Update MD-Express Version

.github/workflows/monai-deploy-express.yml

@@ -12,6 +12,9 @@ on:
         default: 'monai-deploy-express-v'
         required: true
         type: string
+# To address error 403
+permissions:
+  contents: write
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:

.github/workflows/test-monai-deploy-express.yml

@@ -1,5 +1,3 @@
-# This is a basic workflow to help you get started with Actions
-
 name: Test MONAI Deploy Express
 on:
   push:
@@ -9,6 +7,8 @@ on:
   workflow_dispatch:
 # Controls when the workflow will run
 
+permissions:
+  contents: write
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
@@ -23,26 +23,43 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Start MONAI Deploy Express
+        continue-on-error: true
         working-directory: ./deploy/monai-deploy-express
         run: |
           ./init.sh
           docker compose up --wait
 
       - name: Informatics Gateway Health Check
-        continue-on-error: true
+        continue-on-error: false
         run: |
           curl http://localhost:5000/health
 
       - name: Workflow Manager Health Check
-        continue-on-error: true
+        continue-on-error: false
         run: |
           curl http://localhost:5001/health
 
       - name: Task Manager Health Check
-        continue-on-error: true
+        continue-on-error: false
         run: |
           curl http://localhost:5002/health
 
+      - name: Get WorkflowID
+        continue-on-error: false
+        run: |
+          curl -X POST http://localhost:8042/instances --data-binary "@deploy/monai-deploy-express/sample-workflows/ci-test-files/IMG0002.dcm"
+          WORKFLOW_ID=$(curl --request POST --header 'Content-Type: application/json'  --data @deploy/monai-deploy-express/sample-workflows/hello-world.json  http://localhost:5001/workflows | jq '.workflow_id' )
+          SIZE=${#WORKFLOW_ID}
+          echo "GITHUB_SIZE=$(echo $SIZE)" >> $GITHUB_ENV
+          if [[ $SIZE < 32 ]]; then
+              echo "WID=false" >> "$GITHUB_ENV"
+              echo "No WorkflowID"
+              exit 1
+          else
+              echo "WID=true" >> "$GITHUB_ENV"
+              echo "WorkflowID Present"
+          fi
+
       - name: Collect Logs
         working-directory: ./deploy/monai-deploy-express
         continue-on-error: true

.vscode/settings.json

@@ -0,0 +1,5 @@
+{
+    "githubPullRequests.ignoredPullRequestBranches": [
+        "main"
+    ]
+}

deploy/monai-deploy-express/.env

@@ -1,8 +1,8 @@
 # Container Images
 INFORMATICS_GATEWAY_IMAGE=ghcr.io/project-monai/monai-deploy-informatics-gateway:0.4.1
 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-beta.332
+TASK_MANAGER_IMAGE=ghcr.io/project-monai/monai-deploy-task-manager:2023.5.0-beta.332 
 
 MINIO_IMAGE=minio/minio:RELEASE.2023-10-16T04-13-43Z
 MONGODB_IMAGE=mongo:5.0.12
@@ -98,7 +98,7 @@ 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=$PWD/.md/mdtm/
+TASK_MANAGER_DATA=${PWD}/.md/mdtm/
 MONAI_DEPLOY_PLUGINS=plug-ins/ # disabled by default
 
 MINIO_DATA=.md/minio/data/

deploy/monai-deploy-express/configs/task-manager.json

@@ -21,29 +21,16 @@
       },
     },
     "messaging": {
-      "retries": {
-        "retryDelays": "5"
-      },
-      "topics": {
-        "workflowRequest": "md.workflow.request",
-        "exportComplete": "md.export.complete",
-        "exportRequestPrefix": "md.export.request",
-        "taskCallback": "md.tasks.callback"
-      },
-      "dicomAgents": {
-        "dicomWebAgentName": "monaidicomweb",
-        "scuAgentName": "monaiscu"
-      },
       "publisherServiceAssemblyName": "Monai.Deploy.Messaging.RabbitMQ.RabbitMQMessagePublisherService, Monai.Deploy.Messaging.RabbitMQ",
       "publisherSettings": {
         "endpoint": "rabbitmq",
         "username": "admin",
         "password": "admin",
         "virtualHost": "monaideploy",
         "exchange": "monaideploy",
-        "deadLetterExchange": "deadLetterExchange",
-        "deliveryLimit": "5",
-        "requeueDelay": "0"
+        "deadLetterExchange": "deadletterExchange",
+        "deliveryLimit": 3,
+        "requeueDelay": 0
       },
       "subscriberServiceAssemblyName": "Monai.Deploy.Messaging.RabbitMQ.RabbitMQMessageSubscriberService, Monai.Deploy.Messaging.RabbitMQ",
       "subscriberSettings": {
@@ -53,10 +40,25 @@
         "virtualHost": "monaideploy",
         "exchange": "monaideploy",
         "deadLetterExchange": "monaideploy-dead-letter",
-        "exportRequestQueue": "export_tasks",
         "deliveryLimit": 3,
-        "requeueDelay": 30
-      }
+        "requeueDelay": 3,
+        "exportRequestQueue": "export_tasks",
+        "prefetchCount": 5
+      },
+      "retries": {
+        "retryDelays": "localhost"
+      },
+      "topics": {
+        "workflowRequest": "md.workflow.request",
+        "exportComplete": "md.export.complete",
+        "exportRequestPrefix": "md.export.request",
+        "taskCallback": "md.tasks.callback",
+        "exportHl7": "md.export.hl7" 
+      },
+      "dicomAgents": {
+        "dicomWebAgentName": "monaidicomweb",
+        "scuAgentName": "monaiscu"
+      },
     },
     "storage": {
       "serviceAssemblyName": "Monai.Deploy.Storage.MinIO.MinIoStorageService, Monai.Deploy.Storage.MinIO",
@@ -71,52 +73,5 @@
         "serviceName": "test"
       }
     }
-  },
-   "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
-      }
-    }
-  },
-  "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
-        }
-      }
-    ]
   }
 }

deploy/monai-deploy-express/configs/workflow-manager.json

@@ -28,7 +28,10 @@
         "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 +45,7 @@
         "virtualHost": "monaideploy",
         "exchange": "monaideploy",
         "deadLetterExchange": "deadLetterExchange",
-        "deliveryLimit": "5",
+        "deliveryLimit": "3",
         "requeueDelay": "0"
       },
       "subscriberServiceAssemblyName": "Monai.Deploy.Messaging.RabbitMQ.RabbitMQMessageSubscriberService, Monai.Deploy.Messaging.RabbitMQ",
@@ -55,7 +58,8 @@
         "deadLetterExchange": "monaideploy-dead-letter",
         "exportRequestQueue": "export_tasks",
         "deliveryLimit": 3,
-        "requeueDelay": 30
+        "requeueDelay": 3,
+        "prefetchCount": "5"
       }
     },
     "storage": {
@@ -72,7 +76,8 @@
       }
     },
     "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",