MONAI Deploy helm charts

Project-MONAI · Sep 1, 2023 · 20d3ac1 · 20d3ac1
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diff --git a/deploy/helm-charts/Chart.lock b/deploy/helm-charts/Chart.lock
@@ -0,0 +1,9 @@
+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"
diff --git a/deploy/helm-charts/Chart.yaml b/deploy/helm-charts/Chart.yaml
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+apiVersion: v2
+name: monai-deploy
+description: MONAI Deploy for local deployment
+type: application
+
+# This is the chart version. This version number should be incremented each time you make changes
+# to the chart and its templates, including the app version.
+# Versions are expected to follow Semantic Versioning (https://semver.org/)
+version: 0.1.0
+
+# This is the version number of the application being deployed. This version number should be
+# incremented each time you make changes to the application. Versions are not expected to
+# follow Semantic Versioning. They should reflect the version the application is using.
+# It is recommended to use it with quotes.
+appVersion: "0.1.0"
+keywords:
+  - ai
+  - dicom
+  - dicomweb
+  - ehr
+  - emr
+  - fhir
+  - healthcare
+  - hl7
+  - monai-deploy
+  - medical-imaging
+  - radiology
+home: https://github.com/Project-MONAI/monai-deploy
+sources:
+  - https://github.com/Project-MONAI/monai-deploy-informatics-gateway
+  - https://github.com/Project-MONAI/monai-deploy-workflow-manager/
+dependencies:
+  - name: argo-workflows
+    version: 0.33.1
+    repository: https://argoproj.github.io/argo-helm
+  - name: local-path-provisioner
+    version: 0.0.24
+    repository: https://charts.containeroo.ch
diff --git a/deploy/helm-charts/README b/deploy/helm-charts/README
@@ -0,0 +1,75 @@
+# MONAI Deploy Helm Charts
+
+
+## Install Tools
+```bash
+# Install kubernetes tools
+sudo apt-get install -y -q kubelet kubectl kubeadm
+sudo apt-mark hold kubelet kubeadm kubectl
+
+# Install Helm
+curl https://raw.githubusercontent.com/helm/helm/main/scripts/get-helm-3 | bash
+```
+
+## Installing Kubernetes
+Select one of the following Kubernetes distribution:
+- [k3s](https://k3s.io/)
+  ```bash
+  curl -sfL https://get.k3s.io | sh -s - --flannel-backend host-gw --flannel-external-i     
+  # Copy default configuration
+  mkdir -p $HOME/.kube
+  sudo cp -i /etc/rancher/k3s/k3s.yaml $HOME/.kube/config
+  sudo chown $(id -u):$(id -g) $HOME/.kube/config
+  ```
+
+- [K8s](https://kubernetes.io/)
+  ```bash
+  kubeadm init --pod-network-cidr=192.168.0.0/16
+  # Copy default configuration
+  mkdir -p $HOME/.kube
+  sudo cp -i /etc/rancher/k3s/k3s.yaml $HOME/.kube/config
+  sudo chown $(id -u):$(id -g) $HOME/.kube/config
+
+  kubectl taint nodes --all node-role.kubernetes.io/control-plane-
+
+  ```
+
+# Install MONAI Deploy
+
+Build & download dependencies
+
+```bash
+helm dependency build
+```
+
+If you are reinstalling, run the following to remove existing `local-path-provisioner` Storage Class:
+
+```bash
+kubectl delete StorageClass local-path
+```
+
+Install:
+
+```bash
+helm upgrade -i monai-deploy .
+```
+
+Upon successfully installation, optinally follow the on screen instructions to initialize Informatics Gateway & Orthanc.
+
+Uninstall:
+```
+helm uninstall  monai-deploy
+```
+
+
+## Advanced Configuration
+
+Most of the configurations may be found in the following files:
+
+- `values.yaml`: contains container image repo, application secrets, ports, etc...
+- `files/informatics-gateway.json`: Informatics Gateway specific configurations...
