Null pointer exceptions after upgrading source from 1.5.3 to 1.5.4

[David Just]

I Pulled  the latest 1.5.4 sources into my clone, merged my changes and built XNAT.  Unfortunately things don’t seem to be going well.  I’m getting the following in my tomcat logs:

java.lang.NullPointerException
    at org.nrg.xdat.om.base.BaseXnatProjectdata.getArcSpecification(BaseXnatProjectdata.java:1513)
    at org.nrg.xdat.om.base.BaseXnatProjectdata.getRootArchivePath(BaseXnatProjectdata.java:712)
    at org.nrg.xdat.om.base.BaseXnatProjectdata.getExpectedCurrentDirectory(BaseXnatProjectdata.java:2099)
    at org.nrg.xdat.om.base.BaseXnatProjectdata.preSave(BaseXnatProjectdata.java:2055)
    at org.nrg.xft.utils.SaveItemHelper.save(SaveItemHelper.java:58)
    at org.nrg.xft.utils.SaveItemHelper.authorizedSave(SaveItemHelper.java:208)
    at org.nrg.xnat.restlet.resources.ProjectResource.handlePut(ProjectResource.java:225)
    at org.restlet.Finder.handle(Finder.java:359)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at org.restlet.Filter.handle(Filter.java:195)
    at org.restlet.Router.handle(Router.java:504)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at org.restlet.Filter.handle(Filter.java:195)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at org.restlet.Filter.handle(Filter.java:195)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at org.restlet.Filter.handle(Filter.java:195)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at com.noelios.restlet.StatusFilter.doHandle(StatusFilter.java:130)
    at org.restlet.Filter.handle(Filter.java:195)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at org.restlet.Filter.handle(Filter.java:195)
    at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:124)
    at com.noelios.restlet.application.ApplicationHelper.handle(ApplicationHelper.java:112)
    at org.restlet.Application.handle(Application.java:341)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at org.restlet.Filter.handle(Filter.java:195)
    at org.restlet.Router.handle(Router.java:504)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at org.restlet.Filter.handle(Filter.java:195)
    at org.restlet.Router.handle(Router.java:504)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at com.noelios.restlet.StatusFilter.doHandle(StatusFilter.java:130)
    at org.restlet.Filter.handle(Filter.java:195)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at org.restlet.Filter.handle(Filter.java:195)
    at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:124)
    at org.restlet.Component.handle(Component.java:673)
    at org.restlet.Server.handle(Server.java:331)
    at com.noelios.restlet.ServerHelper.handle(ServerHelper.java:68)
    at com.noelios.restlet.http.HttpServerHelper.handle(HttpServerHelper.java:147)
    at com.noelios.restlet.ext.servlet.ServerServlet.service(ServerServlet.java:881)
    at org.nrg.xnat.restlet.servlet.XNATRestletServlet.service(XNATRestletServlet.java:99)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:470)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
    at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)
    at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)
    at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
    at java.lang.Thread.run(Thread.java:680)


