Release/0.1.9

guidelines/mwm-developer-setup.md

@@ -32,6 +32,17 @@ Note. if you already have docker container for Minio Rabbit etc running Stop the
   - `kubectl apply -n argo -f https://raw.githubusercontent.com/argoproj/argo-workflows/master/manifests/quick-start-postgres.yaml`
   - `kubectl config set-context --current --namespace=argo`
 
+To disable argo authentication run
+
+    kubectl patch deployment \
+      argo-server \
+      --namespace argo \
+      --type='json' \
+      -p='[{"op": "replace", "path": "/spec/template/spec/containers/0/args", "value": [
+      "server",
+      "--auth-mode=server"
+    ]}]'
+
 Note. below Im using bash as its my preferred option, But if you to are using bash and your on windows (wsl2) you MUST make sure you windows .kube/config is also pointing to the same K8's cluster, this is because the code running in vs will look in there for the context to write k8's secrets too!
 
 now in a bash window (can be cmd or powershell)

src/TaskManager/API/Migrations/M001_TaskDispatchEventInfo_addVerion.cs

@@ -1,18 +1,18 @@
-// 
-// Copyright 2023 Guy’s and St Thomas’ NHS Foundation Trust
-// 
-// 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.
-
+/*
+ * 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 Monai.Deploy.WorkflowManager.TaskManager.API.Models;
 using Mongo.Migration.Migrations.Document;
 using MongoDB.Bson;

src/TaskManager/API/Migrations/M001_TaskExecutionStats_addVersion.cs

@@ -1,18 +1,19 @@
-// 
-// Copyright 2023 Guy’s and St Thomas’ NHS Foundation Trust
-// 
-// 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 Monai.Deploy.WorkflowManager.TaskManager.API.Models;
+/*
+ * 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 Monai.Deploy.WorkflowManager.TaskManager.API.Models;
 using Mongo.Migration.Migrations.Document;
 using MongoDB.Bson;

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

@@ -88,9 +88,13 @@ private void Initialize()
                 _workflowName = Event.TaskPluginArguments[Keys.WorkflowName];
             }
 
-            if (Event.TaskPluginArguments.ContainsKey(Keys.Notifications))
+            if (Event.TaskPluginArguments.ContainsKey(Keys.Notifications) && Boolean.TryParse(Event.TaskPluginArguments[Keys.Notifications], out var result))
             {
-                _notifications = Boolean.TryParse(Event.TaskPluginArguments[Keys.Notifications], out bool result);
+                _notifications = result;
+            }
+            else
+            {
+                _notifications = true;
             }
 
             if (Event.TaskPluginArguments.ContainsKey(Keys.ReviewedExecutionId))

src/TaskManager/Plug-ins/Argo/ArgoClient.cs

@@ -22,37 +22,9 @@
 
 namespace Monai.Deploy.WorkflowManager.TaskManager.Argo
 {
-    public interface IArgoClient
+    public class ArgoClient : BaseArgoClient, IArgoClient
     {
-        Task<Workflow> Argo_CreateWorkflowAsync(string argoNamespace, WorkflowCreateRequest body, CancellationToken cancellationToken);
-
-        Task<Workflow> Argo_GetWorkflowAsync(string argoNamespace, string name, string getOptions_resourceVersion, string fields, CancellationToken cancellationToken);
-
-        Task<WorkflowTemplate> Argo_GetWorkflowTemplateAsync(string argoNamespace, string name, string getOptions_resourceVersion);
-
-        Task<Workflow> Argo_StopWorkflowAsync(string argoNamespace, string name, WorkflowStopRequest body);
-
-        Task<Workflow> Argo_TerminateWorkflowAsync(string argoNamespace, string name, WorkflowTerminateRequest body);
-
-        Task<Version?> Argo_GetVersionAsync();
-
-        Task<string?> Argo_Get_WorkflowLogsAsync(string argoNamespace, string name, string podName, string logOptions_container);
-
-        Task<WorkflowTemplate> Argo_CreateWorkflowTemplateAsync(string argoNamespace, WorkflowTemplateCreateRequest body, CancellationToken cancellationToken);
-    }
-
-    public class ArgoClient : IArgoClient
-    {
-        private readonly HttpClient _httpClient;
-
-        public string BaseUrl { get; set; } = "http://localhost:2746";
-
-        private string FormattedBaseUrl { get { return BaseUrl != null ? BaseUrl.TrimEnd('/') : ""; } }
-
-        public ArgoClient(HttpClient httpClient)
-        {
-            _httpClient = httpClient;
-        }
+        public ArgoClient(HttpClient httpClient) : base(httpClient) { }
 
