gh-418 Update CLI to support --plugins and update API doc

mocsharp · mocsharp · commit 039e2e98d115 · 2023-08-02T17:54:08.000-07:00
Signed-off-by: Victor Chang &lt;vicchang@nvidia.com&gt;
diff --git a/docs/api/rest/config.md b/docs/api/rest/config.md
@@ -54,7 +54,11 @@ curl --location --request GET 'http://localhost:5000/config/ae'
     "grouping": "0020,000D",
     "timeout": 5,
     "ignoredSopClasses": ["1.2.840.10008.5.1.4.1.1.1.1"],
-    "allowedSopClasses": ["1.2.840.10008.5.1.4.1.1.1.2"]
+    "allowedSopClasses": ["1.2.840.10008.5.1.4.1.1.1.2"],
+    "pluginAssemblies": [
+        "Monai.Deploy.InformaticsGateway.Test.Plugins.TestInputDataPluginAddWorkflow, Monai.Deploy.InformaticsGateway.Test.Plugins",
+        "Monai.Deploy.InformaticsGateway.Test.Plugins.TestInputDataPluginModifyDicomFile, Monai.Deploy.InformaticsGateway.Test.Plugins"
+    ]
   },
   {
     "name": "liver-seg",
@@ -151,6 +155,10 @@ curl --location --request POST 'http://localhost:5000/config/ae/' \
             "timeout": 5,
             "workflows": [
                 "3f6a08a1-0dea-44e9-ab82-1ff1adf43a8e"
+            ],
+            "pluginAssemblies": [
+                "Monai.Deploy.InformaticsGateway.Test.Plugins.TestInputDataPluginAddWorkflow, Monai.Deploy.InformaticsGateway.Test.Plugins",
+                "Monai.Deploy.InformaticsGateway.Test.Plugins.TestInputDataPluginModifyDicomFile, Monai.Deploy.InformaticsGateway.Test.Plugins"
             ]
         }
     }'
@@ -162,7 +170,11 @@ curl --location --request POST 'http://localhost:5000/config/ae/' \
 {
   "name": "breast-tumor",
   "aeTitle": "BREASTV1",
-  "workflows": ["3f6a08a1-0dea-44e9-ab82-1ff1adf43a8e"]
+  "workflows": ["3f6a08a1-0dea-44e9-ab82-1ff1adf43a8e"],
+  "pluginAssemblies": [
+      "Monai.Deploy.InformaticsGateway.Test.Plugins.TestInputDataPluginAddWorkflow, Monai.Deploy.InformaticsGateway.Test.Plugins",
+      "Monai.Deploy.InformaticsGateway.Test.Plugins.TestInputDataPluginModifyDicomFile, Monai.Deploy.InformaticsGateway.Test.Plugins"
+  ]
 }
 ```
 
@@ -210,6 +222,10 @@ curl --location --request PUT 'http://localhost:5000/config/ae/' \
             "timeout": 3,
             "workflows": [
                 "3f6a08a1-0dea-44e9-ab82-1ff1adf43a8e"
+            ],
+            "pluginAssemblies": [
+                "Monai.Deploy.InformaticsGateway.Test.Plugins.TestInputDataPluginAddWorkflow, Monai.Deploy.InformaticsGateway.Test.Plugins",
+                "Monai.Deploy.InformaticsGateway.Test.Plugins.TestInputDataPluginModifyDicomFile, Monai.Deploy.InformaticsGateway.Test.Plugins"
             ]
         }
     }'
@@ -222,6 +238,10 @@ curl --location --request PUT 'http://localhost:5000/config/ae/' \
   "name": "breast-tumor",
   "aeTitle": "BREASTV1",
   "workflows": ["3f6a08a1-0dea-44e9-ab82-1ff1adf43a8e"],
+  "pluginAssemblies": [
+      "Monai.Deploy.InformaticsGateway.Test.Plugins.TestInputDataPluginAddWorkflow, Monai.Deploy.InformaticsGateway.Test.Plugins",
+      "Monai.Deploy.InformaticsGateway.Test.Plugins.TestInputDataPluginModifyDicomFile, Monai.Deploy.InformaticsGateway.Test.Plugins"
+  ],
   "timeout": 3
 }
 ```
diff --git a/docs/setup/setup.md b/docs/setup/setup.md
@@ -311,6 +311,19 @@ mig-cli aet add -a BrainAET -grouping 0020,000E, -t 30
 The command creates a new listening AE Title with AE Title `BrainAET`. The listening AE Title
 will group instances by the Series Instance UID (0020,000E) with a timeout value of 30 seconds.
 
