Installation of XNAT and the installation manual

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Edwin ter Voert

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Sep 14, 2022, 11:52:01 AM9/14/22
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Hi Everyone,

I am trying to install XNAT (on Ubuntu 22.04), but the installation manual is not so clear. i think it could use an update. But time is probably limited.

- The installation of Java 8 is kind of clear. The listed AdoptOpenJDK is however no longer supported. It moved in 2021 to Adoptium and is now Eclipse Temurin.

- The installation of Tomcat 9 is recommended, but a large part of the manual still talks about version 7.

But my question is about PostgreSQL:
- It is unclear to me what version of PostgreSQL is supported by XNAT. In some locations it says version 10 and up. In other locations it mentions 10.x - 12.x.
My question: Does it run with the current 14.x ? or the to be released 15.x ? Did anyone perhaps test this?

Kind regards,
Edwin

Rick Herrick

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Sep 14, 2022, 11:55:37 AM9/14/22
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XNAT is compatible with PostgreSQL up to the latest release of v14. I haven’t had a chance to test with v15 yet, but that’s still in beta and likely a number of months before it’ll be available on most server platforms, so it may be a bit before we get around to testing that at any kind of scale.

Rick Herrick
Senior Software Developer


------ Original Message ------
From "Edwin ter Voert" <e.g.w.t...@gmail.com>
To "xnat_discussion" <xnat_di...@googlegroups.com>
Date 9/14/2022 5:00:51 AM
Subject [XNAT Discussion] Installation of XNAT and the installation manual

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Edwin ter Voert

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Sep 15, 2022, 4:46:53 AM9/15/22
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Dear Rick, all,

Thank you for the answer. It is very useful. It was related to another problem I have:

I tried to manually install XNAT, but it doesn't work. Perhaps you can help me?

Some time ago I successfully installed (a previous version of) XNAT on Debian.
This time I tried the newer version (xnat-web-1.8.5.1a.war) on Ubuntu 22.04.
I again followed the provided installation manual and all looks fine.

But...

When I go to http://192.168.0.8:8080/ I get the XNAT login screen.
I enter "admin / admin" to login and there appears a quickly disappearing message that it is working on something.
Then it forwards me to http://192.168.0.8:8080/setup/ and things go wrong.
The "setup" page shows an error message:

--------------------------
XNAT has encountered an error with your request:

If this error continues to occur, please contact your system administrator with information about how to recreate the problem.
--------------------------

Some details:

Ubuntu 22.04

Java 8:
openjdk version "1.8.0_342"
OpenJDK Runtime Environment (build 1.8.0_342-8u342-b07-0ubuntu1~22.04-b07)
OpenJDK 64-Bit Server VM (build 25.342-b07, mixed mode)

PostgreSQL 14:
postgres (PostgreSQL) 14.5 (Ubuntu 14.5-1.pgdg22.04+1)

Tomcat9:
Server version: Apache Tomcat/9.0.58 (Ubuntu)
Server built:   Jan 6 1970 15:09:28 UTC
Server number:  9.0.58.0
OS Name:        Linux
OS Version:     5.15.0-47-generic
Architecture:   amd64
JVM Version:    1.8.0_342-8u342-b07-0ubuntu1~22.04-b07
JVM Vendor:     Private Build

There is not much in the logfiles, except for a SEVERE error in:
/var/log/tomcat9/localhost.2022-09-15.log

It looks like something is "compiled" with java 11 (55.0) whereas I run java 8 (52.0). But I have no idea what it is or where it belongs to. See below. Does anyone know?

Thanks!