+- `files/workflow-manager.json`: Workflow Manager specific configurations...
+- `files/task-manager.json`: Task Manager specific configurations...
+- `files/orthanc.json`: Orthanc specific configurations...
+
+# 
diff --git a/deploy/helm-charts/charts/.gitignore b/deploy/helm-charts/charts/.gitignore
@@ -0,0 +1 @@
+*.tgz
diff --git a/deploy/helm-charts/files/informatics-gateway.json b/deploy/helm-charts/files/informatics-gateway.json
@@ -0,0 +1,85 @@
+{
+    "MonaiDeployAuthentication": {
+      "bypassAuthentication": true
+    },
+    "ConnectionStrings": {
+        "Type": "mongodb",
+        "DatabaseName": "InformaticsGateway"
+    },
+    "InformaticsGateway": {
+      "dicom": {
+        "scp": {
+          "port": 104,
+          "logDimseDatasets": false,
+          "rejectUnknownSources": true
+        },
+        "scu": {
+          "aeTitle": "MONAISCU",
+          "logDimseDatasets": false,
+          "logDataPDUs": false
+        }
+      },
+      "messaging": {
+        "publisherServiceAssemblyName": "Monai.Deploy.Messaging.RabbitMQ.RabbitMQMessagePublisherService, Monai.Deploy.Messaging.RabbitMQ",
+        "publisherSettings": {
+          "exchange": "monaideploy"
+        },
+        "subscriberServiceAssemblyName": "Monai.Deploy.Messaging.RabbitMQ.RabbitMQMessageSubscriberService, Monai.Deploy.Messaging.RabbitMQ",
+        "subscriberSettings": {
+          "exchange": "monaideploy",
+          "exportRequestQueue": "export_tasks",
+          "deadLetterExchange": "monaideploy-dead-letter",
+          "deliveryLimit": 3,
+          "requeueDelay": 30
+        }
+      },
+      "storage": {
+        "localTemporaryStoragePath": "/payloads",
+        "remoteTemporaryStoragePath": "/incoming",
+        "bucketName": "monaideploy",
+        "storageRootPath": "/payloads",
+        "temporaryBucketName": "monaideploy",
+        "serviceAssemblyName": "Monai.Deploy.Storage.MinIO.MinIoStorageService, Monai.Deploy.Storage.MinIO",
+        "watermarkPercent": 75,
+        "reserveSpaceGB": 5,
+        "settings": {
+          "securedConnection": false,
+          "region": "local",
+          "executableLocation": "/bin/mc",
+          "serviceName": "MinIO",
+          "createBuckets": "monaideploy"
+        }
+      },
+      "hl7": {
+        "port": 2575,
+        "maximumNumberOfConnections": 10,
+        "clientTimeout": 60000,
+        "sendAck": true
+      },
+      "dicomWeb": {
+        "plugins": []
+      },
+      "plugins": {
+        "remoteApp": {
+          "ReplaceTags": "AccessionNumber"
+        }
+      }
+    },
+    "Kestrel": {
+      "EndPoints": {
+        "Http": {
+          "Url": "http://+:5000"
+        }
+      }
+    },
+    "AllowedHosts": "*",
+    "Cli": {
+      "Runner": "Docker",
+      "HostDataStorageMount": "~/.mig/data",
+      "HostPlugInsStorageMount": "~/.mig/plug-ins",
+      "HostDatabaseStorageMount": "~/.mig/database",
+      "HostLogsStorageMount": "~/.mig/logs",
+      "InformaticsGatewayServerEndpoint": "http://localhost:5000",
+      "DockerImagePrefix": "ghcr.io/project-monai/monai-deploy-informatics-gateway"
