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Merge pull request #760 from Project-MONAI/release/2023.04.24.2
Release/0.1.9
2 parents 5a14064 + 01fbb01 commit e64e8b3

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‎guidelines/mwm-developer-setup.md‎

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Original file line numberDiff line numberDiff line change
@@ -32,6 +32,17 @@ Note. if you already have docker container for Minio Rabbit etc running Stop the
3232
- `kubectl apply -n argo -f https://raw.githubusercontent.com/argoproj/argo-workflows/master/manifests/quick-start-postgres.yaml`
3333
- `kubectl config set-context --current --namespace=argo`
3434

35+
To disable argo authentication run
36+
37+
kubectl patch deployment \
38+
argo-server \
39+
--namespace argo \
40+
--type='json' \
41+
-p='[{"op": "replace", "path": "/spec/template/spec/containers/0/args", "value": [
42+
"server",
43+
"--auth-mode=server"
44+
]}]'
45+
3546
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!
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3748
now in a bash window (can be cmd or powershell)

‎src/TaskManager/API/Migrations/M001_TaskDispatchEventInfo_addVerion.cs‎

Lines changed: 15 additions & 15 deletions
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@@ -1,18 +1,18 @@
1-
//
2-
// Copyright 2023 Guy’s and St Thomas’ NHS Foundation Trust
3-
//
4-
// Licensed under the Apache License, Version 2.0 (the "License");
5-
// you may not use this file except in compliance with the License.
6-
// You may obtain a copy of the License at
7-
//
8-
// http://www.apache.org/licenses/LICENSE-2.0
9-
//
10-
// Unless required by applicable law or agreed to in writing, software
11-
// distributed under the License is distributed on an "AS IS" BASIS,
12-
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
13-
// See the License for the specific language governing permissions and
14-
// limitations under the License.
15-
1+
/*
2+
* Copyright 2022 MONAI Consortium
3+
*
4+
* Licensed under the Apache License, Version 2.0 (the "License");
5+
* you may not use this file except in compliance with the License.
6+
* You may obtain a copy of the License at
7+
*
8+
* http://www.apache.org/licenses/LICENSE-2.0
9+
*
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* Unless required by applicable law or agreed to in writing, software
11+
* distributed under the License is distributed on an "AS IS" BASIS,
12+
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
13+
* See the License for the specific language governing permissions and
14+
* limitations under the License.
15+
*/
1616
using Monai.Deploy.WorkflowManager.TaskManager.API.Models;
1717
using Mongo.Migration.Migrations.Document;
1818
using MongoDB.Bson;

‎src/TaskManager/API/Migrations/M001_TaskExecutionStats_addVersion.cs‎

Lines changed: 16 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -1,18 +1,19 @@
1-
//
2-
// Copyright 2023 Guy’s and St Thomas’ NHS Foundation Trust
3-
//
4-
// Licensed under the Apache License, Version 2.0 (the "License");
5-
// you may not use this file except in compliance with the License.
6-
// You may obtain a copy of the License at
7-
//
8-
// http://www.apache.org/licenses/LICENSE-2.0
9-
//
10-
// Unless required by applicable law or agreed to in writing, software
11-
// distributed under the License is distributed on an "AS IS" BASIS,
12-
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
13-
// See the License for the specific language governing permissions and
14-
// limitations under the License.
15-
// using Monai.Deploy.WorkflowManager.TaskManager.API.Models;
1+
/*
2+
* Copyright 2022 MONAI Consortium
3+
*
4+
* Licensed under the Apache License, Version 2.0 (the "License");
5+
* you may not use this file except in compliance with the License.
6+
* You may obtain a copy of the License at
7+
*
8+
* http://www.apache.org/licenses/LICENSE-2.0
9+
*
10+
* Unless required by applicable law or agreed to in writing, software
11+
* distributed under the License is distributed on an "AS IS" BASIS,
12+
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
13+
* See the License for the specific language governing permissions and
14+
* limitations under the License.
15+
*/
16+
1617
using Monai.Deploy.WorkflowManager.TaskManager.API.Models;
1718
using Mongo.Migration.Migrations.Document;
1819
using MongoDB.Bson;

