merge in

Signed-off-by: Neil South <[email protected]>

src/TaskManager/Plug-ins/Docker/DockerPlugin.cs

@@ -14,8 +14,8 @@
  * limitations under the License.
  */
 
+using System.Diagnostics;
 using System.Globalization;
-using Amazon.Runtime.Internal.Transform;
 using Ardalis.GuardClauses;
 using Docker.DotNet;
 using Docker.DotNet.Models;
@@ -364,9 +364,14 @@ private CreateContainerParameters BuildContainerSpecification(IList<ContainerVol
                 {
                     Runtime = Strings.RuntimeNvidia,
                     Mounts = volumeMounts,
-                }
+                },
             };
 
+            if (Event.TaskPluginArguments.ContainsKey(Keys.User))
+            {
+                parameters.User = Event.TaskPluginArguments[Keys.User];
+            }
+
             return parameters;
         }
 
@@ -406,6 +411,7 @@ private async Task<List<ContainerVolumeMount>> SetupInputs(CancellationToken can
                 // eg: /monai/input
                 var volumeMount = new ContainerVolumeMount(input, Event.TaskPluginArguments[input.Name], inputHostDirRoot, inputContainerDirRoot);
                 volumeMounts.Add(volumeMount);
+                _logger.InputVolumeMountAdded(inputHostDirRoot, inputContainerDirRoot);
 
                 // For each file, download from bucket and store in Task Manager Container.
                 foreach (var obj in objects)
@@ -424,6 +430,8 @@ private async Task<List<ContainerVolumeMount>> SetupInputs(CancellationToken can
                 }
             }
 
+            SetPermission(containerPath);
+
             return volumeMounts;
         }
 
@@ -436,7 +444,10 @@ private ContainerVolumeMount SetupIntermediateVolume()
 
                 Directory.CreateDirectory(containerPath);
 
-                return new ContainerVolumeMount(Event.IntermediateStorage, Event.TaskPluginArguments[Keys.WorkingDirectory], hostPath, containerPath);
+                var volumeMount = new ContainerVolumeMount(Event.IntermediateStorage, Event.TaskPluginArguments[Keys.WorkingDirectory], hostPath, containerPath);
+                _logger.IntermediateVolumeMountAdded(hostPath, containerPath);
+                SetPermission(containerPath);
+                return volumeMount;
             }
 
             return default!;
@@ -465,11 +476,32 @@ private List<ContainerVolumeMount> SetupOutputs()
                 Directory.CreateDirectory(containerPath);
 
                 volumeMounts.Add(new ContainerVolumeMount(output, Event.TaskPluginArguments[output.Name], hostPath, containerPath));
+                _logger.OutputVolumeMountAdded(hostPath, containerPath);
             }
 
+            SetPermission(containerRootPath);
+
             return volumeMounts;
         }
 
+        private void SetPermission(string path)
+        {
+            if (Event.TaskPluginArguments.ContainsKey(Keys.User))
+            {
+                if (!System.OperatingSystem.IsWindows())
+                {
+                    var process = Process.Start("chown", $"-R {Event.TaskPluginArguments[Keys.User]} {path}");
+                    process.WaitForExit();
+
+                    if (process.ExitCode != 0)
+                    {
+                        _logger.ErrorSettingDirectoryPermission(path, Event.TaskPluginArguments[Keys.User]);
+                        throw new SetPermissionException($"chown command exited with code {process.ExitCode}");
+                    }
+                }
+            }
+        }
+
         protected override void Dispose(bool disposing)
         {
             if (!DisposedValue && disposing)

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

@@ -33,6 +33,11 @@ internal static class Keys
         /// </summary>
         public static readonly string EntryPoint = "entrypoint";
 