+
+### Optional: Input Data Plug-ins
+
+Each listening AE Title may be configured with zero or more plug-ins to maniulate incoming DICOM files before saving to the storage
+service and dispatching a workflow request. To include input data plug-ins, first create your plug-ins by implementing the
+[IInputDataPlugin](xref:Monai.Deploy.InformaticsGateway.Api.IInputDataPlugin) interface and then use `-p` argument with the fully
+qualified type name with the `mig-cli aet add` command. For example, the following command adds `MyNamespace.AnonymizePlugin`
+and `MyNamespace.FixSeriesData` plug-ins from the `MyNamespace.Plugins` assembly file.
+
+```bash
+mig-cli aet add -a BrainAET -grouping 0020,000E, -t 30 -p "MyNamespace.AnonymizePlugin, MyNamespace.Plugins" "MyNamespace.FixSeriesData, MyNamespace.Plugins"
+```
+
 > [!Note]
 > `-grouping` is optional, with a default value of 0020,000D.
 > `-t` is optional, with a default value of 5 seconds.
diff --git a/src/Api/MonaiApplicationEntity.cs b/src/Api/MonaiApplicationEntity.cs
@@ -72,6 +72,9 @@ public class MonaiApplicationEntity : MongoDBEntityBase
         /// </summary>
         public List<string> Workflows { get; set; } = default!;
 
+        /// <summary>
+        /// Optional list of data input plug-in type names to be executed by the <see cref="IInputDataPluginEngine"/>.
+        /// </summary>
         public List<string> PluginAssemblies { get; set; } = default!;
 
         /// <summary>
diff --git a/src/CLI/Commands/AetCommand.cs b/src/CLI/Commands/AetCommand.cs
@@ -97,6 +97,12 @@ private void SetupAddAetCommand()
                 IsRequired = false,
             };
             addCommand.AddOption(allowedSopsOption);
+            var plugins = new Option<List<string>>(new string[] { "-p", "--plugins" }, description: "A space separated list of fully qualified type names of the plug-ins (surround each plug-in with double quotes)")
+            {
+                AllowMultipleArgumentsPerToken = true,
+                IsRequired = false,
+            };
+            addCommand.AddOption(plugins);
 
             addCommand.Handler = CommandHandler.Create<MonaiApplicationEntity, IHost, bool, CancellationToken>(AddAeTitlehandlerAsync);
         }
@@ -130,6 +136,12 @@ private void SetupEditAetCommand()
                 IsRequired = false,
             };
             addCommand.AddOption(allowedSopsOption);
+            var plugins = new Option<List<string>>(new string[] { "-p", "--plugins" }, description: "A space separated list of fully qualified type names of the plug-ins (surround each plug-in with double quotes)")
+            {
+                AllowMultipleArgumentsPerToken = true,
+                IsRequired = false,
+            };
+            addCommand.AddOption(plugins);
 
             addCommand.Handler = CommandHandler.Create<MonaiApplicationEntity, IHost, bool, CancellationToken>(EditAeTitleHandlerAsync);
         }
@@ -274,8 +286,7 @@ private async Task<int> AddAeTitlehandlerAsync(MonaiApplicationEntity entity, IH
                 }
                 if (result.AllowedSopClasses.Any())
                 {
-                    logger.MonaiAeAllowedSops(string.Join(',', result.AllowedSopClasses));
-                    logger.AcceptedSopClassesWarning();
+                    logger.MonaiAePlugins(string.Join(',', result.AllowedSopClasses));
                 }
             }
             catch (ConfigurationException ex)
@@ -330,6 +341,10 @@ private async Task<int> EditAeTitleHandlerAsync(MonaiApplicationEntity entity, I
                     logger.MonaiAeAllowedSops(string.Join(',', result.AllowedSopClasses));
                     logger.AcceptedSopClassesWarning();
                 }
+                if (result.AllowedSopClasses.Any())
+                {
+                    logger.MonaiAePlugins(string.Join(',', result.AllowedSopClasses));
+                }
             }
             catch (ConfigurationException ex)
             {
diff --git a/src/CLI/Logging/Log.cs b/src/CLI/Logging/Log.cs
@@ -187,6 +187,9 @@ public static partial class Log
         [LoggerMessage(EventId = 30061, Level = LogLevel.Critical, Message = "Error updating SCP Application Entity {aeTitle}: {message}")]
         public static partial void ErrorUpdatingMonaiApplicationEntity(this ILogger logger, string aeTitle, string message);
 
