copyxnat 0.2.8

CopyXnat is a python utility for copying XNAT projects from one XNAT server to another

CopyXnat

A utility for downloading or copying projects between XNAT servers.

This is a prerelease. It may not work as intended, and may lead to data loss. Please use caution when running on production servers

Quick start

Please make sure your XNAT archive and PostgreSQL database are fully backed up before running CopyXnat on a real XNAT server. CopyXnat may modify and overwrite your data.

Install and run using pip (Python 3.6+)

You need Python 3.6 or later. It is recommended that you do not modify your system Python installation. You can use tools such as Homebrew (macOS) to install the latest python version without affecting your system python.

    pip install copyxnat --upgrade
    copyxnat --help

Install and run using Docker

If you have Docker installed you can run CopyXnat in a container. Note that interactive mode (-it) is generally required in order to enter server passwords where prompted.

    docker run --rm -it tomdoel/copyxnat --help

Example use cases

Show project contents

• Print a list of projects, subjects etc on an XNAT server

  copyxnat -s "https://YOUR-SERVER-URL" -u "YOUR-USER-NAME" show
  

Download projects

• Download XNAT projects onto your computer

  copyxnat --src_host "https://YOUR-SERVER-URL" --src_user "YOUR-USER-NAME" --project "PROJECT1,PROJECT2" export
  

• Download all projects you have access to onto your computer

  copyxnat --src_host "https://YOUR-SERVER-URL" --src_user "YOUR-XNAT-USER-NAME" export
  

Copy projects from one XNAT server to another

• Duplicate a project on a destination server

  copyxnat --src_host "https://SOURCE-SERVER-URL" --src_user "XNAT-USER-SOURCE" --project "PROJECT-NAME" copy --dst_host "https://DEST-SERVER-URL" --dst_user "XNAT-USER-DEST"
  

• Duplicate a project and rename

  copyxnat --src_host "https://SOURCE-SERVER-URL" --src_user "XNAT-USER-SOURCE"  --project "PROJECT-NAME:NEW-PROJECT-NAME" copy --dst_host "https://DEST-SERVER-URL" --dst_user "XNAT-USER-DEST"
  

• Duplicate a project on the same server (with a new name)

  copyxnat --src_host "https://SERVER-URL" --src_user "XNAT-USER-SOURCE"  --project "PROJECT-NAME:NEW-PROJECT-NAME" copy --dst_host "https://SERVER-URL" --dst_user "XNAT-USER-DEST"
  

Using CopyXnat in your own code

Importing via pip

You can import and run the module with pip and then import from your code

    from copyxnat.xnat.run_command import run_command
    from copyxnat.commands.show_command import ShowCommand

    result = run_command(command=ShowCommand,
                         src_host=src_host,
                         src_user=src_user,
                         src_pw=src_pw,
                         project_filter=None)

Local development: running the command-line utility directly

You can run directly from the source code. This is primarily useful if you are modifying the code.

   pip install -r requirements-dev.txt
   python copyxnat --help

Links

• Documentation
• Source code
• PyPi
• Docker Hub

Authors

• Tom Doel

Copyright

Copyright 2021 Tom Doel

License

This project is released under the MIT License. Please see the license file for details.