ID3C customizations for the Seattle Flu Study

This repository contains:

• a Sqitch project for managing Seattle Flu-specific static data in the ID3C database, such as organism assignments for targets, extra site details, and bespoke views.

• an ID3C extension which provides additional id3c CLI subcommands and ETL routines.

• additional support data and code

Sqitch

Changes in this Sqitch project can rely on changes in the ID3C Sqitch project by prefixing them with the project name (seattleflu/schema currently, but subject to change after reorganization).

Run the following to deploy all sqitch changes to your local database:

1. Within ID3C:

• sqitch deploy dev @2020-01-14b
• sqitch deploy dev @2020-01-14d --log-only^*
• sqitch deploy dev

2. Within ID3C customizations:

• sqitch deploy dev

* Note: using the --log-only option tells sqitch to log changes without dropping the views that were moved from ID3C core to ID3C customizations.

API

You can also run the customizations portion of the ID3C API from this repository. For local testing, start the API with:

pipenv run python -m id3c.api FLASK_DEBUG=1

and visit http://127.0.0.1:5000/v1/documentation/customizations for documentation on the endpoints contained within this directory.

If you'd like to see how the files get packaged and what is included, simply run

pipenv run python setup.py sdist

Tests

Run all tests with:

pipenv run pytest -v

or name an individual test file, for example:

pipenv run pytest tests/docstrings.py