+        /// <summary>
+        /// Key for specifying the user to the container. Same as -u argument for docker run.
+        /// </summary>
+        public static readonly string User = "user";
+
         /// <summary>
         /// Key for the command to execute by the container.
         /// </summary>

src/TaskManager/Plug-ins/Docker/Logging/Log.cs

@@ -103,5 +103,17 @@ public static partial class Log
 
         [LoggerMessage(EventId = 1027, Level = LogLevel.Information, Message = "Image does not exist '{image}' locally, attempting to pull.")]
         public static partial void ImageDoesNotExist(this ILogger logger, string image);
+
+        [LoggerMessage(EventId = 1028, Level = LogLevel.Information, Message = "Input volume added {hostPath} = {containerPath}.")]
+        public static partial void InputVolumeMountAdded(this ILogger logger, string hostPath, string containerPath);
+
+        [LoggerMessage(EventId = 1029, Level = LogLevel.Information, Message = "Output volume added {hostPath} = {containerPath}.")]
+        public static partial void OutputVolumeMountAdded(this ILogger logger, string hostPath, string containerPath);
+
+        [LoggerMessage(EventId = 1030, Level = LogLevel.Information, Message = "Intermediate volume added {hostPath} = {containerPath}.")]
+        public static partial void IntermediateVolumeMountAdded(this ILogger logger, string hostPath, string containerPath);
+
+        [LoggerMessage(EventId = 1031, Level = LogLevel.Error, Message = "Error setting directory {path} with permission {user}.")]
+        public static partial void ErrorSettingDirectoryPermission(this ILogger logger, string path, string user);
     }
 }

src/TaskManager/Plug-ins/Docker/SetPermissionException.cs

@@ -0,0 +1,40 @@
+/*
+ * Copyright 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.
+ */
+
+using System.Runtime.Serialization;
+
+namespace Monai.Deploy.WorkflowManager.TaskManager.Docker
+{
+    [Serializable]
+    internal class SetPermissionException : Exception
+    {
+        public SetPermissionException()
+        {
+        }
+
+        public SetPermissionException(string? message) : base(message)
+        {
+        }
+
+        public SetPermissionException(string? message, Exception? innerException) : base(message, innerException)
+        {
+        }
+
+        protected SetPermissionException(SerializationInfo info, StreamingContext context) : base(info, context)
+        {
+        }
+    }
+}

src/TaskManager/TaskManager/Services/Http/Startup.cs

@@ -62,6 +62,27 @@ public void ConfigureServices(IServiceCollection services)
             {
                 c.SwaggerDoc("v1", new OpenApiInfo { Title = "MONAI Workflow Manager", Version = "v1" });
                 c.DescribeAllParametersInCamelCase();
+                c.AddSecurityDefinition("basic", new OpenApiSecurityScheme
+                {
+                    Scheme = "basic",
+                    Name = "basic",
+                    In = ParameterLocation.Header,
+                    Type = SecuritySchemeType.Http,
+                });
+                c.AddSecurityRequirement(new OpenApiSecurityRequirement
+                {
+                    {
+                        new OpenApiSecurityScheme
+                            {
+                                Reference = new OpenApiReference
+                                {
+                                    Type = ReferenceType.SecurityScheme,
+                                    Id = "basic",
+                                },
+                            },
+                        System.Array.Empty<string>()
+                    },
+                });
             });
 
             var serviceProvider = services.BuildServiceProvider();

src/WorkflowManager/WorkflowExecuter/Services/WorkflowExecuterService.cs

@@ -271,7 +271,7 @@ private async Task ProcessArtifactReceivedOutputs(ArtifactsReceivedEvent message
                 }
             }
 
-            var currentTask = workflowInstance.Tasks?.FirstOrDefault(t => t.TaskId == taskId);
+            var currentTask = workflowInstance.Tasks?.Find(t => t.TaskId == taskId);
 
             currentTask!.OutputArtifacts = validArtifacts; // added here are the parent function saves the object !
 
@@ -735,7 +735,7 @@ private async Task<bool> HandleOutputArtifacts(WorkflowInstance workflowInstance
                 return false;
             }
 
-            var currentTask = workflowInstance.Tasks?.FirstOrDefault(t => t.TaskId == task.TaskId);
+            var currentTask = workflowInstance.Tasks?.Find(t => t.TaskId == task.TaskId);
 
             if (currentTask is not null)
             {

tests/UnitTests/WorkflowExecuter.Tests/Services/WorkflowExecuterServiceTests.cs

@@ -3184,6 +3184,7 @@ public async Task ArtifactReceveid_Valid_ReturnesTrue()
 
             Assert.True(result);
         }
+
         [Fact]
         public async Task ProcessArtifactReceived_Calls_WorkflowInstanceRepository_UpdateTaskOutputArtifactsAsync()
         {