feat: Added option to pass custom WES Adapter environment variables

packages/cdk/apps/core/app.ts

@@ -42,6 +42,16 @@ if (customTagsJsonString) {
   customTagsMap = JSON.parse(customTagsJsonString);
 }
 
+// If user specified adapter custom envs, add them to the stack parameters, so they will be persisted in SSM Parameter Store.
+const customWesEnvVarsJsonString = getContextOrDefault<Maybe<string>>(app.node, "CUSTOM_WES_ENV_VARS");
+if (customWesEnvVarsJsonString) {
+  stackParameters.push({
+    name: "customWesEnvVars",
+    value: customWesEnvVarsJsonString,
+    description: "JSON string of custom env vars to be passed to the WES adapter",
+  });
+}
+
 new CoreStack(app, `${PRODUCT_NAME}-Core`, {
   vpcId,
   bucketName,

packages/cdk/lib/env/context-app-parameters.ts

@@ -105,6 +105,10 @@ export class ContextAppParameters {
    * Map of custom tags to be applied to all the infrastructure in the context.
    */
   public readonly customTags: { [key: string]: string };
+  /**
+   * Map of custom environment variables to be passed to the WES Adapter.
+   */
+  public readonly customWesEnvVars?: { [key: string]: string };
 
   constructor(node: Node) {
     const instanceTypeStrings = getEnvStringListOrDefault(node, "BATCH_COMPUTE_INSTANCE_TYPES");
@@ -142,6 +146,16 @@ export class ContextAppParameters {
     } else {
       this.customTags = {};
     }
+
+    const customWesEnvVarsString = getEnvStringOrDefault(node, "CUSTOM_WES_ENV_VARS");
+
+    if (customWesEnvVarsString) {
+      const customWesEnvVars: Array<{ Key: string; Value: string }> = JSON.parse(customWesEnvVarsString);
+      if (customWesEnvVars && customWesEnvVars.length) {
+        this.customWesEnvVars = {};
+        customWesEnvVars.forEach((customWesEnvVar) => (this.customWesEnvVars![customWesEnvVar["Key"]] = customWesEnvVar["Value"]));
+      }
+    }
   }
 
   public getContextBucketPath(): string {

packages/cdk/lib/stacks/engines/cromwell-engine-construct.ts

@@ -69,6 +69,7 @@ export class CromwellEngineConstruct extends EngineConstruct {
       contextName: params.contextName,
       userId: params.userId,
       engineEndpoint: this.engine.loadBalancer.loadBalancerDnsName,
+      customEnvs: params.customWesEnvVars,
     });
     this.adapterLogGroup = lambda.logGroup;
 
@@ -130,21 +131,18 @@ export class CromwellEngineConstruct extends EngineConstruct {
     return engine;
   }
 
-  private renderAdapterLambda({ role, jobQueueArn, engineLogGroupName, projectName, contextName, userId, engineEndpoint, vpc }) {
-    return super.renderPythonLambda(
-      this,
-      "CromwellWesAdapterLambda",
-      role,
-      {
-        ENGINE_NAME: "cromwell",
-        ENGINE_ENDPOINT: engineEndpoint,
-        ENGINE_LOG_GROUP: engineLogGroupName,
-        JOB_QUEUE: jobQueueArn,
-        PROJECT_NAME: projectName,
-        CONTEXT_NAME: contextName,
-        USER_ID: userId,
-      },
-      vpc
-    );
+  private renderAdapterLambda({ role, jobQueueArn, engineLogGroupName, projectName, contextName, userId, engineEndpoint, vpc, customEnvs }) {
+    const environment = {
+      ...customEnvs,
+      ENGINE_NAME: "cromwell",
+      ENGINE_ENDPOINT: engineEndpoint,
+      ENGINE_LOG_GROUP: engineLogGroupName,
+      JOB_QUEUE: jobQueueArn,
+      PROJECT_NAME: projectName,
+      CONTEXT_NAME: contextName,
+      USER_ID: userId,
+    };
+
+    return super.renderPythonLambda(this, "CromwellWesAdapterLambda", role, environment, vpc);
   }
 }

packages/cdk/lib/stacks/engines/miniwdl-engine-construct.ts

@@ -93,6 +93,7 @@ export class MiniwdlEngineConstruct extends EngineConstruct {
       jobDefinitionArn: this.miniwdlEngine.headJobDefinition.jobDefinitionArn,
       rootDirS3Uri: rootDirS3Uri,
       vpc: props.contextParameters.usePublicSubnets ? undefined : props.vpc,
+      customEnvs: props.contextParameters.customWesEnvVars,
     });
     this.adapterLogGroup = lambda.logGroup;
 
