254 clinical review reviewed task

guidelines/mwm-workflow-spec.md

@@ -176,7 +176,7 @@ Each Artifact contains at least two elements:
 |------|------|------|-----|
 |name|str|Always|The name of this artifact.|
 |value|Artifact identifier|Required for inputs, optional for outputs.|The context variable for this artifact (see example). If defined for output, that value will be used instead of a Task-generated one.|
-| mandatory| bool | No (default false) | Determines whether this artifact is mandatory. If a mandatory artifact doesn't exist the task is marked as a failure and workflow execution stops. |
+| mandatory| bool | No (default true) | Determines whether this artifact is mandatory. If a mandatory artifact doesn't exist the task is marked as a failure and workflow execution stops. |
 
 
 As you can see in the example below, input artifacts require a _value_. This is a reference to a previously generated artifact, or to `context.input` - a value for an artifact representing the original input that triggered the workflow.
@@ -271,7 +271,6 @@ The Execution object contains the following properties:
 |------|------|------|
 |execution_id|str|The unique ID identifying task execution.|
 |task_id|str|The ID of this task in the workflow.|
-|input_dir|str|Path to the input directory of this task.|
 |output_dir|str|Path to the output directory of this task.|
 |task|dict|The details of the executed task. Similar to the Task definition in the workflow spec.|
 |start_time|timestamp|The UTC timestamp of when this task execution began.

src/ConditionsResolver/Constants/ParameterConstants.cs

@@ -0,0 +1,41 @@
+/*
+ * Copyright 2021-2022 MONAI Consortium
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+namespace Monai.Deploy.WorkflowManager.ConditionsResolver.Constants
+{
+    public static class ParameterConstants
+    {
+        public const string TaskId = "task_id";
+        public const string Status = "status";
+        public const string ExecutionId = "execution_id";
+        public const string OutputDirectory = "output_dir";
+        public const string TaskType = "task_type";
+        public const string PreviousTaskId = "previous_task_id";
+        public const string ErrorMessage = "error_msg";
+        public const string Result = "result";
+        public const string StartTime = "start_time";
+
+        public const string Name = "name";
+        public const string Description = "description";
+
+        public const string PatientId = "id";
+        public const string PatientName = "name";
+        public const string PatientSex = "sex";
+        public const string PatientDob = "dob";
+        public const string PatientAge = "age";
+        public const string PatientHospitalId = "hospital_id";
+    }
+}

src/ConditionsResolver/Parser/ConditionalParameterParser.cs

@@ -14,10 +14,12 @@
  * limitations under the License.
  */
 
+using System.Globalization;
 using System.Text.RegularExpressions;
 using Ardalis.GuardClauses;
 using Microsoft.Extensions.Logging;
 using Monai.Deploy.WorkflowManager.Common.Interfaces;
+using Monai.Deploy.WorkflowManager.ConditionsResolver.Constants;
 using Monai.Deploy.WorkflowManager.ConditionsResolver.Resolver;
 using Monai.Deploy.WorkflowManager.Contracts.Models;
 using Monai.Deploy.WorkflowManager.Storage.Services;
@@ -36,7 +38,7 @@ public enum ParameterContext
 
     public class ConditionalParameterParser : IConditionalParameterParser
     {
-        private const string ExecutionsTask = "context.executions.task";
+        private const string ExecutionsTask = "context.executions";
         private const string ContextDicomSeries = "context.dicom.series";
         private const string PatientDetails = "context.input.patient_details";
         private const string ContextWorkflow = "context.workflow";
@@ -182,7 +184,7 @@ private void ClearWorkflowParser()
         /// <summary>
         /// Resolves a query between two brackets {{ query }}
         /// </summary>
-        /// <param name="value">The query Example: {{ context.executions.task['other task'].'Fred' }}</param>
+        /// <param name="value">The query Example: {{ context.executions.other_task.Result.'Fred' }}</param>
         /// <returns>
         /// Tuple:
         /// Result of the resolution
@@ -243,29 +245,77 @@ private void ClearWorkflowParser()
         private (string? Result, ParameterContext Context) ResolveExecutionTasks(string value)
         {
             var subValue = value.Trim().Substring(ExecutionsTask.Length, value.Length - ExecutionsTask.Length);
-            var subValues = subValue.Split('[', ']');
+            var subValues = subValue.Split('.');
             var id = subValues[1].Trim('\'');
 
-            var task = WorkflowInstance?.Tasks.First(t => t.TaskId == id);
+            var task = WorkflowInstance?.Tasks.FirstOrDefault(t => t.TaskId == id);
 
-            if (task is null || task is not null && !task.Metadata.Any())
+            if (task is null)
             {
                 return (Result: null, Context: ParameterContext.TaskExecutions);
             }
 
-            var metadataKey = subValues[2].Split('\'')[1];
+            var subValueKey = subValues[2];
+            string? keyValue = null;
 
