@quiltdata/benchling-webhook 0.6.3-20251104T170954Z → 0.7.2-20251106T003353Z

package/dist/bin/commands/setup-wizard.js

@@ -1,10 +1,16 @@
+#!/usr/bin/env node
 "use strict";
 /**
- * Setup Wizard Command
+ * Interactive Configuration Wizard (v0.7.0)
  *
- * Launches the interactive setup wizard when npx is run without arguments.
- * This provides a guided experience for first-time users to configure and
- * deploy the Benchling webhook integration.
+ * Complete setup wizard that orchestrates:
+ * 1. Quilt configuration inference
+ * 2. Interactive configuration prompts
+ * 3. Configuration validation
+ * 4. Profile persistence via XDGConfig
+ *
+ * Consolidated from scripts/install-wizard.ts, scripts/config/wizard.ts,
+ * and scripts/config/validator.ts.
  *
  * @module commands/setup-wizard
  */
@@ -46,58 +52,850 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.setupWizardCommand = setupWizardCommand;
+const https = __importStar(require("https"));
+const fs_1 = require("fs");
+const path_1 = require("path");
+const inquirer_1 = __importDefault(require("inquirer"));
 const chalk_1 = __importDefault(require("chalk"));
-const install_wizard_1 = require("../../scripts/install-wizard");
+const boxen_1 = __importDefault(require("boxen"));
+const ora_1 = __importDefault(require("ora"));
+const client_s3_1 = require("@aws-sdk/client-s3");
+const xdg_config_1 = require("../../lib/xdg-config");
+const infer_quilt_config_1 = require("../commands/infer-quilt-config");
+const manifest_1 = require("./manifest");
+const sync_secrets_1 = require("./sync-secrets");
+const deploy_1 = require("./deploy");
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const pkg = require("../../package.json");
+const MANIFEST_FILENAME = "benchling-app-manifest.yaml";
+function getAccountFromStackArn(stackArn) {
+    if (!stackArn) {
+        return undefined;
+    }
+    const parts = stackArn.split(":");
+    if (parts.length < 5) {
+        return undefined;
+    }
+    const account = parts[4];
+    return /^[0-9]{12}$/.test(account) ? account : undefined;
+}
+// =============================================================================
+// VALIDATION FUNCTIONS (from scripts/config/validator.ts)
+// =============================================================================
 /**
- * Setup wizard command handler
- *
- * Provides guided setup experience:
- * 1. Welcome message and prerequisites check
- * 2. Configuration collection via install-wizard
- * 3. Automatic deployment (optional)
- * 4. Integration testing (optional)
- *
- * @returns Promise that resolves when wizard completes
+ * Validates Benchling tenant accessibility
+ */
+async function validateBenchlingTenant(tenant) {
+    const result = {
+        isValid: false,
+        errors: [],
+        warnings: [],
+    };
+    if (!tenant || tenant.trim().length === 0) {
+        result.errors.push("Tenant name cannot be empty");
+        return result;
+    }
+    // Basic format validation
+    if (!/^[a-zA-Z0-9-_]+$/.test(tenant)) {
+        result.errors.push("Tenant name contains invalid characters (only alphanumeric, dash, underscore allowed)");
+        return result;
+    }
+    // Test tenant URL accessibility
+    const tenantUrl = `https://${tenant}.benchling.com`;
+    return new Promise((resolve) => {
+        https
+            .get(tenantUrl, { timeout: 5000 }, (res) => {
+            if (res.statusCode === 200 || res.statusCode === 302 || res.statusCode === 301) {
+                result.isValid = true;
+                console.log(`  ✓ Tenant URL accessible: ${tenantUrl}`);
+            }
+            else {
+                if (!result.warnings)
+                    result.warnings = [];
+                result.warnings.push(`Tenant URL returned status ${res.statusCode}`);
+                result.isValid = true; // Consider this a warning, not an error
+            }
+            resolve(result);
+        })
+            .on("error", (error) => {
+            if (!result.warnings)
+                result.warnings = [];
+            result.warnings.push(`Could not verify tenant URL: ${error.message}`);
+            result.isValid = true; // Allow proceeding with warning
+            resolve(result);
+        });
+    });
+}
+/**
+ * Validates Benchling OAuth credentials