@@ -144,18 +145,15 @@ export class MiniwdlEngineConstruct extends EngineConstruct {
     return [this.batchHead.role, this.batchWorkers.role];
   }
 
-  private renderAdapterLambda({ role, jobQueueArn, jobDefinitionArn, rootDirS3Uri, vpc }) {
-    return super.renderPythonLambda(
-      this,
-      "MiniWDLWesAdapterLambda",
-      role,
-      {
-        ENGINE_NAME: ENGINE_MINIWDL,
-        JOB_QUEUE: jobQueueArn,
-        JOB_DEFINITION: jobDefinitionArn,
-        OUTPUT_DIR_S3_URI: rootDirS3Uri,
-      },
-      vpc
-    );
+  private renderAdapterLambda({ role, jobQueueArn, jobDefinitionArn, rootDirS3Uri, vpc, customEnvs }) {
+    const environment = {
+      ...customEnvs,
+      ENGINE_NAME: ENGINE_MINIWDL,
+      JOB_QUEUE: jobQueueArn,
+      JOB_DEFINITION: jobDefinitionArn,
+      OUTPUT_DIR_S3_URI: rootDirS3Uri,
+    };
+
+    return super.renderPythonLambda(this, "MiniWDLWesAdapterLambda", role, environment, vpc);
   }
 }

packages/cdk/lib/stacks/engines/nextflow-engine-construct.ts

@@ -63,6 +63,7 @@ export class NextflowEngineConstruct extends EngineConstruct {
       jobDefinitionArn: this.nextflowEngine.headJobDefinition.jobDefinitionArn,
       engineLogGroupName: engineLogGroup.logGroupName,
       vpc: props.contextParameters.usePublicSubnets ? undefined : props.vpc,
+      customEnvs: props.contextParameters.customWesEnvVars,
     });
     this.adapterLogGroup = lambda.logGroup;
 
@@ -82,18 +83,15 @@ export class NextflowEngineConstruct extends EngineConstruct {
     };
   }
 
-  private renderAdapterLambda({ role, jobQueueArn, jobDefinitionArn, engineLogGroupName, vpc }) {
-    return super.renderPythonLambda(
-      this,
-      "NextflowWesAdapterLambda",
-      role,
-      {
-        ENGINE_NAME: "nextflow",
-        JOB_QUEUE: jobQueueArn,
-        JOB_DEFINITION: jobDefinitionArn,
-        ENGINE_LOG_GROUP: engineLogGroupName,
-      },
-      vpc
-    );
+  private renderAdapterLambda({ role, jobQueueArn, jobDefinitionArn, engineLogGroupName, vpc, customEnvs }) {
+    const environment = {
+      ...customEnvs,
+      ENGINE_NAME: "nextflow",
+      JOB_QUEUE: jobQueueArn,
+      JOB_DEFINITION: jobDefinitionArn,
+      ENGINE_LOG_GROUP: engineLogGroupName,
+    };
+
+    return super.renderPythonLambda(this, "NextflowWesAdapterLambda", role, environment, vpc);
   }
 }

packages/cdk/lib/stacks/engines/snakemake-engine-construct.ts

@@ -59,6 +59,7 @@ export class SnakemakeEngineConstruct extends EngineConstruct {
       taskQueueArn: this.batchWorkers.jobQueue.jobQueueArn,
       fsapId: this.snakemakeEngine.fsap.accessPointId,
       outputBucket: params.getEngineBucketPath(),
+      customEnvs: contextParameters.customWesEnvVars,
     });
     this.adapterLogGroup = lambda.logGroup;
 
@@ -173,22 +174,19 @@ export class SnakemakeEngineConstruct extends EngineConstruct {
     });
   }
 
