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[Users] Couldn't Store Trigger - UbuntuInstallIssue

Sorry, didn't mean Tomcat ... Postgres, of course :)
Janus Engstrøm
Sent by: [email protected]
18-11-2011 12:28
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[email protected]

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[email protected]
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Re: [Developers] [Users] Couldn't Store Trigger - UbuntuInstallIssue

Hi Shaun,
This about OC not working with Postgres 9.0, is this true for Ubuntu/Linux only, or is it a Windows issue as well? I'm running our production instance on a 9.0 version of Tomcat (OC 3.0.4.2) and haven't encountered any problems? Windows 2008R2 Enterprise.
Best regards,
Janus
Shaun Martin
Sent by: [email protected]
17-11-2011 21:31
Please respond to
[email protected]

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,
cc

Subject
Re: [Developers] [Users] Couldn't Store Trigger - Ubuntu InstallIssue

Hi Michael,
If OpenClinica connects and builds the database your configuration is fine. The issue would then lie with your database itself or the database server. Of the top of my head I would guess you have Postgres 9.0 installed and OpenClinica does not work with 9.0. Please note the OpenClinica installation instructions as written exactly will work on Ubuntu and return you a working OpenClinica system. I recommend rebuilding the server and following our instructions to fix your issue.
Thanks,
Shaun
On 11/17/11 02:57 PM, "Michael Zdanis" wrote:
Hello,
I am attempting to install OpenClinica-3.1.1-Community for evaluation on an Ubuntu 11.10 system that was built from bare iron for the purpose. Ubunutu isn’t wild about having tomcat and java installed per the OC directions, so after a couple of attempts we allowed the main system to install and config PostgreSQL, and tomcat. Removed the pl/pgsql extension from template1 (a default you can’t get around with the base install) and changed the addressing in datainfo.properties to point to catalina.base rather than catalina.home since the OpenClinica files sit in /var/lib/tomcat6/webapps in this installation. On initial run, OpenClinica hits the database, builds 101 tables, 72 sequences, 2 functions, 9 trigger functions, and 1 view and then bombs with a series of errors. An exemplar of the error in the localhost.yyyy-mm-dd.log file is shown below. At this point I’m a bit stuck. Any direction is appreciated.
Nov 16, 2011 4:29:09 PM org.apache.catalina.core.StandardContext listenerStop
SEVERE: Exception sending context destroyed event to listener instance of class org.akaza.openclinica.control.OCServletContextListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'schedulerFactoryBean' defined in URL [jar:file:/var/lib/tomcat6/webapps/OpenClinica/WEB-INF/lib/OpenClinica-core-3.1.1-Community.jar!/org/akaza/openclinica/applicationContext-core-scheduler.xml]: Invocation of init method failed; nested exception is org.quartz.JobPersistenceException: Couldn't store trigger 'legacyJobTrigger' for 'legacyJobDetail' job:invalid stream header: BB656430 [See nested exception: java.io.StreamCorruptedException: invalid stream header: BB656430]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:291)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:563)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:895)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:425)
at org.springframework.web.context.ContextLoader.createWebApplicationContext(ContextLoader.java:276)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:197)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
at org.akaza.openclinica.dao.core.OCContextLoaderListener.contextInitialized(OCContextLoaderListener.java:22)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4206)
at org.apache.catalina.core.StandardContext.start(StandardContext.java:4705)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:943)
at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:778)
at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:504)
at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1315)
at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:324)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1061)
at org.apache.catalina.core.StandardHost.start(StandardHost.java:840)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:463)
at org.apache.catalina.core.StandardService.start(StandardService.java:525)
at org.apache.catalina.core.StandardServer.start(StandardServer.java:754)
at org.apache.catalina.startup.Catalina.start(Catalina.java:595)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
Caused by: org.quartz.JobPersistenceException: Couldn't store trigger 'legacyJobTrigger' for 'legacyJobDetail' job:invalid stream header: BB656430 [See nested exception: java.io.StreamCorruptedException: invalid stream header: BB656430]
at org.quartz.impl.jdbcjobstore.JobStoreSupport.storeTrigger(JobStoreSupport.java:1245)
at org.quartz.impl.jdbcjobstore.JobStoreSupport$5.execute(JobStoreSupport.java:1151)
at org.quartz.impl.jdbcjobstore.JobStoreSupport$40.execute(JobStoreSupport.java:3691)
at org.quartz.impl.jdbcjobstore.JobStoreCMT.executeInLock(JobStoreCMT.java:242)
at org.quartz.impl.jdbcjobstore.JobStoreSupport.executeInLock(JobStoreSupport.java:3687)
at org.quartz.impl.jdbcjobstore.JobStoreSupport.storeTrigger(JobStoreSupport.java:1147)
at org.quartz.core.QuartzScheduler.scheduleJob(QuartzScheduler.java:829)
at org.quartz.impl.StdScheduler.scheduleJob(StdScheduler.java:254)
at org.springframework.scheduling.quartz.SchedulerAccessor.addTriggerToScheduler(SchedulerAccessor.java:340)
at org.springframework.scheduling.quartz.SchedulerAccessor.registerJobsAndTriggers(SchedulerAccessor.java:271)
at org.springframework.scheduling.quartz.SchedulerFactoryBean.afterPropertiesSet(SchedulerFactoryBean.java:513)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1477)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1417)
... 37 more
Caused by: java.io.StreamCorruptedException: invalid stream header: BB656430
at java.io.ObjectInputStream.readStreamHeader(ObjectInputStream.java:800)
at java.io.ObjectInputStream.(ObjectInputStream.java:297)
at org.quartz.impl.jdbcjobstore.PostgreSQLDelegate.getObjectFromBlob(PostgreSQLDelegate.java:99)
at org.quartz.impl.jdbcjobstore.StdJDBCDelegate.selectJobDetail(StdJDBCDelegate.java:904)
at org.quartz.impl.jdbcjobstore.JobStoreSupport.storeTrigger(JobStoreSupport.java:1201)
... 49 more
Nov 16, 2011 4:29:09 PM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext
Best regards,
Michael
Michael R. Zdanis
President
Cetus Group, LLC
224 Schilling Circle, Ste. 240
Hunt Valley, MD 21031
410.403.1161 (direct)
410.615.1112 (cell)
410.403.1159 (fax)

