id3c-customizations/

Extensions of ID3C for the Seattle Flu Study

Source code

github.com/seattleflu/id3c-customizations

Contributors

cooperqmarshall

Latest commits

29 Jul 2022 - Merge pull request #337 from seattleflu/phskc-address-encoding-bugfix Check Existence of Location Before Accessing its Identifier

29 Jul 2022 - Check Existence of Location Before Accessing its Identifier Previously the `encode_addresses` function attempted to directly access the location identifier, however this location has the potential of being a null value. We should first make sure the location exists before accessing its identifier.

22 Jul 2022 - Merge pull request #336 from seattleflu/uw-retros-add-vacc UW-retros ETL add sinovac vaccine and rework mapping

22 Jul 2022 - Simplify UW Retros ETL code by reworking vaccine mapping Adding a dictionary to elimiate some of the repeated lines in the previous mapping. Details for each CSX code are stored in a dictionary, and each vaccine name received from REDCap is mapped to one of those entries.

22 Jul 2022 - Add sinovic vaccine to uw-retros ETL mapping A new value was received that was not previously mapped. Sinovac vaccine is being mapped to CVX code 511 (reference: https://www.cdc.gov/vaccines/programs/iis/COVID-19-related-codes.html)

Pages

/ clinical / uw /

/ locations /

/

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