From 6a876bcfab6e32d3cfdd9da020e7a5282321e14e Mon Sep 17 00:00:00 2001
From: Tristan <tristan.perard@outlook.com>
Date: Mon, 6 Oct 2025 14:32:21 +0300
Subject: [PATCH 1/7] Edit Helm Chart

- Add resources
- Add a key to change the storage mode
  - if RWO, the prowes pods will be deployed on the same nodes
---
 .../templates/flower/flower-deployment.yaml   |  1 +
 .../templates/mongodb/mongodb-deployment.yaml |  4 +-
 deployment/templates/mongodb/mongodb-pvc.yaml |  2 +-
 .../templates/prowes/celery-deployment.yaml   | 15 +++----
 .../templates/prowes/prowes-deployment.yaml   | 20 +++++++++
 .../templates/prowes/prowes-volume.yaml       |  2 +-
 .../rabbitmq/rabbitmq-deployment.yaml         |  3 +-
 .../templates/rabbitmq/rabbitmq-pvc.yaml      |  4 +-
 deployment/values.yaml                        | 42 ++++++++++++++++++-
 9 files changed, 76 insertions(+), 17 deletions(-)

diff --git a/deployment/templates/flower/flower-deployment.yaml b/deployment/templates/flower/flower-deployment.yaml
index 44ada45..4e1cb64 100644
--- a/deployment/templates/flower/flower-deployment.yaml
+++ b/deployment/templates/flower/flower-deployment.yaml
@@ -19,3 +19,4 @@ spec:
         command: ['flower']
         args: ['--broker=amqp://guest:guest@rabbitmq:5672//', '--port=5555', '--basic_auth={{ .Values.flower.basicAuth }}']
         name: flower
+        resources: {{- toYaml .Values.flower.resources | nindent 10 }}
diff --git a/deployment/templates/mongodb/mongodb-deployment.yaml b/deployment/templates/mongodb/mongodb-deployment.yaml
index 22261d7..90f1646 100644
--- a/deployment/templates/mongodb/mongodb-deployment.yaml
+++ b/deployment/templates/mongodb/mongodb-deployment.yaml
@@ -64,9 +64,7 @@ spec:
             periodSeconds: 10
             successThreshold: 1
             timeoutSeconds: 1
-          resources:
-            limits:
-              memory: 512Mi
+          resources: {{- toYaml .Values.mongodb.resources | nindent 10 }}
           volumeMounts:
             - mountPath: /var/lib/mongodb/data
               name: mongodb-data
diff --git a/deployment/templates/mongodb/mongodb-pvc.yaml b/deployment/templates/mongodb/mongodb-pvc.yaml
index 70fc970..dede4b5 100644
--- a/deployment/templates/mongodb/mongodb-pvc.yaml
+++ b/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 }}
\ No newline at end of file
diff --git a/deployment/templates/prowes/celery-deployment.yaml b/deployment/templates/prowes/celery-deployment.yaml
index c8d05d1..578e3c5 100644
--- a/deployment/templates/prowes/celery-deployment.yaml
+++ b/deployment/templates/prowes/celery-deployment.yaml
@@ -16,6 +16,13 @@ spec:
         image: busybox
         command: [ 'mkdir' ]
         args: [ '-p', '/data/db', '/data/output', '/data/tmp' ]
+        resources:
+          limits:
+            memory: 256Mi
+            cpu: 100m
+          requests:
+            memory: 256Mi
+            cpu: 100m
         volumeMounts:
         - mountPath: /data
           name: prowes-volume
@@ -50,13 +57,7 @@ spec:
           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: prowes-volume
diff --git a/deployment/templates/prowes/prowes-deployment.yaml b/deployment/templates/prowes/prowes-deployment.yaml
index 7b54166..2662a2e 100644
--- a/deployment/templates/prowes/prowes-deployment.yaml
+++ b/deployment/templates/prowes/prowes-deployment.yaml
@@ -12,11 +12,24 @@ spec:
       labels:
         app: {{ .Values.prowes.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.prowes.resources | nindent 10 }}
         volumeMounts:
         - mountPath: /data
           name: prowes-volume
@@ -51,6 +64,13 @@ spec:
           value: {{ .Values.rabbitmq.appName }}
         - name: RABBIT_PORT
           value: "5672"
+        resources:
+          limits:
+            cpu: 500m
+            memory: 256Mi
+          requests:
+            cpu: 100m
+            memory: 256Mi
         livenessProbe:
           tcpSocket:
             port: prowes-port
diff --git a/deployment/templates/prowes/prowes-volume.yaml b/deployment/templates/prowes/prowes-volume.yaml
index fc07e34..2e7e6cd 100644
--- a/deployment/templates/prowes/prowes-volume.yaml
+++ b/deployment/templates/prowes/prowes-volume.yaml
@@ -5,7 +5,7 @@ metadata:
   name: {{ .Values.prowes.appName}}-volume
 spec:
   accessModes:
-    - ReadWriteMany
+    - {{ .Values.storageAccessMode }}
   resources:
     requests:
       storage: '1Gi'
diff --git a/deployment/templates/rabbitmq/rabbitmq-deployment.yaml b/deployment/templates/rabbitmq/rabbitmq-deployment.yaml
index 7b8926f..212cfbe 100644
--- a/deployment/templates/rabbitmq/rabbitmq-deployment.yaml
+++ b/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
\ No newline at end of file
+          claimName: {{ .Values.rabbitmq.appName }}-volume
diff --git a/deployment/templates/rabbitmq/rabbitmq-pvc.yaml b/deployment/templates/rabbitmq/rabbitmq-pvc.yaml
index 544e239..9d36f77 100644
--- a/deployment/templates/rabbitmq/rabbitmq-pvc.yaml
+++ b/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 }}
\ No newline at end of file
+      storage: {{ .Values.rabbitmq.volumeSize }}
diff --git a/deployment/values.yaml b/deployment/values.yaml
index d821db7..fdbb672 100644
--- a/deployment/values.yaml
+++ b/deployment/values.yaml
@@ -2,24 +2,47 @@
 # This is a YAML-formatted file.
 # Declare variables to be passed into your templates.
 