-            if (task is not null && task.Metadata.ContainsKey(metadataKey))
+            if (subValues.Length > 3)
             {
-                var result = task.Metadata[metadataKey];
+                keyValue = subValues[3]?.Split('\'')[1];
+            }
+
+            var resultStr = null as string;
+            switch (subValueKey.ToLower())
+            {
+                case ParameterConstants.TaskId:
+                    resultStr = task.TaskId;
+                    break;
+                case ParameterConstants.Status:
+                    resultStr = task.Status.ToString();
+                    break;
+                case ParameterConstants.ExecutionId:
+                    resultStr = task.ExecutionId;
+                    break;
+                case ParameterConstants.OutputDirectory:
+                    resultStr = task.OutputDirectory;
+                    break;
+                case ParameterConstants.TaskType:
+                    resultStr = task.TaskType;
+                    break;
+                case ParameterConstants.PreviousTaskId:
+                    resultStr = task.PreviousTaskId;
+                    break;
+                case ParameterConstants.ErrorMessage:
+                    resultStr = task.Reason.ToString();
+                    break;
+                case ParameterConstants.Result:
+                    resultStr = GetValueFromDictionary(task.ResultMetadata, keyValue);
+                    break;
+                case ParameterConstants.StartTime:
+                    resultStr = task.TaskStartTime?.ToString("dd/MM/yyyy HH:mm:ss");
+                    break;
+                default:
+                    break;
+            }
+
+            return (Result: resultStr, Context: ParameterContext.TaskExecutions);
+        }
 
-                if (result is string resultStr)
+        private static string? GetValueFromDictionary(Dictionary<string, object> dictionary, string? key)
+        {
+            if (key is null)
+            {
+                return null;
+            }
+
+            if (dictionary.TryGetValue(key, out var value))
+            {
+                if (value is string valueStr)
                 {
-                    return (Result: resultStr, Context: ParameterContext.TaskExecutions);
+                    return valueStr;
                 }
             }
 
-            return (Result: null, Context: ParameterContext.TaskExecutions);
+            return null;
         }
 
         private (string? Result, ParameterContext Context) ResolveContextWorkflow(string value)
@@ -288,10 +338,10 @@ private void ClearWorkflowParser()
                 var resultStr = null as string;
                 switch (keyValue)
                 {
-                    case "name":
+                    case ParameterConstants.Name:
                         resultStr = workflowSpecValue.Name;
                         break;
-                    case "description":
+                    case ParameterConstants.Description:
                         resultStr = workflowSpecValue.Description;
                         break;
                     default:
@@ -324,22 +374,22 @@ private void ClearWorkflowParser()
                 var resultStr = null as string;
                 switch (keyValue)
                 {
-                    case "id":
+                    case ParameterConstants.PatientId:
                         resultStr = patientValue.PatientId;
                         break;
-                    case "name":
+                    case ParameterConstants.PatientName:
                         resultStr = patientValue.PatientName;
                         break;
-                    case "sex":
+                    case ParameterConstants.PatientSex:
                         resultStr = patientValue.PatientSex;
                         break;
-                    case "dob":
+                    case ParameterConstants.PatientDob:
                         resultStr = patientValue.PatientDob?.ToString("dd/MM/yyyy");
                         break;
-                    case "age":
+                    case ParameterConstants.PatientAge:
                         resultStr = patientValue.PatientAge;
                         break;
-                    case "hospital_id":
+                    case ParameterConstants.PatientHospitalId:
                         resultStr = patientValue.PatientHospitalId;
                         break;
                     default:

src/Contracts/Models/TaskExecution.cs

@@ -59,8 +59,8 @@ public class TaskExecution
         [JsonProperty(PropertyName = "output_directory")]
         public string OutputDirectory { get; set; }
 
-        [JsonProperty(PropertyName = "metadata")]
-        public Dictionary<string, object> Metadata { get; set; }
+        [JsonProperty(PropertyName = "result")]
+        public Dictionary<string, object> ResultMetadata { get; set; }
 
         [JsonProperty(PropertyName = "input_parameters")]
         public Dictionary<string, object> InputParameters { get; set; }

src/TaskManager/Plug-ins/AideClinicalReview/AideClinicalReviewPlugin.cs

@@ -42,6 +42,8 @@ public class AideClinicalReviewPlugin : TaskPluginBase, IAsyncDisposable
         private string _patientHospitalId;
         private string _queueName;
         private string _workflowName;
+        private string _reviewedTaskId;
+        private string _reviewedExecutionId;
 
