semlookp-deployment

Semantic Lookup Platform - Deployment Configuration

Deploy OLS4 backend

Generate data

Enter the OLS4 project. Do as described here.

In short:

• copy the OWL or RDFS ontology file to the testcases folder
• Then make a new config file for your ontology in dataload/configs (you can use efo.json as a template)
• For the ontology_purl property in the config, use e.g. file:///opt/dataload/testcases/myontology.owl if your ontology is in testcases/myontology.owl

export OLS4_CONFIG=./dataload/configs/meshd-v1.json
docker compose up

The data is generated and saved locally in /var/lib/docker/volumes/<your_project_name>/_data

Create data archives for Solr and Neo4j

sudo tar --use-compress-program="pigz --fast --recursive" -cf /neo4j.tgz -C /var/lib/docker/volumes/<your project name>/_data .
sudo tar --use-compress-program="pigz --fast --recursive" -cf /solr.tgz -C /var/lib/docker/volumes/<your project name>/_data .

Eventually, the permissions need to be changed:

sudo chown -R username:username /neo4j.tgz
sudo chown -R username:username /solr.tgz

Deploy ols4-dataserver

helm repo add semlookp-deployment https://zbmed.github.io/semlookp-deployment/
helm install ols4-dataserver semlookp-deployment/ols4-dataserver

Upload data to ols4-dataserver

kubectl cp /neo4j-meshd-v1.tgz ols4-dataserver-7d9d88cd86-n98fb:/usr/share/nginx/html/neo4j.tgz
kubectl cp /solr-meshd-v1.tgz ols4-dataserver-7d9d88cd86-n98fb:/usr/share/nginx/html/solr.tgz

Deploy ols4-backend

helm install <your release name> \
--set-json='ingress.dns="<your domain>"'  \
--set-json='imageTag="dev"'  \
--set-json='backend.context="/ols4"'  \
--set-json='backend.neo4jTarballUrl="http://ols4-dataserver/neo4j.tgz"'  \
--set-json='backend.solrTarballUrl="http://ols4-dataserver/solr.tgz"'  \
semlookp-deployment/k8s/ols4-backend

Funding

This project is developed by the NFDI4Health consortium and the Terminology Services for NFDI (TS4NFDI) project (as part of the Base4NFDI consortium).

The NFDI4Health Consortium gratefully acknowledges the financial support of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – project number 442326535.

The project is derived from the Semantic Lookup Platform SemLookP which was also developed in part by ZB MED - Information Centre for Life Sciences.