+    }
+  }
diff --git a/deploy/helm-charts/files/orthanc.json b/deploy/helm-charts/files/orthanc.json
@@ -0,0 +1,84 @@
+{
+  "Name": "Orthanc",
+  "StorageDirectory": "/var/lib/orthanc/db",
+  "IndexDirectory": "/var/lib/orthanc/db",
+  "StorageCompression": false,
+  "MaximumStorageSize": 0,
+  "MaximumPatientCount": 0,
+  "LuaScripts": [],
+  "Plugins": [
+    "/usr/share/orthanc/plugins",
+    "/usr/local/share/orthanc/plugins"
+  ],
+  "ConcurrentJobs": 2,
+  "HttpServerEnabled": true,
+  "HttpPort": 8042,
+  "HttpDescribeErrors": true,
+  "HttpCompressionEnabled": true,
+  "DicomServerEnabled": true,
+  "DicomCheckCalledAet": false,
+  "DicomPort": 4242,
+  "DefaultEncoding": "Latin1",
+  "DeflatedTransferSyntaxAccepted": true,
+  "JpegTransferSyntaxAccepted": true,
+  "Jpeg2000TransferSyntaxAccepted": true,
+  "JpegLosslessTransferSyntaxAccepted": true,
+  "JpipTransferSyntaxAccepted": true,
+  "Mpeg2TransferSyntaxAccepted": true,
+  "RleTransferSyntaxAccepted": true,
+  "UnknownSopClassAccepted": true,
+  "DicomScpTimeout": 30,
+  "RemoteAccessAllowed": true,
+  "SslEnabled": false,
+  "SslCertificate": "certificate.pem",
+  "AuthenticationEnabled": false,
+  "DicomModalitiesInDatabase": false,
+  "DicomAlwaysAllowEcho": true,
+  "DicomAlwaysAllowStore": true,
+  "DicomCheckModalityHost": false,
+  "DicomScuTimeout": 10,
+  "OrthancPeers": {},
+  "OrthancPeersInDatabase": false,
+  "HttpProxy": "",
+  "HttpVerbose": true,
+  "HttpTimeout": 10,
+  "HttpsVerifyPeers": true,
+  "HttpsCACertificates": "",
+  "UserMetadata": {},
+  "UserContentType": {},
+  "StableAge": 60,
+  "StrictAetComparison": false,
+  "StoreMD5ForAttachments": true,
+  "LimitFindResults": 0,
+  "LimitFindInstances": 0,
+  "LimitJobs": 10,
+  "LogExportedResources": false,
+  "KeepAlive": true,
+  "TcpNoDelay": true,
+  "HttpThreadsCount": 50,
+  "StoreDicom": true,
+  "DicomAssociationCloseDelay": 5,
+  "QueryRetrieveSize": 10,
+  "CaseSensitivePN": false,
+  "LoadPrivateDictionary": true,
+  "Dictionary": {},
+  "SynchronousCMove": true,
+  "JobsHistorySize": 10,
+  "SaveJobs": true,
+  "OverwriteInstances": true,
+  "MediaArchiveSize": 1,
+  "StorageAccessOnFind": "Always",
+  "MetricsEnabled": true,
+  "RemoteAccessEnabled": true,
+  "DicomWeb": {
+    "Enable": true, // Whether DICOMweb support is enabled
+    "Root": "/dicom-web/", // Root URI of the DICOMweb API (for QIDO-RS, STOW-RS and WADO-RS)
+    "EnableWado": true, // Whether WADO-URI (previously known as WADO) support is enabled
+    "WadoRoot": "/wado", // Root URI of the WADO-URI (aka. WADO) API
+    "Host": "localhost:8042", // Hard-codes the name of the host for subsequent WADO-RS requests
+    "Ssl": false, // Whether HTTPS should be used for subsequent WADO-RS requests
+    "StowMaxInstances": 10, // For STOW-RS client, the maximum number of instances in one single HTTP query (0 = no limit)
+    "StowMaxSize": 10, // For STOW-RS client, the maximum size of the body in one single HTTP query (in MB, 0 = no limit)
+    "QidoCaseSensitive": true // For QIDO-RS server, whether search is case sensitive (since release 0.5)
+  }
+}