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

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -88,9 +88,13 @@ private void Initialize()
8888
_workflowName = Event.TaskPluginArguments[Keys.WorkflowName];
8989
}
9090

91-
if (Event.TaskPluginArguments.ContainsKey(Keys.Notifications))
91+
if (Event.TaskPluginArguments.ContainsKey(Keys.Notifications) && Boolean.TryParse(Event.TaskPluginArguments[Keys.Notifications], out var result))
9292
{
93-
_notifications = Boolean.TryParse(Event.TaskPluginArguments[Keys.Notifications], out bool result);
93+
_notifications = result;
94+
}
95+
else
96+
{
97+
_notifications = true;
9498
}
9599

96100
if (Event.TaskPluginArguments.ContainsKey(Keys.ReviewedExecutionId))

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

Lines changed: 107 additions & 108 deletions
Original file line numberDiff line numberDiff line change
@@ -22,37 +22,9 @@
2222

2323
namespace Monai.Deploy.WorkflowManager.TaskManager.Argo
2424
{
25-
public interface IArgoClient
25+
public class ArgoClient : BaseArgoClient, IArgoClient
2626
{
27-
Task<Workflow> Argo_CreateWorkflowAsync(string argoNamespace, WorkflowCreateRequest body, CancellationToken cancellationToken);
28-
29-
Task<Workflow> Argo_GetWorkflowAsync(string argoNamespace, string name, string getOptions_resourceVersion, string fields, CancellationToken cancellationToken);
30-
31-
Task<WorkflowTemplate> Argo_GetWorkflowTemplateAsync(string argoNamespace, string name, string getOptions_resourceVersion);
32-
33-
Task<Workflow> Argo_StopWorkflowAsync(string argoNamespace, string name, WorkflowStopRequest body);
34-
35-
Task<Workflow> Argo_TerminateWorkflowAsync(string argoNamespace, string name, WorkflowTerminateRequest body);
36-
37-
Task<Version?> Argo_GetVersionAsync();
38-
39-
Task<string?> Argo_Get_WorkflowLogsAsync(string argoNamespace, string name, string podName, string logOptions_container);
40-
41-
Task<WorkflowTemplate> Argo_CreateWorkflowTemplateAsync(string argoNamespace, WorkflowTemplateCreateRequest body, CancellationToken cancellationToken);
42-
}
43-
44-
public class ArgoClient : IArgoClient
45-
{
46-
private readonly HttpClient _httpClient;
47-
48-
public string BaseUrl { get; set; } = "http://localhost:2746";
49-
50-
private string FormattedBaseUrl { get { return BaseUrl != null ? BaseUrl.TrimEnd('/') : ""; } }
51-
52-
public ArgoClient(HttpClient httpClient)
53-
{
54-
_httpClient = httpClient;
55-
}
27+
public ArgoClient(HttpClient httpClient) : base(httpClient) { }
5628

