MONAI Deploy 0.6.0 release (#152)

* MDE 0.6.0 release * Remove obsoleted version tag * Update IG to 0.5.0 and WM to 0.20 Signed-off-by: Victor Chang <[email protected]>
Project-MONAI · Jun 14, 2024 · 4a90d27 · 4a90d27
1 parent 8ebac51
commit 4a90d27
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Showing 6 changed files with 83 additions and 91 deletions.
diff --git a/deploy/monai-deploy-express/.env b/deploy/monai-deploy-express/.env
@@ -1,12 +1,12 @@
 # Container Images
-INFORMATICS_GATEWAY_IMAGE=ghcr.io/project-monai/monai-deploy-informatics-gateway:0.4.1
+INFORMATICS_GATEWAY_IMAGE=ghcr.io/project-monai/monai-deploy-informatics-gateway:0.5.0
 INFORMATICS_GATEWAY_CONFIG_IMAGE=dwdraju/alpine-curl-jq:latest
-WORKFLOW_MANAGER_IMAGE=ghcr.io/project-monai/monai-deploy-workflow-manager:2023.5.0-beta.238
-TASK_MANAGER_IMAGE=ghcr.io/project-monai/monai-deploy-task-manager:2023.5.0-beta.238 
+WORKFLOW_MANAGER_IMAGE=ghcr.io/project-monai/monai-deploy-workflow-manager:0.2.0
+TASK_MANAGER_IMAGE=ghcr.io/project-monai/monai-deploy-task-manager:0.2.0
 
-MINIO_IMAGE=minio/minio:RELEASE.2023-10-16T04-13-43Z
-MONGODB_IMAGE=mongo:5.0.12
-ORTHANC_IMAGE=osimis/orthanc:23.9.2-full
+MINIO_IMAGE=minio/minio:RELEASE.2024-06-11T03-13-30Z
+MONGODB_IMAGE=mongo:5.0.25
+ORTHANC_IMAGE=orthancteam/orthanc:24.6.1-full
 RABBITMQ_IMAGE=rabbitmq:3.12.7-management
 
 ELK_VERSION=8.7.0
@@ -96,9 +96,9 @@ KIBANA_IP=172.29.0.103
 KIBANA_CFG_IP=172.29.0.104
 
 # Host Data Volume Paths
-INFORMATICS_GATEWAY_PAYLOADS=.md/mdig/payloads/
-INFORMATICS_GATEWAY_DATABASE=.md/mdig/database/
-TASK_MANAGER_DATA=$PWD/.md/mdtm/
+INFORMATICS_GATEWAY_PAYLOADS=${PWD}/.md/mdig/payloads/
+INFORMATICS_GATEWAY_DATABASE=${PWD}/.md/mdig/database/
+TASK_MANAGER_DATA=${PWD}/.md/mdtm/
 MONAI_DEPLOY_PLUGINS=plug-ins/ # disabled by default
 