And a bunch of errors in my application.log  

java.lang.NullPointerException
    at org.nrg.xnat.restlet.resources.ScanList.<init>(ScanList.java:55)
    at sun.reflect.GeneratedConstructorAccessor38.newInstance(Unknown Source)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
    at org.restlet.Finder.createTarget(Finder.java:181)
    at org.restlet.Finder.createTarget(Finder.java:226)
    at org.restlet.Finder.findTarget(Finder.java:240)
    at org.restlet.Finder.handle(Finder.java:329)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at org.restlet.Filter.handle(Filter.java:195)
    at org.restlet.Router.handle(Router.java:504)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at org.restlet.Filter.handle(Filter.java:195)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at org.restlet.Filter.handle(Filter.java:195)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at org.restlet.Filter.handle(Filter.java:195)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at com.noelios.restlet.StatusFilter.doHandle(StatusFilter.java:130)
    at org.restlet.Filter.handle(Filter.java:195)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at org.restlet.Filter.handle(Filter.java:195)
    at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:124)
    at com.noelios.restlet.application.ApplicationHelper.handle(ApplicationHelper.java:112)
    at org.restlet.Application.handle(Application.java:341)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at org.restlet.Filter.handle(Filter.java:195)
    at org.restlet.Router.handle(Router.java:504)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at org.restlet.Filter.handle(Filter.java:195)
    at org.restlet.Router.handle(Router.java:504)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at com.noelios.restlet.StatusFilter.doHandle(StatusFilter.java:130)
    at org.restlet.Filter.handle(Filter.java:195)
    at org.restlet.Filter.doHandle(Filter.java:150)
    at org.restlet.Filter.handle(Filter.java:195)
    at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:124)
    at org.restlet.Component.handle(Component.java:673)
    at org.restlet.Server.handle(Server.java:331)
    at com.noelios.restlet.ServerHelper.handle(ServerHelper.java:68)
    at com.noelios.restlet.http.HttpServerHelper.handle(HttpServerHelper.java:147)
    at com.noelios.restlet.ext.servlet.ServerServlet.service(ServerServlet.java:881)
    at org.nrg.xnat.restlet.servlet.XNATRestletServlet.service(XNATRestletServlet.java:99)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:470)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
    at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)
    at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)
    at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
    at java.lang.Thread.run(Thread.java:680)
2012-04-04 10:25:50,346 [org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-6] ERROR org.quartz.core.JobRunShell - Job prearchive-jobs.session-rebuilder threw an unhandled Exception:
java.lang.NullPointerException
    at org.nrg.xnat.helpers.prearchive.SessionXMLRebuilderJob.execute(SessionXMLRebuilderJob.java:67)
    at org.nrg.schedule.DelegatingJobBean.executeInternal(DelegatingJobBean.java:55)
    at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)
    at org.quartz.core.JobRunShell.run(JobRunShell.java:216)
    at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:549)
2012-04-04 10:25:50,346 [org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-6] ERROR org.quartz.core.ErrorLogger - Job (prearchive-jobs.session-rebuilder threw an exception.
org.quartz.SchedulerException: Job threw an unhandled exception. [See nested exception: java.lang.NullPointerException]
    at org.quartz.core.JobRunShell.run(JobRunShell.java:227)
    at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:549)
Caused by: java.lang.NullPointerException
    at org.nrg.xnat.helpers.prearchive.SessionXMLRebuilderJob.execute(SessionXMLRebuilderJob.java:67)
    at org.nrg.schedule.DelegatingJobBean.executeInternal(DelegatingJobBean.java:55)
    at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)
    at org.quartz.core.JobRunShell.run(JobRunShell.java:216)
    ... 1 more

[Olsen, Tim]

David, 

 

It looks like your archive specification wasn’t initialized properly.  When you logged in, did you get routed to the settings page? 

 

Also, I pushed up minor fixes for these NullPointerExceptions (bitbucket/nrg/xnat_builder_1_5dev).

 

Tim

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[David Just]

Pulling your new changes and rebuilding again cleared up a lot of the errors,

But I’m still getting the following on a clean re-build right after setting the default setting( In xdat.log)


2012-04-04 16:14:13,308 [http-8080-2] ERROR org.nrg.xnat.turbine.utils.ArcSpecManager -
java.lang.NullPointerException
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase.getPrearcPath(PrearcDatabase.java:121)
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase.initDatabase(PrearcDatabase.java:100)
    at org.nrg.xnat.turbine.utils.ArcSpecManager.GetInstance(ArcSpecManager.java:214)
    at org.nrg.xnat.turbine.utils.ArcSpecManager.GetInstance(ArcSpecManager.java:48)
    at org.nrg.xnat.turbine.modules.screens.EditArcSpecs.doBuildTemplate(EditArcSpecs.java:24)
    at org.nrg.xdat.turbine.modules.screens.SecureScreen.doBuildTemplate(SecureScreen.java:85)
    at org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:100)
    at org.apache.turbine.modules.Screen.build(Screen.java:57)
    at org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:104)
    at org.apache.turbine.modules.ScreenLoader.exec(ScreenLoader.java:119)
    at org.apache.turbine.modules.screens.TemplateScreen.doRedirect(TemplateScreen.java:163)
    at org.apache.turbine.modules.screens.TemplateScreen.doRedirect(TemplateScreen.java:187)
    at org.nrg.xnat.turbine.modules.screens.Index.doBuildTemplate(Index.java:26)
    at org.nrg.xdat.turbine.modules.screens.SecureScreen.doBuildTemplate(SecureScreen.java:85)
    at org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:100)
    at org.apache.turbine.modules.Screen.build(Screen.java:57)
    at org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:104)
    at org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyLayout.java:92)
    at org.apache.turbine.modules.Layout.build(Layout.java:53)
    at org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)
    at org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:146)
    at org.apache.turbine.modules.Page.build(Page.java:53)
    at org.apache.turbine.modules.PageLoader.exec(PageLoader.java:98)
    at org.apache.turbine.Turbine.doGet(Turbine.java:751)
    at org.apache.turbine.Turbine.doPost(Turbine.java:846)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:637)

