OxO2

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

Running OxO2 using docker

Environment variables

The following environment variables must be set:

1. OXO2_DATA - This where SSSOM files will be downloaded to and where any output of the OxO2 dataload will be written.
2. OXO_CONFIG - Points to the OxO2 config file. This is how OxO2 knows which SSSOM mappings to load. For an example see the

Running OxO2 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_HOME is set.
5. Nemo - download the latest version from Nemo latest or build from source following instructions here. To check your Nemo installation, run nmo --help.

Environment variables

Define the following environment variables:

1. OXO2_DATA - This where SSSOM files will be downloaded to and where any output of the OxO2 dataload will be written.
2. OXO_CONFIG - Points to the OxO2 config file. This is how OxO2 knows which SSSOM mappings to load. For an example see the oxo-config.json in root of the OxO2 source code directory.

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/server/solr/configsets
4. Start solr: $SOLR_HOME/bin/solr start --user-managed
5. Run OxO2 dataload: ./oxo2-dataload/loadData.sh
6. Run OxO backend: ./startBackend.sh
7. 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 from browser at: http://localhost:5173/