Initialised the cttso launch v2 deployment service

lib/workload/stateless/cttso_v2_pipeline_manager/Readme.md

@@ -0,0 +1,170 @@
+# ctTSO v2 pipeline manager
+
+<!-- TOC -->
+* [ctTSO v2 pipeline manager](#cttso-v2-pipeline-manager)
+  * [Inputs](#inputs)
+    * [Example Input](#example-input)
+  * [Outputs](#outputs)
+  * [Lambdas in this directory](#lambdas-in-this-directory)
+    * [Get Cache and Output paths](#get-cache-and-output-paths)
+    * [Generate a trimmed samplesheet](#generate-a-trimmed-samplesheet)
+    * [Upload the samplesheet to the cache path](#upload-the-samplesheet-to-the-cache-path)
+    * [Generate a copy manifest](#generate-a-copy-manifest)
+    * [Launch the nextflow pipeline](#launch-the-nextflow-pipeline)
+  * [SSM Parameters](#ssm-parameters-)
+    * [External Parameters required by CDK](#external-parameters-required-by-cdk)
+<!-- TOC -->
+
+This AWS step functions performs the following actions
+
+* Copies a set of fastq files to a structured location (via the icav2 copy batch utility)
+* Uploads a samplesheet to the same structured location
+* Invokes the ctTSO v2 pipeline calling the structured location as the run folder
+
+![](./images/step_functions_image.png)
+
+## Inputs
+
+The AWS Step functions takes in the following parameters:
+
+* project_id
+* sample_id  (should match the sample_id in the samplesheet, ideally the lab metadata library id)
+* portal_run_id  (unique identifier for this step functions run and determines the data output location)
+* user_reference (an identifier for the run, can also be the same as the portal run id)
+* user_tags: (as a dict)
+  * subject_id
+  * library_id
+  * instrument_run_id
+  * project_owner
+  * project_name
+* technical_tags: 
+  * These are generated by the AWS Step functions and comprise the step_functions_execution_arn and the portal_run_id
+  * So should be left blank for now
+* samplesheet_b64gz: (a base64 encoded and gzipped samplesheet as a dictionary, this can be found as an output of the bssh_icav2_fastq_copy_manager step functions)
+* fastq_list_rows_b64gz: (a base64 encoded and gzipped list of fastq rows as a dictionary, this can be found as an output of the bssh_icav2_fastq_copy_manager step functions)
+  * This will use only the fastq files whose RGSM attribute match the sample id
+
+### Example Input
+
+```json
+{
+  "project_id": "7595e8f2-32d3-4c76-a324-c6a85dae87b5",
+  "sample_id": "L2301368",
+  "portal_run_id": "20240308abcd1234",
+  "user_reference": "PTC-ctTSO-v2-launch-test",
+  "user_tags": {
+    "subject_id": "SBJ04405",
+    "library_id": "L2301368",
+    "instrument_run_id": "231116_A01052_0172_BHVLM5DSX7",
+    "project_owner": "UMCCR",
+    "project_name": "testing"
+  },
+  "samplesheet_b64gz": "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",
+  "fastq_list_rows_b64gz": "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"
+}
+```
+
+## Outputs
+
+The AWS Step functions returns the following parameters:
+
+The analysis ID of the nextflow pipeline run launched by the step functions lambda 
+
+The CreateNextflowAnalysis submission as a JSON object for reproducibility
+
+```json
+{
+  "analysis_id": "3e17b6ff-ff63-43ab-ac15-e939e88932b6",
+  "analysis_launch_payload": {
+    "userReference": "PTC-ctTSO-v2-launch-test",
+    "pipelineId": "fdef5902-3f50-4ee7-ae17-15d38d4b489c",
+    "tags": {
+      "technicalTags": [
+        "portal_run_id=20240308abcd1234",
+        "step_functions_execution_arn=93f7c69b-66eb-4890-8eb4-298ec3b36d37"
+      ],
+      "userTags": [
+        "subject_id=SBJ04405",
+        "library_id=L2301368",
+        "instrument_run_id=231116_A01052_0172_BHVLM5DSX7",
+        "project_owner=UMCCR",
+        "project_name=testing"
+      ],
+      "referenceTags": []
+    },
+    "analysisInput": {
+      "inputs": [
+        {
+          "parameterCode": "run_folder",
+          "dataIds": [
+            "fol.58422302edd141213e0f08dc3cace45e"
+          ]
+        },
+        {
+          "parameterCode": "sample_sheet",
+          "dataIds": [
+            "fil.94813f45b9e94977b0a308dc388cf24f"
+          ]
+        }
+      ],
+      "parameters": [
+        {
+          "code": "StartsFromFastq",
+          "value": "true"
+        },
+        {
+          "code": "sample_pair_ids",
+          "multiValue": [
+            "L2301368"
+          ]
+        }
+      ]
+    },
+    "activationCodeDetailId": "7f03a57e-2cfc-4b35-9cbb-d19e6ce9984b",
+    "analysisStorageId": "3fab13dd-46e7-4b54-bb34-b80a01a99379",
+    "outputParentFolderId": null,
+    "analysisOutput": [
+      {
+        "sourcePath": "out/",
+        "targetProjectId": "7595e8f2-32d3-4c76-a324-c6a85dae87b5",
+        "targetPath": "/ilmn_cttso_fastq_cache/20240308abcd1234/",
+        "type": "FOLDER"
+      }
+    ]
+  }
+}
+```
+
+## Lambdas in this directory
+
+### Get Cache and Output paths
+
+Combine the root cache and root output ssm parameters with the portal run id submitted in the inputs
+
+### Generate a trimmed samplesheet
+
+Generate a samplesheet that only has the TSO500L sections and only for the sample_id submitted in the inputs
+
+### Upload the samplesheet to the cache path
+
+Upload the samplesheet dict as a samplesheet csv to the cache path
+
+### Generate a copy manifest
+
+Generate a copy manifest for submissions to the icav2 copy batch utility
+
+### Launch the nextflow pipeline
+
+Take the fastq output locations, samplesheet location and metadata generated in the inputs and run the launch nextflow object.
+
+## SSM Parameters 
+
+### External Parameters required by CDK
+
+```
+/icav2/umccr-prod/service-user-trial-jwt-token-secret-arn
+/icav2_copy_batch_utility/state_machine_arn
+/icav2/umccr-prod/cache_project_cttso_fastq_path
+/icav2/umccr-prod/output_project_cttso_fastq_path
+/icav2/umccr-prod/tso500_ctdna_2.1_pipeline_id
+```

