The directory specified by base and internal path [${xnat.home}/plugins]/[] does not exist

[Sunil]

Hello Xnat Team

I am facing issue on xnat vagrant setup

Jul 15 12:20:10 xnat-local-release tomcat9[3309]:     ... 37 more
Jul 15 12:20:10 xnat-local-release tomcat9[3309]: Caused by: java.lang.IllegalArgumentException: The directory specified by base and internal path [${xnat.home}/plugins]/[] does not exist.
Jul 15 12:20:10 xnat-local-release tomcat9[3309]:     at org.apache.catalina.webresources.DirResourceSet.checkType(DirResourceSet.java:257)
Jul 15 12:20:10 xnat-local-release tomcat9[3309]:     at org.apache.catalina.webresources.AbstractFileResourceSet.initInternal(AbstractFileResourceSet.java:206)
Jul 15 12:20:10 xnat-local-release tomcat9[3309]:     at org.apache.catalina.webresources.DirResourceSet.initInternal(DirResourceSet.java:265)
Jul 15 12:20:10 xnat-local-release tomcat9[3309]:     at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:136)
Jul 15 12:20:10 xnat-local-release tomcat9[3309]:     ... 44 more
Jul 15 12:20:10 xnat-local-release tomcat9[3309]: Deployment of web application directory [/var/lib/tomcat9/webapps/ROOT.war] has finished in [24] ms
Jul 15 12:20:10 xnat-local-release tomcat9[3309]: Starting ProtocolHandler ["http-nio-8080"]

[Sunil]

Hi Xnat Team,

Thanks, This error fixed  but now facing

   Caused by: org.nrg.framework.exceptions.NrgServiceRuntimeException: Error [Unknown]: Error [Unknown]: An error occurred trying to create the temp folder xnat_23293081767984 in the containing folder /data/xnat/home
                at org.nrg.xnat.initialization.XnatWebAppInitializer.getMultipartConfigElement(XnatWebAppInitializer.java:136)
                at org.nrg.xnat.initialization.XnatWebAppInitializer.customizeRegistration(XnatWebAppInitializer.java:99)
                at org.springframework.web.servlet.support.AbstractDispatcherServletInitializer.registerDispatcherServlet(AbstractDispatcherServletInitializer.java:113)
                at org.springframework.web.servlet.support.AbstractDispatcherServletInitializer.onStartup(AbstractDispatcherServletInitializer.java:71)
                at org.nrg.xnat.initialization.XnatWebAppInitializer.onStartup(XnatWebAppInitializer.java:60)
                at org.springframework.web.SpringServletContainerInitializer.onStartup(SpringServletContainerInitializer.java:169)
                at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5135)
                at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
                ... 38 more
        Caused by: java.nio.file.FileSystemException: /data/xnat/home/work/xnat_232930817679848982889885664969967: Read-only file system
                at sun.nio.fs.UnixException.translateToIOException(UnixException.java:91)
                at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
                at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
                at sun.nio.fs.UnixFileSystemProvider.createDirectory(UnixFileSystemProvider.java:384)
                at java.nio.file.Files.createDirectory(Files.java:674)
                at java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
                at java.nio.file.TempFileHelper.createTempDirectory(TempFileHelper.java:173)
                at java.nio.file.Files.createTempDirectory(Files.java:950)
                at org.nrg.xnat.initialization.XnatWebAppInitializer.getMultipartConfigElement(XnatWebAppInitializer.java:118)

[Rick Herrick]

Is either your /data/xnat/home or /data/xnat/home/work folder mounted as a local share (i.e., mapped to some folder on the host machine)? It could be mounted as a read-only volume.

 

From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of Sunil <sunilsh...@gmail.com>
Date: Tuesday, July 16, 2024 at 8:05 AM
To: xnat_discussion <xnat_di...@googlegroups.com>
Subject: [XNAT Discussion] Re: The directory specified by base and internal path [${xnat.home}/plugins]/[] does not exist

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[Li Wen]

I'm also experiencing this issue. Could you please share how you resolved it?

[Rick Herrick]

Try ssh'ing into the Vagrant VM, cd'ing to /data/xnat/home, then doing something like ls -l plugins. 

If you have that folder mapped to a folder on your host machine, make sure the folder permissions are set properly in your local.yaml file. This is described in the README.md, but for reference it would look something like this:

shares:
    '/local/path/to/plugins':
        - '/data/xnat/home/plugins'
        - ['fmode=644','dmode=755']

While ssh'ed in, you can also check the Tomcat process, something like:

ps ax | egrep tomcat

Look to make sure that -Dxnat.home=/data/xnat/home is somewhere in the command line.

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