  */
-async function setupWizardCommand() {
-    console.log(chalk_1.default.bold.cyan("\n🚀 Benchling Webhook Setup Wizard\n"));
-    console.log("This wizard will guide you through:");
-    console.log("  1. Collecting configuration (Benchling credentials, AWS settings)");
-    console.log("  2. Validating credentials and access");
-    console.log("  3. Saving configuration for deployment");
-    console.log("  4. Deploying to AWS (optional)\n");
-    console.log(chalk_1.default.dim("Press Ctrl+C at any time to exit\n"));
-    // Run the existing install wizard
-    await (0, install_wizard_1.runInstallWizard)({
-        nonInteractive: false,
-        skipValidation: false,
+async function validateBenchlingCredentials(tenant, clientId, clientSecret) {
+    const result = {
+        isValid: false,
+        errors: [],
+        warnings: [],
+    };
+    if (!clientId || clientId.trim().length === 0) {
+        result.errors.push("Client ID cannot be empty");
+    }
+    if (!clientSecret || clientSecret.trim().length === 0) {
+        result.errors.push("Client secret cannot be empty");
+    }
+    if (result.errors.length > 0) {
+        return result;
+    }
+    // Test OAuth token endpoint
+    const tokenUrl = `https://${tenant}.benchling.com/api/v2/token`;
+    const authString = Buffer.from(`${clientId}:${clientSecret}`).toString("base64");
+    return new Promise((resolve) => {
+        const postData = "grant_type=client_credentials";
+        const options = {
+            method: "POST",
+            headers: {
+                "Authorization": `Basic ${authString}`,
+                "Content-Type": "application/x-www-form-urlencoded",
+                "Content-Length": postData.length,
+            },
+            timeout: 10000,
+        };
+        const req = https.request(tokenUrl, options, (res) => {
+            let data = "";
+            res.on("data", (chunk) => {
+                data += chunk;
+            });
+            res.on("end", () => {
+                if (res.statusCode === 200) {
+                    result.isValid = true;
+                    console.log("  ✓ OAuth credentials validated successfully");
+                }
+                else {
+                    result.errors.push(`OAuth validation failed with status ${res.statusCode}: ${data.substring(0, 100)}`);
+                }
+                resolve(result);
+            });
+        });
+        req.on("error", (error) => {
+            if (!result.warnings)
+                result.warnings = [];
+            result.warnings.push(`Could not validate OAuth credentials: ${error.message}`);
+            result.isValid = true; // Allow proceeding with warning
+            resolve(result);
+        });
+        req.write(postData);
+        req.end();
     });
-    console.log(chalk_1.default.green.bold("\n✓ Setup complete!\n"));
-    // Ask if user wants to deploy now
-    const inquirer = (await Promise.resolve().then(() => __importStar(require("inquirer")))).default;
-    const { shouldDeploy } = await inquirer.prompt([
+}
+/**
+ * Validates S3 bucket access
+ */
+async function validateS3BucketAccess(bucketName, region, awsProfile) {
+    const result = {
+        isValid: false,
+        errors: [],
+        warnings: [],
+    };
+    if (!bucketName || bucketName.trim().length === 0) {
+        result.errors.push("Bucket name cannot be empty");
+        return result;
+    }
+    try {
+        const clientConfig = { region };
+        if (awsProfile) {
+            const { fromIni } = await Promise.resolve().then(() => __importStar(require("@aws-sdk/credential-providers")));
+            clientConfig.credentials = fromIni({ profile: awsProfile });
+        }
+        const s3Client = new client_s3_1.S3Client(clientConfig);
+        // Test HeadBucket (verify bucket exists and we have access)
+        const headCommand = new client_s3_1.HeadBucketCommand({ Bucket: bucketName });
+        await s3Client.send(headCommand);
+        console.log(`  ✓ S3 bucket accessible: ${bucketName}`);
+        // Test ListObjects (verify we can list objects)
+        const listCommand = new client_s3_1.ListObjectsV2Command({
+            Bucket: bucketName,
+            MaxKeys: 1,
+        });