         public async Task<Workflow> Argo_CreateWorkflowAsync(string argoNamespace, WorkflowCreateRequest body, CancellationToken cancellationToken)
         {
@@ -164,27 +136,113 @@ public async Task<WorkflowTemplate> Argo_GetWorkflowTemplateAsync(string argoNam
             urlBuilder.Length--;
             return await GetRequest<string>(urlBuilder, true).ConfigureAwait(false);
         }
-        private async Task<T> SendRequest<T>(StringContent stringContent, StringBuilder urlBuilder, string Method, CancellationToken cancellationToken)
+
+        /// <param name="cancellationToken">A cancellation token that can be used by other objects or threads to receive notice of cancellation.</param>
+        /// <returns>A successful response.</returns>
+        /// <exception cref="ApiException">A server side error occurred.</exception>
+        public virtual async Task<WorkflowTemplate> Argo_CreateWorkflowTemplateAsync(string argoNamespace, WorkflowTemplateCreateRequest body, CancellationToken cancellationToken)
+        {
+            Guard.Against.NullOrWhiteSpace(argoNamespace);
+            Guard.Against.Null(body);
+
+            var urlBuilder = new StringBuilder();
+            urlBuilder.Append(CultureInfo.InvariantCulture, $"{FormattedBaseUrl}/api/v1/workflow-templates/{argoNamespace}");
+
+            var method = "POST";
+            var content = new StringContent(Newtonsoft.Json.JsonConvert.SerializeObject(body));
+            return await SendRequest<WorkflowTemplate>(content, urlBuilder, method, cancellationToken).ConfigureAwait(false);
+        }
+
+        /// <param name="cancellationToken">A cancellation token that can be used by other objects or threads to receive notice of cancellation.</param>
+        /// <returns>A successful response.</returns>
+        /// <exception cref="ApiException">A server side error occurred.</exception>
+        public virtual async Task<bool> Argo_DeleteWorkflowTemplateAsync(string argoNamespace, string templateName, CancellationToken cancellationToken)
         {
-            using (var request = new HttpRequestMessage())
+            Guard.Against.NullOrWhiteSpace(argoNamespace);
+
+            var urlBuilder = new StringBuilder();
+            urlBuilder.Append(CultureInfo.InvariantCulture, $"{FormattedBaseUrl}/api/v1/workflow-templates/{argoNamespace}/{templateName}");
+
+            var method = "DELETE";
+            var response = await HttpClient.SendAsync(new HttpRequestMessage(new HttpMethod(method), urlBuilder.ToString()), cancellationToken).ConfigureAwait(false);
+            return (int)response.StatusCode == 200;
+        }
+
+        public static string ConvertToString(object value, CultureInfo cultureInfo)
+        {
+            if (value == null)
             {
-                stringContent.Headers.ContentType = System.Net.Http.Headers.MediaTypeHeaderValue.Parse("application/json");
-                request.Content = stringContent;
-                request.Method = new HttpMethod(Method);
-                request.Headers.Accept.Add(System.Net.Http.Headers.MediaTypeWithQualityHeaderValue.Parse("application/json"));
-                request.RequestUri = new Uri(urlBuilder.ToString(), UriKind.RelativeOrAbsolute);
+                return "";
+            }
 
