@quiltdata/benchling-webhook 0.6.1-20251104T053146Z → 0.6.2

package/README.md

@@ -4,342 +4,46 @@ Connects Benchling lab notebook entries to Quilt data packages via webhooks.
 
 ## Prerequisites
 
-- `npx` from Node.js 18+ ([download](https://nodejs.org))
+- Node.js 18+ with `npx` ([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
+## Quick Start
 
-### 1. Create Benchling App
+Run the guided setup wizard:
 
 ```bash
-npx @quiltdata/benchling-webhook@latest manifest
+npx @quiltdata/benchling-webhook@latest
 ```
 
-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.
+The wizard will:
 
-### 2. Store Benchling Secrets in AWS Secrets Manager
+1. Detect your Quilt stack from AWS CloudFormation
+2. Collect and validate your Benchling credentials
+3. Sync secrets to AWS Secrets Manager
+4. Deploy to AWS
 
-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@latest deploy \
-  --quilt-stack-arn "arn:aws:cloudformation:us-east-1:123456789012:stack/QuiltStack/abc123" \
-  --benchling-secret "benchling-webhook-credentials"
-```
-
-That's it! The deployment automatically resolves:
-
-- 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.
+After deployment, install the webhook URL in your [Benchling app settings](https://docs.benchling.com/docs/getting-started-benchling-apps#installing-your-app).
 
 ## Usage
 
 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:
+## Additional Commands
 
 ```bash
-npx @quiltdata/benchling-webhook@latest --help
+npx @quiltdata/benchling-webhook@latest --help    # Show all commands
+npx @quiltdata/benchling-webhook@latest deploy    # Deploy only
+npx @quiltdata/benchling-webhook@latest test      # Test integration
+npx @quiltdata/benchling-webhook@latest manifest  # Generate app manifest
 ```
 
-### Commands
+## Resources
 
-- `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:
-
-```bash
-git clone https://github.com/quiltdata/benchling-webhook.git
-cd benchling-webhook
-
-# 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
-
-# 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)
+- [Changelog](./CHANGELOG.md) - Version history
+- [Report Issues](https://github.com/quiltdata/benchling-webhook/issues)
 
 ## 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.map

@@ -1 +1 @@
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package/dist/bin/benchling-webhook.js

@@ -44,7 +44,7 @@ const benchling_webhook_stack_1 = require("../lib/benchling-webhook-stack");
 const child_process_1 = require("child_process");
 // Import get-env for library usage
 // eslint-disable-next-line @typescript-eslint/no-require-imports
-const { inferStackConfig } = require("./get-env.js");
+const { inferStackConfig } = require("./get-env");
 exports.inferStackConfig = inferStackConfig;
 /**
  * Check if CDK is bootstrapped for the given account/region

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

@@ -1 +1 @@
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package/dist/bin/check-logs.d.ts

@@ -0,0 +1,7 @@
+#!/usr/bin/env node
+/**
+ * Check CloudWatch logs for the deployed Benchling webhook ECS service
+ * Uses CloudFormation stack outputs to find the correct log group
+ */
+import "dotenv/config";
+//# sourceMappingURL=check-logs.d.ts.map

package/dist/bin/check-logs.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"check-logs.d.ts","sourceRoot":"","sources":["../../bin/check-logs.ts"],"names":[],"mappings":";AACA;;;GAGG;AAEH,OAAO,eAAe,CAAC"}

