# [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
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
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)
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine