This directory contains the files needed to create the Docker images used to run the UBKG Neo4j container. Docker images supporting both x86-64 and arm64 platforms are built. For details on Docker using this image to host the UBKG in Neo4j, consult the README.md at the root of this respository.
- Docker must be installed with Docker BuildX build support. By default Docker BuildX support is installed with Docker Desktop. If you have a version of Docker installed without Desktop you can install Docker BuildX manually.
- The bash shell scripts contained in this directory are intended for use on Mac OS X or Linux. These scripts will not work on Windows. (The resulting Docker images will, however, run on Windows.)
The build-push-multi-arch.sh script is a bash script which will build and push to DockerHub the UBKG Neo4j Docker images with support for both x86-64 and amd64 platforms. The script takes advantage of the Docker Buildx build --platform option to create the multi-platform images.
Before running this script first log into DockerHub with the docker login command using an account that has write privileges in the HuBMAP DockerHub Organization.
usage: ./build-push-multi-arch.sh [-rv version]
If run without the -rv option the script will build the multi-platform images and push them to DockerHub with the tag hubmap/ubkg-neo4j:latest.
If given the -rv <version argument the script will build the multi-platrom images and push them to DockerHub with the addional tags of hubmap/ubkg-neo4j:current-release and hubmap/ubkg-neo4j:<version>, where is replaced with the version entered as the version argument.
e.g. ./build-push-multi-arch.sh -rv 3.2.4
usage: ./build-local.sh
The build-local.sh simply builds a local image for use during development and debugging of the UBKG Neo4j Docker container. The locally built image will be tagged as ubkg-neo4j-local To run the local image use the run.sh script at the top level directory in this repository with the arguments -t local.
| File | Description | Scope |
|---|---|---|
| Dockerfile | Instructions for building the container | Build file |
| neo4j.conf | Configuration file for the neo4j instance | Added to image |
| neo4j.conf.noauth | Version of configuration file used for operations that require disabling authentication | Added to image |
| indexes_constraints.cypher | Set of neo4j Cypher instructions to set constraints and build indices in the UBKG Neo4j database | added to image |
| start.sh | Script that configures the neo4j database per parameters | Added to image |
| File | Description |
|---|---|
| build-local.sh | Builds the Docker image locally (not pushed to DockerHub). The image is built and tagged as ubkg-neo4j-local. |
| build-push-multi-arch.sh | Builds images for x86-64 and arm64 platforms and pushes the images to DockerHub. |
The file indexes_constraints.cypher creates indexes and constraints in the neo4j database. This Cypher script runs after ontology CSVs have been imported into the database, and is called by an external shell script.
The Cypher commands in the script result in the creation of a large number of relationship indexes (from 1800 to over 2000). Because index creation in Cypher is asynchronous, the script causes a large number of parallel processes. For large UBKG instances, the script can result in Out of Memory Errors.
To mitigate the risk of OOMEs, run the Python script create_indexes_and_constraints.py instead of the Shell script create_indexes_and_constraints.sh.