-applicationDomain: rahtiapp.fi
+applicationDomain: ""
 
 # which cluster type proWES is going to be deployed on
 # it can be either 'kubernetes' or 'openshift'
 clusterType: kubernetes
 
+# mongodb-pvc.yaml/rabbitmq-pvc.yaml, change to ReadWriteMany if storageClass can do RWX
+storageAccessMode: ReadWriteOnce
+
 flower:
   appName: prowes-flower
   basicAuth: admin:admin
   image: endocode/flower
-
+  resources:
+    limits:
+      cpu: 500m
+      memory: 1Gi
+    requests:
+      cpu: 300m
+      memory: 500Mi
 prowes:
   appName: prowes
   image: elixircloud/prowes:latest
+  resources:
+    limits:
+      memory: 256Mi
+      cpu: 100m
+    requests:
+      memory: 256Mi
+      cpu: 100m
 
 celeryWorker:
   appName: celery-worker
   image: elixircloud/prowes:latest
+  resources:
+    limits:
+      cpu: 500m
+      memory: 256Mi
+    requests:
+      cpu: 100m
+      memory: 256Mi
 
 mongodb:
   appName: mongodb
@@ -29,8 +52,23 @@ mongodb:
   databaseUser: prowes-user
   volumeSize: 1Gi
   image: centos/mongodb-36-centos7
+  resources:
+    limits:
+      cpu: 500m
+      memory: 512Mi
+    requests:
+      cpu: 500m
+      memory: 512Mi
 
 rabbitmq:
   appName: rabbitmq
   volumeSize: 1Gi
   image: rabbitmq:3-management
+  resources:
+    limits:
+      cpu: 500m
+      memory: 1Gi
+    requests:
+      cpu: 500m
+      memory: 256Mi
+

From 09d546e3f15a52b05aad1cfc898a33a0a35f0b3e Mon Sep 17 00:00:00 2001
From: Tristan <tristan.perard@outlook.com>
Date: Mon, 6 Oct 2025 14:45:53 +0300
Subject: [PATCH 2/7] Add initResources