-                HttpResponseMessage? response = null;
-                try
+            if (value is Enum)
+            {
+                var name = Enum.GetName(value.GetType(), value);
+                if (name != null)
                 {
-                    response = await _httpClient.SendAsync(request, HttpCompletionOption.ResponseHeadersRead, cancellationToken).ConfigureAwait(false);
+                    var field = System.Reflection.IntrospectionExtensions.GetTypeInfo(value.GetType()).GetDeclaredField(name);
+                    if (field != null)
+                    {
+                        if (System.Reflection.CustomAttributeExtensions.GetCustomAttribute(field, typeof(System.Runtime.Serialization.EnumMemberAttribute)) is System.Runtime.Serialization.EnumMemberAttribute attribute)
+                        {
+                            return attribute.Value ?? name;
+                        }
+                    }
+
+                    var converted = Convert.ToString(Convert.ChangeType(value, Enum.GetUnderlyingType(value.GetType()), cultureInfo));
+                    return converted ?? string.Empty;
                 }
-                catch (Exception ex)
+            }
+            else if (value is bool boolean)
+            {
+                return Convert.ToString(boolean, cultureInfo).ToLowerInvariant();
+            }
+            else if (value is byte[] v)
+            {
+                return Convert.ToBase64String(v);
+            }
+            else if (value.GetType().IsArray)
+            {
+                var array = Enumerable.OfType<object>((Array)value);
+                return string.Join(",", Enumerable.Select(array, o => ConvertToString(o, cultureInfo)));
+            }
+
+            var result = Convert.ToString(value, cultureInfo);
+            return result ?? "";
+        }
+    }
+
+    /// <summary>
+    /// <see cref="BaseArgoClient"/> generic functions relating to argo requests
+    /// </summary>
+    public class BaseArgoClient
+    {
+        public string BaseUrl { get; set; } = "http://localhost:2746";
+
+        protected string FormattedBaseUrl { get { return BaseUrl != null ? BaseUrl.TrimEnd('/') : ""; } }
+
+        protected readonly HttpClient HttpClient;
+
+        public BaseArgoClient(HttpClient httpClient)
+        {
+            HttpClient = httpClient;
+        }
+
+        protected async Task<T> SendRequest<T>(StringContent stringContent, StringBuilder urlBuilder, string method, CancellationToken cancellationToken)
+        {
+            using (var request = new HttpRequestMessage())
+            {
+                if (stringContent is not null)
                 {
-                    var mess = ex.Message;
-                    throw;
+                    stringContent.Headers.ContentType = System.Net.Http.Headers.MediaTypeHeaderValue.Parse("application/json");
+                    request.Content = stringContent;
                 }
+                request.Method = new HttpMethod(method);
+                request.Headers.Accept.Add(System.Net.Http.Headers.MediaTypeWithQualityHeaderValue.Parse("application/json"));
+                request.RequestUri = new Uri(urlBuilder.ToString(), UriKind.RelativeOrAbsolute);
 
+                HttpResponseMessage? response = null;
+                response = await HttpClient.SendAsync(request, HttpCompletionOption.ResponseContentRead, cancellationToken).ConfigureAwait(false);
 
                 try
                 {
@@ -222,7 +280,7 @@ private async Task<T> SendRequest<T>(StringContent stringContent, StringBuilder
             }
         }
 
-        private async Task<T?> GetRequest<T>(StringBuilder urlBuilder, bool isLogs = false)
+        protected async Task<T?> GetRequest<T>(StringBuilder urlBuilder, bool isLogs = false)
         {
 
             using (var request = new HttpRequestMessage())
@@ -231,7 +289,7 @@ private async Task<T> SendRequest<T>(StringContent stringContent, StringBuilder
                 request.Headers.Accept.Add(System.Net.Http.Headers.MediaTypeWithQualityHeaderValue.Parse("application/json"));
                 request.RequestUri = new Uri(urlBuilder.ToString(), UriKind.RelativeOrAbsolute);
 
-                var response = await _httpClient.SendAsync(request, HttpCompletionOption.ResponseHeadersRead).ConfigureAwait(false);
+                var response = await HttpClient.SendAsync(request, HttpCompletionOption.ResponseHeadersRead).ConfigureAwait(false);
                 try
                 {
                     var headers_ = Enumerable.ToDictionary(response.Headers, h_ => h_.Key, h_ => h_.Value);
@@ -271,10 +329,9 @@ private async Task<T> SendRequest<T>(StringContent stringContent, StringBuilder
             }
         }
 
