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OpenClinica3.1.3-beta-2 on Debian 6 - net.sf.ehcache.CacheManager NullPointerException - during the

Hi to All,
I’m facing with an error when I try to startup the installed tomcat.

The log is the following:

INFO: Deploying web application archive OpenClinica.war
Sep 11, 2012 8:29:12 AM org.apache.catalina.core.StandardContext start
SEVERE: Error listenerStart
Sep 11, 2012 8:29:12 AM org.apache.catalina.core.StandardContext start
SEVERE: Context [/OpenClinica] startup failed due to previous errors
Sep 11, 2012 8:29:12 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/OpenClinica] appears to have started a thread named [[email protected]] but has failed to stop it. This is very likely to create a memory leak.
Sep 11, 2012 8:29:12 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/OpenClinica] appears to have started a thread named [[email protected]] but has failed to stop it. This is very likely to create a memory leak.
Sep 11, 2012 8:29:12 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/OpenClinica] created a ThreadLocal with key of type [ch.qos.logback.classic.util.CopyOnInheritThreadLocal] (value [[email protected]]) and a value of type [java.util.HashMap] (value [{HOSTNAME=localhost, WEBAPP=/usr/local/apache-tomcat-6.0.32/webapps/OpenClinica/}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Sep 11, 2012 8:29:12 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/OpenClinica] created a ThreadLocal with key of type [ch.qos.logback.classic.util.CopyOnInheritThreadLocal] (value [[email protected]]) and a value of type [java.util.HashMap] (value [{HOSTNAME= localhost, WEBAPP=/usr/local/apache-tomcat-6.0.32/webapps/OpenClinica/}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Sep 11, 2012 8:29:12 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
SEVERE: The web application [/OpenClinica] created a ThreadLocal with key of type [ch.qos.logback.classic.util.CopyOnInheritThreadLocal] (value [[email protected]]) and a value of type [java.util.HashMap] (value [{HOSTNAME= localhost, WEBAPP=/usr/local/apache-tomcat-6.0.32/webapps/OpenClinica/}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
Sep 11, 2012 8:29:13 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory oldwebapps
Sep 11, 2012 8:29:13 AM org.apache.coyote.http11.Http11Protocol start
INFO: Starting Coyote HTTP/1.1 on http-8080
Sep 11, 2012 8:29:13 AM org.apache.jk.common.ChannelSocket init
INFO: JK: ajp13 listening on /0.0.0.0:8009
Sep 11, 2012 8:29:13 AM org.apache.jk.server.JkMain start
INFO: Jk running ID=0 time=0/39 config=null
Sep 11, 2012 8:29:13 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 4869 ms
Sep 11, 2012 8:29:14 AM org.apache.catalina.loader.WebappClassLoader findResourceInternal
INFO: Illegal access: this web application instance has been stopped already. Could not load ehcache-version.properties. The eventual following stack trace is caused by an error thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access, and has no functional impact.
Exception in thread "[email protected]" java.lang.NullPointerException
at ch.qos.logback.classic.Logger.filterAndLog_0_Or3Plus(Logger.java:407)
at ch.qos.logback.classic.Logger.debug(Logger.java:526)
at net.sf.ehcache.util.UpdateChecker.checkForUpdate(UpdateChecker.java:63)
at net.sf.ehcache.util.UpdateChecker.run(UpdateChecker.java:51)
at java.util.TimerThread.mainLoop(Timer.java:512)
at java.util.TimerThread.run(Timer.java:462)
Sep 11, 2012 8:29:14 AM org.apache.catalina.loader.WebappClassLoader findResourceInternal
INFO: Illegal access: this web application instance has been stopped already. Could not load ehcache-version.properties. The eventual following stack trace is caused by an error thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access, and has no functional impact.
Exception in thread "[email protected]" java.lang.NullPointerException
at ch.qos.logback.classic.Logger.filterAndLog_0_Or3Plus(Logger.java:407)
at ch.qos.logback.classic.Logger.debug(Logger.java:526)
at net.sf.ehcache.util.UpdateChecker.checkForUpdate(UpdateChecker.java:63)
at net.sf.ehcache.util.UpdateChecker.run(UpdateChecker.java:51)
at java.util.TimerThread.mainLoop(Timer.java:512)
at java.util.TimerThread.run(Timer.java:462)


I have installed the apache tomcat, java and postgres following the manual.

Even If I can read into the logs “this web application instance has been stopped already”, this error appears even at the first tomcat startup.

Thank you in advance and best Regards,
Ennio

Comments

  • drodriguesdrodrigues Posts: 18
    Hello Ennio,
    This issue is caused by a bug already identified and being worked on at this moment [1]. You're experiencing this error because OpenClinica is failing to create a directory required during startup. You can create it manually, as a workaround.
    - Create a new directory named 'openclinica.data' in your Tomcat directory;
    - Create a directory named 'xslt' inside 'openclinica.data';
    - Extract the contents of the attached zip file to this directory;
    - Start Tomcat.
    The presence of those files should allow OpenClinica to start normally.
    Kindly,
    Douglas
    [1] - https://issuetracker.openclinica.com/view.php?id=15391
    On Tue, Sep 11, 2012 at 9:39 AM, Ennio Masi - Hippocrates Sintech S.r.l. wrote:
    Hi to All,
    I’m facing with an error when I try to startup the installed tomcat.

