Nds helm updates

deploy/helm/Gateway-local.yaml

@@ -0,0 +1,40 @@
+# Copyright 2022 MONAI Consortium
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+replicaCount: 1
+
+image:
+  repository: registry.gitlab.com/answerdigital/londonai/aide/workflow-manager-images/infomatics-gateway
+  pullPolicy: IfNotPresent
+  tag: 2022-08-01
+
+enviromentVariables:
+  InformaticsGateway__messaging__publisherSettings__endpoint: "rabbitmq-monai"
+  InformaticsGateway__messaging__publisherSettings__username: "admin"
+  InformaticsGateway__messaging__publisherSettings__password: "admin"
+  InformaticsGateway__messaging__subscriberSettings__endpoint: "rabbitmq-monai"
+  InformaticsGateway__messaging__subscriberSettings__username: "admin"
+  InformaticsGateway__messaging__subscriberSettings__password: "admin"
+  InformaticsGateway__storage__settings__endpoint: "minio.monai:9000" 
+  InformaticsGateway__storage__settings__accessKey: "admin"
+  InformaticsGateway__storage__settings__accessToken: "password"
+  InformaticsGateway__dicom__scp__rejectUnknownSources: false
+
+
+service:
+  type: ClusterIP
+  port: 5000
+  port2: 104
+
+
+

deploy/helm/Gateway.yaml

@@ -28,8 +28,23 @@ enviromentVariables:
   InformaticsGateway__storage__settings__endpoint: "minio.monai:9000" 
   InformaticsGateway__storage__settings__accessKey: "rootminio"
   InformaticsGateway__storage__settings__accessToken: "rootminio"
+  InformaticsGateway__dicom__scp__rejectUnknownSources: false
+
 
 service:
   type: ClusterIP
   port: 5000
+  port2: 104
+
+
+volumes:
+  name: gateway-storage
+  claimName: gateway-storage-claim
+  namespace: monai
+  storage: 1Gi
+  path: /efs_data/monai/gateway  # path on the host
+
+volumeMounts:
+  mountPath: "/database"
+  name: gateway-storage
 

deploy/helm/MWM.yaml

@@ -29,12 +29,23 @@ enviromentVariables:
   WorkflowManager__storage__settings__executableLocation: "mc"
   WorkflowManager__messaging__publisherSettings__endpoint: "rabbitmq.monai"
   WorkflowManager__messaging__subscriberSettings__endpoint: "rabbitmq.monai"
-  WorkflowManager__messaging__publisherSettings__username: "monaideploy"
-  WorkflowManager__messaging__subscriberSettings__username: "monaideploy"
-  WorkflowManager__messaging__subscriberSettings__password: "monaideploy"
-  WorkflowManager__messaging__publisherSettings__password: "monaideploy"
   WorkloadManagerDatabase__ConnectionString: "mongodb://root:rootpassword@mongo-monai.monai:27017"
 
+enviromentVariablesFromSecrets:
+  secrets:
+    - name: WorkflowManager__messaging__subscriberSettings__username
+      secretName: rabbit-secret-master
+      secretKey: username
+    - name: WorkflowManager__messaging__subscriberSettings__password
+      secretName: rabbit-secret-master
+      secretKey: password
+    - name: WorkflowManager__messaging__publisherSettings__username
+      secretName: rabbit-secret-master
+      secretKey: username
+    - name: WorkflowManager__messaging__publisherSettings__password
+      secretName: rabbit-secret-master
+      secretKey: password
+
 service:
   type: ClusterIP
   port: 5000

deploy/helm/minio-local.yaml

@@ -0,0 +1,42 @@
+
+# Copyright 2022 MONAI Consortium
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+replicaCount: 1
+
+# image:
+  # repository: minio/minio
+  # pullPolicy: IfNotPresent
+  # tag: latest
+  # command: 
+    # - "/bin/sh"
+    # - "-ce"
+    # - "/usr/bin/docker-entrypoint.sh minio server /data"
+
+enviromentVariables:
+  MINIO_ROOT_USER: admin
+  MINIO_ROOT_PASSWORD: password
+
+service:
+  type: NodePort
+  port: 9000
+  nodeport: 30090
+  port2: 9001
+  nodeport2: 30091
+  selector: 
+    app: minio
+
+
+
+

deploy/helm/minio.yaml

@@ -27,7 +27,6 @@ replicaCount: 1
 enviromentVariables:
   MINIO_ROOT_USER: minioadmin
   MINIO_ROOT_PASSWORD: minioadmin
-  WorkflowManager__storage__settings__endpoint: "minio:9000"
 
