@quiltdata/benchling-webhook 0.5.4 → 0.6.1-20251104T043302Z

package/README.md

@@ -7,26 +7,65 @@ Connects Benchling lab notebook entries to Quilt data packages via webhooks.
 - `npx` from Node.js 18+ ([download](https://nodejs.org))
 - [AWS credentials](https://docs.aws.amazon.com/cli/v1/userguide/cli-configure-files.html) configured
 - Existing [Quilt deployment](https://www.quilt.bio/install)
+- Benchling tenant with OAuth app configured
 
 ## Setup
 
 ### 1. Create Benchling App
 
 ```bash
-npx @quiltdata/benchling-webhook manifest
+npx @quiltdata/benchling-webhook@latest manifest
 ```
 
 Follow the displayed instructions to [upload the manifest](https://docs.benchling.com/docs/getting-started-benchling-apps#creating-an-app-from-a-manifest) to Benchling and get your App Definition ID.
 
-### 2. Deploy to AWS
+### 2. Store Benchling Secrets in AWS Secrets Manager
+
+Create a secret in AWS Secrets Manager with your Benchling credentials:
+
+```bash
+aws secretsmanager create-secret \
+  --name benchling-webhook-credentials \
+  --description "Benchling OAuth credentials" \
+  --secret-string '{
+    "client_id": "your-benchling-client-id",
+    "client_secret": "your-benchling-client-secret",
+    "tenant": "your-tenant",
+    "app_definition_id": "your-app-definition-id"
+  }'
+```
+
+> **Note**: The secret must contain `client_id`, `client_secret`, and `tenant`. The `app_definition_id` is optional but recommended.
+
+### 3. Deploy to AWS (Secrets-Only Mode - v0.6.0+)
+
+**Recommended: Secrets-Only Mode** - Minimal configuration, all settings resolved from AWS:
 
 ```bash
-npx @quiltdata/benchling-webhook
+npx @quiltdata/benchling-webhook@latest deploy \
+  --quilt-stack-arn "arn:aws:cloudformation:us-east-1:123456789012:stack/QuiltStack/abc123" \
+  --benchling-secret "benchling-webhook-credentials"
 ```
 
-The interactive wizard will auto-detect or request configuration information, deploy to AWS, and test the webhook automatically.
+That's it! The deployment automatically resolves:
 
-### 3. Install in Benchling
+- Quilt catalog URL from your stack
+- S3 bucket configuration
+- Athena database name
+- SQS queue ARN
+- AWS region and account
+
+**Alternative: Legacy Mode** - For existing deployments or manual configuration:
+
+```bash
+npx @quiltdata/benchling-webhook@latest deploy \
+  --benchling-secrets @benchling-secrets.json \
+  --catalog your-catalog.quiltdata.com
+```
+
+**See [Secrets Configuration Guide](./docs/SECRETS_CONFIGURATION.md) and [Migration Guide](./docs/MIGRATION_GUIDE_V06.md) for more options**
+
+### 4. Install in Benchling
 
 After deployment, you'll receive a webhook URL. Set it in your Benchling app settings and [install the app](https://docs.benchling.com/docs/getting-started-benchling-apps#installing-your-app) in your tenant.
 
@@ -34,12 +73,173 @@ After deployment, you'll receive a webhook URL. Set it in your Benchling app set
 
 In Benchling: Create entry → Insert Canvas → "Quilt Integration" → Create/Update package
 