 MINIO_DATA=.md/minio/data/

diff --git a/deploy/monai-deploy-express/configs/informatics-gateway.json b/deploy/monai-deploy-express/configs/informatics-gateway.json
@@ -5,12 +5,22 @@
   "ConnectionStrings": {
     "Type": "mongodb",
     "InformaticsGatewayDatabase": "mongodb://root:rootpassword@mongodb:27017",
-    "DatabaseName": "InformaticsGateway"
+    "DatabaseOptions": {
+      "DatabaseName": "InformaticsGateway",
+      "retries": {
+        "delays": [
+          "750",
+          "1201",
+          "2500"
+        ]
+      }
+    }
   },
   "InformaticsGateway": {
     "dicom": {
       "scp": {
         "port": 104,
+        "externalAppPort": 105,
         "logDimseDatasets": false,
         "rejectUnknownSources": false
       },
@@ -36,11 +46,17 @@
         "password": "admin",
         "virtualHost": "monaideploy",
         "exchange": "monaideploy",
-        "exportRequestQueue": "export_tasks",
         "deadLetterExchange": "monaideploy-dead-letter",
         "deliveryLimit": 3,
-        "requeueDelay": 30
+        "requeueDelay": 3,
+        "prefetchCount": "5"
+      },
+      "topics": {
+        "externalAppRequest": "md.externalapp.request",
+        "exportHl7": "md.export.hl7",
+        "exportHl7Complete": "md.export.hl7complete"
       }
+
     },
     "storage": {
       "localTemporaryStoragePath": "/payloads",
@@ -49,16 +65,15 @@
       "storageRootPath": "/payloads",
       "temporaryBucketName": "monaideploy",
       "serviceAssemblyName": "Monai.Deploy.Storage.MinIO.MinIoStorageService, Monai.Deploy.Storage.MinIO",
-      "watermarkPercent": 75,
+      "watermarkPercent": 95,
       "reserveSpaceGB": 5,
-      "concurrentUploads": 4,
       "settings": {
         "endpoint": "minio:9000",
         "accessKey": "minioadmin",
         "accessToken": "minioadmin",
         "securedConnection": false,
         "region": "local",
-        "executableLocation": "mc",
+        "executableLocation": "/bin/mc",
         "serviceName": "MinIO",
         "createBuckets": "monaideploy"
       }
@@ -68,23 +83,27 @@
       "maximumNumberOfConnections": 10,
       "clientTimeout": 60000,
       "sendAck": true
-    }
-  },
-  "Kestrel": {
-    "EndPoints": {
-      "Http": {
-        "Url": "http://+:5000"
+    },
+    "dicomWeb": {
+      "plugins": []
+    },
+
+    "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"
     }
-  },
-  "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/monai-deploy-express/configs/task-manager.json b/deploy/monai-deploy-express/configs/task-manager.json
@@ -18,7 +18,7 @@
         "docker": "Monai.Deploy.WorkflowManager.TaskManager.Docker.DockerPlugin, Monai.Deploy.WorkflowManager.TaskManager.Docker"
       },
       "meta-data": {
-      },
+      }
     },
     "messaging": {
       "retries": {
@@ -28,7 +28,8 @@
         "workflowRequest": "md.workflow.request",
         "exportComplete": "md.export.complete",
         "exportRequestPrefix": "md.export.request",
-        "taskCallback": "md.tasks.callback"
+        "taskCallback": "md.tasks.callback",
+        "exportHl7": "md.export.hl7"
       },
       "dicomAgents": {
         "dicomWebAgentName": "monaidicomweb",
@@ -42,7 +43,7 @@
         "virtualHost": "monaideploy",
         "exchange": "monaideploy",
         "deadLetterExchange": "deadLetterExchange",
-        "deliveryLimit": "5",
+        "deliveryLimit": "3",
         "requeueDelay": "0"
       },
       "subscriberServiceAssemblyName": "Monai.Deploy.Messaging.RabbitMQ.RabbitMQMessageSubscriberService, Monai.Deploy.Messaging.RabbitMQ",
@@ -55,7 +56,8 @@
         "deadLetterExchange": "monaideploy-dead-letter",
         "exportRequestQueue": "export_tasks",
         "deliveryLimit": 3,
-        "requeueDelay": 30
+        "requeueDelay": 3,
+        "prefetchCount": 5
       }
     },
     "storage": {
@@ -72,51 +74,15 @@
       }
     }
   },
-   "Logging": {
-    "LogLevel": {
-      "Default": "Information",
-      "System": "Warning",
-      "Microsoft": "Warning",
-      "Microsoft.EntityFrameworkCore": "Warning",
-      "Microsoft.Hosting.Lifetime": "Information",
-      "Microsoft.AspNetCore.Mvc.Infrastructure.ControllerActionInvoker": "Error",
-      "Monai": "Debug"
-    },
-    "Console": {
-      "FormatterOptions": {
-        "ColorBehavior": "Enabled",
-        "IncludeScopes": true,
-        "SingleLine": false,
-        "TimestampFormat": " HH:mm:ss ",
-        "UseUtcTimestamp": true
+  "Kestrel": {
+    "EndPoints": {
+      "Http": {
+        "Url": "http://+:5002"
       }
-    }
-  },
-  "Serilog": {
-    "Enrich": [ "FromLogContext", "WithMachineName", "WithThreadId" ],
-    "Properties": {
-      "enviroment": "Production",
-      "serviceName": "MTM"
     },
-    "WriteTo": [
-      {
-        "Name": "File",
-        "Args": {
-          "path": "logs/MTM-.log",
-          "rollingInterval": "Day",
-          "rollOnFileSizeLimit": true,
-          "fileSizeLimitBytes": "10485760",
-          "retainedFileCountLimit": 30,
