@quiltdata/benchling-webhook 0.4.13

package/AGENTS.md

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+# Benchling Webhook Integration - Complete Guide
+
+Complete deployment and operational guide for the Benchling webhook integration with Quilt.
+
+## Architecture Overview
+
+This AWS CDK application deploys a highly available, auto-scaling webhook processor using:
+
+- **Amazon API Gateway** → Routes HTTPS webhooks with IP-based access control
+- **Application Load Balancer (ALB)** → Distributes traffic across container instances
+- **AWS Fargate on Amazon ECS** → Runs containerized webhook processor (auto-scales 2-10 tasks)
+- **Amazon S3** → Stores webhook payloads and package data
+- **Amazon SQS** → Queues package creation requests for Quilt
+- **AWS Secrets Manager** → Securely stores Benchling OAuth credentials
+- **Amazon CloudWatch** → Provides centralized logging and monitoring
+- **AWS IAM** → Enforces least-privilege access controls
+
+**Request Flow:** Benchling → API Gateway → ALB → Fargate (Flask app) → S3 + SQS
+
+### Code Organization
+
+- **Infrastructure (CDK)**: `bin/` and `lib/` contain TypeScript CDK code for AWS deployment
+  - `lib/benchling-webhook-stack.ts` - Main stack orchestrating all components
+  - `lib/fargate-service.ts` - ECS Fargate service running Flask in Docker
+  - `lib/alb-api-gateway.ts` - API Gateway with HTTP integration to ALB
+  - `lib/ecr-repository.ts` - Docker image repository
+- **Application (Python)**: `docker/` contains Flask webhook processor
+  - See [docker/README.md](docker/README.md) for application development
+
+## Prerequisites
+
+- **AWS Account** with appropriate IAM permissions
+- **AWS CLI** v2.x configured with credentials
+- **Node.js** >= 18.0.0
+- **Docker** for container builds
+- **Quilt Stack** deployed with S3 bucket and SQS queue configured
+- **Benchling Account** with app creation permissions
+
+## Installation
+
+### 1. Clone and Install
+
+```bash
+git clone https://github.com/quiltdata/benchling-webhook.git
+cd benchling-webhook
+npm install
+```
+
+### 2. Configure Environment
+
+#### Option A: Auto-infer from Quilt Catalog (Recommended)
+
+If you have an existing Quilt deployment, you can automatically infer most configuration values:
+
+```bash
+# Infer config from your Quilt catalog
+npm run get-env -- https://quilt-catalog.yourcompany.com --write
+
+# Review the generated env.inferred file
+cat env.inferred
+
+# Copy to .env and fill in Benchling credentials
+cp env.inferred .env
+# Then edit .env to add your Benchling-specific values
+```
+
+The script will:
+
+- Fetch `config.json` from your Quilt catalog
+- Query AWS CloudFormation to find your Quilt stack
+- Extract bucket names, queue names, region, and account ID
+- Generate a `.env.inferred` file with pre-filled AWS/Quilt configuration
+
+**Note:** You'll still need to manually add Benchling credentials (tenant, client ID, client secret, etc.).
+
+#### Option B: Manual Configuration
+
+```bash
+cp env.template .env
+```
+
+Edit `.env` with your configuration:
+
+**Required Variables** (you must provide these):
+
+| Variable | Description |
+|----------|-------------|
+| `QUILT_CATALOG` | Quilt catalog URL (e.g., `quilt-catalog.yourcompany.com`) |
+| `QUILT_USER_BUCKET` | Your S3 bucket for Benchling exports |
+| `BENCHLING_TENANT` | Benchling subdomain (e.g., `myorg` from `myorg.benchling.com`) |
+| `BENCHLING_CLIENT_ID` | OAuth client ID from Benchling app |
+| `BENCHLING_CLIENT_SECRET` | OAuth client secret from Benchling app |
+| `BENCHLING_APP_DEFINITION_ID` | App definition ID for webhook verification |
+
+**Auto-Inferred Variables** (automatically determined from your Quilt catalog):
+
+| Variable | How It's Inferred |
+|----------|-------------------|
+| `CDK_DEFAULT_ACCOUNT` | From AWS STS (your current account) |
+| `CDK_DEFAULT_REGION` | From catalog config.json |
+| `QUEUE_NAME` | From Quilt stack outputs |
+| `SQS_QUEUE_URL` | From Quilt stack outputs |
