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Anyone else installing XNAT 1.6.5 from xnat.org website having the same issue? I followed the same exact steps as in the installation guide here. This issue is happening in step 11. I have finished the prior steps successfully:

Additional log here: http://pastebin.com/vQ6n6DfL

When I browse to localhost:8080/xnat I get :

HTTP Status 404 - /xnat

type Status report

message /xnat

description The requested resource is not available.
Apache Tomcat/8.0.26 (Ubuntu)

I also have nothing copied into tomcat root after I ran these two commands which seemingly changed the .war file:

ls /usr/share/tomcat8-root/default_root/
index.html  META-INF

jalal@klein:~/computer_vision/XNAT/xnat/deployments/xnat/target$ ls
classes  src  test-classes  test-reports  xnat-1.0-dev.jar

Here is the .war file I had before:

    jalal@klein:~/computer_vision/XNAT/xnat/deployments/xnat/target$ ls
    classes  src  test-classes  test-reports 
jalal@klein:~/computer_vision/XNAT/xnat$ ps -ax | grep httpd' and 'killall httpd
grep: httpd: No such file or directory
jalal@klein:~/computer_vision/XNAT/xnat$ sudo netstat -an | fgrep 8080
tcp6       0      0 :::8080                 :::*                    LISTEN     
unix  3      [ ]         STREAM     CONNECTED     38080    
jalal@klein:~/computer_vision/XNAT/xnat$ sudo lsof -i :80
jalal@klein:~/computer_vision/XNAT/xnat$ sudo lsof -i :8080
COMMAND   PID    USER   FD   TYPE  DEVICE SIZE/OFF NODE NAME
java    13228 tomcat8   46u  IPv6 2673854      0t0  TCP *:http-alt (LISTEN)


 xnat  xnat.war
jalal@klein:~/computer_vision/XNAT/xnat$ bin/setup.sh -Ddeploy=true 

Using XDAT Installation: /home/jalal/computer_vision/XNAT/xnat
Using JAVA_HOME:         /usr/lib/jvm/java-8-openjdk-amd64/

Verify Java Version (with java -version)
openjdk version "1.8.0_91"
OpenJDK Runtime Environment (build 1.8.0_91-8u91-b14-3ubuntu1~15.10.1-b14)
OpenJDK 64-Bit Server VM (build 25.91-b14, mixed mode)

Executing /home/jalal/computer_vision/XNAT/xnat/plugin-resources/maven-1.0.2/bin/maven xdat:setup
 __  __
|  \/  |__ _Apache__ ___
| |\/| / _` \ V / -_) ' \  ~ intelligent projects ~
|_|  |_\__,_|\_/\___|_||_|  v. 1.0.2

build:start:

xdat:setup:
    [echo] HOME: /home/jalal/computer_vision/XNAT/xnat
xdat:version:
    [echo] Setting the project version
    [echo] Setting project version to: 1.6.5

BUILD FAILED
File...... /home/jalal/computer_vision/XNAT/xnat/maven.xml
Element... fail
Line...... 40
Column.... 19
--------------------------------------------------------------------------
                | Duplicate Setup Exception |
                --------------------------------------------------------------------------

                This application has already been setup. If you want to redo
                the setup process, delete the /home/jalal/computer_vision/XNAT/xnat/deployments/xnat
                directory and call setup again.

                If you want to update your previously created deployment,
                use the 'update' method rather then the 'setup' one.

                --------------------------------------------------------------------------
Total time: 1 seconds
Finished at: Fri Sep 02 17:01:03 CDT 2016

jalal@klein:~/computer_vision/XNAT/xnat$ bin/update.sh -Ddeploy=true 

Using XDAT Installation: /home/jalal/computer_vision/XNAT/xnat
Using JAVA_HOME:         /usr/lib/jvm/java-8-openjdk-amd64/

Verify Java Version (with java -version)
openjdk version "1.8.0_91"
OpenJDK Runtime Environment (build 1.8.0_91-8u91-b14-3ubuntu1~15.10.1-b14)
OpenJDK 64-Bit Server VM (build 25.91-b14, mixed mode)

Executing /home/jalal/computer_vision/XNAT/xnat/plugin-resources/maven-1.0.2/bin/maven xdat:update
 __  __
|  \/  |__ _Apache__ ___
| |\/| / _` \ V / -_) ' \  ~ intelligent projects ~
|_|  |_\__,_|\_/\___|_||_|  v. 1.0.2

build:start:

xdat:update:

Port information:

jalal@klein:~/computer_vision/XNAT/xnat$ ps -ax | grep httpd' and 'killall httpd
grep: httpd: No such file or directory
jalal@klein:~/computer_vision/XNAT/xnat$ sudo netstat -an | fgrep 8080
tcp6       0      0 :::8080                 :::*                    LISTEN     
unix  3      [ ]         STREAM     CONNECTED     38080    
jalal@klein:~/computer_vision/XNAT/xnat$ sudo lsof -i :80
jalal@klein:~/computer_vision/XNAT/xnat$ sudo lsof -i :8080
COMMAND   PID    USER   FD   TYPE  DEVICE SIZE/OFF NODE NAME
java    13228 tomcat8   46u  IPv6 2673854      0t0  TCP *:http-alt (LISTEN)

Do you know how this issue can be solved?

Mona Jalal
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1 Answers1

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There are a few issues I see here.

XNAT is not validated or tested on Tomcat 8. That's mainly because we've never been able to get it running at all on Tomcat 8. I suspect that's the root cause of the 404: the resource really is not found or available because the application deploy failed during Tomcat start-up.

This is also the reason why you don't see anything running on port 8104, which is where you'd normally see the DICOM SCP receiver running. If XNAT doesn't start at all, the receiver won't be brought up either.

Overall, the output of your setup and update scripts looks fine, so I think there's nothing wrong with the build itself, just where it's being built to.

I'd suggest downloading Tomcat 7 and trying with that.

Also, when you're trying to analyze XNAT issues, you should look two places:

  • In the folder logs inside your deployed XNAT application, in this case ~/computer_vision/XNAT/xnat/deployments/xnat/TOMCAT_HOME/webapps/xnat/logs
  • In the Tomcat logs folder, which would probably be in ~/computer_vision/XNAT/xnat/deployments/xnat/TOMCAT_HOME/logs

That's where you'll find the run-time output from Tomcat and XNAT. My guess is you'd see a lot of messages about xnat:ArcArchivespecification not being found or something like that, which I think is caused by a change in the servlet spec supported by Tomcat 8 that makes it difficult to read files within a web app. We just haven't really had a chance to look that deeply into, however, since Tomcat 8 support is a very low priority for us, given that it's not available on any of the standard install repos for the major distros.

Spanky Quigman
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