INFO ModuleLoader 2018-02-16 07:21:29,617 localhost-startStop-1 : __ || | _ |_ |/ _ (? _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2018-02-16 07:21:32,236 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name: labkeyDataSource Server URL: jdbc:postgresql://localhost/labkey Database Product Name: PostgreSQL Database Product Version: 9.4.13 JDBC Driver Name: PostgreSQL Native Driver JDBC Driver Version: PostgreSQL 9.4.1210 SQL Dialect: PostgreSql94Dialect INFO SqlScriptRunner 2018-02-16 07:21:32,976 localhost-startStop-1 : Running [test-drop.sql] INFO SqlScriptManager 2018-02-16 07:21:32,980 localhost-startStop-1 : start running script : test-drop.sql INFO SqlScriptManager 2018-02-16 07:21:33,103 localhost-startStop-1 : finished running script : test-drop.sql INFO ScriptService$Console 2018-02-16 07:21:33,109 localhost-startStop-1 : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:21:33,119 localhost-startStop-1 : Running [prop-drop.sql] INFO SqlScriptManager 2018-02-16 07:21:33,120 localhost-startStop-1 : start running script : prop-drop.sql INFO SqlScriptManager 2018-02-16 07:21:33,126 localhost-startStop-1 : finished running script : prop-drop.sql INFO ScriptService$Console 2018-02-16 07:21:33,127 localhost-startStop-1 : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:21:33,129 localhost-startStop-1 : Running [core-drop.sql] INFO SqlScriptManager 2018-02-16 07:21:33,130 localhost-startStop-1 : start running script : core-drop.sql INFO SqlScriptManager 2018-02-16 07:21:33,143 localhost-startStop-1 : finished running script : core-drop.sql INFO ScriptService$Console 2018-02-16 07:21:33,145 localhost-startStop-1 : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:21:33,230 localhost-startStop-1 : Running [core-16.30-17.10.sql, core-17.20-17.30.sql] INFO SqlScriptManager 2018-02-16 07:21:33,238 localhost-startStop-1 : start running script : core-16.30-17.10.sql INFO SqlScriptManager 2018-02-16 07:21:33,292 localhost-startStop-1 : finished running script : core-16.30-17.10.sql INFO SqlScriptManager 2018-02-16 07:21:33,364 localhost-startStop-1 : start running script : core-17.20-17.30.sql INFO SqlScriptManager 2018-02-16 07:21:33,550 localhost-startStop-1 : finished running script : core-17.20-17.30.sql INFO ScriptService$Console 2018-02-16 07:21:33,563 localhost-startStop-1 : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:21:33,565 localhost-startStop-1 : Running [core-create.sql] INFO SqlScriptManager 2018-02-16 07:21:33,566 localhost-startStop-1 : start running script : core-create.sql INFO SqlScriptManager 2018-02-16 07:21:33,733 localhost-startStop-1 : finished running script : core-create.sql INFO ScriptService$Console 2018-02-16 07:21:33,735 localhost-startStop-1 : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:21:33,790 localhost-startStop-1 : Running [prop-create.sql] INFO SqlScriptManager 2018-02-16 07:21:33,790 localhost-startStop-1 : start running script : prop-create.sql INFO SqlScriptManager 2018-02-16 07:21:33,795 localhost-startStop-1 : finished running script : prop-create.sql INFO ScriptService$Console 2018-02-16 07:21:33,797 localhost-startStop-1 : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:21:33,843 localhost-startStop-1 : Running [test-create.sql] INFO SqlScriptManager 2018-02-16 07:21:33,844 localhost-startStop-1 : start running script : test-create.sql INFO SqlScriptManager 2018-02-16 07:21:33,864 localhost-startStop-1 : finished running script : test-create.sql INFO ScriptService$Console 2018-02-16 07:21:33,865 localhost-startStop-1 : Purging RhinoService caches INFO ModuleLoader 2018-02-16 07:21:42,211 localhost-startStop-1 : Modules requiring upgrade: [Wiki, Announcements, Internal, Query, BigIron, FCSExpress, Pipeline, Experiment, List, Flow, MS2, ELISpotAssay, TargetedMS, DataIntegration, Study, Luminex, Visualization, Elisa, Microarray, Survey, Search, Issues, API, MS1, Nab, Audit, FileContent] INFO