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merge in from develop
Signed-off-by: Neil South <[email protected]>
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‎docs/changelog.md

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# Changelog
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Added a new Email plugin, this pulls together information and sends a Message (rabbitmq) to a queue for processing via an external application (for the actual sending)
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Renamed the (Generated) Argo client to ArgoGeneratedClient, added a new ArgoClient using just the methods used by this codebase.
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Enhanced the ArgoClient -> Argo_Get_WorkflowLogsAsync method to decode the json better and make the logs extracted from Argo more readable.

‎src/TaskManager/Plug-ins/AideClinicalReview/packages.lock.json

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"monai.deploy.workflowmanager.configuration": {
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"type": "Project",
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"dependencies": {
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"Monai.Deploy.Messaging": "[0.1.23, )",
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"Monai.Deploy.Storage": "[0.2.15, )"
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"Monai.Deploy.Messaging": "0.1.23",
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"Monai.Deploy.Storage": "0.2.15"
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}
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},
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"monai.deploy.workflowmanager.shared": {
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"type": "Project",
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"dependencies": {
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"Ardalis.GuardClauses": "4.0.1",
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"Microsoft.Extensions.Diagnostics.HealthChecks.Abstractions": "6.0.15",
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"Monai.Deploy.WorkflowManager.Configuration": "1.0.0",
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"fo-dicom": "5.0.3"
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"Ardalis.GuardClauses": "[4.0.1, )",
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"Microsoft.Extensions.Diagnostics.HealthChecks.Abstractions": "[6.0.15, )",
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"Monai.Deploy.WorkflowManager.Configuration": "[1.0.0, )",
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"fo-dicom": "[5.0.3, )"
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}
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},
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"monai.deploy.workflowmanager.taskmanager.api": {
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"type": "Project",
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"dependencies": {
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"Monai.Deploy.Messaging": "[0.1.22, )",
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"Mongo.Migration": "[3.1.4, )",
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"MongoDB.Bson": "[2.19.0, )"
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"Monai.Deploy.Messaging": "0.1.23",
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"Mongo.Migration": "3.1.4",
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"MongoDB.Bson": "2.19.0"
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}
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}
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}
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}
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}
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}

‎src/TaskManager/Plug-ins/Argo/packages.lock.json

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"monai.deploy.workflowmanager.configuration": {
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"type": "Project",
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"dependencies": {
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"Monai.Deploy.Messaging": "[0.1.23, )",
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"Monai.Deploy.Storage": "[0.2.15, )"
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"Monai.Deploy.Messaging": "0.1.23",
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"Monai.Deploy.Storage": "0.2.15"
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}
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},
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"monai.deploy.workflowmanager.shared": {
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"type": "Project",
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"dependencies": {
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"Ardalis.GuardClauses": "4.0.1",
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"Microsoft.Extensions.Diagnostics.HealthChecks.Abstractions": "6.0.15",
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"Monai.Deploy.WorkflowManager.Configuration": "1.0.0",
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"fo-dicom": "5.0.3"
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"Ardalis.GuardClauses": "[4.0.1, )",
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"Microsoft.Extensions.Diagnostics.HealthChecks.Abstractions": "[6.0.15, )",
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"Monai.Deploy.WorkflowManager.Configuration": "[1.0.0, )",
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"fo-dicom": "[5.0.3, )"
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}
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},
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"monai.deploy.workflowmanager.taskmanager.api": {
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"type": "Project",
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"dependencies": {
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"Monai.Deploy.Messaging": "[0.1.22, )",
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"Mongo.Migration": "[3.1.4, )",
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"MongoDB.Bson": "[2.19.0, )"
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"Monai.Deploy.Messaging": "0.1.23",
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"Mongo.Migration": "3.1.4",
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"MongoDB.Bson": "2.19.0"
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}
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}
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}
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}
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}
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}