Kind regards,
Edwin


-----------localhost.2022-09-15.log---------------
15-Sep-2022 02:16:20.880 INFO [main] org.apache.catalina.core.ApplicationContext.log 2 Spring WebApplicationInitializers detected on classpath
15-Sep-2022 02:16:21.053 INFO [main] org.apache.catalina.core.ApplicationContext.log Initializing Spring root WebApplicationContext
15-Sep-2022 02:16:56.521 INFO [main] org.apache.catalina.core.ApplicationContext.log Initializing Spring FrameworkServlet 'dispatcher'
15-Sep-2022 02:18:43.989 SEVERE [http-nio-8080-exec-7] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [jsp] in context with path [] threw exception [java.lang.UnsupportedClassVersionError: org/eclipse/jdt/internal/compiler/env/INameEnvironment has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0] with root cause
        java.lang.UnsupportedClassVersionError: org/eclipse/jdt/internal/compiler/env/INameEnvironment has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0
                at java.lang.ClassLoader.defineClass1(Native Method)
                at java.lang.ClassLoader.defineClass(ClassLoader.java:756)
                at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
                at java.net.URLClassLoader.defineClass(URLClassLoader.java:473)
                at java.net.URLClassLoader.access$100(URLClassLoader.java:74)
                at java.net.URLClassLoader$1.run(URLClassLoader.java:369)
                at java.net.URLClassLoader$1.run(URLClassLoader.java:363)
                at java.security.AccessController.doPrivileged(Native Method)
                at java.net.URLClassLoader.findClass(URLClassLoader.java:362)
                at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
                at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
                at java.lang.Class.forName0(Native Method)
                at java.lang.Class.forName(Class.java:264)
                at org.apache.jasper.JspCompilationContext.createCompiler(JspCompilationContext.java:247)
                at org.apache.jasper.JspCompilationContext.createCompiler(JspCompilationContext.java:225)
                at org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:597)
                at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:399)
                at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:379)
                at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:327)
                at javax.servlet.http.HttpServlet.service(HttpServlet.java:764)
                at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:227)
                at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
                at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53)
                at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
                at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
                at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:239)
                at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:215)
                at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
                at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:317)
                at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:127)
                at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:91)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:114)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:137)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.nrg.xnat.security.XnatInitCheckFilter.doFilterInternal(XnatInitCheckFilter.java:62)
                at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:170)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.nrg.xnat.security.XnatExpiredPasswordFilter.doFilterInternal(XnatExpiredPasswordFilter.java:114)
                at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.nrg.xnat.security.XnatBasicAuthenticationFilter.doFilterInternal(XnatBasicAuthenticationFilter.java:115)
                at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.springframework.security.web.session.ConcurrentSessionFilter.doFilter(ConcurrentSessionFilter.java:155)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:200)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:200)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:66)
                at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56)
                at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:99)
                at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.springframework.security.web.access.channel.ChannelProcessingFilter.doFilter(ChannelProcessingFilter.java:157)
                at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:331)
                at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:214)
                at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:177)
                at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:347)
                at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:263)
                at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189)
                at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162)
                at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:197)
                at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97)
                at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:540)
                at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:135)
                at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)
                at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:687)
                at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78)
                at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:359)
                at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:399)
                at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65)
                at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:889)
                at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1735)
                at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
                at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191)
                at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659)
                at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
                at java.lang.Thread.run(Thread.java:750)
15-Sep-2022 02:19:02.039 INFO [Thread-39] org.apache.catalina.core.ApplicationContext.log Destroying Spring FrameworkServlet 'dispatcher'
15-Sep-2022 02:19:02.283 INFO [Thread-39] org.apache.catalina.core.ApplicationContext.log Closing Spring root WebApplicationContext
--------------------------

Op woensdag 14 september 2022 om 17:55:37 UTC+2 schreef Rick Herrick:

Duncan Smith

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Sep 15, 2022, 6:12:37 AM9/15/22
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Hi Edwin,

I recently tried to install XNAT on Ubuntu 22 but I also ran into the issue you are finding. I was eventually able to find this post which explained the problem I was seeing: https://groups.google.com/g/xnat_discussion/c/kBmPvyLL-uw/m/ypr82UkuBQAJ

Duncan

Edwin ter Voert

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Sep 15, 2022, 8:49:58 AM9/15/22
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Hi Duncan,

Thank you for providing this info. It is very helpful. 