-  private renderAdapterLambda({ vpc, role, jobQueueArn, jobDefinitionArn, taskQueueArn, workflowRoleArn, fsapId, outputBucket }) {
-    return super.renderPythonLambda(
-      this,
-      "SnakemakeWesAdapterLambda",
-      role,
-      {
-        ENGINE_NAME: "snakemake",
-        JOB_QUEUE: jobQueueArn,
-        JOB_DEFINITION: jobDefinitionArn,
-        TASK_QUEUE: taskQueueArn,
-        WORKFLOW_ROLE: workflowRoleArn,
-        FSAP_ID: fsapId,
-        OUTPUT_DIR_S3_URI: outputBucket,
-        TIME: Date.now().toString(),
-      },
-      vpc
-    );
+  private renderAdapterLambda({ vpc, role, jobQueueArn, jobDefinitionArn, taskQueueArn, workflowRoleArn, fsapId, outputBucket, customEnvs }) {
+    const environment = {
+      ...customEnvs,
+      ENGINE_NAME: "snakemake",
+      JOB_QUEUE: jobQueueArn,
+      JOB_DEFINITION: jobDefinitionArn,
+      TASK_QUEUE: taskQueueArn,
+      WORKFLOW_ROLE: workflowRoleArn,
+      FSAP_ID: fsapId,
+      OUTPUT_DIR_S3_URI: outputBucket,
+      TIME: Date.now().toString(),
+    };
+
+    return super.renderPythonLambda(this, "SnakemakeWesAdapterLambda", role, environment, vpc);
   }
 }

packages/cli/internal/pkg/cli/context/context_environment.go

@@ -29,26 +29,28 @@ type contextEnvironment struct {
 	AdapterDesignation string
 	AdapterRepository  string
 
-	ArtifactBucketName  string
-	ReadBucketArns      string
-	ReadWriteBucketArns string
-	InstanceTypes       string
-	ResourceType        string
-	MaxVCpus            int
+	ArtifactBucketName   string
+	ReadBucketArns       string
+	ReadWriteBucketArns  string
+	InstanceTypes        string
+	ResourceType         string
+	MaxVCpus             int
+	CustomWesEnvVarsJson string
 
 	RequestSpotInstances bool
 	UsePublicSubnets     bool
 }
 
 func (input contextEnvironment) ToEnvironmentList() []string {
 	return environmentMapToList(map[string]string{
-		"PROJECT":       input.ProjectName,
-		"CONTEXT":       input.ContextName,
-		"USER_ID":       input.UserId,
-		"USER_EMAIL":    input.UserEmail,
-		"OUTPUT_BUCKET": input.OutputBucketName,
-		"AGC_VERSION":   version.Version,
-		"CUSTOM_TAGS":   input.CustomTagsJson,
+		"PROJECT":             input.ProjectName,
+		"CONTEXT":             input.ContextName,
+		"USER_ID":             input.UserId,
+		"USER_EMAIL":          input.UserEmail,
+		"OUTPUT_BUCKET":       input.OutputBucketName,
+		"AGC_VERSION":         version.Version,
+		"CUSTOM_TAGS":         input.CustomTagsJson,
+		"CUSTOM_WES_ENV_VARS": input.CustomWesEnvVarsJson,
 
 		"ENGINE_NAME":               input.EngineName,
 		"FILESYSTEM_TYPE":           input.FilesystemType,

packages/cli/internal/pkg/cli/context/manager.go

@@ -1,6 +1,7 @@
 package context
 
 import (
+	"encoding/json"
 	"fmt"
 	"net/url"
 	"strings"
@@ -214,6 +215,12 @@ func (m *Manager) setContextEnv(contextName string) {
 		return
 	}
 
