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DEPLOYMENT_INSTRUCTIONS.md

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Unified Biomedical Knowledge Graph (UBKG)

Instructions for deploying the Docker neo4j Distribution

Prerequisites

Access

  1. Obtain access to the Globus collection in which the distribution is stored. (Refer to the main README for details on obtaining access.)
  2. Download the distribution Zip archive, using Globus Connect Personal.

Host machine

  1. Install Docker on the host machine.
  2. The host machine will require considerable disk space, depending on the distribution. As of December 2023, distribution sizes were around:
    • HuBMAP/SenNet: 9GB
    • Data Distillery: 20GB

Simple Deployment

This deployment uses default settings.

img_3.png

  1. Expand the Zip archive. The expanded distribution directory will contain:
    • a directory named Data. This directory contains the UBKG neo4j database files.
    • a script named build_container.sh. This script builds a Docker container hosting the UBKG instance of neo4j.
    • container.cfg.example. This is an annotated example of the configuration file required by build_container.sh.
  2. Copy container.cfg.example to a file named container.cfg.
  3. Start Docker Desktop.
  4. Open a Terminal session.
  5. Move to the distribution directory.
  6. Execute ./build_container.sh.
  7. The build_container.sh will run for a short time (1-2 minutes), and will be finished when it displays a message similar to [main] INFO org.eclipse.jetty.server.Server - Started Server@16fa5e34{STARTING}[10.0.15,sto=0] @11686ms

img_6.png

The build_container.sh will create a Docker container with the following default properties:

Property Value
container name ubkg-neo4j-<version>
image name hubmap/ubkg-neo4j
image tag current-release
ports 4000:7474
4500:7687
read-write read-only

img_5.png

  1. Open a browser window. Enter http://localhost:4000/browser/.
  2. The neo4j browser window will appear. Enter connection information:
Property Value
Connect URL bolt://localhost:4000
Authentication Type Username/Password
Username neo4j
Password abcd1234

img_7.png 10. Select Connect.

Custom Deployment

Changes to Docker configuration

To modify the Docker configuration, change values in the configuration file. Keeping the value commented results in the script using a default value.

Value Purpose Recommendation
container_name Name of the Docker container accept default
docker_tag Tag for the Docker container accept default
neo4j_password Password for the neo4j user minimum of 8 characters, including at least one letter and one number
ui_port Port used by the neo4j browser number other than 7474 to prevent possible conflicts with local installations of neo4j
bolt_port Port used by neo4j bolt (Cypher) number other than 7687 to prevent possible conflicts with local installations of neo4j
read_mode Whether the neo4j database is read-only or read-write accept default (read-only)
db_mount_dir Path to the external neo4j database accept default (/data)
all others Not used for deployment; values will be ignored accept default

Rename configuration file

To specify another configuration file, execute the command /.build_container.sh external -c <your configuration file>