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refactor
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jusa3 committed May 6, 2024
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58 changes: 56 additions & 2 deletions README.md
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# 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
```
1 change: 0 additions & 1 deletion k8s/dataserver/templates/ols4-dataserver-pvc.yaml
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Expand Up @@ -4,7 +4,6 @@ metadata:
creationTimestamp: null
name: {{ .Release.Name }}-pvc
spec:
{{/* storageClassName: standard-nfs-production*/}}
accessModes:
- ReadWriteOnce
resources:
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6 changes: 0 additions & 6 deletions k8s/ols4-backend/templates/ols4-configmap.yaml

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2 changes: 1 addition & 1 deletion k8s/ols4-backend/templates/ols4-neo4j-deployment.yaml
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Expand Up @@ -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:
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2 changes: 0 additions & 2 deletions k8s/ols4-backend/templates/ols4-neo4j-pvc.yaml
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Expand Up @@ -3,8 +3,6 @@ kind: PersistentVolumeClaim
metadata:
name: {{ .Release.Name }}-neo4j-pvc
spec:
{{/* storageClassName: local-storage*/}}
{{/* volumeName: ols4-neo4j-pv*/}}
accessModes:
- ReadWriteOnce
resources:
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10 changes: 0 additions & 10 deletions k8s/ols4-backend/templates/ols4-proxy-configmap.yaml

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2 changes: 1 addition & 1 deletion k8s/ols4-backend/templates/ols4-solr-deployment.yaml
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Expand Up @@ -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:
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2 changes: 0 additions & 2 deletions k8s/ols4-backend/templates/ols4-solr-pvc.yaml
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Expand Up @@ -3,8 +3,6 @@ kind: PersistentVolumeClaim
metadata:
name: {{ .Release.Name }}-solr-pvc
spec:
{{/* storageClassName: local-storage*/}}
{{/* volumeName: ols4-solr-pv*/}}
accessModes:
- ReadWriteOnce
resources:
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2 changes: 2 additions & 0 deletions k8s/ols4-backend/values.yaml
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Expand Up @@ -9,4 +9,6 @@ oidc:
bucket:
backend:
context:
neo4jTarballUrl:
solrTarballUrl:

23 changes: 0 additions & 23 deletions k8s/semlookp-ui/.helmignore

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6 changes: 0 additions & 6 deletions k8s/semlookp-ui/Chart.yaml

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4 changes: 0 additions & 4 deletions k8s/semlookp-ui/README.md

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30 changes: 0 additions & 30 deletions k8s/semlookp-ui/templates/semlookp-frontend-deployment.yaml

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11 changes: 0 additions & 11 deletions k8s/semlookp-ui/templates/semlookp-frontend-service.yaml

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33 changes: 0 additions & 33 deletions k8s/semlookp-ui/templates/semlookp-ingress.yaml

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8 changes: 0 additions & 8 deletions k8s/semlookp-ui/values.yaml

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