lib/workload/stateless/cttso_v2_pipeline_manager/deploy/.gitignore

@@ -0,0 +1,8 @@
+*.js
+!jest.config.js
+*.d.ts
+node_modules
+
+# CDK asset staging directory
+.cdk.staging
+cdk.out

lib/workload/stateless/cttso_v2_pipeline_manager/deploy/.npmignore

@@ -0,0 +1,6 @@
+*.ts
+!*.d.ts
+
+# CDK asset staging directory
+.cdk.staging
+cdk.out

lib/workload/stateless/cttso_v2_pipeline_manager/deploy/README.md

@@ -0,0 +1,14 @@
+# 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/stateless/cttso_v2_pipeline_manager/deploy/bin/deploy.ts

@@ -0,0 +1,20 @@
+#!/usr/bin/env node
+import 'source-map-support/register';
+import * as cdk from 'aws-cdk-lib';
+import { ctTSOV2LaunchStateMachineStack } from '../lib/stacks/cttso_v2_launch_stack';
+import {
+  ICAV2_COPY_BATCH_UTILITY_STATE_MACHINE_ARN_SSM_PARAMETER_PATH,
+  ICAV2_JWT_SECRET_ARN_SSM_PARAMETER_PATH,
+  SSM_PARAMETER_LIST_FOR_CTTSO_LAUNCH_LAMBDAS,
+} from '../constants';
+
+const app = new cdk.App();
+new ctTSOV2LaunchStateMachineStack(app, 'ctTSOv2LaunchStatemachineStack', {
+  icav2_jwt_ssm_parameter_path: ICAV2_JWT_SECRET_ARN_SSM_PARAMETER_PATH,
+  ssm_parameter_list: SSM_PARAMETER_LIST_FOR_CTTSO_LAUNCH_LAMBDAS,
+  icav2_copy_batch_utility_state_machine_ssm_parameter_path: ICAV2_COPY_BATCH_UTILITY_STATE_MACHINE_ARN_SSM_PARAMETER_PATH,
+  env: {
+    account: process.env.CDK_DEFAULT_ACCOUNT,
+    region: process.env.CDK_DEFAULT_REGION
+  },
+});

lib/workload/stateless/cttso_v2_pipeline_manager/deploy/cdk.json

@@ -0,0 +1,65 @@
+{
+  "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
+  }
+}

lib/workload/stateless/cttso_v2_pipeline_manager/deploy/constants.ts

@@ -0,0 +1,17 @@
+
+export const DYNAMODB_ARN_SSM_PARAMETER_PATH = "/umccr/orcabus/stateful/cttso_v2_pipeline_dynamo_db/analysis_table_arn"
+
+export const CTTSO_CACHE_ROOT_SSM_PARAMETER_PATH = "/icav2/umccr-prod/cache_project_cttso_fastq_path"
+export const CTTSO_OUTPUT_ROOT_SSM_PARAMETER_PATH = "/icav2/umccr-prod/output_project_cttso_fastq_path"
+
+export const ICAV2_JWT_SECRET_ARN_SSM_PARAMETER_PATH = "/icav2/umccr-prod/service-user-trial-jwt-token-secret-arn"
+export const ICAV2_COPY_BATCH_UTILITY_STATE_MACHINE_ARN_SSM_PARAMETER_PATH = "/icav2_copy_batch_utility/state_machine_arn"
+export const PIPELINE_ID_SSM_PARAMETER_PATH = "/icav2/umccr-prod/tso500_ctdna_2.1_pipeline_id"
+
+
+export const SSM_PARAMETER_LIST_FOR_CTTSO_LAUNCH_LAMBDAS = [
+    CTTSO_CACHE_ROOT_SSM_PARAMETER_PATH,
+    CTTSO_OUTPUT_ROOT_SSM_PARAMETER_PATH,
+    ICAV2_JWT_SECRET_ARN_SSM_PARAMETER_PATH,
+    PIPELINE_ID_SSM_PARAMETER_PATH
+]

lib/workload/stateless/cttso_v2_pipeline_manager/deploy/jest.config.js

@@ -0,0 +1,8 @@
+module.exports = {
+  testEnvironment: 'node',
+  roots: ['<rootDir>/test'],
+  testMatch: ['**/*.test.ts'],
+  transform: {
+    '^.+\\.tsx?$': 'ts-jest'
+  }
+};