‎src/TaskManager/Plug-ins/Email/EmailPlugin.cs

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using System.Net.Mail;
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using System.Text.Json;
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using Ardalis.GuardClauses;
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using FellowOakDicom.Serialization;
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using FellowOakDicom;
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using Microsoft.Extensions.Logging;
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using Microsoft.Extensions.Options;
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}
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}
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public override async Task<ExecutionStatus> ExecuteTask(CancellationToken cancellationToken = default)
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{
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using var loggingScope = _logger.BeginScope(new Dictionary<string, object>
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_logger.SendEmailRequestMessageSent(_requestQueue);
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}
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public override Task<ExecutionStatus> GetStatus(string identity, TaskCallbackEvent callbackEvent, CancellationToken cancellationToken = default) => throw new NotImplementedException();
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public override Task HandleTimeout(string identity) => Task.CompletedTask; // not implemented;
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public override Task<ExecutionStatus> GetStatus(string identity, TaskCallbackEvent callbackEvent, CancellationToken cancellationToken = default)
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{
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var result = new ExecutionStatus() { Status = TaskExecutionStatus.Succeeded };
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return Task.FromResult(result);
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}
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public override Task HandleTimeout(string identity) => Task.CompletedTask;
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}
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}

‎src/TaskManager/TaskManager/Program.cs

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using Monai.Deploy.WorkflowManager.Shared.Services;
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using Microsoft.AspNetCore.Builder;
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namespace Monai.Deploy.WorkflowManager.TaskManager
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{
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public class Program

‎src/TaskManager/TaskManager/packages.lock.json

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"monai.deploy.workflowmanager.configuration": {
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"type": "Project",
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"dependencies": {
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"Monai.Deploy.Messaging": "[0.1.23, )",
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"Monai.Deploy.Storage": "[0.2.15, )"
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"Monai.Deploy.Messaging": "0.1.23",
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"Monai.Deploy.Storage": "0.2.15"
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}
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},
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"monai.deploy.workflowmanager.shared": {
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"type": "Project",
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"dependencies": {
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"Ardalis.GuardClauses": "4.0.1",
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"Microsoft.Extensions.Diagnostics.HealthChecks.Abstractions": "6.0.15",
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"Monai.Deploy.WorkflowManager.Configuration": "1.0.0",
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"fo-dicom": "5.0.3"
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"Ardalis.GuardClauses": "[4.0.1, )",
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"Microsoft.Extensions.Diagnostics.HealthChecks.Abstractions": "[6.0.15, )",
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"Monai.Deploy.WorkflowManager.Configuration": "[1.0.0, )",
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"fo-dicom": "[5.0.3, )"
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}
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},
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"monai.deploy.workflowmanager.taskmanager.aideclinicalreview": {
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"type": "Project",
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"dependencies": {
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"Monai.Deploy.WorkflowManager.Configuration": "1.0.0",
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"Monai.Deploy.WorkflowManager.Shared": "1.0.0",
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"Monai.Deploy.WorkflowManager.TaskManager.API": "1.0.0"
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"Monai.Deploy.WorkflowManager.Configuration": "[1.0.0, )",
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"Monai.Deploy.WorkflowManager.Shared": "[1.0.0, )",
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"Monai.Deploy.WorkflowManager.TaskManager.API": "[1.0.0, )"
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}
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},
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"monai.deploy.workflowmanager.taskmanager.api": {
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"type": "Project",
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"dependencies": {
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"Monai.Deploy.Messaging": "[0.1.22, )",
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"Monai.Deploy.Messaging": "[0.1.23, )",
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"Mongo.Migration": "[3.1.4, )",
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"MongoDB.Bson": "[2.19.0, )"
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}
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},
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"monai.deploy.workflowmanager.taskmanager.argo": {
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"type": "Project",
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"dependencies": {
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"KubernetesClient": "10.1.4",
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"Microsoft.AspNetCore.Mvc.Core": "2.2.5",
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"KubernetesClient": "[10.1.4, )",
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"Microsoft.AspNetCore.Mvc.Core": "[2.2.5, )",
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"Monai.Deploy.WorkflowManager.Configuration": "[1.0.0, )",
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"Monai.Deploy.WorkflowManager.Shared": "[1.0.0, )",
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"Monai.Deploy.WorkflowManager.TaskManager.API": "[1.0.0, )"
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}
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},
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"monai.deploy.workflowmanager.taskmanager.database": {
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"type": "Project",
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"dependencies": {
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"Monai.Deploy.WorkflowManager.TaskManager.API": "[1.0.0, )",
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"MongoDB.Driver": "[2.19.0, )"
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}
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},
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"monai.deploy.workflowmanager.taskmanager.docker": {
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"type": "Project",
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"dependencies": {
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"Docker.DotNet": "3.125.13",
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"Monai.Deploy.WorkflowManager.Configuration": "1.0.0",
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"Monai.Deploy.WorkflowManager.Shared": "1.0.0",
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"Monai.Deploy.WorkflowManager.TaskManager.API": "1.0.0"
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}
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},
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"monai.deploy.workflowmanager.taskmanager.database": {
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"monai.deploy.workflowmanager.taskmanager.email": {
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"type": "Project",
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"dependencies": {
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"Monai.Deploy.WorkflowManager.Configuration": "1.0.0",
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"Monai.Deploy.WorkflowManager.Shared": "1.0.0",
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"Monai.Deploy.WorkflowManager.TaskManager.API": "1.0.0",
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"MongoDB.Driver": "2.19.0"
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"fo-dicom": "5.0.3"
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}
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},
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"monai.deploy.workflowmanager.taskmanager.docker": {
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"monai.deploy.workflowmanager.taskmanager.email": {
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"type": "Project",
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"dependencies": {
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"Docker.DotNet": "[3.125.13, )",
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"Monai.Deploy.WorkflowManager.Configuration": "[1.0.0, )",
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"Monai.Deploy.WorkflowManager.TaskManager.API": "[1.0.0, )"
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"Monai.Deploy.WorkflowManager.Shared": "[1.0.0, )",
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"Monai.Deploy.WorkflowManager.TaskManager.API": "[1.0.0, )",
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"fo-dicom": "[5.0.3, )"
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}
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}
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}
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}
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}
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}