+        [LoggerMessage(EventId = 30062, Level = LogLevel.Information, Message = "\tPlug-ins: {plugins}")]
+        public static partial void MonaiAePlugins(this ILogger logger, string plugins);
+
         // Docker Runner
         [LoggerMessage(EventId = 31000, Level = LogLevel.Debug, Message = "Checking for existing {applicationName} ({version}) containers...")]
         public static partial void CheckingExistingAppContainer(this ILogger logger, string applicationName, string version);
diff --git a/src/CLI/Test/AetCommandTest.cs b/src/CLI/Test/AetCommandTest.cs
@@ -100,7 +100,7 @@ public async Task AetAdd_Command()
             {
                 Name = result.CommandResult.Children[0].Tokens[0].Value,
                 AeTitle = result.CommandResult.Children[1].Tokens[0].Value,
-                Workflows = result.CommandResult.Children[2].Tokens.Select(p => p.Value).ToList()
+                Workflows = result.CommandResult.Children[2].Tokens.Select(p => p.Value).ToList(),
             };
             Assert.Equal("MyName", entity.Name);
             Assert.Equal("MyAET", entity.AeTitle);
@@ -123,6 +123,44 @@ public async Task AetAdd_Command()
                     It.IsAny<CancellationToken>()), Times.Once());
         }
 
+        [Fact(DisplayName = "aet add comand with plug-ins")]
+        public async Task AetAdd_Command_WithPlugins()
+        {
+            var command = "aet add -n MyName -a MyAET --workflows App MyCoolApp TheApp --plugins \"PluginTypeA\" \"PluginTypeB\"";
+            var result = _paser.Parse(command);
+            Assert.Equal(ExitCodes.Success, result.Errors.Count);
+
+            var entity = new MonaiApplicationEntity()
+            {
+                Name = result.CommandResult.Children[0].Tokens[0].Value,
+                AeTitle = result.CommandResult.Children[1].Tokens[0].Value,
+                Workflows = result.CommandResult.Children[2].Tokens.Select(p => p.Value).ToList(),
+                PluginAssemblies = result.CommandResult.Children[3].Tokens.Select(p => p.Value).ToList(),
+            };
+            Assert.Equal("MyName", entity.Name);
+            Assert.Equal("MyAET", entity.AeTitle);
+            Assert.Collection(entity.Workflows,
+                item => item.Equals("App"),
+                item => item.Equals("MyCoolApp"),
+                item => item.Equals("TheApp"));
+            Assert.Collection(entity.PluginAssemblies,
+                item => item.Equals("PluginTypeA"),
+                item => item.Equals("PluginTypeB"));
+
+            _informaticsGatewayClient.Setup(p => p.MonaiScpAeTitle.Create(It.IsAny<MonaiApplicationEntity>(), It.IsAny<CancellationToken>()))
+                .ReturnsAsync(entity);
+
+            int exitCode = await _paser.InvokeAsync(command);
+
+            Assert.Equal(ExitCodes.Success, exitCode);
+
+            _informaticsGatewayClient.Verify(p => p.ConfigureServiceUris(It.IsAny<Uri>()), Times.Once());
+            _informaticsGatewayClient.Verify(
+                p => p.MonaiScpAeTitle.Create(
+                    It.Is<MonaiApplicationEntity>(o => o.AeTitle == entity.AeTitle && o.Name == entity.Name && Enumerable.SequenceEqual(o.Workflows, entity.Workflows)),
+                    It.IsAny<CancellationToken>()), Times.Once());
+        }
+
         [Fact(DisplayName = "aet add comand with allowed & ignored SOP classes")]
         public async Task AetAdd_Command_AllowedIgnoredSopClasses()
         {
@@ -335,7 +373,7 @@ public async Task AetList_Command_Empty()
         [Fact(DisplayName = "aet update command")]
         public async Task AetUpdate_Command()
         {
-            var command = "aet update -n MyName --workflows App MyCoolApp TheApp -i A B C -s D E F";
+            var command = "aet update -n MyName --workflows App MyCoolApp TheApp -i A B C -s D E F -p PlugInAssemblyA PlugInAssemblyB";
             var result = _paser.Parse(command);
             Assert.Equal(ExitCodes.Success, result.Errors.Count);
 
