Merge pull request #404 from Project-MONAI/nds-fix-for-imagepullsecrets

neildsouth · web-flow · commit bb565e144ff9 · 2022-09-06T16:16:50.000+01:00
Nds fix for imagepullsecrets
diff --git a/.gitignore b/.gitignore
@@ -577,3 +577,5 @@ GitExtensions.settings.backup
 *.AssemblyHooks.vb
 /src/WorkflowManager/mc.exe
 *.lutconfig
+/src/TaskManager/TaskManager/Properties/launchSettings.json
+/src/WorkflowManager/WorkflowManager/Properties/launchSettings.json
diff --git a/deploy/helm/Gateway.yaml b/deploy/helm/Gateway.yaml
@@ -16,7 +16,10 @@ replicaCount: 1
 image:
   repository: registry.gitlab.com/answerdigital/londonai/aide/workflow-manager-images/infomatics-gateway
   pullPolicy: IfNotPresent
-  tag: 2022-08-01
+  tag: 2022-08-30-01
+  
+imagePullSecrets:
+ - name: gitlab-image-pull
 
 enviromentVariables:
   InformaticsGateway__messaging__publisherSettings__endpoint: "rabbitmq-monai"
@@ -29,6 +32,8 @@ enviromentVariables:
   InformaticsGateway__storage__settings__accessKey: "rootminio"
   InformaticsGateway__storage__settings__accessToken: "rootminio"
   InformaticsGateway__dicom__scp__rejectUnknownSources: false
+  Kestrel__EndPoints__Http__Url: "http://::5000"
+  InformaticsGateway__storage__watermarkPercent: 95
   
 
 service:
diff --git a/deploy/helm/MTM.yaml b/deploy/helm/MTM.yaml
@@ -0,0 +1,65 @@
+# 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.
+      
+replicaCount: 1
+
+image:
+  repository: registry.gitlab.com/answerdigital/londonai/aide/workflow-manager-images/task-manager
+  pullPolicy: IfNotPresent
+  tag: 2022-09-05-01
+
+imagePullSecrets:
+ - name: gitlab-image-pull
+
+enviromentVariables:
+  WorkflowManager__storage__settings__endpoint: "minio.monai:9000"
+  WorkflowManager__storage__settings__accessKey: "rootminio"
+  WorkflowManager__storage__settings__accessToken: "rootminio"
+  WorkflowManager__storage__settings__executableLocation: "mc"
+  WorkflowManager__messaging__publisherSettings__endpoint: "rabbitmq.monai"
+  WorkflowManager__messaging__subscriberSettings__endpoint: "rabbitmq.monai"
+  WorkloadManagerDatabase__ConnectionString: "mongodb://root:rootpassword@mongo-monai.monai:27017"
+
+enviromentVariablesFromSecrets:
+  secrets:
+    - name: WorkflowManager__messaging__subscriberSettings__username
+      secretName: rabbit-secret-master
+      secretKey: username
+    - name: WorkflowManager__messaging__subscriberSettings__password
+      secretName: rabbit-secret-master
+      secretKey: password
+    - name: WorkflowManager__messaging__publisherSettings__username
+      secretName: rabbit-secret-master
+      secretKey: username
+    - name: WorkflowManager__messaging__publisherSettings__password
+      secretName: rabbit-secret-master
+      secretKey: password
+
+service:
+  type: ClusterIP
+  port: 5000
+
+serviceAccount:
+  create: true
+  name: mtm
+  namespace: monai
+  clusterrole:
+    name: clusterrole-taskmanager-argo-secret-master
+    rules:
+      apiGroups: [""]
+      resources: ["secrets"]
+      verbs: ["get", "list", "watch", "create", "update", "patch", "delete"]
+
+
+  
diff --git a/deploy/helm/MWM.yaml b/deploy/helm/MWM.yaml
@@ -27,9 +27,10 @@ enviromentVariables:
   WorkflowManager__storage__settings__accessKey: "rootminio"
   WorkflowManager__storage__settings__accessToken: "rootminio"
   WorkflowManager__storage__settings__executableLocation: "mc"
-  WorkflowManager__messaging__publisherSettings__endpoint: "rabbitmq.monai"
-  WorkflowManager__messaging__subscriberSettings__endpoint: "rabbitmq.monai"
+  WorkflowManager__messaging__publisherSettings__endpoint: "rabbitmq-monai.monai"
+  WorkflowManager__messaging__subscriberSettings__endpoint: "rabbitmq-monai.monai"
   WorkloadManagerDatabase__ConnectionString: "mongodb://root:rootpassword@mongo-monai.monai:27017"
+  Kestrel__EndPoints__Http__Url: "http://::5000"
 
