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Manual

Operation

To run rest_variantValidator

In dev mode upsing Python

$ python wsgi.py

You will be provided with a link which will open rest_variantValidator in your web browser. http://127.0.0.1:5000/

Swagger documented functions

The rest_variantValidator functions have swagger documentation to help you generate URLs to make direct API calls utilising human readable text-input boxes.

Once the documented page opens in your web-browser, click the variantvalidator link and the documented functions will appear.

A web-hosted version of this rest API can be found at https://rest.variantvalidator.org

Direct request

Direct URL calls can be made to the rest-API. The easiest way to create these URLs is to use the swagger documented functions

In a Docker container

Apache web-server and mod_wsgi

Mounting rest_variantValidator to an Apache web server requires mod_wsgi

Example Apache configuration

Note: you will need to configure the file paths in the example below

<IfModule wsgi_module>

	WSGIPythonPath /local/miniconda3/envs/vvenv/lib:/local/miniconda3/envs/vvenv/lib/python3.6/site-packages
	WSGIDaemonProcess rest_variantValidator user=wwwrun group=www threads=5
	WSGIScriptAlias / /local/py3Repos/rest_variantValidator/wsgi.py
	WSGIPythonHome /local/miniconda3/envs/vvenv
    	    	
    	<Directory /local/py3Repos/rest_variantValidator/>
        	WSGIProcessGroup rest_variantValidator
         	WSGIApplicationGroup %{GLOBAL}
            Order allow,deny
            Allow from all
            Header set Access-Control-Allow-Origin "*"
            Header set Access-Control-Allow-Methods "GET"
     	</Directory>

</IfModule>
LogLevel crit
CustomLog /local/apache2/log/access_log for_pound

Flask configuration

rest_variantValidator is a Flask application. Flask can be configured using its prefixed environment variable configuration mechanism, so documented settings can be set with a prefix of FLASK_.

This mechanism is also used for Flask extensions such as the Flask-Limiter rate limiter this uses, which can be disabled by setting FLASK_RATELIMIT_ENABLED=.

Additional resources

We are compiling a number of jupyter notebook user guides for rest_variantValidator in rest_variantValidator_manuals