From c0f22643d41df46004098afd48784b8bb74f50d8 Mon Sep 17 00:00:00 2001 From: Victor Chang Date: Thu, 13 Jun 2024 09:40:50 -0700 Subject: [PATCH 1/3] MDE 0.6.0 release Signed-off-by: Victor Chang --- deploy/monai-deploy-express/.env | 18 ++--- .../configs/informatics-gateway.json | 65 +++++++++++------- .../configs/task-manager.json | 66 +++++-------------- .../configs/workflow-manager.json | 18 +++-- .../monai-deploy-express/docker-compose.yml | 1 + deploy/monai-deploy-express/init.sh | 4 +- 6 files changed, 83 insertions(+), 89 deletions(-) diff --git a/deploy/monai-deploy-express/.env b/deploy/monai-deploy-express/.env index 5b080ad..1507891 100644 --- 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-beta.96 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:2023.5.0-pr0996.410 +TASK_MANAGER_IMAGE=ghcr.io/project-monai/monai-deploy-task-manager:2023.5.0-pr0996.410 -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 index dd80d8f..a97098e 100644 --- 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" } -} +} \ No newline at end of file diff --git a/deploy/monai-deploy-express/configs/task-manager.json b/deploy/monai-deploy-express/configs/task-manager.json index 3a35f56..cddc884 100644 --- 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": "*" +} \ No newline at end of file diff --git a/deploy/monai-deploy-express/configs/workflow-manager.json b/deploy/monai-deploy-express/configs/workflow-manager.json index 112de1a..766cf0d 100644 --- 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": "*" -} +} \ No newline at end of file diff --git a/deploy/monai-deploy-express/docker-compose.yml b/deploy/monai-deploy-express/docker-compose.yml index fc88dff..788ee54 100644 --- a/deploy/monai-deploy-express/docker-compose.yml +++ b/deploy/monai-deploy-express/docker-compose.yml @@ -112,6 +112,7 @@ services: image: $INFORMATICS_GATEWAY_IMAGE hostname: $INFORMATICS_GATEWAY_HOSTNAME container_name: $INFORMATICS_GATEWAY_CONTAINERNAME + user: root:root volumes: - ./configs/informatics-gateway.json:/opt/monai/ig/appsettings.json - ./configs/nlog.config:/opt/monai/ig/nlog.config diff --git a/deploy/monai-deploy-express/init.sh b/deploy/monai-deploy-express/init.sh index afff762..a6e3be6 100755 --- a/deploy/monai-deploy-express/init.sh +++ b/deploy/monai-deploy-express/init.sh @@ -17,7 +17,7 @@ RUNDIR=$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/" @@ -25,6 +25,6 @@ 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" From 2ced79e891d0cd4a94365b26050f4ef5ba334646 Mon Sep 17 00:00:00 2001 From: Victor Chang Date: Thu, 13 Jun 2024 12:18:13 -0700 Subject: [PATCH 2/3] Remove obsoleted version tag Signed-off-by: Victor Chang --- deploy/monai-deploy-express/docker-compose.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/deploy/monai-deploy-express/docker-compose.yml b/deploy/monai-deploy-express/docker-compose.yml index 788ee54..a84a385 100644 --- 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 From aa1324d1e1626bdee1ca7e10e068fcb87c982cbb Mon Sep 17 00:00:00 2001 From: Victor Chang Date: Thu, 13 Jun 2024 12:18:58 -0700 Subject: [PATCH 3/3] Update IG to 0.5.0 and WM to 0.20 Signed-off-by: Victor Chang --- deploy/monai-deploy-express/.env | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/deploy/monai-deploy-express/.env b/deploy/monai-deploy-express/.env index 1507891..19dd3e6 100644 --- a/deploy/monai-deploy-express/.env +++ b/deploy/monai-deploy-express/.env @@ -1,8 +1,8 @@ # Container Images -INFORMATICS_GATEWAY_IMAGE=ghcr.io/project-monai/monai-deploy-informatics-gateway:0.5.0-beta.96 +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-pr0996.410 -TASK_MANAGER_IMAGE=ghcr.io/project-monai/monai-deploy-task-manager:2023.5.0-pr0996.410 +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.2024-06-11T03-13-30Z MONGODB_IMAGE=mongo:5.0.25