In preparation for the eventual release of XNAT 1.4 we are starting to rebuild our documentation.
Some of you may have seen that I moved the instructions for building XNAT 1.4 from CVS to the WIKI. Please use this from now on (rather than the old discussion group post) as am gradually making tweaks to it.
http://nrg.wikispaces.com/XNAT_Source
I’ve put together a first draft of the 1.4 User Guide. I’ll gradually be moving this to the WIKI and expanding it. In the meantime it’s in the discussion group files:
http://groups.google.com/group/xnat_discussion/files
File Name: XNAT User Guide.doc
We’ll gradually be putting together more specific documentation.
Initial thoughts are:
Store XAR Documentation
Web Service Tools
Pipeline Documentation
Site Administration Documentation
XNAT Extension Guidelines
XNAT Development Best Practices (Eclipse configuration, code structure, etc).
Is there anything else in particular you would like to see?
- Kevin
________________________________________
From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf Of Jon Moody [jbm...@gmail.com]
Sent: Tuesday, May 27, 2008 12:06 PM
To: xnat_discussion
Subject: Re: 1.4 Documentation
Sorry for the delay in getting back to you.
In 1.4 the archive/prearchive/cache/etc paths are touched/created until they are used. So, I wouldn't expect those folders to be created until you begin upload image files.
Your deployment problem is an oddity. I've never encountered a problem like this. It is either an issue with all of the files not being copied into the webapp, the webapp startup failing, or an issue with your database.
Are their any errors in your TOMCAT_HOME/logs/Catalina.out file? Have you tried deleting the generated webapp folder, running update.bat without the auto deploy variable, and copying the generated war file into the webapp?
Tim
-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of david
Sent: Tuesday, May 27, 2008 10:27 AM
To: xnat_discussion
Subject: Re: 1.4 Documentation
The only time I've encountered this error before is when the webapp is not actually deployed to the webapps directory. Did you try the war method?
To try the war:
Delete the TOMCAT/webapps/xnat directory.
From XNAT_HOME run: bin/update.sh
Copy the generated war file into the webapp:
XNAT_HOME/deployments/xnat/target/xnat.war to TOMCAT/webapps/xnat.war
If you are running Tomcat via the GUI manager there is an option in the properties somewhere for setting the java version. A good way to see if this is the issue would be to start tomcat via its bin/startup.bat from within the same terminal you used to run the setup/update scripts. This would guarantee that the same java version was being used for both.
When you attempt to modify the paths in the Default Settings dialog, and it fails, does it log any errors (TOMCAT_HOME/webapp/xnat/logs/*.log)?
Tim
Thanks, Tim,
David
> org.apache.catalina.loader.WebappClassLoader.findClassInternal(WebappClassLoader.java:
> 1853)
> at
> org.apache.catalina.loader.WebappClassLoader.findClass(WebappClassLoader.java:
> 875)
> at
> org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:
> 1330)
> at
> org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:
> org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:
> org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:
> org.apache.catalina.loader.WebappClassLoader.findClassInternal(WebappClassLoader.java:
> 1853)
> at
> org.apache.catalina.loader.WebappClassLoader.findClass(WebappClassLoader.java:
> 875)
> at
> org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:
> 1330)
> at
> org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:
> org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:
Tim
Hi, Tim:
Dabin
> > org.apache.catalina.loader.WebappClassLoader.findClassInternal(WebappClassLoader.java:
> > 1853)
> > at
> > org.apache.catalina.loader.WebappClassLoader.findClass(WebappClassLoader.java:
> > 875)
> > at
> > org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:
> > 1330)
> > at
> > org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:
> > org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:
> > org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:
Most of the paths specified in that page are ignored until they are used. The only path which is used in the page submit is the cache path (where your settings are exported for use by other XNAT tools in development).
Any errors thrown in the process should be logged to the TOMCAT_HOME/webapp/xnat/logs directory. The fact that it isn't logging anything there is a problem.
Have you tried installing XNAT on a different machine to confirm whether or not these issues are limited to your current setup? Perhaps, that would shed some light on what is going on here.
