Add postgres for argo job archive

deploy/helm-charts/docs/01.installation.md

@@ -102,6 +102,7 @@ Use the following commands to install MONAI Deploy Helm charts and its dependenc
 - RabbitMQ
 - [Argo Workflows](https://github.com/argoproj/argo-helm/tree/main/charts/argo-workflows)
 - [local-path-provisioner](https://github.com/rancher/local-path-provisioner)
+- Postgres - archives Argo jobs (can be disabled in `values.yaml` > `argo-workflows` > `controller` > `persistence` > `archive=false`)
 
 ```bash
 helm upgrade -i monai-deploy . # default/current namespace

deploy/helm-charts/docs/03.TriggerNewJobs.md

@@ -35,7 +35,7 @@ click on a study, from the menu on the left, click on *Send to DICOM modality* a
 
 After a minute or two, depending on the size of the DICOM dataset, you may find the job listed in Argo.
 
-Note: The jobs get deleted from the page after a while by Argo GC.
+Note: Check the **Archived Workflows** page if jobs cannot be found on the **Workflows** page.
 
 Enable UI (http://localhost:2746) access with the following command to forward port 2476:
 

deploy/helm-charts/files/sample-workflows/hello-world-argo-template.yml

@@ -7,8 +7,6 @@ spec:
   entrypoint: hello-world-pipeline
   podGC:
     strategy: OnWorkflowSuccess
-    # Uncomment for Argo 3.5
-    # deleteDelayDuration: 300s
   arguments: {}
   templates:
     - name: hello-world-pipeline
@@ -62,4 +60,4 @@ spec:
           - /bin/sh
         args:
           - '-c'
-          - date && cp -r /var/monai/input/* /var/monai/output && date
+          - date && cp -vr /var/monai/input/* /var/monai/output && date

deploy/helm-charts/templates/00-secrets.yaml

@@ -33,4 +33,15 @@ metadata:
   name: {{ .Values.rabbitmq.name }}-secret
 data:
   username: {{ .Values.rabbitmq.username | b64enc | quote }}
-  password: {{ .Values.rabbitmq.password | b64enc | quote }}
+  password: {{ .Values.rabbitmq.password | b64enc | quote }}
+
+
+---
+
+apiVersion: v1
+kind: Secret
+metadata:
+  name: {{ .Values.postgres.name }}-secret
+data:
+  username: {{ .Values.postgres.username | b64enc | quote }}
+  password: {{ .Values.postgres.password | b64enc | quote }}

deploy/helm-charts/templates/05-postgres-deployment.yaml

@@ -0,0 +1,98 @@
+{{- if index .Values "argo-workflows" "controller" "persistence" "archive" -}}
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ .Values.postgres.serviceName }}
+  labels:
+    {{- include "local.labels" . | nindent 4 }}
+spec:
+  {{- if not .Values.autoscaling.enabled }}
+  replicas: {{ .Values.replicaCount }}
+  {{- end }}
+  selector:
+    matchLabels:
+      role: internal-svcs
+      {{- include "local.selectorLabels" . | nindent 6 }}
+  template:
+    metadata:
+      {{- with .Values.podAnnotations }}
+      annotations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      labels:
+        app: postgres
+        role: internal-svcs
+        {{- include "local.selectorLabels" . | nindent 8 }}
+    spec:
+      {{- with .Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      serviceAccountName: {{ include "local.serviceAccountName" . }}
+      securityContext:
+        {{- toYaml .Values.podSecurityContext | nindent 8 }}
+      containers:
+        - name: {{ .Chart.Name }}
+          securityContext:
+            {{- toYaml .Values.securityContext | nindent 12 }}
+          image: "{{ .Values.postgres.repository }}:{{ .Values.postgres.tag }}"
+          imagePullPolicy: {{ .Values.postgres.pullPolicy }}
+          ports:
+            - name: postgres-port
+              containerPort: 5432
+              protocol: TCP
+          volumeMounts:
+          - name: {{ .Release.Name }}-postgresdb
+            mountPath: /var/lib/postgresql/data
+            subPath: data
+          resources:
+            {{- toYaml .Values.postgres.resources | nindent 12 }}
+          env:
+            - name: POSTGRES_USER
+              valueFrom:
+                secretKeyRef:
+                  name: {{ .Values.postgres.name }}-secret
+                  key: username
+            - name: POSTGRES_PASSWORD
+              valueFrom:
+                secretKeyRef:
+                  name: {{ .Values.postgres.name }}-secret
+                  key: password
+          livenessProbe:
+            exec:
+              command: 
+              - /bin/bash 
+              - -c
+              - pg_isready -U postgres
+            initialDelaySeconds: 10
+            periodSeconds: 5
+            timeoutSeconds: 10
+            failureThreshold: 300
+          readinessProbe:
+            exec:
+              command: 
+              - /bin/bash 
+              - -c
+              - pg_isready -U postgres
+            initialDelaySeconds: 15