ModuleLoader 2018-02-16 07:21:42,213 localhost-startStop-1 : LabKey Server startup is complete; modules are being upgraded and initialized in the background INFO ViewServlet 2018-02-16 07:21:42,221 localhost-startStop-1 : ViewServlet initialized INFO ViewServlet 2018-02-16 07:21:42,221 localhost-startStop-1 : WEBAPP: /usr/local/labkey/labkeywebapp INFO ViewServlet 2018-02-16 07:21:42,221 localhost-startStop-1 : PATH: /bin:/usr/bin:/sbin:/usr/sbin INFO DbScope 2018-02-16 07:21:42,293 Module Upgrade : no schema metadata xml file found for schema "umls" INFO SqlScriptRunner 2018-02-16 07:21:42,477 Module Upgrade : Running [study-drop.sql] INFO SqlScriptManager 2018-02-16 07:21:42,478 Module Upgrade : start running script : study-drop.sql INFO SqlScriptManager 2018-02-16 07:21:42,577 Module Upgrade : finished running script : study-drop.sql INFO ScriptService$Console 2018-02-16 07:21:42,579 Module Upgrade : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:21:42,776 Module Upgrade : Running [ms2-drop.sql] INFO SqlScriptManager 2018-02-16 07:21:42,776 Module Upgrade : start running script : ms2-drop.sql INFO SqlScriptManager 2018-02-16 07:21:42,867 Module Upgrade : finished running script : ms2-drop.sql INFO ScriptService$Console 2018-02-16 07:21:42,869 Module Upgrade : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:21:42,894 Module Upgrade : Running [exp-drop.sql] INFO SqlScriptManager 2018-02-16 07:21:42,895 Module Upgrade : start running script : exp-drop.sql INFO SqlScriptManager 2018-02-16 07:21:43,019 Module Upgrade : finished running script : exp-drop.sql INFO ScriptService$Console 2018-02-16 07:21:43,020 Module Upgrade : Purging RhinoService caches INFO DbScope 2018-02-16 07:21:43,080 Module Upgrade : no schema metadata xml file found for schema "junit" INFO SqlScriptRunner 2018-02-16 07:21:43,180 Module Upgrade : Running [comm-drop.sql] INFO SqlScriptManager 2018-02-16 07:21:43,180 Module Upgrade : start running script : comm-drop.sql INFO SqlScriptManager 2018-02-16 07:21:43,205 Module Upgrade : finished running script : comm-drop.sql INFO ScriptService$Console 2018-02-16 07:21:43,206 Module Upgrade : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:21:43,383 Module Upgrade : Running [comm-create.sql] INFO SqlScriptManager 2018-02-16 07:21:43,384 Module Upgrade : start running script : comm-create.sql INFO SqlScriptManager 2018-02-16 07:21:43,471 Module Upgrade : finished running script : comm-create.sql INFO ScriptService$Console 2018-02-16 07:21:43,472 Module Upgrade : Purging RhinoService caches INFO DbScope 2018-02-16 07:21:43,674 Module Upgrade : no schema metadata xml file found for schema "junit" INFO SqlScriptRunner 2018-02-16 07:21:43,712 Module Upgrade : Running [query-17.20-17.30.sql] INFO SqlScriptManager 2018-02-16 07:21:43,713 Module Upgrade : start running script : query-17.20-17.30.sql INFO SqlScriptManager 2018-02-16 07:21:43,879 Module Upgrade : finished running script : query-17.20-17.30.sql INFO ScriptService$Console 2018-02-16 07:21:43,931 Module Upgrade : Purging RhinoService caches INFO DbScope 2018-02-16 07:21:44,178 Module Upgrade : no schema metadata xml file found for schema "junit" INFO SqlScriptRunner 2018-02-16 07:21:44,270 Module Upgrade : Running [pipeline-17.20-17.30.sql] INFO SqlScriptManager 2018-02-16 07:21:44,271 Module Upgrade : start running script : pipeline-17.20-17.30.sql INFO SqlScriptManager 2018-02-16 07:21:44,399 Module Upgrade : finished running script : pipeline-17.20-17.30.sql INFO ScriptService$Console 2018-02-16 07:21:44,413 Module Upgrade : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:21:44,586 Module Upgrade : Running [exp-16.30-17.10.sql, exp-17.10-17.20.sql, exp-17.20-17.30.sql] INFO SqlScriptManager 2018-02-16 07:21:44,587 Module Upgrade : start running script : exp-16.30-17.10.sql INFO SqlScriptExecutor 2018-02-16 07:21:44,624 Module Upgrade : Executing ExperimentUpgradeCode.cleanupQuotedAliases(ModuleContext moduleContext) INFO ScriptService$Console 2018-02-16 07:21:44,625 Module Upgrade : Purging RhinoService caches INFO ScriptService$Console 2018-02-16 07:21:44,945 Module Upgrade : Purging RhinoService caches INFO SqlScriptManager 2018-02-16 07:21:44,981 Module Upgrade : finished running script : exp-16.30-17.10.sql INFO SqlScriptManager 2018-02-16 07:21:45,028 Module Upgrade : start running script : exp-17.10-17.20.sql INFO SqlScriptManager 2018-02-16 07:21:45,188 Module Upgrade : finished running script : exp-17.10-17.20.sql INFO SqlScriptManager 2018-02-16 07:21:45,200 Module Upgrade : start running script : exp-17.20-17.30.sql INFO SqlScriptExecutor 2018-02-16 07:21:45,361 Module Upgrade : Executing ExperimentUpgradeCode.saveMvIndicatorStorageNames(ModuleContext moduleContext) INFO ScriptService$Console 2018-02-16 07:21:45,362 Module Upgrade : Purging RhinoService caches ERROR ExceptionUtil 2018-02-16 07:21:45,787 http-nio-8080-exec-4 : Unhandled exception: 500: Unexpected server error java.lang.ExceptionInInitializerError at org.labkey.api.view.JspView.(JspView.java:89) at org.labkey.api.view.JspView.(JspView.java:79) at org.labkey.core.CoreController$ThemeStylesheetAction.getContent(CoreController.java:318) at org.labkey.core.CoreController$BaseStylesheetAction.export(CoreController.java:279) at org.labkey.core.CoreController$ThemeStylesheetAction.export(CoreController.java:298) at org.labkey.api.action.ExportAction.getView(ExportAction.java:53) at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:82) at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:177) at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:414) at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1228) at org.labkey.api.view.ViewServlet._service(ViewServlet.java:205) at org.labkey.api.view.ViewServlet.service(ViewServlet.java:132) 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:1148) 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:217) 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$AbstractConnectionHandler.process(AbstractProtocol.java:658) at org.apache.coyote.http11.Http11NioProtocol$Http11ConnectionHandler.process(Http11NioProtocol.java:222) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1580) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1537) 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.lang.NullPointerException at org.labkey.api.jsp.JspClassLoader.(JspClassLoader.java:49) at org.labkey.api.jsp.JspLoader.(JspLoader.java:42) ... 47 more ERROR ExceptionUtil 2018-02-16 07:21:45,793 http-nio-8080-exec-4 : Exception detected java.lang.ExceptionInInitializerError at org.labkey.api.view.JspView.(JspView.java:89) at org.labkey.api.view.JspView.(JspView.java:79) at org.labkey.core.CoreController$ThemeStylesheetAction.getContent(CoreController.java:318) at org.labkey.core.CoreController$BaseStylesheetAction.export(CoreController.java:279) at org.labkey.core.CoreController$ThemeStylesheetAction.export(CoreController.java:298) at org.labkey.api.action.ExportAction.getView(ExportAction.java:53) at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:82) at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:177) at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:414) at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1228) at org.labkey.api.view.ViewServlet._service(ViewServlet.java:205) at org.labkey.api.view.ViewServlet.service(ViewServlet.java:132) 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:1148) 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:217) 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.Http11NioProtocol$Http11ConnectionHandler.process(Http11NioProtocol.java:222) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1580) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1537) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:745) Caused by: java.lang.NullPointerException at org.labkey.api.jsp.JspClassLoader.