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 used to pass to 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 };
+  /**
+   * Environment variables to be passed to
+   */
+  public readonly customWesEnvVars?: { [key: string]: string };
 
   constructor(node: Node) {
     const instanceTypeStrings = getEnvStringListOrDefault(node, "BATCH_COMPUTE_INSTANCE_TYPES");
@@ -142,6 +146,12 @@ export class ContextAppParameters {
     } else {
       this.customTags = {};
     }
+
+    const customWesEnvVars = getEnvStringOrDefault(node, "CUSTOM_WES_ENV_VARS");
+
+    if (customWesEnvVars) {
+      this.customWesEnvVars = JSON.parse(customWesEnvVars);
+    }
   }
 
   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/aws/cdk/bootstrap.go

@@ -22,6 +22,7 @@ func (client Client) Bootstrap(appDir string, context []string, executionName st
 	// Add AGC version and custom tags to the bootstrap stack.
 	agcVersionKey := constants.AgcVersionEnvKey + "="
 	customTagsKey := constants.CustomTagEnvKey + "="
+	customWesEnvVarsKey := constants.CustomWesEnvVarEnvKey + "="
 	for _, c := range context {
 		if strings.HasPrefix(c, agcVersionKey) {
 			version := strings.TrimPrefix(c, agcVersionKey)
@@ -38,6 +39,17 @@ func (client Client) Bootstrap(appDir string, context []string, executionName st
 				cmdArgs = append(cmdArgs, "--tags", fmt.Sprintf("%s=%s", k, v))
 			}
 		}
+		if strings.HasPrefix(c, customWesEnvVarsKey) {
+			jsonStr := strings.TrimPrefix(c, customWesEnvVarsKey)
+			customWesEnvVarsMap := make(map[string]interface{})
+			err := json.Unmarshal([]byte(jsonStr), &customWesEnvVarsMap)
+			if err != nil {
+				return nil, err
+			}
+			for k, v := range customWesEnvVarsMap {
+				cmdArgs = append(cmdArgs, "--customWesEnvVars", fmt.Sprintf("%s=%s", k, v))
+			}
+		}
 	}
 
 	cmdArgs = appendContextArguments(cmdArgs, context)

packages/cli/internal/pkg/aws/ssm/get_common_parameter.go

@@ -10,9 +10,10 @@ import (
 )
 
 const (
-	parameterPrefix       = "/agc/_common"
-	outputBucketParameter = "bucket"
-	customTagsParameter   = "customTags"
+	parameterPrefix           = "/agc/_common"
+	outputBucketParameter     = "bucket"
+	customTagsParameter       = "customTags"
+	customWesEnvVarsParameter = "customWesEnvVars"
 )
 
 func (c *Client) GetCommonParameter(parameterSuffix string) (string, error) {
@@ -40,3 +41,10 @@ func (c *Client) GetCustomTags() string {
 	tags, _ := c.GetCommonParameter(customTagsParameter)
 	return tags
 }
+
+func (c *Client) GetCustomWesEnvVars() string {
+	// Adapter custom envs may not exist, so ignore the error
+
+	customWesEnvVars, _ := c.GetCommonParameter(customWesEnvVarsParameter)
+	return customWesEnvVars
+}

packages/cli/internal/pkg/aws/ssm/get_common_parameter_test.go

@@ -75,3 +75,15 @@ func TestClient_GetCustomTags_ExpectedValue(t *testing.T) {
 	actual := client.GetCustomTags()
 	assert.Equal(t, tags, actual)
 }
+
+func TestClient_GetCustomWesEnvVars_ExpectedValue(t *testing.T) {
+	customWesEnvVars := "customWesEnvVars"
+	mockSsm := new(ssmMockClient)
+	client := &Client{mockSsm}
+	ctx := context.Background()
+	mockSsm.On("GetParameter", ctx, &ssm.GetParameterInput{Name: aws.String("/agc/_common/customWesEnvVars")}).
+		Return(&ssm.GetParameterOutput{Parameter: &types.Parameter{Value: aws.String(customWesEnvVars)}}, nil)
+
+	actual := client.GetCustomWesEnvVars()
+	assert.Equal(t, customWesEnvVars, actual)
+}

