XNAT desktop client

238 views
Skip to first unread message

Naveena Gorre

unread,
Jun 16, 2021, 10:50:37 PM6/16/21
to xnat_discussion
Greetings XNAT group,

           I'm currently working on  installing and setting up XNAT desktop client, while going through the documentation I figured that the xnat.server.url is automatically detected by the application but for some reason it's not detecting on my PC, I have also tried hardcoding it but still didn't work. I'm using a windows PC with a native windows OS (no virtual environments) and I have JRE installed on it.
Please let me know if I'm missing out on anything. Thanks in advance
 
Attaching the error screenshot for reference.

Regards
Naveena Gorre
Screenshot (17).png

Mohana Ramaratnam

unread,
Jun 17, 2021, 1:18:29 AM6/17/21
to xnat_discussion
Hi Naveena,

You will have to replace xnat.server.url with  the URL to the xnat instance to which you are trying to upload. For example, the url could be



--
You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to xnat_discussi...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/xnat_discussion/18a63a21-7748-4e14-9201-b66c78b43b78n%40googlegroups.com.

Steve Moore

unread,
Jun 17, 2021, 5:57:53 AM6/17/21
to xnat_discussion
We have also seen cases where the user entered the URL as Mohanna suggested and a DNS problem prevented the connection. If you enter the URL when you define the server and that does not work, try using the IP address of the server.

Steve Moore

Sun, Zhongdong

unread,
Jun 24, 2021, 11:01:32 AM6/24/21
to xnat_di...@googlegroups.com

Hi everyone,

 

Today we download the XNAT desktop client (version 2.0.4) and try to use it to transfer some images. This is an appimage file. We make it executable and run it directly. Our machine runs CentOS 7.4. It can start, but the interface is almost empty. There is no ‘Add new XNAT server’ button in the GUI. See below picture for details. Could anyone please tell us what’s wrong with this?

 

Thanks.

 

Zhongdong Sun

Department of Radiology and Biomedical Imaging

Yale University School of Medicine

 

 

Herrick, Rick

unread,
Jun 24, 2021, 7:21:08 PM6/24/21
to xnat_di...@googlegroups.com

It’s possible to fix part of this error: the first problem I ran into is that a JDK has to be installed on the VM and then linked to a particular location so that the application can find it.

 

sudo yum install java-1.8.0-openjdk-devel

sudo mkdir -p /opt/java/linux-x64/jre/lib/amd64

sudo ln -s /lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64/jre/lib/amd64/server /opt/java/linux-x64/jre/lib/amd64/server

 

However, that just sets it up for another error:

 

/tmp/.mount_XNAT-DmKgpq2/resources/app.asar/renderer-process/index3.js:41 Uncaught Error: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /tmp/.mount_XNAT-DmKgpq2/resources/app.asar.unpacked/node_modules/java/build/Release/nodejavabridge_bindings.node)

Error: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /tmp/.mount_XNAT-DmKgpq2/resources/app.asar.unpacked/node_modules/java/build/Release/nodejavabridge_bindings.node)

    at process.module.(anonymous function) [as dlopen] (ELECTRON_ASAR.js:166:20)

 

It’s worth noting that this same error occurred on CentOS 7.4 and 7.9, which makes sense because the latest version of the ABI library available is 1.3.7 on both of them. I tried testing it on a CentOS 8 VM but the Vagrant box server appears to be down at the moment. It’s possible that CentOS 8 provides a newer version of that library, but I don’t see any easy way to get that working on CentOS 7.4.

 

-- 

Rick Herrick

XNAT Architect/Developer

Computational Imaging Laboratory

Washington University School of Medicine

 

 

From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of Sun, Zhongdong <zhongd...@yale.edu>
Date: Thursday, June 24, 2021 at 10:02 AM
To: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com>
Subject: [XNAT Discussion] XNAT desktop client

* External Email - Caution *

--

You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to xnat_discussi...@googlegroups.com.