+## Configuration
+
+### Deployment Modes (v0.6.0+)
+
+#### Secrets-Only Mode (Recommended)
+
+The simplest deployment method - just provide two parameters:
+
+```bash
+npx @quiltdata/benchling-webhook@latest deploy \
+  --quilt-stack-arn "arn:aws:cloudformation:region:account:stack/QuiltStack/id" \
+  --benchling-secret "my-secret-name"
+```
+
+**Benefits**:
+
+- ✅ Minimal configuration - only 2 parameters needed
+- ✅ Centralized secrets in AWS Secrets Manager
+- ✅ Automatic configuration resolution from CloudFormation
+- ✅ No manual parameter updates when infrastructure changes
+- ✅ Better security - no secrets in CI/CD pipelines
+
+**How to find your Quilt Stack ARN**:
+
+```bash
+# List your CloudFormation stacks
+aws cloudformation describe-stacks --query 'Stacks[?contains(StackName, `Quilt`)].StackId'
+
+# Or from the AWS Console → CloudFormation → Stack Details → Stack info → ARN
+```
+
+#### Legacy Mode
+
+For existing deployments or manual configuration:
+
+```bash
+# Option 1: Inline JSON
+npx @quiltdata/benchling-webhook@latest deploy \
+  --benchling-secrets '{"client_id":"xxx","client_secret":"yyy","tenant":"company"}' \
+  --catalog your-catalog.quiltdata.com
+
+# Option 2: JSON File
+npx @quiltdata/benchling-webhook@latest deploy \
+  --benchling-secrets @benchling-secrets.json \
+  --catalog your-catalog.quiltdata.com
+
+# Option 3: AWS Secrets Manager ARN
+npx @quiltdata/benchling-webhook@latest deploy \
+  --benchling-secrets "arn:aws:secretsmanager:region:account:secret:name" \
+  --catalog your-catalog.quiltdata.com
+```
+
+**📖 [Complete Configuration Guide](./docs/SECRETS_CONFIGURATION.md)**
+**📖 [Migration Guide to v0.6.0](./docs/MIGRATION_GUIDE_V06.md)**
+
+### Secret Format
+
+**Required fields**:
+
+- `client_id`: Benchling OAuth client ID
+- `client_secret`: Benchling OAuth client secret
+- `tenant`: Benchling tenant name (e.g., "company" for company.benchling.com)
+
+**Optional fields**:
+
+- `app_definition_id`: Benchling app definition ID
+- `api_url`: Custom Benchling API URL
+
+**Example**:
+
+```json
+{
+  "client_id": "abc123",
+  "client_secret": "secret_key",
+  "tenant": "mycompany",
+  "app_definition_id": "app_def_123"
+}
+```
+
+### Updating Secrets
+
+To update Benchling credentials after deployment:
+
+**Method 1: Update in AWS Secrets Manager (Recommended)**
+
+```bash
+aws secretsmanager update-secret \
+  --secret-id benchling-webhook/credentials \
+  --secret-string '{"client_id":"new_id","client_secret":"new_secret","tenant":"company"}'
+
+# Restart ECS service to pick up changes
+aws ecs update-service \
+  --cluster benchling-webhook-cluster \
+  --service benchling-webhook-service \
+  --force-new-deployment
+```
+
+**Method 2: Redeploy Stack**
+
+```bash
+npx @quiltdata/benchling-webhook@latest deploy \
+  --benchling-secrets @updated-secrets.json
+```
+
+## All Available Commands
+
 For all available commands, run:
 
 ```bash
-npx @quiltdata/benchling-webhook --help
+npx @quiltdata/benchling-webhook@latest --help
 ```
 
+### Commands
+
+- `deploy` - Deploy the CDK stack to AWS (default command)
+- `init` - Initialize configuration interactively
+- `validate` - Validate configuration without deploying
+- `test` - Test the deployed webhook endpoint
+- `manifest` - Generate Benchling app manifest file
+
+### Deploy Options
+
+```bash
+npx @quiltdata/benchling-webhook@latest deploy [options]
+```
+
+**Secrets-Only Mode (v0.6.0+ - Recommended)**:
+
+- `--quilt-stack-arn <arn>` - ARN of Quilt CloudFormation stack
+- `--benchling-secret <name>` - Name or ARN of Benchling secret in Secrets Manager
+
+**Legacy Mode Configuration**:
+
+- `--benchling-secrets <value>` - Benchling secrets (ARN, JSON, or @file)
+- `--catalog <url>` - Quilt catalog URL
+- `--bucket <name>` - S3 bucket for data
+
+**AWS Configuration**:
+
+- `--profile <name>` - AWS profile to use
+- `--region <region>` - AWS region to deploy to (auto-detected in secrets-only mode)
+- `--image-tag <tag>` - Docker image tag to deploy (default: latest)
+
+**Deployment Options**:
+
+- `--env-file <path>` - Path to .env file (default: .env)
+- `--yes` - Skip confirmation prompts
+- `--no-bootstrap-check` - Skip CDK bootstrap verification
+- `--require-approval <level>` - CDK approval level (default: never)
+
+### Deprecated Parameters (v0.6.0+)
+
+> ⚠️ **Warning**: The following parameters are deprecated and will be removed in v1.0.0
+
+- `--tenant` - Use `--benchling-secrets` or secrets-only mode instead
+- `--client-id` - Use `--benchling-secrets` or secrets-only mode instead
+- `--client-secret` - Use `--benchling-secrets` or secrets-only mode instead
+- `--app-id` - Use `--benchling-secrets` or secrets-only mode instead
+
+**Migration guide**: See [Migration Guide to v0.6.0](./docs/MIGRATION_GUIDE_V06.md)
+
+## Documentation
+
+- 📖 [Secrets Configuration Guide](./docs/SECRETS_CONFIGURATION.md) - Comprehensive secrets management documentation
+- 📖 [Architecture Decision Record: Secrets Management](./docs/ADR-001-SECRETS-MANAGEMENT.md) - Design decisions and rationale
+- 📖 [CHANGELOG.md](./CHANGELOG.md) - Version history and release notes
+
 ## Development
 
