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.
Tests
Run all tests with:
pipenv run pytest -v
or name an individual test file, for example:
pipenv run pytest tests/docstrings.py