(JspClassLoader.java:49) at org.labkey.api.jsp.JspLoader.(JspLoader.java:42) ... 47 more INFO ScriptService$Console 2018-02-16 07:21:45,976 Module Upgrade : Purging RhinoService caches INFO SqlScriptManager 2018-02-16 07:21:45,976 Module Upgrade : finished running script : exp-17.20-17.30.sql INFO ScriptService$Console 2018-02-16 07:21:46,033 Module Upgrade : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:21:46,034 Module Upgrade : Running [exp-create.sql] INFO SqlScriptManager 2018-02-16 07:21:46,039 Module Upgrade : start running script : exp-create.sql INFO SqlScriptManager 2018-02-16 07:21:46,141 Module Upgrade : finished running script : exp-create.sql INFO ScriptService$Console 2018-02-16 07:21:46,142 Module Upgrade : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:21:46,317 Module Upgrade : Running [ms2-16.30-17.10.sql] INFO SqlScriptManager 2018-02-16 07:21:46,317 Module Upgrade : start running script : ms2-16.30-17.10.sql INFO SqlScriptManager 2018-02-16 07:21:46,330 Module Upgrade : finished running script : ms2-16.30-17.10.sql INFO ScriptService$Console 2018-02-16 07:21:46,337 Module Upgrade : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:21:46,338 Module Upgrade : Running [ms2-create.sql] INFO SqlScriptManager 2018-02-16 07:21:46,339 Module Upgrade : start running script : ms2-create.sql INFO SqlScriptManager 2018-02-16 07:21:46,427 Module Upgrade : finished running script : ms2-create.sql INFO ScriptService$Console 2018-02-16 07:21:46,428 Module Upgrade : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:21:46,538 Module Upgrade : Running [targetedms-16.30-17.10.sql, targetedms-17.10-17.20.sql, targetedms-17.20-17.30.sql] INFO SqlScriptManager 2018-02-16 07:21:46,539 Module Upgrade : start running script : targetedms-16.30-17.10.sql INFO SqlScriptManager 2018-02-16 07:22:07,623 Module Upgrade : finished running script : targetedms-16.30-17.10.sql INFO SqlScriptManager 2018-02-16 07:22:07,632 Module Upgrade : start running script : targetedms-17.10-17.20.sql INFO SqlScriptExecutor 2018-02-16 07:22:08,340 Module Upgrade : Executing TargetedMSUpgradeCode.updateExperimentAnnotations(ModuleContext moduleContext) INFO ScriptService$Console 2018-02-16 07:22:08,341 Module Upgrade : Purging RhinoService caches INFO ScriptService$Console 2018-02-16 07:22:08,393 Module Upgrade : Purging RhinoService caches INFO SqlScriptManager 2018-02-16 07:22:08,393 Module Upgrade : finished running script : targetedms-17.10-17.20.sql INFO SqlScriptManager 2018-02-16 07:22:08,445 Module Upgrade : start running script : targetedms-17.20-17.30.sql INFO SqlScriptManager 2018-02-16 07:22:09,240 Module Upgrade : finished running script : targetedms-17.20-17.30.sql INFO ScriptService$Console 2018-02-16 07:22:09,253 Module Upgrade : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:22:09,360 Module Upgrade : Running [study-17.10-17.20.sql, study-17.20-17.30.sql] INFO SqlScriptManager 2018-02-16 07:22:09,361 Module Upgrade : start running script : study-17.10-17.20.sql INFO SqlScriptManager 2018-02-16 07:22:09,517 Module Upgrade : finished running script : study-17.10-17.20.sql INFO SqlScriptManager 2018-02-16 07:22:09,523 Module Upgrade : start running script : study-17.20-17.30.sql INFO SqlScriptExecutor 2018-02-16 07:22:09,529 Module Upgrade : Executing StudyUpgradeCode.moveQCStateToCore(ModuleContext moduleContext) INFO ScriptService$Console 2018-02-16 07:22:09,530 Module Upgrade : Purging RhinoService caches INFO ScriptService$Console 2018-02-16 07:22:09,566 Module Upgrade : Purging RhinoService caches INFO SqlScriptManager 2018-02-16 07:22:09,626 Module Upgrade : finished running script : study-17.20-17.30.sql INFO ScriptService$Console 2018-02-16 07:22:09,668 Module Upgrade : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:22:09,669 Module Upgrade : Running [study-create.sql] INFO SqlScriptManager 2018-02-16 07:22:09,669 Module Upgrade : start running script : study-create.sql INFO SqlScriptManager 2018-02-16 07:22:09,698 Module Upgrade : finished running script : study-create.sql INFO ScriptService$Console 2018-02-16 07:22:09,699 Module Upgrade : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:22:09,806 Module Upgrade : Running [luminex-16.30-17.10.sql] INFO SqlScriptManager 2018-02-16 07:22:09,806 Module Upgrade : start running script : luminex-16.30-17.10.sql INFO SqlScriptManager 2018-02-16 07:22:09,842 Module Upgrade : finished running script : luminex-16.30-17.10.sql INFO ScriptService$Console 2018-02-16 07:22:09,855 Module Upgrade : Purging RhinoService caches INFO SqlScriptRunner 2018-02-16 07:22:09,958 Module Upgrade : Running [microarray-17.20-17.30.sql] INFO SqlScriptManager 2018-02-16 07:22:09,958 Module Upgrade : start running script : microarray-17.20-17.30.sql INFO SqlScriptManager 2018-02-16 07:22:09,968 Module Upgrade : finished running script : microarray-17.20-17.30.sql INFO ScriptService$Console 2018-02-16 07:22:09,976 Module Upgrade : Purging RhinoService caches INFO DbScope 2018-02-16 07:22:10,082 Module Upgrade : no schema metadata xml file found for schema "umls" INFO SqlScriptRunner 2018-02-16 07:22:10,135 Module Upgrade : Running [nab-16.30-17.10.sql] INFO SqlScriptManager 2018-02-16 07:22:10,136 Module Upgrade : start running script : nab-16.30-17.10.sql INFO SqlScriptManager 2018-02-16 07:22:10,239 Module Upgrade : finished running script : nab-16.30-17.10.sql INFO ScriptService$Console 2018-02-16 07:22:10,252 Module Upgrade : Purging RhinoService caches INFO ModuleLoader 2018-02-16 07:22:10,624 Module Upgrade : Starting up modules INFO ModuleLoader 2018-02-16 07:22:10,624 Module Upgrade : Starting module 'Core' INFO ModuleLoader 2018-02-16 07:22:12,428 Module Upgrade : Starting module 'Wiki' INFO ModuleLoader 2018-02-16 07:22:12,434 Module Upgrade : Starting module 'Announcements' INFO ModuleLoader 2018-02-16 07:22:12,586 Module Upgrade : Starting module 'Internal' INFO ModuleLoader 2018-02-16 07:22:12,587 Module Upgrade : Starting module 'Query' INFO ModuleLoader 2018-02-16 07:22:12,914 Module Upgrade : Starting module 'BigIron' INFO ModuleLoader 2018-02-16 07:22:12,915 Module Upgrade : Starting module 'FCSExpress' INFO ModuleLoader 2018-02-16 07:22:12,923 Module Upgrade : Starting module 'Pipeline' INFO SpringModule 2018-02-16 07:22:12,924 Module Upgrade : Loading Spring configuration for the Pipeline module from [/WEB-INF/pipelineContext.xml] INFO SpringModule$1 2018-02-16 07:22:12,926 Module Upgrade : Refreshing Pipeline WebApplicationContext: startup date [Fri Feb 16 07:22:12 UTC 2018]; parent: Root WebApplicationContext INFO ModuleLoader 2018-02-16 07:22:13,399 Module Upgrade : Starting module 'Experiment' INFO SpringModule 2018-02-16 07:22:13,400 Module Upgrade : Loading Spring configuration for the Experiment module from [/WEB-INF/experimentContext.xml] INFO SpringModule$1 2018-02-16 07:22:13,401 Module Upgrade : Refreshing Experiment WebApplicationContext: startup date [Fri Feb 16 07:22:13 UTC 2018]; parent: Root WebApplicationContext INFO ModuleLoader 2018-02-16 07:22:13,809 Module Upgrade : Starting module 'List' INFO ModuleLoader 2018-02-16 07:22:14,056 Module Upgrade : Starting module 'Flow' INFO SpringModule 2018-02-16 07:22:14,057 Module Upgrade : Loading Spring configuration for the Flow module from [/WEB-INF/flowContext.xml] INFO SpringModule$1 2018-02-16 07:22:14,058 Module Upgrade : Refreshing Flow WebApplicationContext: startup date [Fri Feb 16 07:22:14 UTC 2018]; parent: Root WebApplicationContext INFO ModuleLoader 2018-02-16 07:22:14,125 