Tim
David
> > > org.apache.catalina.loader.WebappClassLoader.findClassInternal(WebappClassLoader.java:
> > > 1853)
> > > at
> > > org.apache.catalina.loader.WebappClassLoader.findClass(WebappClassLoader.java:
> > > 875)
> > > at
> > > org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:
> > > 1330)
> > > at
> > > org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:
> > > org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:
> > > org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:
Tim
David
> > > > org.apache.catalina.loader.WebappClassLoader.findClassInternal(WebappClassLoader.java:
> > > > 1853)
> > > > at
> > > > org.apache.catalina.loader.WebappClassLoader.findClass(WebappClassLoader.java:
> > > > 875)
> > > > at
> > > > org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:
> > > > 1330)
> > > > at
> > > > org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:
> > > > org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:
2. test installation instructions
Have you tried steps 11 - 13 on the wiki installation guide? http://nrg.wikispaces.com/XNAT_Source
They were intended to walk you through that process. Is there anything more you are looking for? I can add it to that page.
Tim
Thanks, I got it.
I have other questions:
David
> > > > > org.apache.catalina.loader.WebappClassLoader.findClassInternal(WebappClassLoader.java:
> > > > > 1853)
> > > > > at
> > > > > org.apache.catalina.loader.WebappClassLoader.findClass(WebappClassLoader.java:
> > > > > 875)
> > > > > at
> > > > > org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:
> > > > > 1330)
> > > > > at
> > > > > org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:
> > > > > org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:
Perhaps our DICOM tools are having trouble with your DICOM files. I would recommend downloading DICOMBrowser form the NRG site: http://nrg.wustl.edu/projects/DICOM/DicomBrowser.jsp. It uses the same libraries to process DICOM. If it can read the DICOM, then the webapp should be able to.
The FTP path should not impact anything (unless you've separately setup the XNAT FTP Server). You should be able to put a dummy value in that field, and then ignore it.
The fields which show up in the insert/edit subject dialogs are determined by the field groups you select in the 'Manage Custom Variables' section of the Project report.
David
> > > > > > org.apache.catalina.loader.WebappClassLoader.findClassInternal(WebappClassLoader.java:
If you have a more specific question, I'd be happy to answer it now.
In a default install, you should set the SITE URL to http://localhost:8080/xnat. The wiki doc is a little less forceful, stating you can 'probably' use http://localhost:8080/xnat. That is because some users may configure tomcat in a way which changes the URL. For example, you could substitute localhost for your machine name (to make it accessible from other machines). You could remove the port number, if you configure Apache (or something else) to route requests from port 80 to Tomcat. You could remove the /xnat webapp specification, if you configure Tomcat to route all requests to the XNAT webapp. But in a vanilla, non-customized Tomcat install you should use http://localhost:8080/xnat.
To modify this, login as the admin user. Click 'More Options' under Administration. Click 'Set Default Settings'. Change the Site URL appropriately.
Tim
-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of david
Sent: Friday, June 06, 2008 12:55 PM
To: xnat_discussion
Subject: Re: 1.4 Documentation
More information.
David
> --------------------------------------------------------------------------------
>
> type Status report
>
> message /app/template/XDATScreen_report_xnat_mrSessionData.vm/
> search_field/xnat:mrSessionData.id/search_value/FP_2_MR_1/
> search_element/xnat:mrSessionData/project/FP
>
> description The requested resource (/app/template/
> XDATScreen_report_xnat_mrSessionData.vm/search_field/
> xnat:mrSessionData.id/search_value/FP_2_MR_1/search_element/
> xnat:mrSessionData/project/FP) is not available.
>
> --------------------------------------------------------------------------------
To incorporate the change...
cd $XNAT_HOME
cvs update
cp plugin-resources/webapp/xnat/applet/PlexiViewerLite.jar projects/xnat/src/applet/
bin/update.sh -Ddeploy=true
Then retry the image viewer.
Tim
Tim,
David
> --------------------------------------------------------------------------------
>
> type Status report
>
> message /app/template/XDATScreen_report_xnat_mrSessionData.vm/
> search_field/xnat:mrSessionData.id/search_value/FP_2_MR_1/
> search_element/xnat:mrSessionData/project/FP
>
> description The requested resource (/app/template/
> XDATScreen_report_xnat_mrSessionData.vm/search_field/
> xnat:mrSessionData.id/search_value/FP_2_MR_1/search_element/
> xnat:mrSessionData/project/FP) is not available.
>
> --------------------------------------------------------------------------------