Update Helm Chart

deployment/Chart.yaml

@@ -2,5 +2,5 @@ apiVersion: v2
 name: protes
 description: A proTES Helm chart for Kubernetes
 type: application
-version: 0.1.0
-appVersion: 1.16.0
+version: 2.0.0
+appVersion: 2.0.0

deployment/templates/flower/flower-deployment.yaml

@@ -18,4 +18,5 @@ spec:
       - image: {{ .Values.flower.image }}
         command: ['flower']
         args: ['--broker=amqp://guest:guest@rabbitmq:5672//', '--port=5555', '--basic_auth={{ .Values.flower.basicAuth }}']
-        name: flower
+        name: flower
+        resources: {{- toYaml .Values.flower.resources | nindent 10 }}

deployment/templates/mongodb/mongo-init-script.yaml

@@ -0,0 +1,41 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: mongo-init-script
+data:
+  init-script.js: |
+    db = db.getSiblingDB('taskStore');
+    dbproTES = db.getSiblingDB('{{ tpl .Values.mongodb.secret.databaseName . }}')
+
+    dbproTES.createUser({
+      user: "{{ tpl .Values.mongodb.secret.databaseUser . }}",
+      pwd: "{{ tpl .Values.mongodb.secret.databasePassword . }}",
+      roles: [
+        {
+          role: "readWrite",
+          db: "{{ tpl .Values.mongodb.secret.databaseName . }}"
+        }
+      ]
+    });
+
+    // Create the 'tasks' and 'service_info' collections
+    // Database configuration from https://github.com/elixir-cloud-aai/proTES/blob/2f2d88915d9948b0d2ffbe6799af01bbc413b00a/pro_tes/config.yaml#L30
+    db.createCollection('tasks');
+    db.runs.createIndex(
+      { task_id: 1, worker_id: 1 },
+      { unique: true, sparse: true }
+    );
+    db.createCollection('service_info');
+    db.service_info.createIndex(
+      { id: 1 }
+    );
+
+    dbproWES.createCollection('runs');
+    dbproWES.runs.createIndex(
+      { run_id: 1, task_id: 1 },
+      { unique: true, sparse: true }
+    );
+    dbproWES.createCollection('service_info');
+    dbproWES.service_info.createIndex(
+      { id: 1}
+    );

deployment/templates/mongodb/mongodb-deployment.yaml

@@ -16,25 +16,30 @@ spec:
     spec:
       containers:
         - env:
-          - name: MONGODB_USER
+          - name: MONGO_INITDB_ROOT_USERNAME
             valueFrom:
               secretKeyRef:
-                key: database-user
+                key: databaseRootUsername
                 name: {{ .Values.mongodb.appName }}
-          - name: MONGODB_PASSWORD
+          - name: MONGO_INITDB_ROOT_PASSWORD
             valueFrom:
               secretKeyRef:
-                key: database-password
+                key: databaseRootPassword
                 name: {{ .Values.mongodb.appName }}
-          - name: MONGODB_ADMIN_PASSWORD
+          - name: MONGO_INITDB_DATABASE
             valueFrom:
               secretKeyRef:
-                key: database-admin-password
+                key: databaseName
                 name: {{ .Values.mongodb.appName }}
-          - name: MONGODB_DATABASE
+          - name: MONGO_APP_USERNAME
             valueFrom:
               secretKeyRef:
-                key: database-name
+                key: databaseUser
+                name: {{ .Values.mongodb.appName }}
+          - name: MONGO_APP_PASSWORD
+            valueFrom:
+              secretKeyRef:
+                key: databasePassword
                 name: {{ .Values.mongodb.appName }}
           image: {{ .Values.mongodb.image }}
           imagePullPolicy: IfNotPresent
@@ -57,20 +62,23 @@ spec:
                 - '-i'
                 - '-c'
                 - >-
-                  mongo 127.0.0.1:27017/$MONGODB_DATABASE -u $MONGODB_USER -p
-                  $MONGODB_PASSWORD --eval="quit()"
+                  mongosh --host 127.0.0.1:27017 -u $MONGO_INITDB_ROOT_USERNAME -p $MONGO_INITDB_ROOT_PASSWORD --authenticationDatabase admin $MONGO_INITDB_DATABASE --eval="quit()"
             failureThreshold: 3
-            initialDelaySeconds: 3
+            initialDelaySeconds: 30
             periodSeconds: 10
             successThreshold: 1
             timeoutSeconds: 1
-          resources:
-            limits:
-              memory: 512Mi
+          resources: {{- toYaml .Values.mongodb.resources | nindent 12 }}
           volumeMounts:
-            - mountPath: /var/lib/mongodb/data
+            - mountPath: /data/db
               name: mongodb-data
+            - name: init-script
+              mountPath: /docker-entrypoint-initdb.d/init-script.js
+              subPath: init-script.js
       volumes:
         - name: mongodb-data
           persistentVolumeClaim:
             claimName: {{ .Values.mongodb.appName }}-volume
+        - name: init-script
+          configMap:
+            name: mongo-init-script

