Wrangler

A micro service to lookup and parse a CSV file named after a tube rack barcode provided and return the data in the CSV if found.

The routes of the service are:

Endpoint                           Methods  Rule
---------------------------------  -------  ------------------------------
health_check                       GET      /health
racks.get_tubes_from_rack_barcode  GET      /tube_rack/<tube_rack_barcode>
static                             GET      /static/<path:filename>

Table of Contents

• Requirements for Development
  • Configuring Environment
  • Setup Steps
• Running
• Testing
  • 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)

• Git hooks are executed using lefthook, install lefthook using homebrew and add the pre-commit and pre-push hooks as follows:

  lefthook add pre-commit
  lefthook add pre-push
  

• talisman is used as a credentials checker, to ignore files which it triggers as false positives, follow the instructions in the git commit output by adding the files to be ignore to a .talismanrc file and try commit again.

Configuring Environment

Create a .env file (or copy the .env.example file) with the following values:

SETTINGS_PATH=config/development.py

Setup Steps

1. Create and enter the virtual environment:

    pipenv shell
   

2. Install the required dependencies:

    pipenv install --dev
   

Running

To run the service:

flask run

Testing

Running Tests

To run the test suite:

python -m pytest -vx

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 provided by the mypy library, to run manually:

pipenv run mypy .

Deployment

This project uses a Docker image as the unit of deployment. The image is created by GitHub actions. To trigger the creation of a new image, increment the .release-version version with the corresponding change according to semver.

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