SenNet Entity API

A set of standard RESTful web service that provides CRUD operations into our entity metadata store. A description of the API calls is found here: Entities API.

Entities schema yaml

The yaml file src/resources/hubmap-entities.yaml contains all the attributes of each entity type and generated metadata information of attributes via trigger methods. This file is being used to validate the user input and also as a way of standarding all the details of entities.

Docker build for local/DEV development

There are a few configurable environment variables to keep in mind:

• COMMONS_BRANCH: build argument only to be used during image creation when we need to use a branch of commons from github rather than the published PyPI package. Default to master branch if not set or null.
• HOST_UID: the user id on the host machine to be mapped to the container. Default to 1002 if not set or null.
• HOST_GID: the user's group id on the host machine to be mapped to the container. Default to 1002 if not set or null.

cd docker
./docker-development.sh [check|config|build|start|stop|down]

Docker build for deployment on PROD

cd docker
./docker-deployment.sh [start|stop|down]

Development process

To release via TEST infrastructure

• Make new feature or bug fix branches from main branch (the default branch)
• Make PRs to main
• As a codeowner, Zhou (github username yuanzhou) is automatically assigned as a reviewer to each PR. When all other reviewers have approved, he will approve as well, merge to TEST infrastructure, and redeploy the TEST instance.
• Developer or someone on the team who is familiar with the change will test/qa the change
• When any current changes in the main have been approved after test/qa on TEST, Zhou will release to PROD using the same docker image that has been tested on TEST infrastructure.

To work on features in the development environment before ready for testing and releasing

• Make new feature branches off the main branch
• Make PRs to dev-integrate
• As a codeowner, Zhou is automatically assigned as a reviewer to each PR. When all other reviewers have approved, he will approve as well, merge to devel, and redeploy the DEV instance.
• When a feature branch is ready for testing and release, make a PR to main for deployment and testing on the TEST infrastructure as above.

Updating API Documentation

The documentation for the API calls is hosted on SmartAPI. Modifying the entity-api-spec.yaml file and committing the changes to github should update the API shown on SmartAPI. SmartAPI allows users to register API documents. The documentation is associated with this github account: api-developers@sennetconsortium.org.

Testing

Install the development dependencies using pip install -r src/requirements.dev.txt.

Execute pytest in the root directory to run all unit tests. pytest -W ignore::DeprecationWarning will execute all unit tests without deprecation warnings.