Update Helm Chart

deployment/Chart.yaml

@@ -1,21 +1,6 @@
 apiVersion: v2
 name: cloud-registry
 description: A Helm chart for Kubernetes
-
-# A chart can be either an 'application' or a 'library' chart.
-#
-# Application charts are a collection of templates that can be packaged into versioned archives
-# to be deployed.
-#
-# Library charts provide useful utilities or functions for the chart developer. They're included as
-# a dependency of application charts to inject those utilities and functions into the rendering
-# pipeline. Library charts do not define any templates and therefore cannot be deployed.
 type: application
-
-# This is the chart version. This version number should be incremented each time you make changes
-# to the chart and its templates, including the app version.
-version: 0.1.0
-
-# This is the version number of the application being deployed. This version number should be
-# incremented each time you make changes to the application.
-appVersion: 1.16.0
+version: 2.0.0
+appVersion: 2.0.0

deployment/templates/NOTES.txt

@@ -0,0 +1,11 @@
+Elixir Cloud Service Registry is being deployed!
+
+Once deployed:
+
+  1. Access the API via https://{{ .Values.host_name }}/ga4gh/registry/v1/
+
+     To test the connection, you can run:
+
+       curl -X GET "https://{{ .Values.host_name }}/ga4gh/registry/v1/service-info" -H "Accept: application/json" -H "Authorization: Bearer {TOKEN}"
+
+  2. Access the Swagger UI via https://{{ .Values.host_name }}/ga4gh/registry/v1/ui

deployment/templates/cloud-registry-configmap-job.yaml

@@ -29,10 +29,9 @@ spec:
         - name: HOST_NAME
           value:  {{ .Values.host_name }}
         - name: MONGO_HOST
-          value: mongodb-{{ .Values.cloud-registry.appName }}
+          value: mongodb
       restartPolicy: Never
       serviceAccountName: {{ .Values.cloud_registry.appName }}-configurer
-status: {}
 ---
 apiVersion: v1
 kind: ServiceAccount

deployment/templates/cloud-registry-deploy.yaml

@@ -27,7 +27,7 @@ spec:
         ports:
         - containerPort: 8080
           protocol: TCP
-        resources: {}
+        resources: {{- toYaml .Values.cloud_registry.resources | nindent 10 }}
         terminationMessagePath: /dev/termination-log
         terminationMessagePolicy: File
         volumeMounts:
@@ -47,4 +47,3 @@ spec:
               path: config.yaml
           name: app-config
         name: config-yaml
-status:

deployment/templates/cloud-registry-ingress.yaml

@@ -0,0 +1,29 @@
+{{ if .Values.cloud_registry.ingress.enabled }}
+apiVersion: networking.k8s.io/v1
+kind: Ingress
+metadata:
+  annotations:
+    {{- if .Values.cloud_registry.ingress.https.enabled }}
+    cert-manager.io/cluster-issuer: {{ .Values.cloud_registry.ingress.https.issuer }}
+    kubernetes.io/tls-acme: "true"
+    {{- end }}
+  name: {{ .Values.cloud_registry.appName }}
+spec:
+  rules:
+  - host: {{ .Values.host_name }} 
+    http:
+      paths:
+      - path: /
+        pathType: Prefix
+        backend:
+          service:
+            name: {{ .Values.cloud_registry.appName }} 
+            port:
+              number: 8080
+{{- if .Values.cloud_registry.ingress.https.enabled }}
+  tls:
+  - hosts:
+    - {{ .Values.host_name }}
+    secretName: {{ .Values.cloud_registry.appName }}-ingress-secret
+{{- end }}
+{{ end }}

deployment/templates/cloud-registry-route.yaml

@@ -1,4 +1,4 @@
-{{ if .Capabilities.APIVersions.Has "route.openshift.io/v1" }}
+{{ if (and (.Capabilities.APIVersions.Has "route.openshift.io/v1") (not .Values.cloud_registry.ingress.enabled)) }}
 apiVersion: route.openshift.io/v1
 kind: Route
 metadata:
@@ -15,6 +15,4 @@ spec:
     name: {{ .Values.cloud_registry.appName }}
     weight: 100
   wildcardPolicy: None
-status:
-  ingress: []
 {{ end }}

deployment/templates/cloud-registry-service.yaml

@@ -12,5 +12,3 @@ spec:
     app: {{ .Values.cloud_registry.appName }}
   sessionAffinity: None
   type: ClusterIP
-status:
-  loadBalancer: {}

deployment/templates/mongo-deploy.yaml

@@ -27,12 +27,15 @@ spec:
         ports:
         - containerPort: 27017
           protocol: TCP
-        resources: {}
+        resources: {{- toYaml .Values.mongodb.resources | nindent 10 }}
         terminationMessagePath: /dev/termination-log
         terminationMessagePolicy: File
         volumeMounts:
         - mountPath: /data/db/
           name: mongodb
+        - name: init-script
+          mountPath: /docker-entrypoint-initdb.d/init-script.js
+          subPath: init-script.js
       dnsPolicy: ClusterFirst
       restartPolicy: Always
       schedulerName: default-scheduler
@@ -42,4 +45,6 @@ spec:
       - name: mongodb
         persistentVolumeClaim:
           claimName: mongodb
-status:
+      - name: init-script
+        configMap:
+          name: mongo-init-script

deployment/templates/mongo-init-script.yaml

@@ -0,0 +1,21 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: mongo-init-script
+data:
+  init-script.js: |
+    db = db.getSiblingDB('serviceStore');
+
+    // Create the 'services' and 'service_info' collections
+    // Database configuration from https://github.com/elixir-cloud-aai/cloud-registry/blob/fa8a1b0dd1361751574550116150a630035dc199/cloud_registry/config.yaml#L32
+    db.createCollection('services');
+    db.services.createIndex(
+      { id: 1 },
+      { unique: true }
+    );
+    db.createCollection('service_info');
+    db.service_info.createIndex(
+      { id: 1 },
+      { unique: true }
+    );
+

deployment/templates/mongo-pvc.yaml

@@ -8,4 +8,3 @@ spec:
   resources:
     requests:
       storage: {{ .Values.mongodb.volumeSize }}
-status:

deployment/templates/mongo-service.yaml

@@ -14,5 +14,3 @@ spec:
     app: mongodb
   sessionAffinity: None
   type: ClusterIP
-status:
-  loadBalancer: {}

deployment/values.yaml

@@ -2,14 +2,35 @@
 # This is a YAML-formatted file.
 # Declare variables to be passed into your templates.
 
-host_name: cloud-registry.rahtiapp.fi
+host_name: ""
 
 cloud_registry:
-  image: elixircloud/cloud-registry:0.1.0
+  image: elixircloud/cloud-registry:20240716
   appName: cloud-registry
+  # if ingress.enabled: false, it will deploy an OpenShift Route (https://docs.redhat.com/en/documentation/openshift_container_platform/4.19/html/network_apis/route-route-openshift-io-v1)
+  ingress:
+    enabled: true
+    https:
+      enabled: false
+      issuer: letsencrypt-prod
+  resources:
+    limits:
+      cpu: 100m
+      memory: 128Mi
+    requests:
+      cpu: 100m
+      memory: 128Mi
 
 apiServer: kubernetes.default.svc:443 # address of k8s API server
 
 mongodb:
-  image: mongo:3.6
+  image: docker.io/library/mongo:noble
   volumeSize: 1Gi
+  resources:
+    limits:
+      cpu: 200m
+      memory: 512Mi
+    requests:
+      cpu: 200m
+      memory: 512Mi
+