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xnat-on-azure's Introduction

XNAT on Azure

Deploy to Azure

The goal of this repository is to provide code, templates and best practices for deploying XNAT on Azure.

Overview

xnat overview

The repository is organized in src and docs directory. The src directory contains code for building the docker container and ARM templates. The docs directory contains the following:

  1. Loading Images
  2. Setting up a project
  3. Programmatic access to data
  4. Training ML Model on Azure ML

Contributing

This project welcomes contributions and suggestions. Most contributions require you to agree to a Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us the rights to use your contribution. For details, visit https://cla.opensource.microsoft.com.

When you submit a pull request, a CLA bot will automatically determine whether you need to provide a CLA and decorate the PR appropriately (e.g., status check, comment). Simply follow the instructions provided by the bot. You will only need to do this once across all repos using our CLA.

This project has adopted the Microsoft Open Source Code of Conduct. For more information see the Code of Conduct FAQ or contact [email protected] with any additional questions or comments.

Trademarks

This project may contain trademarks or logos for projects, products, or services. Authorized use of Microsoft trademarks or logos is subject to and must follow Microsoft's Trademark & Brand Guidelines. Use of Microsoft trademarks or logos in modified versions of this project must not cause confusion or imply Microsoft sponsorship. Any use of third-party trademarks or logos are subject to those third-party's policies.

xnat-on-azure's People

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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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