Extensions of ID3C for the Seattle Flu Study

Source code

github.com/seattleflu/id3c-customizations

Contributors

Latest commits

17 Sep 2021 - Merge pull request #244 from seattleflu/uw-reopening-migrated-records-check Skip HCT migrated records with no non-enrollment encounters

15 Sep 2021 - Skip HCT migrated records with no non-enrollment encounters We are postponing processing of enrollment records for the HCT migrated records until the data issues with those record are resolved in REDCap. This is causing warnings when there are DETs being processed for migrated records' enrollment forms that do not have any non-enrollment forms filled out. Each FHIR bundle with a patient resource must contain at least one encounter resource, which typically would be covered because the enrollment itself counts as an encounter. Because those are not being processed for migrated records there needs to be at least one non-enrollment encounter to create a valid FHIR bundle. This change checks to make sure that is the case before generating the FHIR bundle.

14 Sep 2021 - Merge pull request #239 from seattleflu/uw-etl-barcode-swabsend etl uw-reopening: Include kit registration barcodes

10 Sep 2021 - Merge pull request #233 from seattleflu/seidelma/feature/hct_redcap_changes (WIP) Add new HCT REDCap URL

10 Sep 2021 - Merge pull request #243 from seattleflu/reportable-conditions-null-workbook Handle missing provenance workbook value in Slack post function

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).

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