Extensions of ID3C for the Seattle Flu Study

Source code

github.com/seattleflu/id3c-customizations

Contributors

Latest commits

12 Jan 2021 - Correct view to drop DOH view before the view it uses

08 Jan 2021 - Merge pull request #177 from seattleflu/linelists views: Create new view for WA DoH linelists

08 Jan 2021 - Merge pull request #176 from seattleflu/uw-reopening-system-dates Uw reopening system dates

05 Jan 2021 - Use survey timestamps for uw-reopening collection date Favor the survey timestamps over custom date fields.

04 Jan 2021 - views: Create new view for WA DoH linelists There is shockingly no view of hcov19 results with all three barcodes plus a result date. Create a view of this as a source of truth when creating linelist exports for the Washington Dept. of Health.

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