+            periodSeconds: 5
+            timeoutSeconds: 10
+            failureThreshold: 300
+      volumes:
+        - name: {{ .Release.Name }}-postgresdb
+          persistentVolumeClaim:
+            claimName: {{ .Release.Name }}-{{ .Values.postgres.name }}-volume-claim
+
+      {{- with .Values.nodeSelector }}
+      nodeSelector:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.affinity }}
+      affinity:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.tolerations }}
+      tolerations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+{{- end }}

deploy/helm-charts/templates/05-postgres-pvc.yaml

@@ -0,0 +1,13 @@
+{{- if index .Values "argo-workflows" "controller" "persistence" "archive" -}}
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: {{ .Release.Name }}-{{ .Values.postgres.name }}-volume-claim
+spec:
+  accessModes:
+    - ReadWriteOnce
+  storageClassName: local-path
+  resources:
+    requests:
+      storage: {{ .Values.postgres.size }}
+{{- end }}

deploy/helm-charts/templates/05-postgres-service.yaml

@@ -0,0 +1,18 @@
+{{- if index .Values "argo-workflows" "controller" "persistence" "archive" -}}
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Values.postgres.serviceName }}
+  labels:
+    {{- include "local.labels" . | nindent 4 }}
+spec:
+  type: {{ .Values.postgres.serviceType }}
+  ports:
+    - port: {{ .Values.postgres.port }}
+      targetPort: postgres-port
+      protocol: TCP
+      name: postgres
+  selector:
+    role: internal-svcs
+    {{- include "local.selectorLabels" . | nindent 4 }}
+{{- end }}

deploy/helm-charts/values.yaml

@@ -190,6 +190,32 @@ rabbitmq:
     #   cpu: 100m
     #   memory: 128Mi
 
+postgres:
+  name: postgres
+  serviceName: postgres
+  repository: postgres
+  tag: 15.4
+  pullPolicy: IfNotPresent
+  imagePullSecrets: []
+  username: monai
+  password: monai
+  erlangCookie: SWQOKODSQALRPCLNMEQG
+  vhost: monaideploy
+  serviceType: NodePort
+  size: 1Gi
+  port: 5432
+  resources: {}
+    # We usually recommend not to specify default resources and to leave this as a conscious
+    # choice for the user. This also increases chances charts run on environments with little
+    # resources, such as Minikube. If you do want to specify resources, uncomment the following
+    # lines, adjust them as necessary, and remove the curly braces after 'resources:'.
+    # limits:
+    #   cpu: 100m
+    #   memory: 128Mi
+    # requests:
+    #   cpu: 100m
+    #   memory: 128Mi
+
 serviceAccount:
   # Specifies whether a service account should be created
   create: true
@@ -239,6 +265,73 @@ argo-workflows:
     workflowNamespaces:
       # include your namespace here
       - default
+    persistence:
+      archive: true
+      postgresql:
+        host: postgres
+        port: 5432
+        database: postgres
+        tableName: argo_workflows
+        userNameSecret:
+          name: postgres-secret
+          key: username
+        passwordSecret:
+          name: postgres-secret
+          key: password
+    extraInitContainers:
+      # change the servicename and namespace below if needed <serviceName>.<namespace>.svc.cluster.local
+      - name: init-postgres
+        image: docker.io/postgres:14
+        env:
+        - name: PGHOST
+          value: postgres
+        - name: PGUSER
+          valueFrom:
+            secretKeyRef:
+              name: postgres-secret
+              key: username
+        - name: PGPASSWORD
+          valueFrom:
+            secretKeyRef:
+              name: postgres-secret
+              key: password
+        - name: PGDATABASE
+          value: postgres
+        command:
+        - /bin/sh
+        - -c
+        - |
+          while ! psql -c 'select 1' > /dev/null 2>&1; do
+            echo "waiting for Postgres"
+            sleep 1
+          done
   server:
     extraArgs:
-      - --auth-mode=server
+      - --auth-mode=server
+    extraInitContainers:
+      # change the servicename and namespace below if needed <serviceName>.<namespace>.svc.cluster.local
+      - name: init-postgres
+        image: docker.io/postgres:14
+        env:
+        - name: PGHOST
+          value: postgres
+        - name: PGUSER
+          valueFrom:
+            secretKeyRef:
+              name: postgres-secret
+              key: username
+        - name: PGPASSWORD
+          valueFrom:
+            secretKeyRef:
+              name: postgres-secret
+              key: password
+        - name: PGDATABASE
+          value: postgres
+        command:
+        - /bin/sh
+        - -c
+        - |
+          while ! psql -c 'select 1' > /dev/null 2>&1; do
+            echo "waiting for Postgres"
+            sleep 1
+          done