+	customWesEnvVarsJsonBytes, err := json.Marshal(m.contextSpec.CustomWesEnvVars)
+	if err != nil {
+		m.err = err
+		return
+	}
+
 	m.contextEnv = contextEnvironment{
 		ProjectName:          m.projectSpec.Name,
 		ContextName:          contextName,
@@ -225,6 +232,7 @@ func (m *Manager) setContextEnv(contextName string) {
 		ReadBucketArns:       strings.Join(m.readBuckets, listDelimiter),
 		ReadWriteBucketArns:  strings.Join(m.readWriteBuckets, listDelimiter),
 		InstanceTypes:        strings.Join(m.contextSpec.InstanceTypes, listDelimiter),
+		CustomWesEnvVarsJson: string(customWesEnvVarsJsonBytes),
 		MaxVCpus:             m.contextSpec.MaxVCpus,
 		RequestSpotInstances: m.contextSpec.RequestSpotInstances,
 		UsePublicSubnets:     m.contextSpec.UsePublicSubnets,

packages/cli/internal/pkg/cli/context/manager_deploy_test.go

@@ -46,7 +46,7 @@ func TestManager_Deploy(t *testing.T) {
 				mockClients.ssmMock.EXPECT().GetCustomTags().Return(testTags)
 				mockClients.ecrClientMock.EXPECT().VerifyImageExists(environment.CommonImages["NEXTFLOW"]).Return(nil)
 				clearContext := mockClients.cdkMock.EXPECT().ClearContext(filepath.Join(testHomeDir, ".agc/cdk/apps/context")).Return(nil)
-				mockClients.cdkMock.EXPECT().DeployApp(filepath.Join(testHomeDir, ".agc/cdk/apps/context"), gomock.Len(43), testContextName3).After(clearContext).Return(mockClients.progressStream1, nil)
+				mockClients.cdkMock.EXPECT().DeployApp(filepath.Join(testHomeDir, ".agc/cdk/apps/context"), gomock.Len(44), testContextName3).After(clearContext).Return(mockClients.progressStream1, nil)
 				displayProgressBar = mockClients.cdkMock.DisplayProgressBar
 				mockClients.cdkMock.EXPECT().DisplayProgressBar(fmt.Sprintf("Deploying resources for context(s) %s", []string{testContextName3}), []cdk.ProgressStream{mockClients.progressStream1}).Return([]cdk.Result{{Outputs: []string{"some message"}, ExecutionName: testContextName3}})
 				return mockClients
@@ -69,7 +69,7 @@ func TestManager_Deploy(t *testing.T) {
 				mockClients.ssmMock.EXPECT().GetCustomTags().Return("")
 				mockClients.ecrClientMock.EXPECT().VerifyImageExists(environment.CommonImages["NEXTFLOW"]).Return(nil)
 				clearContext := mockClients.cdkMock.EXPECT().ClearContext(filepath.Join(testHomeDir, ".agc/cdk/apps/context")).Return(nil)
-				mockClients.cdkMock.EXPECT().DeployApp(filepath.Join(testHomeDir, ".agc/cdk/apps/context"), gomock.Len(43), testContextName3).After(clearContext).Return(mockClients.progressStream1, nil)
+				mockClients.cdkMock.EXPECT().DeployApp(filepath.Join(testHomeDir, ".agc/cdk/apps/context"), gomock.Len(44), testContextName3).After(clearContext).Return(mockClients.progressStream1, nil)
 				displayProgressBar = mockClients.cdkMock.DisplayProgressBar
 				mockClients.cdkMock.EXPECT().DisplayProgressBar(fmt.Sprintf("Deploying resources for context(s) %s", []string{testContextName3}), []cdk.ProgressStream{mockClients.progressStream1}).Return([]cdk.Result{{Outputs: []string{"some message"}, ExecutionName: testContextName3}})
 				return mockClients
@@ -94,8 +94,8 @@ func TestManager_Deploy(t *testing.T) {
 				mockClients.ecrClientMock.EXPECT().VerifyImageExists(environment.CommonImages["CROMWELL"]).Times(2).Return(nil)
 				clearContext := mockClients.cdkMock.EXPECT().ClearContext(filepath.Join(testHomeDir, ".agc/cdk/apps/context")).Return(nil)
 				clearContext2 := mockClients.cdkMock.EXPECT().ClearContext(filepath.Join(testHomeDir, ".agc/cdk/apps/context")).Return(nil)
-				mockClients.cdkMock.EXPECT().DeployApp(filepath.Join(testHomeDir, ".agc/cdk/apps/context"), gomock.Len(43), testContextName1).After(clearContext).Return(mockClients.progressStream1, nil)
-				mockClients.cdkMock.EXPECT().DeployApp(filepath.Join(testHomeDir, ".agc/cdk/apps/context"), gomock.Len(43), testContextName2).After(clearContext2).Return(mockClients.progressStream2, nil)
+				mockClients.cdkMock.EXPECT().DeployApp(filepath.Join(testHomeDir, ".agc/cdk/apps/context"), gomock.Len(44), testContextName1).After(clearContext).Return(mockClients.progressStream1, nil)
+				mockClients.cdkMock.EXPECT().DeployApp(filepath.Join(testHomeDir, ".agc/cdk/apps/context"), gomock.Len(44), testContextName2).After(clearContext2).Return(mockClients.progressStream2, nil)
 				displayProgressBar = mockClients.cdkMock.DisplayProgressBar
 				expectedCdkResult := []cdk.Result{{Outputs: []string{"some message"}, ExecutionName: testContextName1}, {Outputs: []string{"some other message"}, ExecutionName: testContextName2}}
 				mockClients.cdkMock.EXPECT().DisplayProgressBar(fmt.Sprintf("Deploying resources for context(s) %s", []string{testContextName1, testContextName2}), []cdk.ProgressStream{mockClients.progressStream1, mockClients.progressStream2}).Return(expectedCdkResult)
@@ -235,7 +235,7 @@ func TestManager_Deploy(t *testing.T) {
 				mockClients.ssmMock.EXPECT().GetCommonParameter("installed-artifacts/s3-root-url").Return(testArtifactBucket, nil)
 				mockClients.ssmMock.EXPECT().GetCustomTags().Return(testTags)
 				mockClients.cdkMock.EXPECT().ClearContext(filepath.Join(testHomeDir, ".agc/cdk/apps/context")).Return(nil)
-				mockClients.cdkMock.EXPECT().DeployApp(filepath.Join(testHomeDir, ".agc/cdk/apps/context"), gomock.Len(43), testContextName1).Return(nil, fmt.Errorf("some context error"))
+				mockClients.cdkMock.EXPECT().DeployApp(filepath.Join(testHomeDir, ".agc/cdk/apps/context"), gomock.Len(44), testContextName1).Return(nil, fmt.Errorf("some context error"))
 				mockClients.ecrClientMock.EXPECT().VerifyImageExists(environment.CommonImages["CROMWELL"]).Return(nil)
 				return mockClients
 			},