+| `QUILT_DATABASE` | From Quilt stack outputs |
+
+**Optional Variables** (have sensible defaults):
+
+| Variable | Default | Description |
+|----------|---------|-------------|
+| `PKG_PREFIX` | `benchling` | Quilt package name prefix |
+| `PKG_KEY` | `experiment_id` | Metadata key for linking entries to packages |
+| `LOG_LEVEL` | `INFO` | Logging level (DEBUG, INFO, WARNING, ERROR, CRITICAL) |
+| `ENABLE_WEBHOOK_VERIFICATION` | `true` | Verify webhook signatures |
+| `WEBHOOK_ALLOW_LIST` | (empty) | Comma-separated IP allowlist |
+| `ECR_REPOSITORY_NAME` | `quiltdata/benchling` | Custom ECR repo name |
+
+See [doc/PARAMETERS.md](doc/PARAMETERS.md) for complete reference.
+
+### 3. Deploy Infrastructure
+
+```bash
+# Bootstrap CDK (first time only)
+source .env
+npx cdk bootstrap aws://$CDK_DEFAULT_ACCOUNT/$CDK_DEFAULT_REGION
+
+# Deploy stack
+npm run deploy
+```
+
+The webhook URL will be saved to `.env.deploy`:
+
+```bash
+WEBHOOK_ENDPOINT=https://abc123.execute-api.us-east-1.amazonaws.com/prod
+```
+
+## Post-Deployment Configuration
+
+### Configure Benchling App
+
+1. **Create App**: Benchling → Developer Console → Apps → Create app → From manifest
+2. **Upload Manifest**: Use `app-manifest.yaml` from this repository
+3. **Set Credentials**: Create Client Secret → Copy ID and Secret to `.env`
+4. **Configure Webhook**: Overview → Webhook URL → Paste URL from `.env.deploy`
+5. **Install App**: Version History → Install → Activate
+6. **Grant Permissions**: Tenant Admin → Organizations → Apps → Add app → Set role to Admin
+
+### Verify Deployment
+
+```bash
+# Health check
+source .env.deploy
+curl $WEBHOOK_ENDPOINT/health
+
+# Monitor logs
+aws logs tail /ecs/benchling-webhook --follow
+```
+
+## Usage
+
+1. **Create Entry** in Benchling notebook
+2. **Insert Canvas** → Select "Quilt Integration"
+3. **Create Package** → Generates versioned Quilt package
+4. **Add Files** → Attach experimental data
+5. **Update Package** → Creates new version with attachments
+
+## Development
+
+### Common Commands
+
+**Development:**
+- `npm run build` - Compile TypeScript
+- `npm run test` - Run Jest tests
+- `npm run lint` - Apply ESLint
+
+**Deployment:**
+- `npm run deploy` - Test + deploy (outputs to `.env.deploy`)
+- `npm run docker-push` - Build and push Docker images
+- `npm run docker-check` - Validate Docker images
+- `npm run release` - Create production release
+
+**Python App:**
+- See [docker/README.md](docker/README.md) or run `make help` in docker/ directory
+
+### Coding Style
+
+- **TypeScript**: 4-space indent, double quotes, trailing commas, required semicolons
+- **Types**: Avoid `any` in production; explicit return types on exports
+- **Organization**: Separate CDK constructs in `lib/`; application code in `docker/`
+
+### Commits & PRs
+
+- Use Conventional Commits: `type(scope): summary`
+- Keep commits focused; update `package-lock.json` when needed
+- Include test results and deployment considerations in PRs
+
+## Security Best Practices
+
+- OAuth credentials stored in AWS Secrets Manager
+- IP-based access control via API Gateway resource policies
+- Container images scanned for vulnerabilities via Amazon ECR
+- IAM roles follow least-privilege principle
+- All traffic encrypted in transit (TLS 1.2+)
+- CloudWatch logs encrypted at rest
+
+## Monitoring & Troubleshooting
+
+### Monitoring
+
+- **CloudWatch Logs**: `/ecs/benchling-webhook`
+- **ECS Task Metrics**: CPU, memory, task count
+- **API Gateway Metrics**: Request count, latency, 4XX/5XX errors
+- **ALB Target Health**: Monitor unhealthy targets
+
+### Health Endpoints
+
+- `/health` - General health check
+- `/health/ready` - Readiness probe
+
+### Debugging
+
+- **Deployment**: Check `.env.deploy` for outputs
+- **Logs**: `npm run logs` or `aws logs tail /ecs/benchling-webhook --follow`
+- **Events**: `npm run event` to send test events
+
+## License
+
+Apache-2.0 - See [LICENSE](LICENSE) file for details