---
 deployment/templates/prowes/celery-deployment.yaml |  8 +-------
 deployment/templates/prowes/prowes-deployment.yaml | 10 ++--------
 deployment/values.yaml                             | 14 ++++++++++++++
 3 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/deployment/templates/prowes/celery-deployment.yaml b/deployment/templates/prowes/celery-deployment.yaml
index 578e3c5..8538891 100644
--- a/deployment/templates/prowes/celery-deployment.yaml
+++ b/deployment/templates/prowes/celery-deployment.yaml
@@ -16,13 +16,7 @@ spec:
         image: busybox
         command: [ 'mkdir' ]
         args: [ '-p', '/data/db', '/data/output', '/data/tmp' ]
-        resources:
-          limits:
-            memory: 256Mi
-            cpu: 100m
-          requests:
-            memory: 256Mi
-            cpu: 100m
+        resources: {{- toYaml .Values.celeryWorker.initResources | nindent 10 }}
         volumeMounts:
         - mountPath: /data
           name: prowes-volume
diff --git a/deployment/templates/prowes/prowes-deployment.yaml b/deployment/templates/prowes/prowes-deployment.yaml
index 2662a2e..4bd1f86 100644
--- a/deployment/templates/prowes/prowes-deployment.yaml
+++ b/deployment/templates/prowes/prowes-deployment.yaml
@@ -29,7 +29,7 @@ spec:
         image: busybox
         command: [ 'mkdir' ]
         args: [ '-p', '/data/db', '/data/specs' ]
-        resources: {{- toYaml .Values.prowes.resources | nindent 10 }}
+        resources: {{- toYaml .Values.prowes.initResources | nindent 10 }}
         volumeMounts:
         - mountPath: /data
           name: prowes-volume
@@ -64,13 +64,7 @@ spec:
           value: {{ .Values.rabbitmq.appName }}
         - name: RABBIT_PORT
           value: "5672"
-        resources:
-          limits:
-            cpu: 500m
-            memory: 256Mi
-          requests:
-            cpu: 100m
-            memory: 256Mi
+        resources: {{- toYaml .Values.prowes.resources | nindent 10 }}
         livenessProbe:
           tcpSocket:
             port: prowes-port
diff --git a/deployment/values.yaml b/deployment/values.yaml
index fdbb672..dd10066 100644
--- a/deployment/values.yaml
+++ b/deployment/values.yaml
@@ -25,6 +25,13 @@ flower:
 prowes:
   appName: prowes
   image: elixircloud/prowes:latest
+  initResources:
+    limits:
+      memory: 16Mi
+      cpu: 10m
+    requests:
+      memory: 16Mi
+      cpu: 10m
   resources:
     limits:
       memory: 256Mi
@@ -36,6 +43,13 @@ prowes:
 celeryWorker:
   appName: celery-worker
   image: elixircloud/prowes:latest
+  initResources:
+    limits:
+      memory: 16Mi
+      cpu: 10m
+    requests:
+      memory: 16Mi
+      cpu: 10m
   resources:
     limits:
       cpu: 500m

From 5db765cec56f05e6db50a177abad8e73687072e1 Mon Sep 17 00:00:00 2001
From: Tristan <74349933+trispera@users.noreply.github.com>
Date: Thu, 9 Oct 2025 11:29:19 +0300
Subject: [PATCH 3/7] Fix min requests

---
 deployment/values.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/deployment/values.yaml b/deployment/values.yaml
index dd10066..05658b9 100644
--- a/deployment/values.yaml
+++ b/deployment/values.yaml
@@ -28,10 +28,10 @@ prowes:
   initResources:
     limits:
       memory: 16Mi
-      cpu: 10m
+      cpu: 50m
     requests:
       memory: 16Mi
-      cpu: 10m
+      cpu: 50m
   resources:
     limits:
       memory: 256Mi
@@ -46,10 +46,10 @@ celeryWorker:
   initResources:
     limits:
       memory: 16Mi
-      cpu: 10m
+      cpu: 50m
     requests:
       memory: 16Mi
-      cpu: 10m
+      cpu: 50m
   resources:
     limits:
       cpu: 500m

From f5bc49c97bdb1ea3ef7a2e5738d504f04382b7e6 Mon Sep 17 00:00:00 2001
From: Tristan <tristan.perard@outlook.com>
Date: Fri, 10 Oct 2025 14:26:21 +0300
Subject: [PATCH 4/7] Update mongodb and rabbitMQ

