Installing the app on a virtual environment with a running instance of MongoDB

Prerequisites

To use this server you'll need to have a working instance of MongoDB. from the mongo shell you can create a database and an authenticated user to handle connections using this syntax:

use pmatcher
db.createUser(
   {
     user: "pmUser",
     pwd: "pmPassword",
     roles: [ "dbOwner" ]
   }
)

After setting up the restricted access to the server you'll just have to launch the mongo demon using authentication:

mongod --auth --dbpath path_to_database_data

Clone patientMatcher repository from github using this command:

git clone https://github.com/Clinical-Genomics/patientMatcher.git

Change directory to the cloned folder and from there install the software using the following command:

pip install -r requirements.txt
pip install -e .

To customize the server configuration you'll need to edit the config.py file under the /instance folder.   For testing purposes you can keep the default configuration values as they are, but keep in mind that you should adjust these numbers when in production.

To start the server run this command:

pmatcher run -h custom_host -p custom_port

Please note that the code is NOT guaranteed to be bug-free and it must be customized to be used in production.