package/CHANGELOG.md

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+<!-- markdownlint-disable MD024 -->
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## [Unreleased]
+
+## [0.4.13] - 2025-10-28
+
+### Changed
+
+- **Simplified configuration**: Auto-infer AWS and Quilt config from catalog at deployment time
+- **Reduced required .env variables**: From 20+ to just 6 (catalog URL, user bucket, 4 Benchling credentials)
+- **Renamed `BUCKET_NAME` → `QUILT_USER_BUCKET`**: Clearer distinction between user data bucket and Quilt system buckets
+- **Added CDK bootstrap validation**: Fails fast with helpful error if account/region not bootstrapped
+- **Made LOG_LEVEL configurable**: Override default INFO level for production debugging
+
+### Removed
+
+- Unused environment variables: `BENCHLING_API_KEY`, `PKG_BUCKET_ONLY`, `PREFIX`, `STAGE`, `FLASK_ENV`
+
+### Fixed
+
+- Module import issue: CLI argument parsing now only runs when executed directly, not on import
+
+## [0.4.12] - 2025-10-27
+
+### Added
+
+- Dev release workflow with timestamped pre-release tags for testing CI/CD pipeline
+
+### Changed
+
+- Refactored release script to separate version bumping from tag creation
+- version.js now outputs just the version number when called with no arguments
+
+## [0.4.11] - 2025-10-27
+
+### Added
+
+- Version synchronization test to ensure package.json, docker/pyproject.toml, and docker/app-manifest.yaml remain in sync
+- app-manifest.yaml now published as GitHub release asset for Benchling App installations
+
+### Fixed
+
+- Version bump script (bin/version.js) now updates all three version files instead of just package.json
+- `docker-validate` target now validates ECR repository is publicly accessible without authentication
+- `docker-validate` reads Docker image URI from `cdk-outputs.json` instead of requiring version parameter
+- `docker-validate` will fail if repository requires authentication, ensuring public access is maintained
+
+## [0.4.10] - 2025-10-27
+
+### Added
+
+- Canvas error notification section to display warnings and errors to users
+- Athena permissions (StartQueryExecution, GetQueryExecution, GetQueryResults) to ECS task role
+- Glue Data Catalog permissions for Athena queries
+- S3 permissions for Athena query results bucket
+- Test event file for Athena access denied scenario
+
+### Fixed
+
+- Canvas now displays error notifications instead of failing silently when PackageQuery encounters AWS permission issues
+- Improved error messages for Athena AccessDeniedException with actionable guidance
+
+## [0.4.9] - 2025-10-27
+
+### Added
+
+- Integrated release workflow into CI pipeline for automated GitHub releases, Docker image publishing, and NPM package publishing
+- Support for both production and pre-release (dev) versions
+
+### Changed
+
+- Updated Python to 3.14 in CI workflows
+- Updated aws-actions/configure-aws-credentials to v5
+- Updated actions/setup-python to v6
+- Streamlined release process with automated tagging and publishing
+
+## [0.4.8] - 2025-10-27
+
+### Changed
+
+- **Infrastructure Migration** - Migrated from Lambda to Docker/Fargate for improved scalability and resource management
+- **Improved Deployment** - Streamlined Docker-based deployment workflow with health checks and automated verification
+- **Enhanced Testing** - Added comprehensive test commands for local development and CI/CD workflows
+
+### Fixed
+
+- Resolved CloudFormation deployment conflicts during stack updates
+- Ensured ECR repository exists before Docker push in CI