---
 deployment/README.md                          | 99 ++++---------------
 .../templates/mongodb/mongo-init-script.yaml  | 41 ++++++++
 .../templates/mongodb/mongodb-deployment.yaml | 38 ++++---
 .../templates/mongodb/mongodb-secret.yaml     |  8 +-
 .../templates/prowes/celery-deployment.yaml   |  6 +-
 .../templates/prowes/prowes-deployment.yaml   |  6 +-
 deployment/values.yaml                        | 18 ++--
 7 files changed, 104 insertions(+), 112 deletions(-)
 create mode 100644 deployment/templates/mongodb/mongo-init-script.yaml

diff --git a/deployment/README.md b/deployment/README.md
index 5ba6509..11a7667 100644
--- a/deployment/README.md
+++ b/deployment/README.md
@@ -3,8 +3,6 @@
 - [Kubernetes deployment for proWES](#kubernetes-deployment-for-wes)
     - [Usage](#usage)
         - [Updates](#updates)
-        - [Using with an external MongoDB](#using-with-an-external-mongodb)
-        - [Setting up RabbitMQ for testing on OpenShift](#setting-up-rabbitmq-for-testing-on-openshift)
     - [Technical details](#technical-details)
         - [MongoDB](#mongodb)
         - [RabbitMQ](#rabbitmq)
@@ -53,37 +51,23 @@ Create a Kubernetes Secret from the `.netrc` file:
 kubectl create secret generic netrc --from-file .netrc
 ```
 
-After this you can deploy proWES using `kubectl`:
+You need to edit the `values.yaml` file to specify your `applicationDomain` and the `clusterType`
 
-```bash
-cd deployment/common/wes
-ls wes-* | xargs -L1 kubectl create -f
-```
-
-Once proWES is deployed, you can expose it with the YAML files found under
-`deployment/ingress`. Which file to use depends on your cluster and how ingress
-is configured there.
-
-Creating an OpenShift Route:
+After this you can deploy proWES using `helm`:
 
 ```bash
-cd deployment/ingress
-oc create -f wes-route.yaml
+helm install prowes . -f values.yaml
 ```
 
 ### Updates
 
-If you make changes to any of the Deployments, you can update them with
-`kubectl`. For example, this is how you would update the Celery worker Deployment:
+If you want to edit any of the Deployments, you can update them with
+`helm` and the `values.yaml` file. Once edited, you can run this command:
 
 ```bash
-kubectl replace -f wes-celery-deployment.yaml
+helm upgrade prowes . -f values.yaml
 ```
 
-The OpenShift specific objects need to be updated using the `oc` tool instead.
-Also, if you update the Route you must use the `--force` flag. This removes and
-recreates the Route.
-
 If you want to point to a different FTP server or change the login credentials
 for the current FTP server, you can update the `.netrc` secret like so:
 
@@ -91,57 +75,22 @@ for the current FTP server, you can update the `.netrc` secret like so:
 kubectl create secret generic netrc --from-file .netrc --dry-run -o yaml | kubectl apply -f -
 ```
 
-If you want to update the configuration, you can update the ConfigMap or use a
-different ConfigMap with the same name. The Deployments expect to find the
-`app_config.yaml` ConfigMap with the name `wes-config`. You can update the
-ConfigMap like so:
-
-```bash
-kubectl replace -f wes-configmap.yaml
-```
-
-### Using with an external MongoDB
-
-In certain situations, you may want to run an external MongoDB. There is an
-example headless service file for this case under `deployment/mongodb`.
-
-Make a copy of the example Service:
-
-```bash
-cd deployment/mongodb
-cp mongodb-service-external.yaml.example mongodb-service-external.yaml
-```
-
-Edit the `mongodb-service-external.yaml` file and under `externalName` add your
-external MongoDB's host name. After this, create the Service:
-
-```bash
-kubectl create -f mongodb-service-external.yaml
-```
+## Technical details
 
-It is assumed that the external MongoDB already has a database called
-`prowes-db` created and a user with read-write access available. Next you
-will need to configure the MongoDB user and password in a secret (replace
-`<username>` and `<password>`):
+### MongoDB
 
-```bash
-kubectl create secret generic mongodb --from-literal=database-user=<username> --from-literal=database-password=<password>
-```
+The MongoDB database is deployed using:
 
-Depending on your MongoDB provider, the port may differ from 27017. In this
-case, you will need to modify the Deployment files accordingly to use the
-correct port (replace `<my external mongodb port>`):
+- `templates/mongodb/mongodb-deployment.yaml`
 
-```bash
-cd deployment/common
-find . -name *.yaml | xargs -L1 sed -i -e 's/27017/<my external mongodb port>/g'
-```
+### RabbitMQ
 
-After this you can deploy proWES (see above).
+The message broker RabbitMQ that allows the app to communicate with the worker
+is deployed using:
 
-## Technical details
+- `templates/rabbitmq/rabbitmq-deployment.yaml`
 
-### ApplicaWES
+### WES
 
 proWES consists of five deployments: a Flask server and a Celery worker. These
 are deployed using:
@@ -150,22 +99,14 @@ are deployed using:
 - `templates/prowes/celery-deployment.yaml`
 
 These deployments depend on setting up a shared ReadWriteMany volume between
-Flask and Celery (`wes-volume.yaml`) and a shared ConfigMap
 (`wes-configmap.yaml`).
 