‎src/WorkflowManager/WorkflowManager/Program.cs

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{
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#pragma warning disable SA1600 // Elements should be documented
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internal class Program
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public class Program
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{
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{

‎tests/IntegrationTests/TaskManager.IntegrationTests/Features/ClinicalReview.feature

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# See the License for the specific language governing permissions and
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# limitations under the License.
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@IntergrationTests
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@IntegrationTests
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Feature: ClinicalReview
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Integration tests for the clinical review plugin
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@ClinicalReviewPlugin
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Scenario: Clincial review task dispatch event triggers a clinical review request event with all patient details
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Given I have a bucket in MinIO bucket1
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When A Task Dispatch event is published Task_Dispatch_Clinical_Review_Full_Patient_Details
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Then A Clincial Review Request event is published
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@ClinicalReviewPlugin
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Scenario: Clincial review task dispatch event triggers a clinical review request event with partial patient details
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Given I have a bucket in MinIO bucket1
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When A Task Dispatch event is published Task_Dispatch_Clinical_Review_Partial_Patient_Details
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Then A Clincial Review Request event is published
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@ClinicalReviewPlugin
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Scenario: Clincial review task dispatch event triggers a clinical review request event with no patient details
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Given I have a bucket in MinIO bucket1
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When A Task Dispatch event is published Task_Dispatch_Clinical_Review_No_Patient_Details
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Then A Clincial Review Request event is published
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@ClinicalReviewPlugin
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Scenario: Clincial review task dispatch event triggers a clinical review request event with multiple files
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Given I have a bucket in MinIO bucket1
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When A Task Dispatch event is published Task_Dispatch_Clinical_Review_Multi_File
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Then A Clincial Review Request event is published
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@ClinicalReviewPlugin
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Scenario: Clincial review task dispatch event triggers clincial review event with single reviewer role
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Given I have a bucket in MinIO bucket1
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When A Task Dispatch event is published Task_Dispatch_Clinical_Reviewer_Role_Single_Role
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Then A Clincial Review Request event is published
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@ClinicalReviewPlugin
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Scenario: Clincial review task dispatch event triggers clincial review event with default reviewer role
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Given I have a bucket in MinIO bucket1
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When A Task Dispatch event is published Task_Dispatch_Clinical_Reviewer_Role_Mutiple_Roles
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Then A Clincial Review Request event is published
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@ClinicalReviewPlugin
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Scenario: Clincial review task dispatch event triggers clincial review event with mutiple reviewer roles
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Given I have a bucket in MinIO bucket1
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When A Task Dispatch event is published Task_Dispatch_Clinical_Reviewer_Role_Default_Role
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Then A Clincial Review Request event is published
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@ClinicalReviewPlugin
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Scenario: Clincial review task dispatch event triggers clincial review event with application name
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Given I have a bucket in MinIO bucket1
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When A Task Dispatch event is published Task_Dispatch_Clinical_Review_Application_Name
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Then A Clincial Review Request event is published
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@ClinicalReviewPlugin
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Scenario: Clincial review task dispatch event triggers clincial review event with application version
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Given I have a bucket in MinIO bucket1
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When A Task Dispatch event is published Task_Dispatch_Clinical_Review_Application_Version
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Then A Clincial Review Request event is published
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@ClinicalReviewPlugin
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Scenario: Clincial review task dispatch event triggers clincial review event with QA mode
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Given I have a bucket in MinIO bucket1
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When A Task Dispatch event is published Task_Dispatch_Clinical_Review_QA_Mode
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Then A Clincial Review Request event is published
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@ClinicalReviewPlugin
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Scenario: Clincial review task dispatch event triggers clincial review event with reviewed execution Id
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Given I have a bucket in MinIO bucket1
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When A Task Dispatch event is published Task_Dispatch_Clinical_Review_Reviewed_Execution_Id
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Then A Clincial Review Request event is published
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@ClinicalReviewPlugin
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Scenario Outline: Clincial review task dispatch event triggers clincial review event with notifications
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Given I have a bucket in MinIO bucket1
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When A Task Dispatch event is published <testData>
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Then A Clincial Review Request event is published
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Examples:

‎tests/IntegrationTests/TaskManager.IntegrationTests/Features/EmialNotification.feature

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# Copyright 2023 MONAI Consortium
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
5+
# You may obtain a copy of the License at
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#
7+
# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
10+
# distributed under the License is distributed on an "AS IS" BASIS,
11+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12+
# See the License for the specific language governing permissions and
13+
# limitations under the License.
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@IntegrationTests
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Feature: EmialNotification
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Integration tests for the email plugin
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@EmailPlugin
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Scenario: Email task dispatch event triggers an email request event with all relevant args
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Given I have an input DICOM file saved in MinIO for TaskDispatch Task_Dispatch_Email_All
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When A Task Dispatch event is published Task_Dispatch_Email_All
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Then An email request event is published
25+
26+
@EmailPlugin
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Scenario: Email task dispatch event triggers an email request event with only emails arg
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Given I have an input DICOM file saved in MinIO for TaskDispatch Task_Dispatch_Email_Emails
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When A Task Dispatch event is published Task_Dispatch_Email_Emails
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Then An email request event is published
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@EmailPlugin
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Scenario: Email task dispatch event triggers an email request event with only roles arg
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Given I have an input DICOM file saved in MinIO for TaskDispatch Task_Dispatch_Email_Roles
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When A Task Dispatch event is published Task_Dispatch_Email_Roles
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Then An email request event is published

‎tests/IntegrationTests/TaskManager.IntegrationTests/Features/TaskUpdate.feature

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@TaskDispatch_TaskUpdate
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Scenario: TaskUpdateEvent is published with status Accepted after receiving a valid TaskDispatchEvent
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Given I have a bucket in MinIO bucket1
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When A Task Dispatch event is published Task_Dispatch_Accepted
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Then A Task Update event with status Accepted is published with Task Dispatch details
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@TaskDispatch_TaskUpdate
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Scenario Outline: TaskUpdateEvent is published with status Failed after receiving an invalid TaskDispatchEvent
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Given I have a bucket in MinIO bucket1
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When A Task Dispatch event is published <TaskDispatchEvent>
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Then A Task Update event with status Failed is published with Task Dispatch details
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Examples:
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@Ignore
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@TaskCallback_TaskUpdate
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Scenario Outline: TaskUpdateEvent is published with correct status upon receiving a valid TaskCallbackEvent
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Given I have a bucket in MinIO bucket1
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And I have Task Dispatch Info saved in Mongo Task_Dispatch_Basic_Clinical_Review
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When A Task Callback event is published <taskCallbackEvent>
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Then A Task Update event with status <status> is published with Task Callback details

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