@@ -346,6 +384,7 @@ public async Task AetUpdate_Command()
                 Workflows = result.CommandResult.Children[1].Tokens.Select(p => p.Value).ToList(),
                 IgnoredSopClasses = result.CommandResult.Children[2].Tokens.Select(p => p.Value).ToList(),
                 AllowedSopClasses = result.CommandResult.Children[3].Tokens.Select(p => p.Value).ToList(),
+                PluginAssemblies = result.CommandResult.Children[4].Tokens.Select(p => p.Value).ToList(),
             };
 
             Assert.Equal("MyName", entity.Name);
@@ -362,6 +401,9 @@ public async Task AetUpdate_Command()
                 item => item.Equals("A"),
                 item => item.Equals("B"),
                 item => item.Equals("C"));
+            Assert.Collection(entity.PluginAssemblies,
+                item => item.Equals("PlugInAssemblyA"),
+                item => item.Equals("PlugInAssemblyB"));
 
             _informaticsGatewayClient.Setup(p => p.MonaiScpAeTitle.Update(It.IsAny<MonaiApplicationEntity>(), It.IsAny<CancellationToken>()))
                 .ReturnsAsync(entity);

Original file line number	Diff line number	Diff line change
`@@ -97,6 +97,12 @@ private void SetupAddAetCommand()`
`97`	`97`	`IsRequired = false,`
`98`	`98`	`};`
`99`	`99`	`addCommand.AddOption(allowedSopsOption);`
	`100`	`+ var plugins = new Option<List<string>>(new string[] { "-p", "--plugins" }, description: "A space separated list of fully qualified type names of the plug-ins (surround each plug-in with double quotes)")`
	`101`	`+ {`
	`102`	`+ AllowMultipleArgumentsPerToken = true,`
	`103`	`+ IsRequired = false,`
	`104`	`+ };`
	`105`	`+ addCommand.AddOption(plugins);`
`100`	`106`
`101`	`107`	`addCommand.Handler = CommandHandler.Create<MonaiApplicationEntity, IHost, bool, CancellationToken>(AddAeTitlehandlerAsync);`
`102`	`108`	`}`
`@@ -130,6 +136,12 @@ private void SetupEditAetCommand()`
`130`	`136`	`IsRequired = false,`
`131`	`137`	`};`
`132`	`138`	`addCommand.AddOption(allowedSopsOption);`
	`139`	`+ var plugins = new Option<List<string>>(new string[] { "-p", "--plugins" }, description: "A space separated list of fully qualified type names of the plug-ins (surround each plug-in with double quotes)")`
	`140`	`+ {`
	`141`	`+ AllowMultipleArgumentsPerToken = true,`
	`142`	`+ IsRequired = false,`
	`143`	`+ };`
	`144`	`+ addCommand.AddOption(plugins);`
`133`	`145`
`134`	`146`	`addCommand.Handler = CommandHandler.Create<MonaiApplicationEntity, IHost, bool, CancellationToken>(EditAeTitleHandlerAsync);`
`135`	`147`	`}`
`@@ -274,8 +286,7 @@ private async Task<int> AddAeTitlehandlerAsync(MonaiApplicationEntity entity, IH`
`274`	`286`	`}`
`275`	`287`	`if (result.AllowedSopClasses.Any())`
`276`	`288`	`{`
`277`		`- logger.MonaiAeAllowedSops(string.Join(',', result.AllowedSopClasses));`
`278`		`- logger.AcceptedSopClassesWarning();`
	`289`	`+ logger.MonaiAePlugins(string.Join(',', result.AllowedSopClasses));`
`279`	`290`	`}`
`280`	`291`	`}`
`281`	`292`	`catch (ConfigurationException ex)`
`@@ -330,6 +341,10 @@ private async Task<int> EditAeTitleHandlerAsync(MonaiApplicationEntity entity, I`
`330`	`341`	`logger.MonaiAeAllowedSops(string.Join(',', result.AllowedSopClasses));`
`331`	`342`	`logger.AcceptedSopClassesWarning();`
`332`	`343`	`}`
	`344`	`+ if (result.AllowedSopClasses.Any())`
	`345`	`+ {`
	`346`	`+ logger.MonaiAePlugins(string.Join(',', result.AllowedSopClasses));`
	`347`	`+ }`
`333`	`348`	`}`
`334`	`349`	`catch (ConfigurationException ex)`
`335`	`350`	`{`