 For local development and contributing:
@@ -47,16 +247,99 @@ For local development and contributing:
 ```bash
 git clone https://github.com/quiltdata/benchling-webhook.git
 cd benchling-webhook
-npm install
 
-# Test CLI locally (note the -- separator for passing args)
-npm run cli -- --help
-npm run cli -- deploy
+# Install dependencies and configure (interactive)
+npm run setup
+
+# Build package
+npm run build
+```
+
+### Testing Workflow
+
+```bash
+# 1. Run unit tests (lint + typecheck + mocked tests)
+npm run test
+
+# 2. Run local integration tests (builds Docker, uses real Benchling payloads)
+npm run test:local
+
+# 3. Run remote integration tests (deploys dev stack, tests through API Gateway)
+npm run test:remote
 
-npm test    # Run tests
-npm run build    # Build package
+# Individual test commands
+npm run test:ts          # TypeScript tests only
+npm run test:python      # Python unit tests only
+npm run build:typecheck  # Type checking only
+npm run lint             # Linting only
 ```
 
+### Release Workflow
+
+```bash
+# Create and push version tag (triggers release pipeline)
+npm run release:tag
+
+# CI will run:
+# - npm run test:remote (builds dev image, deploys dev stack, tests)
+# - npm run release (promotes to production after tests pass)
+```
+
+## Troubleshooting
+
+### Common Issues
+
+**Error: "Invalid secret ARN format"**
+
+- Verify ARN format: `arn:aws:secretsmanager:region:account:secret:name`
+- See [Troubleshooting Guide](./docs/SECRETS_CONFIGURATION.md#troubleshooting)
+
+**Error: "Missing required field: client_id"**
+
+- Check secret JSON includes all required fields: `client_id`, `client_secret`, `tenant`
+- Validate JSON syntax: `echo '{"client_id":"..."}' | jq .`
+
+**Deprecation Warning**
+
+- Migrate to `--benchling-secrets` parameter
+- See [Migration Guide](./docs/SECRETS_CONFIGURATION.md#migration-guide)
+
+**For more help**: See [Secrets Configuration - Troubleshooting](./docs/SECRETS_CONFIGURATION.md#troubleshooting)
+
+## Security
+
+- Secrets are stored in AWS Secrets Manager with encryption at rest
+- Secrets are masked in all CLI output
+- CloudFormation parameters use `noEcho: true`
+- IAM policies grant least-privilege access
+- CloudTrail logs all secret access for audit
+
+**Best Practices**:
+
+- Never commit secrets to version control
+- Use AWS Secrets Manager for production deployments
+- Rotate secrets regularly
+- Review IAM policies periodically
+
+**For detailed security guidance**: See [Secrets Configuration - Security](./docs/SECRETS_CONFIGURATION.md#security-best-practices)
+
+## Support
+
+- 🐛 [Report Issues](https://github.com/quiltdata/benchling-webhook/issues)
+- 📧 Security vulnerabilities: <security@quiltdata.com>
+- 📖 [Documentation](./docs/)
+- 💬 [Discussions](https://github.com/quiltdata/benchling-webhook/discussions)
+
 ## License
 
 Apache-2.0
+
+## Version
+
+See [CHANGELOG.md](./CHANGELOG.md) for version history.
+
+**Important:** Always use `@latest` with npx to avoid caching issues:
+
+```bash
+npx @quiltdata/benchling-webhook@latest --help
+```

package/dist/bin/benchling-webhook.d.ts

@@ -43,7 +43,7 @@ export declare function checkCdkBootstrap(account: string, region: string): Prom
 export declare function inferConfiguration(catalogUrl: string): Promise<InferenceResult>;
 /**
  * Create CDK app and stack (synthesis only, no deployment)
- * Pure function - returns app and stack objects
+ * Secrets-only mode (v0.6.0+) - requires QUILT_STACK_ARN and BENCHLING_SECRET
  */
 export declare function createStack(config: Config): DeploymentResult;
 export { inferStackConfig };

