Remove use of local-path-provisioner and create PVs

deploy/helm-charts/.gitignore

@@ -0,0 +1 @@
+charts/*.tgz

deploy/helm-charts/Chart.lock

@@ -2,8 +2,5 @@ dependencies:
 - name: argo-workflows
   repository: https://argoproj.github.io/argo-helm
   version: 0.33.1
-- name: local-path-provisioner
-  repository: https://charts.containeroo.ch
-  version: 0.0.24
-digest: sha256:6c6f22833d7b04577238156ef04787025ff112a3fce93e1b7aef4664cf483b4b
-generated: "2023-09-01T14:33:33.804030468-07:00"
+digest: sha256:bc9fd492011835b2ebb1d418f860eda28691ab8805d3215be2f488fc00cfe236
+generated: "2023-09-07T10:32:16.447050486-07:00"

deploy/helm-charts/Chart.yaml

@@ -31,8 +31,5 @@ sources:
   - https://github.com/Project-MONAI/monai-deploy-workflow-manager/
 dependencies:
   - name: argo-workflows
-    version: 0.33.1
+    version: 0.33.3
     repository: https://argoproj.github.io/argo-helm
-  - name: local-path-provisioner
-    version: 0.0.24
-    repository: https://charts.containeroo.ch

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

@@ -102,14 +102,31 @@ Use the following commands to install MONAI Deploy Helm charts and its dependenc
 - Orthanc
 - 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
 helm upgrade -i monai-deploy -n my-space . # install in namespace "my-namespace"
 ```
 
+> **Note**
+> Persistent volumes are created in `/opt/monai-deploy` by default, please ensure the volume has enough space required for each service:
+> - Informatics Gateway: 1Gi (logs), 10Gi (payloads) - `/opt/monai-deploy/mig`
+> - MinIO: 100Gi (data), 1Gi (config) - `/opt/monai-deploy/minio`
+> - Mongo: 1Gi - `/opt/monai-deploy/mongo`
+> - Orthanc: 100Gi - `/opt/monai-deploy/orthanc`
+> - RabbitMQ: 1Gi - `/opt/monai-deploy/rabbitmq`
+> - Postgres: 1Gi - `/opt/monai-deploy/postgres`
+
+> **Note**
+> Informatics Gateway creates two buckets at startup:
+> 1. monaideploy - stores input and output
+> 2. argologs - archives application logs from Argo
+
+> **Warning**
+> While data can be persisted between reinstallations, you may still need to reconfigure DICOM AE Titles so the IP addresses and ports
+> can be configured correctly.
+
 Upon successfully installation, optionally follow the on screen instructions to initialize Informatics Gateway & Orthanc.
 
 ## Advanced Configuration

deploy/helm-charts/files/informatics-gateway.json

@@ -11,7 +11,7 @@
         "scp": {
           "port": 104,
           "logDimseDatasets": false,
-          "rejectUnknownSources": true
+          "rejectUnknownSources": false
         },
         "scu": {
           "aeTitle": "MONAISCU",
@@ -47,7 +47,7 @@
           "region": "local",
           "executableLocation": "/bin/mc",
           "serviceName": "MinIO",
-          "createBuckets": "monaideploy"
+          "createBuckets": "monaideploy,argologs"
         }
       },
       "hl7": {

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

@@ -55,9 +55,9 @@ spec:
       metadata: {}
       container:
         name: ''
-        image: alpine:latest
+        image: ubuntu:latest
         command:
           - /bin/sh
         args:
           - '-c'
-          - date && cp -vr /var/monai/input/* /var/monai/output && date
+          - date -Ins && cp -r /var/monai/input/* /var/monai/output && date -Ins

deploy/helm-charts/files/sample-workflows/hello-world.json

@@ -5,7 +5,7 @@
 	"informatics_gateway": {
 		"ae_title": "MONAI-DEPLOY",
 		"data_origins": [
-			"ORTHANC"
+			"ORTHANC", "STORESCU"
 		],
 		"export_destinations": [
 			"ORTHANC"

