@quiltdata/benchling-webhook 0.5.1 → 0.5.4-20251031T221509Z

package/README.md

@@ -7,6 +7,7 @@ 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
 
@@ -18,15 +19,35 @@ npx @quiltdata/benchling-webhook 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. Configure Benchling Secrets
+
+Create a JSON file with your Benchling credentials:
+
+```bash
+cat > benchling-secrets.json << EOF
+{
+  "client_id": "your-benchling-client-id",
+  "client_secret": "your-benchling-client-secret",
+  "tenant": "your-tenant"
+}
+EOF
+```
+
+> **Important**: Never commit secrets to version control. Add `benchling-secrets.json` to `.gitignore`.
+
+**See [Secrets Configuration Guide](./docs/SECRETS_CONFIGURATION.md) for detailed configuration options**
+
+### 3. Deploy to AWS
 
 ```bash
-npx @quiltdata/benchling-webhook
+npx @quiltdata/benchling-webhook deploy \
+  --benchling-secrets @benchling-secrets.json \
+  --catalog your-catalog.quiltdata.com
 ```
 
 The interactive wizard will auto-detect or request configuration information, deploy to AWS, and test the webhook automatically.
 
-### 3. Install in Benchling
+### 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 +55,138 @@ 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
+
+### Secrets Management (v0.6.0+)
+
+The webhook supports multiple ways to configure Benchling credentials:
+
+#### Option 1: Inline JSON
+```bash
+npx @quiltdata/benchling-webhook deploy \
+  --benchling-secrets '{"client_id":"xxx","client_secret":"yyy","tenant":"company"}'
+```
+
+#### Option 2: JSON File (Recommended)
+```bash
+npx @quiltdata/benchling-webhook deploy --benchling-secrets @benchling-secrets.json
+```
+
+#### Option 3: AWS Secrets Manager ARN
+```bash
+npx @quiltdata/benchling-webhook deploy \
+  --benchling-secrets "arn:aws:secretsmanager:us-east-1:123456789012:secret:benchling-creds"
+```
+
+#### Option 4: Environment Variable
+```bash
+export BENCHLING_SECRETS='{"client_id":"xxx","client_secret":"yyy","tenant":"company"}'
+npx @quiltdata/benchling-webhook deploy
+```
+
+**📖 [Complete Secrets Configuration Guide](./docs/SECRETS_CONFIGURATION.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 deploy \
+  --benchling-secrets @updated-secrets.json
+```
+
+## All Available Commands
+
 For all available commands, run:
 
 ```bash
 npx @quiltdata/benchling-webhook --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 deploy [options]
+```
+
+**Secrets Configuration**:
+- `--benchling-secrets <value>` - Benchling secrets (ARN, JSON, or @file)
+
+**Quilt Configuration**:
+- `--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
+- `--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` instead
+- `--client-id` - Use `--benchling-secrets` instead
+- `--client-secret` - Use `--benchling-secrets` instead
+- `--app-id` - Use `--benchling-secrets` instead
+
+**Migration guide**: See [Secrets Configuration - Migration Guide](./docs/SECRETS_CONFIGURATION.md#migration-guide)
+
+## 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:
@@ -53,10 +200,76 @@ npm install
 npm run cli -- --help
 npm run cli -- deploy
 
-npm test    # Run tests
-npm run build    # Build package
+npm test        # Run tests
+npm run build   # Build package
+```
+
+### Running Tests
+
+```bash
+# Run all tests (TypeScript + Python)
+npm test
+
+# Run TypeScript tests only
+npm run test:ts
+
+# Run Python tests only
+npm run test:python
+
+# Type checking
+npm run typecheck
+
+# Linting
+npm run lint
 ```
 
+## 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
+
+Current version: 0.5.4 (see [CHANGELOG.md](./CHANGELOG.md))
+
+Next version: 0.6.0 (secrets management integration)

