Extensions of ID3C for the Seattle Flu Study

Source code

github.com/seattleflu/id3c-customizations

Contributors

Latest commits

10 May 2021 - Merge pull request #212 from seattleflu/reportable-conditions-afh-workplace reportable_conditions: notify specific channels for afh/workplace

06 May 2021 - reportable_conditions: notify specific channels for afh/workplace Send reportable conditions notifications to study-specific slack ncov-reporting channels for adult family homes and workplaces clinical testing.

03 May 2021 - Merge branch 'ci/travis→github'

03 May 2021 - Test on both Ubuntu 20.04 and 18.04 Ubuntu 18.04 is what we currently run in production. "Latest" is currently 20.04, which is useful to keep testing on for forward compat. That said, I don't expect this OS version difference to impact the results of tests very often.

30 Apr 2021 - mypy: Ignore untyped third-party module

Pages

/ locations /

/ clinical / uw /

/

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).

Tests

Run all tests with:

pipenv run pytest -v

or name an individual test file, for example:

pipenv run pytest tests/docstrings.py