COVIDnet-meta

pl-covidnet-meta is a ChRIS ds plugin which consumes a prediction-default.json from an upstream COVIDnet prediction file and depending on content, might throw an execption.

Abstract

This meta plugin is part of a COVIDnet analysis compute graph. If an upstream processing has inferred COVID infection, this node will throw an exception and terminate. Within the context of the ChRIS UI, this has the effect of coloring the Feed Graph red in the visual representation - in effect providing a simple visual tag on the final result of the compute graph.

Installation

pl-covidnet-meta 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-covidnet-meta as a container:

singularity exec docker://fnndsc/pl-covidnet-meta covidnet_meta [--args values...] input/ output/

To print its available options, run:

singularity exec docker://fnndsc/pl-covidnet-meta covidnet_meta --help

Examples

covidnet_meta 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/
singularity exec docker://fnndsc/pl-covidnet-meta:latest covidnet_meta [--args] incoming/ outgoing/

Development

Instructions for developers.

Building

Build a local container image:

docker build -t localhost/fnndsc/pl-covidnet-meta .

Running

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

docker run --rm -it --userns=host -u $(id -u):$(id -g) \
    -v $PWD/covidnet_meta.py:/usr/local/lib/python3.10/site-packages/covidnet_meta.py:ro \
    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
    localhost/fnndsc/pl-covidnet-meta covidnet_meta /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-covidnet-meta:dev --build-arg extras_require=dev .
docker run --rm -it localhost/fnndsc/pl-covidnet-meta: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-covidnet-meta:1.2.3 .
docker push docker.io/fnndsc/pl-covidnet-meta:1.2.3

Get JSON Representation

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

docker run --rm localhost/fnndsc/pl-covidnet-meta:dev chris_plugin_info > chris_plugin_info.json