deployment/templates/mongodb/mongodb-pvc.yaml

@@ -4,7 +4,7 @@ metadata:
   name: {{ .Values.mongodb.appName }}-volume
 spec:
   accessModes:
-    - ReadWriteMany
+    - {{ .Values.storageAccessMode }}
   resources:
     requests:
       storage: {{ .Values.mongodb.volumeSize }}

deployment/templates/mongodb/mongodb-secret.yaml

@@ -4,7 +4,7 @@ type: Opaque
 metadata:
   name: {{ .Values.mongodb.appName }}
 data:
-  database-admin-password: {{ .Values.mongodb.databaseAdminPassword  | b64enc }}
-  database-name: {{ .Values.mongodb.databaseName  | b64enc }}
-  database-password: {{ .Values.mongodb.databasePassword  | b64enc }}
-  database-user: {{ .Values.mongodb.databaseUser  | b64enc }}
+  {{- range $key, $val := .Values.mongodb.secret }}
+    "{{ $key }}": "{{ tpl $val $ | b64enc }}"
+  {{- end }}
+

deployment/templates/protes/celery-deployment.yaml

@@ -16,6 +16,7 @@ spec:
         image: busybox
         command: [ 'mkdir' ]
         args: [ '-p', '/data/db', '/data/output', '/data/tmp' ]
+        resources: {{- toYaml .Values.celeryWorker.initResources | nindent 10 }}
         volumeMounts:
         - mountPath: /data
           name: protes-volume
@@ -34,29 +35,23 @@ spec:
         - name: MONGO_USERNAME
           valueFrom:
             secretKeyRef:
-              key: database-user
+              key: databaseUser
               name: {{ .Values.mongodb.appName }}
         - name: MONGO_PASSWORD
           valueFrom:
             secretKeyRef:
-              key: database-password
+              key: databasePassword
               name: {{ .Values.mongodb.appName }}
         - name: MONGO_DBNAME
           valueFrom:
             secretKeyRef:
-              key: database-name
+              key: databaseName
               name: {{ .Values.mongodb.appName }}
         - name: RABBIT_HOST
           value: {{ .Values.rabbitmq.appName }}
         - name: RABBIT_PORT
           value: "5672"
-        resources:
-          requests:
-            memory: "512Mi"
-            cpu: "300m"
-          limits:
-            memory: "8Gi"
-            cpu: "1"
+        resources: {{- toYaml .Values.celeryWorker.resources | nindent 10 }}
         volumeMounts:
         - mountPath: /data
           name: protes-volume

deployment/templates/protes/protes-deployment.yaml

@@ -12,11 +12,24 @@ spec:
       labels:
         app: {{ .Values.protes.appName }}
     spec:
+      {{- if eq .Values.storageAccessMode "ReadWriteOnce" }}
+      affinity:
+        podAffinity:
+          requiredDuringSchedulingIgnoredDuringExecution:
+          - labelSelector:
+              matchExpressions:
+              - key: app
+                operator: In
+                values:
+                - {{ .Values.celeryWorker.appName }}
+            topologyKey: "kubernetes.io/hostname"
+      {{- end }}
       initContainers:
       - name: vol-init
         image: busybox
         command: [ 'mkdir' ]
         args: [ '-p', '/data/db', '/data/specs' ]
+        resources: {{- toYaml .Values.protes.initResources | nindent 10 }}
         volumeMounts:
         - mountPath: /data
           name: protes-volume
@@ -35,22 +48,23 @@ spec:
         - name: MONGO_USERNAME
           valueFrom:
             secretKeyRef:
-              key: database-user
+              key: databaseUser
               name: {{ .Values.mongodb.appName }}
         - name: MONGO_PASSWORD
           valueFrom:
             secretKeyRef:
-              key: database-password
+              key: databasePassword
               name: {{ .Values.mongodb.appName }}
         - name: MONGO_DBNAME
           valueFrom:
             secretKeyRef:
-              key: database-name
+              key: databaseName
               name: {{ .Values.mongodb.appName }}
         - name: RABBIT_HOST
           value: {{ .Values.rabbitmq.appName }}
         - name: RABBIT_PORT
           value: "5672"
+        resources: {{- toYaml .Values.protes.resources | nindent 10 }}
         livenessProbe:
           tcpSocket:
             port: protes-port