Comments

  • Hi Janus, Michael and Shaun,

    I have read a few posts on this error message, and one thing it could be related to is a bug with the useProperties parameter:

    http://jira.opensymphony.com/browse/QUARTZ-269

    http://markmail.org/message/yi6i3tppqicc5j7l

    While both these reports are rather dated, it may point to a fix if you have problems after down-grading the database to 8.x. If you are still running into issues, can you try to add the line

    org.quartz.jobStore.useProperties=true

    in the datainfo.properties file?

    Hope that helps, Tom



    Tom Hickerson | Senior Tier-2 Engineer
    [email protected]
    www.openclinica.com
    Open Source Platform for Clinical Research
  • smartinsmartin Posts: 145
    Re: [Developers] [Users] Couldn't Store Trigger - UbuntuInstallIssue Hi Janus,
    Although users may have gotten OpenClincia to work on postgres 9.0 we do not support it yet. We do not install OpenClinica on 9.0 internally nor do we say OpenClinica is compatible with postgres 9.0. This is true regardless of your Operating System. We support postgres 8.4.X for the 3.1.x version of OpenClinica currently.
    Thanks,
    Shaun
    On 11/18/11 06:44 AM, "Janus Engstrøm" wrote:
    Sorry, didn't mean Tomcat ... Postgres, of course :)
    Janus Engstrøm
    Sent by: [email protected] 18-11-2011 12:28
    Please respond to
    [email protected]
    To
    [email protected]
    cc
    Subject
    Re: [Developers] [Users] Couldn't Store Trigger - UbuntuInstallIssue
    Hi Shaun,
    This about OC not working with Postgres 9.0, is this true for Ubuntu/Linux only, or is it a Windows issue as well? I'm running our production instance on a 9.0 version of Tomcat (OC 3.0.4.2) and haven't encountered any problems? Windows 2008R2 Enterprise.
    Best regards,
    Janus
    Shaun Martin
    Sent by: [email protected] 17-11-2011 21:31
    Please respond to
    [email protected]
    To
    ,
    cc
    Subject
    Re: [Developers] [Users] Couldn't Store Trigger - Ubuntu InstallIssue
    Hi Michael,
    If OpenClinica connects and builds the database your configuration is fine. The issue would then lie with your database itself or the database server. Of the top of my head I would guess you have Postgres 9.0 installed and OpenClinica does not work with 9.0. Please note the OpenClinica installation instructions as written exactly will work on Ubuntu and return you a working OpenClinica system. I recommend rebuilding the server and following our instructions to fix your issue.
    Thanks,
    Shaun
    On 11/17/11 02:57 PM, "Michael Zdanis" wrote:
    Hello,
    I am attempting to install OpenClinica-3.1.1-Community for evaluation on an Ubuntu 11.10 system that was built from bare iron for the purpose. Ubunutu isn’t wild about having tomcat and java installed per the OC directions, so after a couple of attempts we allowed the main system to install and config PostgreSQL, and tomcat. Removed the pl/pgsql extension from template1 (a default you can’t get around with the base install) and changed the addressing in datainfo.properties to point to catalina.base rather than catalina.home since the OpenClinica files sit in /var/lib/tomcat6/webapps in this installation. On initial run, OpenClinica hits the database, builds 101 tables, 72 sequences, 2 functions, 9 trigger functions, and 1 view and then bombs with a series of errors. An exemplar of the error in the localhost.yyyy-mm-dd.log file is shown below. At this point I’m a bit stuck. Any direction is appreciated.
    Nov 16, 2011 4:29:09 PM org.apache.catalina.core.StandardContext listenerStop
    SEVERE: Exception sending context destroyed event to listener instance of class org.akaza.openclinica.control.OCServletContextListener