-          "formatter": "Serilog.Formatting.Json.JsonFormatter, Serilog"
-        }
-      },
-      {
-        "Name": "Http",
-        "Args": {
-          "requestUri": "http://logstash:50000",
-          "queueLimitBytes": null
-        }
-      }
-    ]
-  }
-}
+    "LogHttpRequestQuery": false,
+    "LogHttpRequestBody": false,
+    "LogHttpResponseBody": true
+  },
+  "AllowedHosts": "*"
+}
diff --git a/deploy/monai-deploy-express/configs/workflow-manager.json b/deploy/monai-deploy-express/configs/workflow-manager.json
@@ -14,6 +14,9 @@
     "TaskManager": {
       "concurrency": 1,
       "taskTimeoutMinutes": 60,
+      "perTaskTypeTimeoutMinutes": {
+        "aide_clinical_review": 5760
+      },
       "plug-ins": {
         "docker": "Monai.Deploy.WorkflowManager.TaskManager.Docker.DockerPlugin, Monai.Deploy.WorkflowManager.TaskManager.Docker"
       },
@@ -28,7 +31,10 @@
         "workflowRequest": "md.workflow.request",
         "exportComplete": "md.export.complete",
         "exportRequestPrefix": "md.export.request",
-        "callbackRequest": "md.tasks.callback"
+        "callbackRequest": "md.tasks.callback",
+        "aideClinicalReviewRequest": "aide.clinical_review.request",
+        "exportHl7": "md.export.hl7",
+        "exportHl7Complete": "md.export.hl7complete"
       },
       "dicomAgents": {
         "dicomWebAgentName": "monaidicomweb",
@@ -42,7 +48,7 @@
         "virtualHost": "monaideploy",
         "exchange": "monaideploy",
         "deadLetterExchange": "deadLetterExchange",
-        "deliveryLimit": "5",
+        "deliveryLimit": "3",
         "requeueDelay": "0"
       },
       "subscriberServiceAssemblyName": "Monai.Deploy.Messaging.RabbitMQ.RabbitMQMessageSubscriberService, Monai.Deploy.Messaging.RabbitMQ",
@@ -55,7 +61,8 @@
         "deadLetterExchange": "monaideploy-dead-letter",
         "exportRequestQueue": "export_tasks",
         "deliveryLimit": 3,
-        "requeueDelay": 30
+        "requeueDelay": 3,
+        "prefetchCount": "5"
       }
     },
     "storage": {
@@ -72,7 +79,8 @@
       }
     },
     "dicomTagsDisallowed": "PatientName,PatientID,IssuerOfPatientID,TypeOfPatientID,IssuerOfPatientIDQualifiersSequence,SourcePatientGroupIdentificationSequence,GroupOfPatientsIdentificationSequence,SubjectRelativePositionInImage,PatientBirthDate,PatientBirthTime,PatientBirthDateInAlternativeCalendar,PatientDeathDateInAlternativeCalendar,PatientAlternativeCalendar,PatientSex,PatientInsurancePlanCodeSequence,PatientPrimaryLanguageCodeSequence,PatientPrimaryLanguageModifierCodeSequence,QualityControlSubject,QualityControlSubjectTypeCodeSequence,StrainDescription,StrainNomenclature,StrainStockNumber,StrainSourceRegistryCodeSequence,StrainStockSequence,StrainSource,StrainAdditionalInformation,StrainCodeSequence,GeneticModificationsSequence,GeneticModificationsDescription,GeneticModificationsNomenclature,GeneticModificationsCodeSequence,OtherPatientIDsRETIRED,OtherPatientNames,OtherPatientIDsSequence,PatientBirthName,PatientAge,PatientSize,PatientSizeCodeSequence,PatientBodyMassIndex,MeasuredAPDimension,MeasuredLateralDimension,PatientWeight,PatientAddress,InsurancePlanIdentificationRETIRED,PatientMotherBirthName,MilitaryRank,BranchOfService,MedicalRecordLocatorRETIRED,ReferencedPatientPhotoSequence,MedicalAlerts,Allergies,CountryOfResidence,RegionOfResidence,PatientTelephoneNumbers,PatientTelecomInformation,EthnicGroup,Occupation,SmokingStatus,AdditionalPatientHistory,PregnancyStatus,LastMenstrualDate,PatientReligiousPreference,PatientSpeciesDescription,PatientSpeciesCodeSequence,PatientSexNeutered,AnatomicalOrientationType,PatientBreedDescription,PatientBreedCodeSequence,BreedRegistrationSequence,BreedRegistrationNumber,BreedRegistryCodeSequence,ResponsiblePerson,ResponsiblePersonRole,ResponsibleOrganization,PatientComments,ExaminedBodyThickness",
-    "migExternalAppPlugins": [ "Monai.Deploy.InformaticsGateway.PlugIns.RemoteAppExecution.DicomDeidentifier, Monai.Deploy.InformaticsGateway.PlugIns.RemoteAppExecution, Version=0.0.0.0" ]
+    "migExternalAppPlugins": [ "Monai.Deploy.InformaticsGateway.PlugIns.RemoteAppExecution.DicomDeidentifier, Monai.Deploy.InformaticsGateway.PlugIns.RemoteAppExecution, Version=0.0.0.0" ],
+    "dataRetentionDays": 10 // note. -1 = never delete
   },
   "InformaticsGateway": {
     "apiHost": "http://informatics-gateway:5000",
@@ -90,4 +98,4 @@
     "LogHttpResponseBody": true
   },
   "AllowedHosts": "*"
-}
+}
diff --git a/deploy/monai-deploy-express/docker-compose.yml b/deploy/monai-deploy-express/docker-compose.yml
@@ -12,8 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-version: "3.9"
-
 services:
   minio:
     image: $MINIO_IMAGE
@@ -112,6 +110,7 @@ services:
     image: $INFORMATICS_GATEWAY_IMAGE
     hostname: $INFORMATICS_GATEWAY_HOSTNAME
     container_name: $INFORMATICS_GATEWAY_CONTAINERNAME
+    user: root:root
     volumes:
       - ./configs/informatics-gateway.json:/opt/monai/ig/appsettings.json
       - ./configs/nlog.config:/opt/monai/ig/nlog.config