5729
public async Task<Workflow> Argo_CreateWorkflowAsync(string argoNamespace, WorkflowCreateRequest body, CancellationToken cancellationToken)
5830
{
@@ -164,27 +136,113 @@ public async Task<WorkflowTemplate> Argo_GetWorkflowTemplateAsync(string argoNam
164136
urlBuilder.Length--;
165137
return await GetRequest<string>(urlBuilder, true).ConfigureAwait(false);
166138
}
167-
private async Task<T> SendRequest<T>(StringContent stringContent, StringBuilder urlBuilder, string Method, CancellationToken cancellationToken)
139+
140+
/// <param name="cancellationToken">A cancellation token that can be used by other objects or threads to receive notice of cancellation.</param>
141+
/// <returns>A successful response.</returns>
142+
/// <exception cref="ApiException">A server side error occurred.</exception>
143+
public virtual async Task<WorkflowTemplate> Argo_CreateWorkflowTemplateAsync(string argoNamespace, WorkflowTemplateCreateRequest body, CancellationToken cancellationToken)
144+
{
145+
Guard.Against.NullOrWhiteSpace(argoNamespace);
146+
Guard.Against.Null(body);
147+
148+
var urlBuilder = new StringBuilder();
149+
urlBuilder.Append(CultureInfo.InvariantCulture, $"{FormattedBaseUrl}/api/v1/workflow-templates/{argoNamespace}");
150+
151+
var method = "POST";
152+
var content = new StringContent(Newtonsoft.Json.JsonConvert.SerializeObject(body));
153+
return await SendRequest<WorkflowTemplate>(content, urlBuilder, method, cancellationToken).ConfigureAwait(false);
154+
}
155+
156+
/// <param name="cancellationToken">A cancellation token that can be used by other objects or threads to receive notice of cancellation.</param>
157+
/// <returns>A successful response.</returns>
158+
/// <exception cref="ApiException">A server side error occurred.</exception>
159+
public virtual async Task<bool> Argo_DeleteWorkflowTemplateAsync(string argoNamespace, string templateName, CancellationToken cancellationToken)
168160
{
169-
using (var request = new HttpRequestMessage())
161+
Guard.Against.NullOrWhiteSpace(argoNamespace);
162+
163+
var urlBuilder = new StringBuilder();
164+
urlBuilder.Append(CultureInfo.InvariantCulture, $"{FormattedBaseUrl}/api/v1/workflow-templates/{argoNamespace}/{templateName}");
165+
166+
var method = "DELETE";
167+
var response = await HttpClient.SendAsync(new HttpRequestMessage(new HttpMethod(method), urlBuilder.ToString()), cancellationToken).ConfigureAwait(false);
168+
return (int)response.StatusCode == 200;
169+
}
170+
171+
public static string ConvertToString(object value, CultureInfo cultureInfo)
172+
{
173+
if (value == null)
170174
{
171-
stringContent.Headers.ContentType = System.Net.Http.Headers.MediaTypeHeaderValue.Parse("application/json");
172-
request.Content = stringContent;
173-
request.Method = new HttpMethod(Method);
174-
request.Headers.Accept.Add(System.Net.Http.Headers.MediaTypeWithQualityHeaderValue.Parse("application/json"));
175-
request.RequestUri = new Uri(urlBuilder.ToString(), UriKind.RelativeOrAbsolute);
175+
return "";
176+
}
176177