    The log is the following:

    INFO: Deploying web application archive OpenClinica.war
    Sep 11, 2012 8:29:12 AM org.apache.catalina.core.StandardContext start
    SEVERE: Error listenerStart
    Sep 11, 2012 8:29:12 AM org.apache.catalina.core.StandardContext start
    SEVERE: Context [/OpenClinica] startup failed due to previous errors
    Sep 11, 2012 8:29:12 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    SEVERE: The web application [/OpenClinica] appears to have started a thread named [[email protected]] but has failed to stop it. This is very likely to create a memory leak.
    Sep 11, 2012 8:29:12 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
    SEVERE: The web application [/OpenClinica] appears to have started a thread named [[email protected]] but has failed to stop it. This is very likely to create a memory leak.
    Sep 11, 2012 8:29:12 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
    SEVERE: The web application [/OpenClinica] created a ThreadLocal with key of type [ch.qos.logback.classic.util.CopyOnInheritThreadLocal] (value [[email protected]]) and a value of type [java.util.HashMap] (value [{HOSTNAME=localhost, WEBAPP=/usr/local/apache-tomcat-6.0.32/webapps/OpenClinica/}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
    Sep 11, 2012 8:29:12 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
    SEVERE: The web application [/OpenClinica] created a ThreadLocal with key of type [ch.qos.logback.classic.util.CopyOnInheritThreadLocal] (value [[email protected]]) and a value of type [java.util.HashMap] (value [{HOSTNAME= localhost, WEBAPP=/usr/local/apache-tomcat-6.0.32/webapps/OpenClinica/}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
    Sep 11, 2012 8:29:12 AM org.apache.catalina.loader.WebappClassLoader clearThreadLocalMap
    SEVERE: The web application [/OpenClinica] created a ThreadLocal with key of type [ch.qos.logback.classic.util.CopyOnInheritThreadLocal] (value [[email protected]]) and a value of type [java.util.HashMap] (value [{HOSTNAME= localhost, WEBAPP=/usr/local/apache-tomcat-6.0.32/webapps/OpenClinica/}]) but failed to remove it when the web application was stopped. This is very likely to create a memory leak.
    Sep 11, 2012 8:29:13 AM org.apache.catalina.startup.HostConfig deployDirectory
    INFO: Deploying web application directory oldwebapps
    Sep 11, 2012 8:29:13 AM org.apache.coyote.http11.Http11Protocol start
    INFO: Starting Coyote HTTP/1.1 on http-8080
    Sep 11, 2012 8:29:13 AM org.apache.jk.common.ChannelSocket init
    INFO: JK: ajp13 listening on /0.0.0.0:8009
    Sep 11, 2012 8:29:13 AM org.apache.jk.server.JkMain start
    INFO: Jk running ID=0 time=0/39 config=null
    Sep 11, 2012 8:29:13 AM org.apache.catalina.startup.Catalina start
    INFO: Server startup in 4869 ms
    Sep 11, 2012 8:29:14 AM org.apache.catalina.loader.WebappClassLoader findResourceInternal
    INFO: Illegal access: this web application instance has been stopped already. Could not load ehcache-version.properties. The eventual following stack trace is caused by an error thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access, and has no functional impact.
    Exception in thread "[email protected]" java.lang.NullPointerException
    at ch.qos.logback.classic.Logger.filterAndLog_0_Or3Plus(Logger.java:407)
    at ch.qos.logback.classic.Logger.debug(Logger.java:526)
    at net.sf.ehcache.util.UpdateChecker.checkForUpdate(UpdateChecker.java:63)
    at net.sf.ehcache.util.UpdateChecker.run(UpdateChecker.java:51)
    at java.util.TimerThread.mainLoop(Timer.java:512)
    at java.util.TimerThread.run(Timer.java:462)
    Sep 11, 2012 8:29:14 AM org.apache.catalina.loader.WebappClassLoader findResourceInternal
    INFO: Illegal access: this web application instance has been stopped already. Could not load ehcache-version.properties. The eventual following stack trace is caused by an error thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access, and has no functional impact.
    Exception in thread "[email protected]" java.lang.NullPointerException
    at ch.qos.logback.classic.Logger.filterAndLog_0_Or3Plus(Logger.java:407)
    at ch.qos.logback.classic.Logger.debug(Logger.java:526)
    at net.sf.ehcache.util.UpdateChecker.checkForUpdate(UpdateChecker.java:63)
    at net.sf.ehcache.util.UpdateChecker.run(UpdateChecker.java:51)
    at java.util.TimerThread.mainLoop(Timer.java:512)
    at java.util.TimerThread.run(Timer.java:462)


    I have installed the apache tomcat, java and postgres following the manual.

    Even If I can read into the logs “this web application instance has been stopped already”, this error appears even at the first tomcat startup.

    Thank you in advance and best Regards,
    Ennio
This discussion has been closed.