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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" |
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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 |
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# MONAI Deploy Helm Charts | ||
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||
|
||
## Install Tools | ||
```bash | ||
# Install kubernetes tools | ||
sudo apt-get install -y -q kubelet kubectl kubeadm | ||
sudo apt-mark hold kubelet kubeadm kubectl | ||
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||
# 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 | ||
``` | ||
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||
- [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 | ||
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kubectl taint nodes --all node-role.kubernetes.io/control-plane- | ||
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``` | ||
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# Install MONAI Deploy | ||
|
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Build & download dependencies | ||
|
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```bash | ||
helm dependency build | ||
``` | ||
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If you are reinstalling, run the following to remove existing `local-path-provisioner` Storage Class: | ||
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```bash | ||
kubectl delete StorageClass local-path | ||
``` | ||
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Install: | ||
|
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```bash | ||
helm upgrade -i monai-deploy . | ||
``` | ||
|
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Upon successfully installation, optinally follow the on screen instructions to initialize Informatics Gateway & Orthanc. | ||
|
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Uninstall: | ||
``` | ||
helm uninstall monai-deploy | ||
``` | ||
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||
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## 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... | ||
|
||
# |
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*.tgz |
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{ | ||
"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" | ||
} | ||
} |
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{ | ||
"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) | ||
} | ||
} |
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