package/dist/bin/benchling-webhook.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"benchling-webhook.d.ts","sourceRoot":"","sources":["../../bin/benchling-webhook.ts"],"names":[],"mappings":";AACA,OAAO,eAAe,CAAC;AACvB,OAAO,KAAK,GAAG,MAAM,aAAa,CAAC;AACnC,OAAO,EAAE,qBAAqB,EAAE,MAAM,gCAAgC,CAAC;AAEvE,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,qBAAqB,CAAC;AAIlD,QAAA,MAAQ,gBAAgB,KAA4B,CAAC;AAErD;;GAEG;AACH,MAAM,WAAW,eAAe;IAC9B,YAAY,EAAE,OAAO,CAAC;IACtB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B,GAAG,EAAE,GAAG,CAAC,GAAG,CAAC;IACb,KAAK,EAAE,qBAAqB,CAAC;IAC7B,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED;;GAEG;AACH,MAAM,WAAW,eAAe;IAC9B,OAAO,EAAE,OAAO,CAAC;IACjB,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACrC,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED;;;GAGG;AACH,wBAAsB,iBAAiB,CACnC,OAAO,EAAE,MAAM,EACf,MAAM,EAAE,MAAM,GACf,OAAO,CAAC,eAAe,CAAC,CAsC1B;AAED;;;GAGG;AACH,wBAAsB,kBAAkB,CAAC,UAAU,EAAE,MAAM,GAAG,OAAO,CAAC,eAAe,CAAC,CAoBrF;AAED;;;GAGG;AACH,wBAAgB,WAAW,CAAC,MAAM,EAAE,MAAM,GAAG,gBAAgB,CAuB5D;AAuKD,OAAO,EAAE,gBAAgB,EAAE,CAAC"}

package/dist/bin/benchling-webhook.js

@@ -107,7 +107,7 @@ async function inferConfiguration(catalogUrl) {
 }
 /**
  * Create CDK app and stack (synthesis only, no deployment)
- * Pure function - returns app and stack objects
+ * Secrets-only mode (v0.6.0+) - requires QUILT_STACK_ARN and BENCHLING_SECRET
  */
 function createStack(config) {
     const app = new cdk.App();
@@ -116,16 +116,9 @@ function createStack(config) {
             account: config.cdkAccount,
             region: config.cdkRegion,
         },
-        bucketName: config.quiltUserBucket,
-        queueArn: config.queueArn,
-        environment: "production",
-        prefix: config.pkgPrefix || "benchling",
-        benchlingClientId: config.benchlingClientId,
-        benchlingClientSecret: config.benchlingClientSecret,
-        benchlingTenant: config.benchlingTenant,
-        quiltCatalog: config.quiltCatalog,
-        quiltDatabase: config.quiltDatabase,
-        webhookAllowList: config.webhookAllowList,
+        // Secrets-only mode parameters (v0.6.0+)
+        quiltStackArn: config.quiltStackArn,
+        benchlingSecret: config.benchlingSecret,
         logLevel: config.logLevel || "INFO",
         createEcrRepository: config.createEcrRepository === "true",
         ecrRepositoryName: config.ecrRepositoryName || "quiltdata/benchling",
@@ -241,23 +234,20 @@ async function legacyMain() {
     else {
         console.log(`✓ CDK is bootstrapped (CDKToolkit stack: ${bootstrapStatus.status})\n`);
     }
-    // Create stack
+    // Create stack - Secrets-only mode (v0.6.0+)
     const app = new cdk.App();
+    // Get parameters from environment (set by CLI deploy command)
+    // These take precedence over legacy config
+    const quiltStackArn = process.env.QUILT_STACK_ARN || config.QUILT_STACK_ARN;
+    const benchlingSecret = process.env.BENCHLING_SECRET || config.BENCHLING_SECRET;
     new benchling_webhook_stack_1.BenchlingWebhookStack(app, "BenchlingWebhookStack", {
         env: {
             account: config.CDK_DEFAULT_ACCOUNT,
             region: config.CDK_DEFAULT_REGION,
         },
-        bucketName: config.QUILT_USER_BUCKET, // User's data bucket
-        queueArn: config.QUEUE_ARN,
-        environment: "production",
-        prefix: config.PKG_PREFIX || "benchling",
-        benchlingClientId: config.BENCHLING_CLIENT_ID,
-        benchlingClientSecret: config.BENCHLING_CLIENT_SECRET,
-        benchlingTenant: config.BENCHLING_TENANT,
-        quiltCatalog: config.QUILT_CATALOG,
-        quiltDatabase: config.QUILT_DATABASE,
-        webhookAllowList: config.WEBHOOK_ALLOW_LIST,
+        // Secrets-only mode parameters (v0.6.0+)
+        quiltStackArn: quiltStackArn,
+        benchlingSecret: benchlingSecret,
         logLevel: config.LOG_LEVEL || "INFO",
         // ECR repository configuration
         createEcrRepository: config.CREATE_ECR_REPOSITORY === "true",