packages/cli/internal/pkg/aws/ssm/interface.go

@@ -10,6 +10,7 @@ type Interface interface {
 	GetOutputBucket() (string, error)
 	GetCommonParameter(parameterSuffix string) (string, error)
 	GetCustomTags() string
+	GetCustomWesEnvVars() string
 }
 
 type ssmInterface interface {

packages/cli/internal/pkg/cli/account_activate.go

@@ -32,6 +32,7 @@ const (
 	accountVpcFlag               = "vpc"
 	publicSubnetsFlag            = "usePublicSubnets"
 	accountTagsFlag              = "tags"
+	accountCustomWesEnvVarsFlag  = "customWesEnvVars"
 	accountBucketFlagDescription = `The name of an S3 bucket that AGC will use to store its data.
 An autogenerated name will be used if not specified. A new bucket will be created if the bucket does not exist.`
 	accountVpcFlagDescription = `The ID of a VPC that AGC will run in. 
@@ -41,17 +42,21 @@ You must enable the usePublicSubnets option in your project context if you use t
 	accountTagsDescription = `A list of comma separated tags to be applied to all AGC resources in this account
 (i.e. --tags "k1=v1","k2=v2"). Each key-value pair must be quoted as shown in the example,
 otherwise the parsing will fail.`
+	customWesEnvVarsDescription = `A list of comma separated WES adapter custom env vars to be passed to WES adapter
+(i.e. --customWesEnvVars "k1=v1","k2=v2","k3=[{ \"k4\": { \"k5\": \"v5\" } }]").
+Each key-value pair must be quoted as shown in the example, otherwise the parsing will fail.`
 	cdkCoreDir   = ".agc/cdk/apps/core"
 	bucketPrefix = "agc"
 	activateKey  = "activate"
 	bootstrapKey = "bootstrap"
 )
 
 type accountActivateVars struct {
-	bucketName    string
-	vpcId         string
-	publicSubnets bool
-	customTags    map[string]string
+	bucketName       string
+	vpcId            string
+	publicSubnets    bool
+	customTags       map[string]string
+	customWesEnvVars map[string]string
 }
 
 type accountActivateOpts struct {
@@ -135,6 +140,14 @@ func (o accountActivateOpts) generateEnvVars() ([]string, error) {
 		environmentVars = append(environmentVars, fmt.Sprintf("%s=%s", constants.CustomTagEnvKey, string(jsonBytes)))
 	}
 
+	if o.customWesEnvVars != nil {
+		jsonBytes, err := json.Marshal(o.customWesEnvVars)
+		if err != nil {
+			return nil, err
+		}
+		environmentVars = append(environmentVars, fmt.Sprintf("%s=%s", constants.CustomWesEnvVarEnvKey, string(jsonBytes)))
+	}
+
 	vpcId, err := o.getVpcId()
 	if err != nil {
 		return nil, err
@@ -236,5 +249,6 @@ Activate AGC in your AWS account with a custom S3 bucket and VPC.
 	cmd.Flags().StringVar(&vars.vpcId, accountVpcFlag, "", accountVpcFlagDescription)
 	cmd.Flags().BoolVar(&vars.publicSubnets, publicSubnetsFlag, false, publicSubnetsFlagDescription)
 	cmd.Flags().StringToStringVar(&vars.customTags, accountTagsFlag, nil, accountTagsDescription)
+	cmd.Flags().StringToStringVar(&vars.customWesEnvVars, accountCustomWesEnvVarsFlag, nil, customWesEnvVarsDescription)
 	return cmd
 }

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

@@ -26,6 +26,7 @@ const (
 	testUserEmail          = "[email protected]"
 	testUserId             = "bender123"
 	testTags               = "{\"k1\":\"v1\",\"k2\":\"v2\"}"
+	testCustomWesEnvVars   = "{\"k1\":\"v1\",\"k2\":\"v2\"}"
 )
 
 var (

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

@@ -11,12 +11,13 @@ const (
 )
 
 type contextEnvironment struct {
-	ProjectName      string
-	ContextName      string
-	UserId           string
-	UserEmail        string
-	OutputBucketName string
-	CustomTagsJson   string
+	ProjectName          string
+	ContextName          string
+	UserId               string
+	UserEmail            string
+	OutputBucketName     string
+	CustomTagsJson       string
+	CustomWesEnvVarsJson string
 
 	EngineName              string
 	FilesystemType          string
@@ -42,13 +43,14 @@ type contextEnvironment struct {
 
 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,