Refactored project setup on initial structure

* Changed CDK to be coded in TypeScript
* Followed CDK CodePipeline best practise and reference architecture
  by introducing concepts: workload, stateful, stateless, component
* Split CDK entry points: manual and self-mutating pipeline
* Initial mark up for unit tests structure for both TS/Py
  * deploy time code in TypeScript
  * run time code in Python

.eslintrc.json

@@ -0,0 +1,43 @@
+{
+  "env": {
+    "browser": true,
+    "es2021": true,
+    "node": true
+  },
+  "extends": [
+    "eslint:recommended",
+    "plugin:prettier/recommended",
+    "plugin:@typescript-eslint/recommended",
+    "prettier"
+  ],
+  "globals": {
+    "Atomics": "readonly",
+    "SharedArrayBuffer": "readonly"
+  },
+  "parser": "@typescript-eslint/parser",
+  "parserOptions": {
+    "ecmaVersion": "latest",
+    "sourceType": "module",
+    "ecmaFeatures": {
+      "jsx": true,
+      "restParams": true,
+      "spread": true
+    }
+  },
+  "plugins": ["prettier", "@typescript-eslint"],
+  "rules": {
+    "prettier/prettier": "error",
+    "react/react-in-jsx-scope": "off",
+    "react/jsx-filename-extension": [
+      1,
+      {
+        "extensions": [".js", ".jsx", ".ts", ".tsx"]
+      }
+    ]
+  },
+  "settings": {
+    "react": {
+      "version": "detect"
+    }
+  }
+}

.gitignore

@@ -1,30 +1,17 @@
 # Distribution / packaging
 .Python
-env/
-build/
+
 develop-eggs/
-dist/
-downloads/
 eggs/
 .eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
 venv/
 .venv/
+env/
 .env
 *.egg-info/
-.installed.cfg
 *.egg
 *__pycache__*
-lambdas/layers/**/*.zip
-
-# Serverless
-.aws-sam
-.serverless/
-node_modules/
+.pytest_cache/
 
 # IDE
 .idea
@@ -33,5 +20,15 @@ node_modules/
 
 # Environment files
 *.log
-/lambdas/layers/python/
-/cdk.out/
+**/layers/python/
+**/layers/**/*.zip
+
+*.js
+!jest.config.js
+*.d.ts
+node_modules
+
+# CDK asset staging directory
+.cdk.staging
+cdk.out/
+cdk.context.json

.npmignore

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

.prettierignore

@@ -0,0 +1,17 @@
+# See https://prettier.io/docs/en/ignore.html
+
+# Ignore artifacts:
+build
+coverage
+local_ignore
+bams
+vcfs
+
+# Ignore all HTML files:
+*.html
+
+.pre-commit-config.yaml
+buildspec.yml
+docker-compose.yml
+README.md
+start.sh

.prettierrc.json

@@ -0,0 +1,12 @@
+{
+  "arrowParens": "always",
+  "bracketSpacing": true,
+  "bracketSameLine": true,
+  "printWidth": 100,
+  "semi": true,
+  "singleQuote": true,
+  "jsxSingleQuote": true,
+  "tabWidth": 2,
+  "trailingComma": "es5",
+  "useTabs": false
+}

Makefile

@@ -1,17 +1,17 @@
+.PHONY: test
+
 install:
+	@yarn install
+	@find ./lib -name 'requirements.txt' -exec pip install -r {} \;
 	@pip install -r requirements-dev.txt
 	@pre-commit install
 
 check:
 	@pre-commit run --all-files
 
-run:
-	sam local invoke
-
 build:
-	for dir in $(shell find ./lambdas/layers -maxdepth 1 -mindepth 1 -type d -exec basename {} \;); do ./lambdas/layers/create_layer_package.sh $$dir; done
-	cdk synth
+	for dir in $(shell find ./lib/workload/stateless/layers -maxdepth 1 -mindepth 1 -type d -exec basename {} \;); do ./lib/workload/stateless/layers/create_layer_package.sh $$dir; done
 
-deploy: build
-	cdk deploy OrcaBus
-	cdk deploy OrcaBusSchemaStack
+test:
+	@yarn test
+	@pytest

README.md

@@ -2,95 +2,19 @@
 
 UMCCR Orchestration Bus that leverage AWS EventBridge as Event Bus to automate the BioInformatics Workflows Pipeline.
 
