Merge pull request #744 from Project-MONAI/release/0.1.18

Release/0.1.18

Author: neildsouth

.github/workflows/test.yml

@@ -251,7 +251,7 @@ jobs:
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-      run: dotnet sonarscanner begin /k:"Project-MONAI_monai-deploy-workflow-manager" /o:"project-monai" /d:sonar.login="${{ secrets.SONAR_TOKEN }}" /d:sonar.host.url="https://sonarcloud.io" /d:sonar.cs.opencover.reportsPaths="../**/coverage.opencover.xml" /d:sonar.coverage.exclusions="src/WorkflowManager/Database/Repositories/**/*,src/TaskManager/Database/TaskDispatchEventRepository.cs"
+      run: dotnet sonarscanner begin /k:"Project-MONAI_monai-deploy-workflow-manager" /o:"project-monai" /d:sonar.login="${{ secrets.SONAR_TOKEN }}" /d:sonar.host.url="https://sonarcloud.io" /d:sonar.cs.opencover.reportsPaths="../**/coverage.opencover.xml" /d:sonar.coverage.exclusions="src/WorkflowManager/Database/Repositories/**/*,src/TaskManager/Database/TaskDispatchEventRepository.cs,**/Migrations/M0*.cs"
       working-directory: ./src
 
     - name: Restore Solution

doc/dependency_decisions.yml

@@ -2506,3 +2506,33 @@
     :versions:
     - 4.3.0
     :when: 2023-02-02 15:35:00.000000000 Z
+
+- - :approve
+  - System.IO.Pipelines
+  - :who: neildsouth
+    :why: MIT (https://github.com/dotnet/runtime/raw/main/LICENSE.TXT)
+    :versions:
+    - 6.0.3
+    :when: 2023-04-11 13:37:00.000000000 Z
+- - :approve
+  - Microsoft.Extensions.DependencyModel
+  - :who: neildsouth
+    :why: MIT (https://github.com/dotnet/runtime/raw/main/LICENSE.TXT)
+    :versions:
+    - 6.0.0
+    :when: 2023-04-11 13:37:00.000000000 Z
+- - :approve
+  - Microsoft.AspNetCore.TestHost
+  - :who: neildsouth
+    :why: MIT (https://github.com/dotnet/runtime/raw/main/LICENSE.TXT)
+    :versions:
+    - 6.0.15
+    :when: 2023-04-11 13:37:00.000000000 Z
+- - :approve
+  - Microsoft.AspNetCore.Mvc.Testing
+  - :who: neildsouth
+    :why: MIT (https://github.com/dotnet/runtime/raw/main/LICENSE.TXT)
+    :versions:
+    - 6.0.15
+    :when: 2023-04-11 13:37:00.000000000 Z
+

src/.sonarlint/sonar.settings.json

@@ -1 +1 @@
-{"sonar.exclusions":[],"sonar.global.exclusions":["**/build-wrapper-dump.json"],"sonar.inclusions":[]}
+{"sonar.exclusions":[],"sonar.global.exclusions":["**/build-wrapper-dump.json","**/Migrations/*.cs"],"sonar.inclusions":[]}

src/Shared/Configuration/MessageBrokerConfigurationKeys.cs

@@ -64,16 +64,23 @@ public class MessageBrokerConfigurationKeys
 
         /// <summary>
         /// Gets or sets the topic for publishing task update events.
-        /// Defaults to `md.tasks.update`.
+        /// Defaults to `md.tasks.cancellation`.
         /// </summary>
         [ConfigurationKeyName("taskCancellation")]
         public string TaskCancellationRequest { get; set; } = "md.tasks.cancellation";
 
         /// <summary>
         /// Gets or sets the topic for publishing clinical review request events.
-        /// Defaults to `md.tasks.update`.
+        /// Defaults to `aide.clinical_review.request`.
         /// </summary>
         [ConfigurationKeyName("aideClinicalReviewRequest")]
         public string AideClinicalReviewRequest { get; set; } = "aide.clinical_review.request";
+
+        /// <summary>
+        /// Gets or sets the topic for publishing clinical review cancelation events.
+        /// Defaults to `aide.clinical_review.cancellation`.
+        /// </summary>
+        [ConfigurationKeyName("aideClinicalReviewCancelation")]
+        public string AideClinicalReviewCancelation { get; set; } = "aide.clinical_review.cancellation";
     }
 }

