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: about 2 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 (over 5 years ago)
• Default Branch: master
• Last Pushed: 2024-09-16T23:55:55.000Z (3 months ago)
• Last Synced: 2024-09-17T20:54:09.868Z (3 months ago)
• Topics: id3c, scan-study, seattle-flu-study
• Language: PLpgSQL
• Homepage:
• Size: 3.52 MB
• Stars: 3
• Watchers: 3
• Forks: 0
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Codeowners: docs/CODEOWNERS

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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

```