-
         protected virtual async Task<ObjectResponseResult<T?>> ReadObjectResponseAsync<T>(HttpResponseMessage response, IReadOnlyDictionary<string, IEnumerable<string>> headers, bool isLogs = false)
         {
-            if (response == null || response.Content == null)
+            if (response == null || response.Content == null || response.Content.GetType().Name == "EmptyContent")
             {
                 return new ObjectResponseResult<T?>(default, string.Empty);
             }
@@ -306,7 +363,7 @@ private async Task<T> SendRequest<T>(StringContent stringContent, StringBuilder
             }
         }
 
-        protected static string DecodeLogs(string logInput)
+        public static string DecodeLogs(string logInput)
         {
             var rows = logInput.Split(new String[] { "\n" }, StringSplitOptions.None);
             var jsonBody = $"[{string.Join(",", rows)}]";
@@ -348,23 +405,7 @@ protected virtual async Task<ObjectResponseResult<string>> ReadLogResponseAsync(
             }
         }
 
-        /// <param name="cancellationToken">A cancellation token that can be used by other objects or threads to receive notice of cancellation.</param>
-        /// <returns>A successful response.</returns>
-        /// <exception cref="ApiException">A server side error occurred.</exception>
-        public virtual async Task<WorkflowTemplate> Argo_CreateWorkflowTemplateAsync(string argoNamespace, WorkflowTemplateCreateRequest body, CancellationToken cancellationToken)
-        {
-            Guard.Against.NullOrWhiteSpace(argoNamespace);
-            Guard.Against.Null(body);
-
-            var urlBuilder = new StringBuilder();
-            urlBuilder.Append(CultureInfo.InvariantCulture, $"{FormattedBaseUrl}/api/v1/workflow-templates/{argoNamespace}");
-
-            var Method = "POST";
-            var content = new StringContent(Newtonsoft.Json.JsonConvert.SerializeObject(body));
-            return await SendRequest<WorkflowTemplate>(content, urlBuilder, Method, cancellationToken).ConfigureAwait(false);
-        }
-
-        protected struct ObjectResponseResult<T>
+        protected readonly struct ObjectResponseResult<T>
         {
             public ObjectResponseResult(T responseObject, string responseText)
             {
@@ -377,61 +418,19 @@ public ObjectResponseResult(T responseObject, string responseText)
             public string Text { get; }
         }
 
-        private string ConvertToString(object value, CultureInfo cultureInfo)
-        {
-            if (value == null)
-            {
-                return "";
-            }
-
-            if (value is Enum)
-            {
-                var name = Enum.GetName(value.GetType(), value);
-                if (name != null)
-                {
-                    var field = System.Reflection.IntrospectionExtensions.GetTypeInfo(value.GetType()).GetDeclaredField(name);
-                    if (field != null)
-                    {
-                        if (System.Reflection.CustomAttributeExtensions.GetCustomAttribute(field, typeof(System.Runtime.Serialization.EnumMemberAttribute)) is System.Runtime.Serialization.EnumMemberAttribute attribute)
-                        {
-                            return attribute.Value ?? name;
-                        }
-                    }
-
-                    var converted = Convert.ToString(Convert.ChangeType(value, Enum.GetUnderlyingType(value.GetType()), cultureInfo));
-                    return converted ?? string.Empty;
-                }
-            }
-            else if (value is bool boolean)
-            {
-                return Convert.ToString(boolean, cultureInfo).ToLowerInvariant();
-            }
-            else if (value is byte[] v)
-            {
-                return Convert.ToBase64String(v);
-            }
-            else if (value.GetType().IsArray)
-            {
-                var array = Enumerable.OfType<object>((Array)value);
-                return string.Join(",", Enumerable.Select(array, o => ConvertToString(o, cultureInfo)));
-            }
-
-            var result = Convert.ToString(value, cultureInfo);
-            return result ?? "";
-        }
         class ArgoLogEntry
         {
             public string Content { get; set; } = "";
 
             public string PodName { get; set; } = "";
         }
+
         class ArgoLogEntryResult
         {
             public ArgoLogEntry Result { get; set; } = new ArgoLogEntry();
         }
     }
 
-
     public class Version
     {
         [Newtonsoft.Json.JsonProperty("buildDate", Required = Newtonsoft.Json.Required.Always)]