    at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:470)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
    at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)
    at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)
    at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
    at java.lang.Thread.run(Thread.java:680)

2012-04-04 16:14:14,914 [org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-3] ERROR org.nrg.xnat.helpers.prearchive.PrearcTableBuilder -
org.postgresql.util.PSQLException: ERROR: relation "xdat_search.prearchive" does not exist

    at org.postgresql.util.PSQLException.parseServerError(PSQLException.java:139)
    at org.postgresql.core.QueryExecutor.executeV3(QueryExecutor.java:152)
    at org.postgresql.core.QueryExecutor.execute(QueryExecutor.java:100)
    at org.postgresql.core.QueryExecutor.execute(QueryExecutor.java:43)
    at org.postgresql.jdbc1.AbstractJdbc1Statement.execute(AbstractJdbc1Statement.java:517)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:50)
    at org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc1Statement.java:233)
    at org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc1Statement.java:221)
    at org.apache.commons.dbcp.DelegatingStatement.executeQuery(DelegatingStatement.java:205)
    at org.nrg.xft.db.PoolDBUtils.executeQuery(PoolDBUtils.java:876)
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase$22.op(PrearcDatabase.java:1249)
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase$22.op(PrearcDatabase.java:1247)
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase$SessionOp.run(PrearcDatabase.java:1661)
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase.getAllSessions(PrearcDatabase.java:1247)
    at org.nrg.xnat.helpers.prearchive.SessionXMLRebuilderJob.execute(SessionXMLRebuilderJob.java:57)

    at org.nrg.schedule.DelegatingJobBean.executeInternal(DelegatingJobBean.java:55)
    at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)
    at org.quartz.core.JobRunShell.run(JobRunShell.java:216)
    at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:549)

2012-04-04 16:14:14,915 [org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-3] ERROR org.nrg.xnat.helpers.prearchive.SessionXMLRebuilderJob -
org.postgresql.util.PSQLException: ERROR: relation "xdat_search.prearchive" does not exist

    at org.postgresql.util.PSQLException.parseServerError(PSQLException.java:139)
    at org.postgresql.core.QueryExecutor.executeV3(QueryExecutor.java:152)
    at org.postgresql.core.QueryExecutor.execute(QueryExecutor.java:100)
    at org.postgresql.core.QueryExecutor.execute(QueryExecutor.java:43)
    at org.postgresql.jdbc1.AbstractJdbc1Statement.execute(AbstractJdbc1Statement.java:517)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:50)
    at org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc1Statement.java:233)
    at org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc1Statement.java:221)
    at org.apache.commons.dbcp.DelegatingStatement.executeQuery(DelegatingStatement.java:205)
    at org.nrg.xft.db.PoolDBUtils.executeQuery(PoolDBUtils.java:876)
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase$22.op(PrearcDatabase.java:1249)
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase$22.op(PrearcDatabase.java:1247)
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase$SessionOp.run(PrearcDatabase.java:1661)
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase.getAllSessions(PrearcDatabase.java:1247)
    at org.nrg.xnat.helpers.prearchive.SessionXMLRebuilderJob.execute(SessionXMLRebuilderJob.java:57)

[Herrick, Rick]

Yeah, that’s a very annoying but ultimately harmless message. The scheduled XML rebuild task is trying to access the prearchive folder and database, but it just doesn’t exist yet. This task never learns its lesson and will continue doing that until such time as you first log in and initialize the prearchive infrastructure. We have a bug filed for that, but it hasn’t gotten fixed yet.

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