 

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

Herrick, Rick

unread,
Jun 25, 2021, 11:20:22 AM6/25/21
to xnat_discussion

I was able to start up a CentOS 8.4 VM this morning using the gbailey/centos8-mate Vagrant base box. I still needed to link the Java server JRE as described below, but libstdc++ on CentOS 8 supports up to 1.3.11 of the C++ ABI and XNAT desktop client ran with no issue.

 

Unfortunately the version of the C++ ABI that gets set for the application is a function of the build environment and we can’t really change that because the version on the build container is out of our control. Which means, basically, the desktop client can’t support CentOS 7.x without a migration of the overall build environment.

Sun, Zhongdong

unread,
Jun 25, 2021, 12:35:34 PM6/25/21
to xnat_di...@googlegroups.com

Hi Rick,

 

Thank you for your replies.

 

As you mentioned, the XNAT desktop client doesn’t support CentOS 7, only CentOS 8. Unfortunately, we’re still running CentOS 7. I wonder if you have an older version that supports CentOS 7.

 

If unavailable, I wonder if any versions of the desktop client can run in Ubuntu 18.04.

 

Does this desktop client only support JRE 1.8? Ubuntu seems to have a different of JRE.

 

I download the source code for XNAT desktop client and build it in CentOS 7. The building is ok, but the resulted program still has the same problem.

 

Also, I tried the desktop client in CentOS 8 virtual machine, and it works well in it. But we cannot run this in a virtual machine. This program will be used routinely for Dicom image exchange with other sites.

 

Thanks.

Zhongdong

Herrick, Rick

unread,
Jun 25, 2021, 4:57:52 PM6/25/21
to xnat_di...@googlegroups.com

The current version of the desktop client should work fine with Ubuntu 18.04, with a couple caveats:

 

  • The base version of Ubuntu 18.04 doesn’t have gcc (and therefore libstdc++) installed by default. This may not be true on Ubuntu 18.04 desktop (I’m on a headless server version atm), but if you don’t have the file /usr/lib/x86_64-linux-gnu/libstdc++.so.6 on the machine you just need to do apt install gcc. That installs the required library, which supports ABI up to 1.3.11.
  • 18.04 has Java 8 available in its default repositories. The package name and install location are just a bit different:

 

sudo apt install openjdk-8-jre

sudo mkdir -p /opt/java/linux-x64/jre/lib/amd64

sudo ln -s /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server /opt/java/linux-x64/jre/lib/amd64/server

 

Note that this is installing the JRE rather than the JDK. That should be sufficient.

 

Re: “I download the source code for XNAT desktop client and build it in CentOS 7. The building is ok, but the resulted program still has the same problem.”

 

I took a look at the dependencies for the desktop client and I can’t be sure but it looks like the ABI version dependency may actually be in Electron itself, which is the framework that supports running node.js applications as stand-alone GUI applications. Which would indicate that no applications that use Electron after some version would run on CentOS 7.x. And we definitely can’t roll back the version of Electron because we already went through the process to migrate to newer versions of node.js and Electron because they were required by other dependencies we were integrating into the application.

Sun, Zhongdong

unread,
Jun 25, 2021, 7:43:26 PM6/25/21
to xnat_di...@googlegroups.com

Hi Rick,

 

I followed your instruction and setup JRE in one Ubuntu 18.04 machine. The XNAT desktop client worked well in it.

 

Thanks a lot for your helps in this issue. Maybe you can add your instruction into XNAT desktop client installation documentation so that more users can read them.

Herrick, Rick

unread,
Jun 28, 2021, 7:10:26 PM6/28/21
to xnat_di...@googlegroups.com

Sun, Zhongdong

unread,
Jun 28, 2021, 7:23:32 PM6/28/21
to xnat_di...@googlegroups.com

Hi Rick,

 

It’s great. Thanks for updating the documentation. Now it’s more clear how to install the XNAT desktop client on a Linux system. I’m sure more users will find it helpful in future.

Reply all
Reply to author
Forward
0 new messages