+        await s3Client.send(listCommand);
+        console.log("  ✓ S3 bucket list permission confirmed");
+        result.isValid = true;
+    }
+    catch (error) {
+        const err = error;
+        result.errors.push(`S3 bucket validation failed: ${err.message}`);
+    }
+    return result;
+}
+/**
+ * Validates complete ProfileConfig
+ */
+async function validateConfig(config, options = {}) {
+    const result = {
+        isValid: true,
+        errors: [],
+        warnings: [],
+    };
+    if (options.skipValidation) {
+        return result;
+    }
+    // Validate Benchling tenant
+    const tenantValidation = await validateBenchlingTenant(config.benchling.tenant);
+    if (!tenantValidation.isValid) {
+        result.isValid = false;
+        result.errors.push(...tenantValidation.errors);
+    }
+    if (tenantValidation.warnings && tenantValidation.warnings.length > 0) {
+        if (!result.warnings)
+            result.warnings = [];
+        result.warnings.push(...tenantValidation.warnings);
+    }
+    // Validate OAuth credentials (if secret is provided)
+    if (config.benchling.clientSecret) {
+        const credValidation = await validateBenchlingCredentials(config.benchling.tenant, config.benchling.clientId, config.benchling.clientSecret);
+        if (!credValidation.isValid) {
+            result.isValid = false;
+            result.errors.push(...credValidation.errors);
+        }
+        if (credValidation.warnings && credValidation.warnings.length > 0) {
+            if (!result.warnings)
+                result.warnings = [];
+            result.warnings.push(...credValidation.warnings);
+        }
+    }
+    // Validate S3 bucket access
+    const bucketValidation = await validateS3BucketAccess(config.packages.bucket, config.deployment.region, options.awsProfile);
+    if (!bucketValidation.isValid) {
+        result.isValid = false;
+        result.errors.push(...bucketValidation.errors);
+    }
+    if (bucketValidation.warnings && bucketValidation.warnings.length > 0) {
+        if (!result.warnings)
+            result.warnings = [];
+        result.warnings.push(...bucketValidation.warnings);
+    }
+    return result;
+}
+/**
+ * Runs interactive configuration wizard
+ */
+async function runConfigWizard(options = {}) {
+    const { existingConfig = {}, nonInteractive = false, inheritFrom } = options;
+    console.log("╔═══════════════════════════════════════════════════════════╗");
+    console.log("║   Benchling Webhook Configuration Wizard                 ║");
+    console.log("╚═══════════════════════════════════════════════════════════╝\n");
+    if (inheritFrom) {
+        console.log(`Creating profile inheriting from: ${inheritFrom}\n`);
+    }
+    const config = { ...existingConfig };
+    // If non-interactive, validate that all required fields are present
+    if (nonInteractive) {
+        if (!config.benchling?.tenant || !config.benchling?.clientId || !config.benchling?.clientSecret) {
+            throw new Error("Non-interactive mode requires benchlingTenant, benchlingClientId, and benchlingClientSecret to be already configured");
+        }
+        return config;
+    }
+    // Prompt for Quilt configuration (if not inherited)
+    if (!inheritFrom) {
+        // Check if all required Quilt fields are already present (from inference)
+        // Note: bucket is optional and can be inferred from other sources if missing
+        const hasAllQuiltFields = config.quilt?.stackArn &&
+            config.quilt?.catalog &&
+            config.quilt?.database &&
+            config.quilt?.queueArn;
+        let shouldPromptForQuilt = !hasAllQuiltFields;
+        if (hasAllQuiltFields) {
+            console.log("Step 1: Quilt Configuration (inferred from AWS)\n");
+            console.log(`  Stack ARN: ${config.quilt.stackArn}`);
+            console.log(`  Catalog: ${config.quilt.catalog}`);
+            console.log(`  Database: ${config.quilt.database}`);
+            console.log(`  Queue ARN: ${config.quilt.queueArn}`);
+            if (config.quilt.bucket) {
+                console.log(`  Bucket: ${config.quilt.bucket}`);
+            }
+            console.log("");
+            const { confirmQuilt } = await inquirer_1.default.prompt([
+                {