src/Shared/Configuration/PagedOptions.cs

@@ -0,0 +1,28 @@
+/*
+ * Copyright 2023 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.
+ */
+using Microsoft.Extensions.Configuration;
+
+namespace Monai.Deploy.WorkflowManager.Configuration
+{
+    public class PagedOptions
+    {
+        /// <summary>
+        /// Represents the <c>endpointSettings</c> section of the configuration file.
+        /// </summary>
+        [ConfigurationKeyName("endpointSettings")]
+        public EndpointSettings EndpointSettings { get; set; }
+    }
+}

src/Shared/Configuration/WorkflowManagerOptions.cs

@@ -15,11 +15,12 @@
  */
 
 using System;
+using System.Collections.Generic;
 using Microsoft.Extensions.Configuration;
 
 namespace Monai.Deploy.WorkflowManager.Configuration
 {
-    public class WorkflowManagerOptions
+    public class WorkflowManagerOptions : PagedOptions
     {
         /// <summary>
         /// Name of the key for retrieve database connection string.
@@ -44,15 +45,13 @@ public class WorkflowManagerOptions
         [ConfigurationKeyName("taskManager")]
         public TaskManagerConfiguration TaskManager { get; set; }
 
-        /// <summary>
-        /// Represents the <c>endpointSettings</c> section of the configuration file.
-        /// </summary>
-        [ConfigurationKeyName("endpointSettings")]
-        public EndpointSettings EndpointSettings { get; set; }
-
         [ConfigurationKeyName("taskTimeoutMinutes")]
         public double TaskTimeoutMinutes { get; set; } = 60;
 
+        [ConfigurationKeyName("perTaskTypeTimeoutMinutes")]
+        public Dictionary<string, double> PerTaskTypeTimeoutMinutes { get; set; }
+
+
         public TimeSpan TaskTimeout { get => TimeSpan.FromMinutes(TaskTimeoutMinutes); }
 
         /// <summary>

src/WorkflowManager/WorkflowManager/Controllers/ApiControllerBase.cs renamed to src/Shared/Shared/ApiControllerBase.cs

@@ -14,34 +14,33 @@
  * limitations under the License.
  */
 
-using System;
-using System.Collections.Generic;
 using System.Net;
 using Ardalis.GuardClauses;
 using Microsoft.AspNetCore.Mvc;
 using Microsoft.Extensions.Options;
 using Monai.Deploy.WorkflowManager.Configuration;
-using Monai.Deploy.WorkflowManager.Filter;
-using Monai.Deploy.WorkflowManager.Services;
-using Monai.Deploy.WorkflowManager.Wrappers;
+using Monai.Deploy.WorkflowManager.Shared.Filter;
+using Monai.Deploy.WorkflowManager.Shared.Wrappers;
+using Monai.Deploy.WorkflowManager.Shared.Services;
+using Microsoft.AspNetCore.Routing;
 
-namespace Monai.Deploy.WorkflowManager.Controllers
+namespace Monai.Deploy.WorkflowManager.ControllersShared
 {
     /// <summary>
     /// Base Api Controller.
     /// </summary>
     [ApiController]
     public class ApiControllerBase : ControllerBase
     {
-        private readonly IOptions<WorkflowManagerOptions> _options;
+        public IOptions<WorkflowManagerOptions> Options { get; set; }
 
         /// <summary>
         /// Initializes a new instance of the <see cref="ApiControllerBase"/> class.
         /// </summary>
         /// <param name="options">Workflow manager options.</param>
-        public ApiControllerBase(IOptions<WorkflowManagerOptions> options)
+        public ApiControllerBase(IOptions<WorkflowManagerOptions> Options)
         {
-            _options = options ?? throw new ArgumentNullException(nameof(options));
+            this.Options = Options ?? throw new ArgumentNullException(nameof(Options));
         }
 
         /// <summary>
@@ -69,34 +68,26 @@ public ApiControllerBase(IOptions<WorkflowManagerOptions> options)
         /// <param name="uriService">Uri service.</param>
         /// <param name="route">Route.</param>
         /// <returns>Returns <see cref="PagedResponse{T}"/>.</returns>
-        public PagedResponse<List<T>> CreatePagedReponse<T>(List<T> pagedData, PaginationFilter validFilter, long totalRecords, IUriService uriService, string route)
+        public PagedResponse<IEnumerable<T>> CreatePagedReponse<T>(IEnumerable<T> pagedData, PaginationFilter validFilter, long totalRecords, IUriService uriService, string route)
         {
             Guard.Against.Null(pagedData);
             Guard.Against.Null(validFilter);
             Guard.Against.Null(route);
             Guard.Against.Null(uriService);
 
