EpistasisLab / alzkb-site

Alzheimer's Knowledgebase (AlzKB) Site

This repository is comprised of the following components:

• Website: site with some general information about this project. The source code for this website is found in the app directory

• Neo4j: used to store the graph database for this Knowledgebase.

• Nginx: used as a reverse proxy for the Website and the Neo4j Browser

• Docker Compose files

  • The .yml files contain definitions for building a docker image.

• Environmental Variables

  • The environmental variables in .env_sample are used by the different docker services.

Installation

Prerequisites

Docker

• Automated Installation
  • Run install-docker.sh to install Docker Engine
• Manual Installation
  • Install either Docker Desktop or Docker Engine based on your needs.
  • Docker Compose

Building and Running

Building and deploying all services

1. Get a dump file of the database here and put this file in neo4j/dump/, make sure the filename is alzkb.dump (rename it if necessary)
2. Copy the .env_sample as .env and set the variable values as needed for your environment.
3. On the very first run, uncomment the lines for the neo4j-admin service in the docker-compose.yml file, after the first run, the neo4j-admin service is not needed.
4. To deploy the Website, Neo4j, Nginx and dump the database into neo4j run: docker compose up -d --build

Building and deploying the services independently

The services can be built independently of each other as needed.
First, copy the .env_sample as .env and update the variable values as needed for your environment.

• Website
  • Run docker compose -f ./app.yml up -d --build
• Load the database dump
  1. Ensure that the neo4j docker container is not running, it must be stopped if it is.
  2. Get a dump file of the database here and put this file in neo4j/dump/, make sure the filename is alzkb.dump (rename it if necessary)
  3. Run docker compose -f ./neo4j-admin.yml up -d --build
• Neo4j
  • Run docker compose -f ./neo4j.yml up -d --build
• Nginx
  • Run docker compose -f ./nginx.yml up -d --build

Environmental Variables

The .env_sample file contains the following environmental variables:

• COMPOSE_PROJECT_NAME Base name of this project.
  • See the docker documentation for more details.
• ALZKB_HOST IP address (or URL) of the host server where the Website will be deployed.
• ALZKB_NEO4J_BROWSER URL used for the Neo4J Browser, (may be different from ALZKB_HOST)
• ALZKB_APP_SERVICE Name of the docker service where the Website will run. This value is used by Nginx to forward requests to this service.
• ALZKB_PORT Port used by ExpressJS to serve the Website, Nginx will forward requests to ALZKB_HOST to this port.
• ALZKB_DATA_ROOT Directory where the data from Neo4J will be stored on the host machine (data, logs, etc.)
• NEO4J_* variables to configure Neo4j
  • For more information about these varibales, see the neo4j.conf documenation.
  • More details about how these variables map to the neo4j.conf file can be found here
• NODE_ENV Set to either prod or dev
  • see here for more details.