Extensions of ID3C for the Seattle Flu Study

Source code

github.com/seattleflu/id3c-customizations

Contributors

Latest commits

24 Feb 2021 - Merge pull request #197 from seattleflu/prioritize-clia-results Prioritize Clia results

24 Feb 2021 - Tag schema

24 Feb 2021 - Update order in shipping.hcov19_presence_absence_result_v1 Prioritize 'Clia' results over other `assay_type` in this view so that Clia results are always included if available. This change was prompted by certain barcodes showing as 'Pending' in the results portal even though the results were available. When Research results come in after the Clia results, they replace the Clia results in this view. These Research results are then filtered out in `shipping.return_results_v3`, leading to samples showing up as 'Pending'.

22 Feb 2021 - Merge pull request #196 from seattleflu/childcare-etl-fix Childcare ETL: replace 'illness_q_date'

19 Feb 2021 - Childcare ETL: replace 'illness_q_date' The 2021 Childcare project doesn't have the `illness_q_date` variable like the pilot version ("Childcare") does. Both projects have this info collected on a "Symptom Check" survey, so both have `symptom_check_timestamp' available, so we can use that variable. The revision is bumped so that we will have this collected consistently across the two studies.

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