initialised umccrise pipeline manager

config/config.ts

@@ -39,6 +39,10 @@ import {
   getWtsIcav2PipelineManagerStackProps,
   getWtsIcav2PipelineTableStackProps,
 } from './stacks/wtsPipelineManager';
+import {
+  getUmccriseIcav2PipelineManagerStackProps,
+  getUmccriseIcav2PipelineTableStackProps,
+} from './stacks/umccrisePipelineManager';
 
 interface EnvironmentConfig {
   name: string;
@@ -70,6 +74,7 @@ export const getEnvironmentConfig = (stage: AppStage): EnvironmentConfig | null
       wgtsQcIcav2PipelineTableStackProps: getWgtsQcIcav2PipelineTableStackProps(),
       tnIcav2PipelineTableStackProps: getTnIcav2PipelineTableStackProps(),
       wtsIcav2PipelineTableStackProps: getWtsIcav2PipelineTableStackProps(),
+      umccriseIcav2PipelineTableStackProps: getUmccriseIcav2PipelineTableStackProps(),
       BclConvertTableStackProps: getBclConvertManagerTableStackProps(stage),
       stackyStatefulTablesStackProps: getStatefulGlueStackProps(),
     },
@@ -85,6 +90,7 @@ export const getEnvironmentConfig = (stage: AppStage): EnvironmentConfig | null
       wgtsQcIcav2PipelineManagerStackProps: getWgtsQcIcav2PipelineManagerStackProps(stage),
       tnIcav2PipelineManagerStackProps: getTnIcav2PipelineManagerStackProps(stage),
       wtsIcav2PipelineManagerStackProps: getWtsIcav2PipelineManagerStackProps(stage),
+      umccriseIcav2PipelineManagerStackProps: getUmccriseIcav2PipelineManagerStackProps(stage),
       eventSchemaStackProps: getEventSchemaStackProps(),
       dataSchemaStackProps: getDataSchemaStackProps(),
       bclConvertManagerStackProps: getBclConvertManagerStackProps(stage),

config/constants.ts

@@ -396,6 +396,56 @@ export const wtsDefaultArribaVersion = '2.4.0';
 
 export const wtsDefaultQcReferenceSamplesVersion = '2023-07-21--4.2.4';
 
+/*
+Resources required by the umccrise stacks
+*/
+
+// Deployed under dev/stg/prod
+// '
+//   [
+//     {
+//       "name": "202303",
+//       "uri": "icav2://reference-data/umccrise/202303/genomes.tar.gz"
+//     }
+//   ]
+// '
+export const icav2UmccriseGenomesReferenceUriMappingSSMParameterPath =
+  '/icav2/umccr-prod/umccrise_genomes_reference_mapping'; //
+
+/*
+Resources generated by the UMCCRise Stateful Stack
+*/
+export const umccriseIcav2PipelineManagerSSMRoot = '/orcabus/umccrise';
+
+/*
+UMCCRise Stateful stack
+*/
+export const umccriseIcav2PipelineManagerDynamodbTableName = 'umccriseICAv2AnalysesDynamoDBTable';
+export const umccriseDynamoDbTableSSMName = path.join(
+  umccriseIcav2PipelineManagerSSMRoot,
+  'dynamodb_table_name'
+);
+export const umccriseDynamoDbTableSSMArn = path.join(
+  umccriseIcav2PipelineManagerSSMRoot,
+  'dynamodb_table_arn'
+);
+
+/*
+UMCCRise Stateless stack
+*/
+
+// Deployed in dev/stg/prod
+export const umccriseIcav2PipelineIdSSMParameterPath =
+  '/icav2/umccr-prod/umccrise_2.3.1_pipeline_id'; // 61254f38-b56e-4576-a8a1-341e5c412d11
+export const umccriseIcav2PipelineWorkflowType = 'umccrise';
+export const umccriseIcav2PipelineWorkflowTypeVersion = '2.3.1';
+export const umccriseIcav2ServiceVersion = '2024.07.01';
+export const umccriseIcav2ReadyEventSource = 'orcabus.workflowmanager';
+export const umccriseIcav2EventSource = 'orcabus.umccrise';
+export const umccriseIcav2EventDetailType = 'WorkflowRunStateChange';
+export const umccriseStateMachinePrefix = 'umccriseSfn';
+export const umccriseDefaultGenomeVersion = '202303';
+
 // Mock Stack
 export const mockEventBusName = eventBusName;
 export const mockInstrumentRunTableName = 'stacky-instrument-run-table';
@@ -405,7 +455,6 @@ export const mockWgtsQcGlueTableName = 'stacky-wgts-qc-glue-table';
 export const mockTnGlueTableName = 'stacky-tn-glue-table';
 export const mockWtsGlueTableName = 'stacky-wts-glue-table';
 export const mockUmccriseGlueTableName = 'stacky-umccrise-glue-table';
-
 export const mockWorkflowManagerTableName = 'stacky-workflow-manager-table';
 