177-
HttpResponseMessage? response = null;
178-
try
178+
if (value is Enum)
179+
{
180+
var name = Enum.GetName(value.GetType(), value);
181+
if (name != null)
179182
{
180-
response = await _httpClient.SendAsync(request, HttpCompletionOption.ResponseHeadersRead, cancellationToken).ConfigureAwait(false);
183+
var field = System.Reflection.IntrospectionExtensions.GetTypeInfo(value.GetType()).GetDeclaredField(name);
184+
if (field != null)
185+
{
186+
if (System.Reflection.CustomAttributeExtensions.GetCustomAttribute(field, typeof(System.Runtime.Serialization.EnumMemberAttribute)) is System.Runtime.Serialization.EnumMemberAttribute attribute)
187+
{
188+
return attribute.Value ?? name;
189+
}
190+
}
191+
192+
var converted = Convert.ToString(Convert.ChangeType(value, Enum.GetUnderlyingType(value.GetType()), cultureInfo));
193+
return converted ?? string.Empty;
181194
}
182-
catch (Exception ex)
195+
}
196+
else if (value is bool boolean)
197+
{
198+
return Convert.ToString(boolean, cultureInfo).ToLowerInvariant();
199+
}
200+
else if (value is byte[] v)
201+
{
202+
return Convert.ToBase64String(v);
203+
}
204+
else if (value.GetType().IsArray)
205+
{
206+
var array = Enumerable.OfType<object>((Array)value);
207+
return string.Join(",", Enumerable.Select(array, o => ConvertToString(o, cultureInfo)));
208+
}
209+
210+
var result = Convert.ToString(value, cultureInfo);
211+
return result ?? "";
212+
}
213+
}
214+
215+
/// <summary>
216+
/// <see cref="BaseArgoClient"/> generic functions relating to argo requests
217+
/// </summary>
218+
public class BaseArgoClient
219+
{
220+
public string BaseUrl { get; set; } = "http://localhost:2746";
221+
222+
protected string FormattedBaseUrl { get { return BaseUrl != null ? BaseUrl.TrimEnd('/') : ""; } }
223+
224+
protected readonly HttpClient HttpClient;
225+
226+
public BaseArgoClient(HttpClient httpClient)
227+
{
228+
HttpClient = httpClient;
229+
}
230+
231+
protected async Task<T> SendRequest<T>(StringContent stringContent, StringBuilder urlBuilder, string method, CancellationToken cancellationToken)
232+
{
233+
using (var request = new HttpRequestMessage())
234+
{
235+
if (stringContent is not null)
183236
{
184-
var mess = ex.Message;
185-
throw;
237+
stringContent.Headers.ContentType = System.Net.Http.Headers.MediaTypeHeaderValue.Parse("application/json");
238+
request.Content = stringContent;
186239
}
240+
request.Method = new HttpMethod(method);
241+
request.Headers.Accept.Add(System.Net.Http.Headers.MediaTypeWithQualityHeaderValue.Parse("application/json"));
242+
request.RequestUri = new Uri(urlBuilder.ToString(), UriKind.RelativeOrAbsolute);
187243

244+
HttpResponseMessage? response = null;
245+
response = await HttpClient.SendAsync(request, HttpCompletionOption.ResponseContentRead, cancellationToken).ConfigureAwait(false);
188246

189247
try
190248
{
@@ -222,7 +280,7 @@ private async Task<T> SendRequest<T>(StringContent stringContent, StringBuilder
222280
}
223281
}
224282

225-
private async Task<T?> GetRequest<T>(StringBuilder urlBuilder, bool isLogs = false)
283+
protected async Task<T?> GetRequest<T>(StringBuilder urlBuilder, bool isLogs = false)
226284
{
227285

228286
using (var request = new HttpRequestMessage())
@@ -231,7 +289,7 @@ private async Task<T> SendRequest<T>(StringContent stringContent, StringBuilder
231289
request.Headers.Accept.Add(System.Net.Http.Headers.MediaTypeWithQualityHeaderValue.Parse("application/json"));
232290
request.RequestUri = new Uri(urlBuilder.ToString(), UriKind.RelativeOrAbsolute);
233291

234-
var response = await _httpClient.SendAsync(request, HttpCompletionOption.ResponseHeadersRead).ConfigureAwait(false);
292+
var response = await HttpClient.SendAsync(request, HttpCompletionOption.ResponseHeadersRead).ConfigureAwait(false);
235293
try
236294
{
237295
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
271329
}
272330
}
273331

274-
275332
protected virtual async Task<ObjectResponseResult<T?>> ReadObjectResponseAsync<T>(HttpResponseMessage response, IReadOnlyDictionary<string, IEnumerable<string>> headers, bool isLogs = false)
276333
{
277-
if (response == null || response.Content == null)
334+
if (response == null || response.Content == null || response.Content.GetType().Name == "EmptyContent")
278335
{
279336
return new ObjectResponseResult<T?>(default, string.Empty);
280337
}
@@ -306,7 +363,7 @@ private async Task<T> SendRequest<T>(StringContent stringContent, StringBuilder
306363
}
307364
}
308365

