Add pieriandx pipeline manager

lib/workload/stateful/pieriandx_pipeline_dynamo_db/Readme.md

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+# PierianDx Dynamo Db
+
+The dynamo db service that stores pieriandx analyses
+
+Analysis are stored by their step function invocation but can also be accessed via the following methods:
+
+* case_accession_number
+* case_id
+* informaticsjob_id
+* sequencerrun_id
+* portal_run_id
+

lib/workload/stateful/pieriandx_pipeline_dynamo_db/deploy/.gitignore

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+*.js
+!jest.config.js
+*.d.ts
+node_modules
+
+# CDK asset staging directory
+.cdk.staging
+cdk.out

lib/workload/stateful/pieriandx_pipeline_dynamo_db/deploy/.npmignore

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+*.ts
+!*.d.ts
+
+# CDK asset staging directory
+.cdk.staging
+cdk.out

lib/workload/stateful/pieriandx_pipeline_dynamo_db/deploy/README.md

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+# Welcome to your CDK TypeScript project
+
+This is a blank project for CDK development with TypeScript.
+
+The `cdk.json` file tells the CDK Toolkit how to execute your app.
+
+## Useful commands
+
+* `npm run build`   compile typescript to js
+* `npm run watch`   watch for changes and compile
+* `npm run test`    perform the jest unit tests
+* `npx cdk deploy`  deploy this stack to your default AWS account/region
+* `npx cdk diff`    compare deployed stack with current state
+* `npx cdk synth`   emits the synthesized CloudFormation template

lib/workload/stateful/pieriandx_pipeline_dynamo_db/deploy/bin/deploy.ts

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+#!/usr/bin/env node
+import 'source-map-support/register';
+import * as cdk from 'aws-cdk-lib';
+import { PieriandxDynamodbStack } from '../lib/pieriandx-dynamodb-stack';
+
+const app = new cdk.App();
+new PieriandxDynamodbStack(app, 'DeployStack', {
+  /* If you don't specify 'env', this stack will be environment-agnostic.
+   * Account/Region-dependent features and context lookups will not work,
+   * but a single synthesized template can be deployed anywhere. */
+
+  /* Uncomment the next line to specialize this stack for the AWS Account
+   * and Region that are implied by the current CLI configuration. */
+  // env: { account: process.env.CDK_DEFAULT_ACCOUNT, region: process.env.CDK_DEFAULT_REGION },
+
+  /* Uncomment the next line if you know exactly what Account and Region you
+   * want to deploy the stack to. */
+  // env: { account: '123456789012', region: 'us-east-1' },
+
+  /* For more information, see https://docs.aws.amazon.com/cdk/latest/guide/environments.html */
+  env: {
+    account: process.env.CDK_DEFAULT_ACCOUNT,
+    region: process.env.CDK_DEFAULT_REGION,
+  },
+});