deploy/helm-charts/files/welcome.sh

@@ -102,13 +102,18 @@ printf "\nDeleting existing MONAI Deploy AE Title..."
 curl -s --request DELETE "http://$NODE_IP:$MIG_API_PORT/config/ae/MONAI-DEPLOY" >/dev/null
 printf "\nDeleting existing DICOM Source..."
 curl -s --request DELETE "http://$NODE_IP:$MIG_API_PORT/config/source/ORTHANC" >/dev/null
+curl -s --request DELETE "http://$NODE_IP:$MIG_API_PORT/config/source/STORESCU" >/dev/null
 printf "\nDeleting existing DICOM Destination..."
 curl -s --request DELETE "http://$NODE_IP:$MIG_API_PORT/config/destination/ORTHANC" >/dev/null
 
-printf "\nAdding MONAI Deploy AE Title..."
-curl -s --request POST "http://$NODE_IP:$MIG_API_PORT/config/ae" --header "Content-Type: application/json" --data-raw "{\"name\": \"MONAI-DEPLOY\",\"aeTitle\": \"MONAI-DEPLOY\"}" >/dev/null
-printf "\nAdding DICOM Source..."
+printf "\nAdding MONAI Deploy AE Title (MONAI-DEPLOY)..."
+curl -s --request POST "http://$NODE_IP:$MIG_API_PORT/config/ae" --header "Content-Type: application/json" --data-raw "{\"name\": \"MONAI-DEPLOY\",\"aeTitle\": \"MONAI-DEPLOY\", \"timeout\": 3}" >/dev/null
+printf "\nAdding DICOM Source (ORTHANC)..."
 curl -s --request POST "http://$NODE_IP:$MIG_API_PORT/config/source" --header "Content-Type: application/json" --data-raw "{\"name\": \"ORTHANC\",\"hostIp\": \"$ORTHANC_IP\",\"aeTitle\": \"ORTHANC\"}" >/dev/null
+
+HOST_IP=$(hostname -I | awk '{print $1}')
+printf "\nAdding DICOM Source (STORESCU @ $HOST_IP)..."
+curl -s --request POST "http://$NODE_IP:$MIG_API_PORT/config/source" --header "Content-Type: application/json" --data-raw "{\"name\": \"STORESCU\",\"hostIp\": \"$HOST_IP\",\"aeTitle\": \"STORESCU\"}" >/dev/null
 printf "\nAdding DICOM Destination..."
 curl -s --request POST "http://$NODE_IP:$MIG_API_PORT/config/destination" --header "Content-Type: application/json" --data-raw "{\"name\": \"ORTHANC\",\"hostIp\": \"$NODE_IP\",\"port\": $ORTHANC_DIMSE_PORT,\"aeTitle\": \"ORTHANC\"}" >/dev/null
 

deploy/helm-charts/templates/01-mongodb-pv.yaml

@@ -0,0 +1,28 @@
+apiVersion: v1
+kind: PersistentVolume
+metadata:
+  name: {{ .Release.Name }}-{{ .Values.mongo.name }}-volume
+  labels:
+    type: local
+spec:
+  storageClassName: {{ .Release.Name }}-{{ .Values.mongo.name }}-volume-class
+  capacity:
+    storage: {{ .Values.mongo.size }}
+  volumeMode: Filesystem
+  accessModes:
+    - ReadWriteOnce
+  hostPath:
+    path: {{ .Values.mongo.storagePath }}
+    type: "DirectoryOrCreate"
+---
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: {{ .Release.Name }}-{{ .Values.mongo.name }}-volume-claim
+spec:
+  storageClassName: {{ .Release.Name }}-{{ .Values.mongo.name }}-volume-class
+  accessModes:
+    - ReadWriteOnce
+  resources:
+    requests:
+      storage: {{ .Values.mongo.size }}

deploy/helm-charts/templates/02-rabbitmq-pv.yaml

@@ -0,0 +1,28 @@
+apiVersion: v1
+kind: PersistentVolume
+metadata:
+  name: {{ .Release.Name }}-{{ .Values.rabbitmq.name }}-volume
+  labels:
+    type: local
+spec:
+  storageClassName: {{ .Release.Name }}-{{ .Values.rabbitmq.name }}-volume-class
+  capacity:
+    storage: {{ .Values.rabbitmq.size }}
+  volumeMode: Filesystem
+  accessModes:
+    - ReadWriteOnce
+  hostPath:
+    path: {{ .Values.rabbitmq.storagePath }}
+    type: "DirectoryOrCreate"
+---
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: {{ .Release.Name }}-{{ .Values.rabbitmq.name }}-volume-claim
+spec:
+  storageClassName: {{ .Release.Name }}-{{ .Values.rabbitmq.name }}-volume-class
+  accessModes:
