🏥 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
🔧 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 --debugTo create and register the image:
docker image build --tag mcl-infirmary:latest .
docker image tag mcl-infirmary:latest nutjob4life/mcl-infirmary:latest
docker login
docker image push nutjob4life/mcl-infirmary:latestTo explore the image:
docker container run --rm --interactive --tty --entrypoint /bin/sh mcl-infirmary:latest
