema._getTableOrQuery(UserSchema.java:212) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:157) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:149) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:248) at org.labkey.audit.model.LogManager._insertEvent(LogManager.java:92) at org.labkey.audit.AuditLogImpl._addEvent(AuditLogImpl.java:157) at org.labkey.audit.AuditLogImpl.addEvent(AuditLogImpl.java:100) at org.labkey.api.settings.AbstractWriteableSettingsGroup.writeAuditLogEvent(AbstractWriteableSettingsGroup.java:106) at org.labkey.core.admin.AdminController$CustomizeSiteAction.handlePost(AdminController.java:1294) at org.labkey.core.admin.AdminController$CustomizeSiteAction.handlePost(AdminController.java:1159) at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:101) at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:80) at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:216) at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:412) at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1281) at org.labkey.api.view.ViewServlet._service(ViewServlet.java:190) at org.labkey.api.view.ViewServlet.service(ViewServlet.java:124) at javax.servlet.http.HttpServlet.service(HttpServlet.java:725) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1144) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:180) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:506) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:537) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1081) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:658) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:277) at org.apache.tomcat.util.net.AprEndpoint$SocketWithOptionsProcessor.run(AprEndpoint.java:2340) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:745) ERROR AuditLogImpl 2016-04-05 12:41:26,144 http-apr-8443-exec-4 : Failed to insert audit log event java.lang.NullPointerException: Could not find domain for AppPropsEvent at org.labkey.api.audit.AbstractAuditTypeProvider.createStorageTableInfo(AbstractAuditTypeProvider.java:227) at org.labkey.api.audit.provider.SiteSettingsAuditProvider.createTableInfo(SiteSettingsAuditProvider.java:90) at org.labkey.audit.query.AuditQuerySchema.createTable(AuditQuerySchema.java:90) at org.labkey.api.query.UserSchema._getTableOrQuery(UserSchema.java:212) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:157) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:149) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:248) at org.labkey.audit.model.LogManager._insertEvent(LogManager.java:92) at org.labkey.audit.AuditLogImpl._addEvent(AuditLogImpl.java:157) at org.labkey.audit.AuditLogImpl.addEvent(AuditLogImpl.java:100) at org.labkey.api.settings.AbstractWriteableSettingsGroup.writeAuditLogEvent(AbstractWriteableSettingsGroup.java:106) at org.labkey.core.admin.AdminController$CustomizeSiteAction.handlePost(AdminController.java:1294) at org.labkey.core.admin.AdminController$CustomizeSiteAction.handlePost(AdminController.java:1159) at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:101) at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:80) at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:216) at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:412) at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1281) at org.labkey.api.view.ViewServlet._service(ViewServlet.java:190) at org.labkey.api.view.ViewServlet.service(ViewServlet.java:124) at javax.servlet.http.HttpServlet.service(HttpServlet.java:725) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1144) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:180) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:506) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:537) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1081) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:658) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:277) at org.apache.tomcat.util.net.AprEndpoint$SocketWithOptionsProcessor.run(AprEndpoint.java:2340) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:745) ERROR ExceptionUtil 2016-04-05 12:41:26,145 http-apr-8443-exec-4 : Exception detected and logged to mothership java.lang.NullPointerException: Could not find domain for AppPropsEvent at org.labkey.api.audit.AbstractAuditTypeProvider.createStorageTableInfo(AbstractAuditTypeProvider.java:227) at org.labkey.api.audit.provider.SiteSettingsAuditProvider.createTableInfo(SiteSettingsAuditProvider.java:90) at org.labkey.audit.query.AuditQuerySchema.createTable(AuditQuerySchema.java:90) at org.labkey.api.query.UserSchema._getTableOrQuery(UserSchema.java:212) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:157) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:149) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:248) at org.labkey.audit.model.LogManager._insertEvent(LogManager.java:92) at