deployment/templates/protes/protes-volume.yaml

@@ -5,7 +5,7 @@ metadata:
   name: {{ .Values.protes.appName}}-volume
 spec:
   accessModes:
-    - ReadWriteMany
+    - {{ .Values.storageAccessMode }} 
   resources:
     requests:
-      storage: '1Gi'
+      storage: '1Gi'

deployment/templates/rabbitmq/rabbitmq-deployment.yaml

@@ -17,10 +17,11 @@ spec:
       containers:
       - name: rabbitmq
         image: {{ .Values.rabbitmq.image }}
+        resources: {{- toYaml .Values.rabbitmq.resources | nindent 10 }}
         volumeMounts:
         - mountPath: /var/lib/rabbitmq
           name: rabbitmq-volume
       volumes:
       - name: rabbitmq-volume
         persistentVolumeClaim:
-          claimName: {{ .Values.rabbitmq.appName }}-volume
+          claimName: {{ .Values.rabbitmq.appName }}-volume

deployment/templates/rabbitmq/rabbitmq-pvc.yaml

@@ -5,7 +5,7 @@ metadata:
   name: {{ .Values.rabbitmq.appName }}-volume
 spec:
   accessModes:
-    - ReadWriteMany
+    - {{ .Values.storageAccessMode }}
   resources:
     requests:
       storage: {{ .Values.rabbitmq.volumeSize }}

deployment/values.yaml

@@ -2,35 +2,81 @@
 # This is a YAML-formatted file.
 # Declare variables to be passed into your templates.
 
-applicationDomain: rahtiapp.fi
+applicationDomain: ""
 
 # which cluster type proTES is going to be deployed on
 # it can be either 'kubernetes' or 'openshift'
-clusterType: openshift
+clusterType: kubernetes
+
+# mongodb-pvc.yaml/rabbitmq-pvc.yaml, change to ReadWriteMany if storageClass can do RWX
+storageAccessMode: ReadWriteOnce
 
 flower:
   appName: protes-flower
   basicAuth: admin:admin
   image: endocode/flower
+  resources:
+    limits:
+      cpu: 200m
+      memory: 1Gi
+    requests:
+      cpu: 200m
+      memory: 500Mi
 
 protes:
   appName: protes
   image: elixircloud/protes:latest
+  initResources:
+    limits:
+      memory: 16Mi
+      cpu: 50m
+    requests:
+      memory: 16Mi
+  resources:
+    limits:
+      memory: 256Mi
+      cpu: 100m
+    requests:
+      memory: 256Mi
+      cpu: 100m
 
 celeryWorker:
   appName: celery-worker
   image: elixircloud/protes:latest
+  initResources:
+    limits:
+      memory: 16Mi
+      cpu: 50m
+    requests:
+      memory: 16Mi
+      cpu: 50m
+  resources:
+    limits:
+      cpu: 200m
+      memory: 256Mi
+    requests:
+      cpu: 100m
+      memory: 256Mi
 
 mongodb:
   appName: mongodb
-  databaseAdminPassword: adminpasswd
-  databaseName: protes-db
-  databasePassword: protes-db-passwd
-  databaseUser: protes-user
+  secret:
+    databaseRootUsername: prowes-adm
+    databaseRootPassword: adminpasswd
+    databaseUser: prowes-user
+    databasePassword: prowes-db-passwd
+    databaseName: prowes-db
   volumeSize: 1Gi
-  image: centos/mongodb-36-centos7
+  image: docker.io/library/mongo:noble
 
 rabbitmq:
   appName: rabbitmq
   volumeSize: 1Gi
-  image: rabbitmq:3-management
+  image: rabbitmq:4.1.4-management
+  resources:
+    limits:
+      cpu: 200m
+      memory: 1Gi
+    requests:
+      cpu: 200m
+      memory: 256Mi