HuBMAP Data Ingest API

A restful web service exposing calls needed for the Ingest UI React application. The API is documented here.

Working with submodule

This repository relies on the ingest-validation-tools as a submodule for metadata validation. The file .gitmodules contains the configuration for the URL and specific branch of the submodule that is to be used. Once you already have cloned this repository and switched to the target branch, to load the latest ingest-validation-tools submodule:

git submodule update --init --remote

Flask app configuration

This application is written in Flask and it includes an app.cfg.example file in the instance directory. Copy the file and rename it app.cfg and modify with the appropriate information.

Standalone local development

This assumes you are developing the code with the Flask development server and you have access to the remote neo4j database.

Generate the BUILD file

In the project root directory:

./generate-build-version.sh

Install dependencies

Create a new Python 3.x virtual environment:

python3 -m venv venv-hm-ingest-api
source venv-hm-ingest-api/bin/activate

Upgrade pip:

python3 -m pip install --upgrade pip

Then install the dependencies with using the main branch code of commons:

export COMMONS_BRANCH=main
pip install -r requirements.txt

Start the server

Either methods below will run the search-api web service at http://localhost:5005. Choose one:

Directly via Python

python3 app.py

With the Flask Development Server

cd src
export FLASK_APP=app.py
export FLASK_ENV=development
python3 -m flask run -p 5000

Updating API Documentation

The documentation for the API calls is hosted on SmartAPI. Modifying the ingest-api-spec.yaml file and commititng 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@hubmapconsortium.org.

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.