A dynamic registration workflow control plugin

pl-dy_regiFlow is a ChRIS ds plugin that dynamically orchestrates a registration and anonymization workflow. It interfaces with a PACS endpoint to retrieve DICOM data, triggers downstream anonymization and conversion pipelines in CUBE/ChRIS, and manages workflow execution through polling and optional parallelization.

Abstract

Clinical imaging workflows often require conditional execution, polling, and coordination across multiple systems such as PACS archives and ChRIS/CUBE. pl-dy_regiFlow provides a dynamic control layer that retrieves DICOM studies based on a provided JSON specification, interacts with a PACS endpoint for registration and query/retrieve, launches anonymization and conversion pipelines in ChRIS, and monitors workflow progress until completion.

Installation

pl-dy_regiFlow is a ChRIS plugin, meaning it can run from either within ChRIS or the command-line.

Local Usage

To get started with local command-line usage, use Apptainer (a.k.a. Singularity) to run pl-dy_regiFlow as a container:

apptainer exec docker://fnndsc/pl-dy_regiFlow reg_iFlow [--args values...] input/ output/

To print its available options, run:

apptainer exec docker://fnndsc/pl-dy_regiFlow reg_iFlow --help

Examples

reg_iFlow requires two positional arguments: a directory containing input data, and a directory where to create output data. First, create the input directory and move input data into it.

mkdir incoming/ outgoing/
mv some.dat other.dat incoming/
apptainer exec docker://fnndsc/pl-dy_regiFlow:latest reg_iFlow [--args] incoming/ outgoing/

Development

Instructions for developers.

Building

Build a local container image:

docker build -t localhost/fnndsc/pl-dy_regiFlow .

Running

Mount the source code reg_iFlow.py into a container to try out changes without rebuild.

docker run --rm -it --userns=host -u $(id -u):$(id -g) \
    -v $PWD/dy_regiFlow.py:/usr/local/lib/python3.12/site-packages/dy_regiFlow.py:ro \
    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
    localhost/fnndsc/pl-dy_regiFlow reg_iFlow /incoming /outgoing

Testing

Run unit tests using pytest. It's recommended to rebuild the image to ensure that sources are up-to-date. Use the option --build-arg extras_require=dev to install extra dependencies for testing.

docker build -t localhost/fnndsc/pl-dy_regiFlow:dev --build-arg extras_require=dev .
docker run --rm -it localhost/fnndsc/pl-dy_regiFlow:dev pytest

Release

Steps for release can be automated by Github Actions. This section is about how to do those steps manually.

Increase Version Number

Increase the version number in setup.py and commit this file.

Push Container Image

Build and push an image tagged by the version. For example, for version 1.2.3:

docker build -t docker.io/fnndsc/pl-dy_regiFlow:1.2.3 .
docker push docker.io/fnndsc/pl-dy_regiFlow:1.2.3

Get JSON Representation

Run chris_plugin_info to produce a JSON description of this plugin, which can be uploaded to ChRIS.

docker run --rm docker.io/fnndsc/pl-dy_regiFlow:1.2.3 chris_plugin_info -d docker.io/fnndsc/pl-dy_regiFlow:1.2.3 > chris_plugin_info.json

Intructions on how to upload the plugin to ChRIS can be found here: https://chrisproject.org/docs/tutorials/upload_plugin