+    - ReadWriteOnce
+  resources:
+    requests:
+      storage: {{ .Values.rabbitmq.size }}

deploy/helm-charts/templates/03-minio-pv.yaml

@@ -0,0 +1,59 @@
+# MinIO data volume and volume claim
+apiVersion: v1
+kind: PersistentVolume
+metadata:
+  name: {{ .Release.Name }}-{{ .Values.minio.name }}-data-volume
+  labels:
+    type: local
+spec:
+  storageClassName: {{ .Release.Name }}-{{ .Values.minio.name }}-data-volume-class
+  capacity:
+    storage: {{ .Values.minio.dataSize }}
+  volumeMode: Filesystem
+  accessModes:
+    - ReadWriteOnce
+  hostPath:
+    path: {{ .Values.minio.storagePath }}
+    type: "DirectoryOrCreate"
+---
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: {{ .Release.Name }}-{{ .Values.minio.name }}-data-volume-claim
+spec:
+  storageClassName: {{ .Release.Name }}-{{ .Values.minio.name }}-data-volume-class
+  accessModes:
+    - ReadWriteOnce
+  resources:
+    requests:
+      storage: {{ .Values.minio.dataSize }}
+---
+# MinIO config volume and volume claim
+apiVersion: v1
+kind: PersistentVolume
+metadata:
+  name: {{ .Release.Name }}-{{ .Values.minio.name }}-config-volume
+  labels:
+    type: local
+spec:
+  storageClassName: {{ .Release.Name }}-{{ .Values.minio.name }}-config-volume-class
+  capacity:
+    storage: {{ .Values.minio.configSize }}
+  volumeMode: Filesystem
+  accessModes:
+    - ReadWriteOnce
+  hostPath:
+    path: {{ .Values.minio.storagePath }}
+    type: "DirectoryOrCreate"
+---
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: {{ .Release.Name }}-{{ .Values.minio.name }}-config-volume-claim
+spec:
+  storageClassName: {{ .Release.Name }}-{{ .Values.minio.name }}-config-volume-class
+  accessModes:
+    - ReadWriteOnce
+  resources:
+    requests:
+      storage: {{ .Values.minio.configSize }}

deploy/helm-charts/templates/04-orthanc-pv.yaml

@@ -0,0 +1,28 @@
+apiVersion: v1
+kind: PersistentVolume
+metadata:
+  name: {{ .Release.Name }}-{{ .Values.orthanc.name }}-volume
+  labels:
+    type: local
+spec:
+  storageClassName: {{ .Release.Name }}-{{ .Values.orthanc.name }}-volume-class
+  capacity:
+    storage: {{ .Values.orthanc.size }}
+  volumeMode: Filesystem
+  accessModes:
+    - ReadWriteOnce
+  hostPath:
+    path: {{ .Values.orthanc.storagePath }}
+    type: "DirectoryOrCreate"
+---
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: {{ .Release.Name }}-{{ .Values.orthanc.name }}-volume-claim
+spec:
+  storageClassName: {{ .Release.Name }}-{{ .Values.orthanc.name }}-volume-class
+  accessModes:
+    - ReadWriteOnce
+  resources:
+    requests:
+      storage: {{ .Values.orthanc.size }}

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

@@ -0,0 +1,30 @@
+{{- if index .Values "argo-workflows" "controller" "persistence" "archive" -}}
+apiVersion: v1
+kind: PersistentVolume
+metadata:
+  name: {{ .Release.Name }}-{{ .Values.postgres.name }}-volume
+  labels:
+    type: local
+spec:
+  storageClassName: {{ .Release.Name }}-{{ .Values.postgres.name }}-volume-class
+  capacity:
+    storage: {{ .Values.postgres.size }}
+  volumeMode: Filesystem
+  accessModes:
+    - ReadWriteOnce
+  hostPath:
+    path: {{ .Values.postgres.storagePath }}
+    type: "DirectoryOrCreate"
+---
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: {{ .Release.Name }}-{{ .Values.postgres.name }}-volume-claim
+spec:
+  storageClassName: {{ .Release.Name }}-{{ .Values.postgres.name }}-volume-class
+  accessModes:
+    - ReadWriteOnce
+  resources:
+    requests:
+      storage: {{ .Values.postgres.size }}
+{{- end }}