 // {

config/stacks/umccrisePipelineManager.ts

@@ -0,0 +1,58 @@
+import {
+  AppStage,
+  eventBusName,
+  icaEventPipeStackName,
+  icav2AccessTokenSecretName,
+  dragenIcav2ReferenceUriMappingSSMParameterPath,
+  umccriseIcav2PipelineIdSSMParameterPath,
+  umccriseIcav2PipelineManagerDynamodbTableName,
+  umccriseIcav2PipelineWorkflowType,
+  umccriseIcav2PipelineWorkflowTypeVersion,
+  umccriseIcav2ServiceVersion,
+  umccriseIcav2ReadyEventSource,
+  umccriseIcav2EventSource,
+  umccriseIcav2EventDetailType,
+  umccriseStateMachinePrefix,
+  umccriseDefaultGenomeVersion,
+  umccriseDynamoDbTableSSMArn,
+  umccriseDynamoDbTableSSMName,
+} from '../constants';
+import { UmccriseIcav2PipelineManagerConfig } from '../../lib/workload/stateless/stacks/umccrise-pipeline-manager/deploy';
+import { UmccriseIcav2PipelineTableConfig } from '../../lib/workload/stateful/stacks/umccrise-pipeline-dynamo-db/deploy/stack';
+
+// Stateful
+export const getUmccriseIcav2PipelineTableStackProps = (): UmccriseIcav2PipelineTableConfig => {
+  return {
+    umccriseIcav2DynamodbTableArnSsmParameterPath: umccriseDynamoDbTableSSMArn,
+    umccriseIcav2DynamodbTableNameSsmParameterPath: umccriseDynamoDbTableSSMName,
+    dynamodbTableName: umccriseIcav2PipelineManagerDynamodbTableName,
+  };
+};
+
+// Stateless
+export const getUmccriseIcav2PipelineManagerStackProps = (
+  stage: AppStage
+): UmccriseIcav2PipelineManagerConfig => {
+  return {
+    /* ICAv2 Pipeline analysis essentials */
+    icav2TokenSecretId: icav2AccessTokenSecretName[stage], // "/icav2/umccr-prod/service-production-jwt-token-secret-arn"
+    pipelineIdSsmPath: umccriseIcav2PipelineIdSSMParameterPath, // List of parameters the workflow session state machine will need access to
+    /* Table to store analyis metadata */
+    dynamodbTableName: umccriseIcav2PipelineManagerDynamodbTableName,
+    /* Internal and external buses */
+    eventBusName: eventBusName,
+    icaEventPipeName: `${icaEventPipeStackName}Pipe`,
+    /* Event handling */
+    workflowType: umccriseIcav2PipelineWorkflowType,
+    workflowVersion: umccriseIcav2PipelineWorkflowTypeVersion,
+    serviceVersion: umccriseIcav2ServiceVersion,
+    triggerLaunchSource: umccriseIcav2ReadyEventSource,
+    internalEventSource: umccriseIcav2EventSource,
+    detailType: umccriseIcav2EventDetailType,
+    /* Names for statemachines */
+    stateMachinePrefix: umccriseStateMachinePrefix,
+    /* SSM Workflow Parameters */
+    defaultReferenceVersion: umccriseDefaultGenomeVersion,
+    referenceUriSsmPath: dragenIcav2ReferenceUriMappingSSMParameterPath,
+  };
+};