package/dist/bin/benchling-webhook.js.map

@@ -1 +1 @@
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+{"version":3,"file":"benchling-webhook.js","sourceRoot":"","sources":["../../bin/benchling-webhook.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AA6CA,8CAyCC;AAMD,gDAoBC;AAMD,kCAuBC;AA5ID,yBAAuB;AACvB,iDAAmC;AACnC,4EAAuE;AACvE,iDAAyC;AAGzC,mCAAmC;AACnC,iEAAiE;AACjE,MAAM,EAAE,gBAAgB,EAAE,GAAG,OAAO,CAAC,cAAc,CAAC,CAAC;AA2S5C,4CAAgB;AA3QzB;;;GAGG;AACI,KAAK,UAAU,iBAAiB,CACnC,OAAe,EACf,MAAc;IAEd,IAAI,CAAC;QACD,MAAM,MAAM,GAAG,IAAA,wBAAQ,EACnB,+CAA+C,MAAM,6EAA6E,EAClI,EAAE,QAAQ,EAAE,OAAO,EAAE,CACxB,CAAC;QAEF,MAAM,WAAW,GAAG,MAAM,CAAC,IAAI,EAAE,CAAC;QAElC,IACI,WAAW,CAAC,QAAQ,CAAC,gBAAgB,CAAC;YAC5C,WAAW,CAAC,QAAQ,CAAC,iBAAiB,CAAC,EACnC,CAAC;YACC,OAAO;gBACH,YAAY,EAAE,KAAK;gBACnB,OAAO,EAAE,uCAAuC,OAAO,cAAc,MAAM,EAAE;gBAC7E,OAAO,EAAE,2BAA2B,OAAO,IAAI,MAAM,EAAE;aAC1D,CAAC;QACN,CAAC;QAED,IAAI,CAAC,WAAW,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC;YACpC,OAAO;gBACH,YAAY,EAAE,IAAI;gBAClB,MAAM,EAAE,WAAW;gBACnB,OAAO,EAAE,iCAAiC,WAAW,qCAAqC;aAC7F,CAAC;QACN,CAAC;QAED,OAAO;YACH,YAAY,EAAE,IAAI;YAClB,MAAM,EAAE,WAAW;SACtB,CAAC;IACN,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACb,OAAO;YACH,YAAY,EAAE,KAAK;YACnB,OAAO,EAAE,0CAA2C,KAAe,CAAC,OAAO,EAAE;SAChF,CAAC;IACN,CAAC;AACL,CAAC;AAED;;;GAGG;AACI,KAAK,UAAU,kBAAkB,CAAC,UAAkB;IACvD,IAAI,CAAC;QACL,gBAAgB;QACZ,MAAM,aAAa,GAAG,UAAU,CAAC,UAAU,CAAC,MAAM,CAAC;YAC/C,CAAC,CAAC,UAAU;YACZ,CAAC,CAAC,WAAW,UAAU,EAAE,CAAC;QAE9B,MAAM,MAAM,GAAG,MAAM,gBAAgB,CAAC,aAAa,CAAC,CAAC;QAErD,OAAO;YACH,OAAO,EAAE,IAAI;YACb,YAAY,EAAE,MAAM,CAAC,YAAY;SACpC,CAAC;IACN,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACb,OAAO;YACH,OAAO,EAAE,KAAK;YACd,YAAY,EAAE,EAAE;YAChB,KAAK,EAAG,KAAe,CAAC,OAAO;SAClC,CAAC;IACN,CAAC;AACL,CAAC;AAED;;;GAGG;AACH,SAAgB,WAAW,CAAC,MAAc;IACtC,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,GAAG,EAAE,CAAC;IAE1B,MAAM,KAAK,GAAG,IAAI,+CAAqB,CAAC,GAAG,EAAE,uBAAuB,EAAE;QAClE,GAAG,EAAE;YACD,OAAO,EAAE,MAAM,CAAC,UAAU;YAC1B,MAAM,EAAE,MAAM,CAAC,SAAS;SAC3B;QACD,yCAAyC;QACzC,aAAa,EAAE,MAAM,CAAC,aAAc;QACpC,eAAe,EAAE,MAAM,CAAC,eAAgB;QACxC,QAAQ,EAAE,MAAM,CAAC,QAAQ,IAAI,MAAM;QACnC,mBAAmB,EAAE,MAAM,CAAC,mBAAmB,KAAK,MAAM;QAC1D,iBAAiB,EAAE,MAAM,CAAC,iBAAiB,IAAI,qBAAqB;QACpE,QAAQ,EAAE,MAAM,CAAC,QAAQ,IAAI,QAAQ;KACxC,CAAC,CAAC;IAEH,OAAO;QACH,GAAG;QACH,KAAK;QACL,SAAS,EAAE,KAAK,CAAC,SAAS;QAC1B,OAAO,EAAE,KAAK,CAAC,OAAO;KACzB,CAAC;AACN,CAAC;AAED;;;;GAIG;AACH,KAAK,UAAU,eAAe;IAC1B,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC;IAC5B,IAAI,WAAW,GAA2B,EAAE,CAAC;IAE7C,sEAAsE;IACtE,IAAI,OAAO,CAAC,aAAa,EAAE,CAAC;QACxB,IAAI,CAAC;YACD,OAAO,CAAC,GAAG,CAAC,yCAAyC,OAAO,CAAC,aAAa,EAAE,CAAC,CAAC;YAC9E,MAAM,MAAM,GAAG,MAAM,gBAAgB,CACjC,WAAW,OAAO,CAAC,aAAa,CAAC,OAAO,CAAC,