package/dist/bin/check-logs.js

@@ -1,63 +1,58 @@
 #!/usr/bin/env node
+"use strict";
 /**
  * Check CloudWatch logs for the deployed Benchling webhook ECS service
  * Uses CloudFormation stack outputs to find the correct log group
  */
-
+Object.defineProperty(exports, "__esModule", { value: true });
 require("dotenv/config");
-const { execSync } = require("child_process");
-
+const child_process_1 = require("child_process");
 const STACK_NAME = "BenchlingWebhookStack";
-
 // Validate required environment variables
 if (!process.env.CDK_DEFAULT_REGION) {
     console.error("Error: CDK_DEFAULT_REGION is not set in .env file");
     console.error("Please set CDK_DEFAULT_REGION in your .env file");
     process.exit(1);
 }
-
 const AWS_REGION = process.env.CDK_DEFAULT_REGION;
-
 function getStackOutputs() {
     try {
-        const output = execSync(
-            `aws cloudformation describe-stacks --stack-name ${STACK_NAME} --region ${AWS_REGION} --query 'Stacks[0].Outputs' --output json`,
-            { encoding: "utf-8" },
-        );
+        const output = (0, child_process_1.execSync)(`aws cloudformation describe-stacks --stack-name ${STACK_NAME} --region ${AWS_REGION} --query 'Stacks[0].Outputs' --output json`, { encoding: "utf-8" });
         return JSON.parse(output);
-    } catch (error) {
+    }
+    catch (_error) {
         console.error(`Error: Could not get stack outputs for ${STACK_NAME}`);
         console.error("Make sure the stack is deployed and AWS credentials are configured.");
         process.exit(1);
     }
 }
-
 function getLogGroupFromOutputs(outputs, logType) {
     let outputKey;
     if (logType === "ecs") {
         outputKey = "EcsLogGroup";
-    } else if (logType === "api") {
+    }
+    else if (logType === "api") {
         outputKey = "ApiGatewayLogGroup";
-    } else if (logType === "api-exec") {
+    }
+    else if (logType === "api-exec") {
         outputKey = "ApiGatewayExecutionLogGroup";
     }
-
+    else {
+        console.error(`Error: Invalid log type '${logType}'`);
+        process.exit(1);
+    }
     const logGroupOutput = outputs.find((o) => o.OutputKey === outputKey);
-
     if (!logGroupOutput) {
         console.error(`Error: Could not find ${outputKey} in stack outputs`);
         console.error("Make sure the stack has been deployed with the latest changes.");
         process.exit(1);
     }
-
     return logGroupOutput.OutputValue;
 }
-
 function printStackInfo(outputs, logGroup, logType) {
     console.log("=".repeat(80));
     console.log("Benchling Webhook Stack Information");
     console.log("=".repeat(80));
-
     const clusterName = outputs.find((o) => o.OutputKey === "FargateServiceClusterNameCD3B109F");
     const serviceName = outputs.find((o) => o.OutputKey === "FargateServiceServiceName24CFD869");
     const webhookEndpoint = outputs.find((o) => o.OutputKey === "WebhookEndpoint");
@@ -66,23 +61,27 @@ function printStackInfo(outputs, logGroup, logType) {
     const apiLogGroup = outputs.find((o) => o.OutputKey === "ApiGatewayLogGroup");
     const apiExecLogGroup = outputs.find((o) => o.OutputKey === "ApiGatewayExecutionLogGroup");
     const albDns = outputs.find((o) => o.OutputKey === "LoadBalancerDNS");
-
-    if (clusterName) console.log(`Cluster:   ${clusterName.OutputValue}`);
-    if (serviceName) console.log(`Service:   ${serviceName.OutputValue}`);
-    if (webhookEndpoint) console.log(`Endpoint:  ${webhookEndpoint.OutputValue}`);
-    if (albDns) console.log(`ALB DNS:   ${albDns.OutputValue}`);
-    if (version) console.log(`Version:   ${version.OutputValue}`);
-
+    if (clusterName)
+        console.log(`Cluster:   ${clusterName.OutputValue}`);
+    if (serviceName)
+        console.log(`Service:   ${serviceName.OutputValue}`);
+    if (webhookEndpoint)
+        console.log(`Endpoint:  ${webhookEndpoint.OutputValue}`);
+    if (albDns)
+        console.log(`ALB DNS:   ${albDns.OutputValue}`);
+    if (version)
+        console.log(`Version:   ${version.OutputValue}`);
     console.log("");
     console.log("Log Groups:");
-    if (ecsLogGroup) console.log(`  ECS:         ${ecsLogGroup.OutputValue}${logType === "ecs" ? " (viewing)" : ""}`);
-    if (apiLogGroup) console.log(`  API Access:  ${apiLogGroup.OutputValue}${logType === "api" ? " (viewing)" : ""}`);
-    if (apiExecLogGroup) console.log(`  API Exec:    ${apiExecLogGroup.OutputValue}${logType === "api-exec" ? " (viewing)" : ""}`);
-
+    if (ecsLogGroup)
+        console.log(`  ECS:         ${ecsLogGroup.OutputValue}${logType === "ecs" ? " (viewing)" : ""}`);
+    if (apiLogGroup)
+        console.log(`  API Access:  ${apiLogGroup.OutputValue}${logType === "api" ? " (viewing)" : ""}`);
+    if (apiExecLogGroup)
+        console.log(`  API Exec:    ${apiExecLogGroup.OutputValue}${logType === "api-exec" ? " (viewing)" : ""}`);
     console.log("=".repeat(80));
     console.log("");
 }
-
 function main() {
     const args = process.argv.slice(2);
     const logType = args.find((arg) => arg.startsWith("--type="))?.split("=")[1] || "all";
@@ -90,27 +89,22 @@ function main() {
