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[bioontology-support] Bioportal installation at ORNL

Kettani, Mouna kettanim at ornl.gov
Fri Jul 2 13:48:09 PDT 2010


Yes, we are using tomcat6 under Ubuntu 10.04. If this can help. You'll find below a complete trace of the error in catalina.log. Thanks
Mouna

Jul 2, 2010 4:42:32 PM org.apache.catalina.loader.WebappClassLoader loadClass
INFO: Illegal access: this web application instance has been stopped already.  Could not load com.sun.org.apache.xerces.internal.impl.dv.dtd.DTDDVFactoryImpl.  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.
java.lang.IllegalStateException
	at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1370)
	at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1329)
	at com.sun.org.apache.xerces.internal.impl.dv.ObjectFactory.findProviderClass(ObjectFactory.java:398)
	at com.sun.org.apache.xerces.internal.impl.dv.ObjectFactory.newInstance(ObjectFactory.java:353)
	at com.sun.org.apache.xerces.internal.impl.dv.DTDDVFactory.getInstance(DTDDVFactory.java:62)
	at com.sun.org.apache.xerces.internal.impl.dv.DTDDVFactory.getInstance(DTDDVFactory.java:47)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.<init>(XML11Configuration.java:542)
	at com.sun.org.apache.xerces.internal.parsers.XIncludeAwareParserConfiguration.<init>(XIncludeAwareParserConfiguration.java:128)
	at com.sun.org.apache.xerces.internal.parsers.XIncludeAwareParserConfiguration.<init>(XIncludeAwareParserConfiguration.java:89)
	at sun.reflect.GeneratedConstructorAccessor29.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
	at java.lang.Class.newInstance0(Class.java:372)
	at java.lang.Class.newInstance(Class.java:325)
	at com.sun.org.apache.xerces.internal.parsers.ObjectFactory.newInstance(ObjectFactory.java:352)
	at com.sun.org.apache.xerces.internal.parsers.ObjectFactory.createObject(ObjectFactory.java:157)
	at com.sun.org.apache.xerces.internal.parsers.ObjectFactory.createObject(ObjectFactory.java:100)
	at com.sun.org.apache.xerces.internal.parsers.SAXParser.<init>(SAXParser.java:106)
	at com.sun.org.apache.xerces.internal.parsers.SAXParser.<init>(SAXParser.java:91)
	at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.<init>(SAXParserImpl.java:335)
	at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.<init>(SAXParserImpl.java:125)
	at com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl.newSAXParser(SAXParserFactoryImpl.java:81)
	at org.jdom.input.JAXPParserFactory.createParser(JAXPParserFactory.java:131)
	at sun.reflect.GeneratedMethodAccessor62.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:616)
	at org.jdom.input.SAXBuilder.createParser(SAXBuilder.java:548)
	at org.jdom.input.SAXBuilder.build(SAXBuilder.java:424)
	at org.jdom.input.SAXBuilder.build(SAXBuilder.java:810)
	at org.jdom.input.SAXBuilder.build(SAXBuilder.java:789)
	at org.LexGrid.LexBIG.Impl.dataAccess.WriteLockManager.readFile(WriteLockManager.java:447)
	at org.LexGrid.LexBIG.Impl.dataAccess.WriteLockManager.checkForRegistryUpdates(WriteLockManager.java:298)
	at org.LexGrid.LexBIG.Impl.dataAccess.WriteLockManager$PingThread.run(WriteLockManager.java:244)
	at java.lang.Thread.run(Thread.java:636)
________________________________________
From: Paul R Alexander [palexander at stanford.edu]
Sent: Friday, July 02, 2010 2:29 PM
To: Kettani, Mouna; Michael Dorf
Cc: Natasha Noy; support at bioontology.org; Pouchard, Line Catherine
Subject: Re: Bioportal installation at ORNL

On 7/2/10 10:34 AM, Mouna Kettani wrote:
Paul - we are still not able to access bioportal_admin via browser: http://localhost:8080/bioportal_admin/ gives:  The requested resource () is not available. Could you please tell us how to resolve this problem? Thanks a lot.
This sounds like there was an error when Tomcat was trying to deploy the BioPortal Admin app during startup. You can view the catalina.out log in the Tomcat folder to see what's happening.

I think I remember somewhere you saying that you were using Tomcat 6. We have had some problems with the Admin app in Tomcat 6 and have recently made some improvements to fix these, however they may not be available yet. I've CCed Michael Dorf on this email so that he can give you some more information on this code.

Paul Alexander
Web / UI Developer
NCBO BioPortal



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