Module Upgrade : Starting module 'MS2' INFO SpringModule 2018-02-16 07:22:14,126 Module Upgrade : Loading Spring configuration for the MS2 module from [/WEB-INF/ms2Context.xml] INFO SpringModule$1 2018-02-16 07:22:14,132 Module Upgrade : Refreshing MS2 WebApplicationContext: startup date [Fri Feb 16 07:22:14 UTC 2018]; parent: Root WebApplicationContext INFO ModuleLoader 2018-02-16 07:22:14,743 Module Upgrade : Starting module 'ELISpotAssay' INFO ModuleLoader 2018-02-16 07:22:14,750 Module Upgrade : Starting module 'TargetedMS' INFO SpringModule 2018-02-16 07:22:14,750 Module Upgrade : Loading Spring configuration for the TargetedMS module from [/WEB-INF/targetedmsContext.xml] INFO SpringModule$1 2018-02-16 07:22:14,751 Module Upgrade : Refreshing TargetedMS WebApplicationContext: startup date [Fri Feb 16 07:22:14 UTC 2018]; parent: Root WebApplicationContext INFO ModuleLoader 2018-02-16 07:22:14,918 Module Upgrade : Starting module 'DataIntegration' INFO ModuleLoader 2018-02-16 07:22:14,928 Module Upgrade : Starting module 'Study' INFO SpringModule 2018-02-16 07:22:14,929 Module Upgrade : Loading Spring configuration for the Study module from [/WEB-INF/studyContext.xml] INFO SpringModule$1 2018-02-16 07:22:14,930 Module Upgrade : Refreshing Study WebApplicationContext: startup date [Fri Feb 16 07:22:14 UTC 2018]; parent: Root WebApplicationContext INFO ModuleLoader 2018-02-16 07:22:15,564 Module Upgrade : Starting module 'Luminex' INFO ModuleLoader 2018-02-16 07:22:15,576 Module Upgrade : Starting module 'Visualization' INFO ModuleLoader 2018-02-16 07:22:15,579 Module Upgrade : Starting module 'Elisa' INFO ModuleLoader 2018-02-16 07:22:15,582 Module Upgrade : Starting module 'Microarray' INFO SpringModule 2018-02-16 07:22:15,583 Module Upgrade : Loading Spring configuration for the Microarray module from [/WEB-INF/microarrayContext.xml] INFO SpringModule$1 2018-02-16 07:22:15,584 Module Upgrade : Refreshing Microarray WebApplicationContext: startup date [Fri Feb 16 07:22:15 UTC 2018]; parent: Root WebApplicationContext INFO ModuleLoader 2018-02-16 07:22:15,612 Module Upgrade : Starting module 'Survey' INFO ModuleLoader 2018-02-16 07:22:15,613 Module Upgrade : Starting module 'Search' INFO ModuleLoader 2018-02-16 07:22:15,653 Module Upgrade : Starting module 'Issues' INFO ModuleLoader 2018-02-16 07:22:15,669 Module Upgrade : Starting module 'API' INFO ModuleLoader 2018-02-16 07:22:15,669 Module Upgrade : Starting module 'MS1' INFO SpringModule 2018-02-16 07:22:15,670 Module Upgrade : Loading Spring configuration for the MS1 module from [/WEB-INF/ms1Context.xml] INFO SpringModule$1 2018-02-16 07:22:15,671 Module Upgrade : Refreshing MS1 WebApplicationContext: startup date [Fri Feb 16 07:22:15 UTC 2018]; parent: Root WebApplicationContext INFO ModuleLoader 2018-02-16 07:22:15,756 Module Upgrade : Starting module 'Nab' INFO ModuleLoader 2018-02-16 07:22:15,778 Module Upgrade : Starting module 'Audit' INFO ModuleLoader 2018-02-16 07:22:15,816 Module Upgrade : Starting module 'FileContent' INFO ModuleLoader 2018-02-16 07:22:15,822 Module Upgrade : Running startup listener: Audit Log INFO ModuleLoader 2018-02-16 07:22:16,283 Module Upgrade : Running startup listener: Search Service: clear indexes INFO ModuleLoader 2018-02-16 07:22:16,536 Module Upgrade : Running startup listener: Schedule Upgrade Check INFO ModuleLoader 2018-02-16 07:22:16,538 Module Upgrade : Running startup listener: PipelineJobRestarter INFO ModuleLoader 2018-02-16 07:22:16,540 Module Upgrade : Running startup listener: DataIntegration INFO ModuleLoader 2018-02-16 07:22:16,561 Module Upgrade : Running startup listener: Search Service INFO ModuleLoader 2018-02-16 07:22:16,835 Module Upgrade : Module startup complete WARN AuthenticationManager 2018-02-16 07:22:20,748 http-nio-8080-exec-6 : qc_munin@omics.se failed to login: invalid credentials