     const since = args.find((arg) => arg.startsWith("--since="))?.split("=")[1] || "5m";
     const follow = args.includes("--follow") || args.includes("-f");
     const tail = args.find((arg) => arg.startsWith("--tail="))?.split("=")[1] || "100";
-
     // Validate log type
     if (!["ecs", "api", "api-exec", "all"].includes(logType)) {
         console.error("Error: --type must be 'ecs', 'api', 'api-exec', or 'all'");
         process.exit(1);
     }
-
     // Get stack outputs
     const outputs = getStackOutputs();
-
     // Handle 'all' type - show all three log groups
     if (logType === "all") {
         printStackInfo(outputs, null, "all");
         console.log("Showing logs from all sources (most recent first):\n");
-
         const logGroupDefs = [
             { type: "ECS", group: outputs.find((o) => o.OutputKey === "EcsLogGroup")?.OutputValue },
             { type: "API-Access", group: outputs.find((o) => o.OutputKey === "ApiGatewayLogGroup")?.OutputValue },
             { type: "API-Exec", group: outputs.find((o) => o.OutputKey === "ApiGatewayExecutionLogGroup")?.OutputValue },
         ];
-
         // Warn about missing log groups
         const missingGroups = logGroupDefs.filter(lg => !lg.group);
         if (missingGroups.length > 0) {
@@ -120,63 +114,60 @@ function main() {
             });
             console.log("");
         }
-
         const logGroups = logGroupDefs.filter(lg => lg.group);
-
         for (const { type, group } of logGroups) {
             console.log(`\n${"=".repeat(80)}`);
             console.log(`${type}: ${group}`);
             console.log("=".repeat(80));
-
             let command = `aws logs tail "${group}"`;
             command += ` --region ${AWS_REGION}`;
             command += ` --since ${since}`;
-            command += ` --format short`;
+            command += " --format short";
             if (filterPattern) {
                 command += ` --filter-pattern "${filterPattern}"`;
             }
             command += ` 2>&1 | tail -${tail}`;
-
             try {
-                const output = execSync(command, { encoding: "utf-8", shell: "/bin/bash" });
+                const output = (0, child_process_1.execSync)(command, { encoding: "utf-8", shell: "/bin/bash" });
                 if (output.trim()) {
                     console.log(output);
-                } else {
+                }
+                else {
                     console.log(`(No logs in the last ${since})`);
                 }
-            } catch (error) {
-                console.log(`Error reading ${type} logs: ${error.message}`);
+            }
+            catch (error) {
+                const errorMessage = error instanceof Error ? error.message : String(error);
+                console.log(`Error reading ${type} logs: ${errorMessage}`);
             }
         }
         return;
     }
-
     const logGroup = getLogGroupFromOutputs(outputs, logType);
     printStackInfo(outputs, logGroup, logType);
-
     // Build AWS logs command
     let command = `aws logs tail ${logGroup}`;
     command += ` --region ${AWS_REGION}`;
     command += ` --since ${since}`;
-    command += ` --format short`;
-
+    command += " --format short";
     if (filterPattern) {
         command += ` --filter-pattern "${filterPattern}"`;
     }
-
     if (follow) {
         command += " --follow";
         console.log("Following logs (Press Ctrl+C to stop)...\n");
-    } else {
+    }
+    else {
         command += ` | tail -${tail}`;
         console.log(`Showing last ${tail} log entries from the past ${since}...\n`);
     }
-
     // Execute logs command
     try {
-        execSync(command, { stdio: "inherit" });
-    } catch (error) {
-        if (error.status !== 130) {
+        (0, child_process_1.execSync)(command, { stdio: "inherit" });
+    }
+    catch (error) {
+        const hasStatus = error && typeof error === "object" && "status" in error;
+        if (hasStatus && error.status !== 130) {
             // Ignore Ctrl+C exit (status 130)
             console.error("\nError fetching logs. Make sure:");
             console.error("1. The stack is deployed");
@@ -186,7 +177,6 @@ function main() {
         }
     }
 }
-
 function printHelp() {
     console.log("Usage: npm run logs [options]");
     console.log("");
@@ -214,18 +204,19 @@ function printHelp() {
     console.log("  npm run logs -- --type=ecs --follow            # Follow ECS logs");
     console.log("  npm run logs -- --type=api-exec --since=10m    # Last 10 min of execution logs");
 }
-
 if (require.main === module) {
     const args = process.argv.slice(2);
     if (args.includes("--help") || args.includes("-h")) {
         printHelp();
         process.exit(0);
     }
-
     try {
         main();
-    } catch (error) {
-        console.error("Error:", error.message);
+    }
+    catch (error) {
+        const errorMessage = error instanceof Error ? error.message : String(error);
+        console.error("Error:", errorMessage);
         process.exit(1);
     }
 }
+//# sourceMappingURL=check-logs.js.map