lib/workload/stateful/pieriandx_pipeline_dynamo_db/deploy/cdk.json

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+{
+  "app": "npx ts-node --prefer-ts-exts bin/deploy.ts",
+  "watch": {
+    "include": [
+      "**"
+    ],
+    "exclude": [
+      "README.md",
+      "cdk*.json",
+      "**/*.d.ts",
+      "**/*.js",
+      "tsconfig.json",
+      "package*.json",
+      "yarn.lock",
+      "node_modules",
+      "test"
+    ]
+  },
+  "context": {
+    "@aws-cdk/aws-lambda:recognizeLayerVersion": true,
+    "@aws-cdk/core:checkSecretUsage": true,
+    "@aws-cdk/core:target-partitions": [
+      "aws",
+      "aws-cn"
+    ],
+    "@aws-cdk-containers/ecs-service-extensions:enableDefaultLogDriver": true,
+    "@aws-cdk/aws-ec2:uniqueImdsv2TemplateName": true,
+    "@aws-cdk/aws-ecs:arnFormatIncludesClusterName": true,
+    "@aws-cdk/aws-iam:minimizePolicies": true,
+    "@aws-cdk/core:validateSnapshotRemovalPolicy": true,
+    "@aws-cdk/aws-codepipeline:crossAccountKeyAliasStackSafeResourceName": true,
+    "@aws-cdk/aws-s3:createDefaultLoggingPolicy": true,
+    "@aws-cdk/aws-sns-subscriptions:restrictSqsDescryption": true,
+    "@aws-cdk/aws-apigateway:disableCloudWatchRole": true,
+    "@aws-cdk/core:enablePartitionLiterals": true,
+    "@aws-cdk/aws-events:eventsTargetQueueSameAccount": true,
+    "@aws-cdk/aws-iam:standardizedServicePrincipals": true,
+    "@aws-cdk/aws-ecs:disableExplicitDeploymentControllerForCircuitBreaker": true,
+    "@aws-cdk/aws-iam:importedRoleStackSafeDefaultPolicyName": true,
+    "@aws-cdk/aws-s3:serverAccessLogsUseBucketPolicy": true,
+    "@aws-cdk/aws-route53-patters:useCertificate": true,
+    "@aws-cdk/customresources:installLatestAwsSdkDefault": false,
+    "@aws-cdk/aws-rds:databaseProxyUniqueResourceName": true,
+    "@aws-cdk/aws-codedeploy:removeAlarmsFromDeploymentGroup": true,
+    "@aws-cdk/aws-apigateway:authorizerChangeDeploymentLogicalId": true,
+    "@aws-cdk/aws-ec2:launchTemplateDefaultUserData": true,
+    "@aws-cdk/aws-secretsmanager:useAttachedSecretResourcePolicyForSecretTargetAttachments": true,
+    "@aws-cdk/aws-redshift:columnId": true,
+    "@aws-cdk/aws-stepfunctions-tasks:enableEmrServicePolicyV2": true,
+    "@aws-cdk/aws-ec2:restrictDefaultSecurityGroup": true,
+    "@aws-cdk/aws-apigateway:requestValidatorUniqueId": true,
+    "@aws-cdk/aws-kms:aliasNameRef": true,
+    "@aws-cdk/aws-autoscaling:generateLaunchTemplateInsteadOfLaunchConfig": true,
+    "@aws-cdk/core:includePrefixInUniqueNameGeneration": true,
+    "@aws-cdk/aws-efs:denyAnonymousAccess": true,
+    "@aws-cdk/aws-opensearchservice:enableOpensearchMultiAzWithStandby": true,
+    "@aws-cdk/aws-lambda-nodejs:useLatestRuntimeVersion": true,
+    "@aws-cdk/aws-efs:mountTargetOrderInsensitiveLogicalId": true,
+    "@aws-cdk/aws-rds:auroraClusterChangeScopeOfInstanceParameterGroupWithEachParameters": true,
+    "@aws-cdk/aws-appsync:useArnForSourceApiAssociationIdentifier": true,
+    "@aws-cdk/aws-rds:preventRenderingDeprecatedCredentials": true,
+    "@aws-cdk/aws-codepipeline-actions:useNewDefaultBranchForCodeCommitSource": true,
+    "@aws-cdk/aws-cloudwatch-actions:changeLambdaPermissionLogicalIdForLambdaAction": true,
+    "@aws-cdk/aws-codepipeline:crossAccountKeysDefaultValueToFalse": true,
+    "@aws-cdk/aws-codepipeline:defaultPipelineTypeToV2": true,
+    "@aws-cdk/aws-kms:reduceCrossAccountRegionPolicyScope": true
+  }
+}

lib/workload/stateful/pieriandx_pipeline_dynamo_db/deploy/constants.ts

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+const ROOT_SSM_PARAMETER_PATH = '/umccr/orcabus/stateful/pieriandx_dynamodb';
+
+export const DYNAMODB_TABLE_ARN_SSM_PARAMETER_PATH = `${ROOT_SSM_PARAMETER_PATH}/analysis_table_arn`;
+export const DYNAMODB_TABLE_NAME_SSM_PARAMETER_PATH = `${ROOT_SSM_PARAMETER_PATH}/analysis_table_name`;
+
+export const DYNAMODB_TABLE_NAME = 'pierianDxAnalysesDynamoDBTable';

lib/workload/stateful/pieriandx_pipeline_dynamo_db/deploy/jest.config.js

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+module.exports = {
+  testEnvironment: 'node',
+  roots: ['<rootDir>/test'],
+  testMatch: ['**/*.test.ts'],
+  transform: {
+    '^.+\\.tsx?$': 'ts-jest'
+  }
+};

lib/workload/stateful/pieriandx_pipeline_dynamo_db/deploy/lib/pieriandx-dynamodb-stack.ts

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+import * as cdk from 'aws-cdk-lib';
+import { Construct } from 'constructs';
+// import * as sqs from 'aws-cdk-lib/aws-sqs';
+import * as dynamodb from 'aws-cdk-lib/aws-dynamodb';
+import { DYNAMODB_TABLE_ARN_SSM_PARAMETER_PATH, DYNAMODB_TABLE_NAME, DYNAMODB_TABLE_NAME_SSM_PARAMETER_PATH } from '../constants';
+import * as ssm from 'aws-cdk-lib/aws-ssm';
+
+
+export class PieriandxDynamodbStack extends cdk.Stack {
+
+  public readonly pieriandx_dynamodb_arn_ssm_parameter_path: string;
+  public readonly pieriandx_dynamodb_table_name_ssm_parameter_path: string;
+
+  constructor(scope: Construct, id: string, props?: cdk.StackProps) {
+    super(scope, id, props);
+
+    /*
+    Initialise dynamodb table, where portal_run_id is the primary sort key
+    */
+    const dynamodb_table = new dynamodb.TableV2(this, 'PierianDxDynamoDBTable', {
+      /* Either a db_uuid or an icav2 analysis id or a portal run id */
+      partitionKey: {
+        name: 'id',
+        type: dynamodb.AttributeType.STRING,
+      },
+      /* One of 'db_uuid', 'portal_run_id', 'case_id', 'case_accession_number', 'informaticsjob_id' */
+      sortKey: {
+        name: 'id_type',
+        type: dynamodb.AttributeType.STRING,
+      },
+      tableName: DYNAMODB_TABLE_NAME,
+    });
+
+    /*
+    Generate a ssm parameter to store the table arn so it can be referred to be other stacks
+    */
+    this.pieriandx_dynamodb_arn_ssm_parameter_path = new ssm.StringParameter(
+      this,
+      'PierianDxDynamoDBTableArn',
+      {
+        parameterName: DYNAMODB_TABLE_ARN_SSM_PARAMETER_PATH,
+        stringValue: dynamodb_table.tableArn,
+      }
+    ).parameterName;
+
+    this.pieriandx_dynamodb_table_name_ssm_parameter_path = new ssm.StringParameter(
+      this,
+      'PierianDxDynamoDBTableName',
+      {
+        parameterName: DYNAMODB_TABLE_NAME_SSM_PARAMETER_PATH,
+        stringValue: dynamodb_table.tableName,
+      }
+    ).parameterName;
+  }
+}

lib/workload/stateful/pieriandx_pipeline_dynamo_db/deploy/package.json

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+{
+  "name": "deploy",
+  "version": "0.1.0",
+  "bin": {
+    "deploy": "bin/deploy.js"
+  },
+  "scripts": {
+    "build": "tsc",
+    "watch": "tsc -w",
+    "test": "jest",
+    "cdk": "cdk"
+  },
+  "devDependencies": {
+    "@types/jest": "^29.5.12",
+    "@types/node": "20.11.30",
+    "jest": "^29.7.0",
+    "ts-jest": "^29.1.2",
+    "aws-cdk": "2.135.0",
+    "ts-node": "^10.9.2",
+    "typescript": "~5.4.3"
+  },
+  "dependencies": {
+    "aws-cdk-lib": "2.135.0",
+    "constructs": "^10.0.0",
+    "source-map-support": "^0.5.21"
+  }
+}

lib/workload/stateful/pieriandx_pipeline_dynamo_db/deploy/test/deploy.test.ts

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+// import * as cdk from 'aws-cdk-lib';
+// import { Template } from 'aws-cdk-lib/assertions';
+// import * as Deploy from '../lib/deploy-stack';
+
+// example test. To run these tests, uncomment this file along with the
+// example resource in lib/pieriandx-dynamodb-stack.ts
+test('SQS Queue Created', () => {
+//   const app = new cdk.App();
+//     // WHEN
+//   const stack = new Deploy.PieriandxDynamodbStack(app, 'MyTestStack');
+//     // THEN
+//   const template = Template.fromStack(stack);
+
+//   template.hasResourceProperties('AWS::SQS::Queue', {
+//     VisibilityTimeout: 300
+//   });
+});

lib/workload/stateful/pieriandx_pipeline_dynamo_db/deploy/tsconfig.json

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+{
+  "compilerOptions": {
+    "target": "ES2020",
+    "module": "commonjs",
+    "lib": [
+      "es2020",
+      "dom"
+    ],
+    "declaration": true,
+    "strict": true,
+    "noImplicitAny": true,
+    "strictNullChecks": true,
+    "noImplicitThis": true,
+    "alwaysStrict": true,
+    "noUnusedLocals": false,
+    "noUnusedParameters": false,
+    "noImplicitReturns": true,
+    "noFallthroughCasesInSwitch": false,
+    "inlineSourceMap": true,
+    "inlineSources": true,
+    "experimentalDecorators": true,
+    "strictPropertyInitialization": false,
+    "typeRoots": [
+      "./node_modules/@types"
+    ]
+  },
+  "exclude": [
+    "node_modules",
+    "cdk.out"
+  ]
+}