cAAc,EAAE,EAAE,CAAC,EAAE,CACjE,CAAC;YACF,WAAW,GAAG,MAAM,CAAC,YAAY,CAAC;YAClC,OAAO,CAAC,GAAG,CAAC,+CAA+C,CAAC,CAAC;QACjE,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACb,OAAO,CAAC,KAAK,CACT,wDAAyD,KAAe,CAAC,OAAO,EAAE,CACrF,CAAC;YACF,OAAO,CAAC,KAAK,CAAC,+CAA+C,CAAC,CAAC;QACnE,CAAC;IACL,CAAC;IAED,wDAAwD;IACxD,MAAM,MAAM,GAAG,EAAE,GAAG,WAAW,EAAE,GAAG,OAAO,EAAE,CAAC;IAE9C,yCAAyC;IACzC,MAAM,gBAAgB,GAAG;QACrB,eAAe;QACf,mBAAmB;QACnB,qBAAqB;QACrB,yBAAyB;QACzB,kBAAkB;KACrB,CAAC;IAEF,MAAM,WAAW,GAAG,gBAAgB,CAAC,MAAM,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC;IAE3E,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACzB,OAAO,CAAC,KAAK,CAAC,gDAAgD,CAAC,CAAC;QAChE,WAAW,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE;YAC5B,OAAO,CAAC,KAAK,CAAC,OAAO,OAAO,EAAE,CAAC,CAAC;QACpC,CAAC,CAAC,CAAC;QACH,OAAO,CAAC,KAAK,CAAC,iDAAiD,CAAC,CAAC;QACjE,OAAO,CAAC,KAAK,CAAC,gCAAgC,CAAC,CAAC;QAChD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IACpB,CAAC;IAED,uCAAuC;IACvC,MAAM,oBAAoB,GAAG;QACzB,qBAAqB;QACrB,oBAAoB;QACpB,WAAW;QACX,gBAAgB;KACnB,CAAC;IAEF,MAAM,mBAAmB,GAAG,oBAAoB,CAAC,MAAM,CACnD,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAChC,CAAC;IAEF,IAAI,mBAAmB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACjC,OAAO,CAAC,KAAK,CAAC,gDAAgD,CAAC,CAAC;QAChE,mBAAmB,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE;YACpC,OAAO,CAAC,KAAK,CAAC,OAAO,OAAO,EAAE,CAAC,CAAC;QACpC,CAAC,CAAC,CAAC;QACH,OAAO,CAAC,KAAK,CACT,0EAA0E,CAC7E,CAAC;QACF,OAAO,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC;QAChC,OAAO,CAAC,KAAK,CAAC,qCAAqC,CAAC,CAAC;QACrD,OAAO,CAAC,KAAK,CAAC,gEAAgE,CAAC,CAAC;QAChF,OAAO,CAAC,KAAK,CAAC,iDAAiD,CAAC,CAAC;QACjE,OAAO,CAAC,KAAK,CAAC,uEAAuE,CAAC,CAAC;QACvF,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IACpB,CAAC;IAED,qCAAqC;IACrC,MAAM,uBAAuB,GAAG;QAC5B,kBAAkB;QAClB,qBAAqB;QACrB,yBAAyB;QACzB,6BAA6B;KACvB,CAAC;IAEX,MAAM,gBAAgB,GAAG,uBAAuB,CAAC,MAAM,CACnD,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAC5B,CAAC;IAEF,IAAI,gBAAgB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC9B,OAAO,CAAC,KAAK,CACT,mEAAmE,CACtE,CAAC;QACF,gBAAgB,CAAC,OAAO,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,OAAO,KAAK,EAAE,CAAC,CAAC,CAAC;QACnE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IACpB,CAAC;IAED,OAAO,MAAM,CAAC;AAClB,CAAC;AAED;;;GAGG;AACH,KAAK,UAAU,UAAU;IACrB,MAAM,MAAM,GAAG,MAAM,eAAe,EAAE,CAAC;IAEvC,kBAAkB;IAClB,MAAM,eAAe,GAAG,MAAM,iBAAiB,CAC/C,MAAM,CAAC,mBAAoB,EAC3B,MAAM,CAAC,kBAAmB,CACzB,CAAC;IAEF,IAAI,CAAC,eAAe,CAAC,YAAY,EAAE,CAAC;QAChC,OAAO,CAAC,KAAK,CAAC,yBAAyB,CAAC,CAAC;QACzC,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC,CAAC;QAC9B,OAAO,CAAC,KAAK,CAAC,eAAe,CAAC,OA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package/dist/bin/cdk-dev.js