So, as XNAT uses Tomcat9 and the newer Linux distributions (like Debian, Ubuntu) appear to no longer support Java 8, and build libraries for Java 11, XNAT will no longer run on those newer systems. 
Unless XNAT switches to Java 11 too, of course. I also hope they do soon. Java 8 LTS is from 20014 and already some years old. But it probably requires a lot of time to transfer to the newer Java 11 LTS.

I think XNAT should mention this limitation on their installation website as "requirement" or so. As more and more people will run into this installation problem. 

Thanks,
Edwin

Op donderdag 15 september 2022 om 12:12:37 UTC+2 schreef Duncan Smith:

Pauline Laufer

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Apr 17, 2023, 10:21:33 AM4/17/23
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Dear all,

I am currently setting up a server that should be used for XNAT and choosing the right OS. Ubuntu 22.04 would be my first choice. Is there already a fix for this incompatibility?
Or have you found a workaround Edwin and Duncan?

What version of Ubuntu would you recommend for the use with XNAT?

Thanks a lot in advance,
Pauline

Edwin ter Voert

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Apr 17, 2023, 10:33:42 AM4/17/23
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I installed it on an older Ubuntu version. That worked. It is terrible that they still use(d?) the old java 8 for XNAT.

But there is a newer version of XNAT now. Perhaps it was fixed. 

Best,
Edwin


Op ma 17 apr. 2023 16:21 schreef Pauline Laufer <paulin...@gmail.com>:
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Brad Zoltick

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Apr 17, 2023, 11:12:10 AM4/17/23
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Hi Pauline

I just tried installing the latest version of XNAT with the stock release of Tomcat 9, openjdk-8 and PostgreSQL 14.

Everything works perfectly until you try to do the initial admin:admin setup and you hit the Tomcat 9 — Java 8 incompatibility with some eclipse library.

I understand the difficulty of migrating from
Java 8 to anything > 8.  We also have a Java 8 App that depends on a Java library that was never ported to a later version of Java.

Brad Zoltick

Sent from my iPhone

On Apr 17, 2023, at 10:21 AM, Pauline Laufer <paulin...@gmail.com> wrote:

Dear all,

Rick Herrick

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Apr 17, 2023, 11:32:02 AM4/17/23
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As I noted here, I’m successfully running Ubuntu 22.04.2 with Java 8 (openjdk-8-jdk-headless 1.8.0_362) and Tomcat 9.0.58.0. These are the latest available versions that are showing up on my VM.

How do the versions of these packages on your servers compare with what I posted above?

Rick Herrick
Senior Software Developer


------ Original Message ------
From "Brad Zoltick" <zolt...@gmail.com>
Date 4/17/2023 10:11:57 AM
Subject Re: [XNAT Discussion] Installation of XNAT and the installation manual

Edwin ter Voert

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Apr 18, 2023, 1:08:36 AM4/18/23
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Dear Rick,

Good to know. Then probably somebody fixed the problem in the meantime.

(The packages I used are listed in the post, but they were older, from around Sept 2022)

I am glad to hear that it is working now. I'll try the newer version soon.

Thanks,
Edwin




Op ma 17 apr. 2023 17:32 schreef Rick Herrick <rickh...@flywheel.io>:
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Rick Herrick

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Apr 18, 2023, 10:31:04 AM4/18/23
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Please let us know what you find out.

Rick Herrick
Senior Software Developer


------ Original Message ------
From "Edwin ter Voert" <e.g.w.t...@gmail.com>
Date 4/18/2023 12:08:22 AM
Subject Re: Re[2]: [XNAT Discussion] Installation of XNAT and the installation manual

Brad Zoltick

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Apr 18, 2023, 11:15:09 AM4/18/23
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Hi Rick,

In reference to your earlier reply, I compared the versions of openjdk-8-jdk and tomcat-9 and they match.  I am running the same release of Ubuntu.

