refactor

README.md

@@ -1,2 +1,56 @@
-# semlookp-deployment
-Semantic Lookup Platform - Deployment Configuration
+# OLS4 backend deployment
+OLS4 backend - Deployment Configuration
+
+
+## Deploy OLS4 backend
+
+### Generate data
+
+Enter the OLS4 project. Do as described [here](https://github.com/EBISPOT/ols4?tab=readme-ov-file#deploying-ols4).
+
+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
+
+```bash
+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
+```bash
+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:
+```bash
+sudo chown -R username:username /neo4j.tgz
+sudo chown -R username:username /solr.tgz
+```
+
+### Deploy ols4-dataserver
+```bash
+helm repo add semlookp-deployment https://zbmed.github.io/semlookp-deployment/
+helm install ols4-dataserver semlookp-deployment/ols4-dataserver
+```
+
+### Upload data to ols4-dataserver
+```bash
+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
+```bash
+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
+```

k8s/dataserver/templates/ols4-dataserver-pvc.yaml

@@ -4,7 +4,6 @@ metadata:
   creationTimestamp: null
   name: {{ .Release.Name }}-pvc
 spec:
-{{/*  storageClassName: standard-nfs-production*/}}
   accessModes:
     - ReadWriteOnce
   resources:

k8s/ols4-backend/templates/ols4-neo4j-deployment.yaml

@@ -37,7 +37,7 @@ spec:
             - name: NEO4J_dbms_memory_heap_maxSize
               value: 8g
             - name: NEO4J_TARBALL_URL
-              value: {{.Values.neo4jTarballUrl}}
+              value: {{.Values.backend.neo4jTarballUrl}}
             - name: NEO4J_AUTH
               value: none
           ports:

k8s/ols4-backend/templates/ols4-neo4j-pvc.yaml

@@ -3,8 +3,6 @@ kind: PersistentVolumeClaim
 metadata:
   name: {{ .Release.Name }}-neo4j-pvc
 spec:
-{{/*  storageClassName: local-storage*/}}
-{{/*  volumeName: ols4-neo4j-pv*/}}
   accessModes:
     - ReadWriteOnce
   resources:

k8s/ols4-backend/templates/ols4-solr-deployment.yaml

@@ -35,7 +35,7 @@ spec:
               memory: 2000Mi
           env:
             - name: SOLR_TARBALL_URL
-              value: {{.Values.solrTarballUrl}}
+              value: {{.Values.backend.solrTarballUrl}}
             - name: SOLR_HOME
               value: /data
           ports:

k8s/ols4-backend/templates/ols4-solr-pvc.yaml

@@ -3,8 +3,6 @@ kind: PersistentVolumeClaim
 metadata:
   name: {{ .Release.Name }}-solr-pvc
 spec:
-{{/*  storageClassName: local-storage*/}}
-{{/*  volumeName: ols4-solr-pv*/}}
   accessModes:
     - ReadWriteOnce
   resources:

k8s/ols4-backend/values.yaml

@@ -9,4 +9,6 @@ oidc:
     bucket:
 backend:
   context:
+  neo4jTarballUrl:
+  solrTarballUrl: