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.
Project description
GIDEON - Python Interface (BETA)
A package for accessing the GIDEON API using Python.
The gideon_api
package provides functions to access the GIDEON API without the need of writing your own REST API queries.
GIDEON Authentication
- The GIDEON API requires the use of an API key, which can be set in two ways:
- 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 either in the terminal for the current terminal session only or the
$HOME/.bashrc
file for persistent storage. In either case, set the API key with the lineexport GIDEON_API_KEY=<YOUR API KEY>
- The API key can be set either in the terminal for the current terminal session only or the
- The GIDEON API key can be updated within Python by calling the function
gideon_api.set_api_key(<YOUR API KEY>)
. Be sure to protect your key and not store it in code or a repository shared with others.
Basic Installation
$ pip install --user gideon-api
Developer Installation
Install the Python Virtual Environment
- Install the
pipenv
Python environment manager.- Install the
pipenv
Python package to your Python user install directory with the following terminal command:$python3 -m pip install --user pipenv
- Install the
- Install the developer virtual environment.
Change directory to the repository root and execute the terminal command
$python3 -m pipenv install --dev
- From the repository root or an of its subdirectories, 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
- Activate the project's pipenv environment. Follow step #3 from the "Install the Virtual Environment" section.
- Change directory to the repository's
docs/
directory, one level below the root of the repository. - Run
make html
to build the HTML documents in thebuild/
subdirectory. If thebuild/
directory does not exist, it will be generated by themake html
command.
Functionality Overview
GIDEON ID Codes
Many of the items in the GIDEON database use a unique identifier code, such as diseases, bacteria, drugs, etc. Refer to the GIDEON ID Codes Documentation for a list of lookup functions.
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 APIgideon_api.query_online
: This version should be used to process the request without interacting with the cache and provides lower level response data.
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