diff --git a/deploy/monai-deploy-express/init.sh b/deploy/monai-deploy-express/init.sh
@@ -17,14 +17,14 @@ RUNDIR=$PWD/.md
 
 echo "Initializing directories..."
 [ -d $RUNDIR ] && echo "Removing existin $RUNDIR" && sudo rm -r $RUNDIR
-mkdir -p $RUNDIR/esdata/ && echo "Created $RUNDIR/"
+mkdir -p $RUNDIR/esdata/ && echo "Created $RUNDIR/esdata/"
 mkdir -p $RUNDIR/minio/ && echo "Created $RUNDIR/minio/"
 mkdir -p $RUNDIR/rabbitmq/ && echo "Created $RUNDIR/rabbitmq/"
 mkdir -p $RUNDIR/orthanc/ && echo "Created $RUNDIR/orthanc/"
 mkdir -p $RUNDIR/mongodb/ && echo "Created $RUNDIR/mongodb/"
 mkdir -p $RUNDIR/mdwm/ && echo "Created $RUNDIR/mdwm/"
 mkdir -p $RUNDIR/mdtm/ && echo "Created $RUNDIR/mdtm/"
 mkdir -p $RUNDIR/mdig/ && echo "Created $RUNDIR/mdig/"
-sudo chown $(id -u):$(id -g) -R $RUNDIR/esdata && echo "Permission updated"
+sudo chown $(id -u):$(id -g) -R $RUNDIR/ && echo "Permission updated"
 echo "Directories setup"
 echo "Ready to run docker compose up"