org.labkey.audit.AuditLogImpl._addEvent(AuditLogImpl.java:157) at org.labkey.audit.AuditLogImpl.addEvent(AuditLogImpl.java:100) at org.labkey.api.settings.AbstractWriteableSettingsGroup.writeAuditLogEvent(AbstractWriteableSettingsGroup.java:106) at org.labkey.core.admin.AdminController$CustomizeSiteAction.handlePost(AdminController.java:1294) at org.labkey.core.admin.AdminController$CustomizeSiteAction.handlePost(AdminController.java:1159) at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:101) at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:80) at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:216) at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:412) at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1281) at org.labkey.api.view.ViewServlet._service(ViewServlet.java:190) at org.labkey.api.view.ViewServlet.service(ViewServlet.java:124) at javax.servlet.http.HttpServlet.service(HttpServlet.java:725) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1144) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:180) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:506) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:537) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1081) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:658) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:277) at org.apache.tomcat.util.net.AprEndpoint$SocketWithOptionsProcessor.run(AprEndpoint.java:2340) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:745) ERROR ExceptionUtil 2016-04-05 12:41:26,146 http-apr-8443-exec-4 : Unhandled exception: 500: Unexpected server error java.lang.NullPointerException: Could not find domain for AppPropsEvent at org.labkey.api.audit.AbstractAuditTypeProvider.createStorageTableInfo(AbstractAuditTypeProvider.java:227) at org.labkey.api.audit.provider.SiteSettingsAuditProvider.createTableInfo(SiteSettingsAuditProvider.java:90) at org.labkey.audit.query.AuditQuerySchema.createTable(AuditQuerySchema.java:90) at org.labkey.api.query.UserSchema._getTableOrQuery(UserSchema.java:212) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:157) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:149) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:248) at org.labkey.audit.model.LogManager._insertEvent(LogManager.java:92) at org.labkey.audit.AuditLogImpl._addEvent(AuditLogImpl.java:157) at org.labkey.audit.AuditLogImpl.addEvent(AuditLogImpl.java:100) at org.labkey.api.settings.AbstractWriteableSettingsGroup.writeAuditLogEvent(AbstractWriteableSettingsGroup.java:106) at org.labkey.core.admin.AdminController$CustomizeSiteAction.handlePost(AdminController.java:1294) at org.labkey.core.admin.AdminController$CustomizeSiteAction.handlePost(AdminController.java:1159) at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:101) at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:80) at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:216) at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:412) at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1281) at org.labkey.api.view.ViewServlet._service(ViewServlet.java:190) at org.labkey.api.view.ViewServlet.service(ViewServlet.java:124) at javax.servlet.http.HttpServlet.service(HttpServlet.java:725) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1144) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:180) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:506) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:537) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1081) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:658) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:277) at org.apache.tomcat.util.net.AprEndpoint$SocketWithOptionsProcessor.run(AprEndpoint.java:2340) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:745) ERROR ExceptionUtil 2016-04-05 12:51:37,225 FifteenMinuteDigest : Exception detected and logged to mothership java.lang.NullPointerException: Could not find domain for FileSystem at org.labkey.api.audit.AbstractAuditTypeProvider.createStorageTableInfo(AbstractAuditTypeProvider.java:227) at org.labkey.api.audit.AbstractAuditTypeProvider.createTableInfo(AbstractAuditTypeProvider.java:234) at org.labkey.audit.query.AuditQuerySchema.createTable(AuditQuerySchema.java:90) at org.labkey.api.query.UserSchema._getTableOrQuery(UserSchema.java:212) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:157) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:149) at org.labkey.api.query.UserSchema.getTable(UserSchema.java:248) at org.labkey.filecontent.message.FileContentDigestProvider.sendDigestForAllContainers(FileContentDigestProvider.java:87) at org.labkey.api.message.digest.MessageDigest.sendMessageDigest(MessageDigest.java:69) at org.labkey.api.message.digest.MessageDigest$MessageDigestTask.run(MessageDigest.java:142) at java.util.TimerThread.mainLoop(Timer.java:555) at java.util.TimerThread.run(Timer.java:505)