Extensions of ID3C for the Seattle Flu Study

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


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.


Run all tests with:

pipenv run pytest -v

or name an individual test file, for example:

pipenv run pytest tests/docstrings.py