XNAT upgrade issues

[Simon Doran]

Hi Rick,

  Hope you are around to respond to a couple of issues.

  The first is already solved - just one to think about when packaging the 1.6.5 release. The second I'm a bit stuck on and could do with some help urgently if possible.

1. It's probably worth having pity on those poor people who, like me, have to install XNAT on a machine that has no internet access, such as behind a hospital firewall. I came across the following two issues with bin/setup.sh:

#    [exec] persistence-api-1.0.2.jar

#    [exec] 

#    [exec] Error retrieving artifact from [http://repo1.maven.org/maven/javax.persistence/jars/persistence-api-1.0.2.jar]: java.net.ConnectException: Connection timed out

#    [exec] WARNING: Failed to download persistence-api-1.0.2.jar.

   This one is solved simply via Googling and downloading the jar file on a machine that does have internet access and transferring it (by some institution-approved means!) into the $XNAT_HOME/plugin-resources/repository/javax.persistence/jars/.

You might want to consider shipping the distribution with this file included.

# Downloading https://services.gradle.org/distributions/gradle-2.2.1-bin.zip

#    [exec] 

#    [exec] Exception in thread "main" java.net.ConnectException: Connection timed out

  This occurs during the pipeline build and the way I fixed it was to download gradle-2.2.1-bin.zip from the gradle website and  transfer it to $XNAT_HOME/pipeline-installer. Then I needed to edit the file

/pipeline-installer/gradle/wrapper/gradle-wrapper.properties to comment out the line:

distributionUrl=https\://services.gradle.org/distributions/gradle-2.2.1-bin.zip

and replace it with

distributionUrl=file:///home/xnat/XNAT/Home/code/Current/pipeline-installer/gradle-2.2.1-bin.zip

2. This I need some help on. Everything built nicely - no errors apart from the above. Looking at catalina.out gives me a clean bill of health when I start Tomcat back up. However, when I go to my XNAT page, I find that the browser can't find the required resources:

[Error] Failed to load resource: the server responded with a status of 500 (Internal Server Error) (globals.js, line 0) https://ourserver.icr.ac.uk:8443/XNAT_anonymised/scripts/globals.js

[Error] Failed to load resource: the server responded with a status of 500 (Internal Server Error) (xdat.js, line 0) https://ourserver.icr.ac.uk:8443/XNAT_anonymised/scripts/xdat.js

[Error] Failed to load resource: the server responded with a status of 500 (Internal Server Error) (jquery-1.8.3.min.js, line 0)https://ourserver.icr.ac.uk:8443/XNAT_anonymised/scripts/jquery/jquery-1.8.3.min.js

[Error] ReferenceError: Can't find variable: jQuery

global code (ForgotLogin.vm, line 62)

[Error] Failed to load resource: the server responded with a status of 500 (Internal Server Error) (icons.css, line 0)https://ourserver.icr.ac.uk:8443/XNAT_anonymised/style/icons.css

[Error] Failed to load resource: the server responded with a status of 500 (Internal Server Error) (skin.css, line 0)https://ourserver.icr.ac.uk:8443/XNAT_anonymised/scripts/yui/build/assets/skins/sam/skin.css

[Error] Failed to load resource: the server responded with a status of 500 (Internal Server Error) (calendar.css, line 0)https://ourserver.icr.ac.uk:8443/XNAT_anonymised/scripts/yui/build/calendar/assets/skins/sam/calendar.css

  I am guessing that one of the settings in the existing database that I am upgrading is incompatible with something in the build.properties file that I used in the bin/setup.sh step of the installation. But what might it be and how do I go about sorting things out.

  Best wishes,

Simon

[Herrick, Rick]

Simon,

Do you have any trouble with downloading the files geronimo-j2ee-management_1.1_spec-1.0.1.jar and geronimo-jms_1.1_spec-1.1.1.jar?

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 740-5961

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[Simon Doran]

Hi Rick,

  Thanks for the rapid response. It turns out the the cause of Problem 2 above was easy to fix, but sufficiently unexpected (to me, at least) that it is worth posting here and it shows that one should always look at the logs even when one thinks one knows the answer!

  The problem manifested itself by the XNAT login webpage appearing with no style sheets, images, etc. I went down the root of chasing after a debug of the webpage itself and wondering whether my new build had somehow ended up with all these resources in the wrong place.

  In fact, a quick check of application.log would have showed me the following:

2015-07-01 16:22:44,203 [localhost-startStop-1] ERROR org.springframework.web.servlet.DispatcherServlet - Context initialization failed

org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'scriptRunnerService': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire method: public void org.nrg.automation.services.impl.DefaultScriptRunnerService.setOutputAdapter(org.nrg.automation.runners.ScriptRunnerOutputAdapter); nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.nrg.xnat.utils.BuildDirScriptRunnerOutputAdapter#0' defined in ServletContext resource [/WEB-INF/conf/automation-services-config.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [org.nrg.xnat.utils.BuildDirScriptRunnerOutputAdapter]: Constructor threw exception; nested exception is org.nrg.framework.exceptions.NrgServiceRuntimeException: Error [Unknown]: Error [Unknown]: The path /home/xnat/XNAT/Home/build/ doesn't exist.

        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:287)

  For some reason, I had never created this directory, even though I had referred to it in the build.properties specification.

  Solution: easy!

 mkdir /home/xnat/XNAT/Home/build/

  Thanks again for your help, Rick.

  Best wishes,

Simon

[Herrick, Rick]

Cool, thanks for sending out the update on that, Simon!

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 827-4250

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From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] on behalf of Simon Doran [simon...@icr.ac.uk]
Sent: Tuesday, July 07, 2015 12:49 PM
To: xnat_di...@googlegroups.com
Subject: Re: [XNAT Discussion] XNAT upgrade issues