-### MongoDB
 
-The MongoDB database is deployed using:
-
-- `templates/mongodb/mongodb-deployment.yaml`
-
-### RabbitMQ
+## Destroy
 
-The message broker RabbitMQ that allows the app to communicate with the worker
-is deployed using:
+Simply run:
 
-- `templates/rabbitmq/rabbitmq-deployment.yaml`
+```bash
+helm uninstall prowes
+```
 
-The disadvantage with this template is that it only works with OpenShift because
-it uses objects that are only available in OpenShift. For plain Kubernetes a
-different approach needs to be used.
diff --git a/deployment/templates/mongodb/mongo-init-script.yaml b/deployment/templates/mongodb/mongo-init-script.yaml
new file mode 100644
index 0000000..937f66c
--- /dev/null
+++ b/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('runStore');
+    dbproWES = db.getSiblingDB('{{ tpl .Values.mongodb.secret.databaseName . }}')
+
+    dbproWES.createUser({
+      user: "{{ tpl .Values.mongodb.secret.databaseUser . }}",
+      pwd: "{{ tpl .Values.mongodb.secret.databasePassword . }}",
+      roles: [
+        {
+          role: "readWrite",
+          db: "{{ tpl .Values.mongodb.secret.databaseName . }}"
+        }
+      ]
+    });
+
+    // Create the 'runs' and 'service_info' collections
+    // Database configuration from https://github.com/elixir-cloud-aai/proWES/blob/59b53a4bdd06dd83ff41754b27d97309073ed237/pro_wes/config.yaml#L30
+    db.createCollection('runs');
+    db.runs.createIndex(
+      { run_id: 1, task_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}
+    );
diff --git a/deployment/templates/mongodb/mongodb-deployment.yaml b/deployment/templates/mongodb/mongodb-deployment.yaml
index 90f1646..3cfd44f 100644
--- a/deployment/templates/mongodb/mongodb-deployment.yaml
+++ b/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
@@ -57,18 +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: {{- toYaml .Values.mongodb.resources | nindent 10 }}
+            timeoutSeconds: 50
+          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
diff --git a/deployment/templates/mongodb/mongodb-secret.yaml b/deployment/templates/mongodb/mongodb-secret.yaml
index 57949b7..e634e49 100644
--- a/deployment/templates/mongodb/mongodb-secret.yaml
+++ b/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 }}
+
diff --git a/deployment/templates/prowes/celery-deployment.yaml b/deployment/templates/prowes/celery-deployment.yaml
index 8538891..3739a8c 100644
--- a/deployment/templates/prowes/celery-deployment.yaml
+++ b/deployment/templates/prowes/celery-deployment.yaml
@@ -35,17 +35,17 @@ 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 }}
diff --git a/deployment/templates/prowes/prowes-deployment.yaml b/deployment/templates/prowes/prowes-deployment.yaml
index 4bd1f86..bab88f2 100644
--- a/deployment/templates/prowes/prowes-deployment.yaml
+++ b/deployment/templates/prowes/prowes-deployment.yaml
@@ -48,17 +48,17 @@ 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 }}
diff --git a/deployment/values.yaml b/deployment/values.yaml
index 05658b9..01e681b 100644
--- a/deployment/values.yaml
+++ b/deployment/values.yaml
@@ -17,10 +17,10 @@ flower:
   image: endocode/flower
   resources:
     limits:
-      cpu: 500m
+      cpu: 200m
       memory: 1Gi
     requests:
-      cpu: 300m
+      cpu: 200m
       memory: 500Mi
 prowes:
   appName: prowes
@@ -52,7 +52,7 @@ celeryWorker:
       cpu: 50m
   resources:
     limits:
-      cpu: 500m
+      cpu: 200m
       memory: 256Mi
     requests:
       cpu: 100m
@@ -65,24 +65,24 @@ mongodb:
   databasePassword: prowes-db-passwd
   databaseUser: prowes-user
   volumeSize: 1Gi
-  image: centos/mongodb-36-centos7
+  image: docker.io/library/mongo:noble 
   resources:
     limits:
-      cpu: 500m
+      cpu: 200m
       memory: 512Mi
     requests:
-      cpu: 500m
+      cpu: 200m
       memory: 512Mi
 
 rabbitmq:
   appName: rabbitmq
   volumeSize: 1Gi
-  image: rabbitmq:3-management
+  image: rabbitmq:4.1.4-management
   resources:
     limits:
-      cpu: 500m
+      cpu: 200m
       memory: 1Gi
     requests:
-      cpu: 500m
+      cpu: 200m
       memory: 256Mi
 