         public AideClinicalReviewPlugin(
             IServiceScopeFactory serviceScopeFactory,
@@ -102,6 +104,16 @@ private void Initialize()
             {
                 _workflowName = Event.TaskPluginArguments[Keys.WorkflowName];
             }
+
+            if (Event.TaskPluginArguments.ContainsKey(Keys.ReviewedExecutionId))
+            {
+                _reviewedExecutionId = Event.TaskPluginArguments[Keys.ReviewedExecutionId];
+            }
+
+            if (Event.TaskPluginArguments.ContainsKey(Keys.ReviewedTaskId))
+            {
+                _reviewedTaskId = Event.TaskPluginArguments[Keys.ReviewedTaskId];
+            }
         }
 
         private void ValidateEventAndInit()
@@ -144,6 +156,8 @@ private JsonMessage<ClinicalReviewRequestEvent> GenerateClinicalReviewRequestEve
                 CorrelationId = Event.CorrelationId,
                 ExecutionId = Event.ExecutionId,
                 TaskId = Event.TaskId,
+                ReviewedTaskId = _reviewedTaskId,
+                ReviewedExecutionId = _reviewedExecutionId,
                 WorkflowName = _workflowName,
                 Files = Event.Inputs,
                 PatientMetadata = new PatientMetadata

src/TaskManager/Plug-ins/AideClinicalReview/Events/ClinicalReviewRequestEvent.cs

@@ -37,6 +37,20 @@ public class ClinicalReviewRequestEvent : EventBase
         [JsonProperty(PropertyName = "task_id")]
         public string TaskId { get; set; }
 
+        /// <summary>
+        /// Gets or sets the ID of the reviewed task ID.
+        /// </summary>
+        [Required]
+        [JsonProperty(PropertyName = "reviewed_task_id")]
+        public string ReviewedTaskId { get; set; }
+
+        /// <summary>
+        /// Gets or sets the ID of the reviewed execution ID.
+        /// </summary>
+        [Required]
+        [JsonProperty(PropertyName = "reviewed_execution_id")]
+        public string ReviewedExecutionId { get; set; }
+
         /// <summary>
         /// Gets or sets the correlation ID.
         /// </summary>

src/TaskManager/Plug-ins/AideClinicalReview/Keys.cs

@@ -54,9 +54,14 @@ public class Keys
         public static readonly string WorkflowName = "workflow_name";
 
         /// <summary>
-        /// Key for the reviewed task details.
+        /// Key for the reviewed task id.
         /// </summary>
-        public static readonly string ReviewedTaskDetails = "reviewed_task_details";
+        public static readonly string ReviewedTaskId = "reviewed_task_id";
+
+        /// <summary>
+        /// Key for the reviewed execution id.
+        /// </summary>
+        public static readonly string ReviewedExecutionId = "reviewed_execution_id";
 
         /// <summary>
         /// Key for the queue name to send the clinical review message.
@@ -69,7 +74,8 @@ public class Keys
         public static readonly IReadOnlyList<string> RequiredParameters =
             new List<string> {
                 QueueName,
-                WorkflowName
+                WorkflowName,
+                ReviewedTaskId
             };
     }
 }

src/WorkflowExecuter/Common/EventMapper.cs

@@ -78,7 +78,7 @@ public static TaskDispatchEvent ToTaskDispatchEvent(TaskExecution task, Workflow
                 Inputs = inputs,
                 Outputs = outputs,
                 TaskPluginType = task.TaskType,
-                Metadata = task.Metadata,
+                Metadata = { },
                 PayloadId = workflowInstance.PayloadId,
                 IntermediateStorage = new Messaging.Common.Storage
                 {

src/WorkflowExecuter/Services/WorkflowExecuterService.cs

@@ -240,7 +240,7 @@ public async Task<bool> ProcessTaskUpdate(TaskUpdateEvent message)
 
             if (message.Metadata.Any())
             {
-                currentTask.Metadata = message.Metadata;
+                currentTask.ResultMetadata = message.Metadata;
             }
 
             await HandleOutputArtifacts(workflowInstance, message.Outputs, currentTask);
@@ -592,9 +592,10 @@ private async Task<TaskExecution> CreateTaskExecutionAsync(TaskObject task,
                 TaskStartTime = DateTime.UtcNow,
                 TaskId = task.Id,
                 Status = TaskExecutionStatus.Created,
-                InputArtifacts = await _artifactMapper.ConvertArtifactVariablesToPath(task?.Artifacts?.Input ?? new Artifact[] { }, payloadId, workflowInstanceId, bucketName),
+                Reason = FailureReason.None,
+                InputArtifacts = await _artifactMapper.ConvertArtifactVariablesToPath(task?.Artifacts?.Input ?? Array.Empty<Artifact>(), payloadId, workflowInstanceId, bucketName),
                 OutputDirectory = $"{payloadId}/workflows/{workflowInstanceId}/{executionId}",
-                Metadata = { },
+                ResultMetadata = { },
                 InputParameters = newInputParameters,
                 PreviousTaskId = previousTaskId
             };