 enviromentVariablesFromSecrets:
   secrets:
diff --git a/deploy/helm/templates/deployment.yaml b/deploy/helm/templates/deployment.yaml
@@ -63,7 +63,7 @@ spec:
               value: {{ $value | quote }}
               {{- end }}
         
-              {{- range .Values.enviromentVariablesFromSecrets.secrets }}
+              {{- range (.Values.enviromentVariablesFromSecrets).secrets }}
             - name: {{ .name }}
               valueFrom:
                 secretKeyRef:
diff --git a/deploy/helm/templates/volume.yml b/deploy/helm/templates/volume.yml
@@ -11,7 +11,7 @@
 # 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.
-{{- if .Values.volumeMounts -}}
+{{- if .Values.volumeMounts }}
 apiVersion: v1
 kind: PersistentVolume
 metadata:
diff --git a/deploy/helm/templates/volumeclaim.yml b/deploy/helm/templates/volumeclaim.yml
@@ -11,7 +11,7 @@
 # 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.
-{{- if .Values.volumeMounts -}}
+{{- if .Values.volumeMounts }}
 apiVersion: v1
 kind: PersistentVolumeClaim
 metadata:
diff --git a/src/TaskManager/Plug-ins/Argo/ArgoPlugin.cs b/src/TaskManager/Plug-ins/Argo/ArgoPlugin.cs
@@ -486,6 +486,19 @@ private async Task CopyWorkflowTemplateToWorkflow(WorkflowTemplate workflowTempl
 
             await CopyTemplateSteps(template.Steps, workflowTemplate, name, workflow, cancellationToken).ConfigureAwait(false);
             await CopyTemplateDags(template.Dag, workflowTemplate, name, workflow, cancellationToken).ConfigureAwait(false);
+            CopyImagePullSecrets(workflowTemplate, workflow);
+        }
+
+        private void CopyImagePullSecrets(WorkflowTemplate workflowTemplate, Workflow workflow)
+        {
+            if (workflowTemplate.Spec.ImagePullSecrets?.Any() is true)
+            {
+                workflow.Spec.ImagePullSecrets = new List<LocalObjectReference>();
+                foreach (var secret in workflowTemplate.Spec.ImagePullSecrets)
+                {
+                    workflow.Spec.ImagePullSecrets.Add(secret);
+                }
+            }
         }
 
         /// <summary>
diff --git a/src/TaskManager/TaskManager/appsettings.Local.json b/src/TaskManager/TaskManager/appsettings.Local.json
@@ -1,6 +1,6 @@
 {
   "WorkloadManagerDatabase": {
-    "ConnectionString": "mongodb://root:rootpassword@localhost:27017",
+    "ConnectionString": "mongodb://root:rootpassword@localhost:30017",
     "DatabaseName": "WorkloadManager",
     "WorkflowCollectionName": "Workflows",
     "WorkflowInstanceCollectionName": "WorkflowInstances",
diff --git a/src/WorkflowManager/WorkflowManager/appsettings.Local.json b/src/WorkflowManager/WorkflowManager/appsettings.Local.json
@@ -1,6 +1,6 @@
 {
   "WorkloadManagerDatabase": {
-    "ConnectionString": "mongodb://root:rootpassword@localhost:27017",
+    "ConnectionString": "mongodb://root:rootpassword@localhost:30017",
     "DatabaseName": "WorkloadManager",
     "WorkflowCollectionName": "Workflows",
     "WorkflowInstanceCollectionName": "WorkflowInstances",
diff --git a/tests/UnitTests/TaskManager.Argo.Tests/ArgoPluginTest.cs b/tests/UnitTests/TaskManager.Argo.Tests/ArgoPluginTest.cs
@@ -17,6 +17,7 @@
 using System;
 using System.Collections.Generic;
 using System.IO;
+using System.IO.Abstractions;
 using System.Linq;
 using System.Net.Http;
 using System.Threading;
@@ -586,6 +587,46 @@ public async Task ArgoPlugin_GetStatus_ReturnsExecutionStatusOnFailure()
         _argoClient.Verify(p => p.WorkflowService_GetWorkflowAsync(It.Is<string>(p => p.Equals("namespace", StringComparison.OrdinalIgnoreCase)), It.Is<string>(p => p.Equals("identity", StringComparison.OrdinalIgnoreCase)), It.IsAny<string>(), It.IsAny<string>(), It.IsAny<CancellationToken>()), Times.Once());
     }
 
