sanger / cherrytrack

Cherrytrack

A microservice which defines the database used to store automation system run information and exposes endpoints to ease querying.

Table of Contents

• Requirements for Development
• Getting Started
  • Setup Steps
  • Migrations
• Running
• Testing
  • Testing Requirements
  • Running Tests
• Formatting, Linting and Type Checking
  • Formatting
  • Linting
  • Type Checking
• Deployment
• Miscellaneous
  • Updating the Table of Contents

Requirements for Development

The following tools are required for development:

• python (use pyenv or something similar to install the python version specified in the Pipfile)
• mySQL 8.0 (a docker-compose.yml is included to easily get the database server up and running)

Getting Started

Setup Steps

Install the require dependencies:

pipenv install --dev

Create the following database (currently manually):

• psd_cherrytrack_dev

To generate dummy data for this project you can use SQL statements from:

• Biosero-SQL. In particular see biosero-sql/example-queries which can be run manually on psd_cherrytrack_dev

Migrations

Flask Migrate is a wrapper around Alembic

To check the current state of the migrations, run:

flask db current

To run the migrations:

flask db upgrade

Running

To run the application:

flask run

Testing

Testing Requirements

Create the following database (currently manually):

• psd_cherrytrack_test

Migrate the test database:

SETTINGS_PATH=config/test.py flask db upgrade

Running Tests

To run the test suite:

python -m pytest

Formatting, Linting and Type Checking

Formatting

This project is formatted using black. To run formatting checks, run:

pipenv run black .

Linting

This project is linted using flake8. To lint the code, run:

pipenv run flake8

Type Checking

This project uses static type checking using the mypy library, to run:

pipenv run mypy .

Deployment

This project uses a Docker image as the unit of deployment. To create a release for deployment, create a release in GitHub and wait for the GitHub action to create the Docker image.

The release version should align with the standards.

Miscellaneous

Updating the Table of Contents

To update the table of contents after adding things to this README you can use the markdown-toc node module. To run:

npx markdown-toc -i README.md