https://github.com/seattleflu/id3c-customizations
Extensions of ID3C for the Seattle Flu Study
https://github.com/seattleflu/id3c-customizations
id3c scan-study seattle-flu-study
Last synced: 3 months ago
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Extensions of ID3C for the Seattle Flu Study
- Host: GitHub
- URL: https://github.com/seattleflu/id3c-customizations
- Owner: seattleflu
- License: mit
- Created: 2019-06-24T18:14:26.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2025-02-04T21:40:25.000Z (over 1 year ago)
- Last Synced: 2025-03-01T18:45:56.250Z (over 1 year ago)
- Topics: id3c, scan-study, seattle-flu-study
- Language: PLpgSQL
- Homepage:
- Size: 3.54 MB
- Stars: 3
- Watchers: 3
- Forks: 0
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Codeowners: docs/CODEOWNERS
Awesome Lists containing this project
README
# 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](https://github.com/seattleflu/id3c/pull/96).
## API
You can also run the customizations portion of the ID3C API from this repository.
For local testing, start the API with:
```
pipenv run python -m id3c.api FLASK_DEBUG=1
```
and visit http://127.0.0.1:5000/v1/documentation/customizations for documentation on
the endpoints contained within this directory.
If you'd like to see how the files get packaged and what is included, simply run
```
pipenv run python setup.py sdist
```
## Tests
Run all tests with:
```sh
pipenv run pytest -v
```
or name an individual test file, for example:
```sh
pipenv run pytest tests/docstrings.py
```