packages/cli/internal/pkg/cli/spec/context.go

@@ -14,12 +14,17 @@ type Engine struct {
 	Engine     string     `yaml:"engine"`
 	Filesystem Filesystem `yaml:"filesystem,omitempty"`
 }
+type CustomWesEnvVar struct {
+	Key   string `yaml:"key"`
+	Value string `yaml:"value"`
+}
 type Context struct {
-	InstanceTypes        []string `yaml:"instanceTypes,omitempty"`
-	RequestSpotInstances bool     `yaml:"requestSpotInstances,omitempty"`
-	MaxVCpus             int      `yaml:"maxVCpus,omitempty"`
-	UsePublicSubnets     bool     `yaml:"usePublicSubnets,omitempty"`
-	Engines              []Engine `yaml:"engines"`
+	InstanceTypes        []string          `yaml:"instanceTypes,omitempty"`
+	RequestSpotInstances bool              `yaml:"requestSpotInstances,omitempty"`
+	MaxVCpus             int               `yaml:"maxVCpus,omitempty"`
+	UsePublicSubnets     bool              `yaml:"usePublicSubnets,omitempty"`
+	Engines              []Engine          `yaml:"engines"`
+	CustomWesEnvVars     []CustomWesEnvVar `yaml:"customWesEnvVars"`
 }
 
 func (context *Context) UnmarshalYAML(unmarshal func(interface{}) error) error {

packages/cli/internal/pkg/cli/spec/project_schema.json

@@ -151,6 +151,27 @@
                 },
                 "required": ["type", "engine"]
               }
+            },
+            "customWesEnvVars": {
+              "type":[
+                "array",
+                "null"
+              ],
+              "items": {
+                "type": "object",
+                "additionalProperties": false,
+                "properties": {
+                  "key": {
+                    "type": "string",
+                    "minLength": 1
+                  },
+                  "value": {
+                    "type": "string",
+                    "minLength": 1
+                  }
+                 },
+                "required": ["key", "value"]
+              }
             }
           },
           "required": [