/data/xnat> more /etc/os-release
PRETTY_NAME="Ubuntu 22.04.2 LTS"
NAME="Ubuntu"
VERSION_ID="22.04"
VERSION="22.04.2 LTS (Jammy Jellyfish)"
VERSION_CODENAME=jammy
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=jammy

The web server crashes at the initial setup
image.png
And the logs still indicate a version mismatch with the Java class level.   I don't understand why you don't encounter the same error with the docker instance?
Here are the java packages installed on my Ubuntu 22.04.2 LTS system.

Brad Zoltick

root@darwin:/var/log/tomcat9# dpkg --get-selections | grep java
ca-certificates-java install
gir1.2-javascriptcoregtk-4.0:amd64 install
java-common install
javascript-common install
libapache-pom-java install
libatk-wrapper-java install
libatk-wrapper-java-jni:amd64 install
libbcel-java install
libcommons-compress-java install
libcommons-io-java install
libcommons-logging-java install
libcommons-parent-java install
libeclipse-jdt-core-java install
libel-api-java install
libfontbox-java install
libglpk-java:amd64 install
libhsqldb1.8.0-java install
libjavascriptcoregtk-4.0-18:amd64 install
libjavascriptcoregtk-4.1-0:amd64 install
libjsp-api-java install
liblibreoffice-java install
libpdfbox-java install
libreoffice-java-common install
libservlet-api-java install
libservlet3.1-java install
libtaglibs-standard-impl-java install
libtaglibs-standard-spec-java install
libtomcat9-java install
libunoloader-java install
libwebsocket-api-java install
ure-java install
root@darwin:/var/log/tomcat9# dpkg --get-selections | grep jdk
openjdk-8-demo install
openjdk-8-doc install
openjdk-8-jdk:amd64 install
openjdk-8-jdk-headless:amd64 install
openjdk-8-jre:amd64 install
openjdk-8-jre-dcevm:amd64 install
openjdk-8-jre-headless:amd64 install
openjdk-8-jre-zero:amd64 install
openjdk-8-source install
root@darwin:/var/log/tomcat9# dpkg --get-selections | grep eclipse
libeclipse-jdt-core-java install


18-Apr-2023 10:57:49.071 INFO [main] org.apache.catalina.core.ApplicationContext.log 2 Spring WebApplicationInitializers detected on classpath
18-Apr-2023 10:57:49.271 INFO [main] org.apache.catalina.core.ApplicationContext.log Initializing Spring root WebApplicationContext
18-Apr-2023 10:58:15.905 INFO [main] org.apache.catalina.core.ApplicationContext.log Initializing Spring FrameworkServlet 'dispatcher'
18-Apr-2023 10:58:21.623 INFO [main] org.apache.catalina.core.ApplicationContext.log 2 Spring WebApplicationInitializers detected on classpath
18-Apr-2023 10:58:21.721 INFO [main] org.apache.catalina.core.ApplicationContext.log Initializing Spring root WebApplicationContext
18-Apr-2023 10:58:48.372 INFO [main] org.apache.catalina.core.ApplicationContext.log Initializing Spring FrameworkServlet 'dispatcher'
18-Apr-2023 10:59:03.346 SEVERE [http-nio-8080-exec-7] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [jsp] in context with path [] threw exception [java.lang.U

John Flavin

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Apr 19, 2023, 10:54:21 AM4/19/23
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Brad,

I'm not familiar with the libeclipse-jdt-core-java package. But my hypothesis is that you have things configured so that tomcat is trying to start under that java version, not openjdk-8, and under the eclipse version it fails.

I was led to this hypothesis by this line from your error message:
18-Apr-2023 10:59:03.346 SEVERE [http-nio-8080-exec-7] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [jsp] in context with path [] threw exception [java.lang.UnsupportedClassVersionError: org/eclipse/jdt/internal/compiler/env/INameEnvironment has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0]
(Emphasis mine)

Can you check the tomcat configuration or the JAVA_HOME or things like that to see which java version is being used?

John Flavin
Backend Team Lead
He/Him



Brad Zoltick

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Apr 19, 2023, 4:42:58 PM4/19/23
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Hi John,
It looks like a problem with Ubuntu 22.04 LTS


I will follow the recommendations from this posting.

Brad Zoltick


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