@@ -230,13 +230,69 @@ async function main() {
 
   await waitForWorkflow(commitSha);
 
-  // 5. Deploy CDK stack with CI-built image tag
+  // 5. Deploy CDK stack with CI-built image tag using secrets-only mode
   console.log('');
-  console.log(`Step 5: Deploying CDK stack with CI-built image...`);
+  console.log(`Step 5: Deploying CDK stack with CI-built image (secrets-only mode)...`);
   process.chdir(path.join(__dirname, '..'));
   // Use the full version with timestamp (without 'v' prefix)
   const imageTag = devTag.replace(/^v/, '');
-  run(`npm run cli -- --image-tag ${imageTag} --yes`);
+
+  // Secrets-only mode parameters
+  const quiltStackArn = 'arn:aws:cloudformation:us-east-1:712023778557:stack/quilt-staging/e51b0c10-10c9-11ee-9b41-12fda87498a3';
+  const benchlingSecret = 'benchling-webhook-dev';
+
+  run(`npm run deploy:prod -- --quilt-stack-arn ${quiltStackArn} --benchling-secret ${benchlingSecret} --image-tag ${imageTag} --yes`);
+
+  // 6. Get and store the deployment endpoint
+  console.log('');
+  console.log('Step 6: Retrieving deployment endpoint...');
+
+  try {
+    const { CloudFormationClient, DescribeStacksCommand } = require('@aws-sdk/client-cloudformation');
+    const os = require('os');
+
+    const cloudformation = new CloudFormationClient({ region: 'us-east-1' });
+    const command = new DescribeStacksCommand({ StackName: 'BenchlingWebhookStack' });
+    const response = await cloudformation.send(command);
+
+    if (response.Stacks && response.Stacks.length > 0) {
+      const stack = response.Stacks[0];
+      const endpointOutput = stack.Outputs?.find(o => o.OutputKey === 'WebhookEndpoint');
+      const webhookUrl = endpointOutput?.OutputValue || '';
+
+      if (webhookUrl) {
+        // Store endpoint in XDG config
+        const configDir = path.join(os.homedir(), '.config', 'benchling-webhook');
+        const deployJsonPath = path.join(configDir, 'deploy.json');
+
+        // Read existing deploy.json or create new one
+        let deployConfig = {};
+        if (fs.existsSync(deployJsonPath)) {
+          deployConfig = JSON.parse(fs.readFileSync(deployJsonPath, 'utf8'));
+        }
+
+        // Update dev section
+        deployConfig.dev = {
+          endpoint: webhookUrl,
+          imageTag: imageTag,
+          deployedAt: new Date().toISOString(),
+          stackName: 'BenchlingWebhookStack'
+        };
+
+        // Ensure config directory exists
+        if (!fs.existsSync(configDir)) {
+          fs.mkdirSync(configDir, { recursive: true });
+        }
+
+        // Write deploy.json
+        fs.writeFileSync(deployJsonPath, JSON.stringify(deployConfig, null, 2));
+        console.log(`✅ Stored deployment endpoint in ${deployJsonPath}`);
+        console.log(`   Endpoint: ${webhookUrl}`);
+      }
+    }
+  } catch (error) {
+    console.warn(`⚠️  Could not retrieve/store deployment endpoint: ${error.message}`);
+  }
 
