Extensions of ID3C for the Seattle Flu Study

Source code

github.com/seattleflu/id3c-customizations

Contributors

Latest commits

25 Nov 2020 - Merge pull request #168 from seattleflu/fix-zipcode-error etl redcap-det scan: Fix error when the zip code field is empty

23 Nov 2020 - etl redcap-det scan: Update zip code field handling 1. Update :func: `zipcode_map` to check if the provided *redcap_code* is an emptry string to catch the edge case of when the zipcode field is empty. This field may be an empty string if edited by internal SFS members for participants that live outside the SCAN coverage zip codes. We've been doing in person dropoffs for priority codes that can be outside of the normal SCAN coverage. 2. Replace the UnknownRedcapZipCode error with a warning that does not stop the entire ETL pipeline. We want a notification when we run into an unknown zip code, but it shouldn't stop the ingest process. There's no need to update the geocoding process because SmartyStreets can handle address lookups without a zipcode.

19 Nov 2020 - Merge pull request #167 from seattleflu/childcare-add-event Accommodate unscheduled event in childcare ETL

19 Nov 2020 - Accommodate unscheduled event in childcare ETL The unscheduled event has fewer instruments than a regular scheduled encounter event but is similar enough that this ETL job can treat it just like a scheduled encounter event.

19 Nov 2020 - Merge pull request #164 from seattleflu/season-3 views: Edit S2 end date, add S3

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