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

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

@@ -117,7 +117,7 @@ function createStack(config) {
             region: config.cdkRegion,
         },
         bucketName: config.quiltUserBucket,
-        queueName: config.queueName,
+        queueArn: config.queueArn,
         environment: "production",
         prefix: config.pkgPrefix || "benchling",
         benchlingClientId: config.benchlingClientId,
@@ -129,6 +129,7 @@ function createStack(config) {
         logLevel: config.logLevel || "INFO",
         createEcrRepository: config.createEcrRepository === "true",
         ecrRepositoryName: config.ecrRepositoryName || "quiltdata/benchling",
+        imageTag: config.imageTag || "latest",
     });
     return {
         app,
@@ -182,8 +183,7 @@ async function legacyGetConfig() {
     const requiredInferredVars = [
         "CDK_DEFAULT_ACCOUNT",
         "CDK_DEFAULT_REGION",
-        "QUEUE_NAME",
-        "SQS_QUEUE_URL",
+        "QUEUE_ARN",
         "QUILT_DATABASE",
     ];
     const missingInferredVars = requiredInferredVars.filter((varName) => !config[varName]);
@@ -200,11 +200,17 @@ async function legacyGetConfig() {
         console.error("\nAlternatively, you can manually set these values in your .env file.");
         process.exit(1);
     }
-    // Validate conditional requirements
-    if (config.ENABLE_WEBHOOK_VERIFICATION !== "false" &&
-        !config.BENCHLING_APP_DEFINITION_ID) {
-        console.error("Error: BENCHLING_APP_DEFINITION_ID is required when webhook verification is enabled.");
-        console.error("Either set BENCHLING_APP_DEFINITION_ID or set ENABLE_WEBHOOK_VERIFICATION=false");
+    // Validate required Benchling fields
+    const requiredBenchlingFields = [
+        "BENCHLING_TENANT",
+        "BENCHLING_CLIENT_ID",
+        "BENCHLING_CLIENT_SECRET",
+        "BENCHLING_APP_DEFINITION_ID",
+    ];
+    const missingBenchling = requiredBenchlingFields.filter((field) => !config[field]);
+    if (missingBenchling.length > 0) {
+        console.error("Error: The following required Benchling configuration is missing:");
+        missingBenchling.forEach((field) => console.error(`  - ${field}`));
         process.exit(1);
     }
     return config;
@@ -243,7 +249,7 @@ async function legacyMain() {
             region: config.CDK_DEFAULT_REGION,
         },
         bucketName: config.QUILT_USER_BUCKET, // User's data bucket
-        queueName: config.QUEUE_NAME,
+        queueArn: config.QUEUE_ARN,
         environment: "production",
         prefix: config.PKG_PREFIX || "benchling",
         benchlingClientId: config.BENCHLING_CLIENT_ID,

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

@@ -1 +1 @@
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package/dist/bin/cdk-dev.js