   console.log('');
   console.log('✅ Development deployment complete!');

package/dist/bin/cli.js

@@ -11,6 +11,7 @@ const init_1 = require("./commands/init");
 const validate_1 = require("./commands/validate");
 const test_1 = require("./commands/test");
 const manifest_1 = require("./commands/manifest");
+const setup_wizard_1 = require("./commands/setup-wizard");
 // Load package.json for version
 // eslint-disable-next-line @typescript-eslint/no-require-imports
 const pkg = require("../package.json");
@@ -24,19 +25,29 @@ program
 program
     .command("deploy", { isDefault: true })
     .description("Deploy the CDK stack to AWS")
-    .option("--catalog <url>", "Quilt catalog URL")
-    .option("--bucket <name>", "S3 bucket for data")
-    .option("--tenant <name>", "Benchling tenant")
-    .option("--client-id <id>", "Benchling OAuth client ID")
-    .option("--client-secret <secret>", "Benchling OAuth client secret")
-    .option("--app-id <id>", "Benchling app definition ID")
+    .option("--quilt-stack-arn <arn>", "ARN of Quilt CloudFormation stack")
+    .option("--benchling-secret <name>", "Name or ARN of Benchling secret in Secrets Manager (defaults to package name)", "@quiltdata/benchling-webhook")
     .option("--env-file <path>", "Path to .env file", ".env")
+    // Common options
     .option("--no-bootstrap-check", "Skip CDK bootstrap verification")
     .option("--require-approval <level>", "CDK approval level", "never")
     .option("--profile <name>", "AWS profile to use")
     .option("--region <region>", "AWS region to deploy to")
     .option("--image-tag <tag>", "Docker image tag to deploy (default: latest)")
     .option("--yes", "Skip confirmation prompts")
+    .addHelpText("after", `
+Examples:
+  Deploy with default secret name:
+    $ npx @quiltdata/benchling-webhook deploy \\
+        --quilt-stack-arn "arn:aws:cloudformation:us-east-1:123456789012:stack/QuiltStack/abc123"
+
+  Deploy with custom secret name:
+    $ npx @quiltdata/benchling-webhook deploy \\
+        --quilt-stack-arn "arn:aws:cloudformation:us-east-1:123456789012:stack/QuiltStack/abc123" \\
+        --benchling-secret "my-benchling-credentials"
+
+For more information: https://github.com/quiltdata/benchling-webhook#deployment
+`)
     .action(async (options) => {
     try {
         await (0, deploy_1.deployCommand)(options);
@@ -106,9 +117,16 @@ program
         process.exit(1);
     }
 });
-// Show help when no command provided
+// Run setup wizard when no command provided
 if (!process.argv.slice(2).length) {
-    program.outputHelp();
+    (0, setup_wizard_1.setupWizardCommand)()
+        .then(() => process.exit(0))
+        .catch((error) => {
+        console.error(chalk_1.default.red(error.message));
+        process.exit(1);
+    });
+}
+else {
+    program.parse();
 }
-program.parse();
 //# sourceMappingURL=cli.js.map

package/dist/bin/cli.js.map

@@ -1 +1 @@
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package/dist/bin/commands/deploy.d.ts

@@ -1,7 +1,11 @@
-import { type ConfigOptions } from "../../lib/utils/config";
-export declare function deployCommand(options: ConfigOptions & {
+export declare function deployCommand(options: {
     yes?: boolean;
     bootstrapCheck?: boolean;
     requireApproval?: string;
+    quiltStackArn?: string;
+    benchlingSecret?: string;
+    imageTag?: string;
+    region?: string;
+    envFile?: string;
 }): Promise<void>;
 //# sourceMappingURL=deploy.d.ts.map

package/dist/bin/commands/deploy.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"deploy.d.ts","sourceRoot":"","sources":["../../../bin/commands/deploy.ts"],"names":[],"mappings":"AAaA,wBAAsB,aAAa,CAAC,OAAO,EAAE;IAAE,GAAG,CAAC,EAAE,OAAO,CAAC;IAAC,cAAc,CAAC,EAAE,OAAO,CAAC;IAAC,eAAe,CAAC,EAAE,MAAM,CAAC;IAAC,aAAa,CAAC,EAAE,MAAM,CAAC;IAAC,eAAe,CAAC,EAAE,MAAM,CAAC;IAAC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IAAC,OAAO,CAAC,EAAE,MAAM,CAAA;CAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAgCzO"}