Reactome Data Image Generation Documentation

This repository does not follow the standard AGR branching strategy, but instead adopts a NEO4j release based branching as neo-x.y. In doing so, it supports an automatic stable GoCD build from such NEO4j versioned branch(es) for use in the staging (and production) environments, while enabling testing of new NEO4j versions on the build environment (on other branches). Any updates within a neo4j release should be done on the matching neo-x.y branch, and then merged into master.

Neo4j edition and plugins

The image is built on Neo4j Community 4.4 (neo4j:4.4.48-community). It serves one database, graph.db, and uses nothing from Enterprise, so there is no Enterprise licence to accept. APOC is fetched at build time for the matching Neo4j minor version and checked against its SHA-256 (APOC_VERSION / APOC_SHA256 in the Dockerfile); to move to a new APOC release, change both.

A dump produced by an older 4.x release loads with neo4j-admin load as before. Queries without an ORDER BY can return rows in a different order on a different Neo4j version, so clients that compare answers byte for byte should compare against the same database.

After a version has been created, the user should create a tagged docker container with the following command

make create-data-image VERSION=<version>
make push-to-dockerhub VERSION=<version>

This will make it so that there is a graphdb_env container available via ECR (by default). If you would like to use this version feel free to specify the version in the add_data's Dockerfile or just use latest.

In order to make changes and test them you might want to create a "develop" container. To do this you can use commands available in the Makefile:

*These are commands done on the development machine. If you are developing locally feel free to use the commands but don't push to ECR

Building develop container

make create-data-image

Make data image

make create-data-image

Share by pushing to container registry

 make push-to-dockerhub VERSION=<VERSION>

Using develop container from container registry

make pull

Make readonly container for production

make create-readonly-image VERSION=<version>

Running Bash inside container

make bash

Run data container

make run

Making Queries

Either go to Localhost:7474 and browse using the UI or use the bolt port within an application