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kyulee-jeon

xnat-on-azure's Issues

Lessons Learned Feedback from JH

I just wanted to suggest some improvements to the XNAT Docker implementation, based on what we learned while deploying to the JH environment:

ARG XNAT_HOME=/xnat/home

This should be under XNAT_ROOT (e.g. /data/xnat/home)

ADD run.sh /usr/local/bin/run.sh

Because of the way Docker containers are built in layers that are cached, this line should be much lower in the Dockerfile so that if the script changes, the rest of the container will be able to be loaded from the cache if there are no other changes.

RUN apt-get update && apt-get install -y postgresql-client wget

This will install the latest PSQL client. It needs to match the version of PSQL that you're connecting to instead.

${XNAT_HOME}/config \
${XNAT_HOME}/logs \
${XNAT_HOME}/plugins \
${XNAT_HOME}/work

These folders should not be created here, as they're being made before the external storage is attached to the container so they won't persist. They should be added to the run.sh file instead.

RUN wget --no-verbose --output-document=/root/ohif-viewer.jar https://bitbucket.org/icrimaginginformatics/ohif-viewer-xnat-plugin/downloads/ohif-viewer-${XNAT_OHIF_VERSION}.jar

Since this plugin persists outside of the actual XNAT install, it should probably be managed separately from the Docker/start scripts. This would also allow for upgrades to the plugin without rebuilding and redeploying the container.

mkdir -p /usr/local/share/xnat
find $XNAT_HOME/config -mindepth 1 -maxdepth 1 -type f -exec cp {} /usr/local/share/xnat \;

What is the purpose of copying the config directory? That new folder only lives on the container and isn't referenced anywhere.

"xnatHomeDir": "/xnat/home",

This needs to live under XNAT_ROOT (similar to the first improvement note)

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