-## Quickstart
-
-### Pre-requisites
-
-```
-brew tap aws/tap
-brew install aws-sam-cli
-
-sam --version
-SAM CLI, version 1.43.0
-
-npm install -g aws-cdk
-
-cdk version
-2.19.0 (build e0d3e62)
-```
-
-### Pre-commit hooks
-
-We are using pre-commit hooks to check for any secret-key leaks and for linting purposes.
-Check [UMCCR wiki](https://github.com/umccr/wiki/blob/master/computing/dev-environment/git-hooks.md) for details.
-
-```
-brew install pre-commit detect-secrets
-
-pre-commit --version
-pre-commit 2.18.1
-
-detect-secrets --version
-1.2.0
-```
-
-### Development
-
-- Create Python environment; we recommend conda or mamba.
+## Development
 
 ```
 conda create -n orcabus python=3.9
 conda activate orcabus
 
-python -V
-Python 3.9.12
-
 make install
-make check
-make run
-```
+make test
 
-### Build & Deploy
-
-```
-make build
-cdk diff
-make deploy
+npx cdk list
+npx cdk synth OrcaBusStatefulStack
+npx cdk synth
+npx cdk diff
+npx cdk deploy OrcaBusStatefulStack
+npx cdk deploy --all
 ```
-
-## Current mock event handling
-
-The mock setup consists of two stacks:
-- oen to configure the event bus and event schemas used by the application
-- the other to manage the application itself
-
-The application is a series of Lambda function that produce/consume events from the event bus. Two Lambdas have a special role, as they provide the interface with external services (ICA ENS/WES).
-
-### Lambdas
-Functions to prepare WES workflow executions. These functions normally receive events from the orchestrator, signaling a specific state has been reached and further actions can be triggered
-- bcl_convert (prepare BCL Convert WES workflow)
-- dragen_wgs_qc (prepare DRAGEN WGS QC WES workflow)
-- dragen_wgs_somatic (prepare DRAGEN WGS SOMATIC WES workflow)
-
-Functions as interface to external services
-- ens_event_manager (manage events received by ICA ENS via SQS. Its job is to translate external events into internal ones, check event consistency/duplication and persist the current state)
-- wes_launcher (send WES execution requests to ICA. Its job to interface with the ICA WES service and launch requested WES workflows) NOTE: the mock version will instead send SQS formatted events directly to the ens_event_manager
-
-- orchestrator (manage and distribute events as needed, based on external triggers and internal state. Its job is to react to external events and decide which, if any, action to take)
-- gds_manager {file level event monitor; may not be needed if functionality is covered by ens_event_manager}
-
-Schemas:
-- SequenceRunStateChange (internal version of ENS `bssh.runs` events; represents a change in sequencing state; emitted by ens_event_manager)
-- WorkflowRunStateChange (internal version of ENS `wes.runs` events; represents a change in workflow state; emitted by ens_event_manager)
-- WesLaunchRequest (event to request a WES workflow launch; usually emitted by workflow prep lambdas)
-- WorkflowRequest (event to trigger a workflow prep lambda, may/may not result in WES workflow request)
-
-
-#### Layers
-Lambda layers are used to make common libs (like utils and schema) available to all Lambdas.
-
-
-## Possible next steps
-
-    1. Ask illumina to have a partner event source integration for ICA with AWS EventBridge. It would cleanup the microservices integration, for instance: instead of connecting SQS queues between accounts, providing an API abstraction that can be consumed/reused in multiple ways.
-    1. Add an extra target that dumps the GDS event in DynamoDB, perhaps a first step to get rid of the heavy Django ORM abstraction.

bin/orcabus.ts

@@ -0,0 +1,15 @@
+#!/usr/bin/env node
+import 'source-map-support/register';
+import * as cdk from 'aws-cdk-lib';
+import { OrcaBusStatelessStack } from '../lib/workload/orcabus-stateless-stack';
+import { OrcaBusStatefulStack } from '../lib/workload/orcabus-stateful-stack';
+
+const app = new cdk.App();
+
+new OrcaBusStatefulStack(app, 'OrcaBusStatefulStack', {
+  env: { account: process.env.CDK_DEFAULT_ACCOUNT, region: process.env.CDK_DEFAULT_REGION },
+});
+
+new OrcaBusStatelessStack(app, 'OrcaBusStatelessStack', {
+  env: { account: process.env.CDK_DEFAULT_ACCOUNT, region: process.env.CDK_DEFAULT_REGION },
+});

bin/pipeline.ts

@@ -0,0 +1 @@
+// TODO impl