 service:
   type: NodePort

deploy/helm/mongo.yaml

@@ -33,7 +33,7 @@ volumes:
   claimName: mongo-storage-claim
   namespace: monai
   storage: 5Gi
-  path: /var/local/mongodata  # path on the host
+  path: /efs_data/monai/mongodata  # path on the host
 
 volumeMounts:
   mountPath: "/data/db"

deploy/helm/rabbitmq-local.yaml

@@ -0,0 +1,37 @@
+# Copyright 2022 MONAI Consortium
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+replicaCount: 1
+
+image:
+  repository: rabbitmq
+  pullPolicy: IfNotPresent
+  tag: 3.8.18-management
+
+enviromentVariables:
+  RABBITMQ_ERLANG_COOKIE: "SWQOKODSQALRPCLNMEQG"
+  RABBITMQ_DEFAULT_USER: "admin"
+  RABBITMQ_DEFAULT_PASS: "admin"
+  RABBITMQ_DEFAULT_VHOST: "monaideploy"
+
+
+service:
+  type: NodePort
+  port: 5672
+  nodeport: 30072
+  port2: 15672
+  nodeport2: 30672
+
+
+

deploy/helm/rabbitmq.yaml

@@ -21,8 +21,8 @@ image:
 
 enviromentVariables:
   RABBITMQ_ERLANG_COOKIE: "SWQOKODSQALRPCLNMEQG"
-  RABBITMQ_DEFAULT_USER: "admin"
-  RABBITMQ_DEFAULT_PASS: "admin"
+  RABBITMQ_DEFAULT_USER: "monaideploy"
+  RABBITMQ_DEFAULT_PASS: "monaideploy"
   RABBITMQ_DEFAULT_VHOST: "monaideploy"
 
 

deploy/helm/templates/deployment.yaml

@@ -60,8 +60,17 @@ spec:
           env:
               {{- range $name, $value := .Values.enviromentVariables }}
             - name: {{ $name }}
-              value: {{ $value }}
-        {{- end }}
+              value: {{ $value | quote }}
+              {{- end }}
+
+              {{- range .Values.enviromentVariablesFromSecrets.secrets }}
+            - name: {{ .name }}
+              valueFrom:
+                secretKeyRef:
+                  name: {{ .secretName}}
+                  key: {{ .secretKey}}
+              {{- end }} 
+
           {{- end }}
           ports:
             - name: http

guidelines/mwm-developer-setup.md

@@ -57,7 +57,7 @@ save the file, now `http://minio:9000` will route to you local machine
 install Helm 3 https://helm.sh/docs/intro/install/
 from a bash terminal in the root folder of the project
 - `helm upgrade -i -n argo -f deploy/helm/mongo-local.yaml mongo deploy/helm`
-- `helm upgrade -i -n argo -f deploy/helm/rabbitmq.yaml rabbit deploy/helm`
+- `helm upgrade -i -n argo -f deploy/helm/rabbitmq-local.yaml rabbit deploy/helm`
 
 ### running in VisualStudio
 Now assuming your launchSettings has the line 
@@ -74,7 +74,7 @@ Open the post/workflows tab and click `try it out`, paste in the following to th
 	"version": "1.0.0",
 	"description": "Attempt at making a workflow",
 	"informatics_gateway": {
-		"ae_title": "MYAET",
+		"ae_title": "MonaiSCU",
 		"data_origins": [
 			"MY_SCANNER"
 		],
@@ -212,4 +212,17 @@ then
 - `mc ls --recursive mwm/bucket1` list all files in bucket
 
 
+## Informatics Gateway
+Although it has its own repo and is separate from the Workflow Manager, I have included a Helm file for it in here, its called Gateway and to deploy it use.
+`helm -n monai upgrade -i -f deploy/helm/Gateway-local.yaml mig helm` Obviously change the namespace, name and path to suit.
+
+Once deployed
+- exec into the running container ie `kubectl -n monai exec -it mig-monai-797f584bf9-9tw8j -- bash`
+- install curl `apt update;apy install curl -y` 
+- add the default AETitle `curl -H 'Content-Type: application/json-patch+json' -d '{"aeTitle": "MonaiSCU","name": "Monai WFM"}' mig-monai:5000/config/ae`
+- `exit`
+
+The Informatics Gateway is now set up to recieve and pass on data from the PACS or Orthanc servers
+
+if using orthanc something like this `"DicomModalities": {"monai" : [ "MonaiSCU", "mig-monai.monai", 104 ]}` would need to be in its config file.