lib/workload/stateful/stacks/umccrise-pipeline-dynamo-db/deploy/stack.ts

@@ -0,0 +1,54 @@
+import * as cdk from 'aws-cdk-lib';
+import { Construct } from 'constructs';
+import * as ssm from 'aws-cdk-lib/aws-ssm';
+import { DynamodbPartitionedPipelineConstruct } from '../../../../components/dynamodb-partitioned-table';
+
+export interface UmccriseIcav2PipelineTableConfig {
+  dynamodbTableName: string;
+  umccriseIcav2DynamodbTableArnSsmParameterPath: string;
+  umccriseIcav2DynamodbTableNameSsmParameterPath: string;
+}
+
+export type UmccriseIcav2PipelineTableStackProps = UmccriseIcav2PipelineTableConfig &
+  cdk.StackProps;
+
+export class UmccriseIcav2PipelineTable extends cdk.Stack {
+  public readonly umccriseIcav2DynamodbTableArnSsmParameterPath: string;
+  public readonly umccriseIcav2DynamodbTableNameSsmParameterPath: string;
+
+  constructor(scope: Construct, id: string, props: UmccriseIcav2PipelineTableStackProps) {
+    super(scope, id, props);
+
+    /*
+    Initialise dynamodb table, where portal_run_id is the primary sort key
+    */
+    const dynamodb_table = new DynamodbPartitionedPipelineConstruct(
+      this,
+      'umccrise_icav2_pipeline_table',
+      {
+        tableName: props.dynamodbTableName,
+      }
+    );
+
+    /*
+    Generate a ssm parameter to store the table arn so it can be referred to be other stacks
+    */
+    this.umccriseIcav2DynamodbTableArnSsmParameterPath = new ssm.StringParameter(
+      this,
+      'umccrise_icav2_pipeline_table_arn_ssm_path',
+      {
+        parameterName: props.umccriseIcav2DynamodbTableArnSsmParameterPath,
+        stringValue: dynamodb_table.tableNameArn,
+      }
+    ).parameterName;
+
+    this.umccriseIcav2DynamodbTableNameSsmParameterPath = new ssm.StringParameter(
+      this,
+      'umccrise_icav2_pipeline_table_name_ssm_path',
+      {
+        parameterName: props.umccriseIcav2DynamodbTableNameSsmParameterPath,
+        stringValue: props.dynamodbTableName,
+      }
+    ).parameterName;
+  }
+}

lib/workload/stateful/statefulStackCollectionClass.ts

@@ -37,6 +37,10 @@ import {
   WtsIcav2PipelineTable,
   WtsIcav2PipelineTableStackProps,
 } from './stacks/wts-dynamo-db/deploy/stack';
+import {
+  UmccriseIcav2PipelineTable,
+  UmccriseIcav2PipelineTableStackProps,
+} from './stacks/umccrise-pipeline-dynamo-db/deploy/stack';
 
 export interface StatefulStackCollectionProps {
   dataBucketStackProps: DataBucketStackProps;
@@ -49,6 +53,7 @@ export interface StatefulStackCollectionProps {
   wgtsQcIcav2PipelineTableStackProps: WgtsQcIcav2PipelineTableStackProps;
   tnIcav2PipelineTableStackProps: TnIcav2PipelineTableStackProps;
   wtsIcav2PipelineTableStackProps: WtsIcav2PipelineTableStackProps;
+  umccriseIcav2PipelineTableStackProps: UmccriseIcav2PipelineTableStackProps;
   BclConvertTableStackProps: BclConvertTableStackProps;
   stackyStatefulTablesStackProps: StackyStatefulTablesStackProps;
 }
@@ -66,6 +71,7 @@ export class StatefulStackCollection {
   readonly wgtsQcIcav2PipelineTableStack: Stack;
   readonly tnIcav2PipelineTableStack: Stack;
   readonly wtsIcav2PipelineTableStack: Stack;
+  readonly umccriseIcav2PipelineTableStack: Stack;
   readonly BclConvertTableStack: Stack;
   readonly stackyStatefulTablesStack: Stack;
 
@@ -144,6 +150,15 @@ export class StatefulStackCollection {
       }
     );
 
+    this.umccriseIcav2PipelineTableStack = new UmccriseIcav2PipelineTable(
+      scope,
+      'UmccriseIcav2PipelineTableStack',
+      {
+        ...this.createTemplateProps(env, 'UmccriseIcav2PipelineTableStack'),
+        ...statefulConfiguration.umccriseIcav2PipelineTableStackProps,
+      }
+    );
+
     this.BclConvertTableStack = new BclConvertTable(scope, 'BclConvertTableStack', {
       ...this.createTemplateProps(env, 'BclConvertTableStack'),
       ...statefulConfiguration.BclConvertTableStackProps,