OxO2

A SSSOM compliant implementation of OxO that is backwards compatible with OxO version 1

Running OxO2 using Docker

Prerequisites

1. Ensure docker is installed in your environment.

Environment variables

1. Set OXO2_CONFIG environment variable - It should point to the OxO2 config file. This is how OxO2 knows which SSSOM mappings to load. For an example config file see the oxo-config.json in the root of the OxO2 code base. Copy your desired configuration file into the root directory of OXO2. E.g. if your configuration file is my_oxo2_config.json, set OXO2_CONFIG=./my_oxo2_config.json by running export OXO2_CONFIG=./my_oxo2_config.json.

Steps

1. To run OxO2 using docker, run docker compose up. This will start Solr, the OxO2 backend and OxO2 frontend. The frontend will be available at http://localhost:8080, the backend at http://localhost:8081 and Solr at http://localhost:8983.
2. To stop OxO2 run docker compose down.

Running OxO2 locally in Kubernetes using Minikube

Prerequisites

1. Ensure you have a kubernetes cluster available. E.g. for a local k8s cluster using minikube run minikube start --driver=docker.
2. Ensure you have helm installed.

Environment variables

1. Ensure that you have a data release such that have the complete OxO2 available at a $SOLR_HOME.

Mount your data into minikube

1. Mount into minikube: minikube mount --port=39000 $SOLR_HOME:/mnt/oxo/solr-data.

Note: You may need to allow port 39000 through firewall. If so, run: sudo ufw allow 39000/tcp.

Deployment

1. From the root directory run:

helm install oxo2 ./k8chart-local/oxo2 -n ontotools --create-namespace

2. To access locally run:

kubectl port-forward deployment/oxo2-frontend 8080:8080 -n ontotools
kubectl port-forward deployment/oxo2-backend 8081:8081 -n ontotools
kubectl port-forward deployment/oxo2-solr 8983:8983 -n ontotools

and the point your browser to http://localhost:8080. The OxO2 backend will be accessible at http://localhost:8081/ and solr at http://localhost:8983.

To undeploy

1. Run: helm uninstall oxo2 -n ontotools.

Running OxO2 locally from the commandline.

Prerequisites

Ensure the following software is installed and available on the user path.

1. Java 17 or later
2. Maven 3.x
3. Git
4. Solr 9.x - Ensure SOLR_SCRIPT is set to /bin dir SOLR_HOME is set to /server/solr dir of your Solr installation.
5. Nemo - download the latest version from Nemo latest or build from source following instructions here. To check your Nemo installation, run nmo --help. Ensure that nmo is available on the path.

Environment variables

Define the following environment variables:

1. OXO2_DATA - This is where SSSOM files will be downloaded to and where any output of the OxO2 dataload will be written.
2. OXO2_CONFIG - Points to the OxO2 config file. This is how OxO2 knows which SSSOM mappings to load. For an example config file see the oxo-config.json in the root of the OxO2 source code directory. NOTE: This must be the absolute path to the file.
3. SOLR_SCRIPT - This should point to the bin directory of your Solr installation.
4. SOLR_HOME - This should point to the root of your Solr data directory.
5. OXO2_SOLR_HOST - This is the URL to your Solr installation.

Here is an example script for setting environment variables:

export SOLR_SCRIPT=/home/myhome/solr-9.9.0/bin
export SOLR_HOME=/home/myhome/oxo2-data/solr
export PATH=$PATH:/home/myhome/nemo
export OXO2_DATA=/home/myhome/oxo2-data/dataload
export JAVA_OPTS="-Xmx16G"
export OXO2_CONFIG=/home/myhome/oxo2/my_oxo2_config.json
export OXO2_SOLR_HOST=http://localhost:8983/solr

Steps

1. Checkout OxO2: git clone [email protected]:EBISPOT/oxo2.git and change to OxO2 source directory.
2. To build, run: mvn clean install
3. Copy solr config to solr: cp ./oxo2-dataload/solr-config/* $SOLR_HOME
4. Change to dataload directory: cd ./oxo2-dataload
5. Run OxO2 dataload: ./loadData.sh
6. Return to OxO2 root dir: cd ..
7. Start Solr: $SOLR_SCRIPT/solr start --user-managed
8. Run OxO backend: ./startBackend.sh
9. To build and run frontend:
   1. Change directory to frontend: cd oxo2-frontend
   2. Build frontend: npm install
   3. Start frontend: npm run dev
   4. Access frontend from browser at: http://localhost:8080/
   5. Backend is accessible at: http://localhost:8081.