From b2bb1c3c491c311168300dee110a3dfe5dd354d9 Mon Sep 17 00:00:00 2001
From: Tristan <tristan.perard@outlook.com>
Date: Fri, 10 Oct 2025 15:19:19 +0300
Subject: [PATCH 5/7] Fix secrets

---
 deployment/values.yaml | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/deployment/values.yaml b/deployment/values.yaml
index 01e681b..ad28927 100644
--- a/deployment/values.yaml
+++ b/deployment/values.yaml
@@ -2,11 +2,11 @@
 # This is a YAML-formatted file.
 # Declare variables to be passed into your templates.
 
-applicationDomain: ""
+applicationDomain: "rahtiapp.fi"
 
 # which cluster type proWES is going to be deployed on
 # it can be either 'kubernetes' or 'openshift'
-clusterType: kubernetes
+clusterType: openshift 
 
 # mongodb-pvc.yaml/rabbitmq-pvc.yaml, change to ReadWriteMany if storageClass can do RWX
 storageAccessMode: ReadWriteOnce
@@ -60,10 +60,12 @@ celeryWorker:
 
 mongodb:
   appName: mongodb
-  databaseAdminPassword: adminpasswd
-  databaseName: prowes-db
-  databasePassword: prowes-db-passwd
-  databaseUser: prowes-user
+  secret:
+    databaseRootUsername: prowes-adm
+    databaseRootPassword: adminpasswd
+    databaseUser: prowes-user
+    databasePassword: prowes-db-passwd
+    databaseName: prowes-db
   volumeSize: 1Gi
   image: docker.io/library/mongo:noble 
   resources:

From b2f94922f879fafffc94626a6b801e198335a66c Mon Sep 17 00:00:00 2001
From: Tristan <tristan.perard@outlook.com>
Date: Fri, 10 Oct 2025 15:33:39 +0300
Subject: [PATCH 6/7] Update Chart.yaml version

---
 deployment/Chart.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/deployment/Chart.yaml b/deployment/Chart.yaml
index af715dc..0260d08 100644
--- a/deployment/Chart.yaml
+++ b/deployment/Chart.yaml
@@ -2,5 +2,5 @@ apiVersion: v2
 name: prowes
 description: A proWES Helm chart for Kubernetes
 type: application
-version: 0.1.0
-appVersion: 1.16.0
+version: 2.0.0
+appVersion: 2.0.0

From ace449166480bedb655bfeb17bc8f0448f2ef1ca Mon Sep 17 00:00:00 2001
From: Tristan <tristan.perard@outlook.com>
Date: Fri, 17 Oct 2025 14:04:36 +0300
Subject: [PATCH 7/7] Fix

---
 deployment/values.yaml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/deployment/values.yaml b/deployment/values.yaml
index ad28927..109c2c4 100644
--- a/deployment/values.yaml
+++ b/deployment/values.yaml
@@ -2,11 +2,11 @@
 # This is a YAML-formatted file.
 # Declare variables to be passed into your templates.
 
-applicationDomain: "rahtiapp.fi"
+applicationDomain: ""
 
 # which cluster type proWES 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
@@ -61,13 +61,13 @@ celeryWorker:
 mongodb:
   appName: mongodb
   secret:
-    databaseRootUsername: prowes-adm
-    databaseRootPassword: adminpasswd
-    databaseUser: prowes-user
-    databasePassword: prowes-db-passwd
-    databaseName: prowes-db
+    databaseRootUsername: ""
+    databaseRootPassword: ""
+    databaseUser: ""
+    databasePassword: ""
+    databaseName: ""
   volumeSize: 1Gi
-  image: docker.io/library/mongo:noble 
+  image: docker.io/library/mongo:noble
   resources:
     limits:
       cpu: 200m