package/LICENSE

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package/README.benchling.md

@@ -0,0 +1,77 @@
+# **Connecting a Webhook to Benchling via an App**
+
+This guide walks you through integrating an **existing webhook** with Benchling by creating a **Benchling App** and subscribing to events.
+
+---
+
+## **1. Prerequisites**
+
+Before proceeding, ensure you have:
+
+- **Benchling Tenant Admin Access**: Permissions to create and manage apps.
+- **A Public HTTPS Endpoint**: Your webhook URL that can receive POST requests.
+- **API Credentials** (if required for authentication).
+
+---
+
+## **2. Creating a Benchling App**
+
+Benchling requires an **app** to manage webhook subscriptions. Follow these steps to create one.
+
+### **Step 1: Access the Developer Console**
+
+1. **Log in to Benchling**.
+2. **Navigate to the Developer Console**:
+   - Click on your **profile icon** (lower-left corner).
+   - Select **"Feature Settings"**.
+   - Click on **"Developer Console"**.
+
+### **Step 2: Create a New App**
+
+1. In the **"Apps"** section, click **"Create app"**.
+2. Choose **"From scratch"**.
+3. Provide the following details:
+   - **Name**: A short label (e.b., "entry-webhook").
+   - **Description**: A brief summary of the app's purpose.
+4. Leave it as Private, or make Public.
+5. Click **"Create"**.
+
+---
+
+## **3. Configuring the Webhook Subscription**
+
+Now, configure the app to send data to your webhook.
+
+### **Step 1: Define Event Subscriptions**
+
+1. In the app's settings, find "Webhook URL" (under Overview -> Global Information).
+2. Click the edit icon
+3. Paste in your webhook URL.
+4. Click checkmark to save.
+
+NOTE: Enter the top-level endpoint; Benchling will send to the appropriate
+path underneath that:
+
+- assayRun: /event
+- configuration: /lifecycle
+- canvas: /canvas
+- entry: /event
+- request: /event
+- workflow: /event
+
+### **Step 2: Webhook Testing**
+
+1. Go to the **"Webhook Testing"** tab.
+2. Under "**Preview**", select one of the "/event" options.
+3. Click **"Send Test"**.
+4. Confirm that the "**Test**" tab shows "Success"
+5. Verify that a package was properly created.
+
+### **Step 3: Add App To Your Tenant**
+
+1. Go back to Home (the Benchling jellyfish logo in the upper right).
+2. Go to the Tenant Admin Console (from your profile icon).
+3. Select your organization.
+4. Select Apps under your organization (NOT from your Tenant)
+
+---

package/README.md

@@ -0,0 +1,53 @@
+# Benchling Webhook Integration for Quilt
+
+Connects Benchling lab notebook entries to Quilt data packages via webhooks.
+
+## Quick Install
+
+**Prerequisites:** AWS account, Node.js 18+, Docker, existing Quilt deployment
+
+```bash
+# 1. Clone and install
+git clone https://github.com/quiltdata/benchling-webhook.git
+cd benchling-webhook
+npm install
+
+# 2. Configure minimal .env
+cp env.template .env
+# Edit .env to set:
+# - QUILT_CATALOG=quilt-catalog.yourcompany.com
+# - QUILT_USER_BUCKET=your-data-bucket
+# - Benchling credentials (5 values)
+# Everything else is auto-inferred at deploy time!
+
+# 3. Deploy
+source .env
+npx cdk bootstrap aws://$CDK_DEFAULT_ACCOUNT/$CDK_DEFAULT_REGION  # first time only
+npm run deploy
+
+# 4. Configure Benchling app
+# - Create app from app-manifest.yaml
+# - Set webhook URL from .env.deploy
+# - Install and activate
+
+# 5. Verify
+source .env.deploy
+curl $WEBHOOK_ENDPOINT/health
+```
+
+## Usage
+
+1. Create entry in Benchling
+2. Insert Canvas → "Quilt Integration"
+3. Click "Create" to make package
+4. Add files and click "Update package"
+
+## Documentation
+
+- [AGENTS.md](AGENTS.md) - Complete deployment guide, architecture, configuration
+- [docker/README.md](docker/README.md) - Development workflows
+- [doc/RELEASE.md](doc/RELEASE.md) - Release process
+
+## License
+
+Apache-2.0