@quiltdata/benchling-webhook 0.5.4 → 0.6.0

package/env.template

@@ -1,66 +1,79 @@
-# ==============================================================================
-# REQUIRED USER VALUES
-# ==============================================================================
-# These are the ONLY values you need to provide. Everything else is inferred
-# from your Quilt catalog configuration at deployment time.
+#
+# ALWAYS REQUIRED PARAMETERS
+#
 
-# ==============================================================================
-# Quilt Configuration
-# ==============================================================================
+# --- Benchling OAuth Configuration ---
+# Tenant: Use XXX if you login at XXX.benchling.com
+BENCHLING_TENANT=your-tenant
 
-# Your Quilt catalog URL (just the domain, without https://)
-QUILT_CATALOG=quilt-catalog.yourcompany.com
+# OAuth credentials from your Benchling app
+BENCHLING_CLIENT_ID=your-client-id
+BENCHLING_CLIENT_SECRET=your-client-secret
 
-# The S3 bucket where you want to store Benchling exports
-# This is YOUR data bucket, not the Quilt system buckets
-QUILT_USER_BUCKET=your-data-bucket
+# App definition ID from Benchling app manifest
+BENCHLING_APP_DEFINITION_ID=appdef_your_id_here
 
-# ==============================================================================
-# Benchling Configuration
-# ==============================================================================
-# BENCHLING_TENANT: Use XXX if you login to Benchling at XXX.benchling.com
+# S3 bucket for storing Benchling exports (YOUR data bucket)
+BENCHLING_PKG_BUCKET=your-data-bucket # (without s3:// prefix)
 
-BENCHLING_TENANT=your-tenant
-BENCHLING_APP_DEFINITION_ID=appdef_your_id_here
-BENCHLING_CLIENT_ID=your-client-id
-BENCHLING_CLIENT_SECRET=your-client-secret
+#
+# POSSIBLY REQUIRED PARAMETERS
+#
 
-# BENCHLING_API_KEY=your-api-key  # not currently used
+QUILT_CATALOG=quilt-stack.your-company.com
+# Required UNLESS available from 'quilt3 config'
 
-# ==============================================================================
-# OPTIONAL VALUES (Override defaults if needed)
-# ==============================================================================
+BENCHLING_TEST_ENTRY=etr_123456789
+# Actual entry ID from your tenant, needed to run integration tests
 
+#
+# Optional PARAMETERS
+#
 
-# Package Configuration
-PKG_PREFIX=benchling   # Prefix for Quilt package names (e.g., "benchling/my-experiment")
-PKG_KEY=experiment_id  # Metadata key used to link Benchling entries to packages
+# --- Package Configuration ---
+# Prefix for Quilt package names (e.g., "benchling/my-experiment")
+BENCHLING_PKG_PREFIX=benchling
 
+# Metadata key to link Benchling entries to packages
+BENCHLING_PKG_KEY=experiment_id
 
-# Webhook Security
-ENABLE_WEBHOOK_VERIFICATION=true  # Set to false ONLY for local development
 
-# Logging (optional - defaults to INFO)
-# LOG_LEVEL=DEBUG  # Options: DEBUG, INFO, WARNING, ERROR, CRITICAL
+# --- Application Configuration (Required) ---
+# Logging level: DEBUG, INFO, WARNING, ERROR, CRITICAL
+BENCHLING_LOG_LEVEL=INFO
 
-# Test Configuration (for running tests)
-BENCHLING_TEST_ENTRY=etr_123456789
+# Enable/disable webhook signature verification (true/false)
+BENCHLING_ENABLE_WEBHOOK_VERIFICATION=true
 
-# Ngrok Configuration (optional - for local development)
-# Get your authtoken from: https://dashboard.ngrok.com/get-started/your-authtoken
-# NGROK_AUTHTOKEN=your_ngrok_authtoken_here
-# NGROK_DOMAIN=your-subdomain.ngrok-free.app
+# Comma-separated list of allowed source IPs (leave empty to allow all)
+# Example: 34.216.192.90,34.217.183.162
+BENCHLING_WEBHOOK_ALLOW_LIST=
 
 # ==============================================================================
-# AUTOMATICALLY INFERRED VALUES
+# NOTES
 # ==============================================================================
-# The following values are automatically inferred from your Quilt catalog
-# at deployment time via bin/get-env.js:
 #
-# - CDK_DEFAULT_ACCOUNT    (from AWS STS)
-# - CDK_DEFAULT_REGION     (from catalog config)
-# - QUEUE_ARN              (from Quilt stack outputs)
-# - QUILT_DATABASE         (from Quilt stack outputs)
+# Quick Start:
+#   1. Copy this file to .env: cp env.template .env
+#   2. Fill in BENCHLING_* variables (section 2)
+#   3. Create secret: npm run config
+#   4. Fill in QuiltStackARN (section 1)
+#   5. Deploy: npm run deploy
+#
+# Configuration at Runtime:
+#   The deployed stack resolves ALL configuration from just 2 sources:
+#   - QuiltStackARN → gets Quilt catalog, database, SQS queue from CloudFormation
+#   - BenchlingSecret → gets all Benchling credentials and app config from Secrets Manager
+#
+#   No other environment variables are needed for production deployment.
+#
+# Local Development:
+#   For testing locally without AWS:
+#   - make -C docker run-local   (starts Flask with mocked AWS)
+#   - make -C docker test-local  (runs tests against local server)
+#
+# For More Information:
+#   - See docs/PARAMETERS.md for parameter reference
+#   - See README.md for complete setup guide
+#   - Run: npm run cli -- --help
 #
-# You do NOT need to set these unless you want to override the inferred values.
-# ==============================================================================

