README.md

🏥 Infirmary

Welcome to "Infirmary", the ReST-based application programming interface for the Clinical Data component of the the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions. This project, along with Sickbay form a database for discovering clinical data.

⚙️ Endpoints

Once deployed, this package provides the following ReST API endpoints:

Endpoint	Auth	Purpose
/ping		Test if the server is working
/hello/{greeting}	🔐	Test if authentication is working
/clinicalCores	🔐	Return all Clinical Cores in the database, fully serialized
/clinicalCores/{participant_ID}	🔐	Return the single Clinical Core for the named participant_ID
/organs	🔐	Return all organs in the database
/organs/{identifier}	🔐	Return the single organ with the numeric identifier
/specimens	🔐	Return all biospecimens in the database
/specimens/{specimen_ID}	🔐	Return the single biospecimen with the given specimen_ID
/genomics	🔐	Return all genomics in the database
/genomics/{specimen_ID}	🔐	Return the genomics information with the given specimens_ID
/images	🔐	Return all imaging information in the database
/images/{identifier}	🔐	Return the imaging information with the numeric identifier

For those endpoints where the "Auth" column is dispays 🔐, you must provide an HTTP Basic Authentication header with a username and password of a member of the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions. All of the endpoints return a JSON payload.

🔧 Development

To develop locally with a local Postgres database:

python3 -m venv venv
venv/bin/pip install --quiet --upgrade setuptools pip wheel build
venv/bin/pip install --editable '.[dev]'
venv/bin/infirmary --debug

To create and register the image:

docker image build --tag mcl-infirmary:latest .
docker image tag mcl-infirmary:latest edrndocker/mcl-infirmary:latest
docker login
docker image push edrndocker/mcl-infirmary:latest

To explore the image:

docker container run --rm --interactive --tty --entrypoint /bin/sh mcl-infirmary:latest