+    [Fact(DisplayName = "ImagePullSecrets - get copied accross")]
+    public async Task ArgoPlugin_Copies_ImagePullSecrets()
+    {
+        var argoTemplate = LoadArgoTemplate("SimpleTemplate.yml");
+
+        Assert.NotNull(argoTemplate);
+        var secret = new LocalObjectReference() { Name = "ImagePullSecret" };
+        argoTemplate.Spec.ImagePullSecrets = new List<LocalObjectReference>() { secret };
+
+        var message = GenerateTaskDispatchEventWithValidArguments();
+        message.TaskPluginArguments["resources"] = "{\"memory_reservation\": \"string\",\"cpu_reservation\": \"string\",\"gpu_limit\": 1,\"memory_limit\": \"string\",\"cpu_limit\": \"string\"}";
+        message.TaskPluginArguments["priorityClass"] = "Helo";
+        Workflow? submittedArgoTemplate = null;
+
+        _argoClient.Setup(p => p.WorkflowTemplateService_GetWorkflowTemplateAsync(It.IsAny<string>(), It.IsAny<string>(), It.IsAny<string>()))
+            .ReturnsAsync(argoTemplate);
+        _argoClient.Setup(p => p.WorkflowService_CreateWorkflowAsync(It.IsAny<string>(), It.IsAny<WorkflowCreateRequest>(), It.IsAny<CancellationToken>()))
+            .Callback((string ns, WorkflowCreateRequest body, CancellationToken cancellationToken) =>
+            {
+                submittedArgoTemplate = body.Workflow;
+            })
+            .ReturnsAsync((string ns, WorkflowCreateRequest body, CancellationToken cancellationToken) =>
+            {
+                return new Workflow { Metadata = new ObjectMeta { Name = "workflow" } };
+            });
+
+        SetupKubbernetesSecrets()
+            .ReturnsAsync((V1Secret body, string ns, string dr, string fm, string fv, bool? pretty, IReadOnlyDictionary<string, IReadOnlyList<string>> headers, CancellationToken ct) =>
+            {
+                return new HttpOperationResponse<V1Secret> { Body = body, Response = new HttpResponseMessage { } };
+            });
+        SetupKubernetesDeleteSecret();
+
+        var runner = new ArgoPlugin(_serviceScopeFactory.Object, _logger.Object, message);
+        var result = await runner.ExecuteTask(CancellationToken.None).ConfigureAwait(false);
+
+        Assert.Equal(TaskExecutionStatus.Accepted, result.Status);
+        Assert.Equal(secret, submittedArgoTemplate?.Spec.ImagePullSecrets.First());
+    }
+
     private static TaskDispatchEvent GenerateTaskDispatchEventWithValidArguments()
     {
         var message = GenerateTaskDispatchEvent();

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"WorkloadManagerDatabase": {`
`3`		`- "ConnectionString": "mongodb://root:rootpassword@localhost:27017",`
	`3`	`+ "ConnectionString": "mongodb://root:rootpassword@localhost:30017",`
`4`	`4`	`"DatabaseName": "WorkloadManager",`
`5`	`5`	`"WorkflowCollectionName": "Workflows",`
`6`	`6`	`"WorkflowInstanceCollectionName": "WorkflowInstances",`