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[bioontology-support] Bioportal installation at ORNL

Kettani, Mouna kettanim at ornl.gov
Tue Jul 6 12:35:39 PDT 2010


Thank you Michael. We have checked the lastest bioportal_admin trunk code from SVN and we placed the folder both is the ROOT of the tomcat folder and in the root of the machine. The browser still does not recognize the resources (snapshot attached). Any other suggestions?

Best Regards,

Mouna
_______________________________________
From: Michael Dorf [mdorf at stanford.edu]
Sent: Friday, July 02, 2010 8:15 PM
To: Kettani, Mouna; 'Paul R Alexander'
Cc: 'Natasha Noy'; support at bioontology.org; Pouchard, Line Catherine
Subject: RE: Bioportal installation at ORNL

Mouna,

Please try pulling the latest bioportal_admin trunk code from SVN.  I have
checked in an updated set of libraries that should work under Tomcat 6.
Note that we haven't had a chance to test this latest release yet.  Please
let me know if you run into any further issues.

Thanks,

Misha

-----Original Message-----
From: Kettani, Mouna [mailto:kettanim at ornl.gov]
Sent: Friday, July 02, 2010 1:48 PM
To: Paul R Alexander; Michael Dorf
Cc: Natasha Noy; support at bioontology.org; Pouchard, Line Catherine
Subject: RE: Bioportal installation at ORNL

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.j
ava:1370)
        at
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.j
ava: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(Objec
tFactory.java:353)
        at
com.sun.org.apache.xerces.internal.impl.dv.DTDDVFactory.getInstance(DTDDVF
actory.java:62)
        at
com.sun.org.apache.xerces.internal.impl.dv.DTDDVFactory.getInstance(DTDDVF
actory.java:47)
        at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.<init>(XML11
Configuration.java:542)
        at
com.sun.org.apache.xerces.internal.parsers.XIncludeAwareParserConfiguratio
n.<init>(XIncludeAwareParserConfiguration.java:128)
        at
com.sun.org.apache.xerces.internal.parsers.XIncludeAwareParserConfiguratio
n.<init>(XIncludeAwareParserConfiguration.java:89)
        at sun.reflect.GeneratedConstructorAccessor29.newInstance(Unknown
Source)
        at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstr
uctorAccessorImpl.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(Objec
tFactory.java:352)
        at
com.sun.org.apache.xerces.internal.parsers.ObjectFactory.createObject(Obje
ctFactory.java:157)
        at
com.sun.org.apache.xerces.internal.parsers.ObjectFactory.createObject(Obje
ctFactory.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$JAXPSAXParser.<init>
(SAXParserImpl.java:335)
        at
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.<init>(SAXParserImpl
.java:125)
        at
com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl.newSAXParser(
SAXParserFactoryImpl.java:81)
        at
org.jdom.input.JAXPParserFactory.createParser(JAXPParserFactory.java:131)
        at sun.reflect.GeneratedMethodAccessor62.invoke(Unknown Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorIm
pl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:616)
        at org.jdom.input.SAXBuilder.createParser(SAXBuilder.java:548)
        at org.jdom.input.SAXBuilder.build(SAXBuilder.java:424)
        at org.jdom.input.SAXBuilder.build(SAXBuilder.java:810)
        at org.jdom.input.SAXBuilder.build(SAXBuilder.java:789)
        at
org.LexGrid.LexBIG.Impl.dataAccess.WriteLockManager.readFile(WriteLockMana
ger.java:447)
        at
org.LexGrid.LexBIG.Impl.dataAccess.WriteLockManager.checkForRegistryUpdate
s(WriteLockManager.java:298)
        at
org.LexGrid.LexBIG.Impl.dataAccess.WriteLockManager$PingThread.run(WriteLo
ckManager.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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