-            var pageSize = validFilter.PageSize ?? _options.Value.EndpointSettings.DefaultPageSize;
-            var respose = new PagedResponse<List<T>>(pagedData, validFilter.PageNumber, pageSize);
-            var totalPages = (double)totalRecords / pageSize;
-            var roundedTotalPages = Convert.ToInt32(Math.Ceiling(totalPages));
+            var pageSize = validFilter.PageSize ?? Options.Value.EndpointSettings.DefaultPageSize;
+            var respose = new PagedResponse<IEnumerable<T>>(pagedData, validFilter.PageNumber, pageSize);
 
-            respose.NextPage =
-                validFilter.PageNumber >= 1 && validFilter.PageNumber < roundedTotalPages
-                ? uriService.GetPageUriString(new PaginationFilter(validFilter.PageNumber + 1, pageSize), route)
-                : null;
-
-            respose.PreviousPage =
-                validFilter.PageNumber - 1 >= 1 && validFilter.PageNumber <= roundedTotalPages
-                ? uriService.GetPageUriString(new PaginationFilter(validFilter.PageNumber - 1, pageSize), route)
-                : null;
+            respose.SetUp(validFilter, totalRecords, uriService, route);
+            return respose;
+        }
 
-            respose.FirstPage = uriService.GetPageUriString(new PaginationFilter(1, pageSize), route);
-            respose.LastPage = uriService.GetPageUriString(new PaginationFilter(roundedTotalPages, pageSize), route);
-            respose.TotalPages = roundedTotalPages;
-            respose.TotalRecords = totalRecords;
 
-            return respose;
+        public StatsPagedResponse<IEnumerable<T>> CreateStatsPagedReponse<T>(IEnumerable<T> pagedData, PaginationFilter validFilter, long totalRecords, IUriService uriService, string route)
+        {
+            var response = new StatsPagedResponse<IEnumerable<T>>(pagedData, validFilter.PageNumber, validFilter.PageSize.Value);
+            response.SetUp(validFilter, totalRecords, uriService, route);
+            return response;
         }
     }
 }

src/WorkflowManager/WorkflowManager/Filter/PaginationFilter.cs renamed to src/Shared/Shared/Filter/PaginationFilter.cs

@@ -1,5 +1,5 @@
 /*
- * Copyright 2022 MONAI Consortium
+ * Copyright 2023 MONAI Consortium
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-namespace Monai.Deploy.WorkflowManager.Filter
+namespace Monai.Deploy.WorkflowManager.Shared.Filter
 {
     /// <summary>
     /// Pagination Filter class.

src/Shared/Shared/Monai.Deploy.WorkflowManager.Shared.csproj

@@ -51,6 +51,10 @@
     <PackageReference Include="Microsoft.Extensions.Diagnostics.HealthChecks.Abstractions" Version="6.0.15" />
   </ItemGroup>
 
+  <ItemGroup>
+    <ProjectReference Include="..\Configuration\Monai.Deploy.WorkflowManager.Configuration.csproj" />
+  </ItemGroup>
+
   <PropertyGroup>
     <RestorePackagesWithLockFile>true</RestorePackagesWithLockFile>
     <DisableImplicitNuGetFallbackFolder>true</DisableImplicitNuGetFallbackFolder>

src/WorkflowManager/WorkflowManager/Services/IUriService.cs renamed to src/Shared/Shared/Services/IUriService.cs

@@ -1,5 +1,5 @@
 /*
- * Copyright 2022 MONAI Consortium
+ * Copyright 2023 MONAI Consortium
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -14,9 +14,9 @@
  * limitations under the License.
  */
 
-using Monai.Deploy.WorkflowManager.Filter;
+using Monai.Deploy.WorkflowManager.Shared.Filter;
 
-namespace Monai.Deploy.WorkflowManager.Services
+namespace Monai.Deploy.WorkflowManager.Shared.Services
 {
     /// <summary>
     /// Uri Serivce.