@@ -0,0 +1,252 @@
+#!/usr/bin/env node
+
+/**
+ * Development deployment workflow script
+ *
+ * This script:
+ * 1. Creates a dev git tag with timestamp (v{version}-{timestamp})
+ * 2. Pushes the tag to GitHub (triggers CI to build Docker image)
+ * 3. Waits for CI/CD pipeline to complete (monitors GitHub Actions)
+ * 4. Deploys CDK stack using the CI-built image tag
+ *
+ * Usage:
+ *   npm run cdk:dev                    # Full workflow
+ *   npm run cdk:dev -- --continue      # Skip tag creation, wait for CI and deploy
+ *   npm run cdk:dev -- --tag <tag>     # Use specific existing tag
+ *
+ * IMPORTANT: This uses CI-built images (x86_64), NOT local builds.
+ * Local ARM builds would fail in AWS which runs on x86_64.
+ */
+
+const { execSync } = require('child_process');
+const fs = require('fs');
+const path = require('path');
+
+// Read package.json for version
+const packagePath = path.join(__dirname, '..', 'package.json');
+const pkg = JSON.parse(fs.readFileSync(packagePath, 'utf8'));
+
+function run(command, options = {}) {
+  const silent = options.silent || false;
+  if (!silent) {
+    console.log(`\n$ ${command}\n`);
+  }
+  try {
+    return execSync(command, {
+      stdio: silent ? 'pipe' : 'inherit',
+      encoding: 'utf-8',
+      ...options
+    });
+  } catch (error) {
+    if (!silent) {
+      console.error(`\n❌ Command failed: ${command}`);
+    }
+    if (options.allowFailure) {
+      return null;
+    }
+    process.exit(1);
+  }
+}
+
+async function waitForWorkflow(commitSha, timeoutMinutes = 15) {
+  console.log('');
+  console.log(`Waiting for CI workflow to complete (timeout: ${timeoutMinutes} minutes)...`);
+  console.log('');
+
+  // Check if gh CLI is available
+  try {
+    execSync('gh --version', { stdio: 'ignore' });
+  } catch (e) {
+    console.error('❌ GitHub CLI (gh) is not installed or not in PATH');
+    console.error('   Install from: https://cli.github.com/');
+    console.error('\n   Alternatively, monitor the workflow manually and deploy when complete:');
+    console.error('   1. Watch: https://github.com/quiltdata/benchling-webhook/actions');
+    console.error('   2. Deploy: npm run cli -- --image-tag <version> --yes');
+    process.exit(1);
+  }
+
+  const startTime = Date.now();
+  const timeoutMs = timeoutMinutes * 60 * 1000;
+  let attempt = 0;
+  let workflowUrl = null;
+
+  while (Date.now() - startTime < timeoutMs) {
+    attempt++;
+
+    try {
+      // Use gh to list recent workflow runs for this commit
+      const result = run(`gh run list --commit ${commitSha} --json status,conclusion,url,databaseId --limit 5`, {
+        silent: true,
+        allowFailure: true
+      });
+
+      if (!result) {
+        process.stdout.write(`\r  Attempt ${attempt}: Waiting for workflow to start (commit ${commitSha.substring(0, 7)})...`);
+        await new Promise(resolve => setTimeout(resolve, 10000));
+        continue;
+      }
+
+      const runs = JSON.parse(result);
+
+      if (runs && runs.length > 0) {
+        const workflowRun = runs[0]; // Most recent run for this commit
+        const status = workflowRun.status;
+        const conclusion = workflowRun.conclusion;
+        workflowUrl = workflowRun.url;
+
+        process.stdout.write(`\r  Attempt ${attempt}: Status=${status}, Conclusion=${conclusion || 'pending'}... ${workflowUrl}`);
+
+        if (status === 'completed') {
+          console.log('\n');
+          if (conclusion === 'success') {
+            console.log(`✅ CI workflow completed successfully!`);
+            console.log(`   Run: ${workflowUrl}`);
+            return true;
+          } else {
+            console.error(`\n❌ CI workflow failed with conclusion: ${conclusion}`);
+            console.error(`   Run: ${workflowUrl}`);
+            console.error('   Please check the workflow logs and fix any issues.');
+            process.exit(1);
+          }
+        }
+      } else {
+        process.stdout.write(`\r  Attempt ${attempt}: Waiting for workflow to start (commit ${commitSha.substring(0, 7)})...`);
+      }
+    } catch (error) {
+      // Errors are non-fatal, just retry
+      if (attempt % 10 === 0) {
+        console.log(`\n  Warning: ${error.message}`);
+      }
+    }
+
+    // Wait 10 seconds between checks
+    await new Promise(resolve => setTimeout(resolve, 10000));
+  }
+
+  console.error('\n\n❌ Timeout waiting for CI workflow to complete');
+  console.error(`   Waited ${timeoutMinutes} minutes`);
+  if (workflowUrl) {
+    console.error(`   Check status at: ${workflowUrl}`);
+  } else {
+    console.error(`   Check status at: https://github.com/quiltdata/benchling-webhook/actions`);
+  }
+  console.error('\n   Once the workflow completes, you can deploy manually with:');
+  console.error(`   npm run cli -- --image-tag <version> --yes`);
+  process.exit(1);
+}
+
+async function main() {
+  console.log('🚀 Starting development deployment workflow...');
+  console.log('');
+  console.log('This workflow uses CI-built Docker images (x86_64 for AWS).');
+  console.log('Local ARM builds are NOT used as they would fail in AWS.');
+  console.log('');
+
+  // Parse command line arguments
+  const args = process.argv.slice(2);
+  const continueMode = args.includes('--continue');
+  const tagIndex = args.indexOf('--tag');
+  const specificTag = tagIndex !== -1 ? args[tagIndex + 1] : null;
+
+  let devTag;
+  let version;
+
+  if (specificTag) {
+    // Use specific tag provided by user
+    devTag = specificTag;
+    version = specificTag.replace(/^v/, '').split('-')[0]; // Extract version from tag
+    console.log(`Using specified tag: ${devTag}`);
+    console.log(`Extracted version: ${version}`);
+  } else if (continueMode) {
+    // Continue mode - find most recent dev tag
+    console.log('Continue mode: Finding most recent dev tag...');
+    try {
+      const tags = run('git tag --sort=-creatordate', { silent: true }).trim().split('\n');
+      const recentDevTag = tags.find(t => t.match(/^v[\d.]+-.+Z$/));
+
+      if (!recentDevTag) {
+        console.error('❌ No dev tags found');
+        console.error('   Run without --continue to create a new dev tag first');
+        process.exit(1);
+      }
+
+      devTag = recentDevTag;
+      version = devTag.replace(/^v/, '').split('-')[0];
+      console.log(`✅ Found recent dev tag: ${devTag}`);
+      console.log(`   Version: ${version}`);
+    } catch (e) {
+      console.error('❌ Failed to find recent dev tag');
+      process.exit(1);
+    }
+  } else {
+    // Normal mode - create new tag
+    // 1. Check for uncommitted changes
+    console.log('Step 1: Checking for uncommitted changes...');
+    try {
+      execSync('git diff-index --quiet HEAD --', { stdio: 'ignore' });
+    } catch (e) {
+      console.error('❌ You have uncommitted changes');
+      console.error('   Commit or stash your changes before creating a dev deployment');
+      process.exit(1);
+    }
+    console.log('✅ Working directory is clean');
+
+    // 2. Generate dev tag name
+    version = pkg.version;
+    const timestamp = new Date().toISOString().replace(/[-:]/g, '').replace(/\.\d+Z$/, 'Z');
+    devTag = `v${version}-${timestamp}`;
+
+    console.log('');
+    console.log(`Step 2: Creating dev tag: ${devTag}`);
+
+    // Check if tag already exists
+    try {
+      execSync(`git rev-parse ${devTag}`, { stdio: 'ignore' });
+      console.error(`❌ Tag ${devTag} already exists`);
+      process.exit(1);
+    } catch (e) {
+      // Tag doesn't exist, continue
+    }
+
+    // Create tag
+    const message = `Development release ${devTag}\n\nThis is a pre-release for testing purposes.`;
+    run(`git tag -a ${devTag} -m "${message}"`);
+    console.log(`✅ Created git tag ${devTag}`);
+
+    // 3. Push tag to origin (triggers CI)
+    console.log('');
+    console.log(`Step 3: Pushing tag to origin (this triggers CI/CD)...`);
+    run(`git push origin ${devTag}`);
+    console.log(`✅ Pushed tag ${devTag} to origin`);
+    console.log('   CI will now build Docker image for x86_64 (AWS-compatible)');
+  }
+
+  // 4. Wait for CI to complete
+  console.log('');
+  console.log(`Step 4: Waiting for CI to build Docker image...`);
+
+  // Get the commit SHA for the tag (use ^{commit} to dereference annotated tags)
+  const commitSha = run(`git rev-parse ${devTag}^{commit}`, { silent: true }).trim();
+
+  await waitForWorkflow(commitSha);
+
+  // 5. Deploy CDK stack with CI-built image tag
+  console.log('');
+  console.log(`Step 5: Deploying CDK stack with CI-built image...`);
+  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`);
+
+  console.log('');
+  console.log('✅ Development deployment complete!');
+  console.log('');
+  console.log(`Dev tag: ${devTag}`);
+  console.log(`Image tag: ${imageTag} (built by CI for x86_64)`);
+  console.log('');
+}
+
+main().catch(error => {
+  console.error('\n❌ Error:', error.message);
+  process.exit(1);
+});

