DeepPhe-Viz

Visualization of cancer patient summaries as generated by the DeepPhe NLP tools.

Prerequisites

You must have the following tools install to build this project:

• Nodejs 6.11.1 (includes npm 3.10.10)
• Neo4j 3.2.1 is used to store the graph output

Currently, we have been successfully using the nvm tool to configure and manage our NodeJS environment; nvm enables a user to associate a paritcular NodeJS and NPM version with their Unix shell, allowing for each switching between NodeJS versions across different projects.

Getting Started

First download/clone the DeepPhe-Viz repo and do a maven build:

git clone https://github.com/DeepPhe/DeepPhe-Viz.git
cd DeepPhe-Viz

Installation & Configuration

Installing this package and all its depedencies can be done with a simple command in the package root directory with no arguments:

npm install

Then put your neo4j database connection username and password in config.json. This assumes that you've loaded the DeepPhe NLP gerenated data into your Neo4j database.

Launching The Viz Server

Now you can start the node server with

node server.js

This will start the web server on port 8383 by default. You can go to http://localhost:8383/patients to see the result.

Note: you can type lsof -i :8383 to see if port 8383 is being used.

Development Mode

During development, you don't want to restart the server with node server.js every time after you make changes in the source code. Nodemon is a utility that will monitor for any changes in your source and automatically restart your server. Perfect for development. To install,

npm install -g nodemon

Then just use nodemon instead of node to run your code, and now your process will automatically restart when your code changes.

nodemon server.js