    org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'schedulerFactoryBean' defined in URL [jar:file:/var/lib/tomcat6/webapps/OpenClinica/WEB-INF/lib/OpenClinica-core-3.1.1-Community.jar!/org/akaza/openclinica/applicationContext-core-scheduler.xml]: Invocation of init method failed; nested exception is org.quartz.JobPersistenceException: Couldn't store trigger 'legacyJobTrigger' for 'legacyJobDetail' job:invalid stream header: BB656430 [See nested exception: java.io.StreamCorruptedException: invalid stream header: BB656430]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:291)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:563)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:895)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:425)
    at org.springframework.web.context.ContextLoader.createWebApplicationContext(ContextLoader.java:276)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:197)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
    at org.akaza.openclinica.dao.core.OCContextLoaderListener.contextInitialized(OCContextLoaderListener.java:22)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4206)
    at org.apache.catalina.core.StandardContext.start(StandardContext.java:4705)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:943)
    at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:778)
    at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:504)
    at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1315)
    at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:324)
    at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142)
    at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1061)
    at org.apache.catalina.core.StandardHost.start(StandardHost.java:840)
    at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
    at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:463)
    at org.apache.catalina.core.StandardService.start(StandardService.java:525)
    at org.apache.catalina.core.StandardServer.start(StandardServer.java:754)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:595)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:616)
    at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
    Caused by: org.quartz.JobPersistenceException: Couldn't store trigger 'legacyJobTrigger' for 'legacyJobDetail' job:invalid stream header: BB656430 [See nested exception: java.io.StreamCorruptedException: invalid stream header: BB656430]
    at org.quartz.impl.jdbcjobstore.JobStoreSupport.storeTrigger(JobStoreSupport.java:1245)
    at org.quartz.impl.jdbcjobstore.JobStoreSupport$5.execute(JobStoreSupport.java:1151)
    at org.quartz.impl.jdbcjobstore.JobStoreSupport$40.execute(JobStoreSupport.java:3691)
    at org.quartz.impl.jdbcjobstore.JobStoreCMT.executeInLock(JobStoreCMT.java:242)
    at org.quartz.impl.jdbcjobstore.JobStoreSupport.executeInLock(JobStoreSupport.java:3687)
    at org.quartz.impl.jdbcjobstore.JobStoreSupport.storeTrigger(JobStoreSupport.java:1147)
    at org.quartz.core.QuartzScheduler.scheduleJob(QuartzScheduler.java:829)
    at org.quartz.impl.StdScheduler.scheduleJob(StdScheduler.java:254)
    at org.springframework.scheduling.quartz.SchedulerAccessor.addTriggerToScheduler(SchedulerAccessor.java:340)
    at org.springframework.scheduling.quartz.SchedulerAccessor.registerJobsAndTriggers(SchedulerAccessor.java:271)
    at org.springframework.scheduling.quartz.SchedulerFactoryBean.afterPropertiesSet(SchedulerFactoryBean.java:513)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1477)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1417)
    ... 37 more
    Caused by: java.io.StreamCorruptedException: invalid stream header: BB656430
    at java.io.ObjectInputStream.readStreamHeader(ObjectInputStream.java:800)
    at java.io.ObjectInputStream.(ObjectInputStream.java:297)
    at org.quartz.impl.jdbcjobstore.PostgreSQLDelegate.getObjectFromBlob(PostgreSQLDelegate.java:99)
    at org.quartz.impl.jdbcjobstore.StdJDBCDelegate.selectJobDetail(StdJDBCDelegate.java:904)
    at org.quartz.impl.jdbcjobstore.JobStoreSupport.storeTrigger(JobStoreSupport.java:1201)
    ... 49 more
    Nov 16, 2011 4:29:09 PM org.apache.catalina.core.ApplicationContext log
    INFO: Closing Spring root WebApplicationContext
    Best regards,
    Michael
    Michael R. Zdanis
    President
    Cetus Group, LLC
    224 Schilling Circle, Ste. 240
    Hunt Valley, MD 21031
    410.403.1161 (direct)
    410.615.1112 (cell)
    410.403.1159 (fax)
This discussion has been closed.