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@quiltdata/benchling-webhook",
-  "version": "0.5.4",
+  "version": "0.6.0",
   "description": "AWS CDK deployment for Benchling webhook processing using Fargate - Deploy directly with npx",
   "main": "dist/lib/index.js",
   "types": "dist/lib/index.d.ts",
@@ -14,32 +14,29 @@
     "benchling-webhook": "./dist/bin/cli.js"
   },
   "scripts": {
-    "clean": "rm -rf cdk.out */{*.js,*.d.ts}",
-    "test": "npm run typecheck && npm run test:ts && npm run test:python",
-    "test-ci": "npm run typecheck && npm run test:ts",
-    "typecheck": "tsc --noEmit",
-    "test:ts": "NODE_ENV=test TMPDIR=./.tmp node --max-old-space-size=4096 ./node_modules/.bin/jest",
-    "test:python": "make -C docker test-unit",
-    "cdk": "npm run test && npm run cli -- --yes",
-    "cdk:dev": "node bin/cdk-dev.js",
-    "lint": "eslint . --ext .ts --fix",
     "build": "tsc",
+    "build:clean": "rm -rf cdk.out dist */{*.js,*.d.ts}",
+    "build:synth": "npx cdk synth",
+    "build:typecheck": "tsc --noEmit",
+    "cli": "node dist/bin/cli.js",
+    "lint": "eslint . --ext .ts --fix && make -C docker lint",
     "prebuild": "rm -rf dist",
+    "prepublishOnly": "npm run build",
     "postbuild": "chmod +x dist/bin/cli.js && cp bin/*.js dist/bin/ 2>/dev/null || true",
-    "cli": "ts-node bin/cli.ts",
-    "synth": "npx cdk synth",
-    "logs": "node bin/check-logs.js",
-    "event": "node bin/send-event.js",
-    "check": "npm run cdk && npm run event && sleep 45 && npm run logs",
-    "docker:test": "make -C docker test",
-    "docker-push": "make -C docker push-local",
-    "docker-check": "make -C docker docker-validate",
-    "release": "npm run test && node bin/release.js",
-    "release:dev": "npm run test && node bin/release.js dev",
-    "notes": "bin/release-notes.sh \"$(jq -r .version package.json)\" \"712023778557.dkr.ecr.us-east-1.amazonaws.com/quiltdata/benchling:$(jq -r .version package.json)\" \"false\" \"$(jq -r .name package.json)\"",
-    "version": "node bin/version.js patch",
-    "version:patch": "npm run version -- patch",
-    "prepublishOnly": "npm run build"
+    "release": "npm run test && node bin/release.js && make -C docker push-ci",
+    "release:dev": "npm run test && node bin/cdk-dev.js",
+    "release:tag": "node bin/version.js && git push --tags",
+    "setup": "ts-node scripts/install-wizard.ts",
+    "setup:health": "ts-node scripts/config-health-check.ts",
+    "setup:infer": "ts-node scripts/infer-quilt-config.ts",
+    "setup:sync-secrets": "ts-node scripts/sync-secrets.ts",
+    "test": "npm run build:typecheck && npm run test:ts && npm run test:python",
+    "test:ci": "npm run build:typecheck && npm run test:ts",
+    "test:local": "make -C docker build && make -C docker test-local",
+    "test:python": "make -C docker test-unit",
+    "test:remote": "npm run release:dev && make -C docker test-deployed-dev",
+    "test:ts": "cross-env NODE_ENV=test jest --maxWorkers=50%",
+    "version": "node bin/version.js"
   },
   "keywords": [
     "benchling",
@@ -67,8 +64,10 @@
     "@typescript-eslint/eslint-plugin": "^8.26.1",
     "@typescript-eslint/parser": "^8.26.1",
     "aws-cdk": "2.1031.1",
+    "aws-sdk-client-mock": "^4.1.0",
+    "cross-env": "^10.1.0",
     "dotenv": "^17.2.3",
-    "esbuild": "0.25.11",
+    "esbuild": "0.25.12",
     "eslint": "^9.22.0",
     "globals": "^16.0.0",
     "jest": "^30.0.0",
@@ -79,7 +78,13 @@
   "dependencies": {
     "@aws-sdk/client-cloudformation": "^3.920.0",
     "@aws-sdk/client-s3": "^3.758.0",
+    "@aws-sdk/client-secrets-manager": "^3.922.0",
+    "@aws-sdk/client-sts": "^3.922.0",
+    "@aws-sdk/credential-providers": "^3.922.0",
+    "@types/inquirer": "^9.0.9",
+    "@types/lodash.merge": "^4.6.9",
     "adm-zip": "^0.5.10",
+    "ajv": "^8.17.1",
     "aws-cdk-lib": "2.221.1",
     "aws-sdk": "^2.1574.0",
     "boxen": "^8.0.0",
@@ -88,6 +93,9 @@
     "constructs": "^10.0.0",
     "dotenv-expand": "^12.0.3",
     "enquirer": "^2.4.1",
+    "execa": "^5.1.1",
+    "inquirer": "^12.10.0",
+    "lodash.merge": "^4.6.2",
     "ora": "^9.0.0"
   },
   "engines": {