Geneweaver 3 API

Description: The API for the Geneweaver v3 application ecosystem.

Setup

Local

Requirements

• Python Poetry
• Python 3.9 or higher
• A connection to a copy of the Geneweaver Database

Setup

1. Clone the repository
2. Run poetry install in project root to install dependencies
3. Configure environment settings with environment variables or a .env file.
4. Run the application

To run the app execute either uvicorn geneweaver.api.main:app --reload with the poetry virtualenv activated, or just run poetry run uvicorn geneweaver.api.main:app --reload.

This will host the application on http://127.0.0.1:8000/ which means the swagger docs page is available at http://127.0.0.1:8000/docs.

Code linters

Ruff rules: (https://docs.astral.sh/ruff/rules/)

From active local environment on command line run:

ruff src/ tests/ --fix

then run black (code formatter: https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html)

black src/ tests/

Unit test

Create appropriate test per code modifications without dependencies to external resources such as DB, Webserver, or APIs. Create appropriate mocks for external resources and data as needed.

Tests directory: geneweaver-api/tests

To execute tests, from the command line run:

pytest tests --cov=geneweaver.api --cov-report term  --cov-report html 

Continuous Integration & Deployment

When a PR is crated in GitHub, it will automatically trigger a workflow that will run the tests and build the docker images, and then deploy to dev. Please be aware of this when creating tests in order to avoid conflicts with other PRs.

When a PR is merged into main, it will automatically trigger a workflow that will run the tests and build the docker images, and then deploy to sqa.

In order for any deployment to run, other than to dev, two things must be true: - the deployment must be approved by SQA. - the version number in pyproject.toml must be incremented.

In order for the stage and prod deployments to run, the version number in pyproject.toml must not contain a letter. This indicates that it is a release version.

Version Numbers

When creating a bugfix or feature addition PR, it is required that your version number contains a letter. This indicates to SQA that the code needs to be tests before it is released.

For example, if the current version is 0.1.0, then your PR should increment the version number to 0.1.1a0 when creating a bugfix PR. The SQA team will then test your code in the sqa environment.

If the code passes SQA testing, they will inform you that 0.1.1a0 has passed QA, at which point you should create a PR with a single line change that increments the version number to 0.1.1.

If 0.1.1a0 fails QA, then you will need to create a fix, and increment the version number to 0.1.1a1. This process will continue until the code passes QA, at which point you will increment the version number to 0.1.1 and create a PR to merge into