309-
protected static string DecodeLogs(string logInput)
366+
public static string DecodeLogs(string logInput)
310367
{
311368
var rows = logInput.Split(new String[] { "\n" }, StringSplitOptions.None);
312369
var jsonBody = $"[{string.Join(",", rows)}]";
@@ -348,23 +405,7 @@ protected virtual async Task<ObjectResponseResult<string>> ReadLogResponseAsync(
348405
}
349406
}
350407

351-
/// <param name="cancellationToken">A cancellation token that can be used by other objects or threads to receive notice of cancellation.</param>
352-
/// <returns>A successful response.</returns>
353-
/// <exception cref="ApiException">A server side error occurred.</exception>
354-
public virtual async Task<WorkflowTemplate> Argo_CreateWorkflowTemplateAsync(string argoNamespace, WorkflowTemplateCreateRequest body, CancellationToken cancellationToken)
355-
{
356-
Guard.Against.NullOrWhiteSpace(argoNamespace);
357-
Guard.Against.Null(body);
358-
359-
var urlBuilder = new StringBuilder();
360-
urlBuilder.Append(CultureInfo.InvariantCulture, $"{FormattedBaseUrl}/api/v1/workflow-templates/{argoNamespace}");
361-
362-
var Method = "POST";
363-
var content = new StringContent(Newtonsoft.Json.JsonConvert.SerializeObject(body));
364-
return await SendRequest<WorkflowTemplate>(content, urlBuilder, Method, cancellationToken).ConfigureAwait(false);
365-
}
366-
367-
protected struct ObjectResponseResult<T>
408+
protected readonly struct ObjectResponseResult<T>
368409
{
369410
public ObjectResponseResult(T responseObject, string responseText)
370411
{
@@ -377,61 +418,19 @@ public ObjectResponseResult(T responseObject, string responseText)
377418
public string Text { get; }
378419
}
379420

380-
private string ConvertToString(object value, CultureInfo cultureInfo)
381-
{
382-
if (value == null)
383-
{
384-
return "";
385-
}
386-
387-
if (value is Enum)
388-
{
389-
var name = Enum.GetName(value.GetType(), value);
390-
if (name != null)
391-
{
392-
var field = System.Reflection.IntrospectionExtensions.GetTypeInfo(value.GetType()).GetDeclaredField(name);
393-
if (field != null)
394-
{
395-
if (System.Reflection.CustomAttributeExtensions.GetCustomAttribute(field, typeof(System.Runtime.Serialization.EnumMemberAttribute)) is System.Runtime.Serialization.EnumMemberAttribute attribute)
396-
{
397-
return attribute.Value ?? name;
398-
}
399-
}
400-
401-
var converted = Convert.ToString(Convert.ChangeType(value, Enum.GetUnderlyingType(value.GetType()), cultureInfo));
402-
return converted ?? string.Empty;
403-
}
404-
}
405-
else if (value is bool boolean)
406-
{
407-
return Convert.ToString(boolean, cultureInfo).ToLowerInvariant();
408-
}
409-
else if (value is byte[] v)
410-
{
411-
return Convert.ToBase64String(v);
412-
}
413-
else if (value.GetType().IsArray)
414-
{
415-
var array = Enumerable.OfType<object>((Array)value);
416-
return string.Join(",", Enumerable.Select(array, o => ConvertToString(o, cultureInfo)));
417-
}
418-
419-
var result = Convert.ToString(value, cultureInfo);
420-
return result ?? "";
421-
}
422421
class ArgoLogEntry
423422
{
424423
public string Content { get; set; } = "";
425424

426425
public string PodName { get; set; } = "";
427426
}
427+
428428
class ArgoLogEntryResult
429429
{
430430
public ArgoLogEntry Result { get; set; } = new ArgoLogEntry();
431431
}
432432
}
433433

434-
435434
public class Version
436435
{
437436
[Newtonsoft.Json.JsonProperty("buildDate", Required = Newtonsoft.Json.Required.Always)]

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