gideon-api 0.1.0

GIDEON provides epidemiological data going back to 1348 AD. This package provides an interface with the GIDEON API to access its Infectous Disease database within Python.

GIDEON - Python Interface (BETA)

GIDEON Authentication

• The package will attempt to read the environment variable $GIDEON_API_KEY, which is set to your GIDEON API key.
• The API key can be set in the terminal or .bashrc file as export GIDEON_API_KEY=<YOUR API KEY>
• The GIDEON API key can be updated within Python by calling the function gideon_api.set_api_key(<YOUR API KEY>)

Developer Setup

Install the Virtual Environment

1. Install the pipenv Python package by installing it to your Python user install directory with the following terminal command: $python3 -m pip install --user pipenv
2. Setup the developer virtual environment. Enter the root of the project and execute the terminal command $python3 -m pipenv install --dev
3. Enter the virtual environment with the command $python3 -m pipenv shell

Build and Install the gideon_api Package.

• From the root directory, $pip install -e .
• The -e/--editable flag allows the developer to not have to reinstall the package when the Python files are updated.

Build the HTML Documentation

1. Activate the pipenv environment
2. Navigate to the docs/ directory
3. Run make html to build the HTML documents in the build/ subdirectory

Functionality Overview

GIDEON ID Codes

Many of the items in the GIDEON database use an id code, such as diseases, bacteria, drugs, etc. Use gideon_api.lookup_item to get specific item code to use when calling the GIDEON API.

Outbreak Data

The following command will query the GIDEON API for particular outbreak data:

• gideon_api.outbreaks_by_year
• gideon_api.outbreaks_by_country_year
• gideon_api.latest_outbreaks_by_country
• gideon_api.outbreaks_by_disease
• gideon_api.endemic_countries_by_disease
• gideon_api.endemic_diseases_by_country

Query the GIDEON API Directly

• gideon_api.query: This is the main function users should use to send commands to the GIDEON API
• gideon_api.query_online: This version should be used to process the request without interacting with the cache and provides lower level response data.