package/dist/bin/cli.js

@@ -26,16 +26,35 @@ program
     .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("--benchling-secrets <value>", "Benchling secrets configuration (ARN, JSON, or @file)")
+    .option("--tenant <name>", "Benchling tenant (deprecated, use --benchling-secrets)")
+    .option("--client-id <id>", "Benchling OAuth client ID (deprecated, use --benchling-secrets)")
+    .option("--client-secret <secret>", "Benchling OAuth client secret (deprecated, use --benchling-secrets)")
+    .option("--app-id <id>", "Benchling app definition ID (deprecated, use --benchling-secrets)")
     .option("--env-file <path>", "Path to .env file", ".env")
     .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:
+  Using AWS Secrets Manager ARN:
+    $ npx @quiltdata/benchling-webhook deploy --benchling-secrets "arn:aws:secretsmanager:us-east-1:123456789012:secret:benchling-credentials"
+
+  Using inline JSON:
+    $ npx @quiltdata/benchling-webhook deploy --benchling-secrets '{"client_id":"xxx","client_secret":"yyy","tenant":"company"}'
+
+  Using JSON file:
+    $ npx @quiltdata/benchling-webhook deploy --benchling-secrets @secrets.json
+
+  Using environment variable:
+    $ export BENCHLING_SECRETS='{"client_id":"xxx","client_secret":"yyy","tenant":"company"}'
+    $ npx @quiltdata/benchling-webhook deploy
+
+For more information: https://github.com/quiltdata/benchling-webhook#secrets-configuration
+`)
     .action(async (options) => {
     try {
         await (0, deploy_1.deployCommand)(options);

package/dist/bin/cli.js.map

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