+                    type: "confirm",
+                    name: "confirmQuilt",
+                    message: "Use these inferred Quilt settings?",
+                    default: true,
+                },
+            ]);
+            if (!confirmQuilt) {
+                console.log("\nPlease enter Quilt configuration manually:\n");
+                shouldPromptForQuilt = true;
+            }
+        }
+        // Only prompt for Quilt fields if not all are present OR user chose to enter manually
+        if (shouldPromptForQuilt) {
+            if (!hasAllQuiltFields) {
+                console.log("Step 1: Quilt Configuration\n");
+                console.log("Note: Run 'npm run setup:infer' first to auto-detect Quilt stack\n");
+            }
+            const quiltAnswers = await inquirer_1.default.prompt([
+                {
+                    type: "input",
+                    name: "stackArn",
+                    message: "Quilt Stack ARN:",
+                    default: config.quilt?.stackArn,
+                    validate: (input) => input.trim().length > 0 && input.startsWith("arn:aws:cloudformation:") ||
+                        "Stack ARN is required and must start with arn:aws:cloudformation:",
+                },
+                {
+                    type: "input",
+                    name: "catalog",
+                    message: "Quilt Catalog URL (domain or full URL):",
+                    default: config.quilt?.catalog,
+                    validate: (input) => {
+                        const trimmed = input.trim();
+                        if (trimmed.length === 0) {
+                            return "Catalog URL is required";
+                        }
+                        return true;
+                    },
+                    filter: (input) => {
+                        // Strip protocol if present, store only domain
+                        return input.trim().replace(/^https?:\/\//, "").replace(/\/$/, "");
+                    },
+                },
+                {
+                    type: "input",
+                    name: "bucket",
+                    message: "Quilt S3 Bucket:",
+                    default: config.quilt?.bucket,
+                    validate: (input) => input.trim().length > 0 || "Bucket name is required",
+                },
+                {
+                    type: "input",
+                    name: "database",
+                    message: "Quilt Athena Database:",
+                    default: config.quilt?.database || "quilt_catalog",
+                    validate: (input) => input.trim().length > 0 || "Database name is required",
+                },
+                {
+                    type: "input",
+                    name: "queueArn",
+                    message: "SQS Queue ARN:",
+                    default: config.quilt?.queueArn,
+                    validate: (input) => input.trim().length > 0 && input.startsWith("arn:aws:sqs:") ||
+                        "Queue ARN is required and must start with arn:aws:sqs:",
+                },
+            ]);
+            // Extract region from stack ARN
+            const arnMatch = quiltAnswers.stackArn.match(/^arn:aws:cloudformation:([^:]+):/);
+            const quiltRegion = arnMatch ? arnMatch[1] : "us-east-1";
+            config.quilt = {
+                stackArn: quiltAnswers.stackArn,
+                catalog: quiltAnswers.catalog,
+                bucket: quiltAnswers.bucket,
+                database: quiltAnswers.database,
+                queueArn: quiltAnswers.queueArn,
+                region: quiltRegion,
+            };
+        }
+    }
+    // Prompt for Benchling configuration & guide app setup
+    console.log("\nStep 2: Create Benchling App\n");
+    let benchlingTenant = config.benchling?.tenant?.trim();
+    benchlingTenant = benchlingTenant && benchlingTenant.length > 0 ? benchlingTenant : undefined;
+    if (nonInteractive) {
+        if (!benchlingTenant) {
+            throw new Error("Benchling tenant must be provided in non-interactive mode");
+        }
+    }
+    else {
+        while (!benchlingTenant) {
+            const tenantAnswer = await inquirer_1.default.prompt([
+                {
+                    type: "input",
+                    name: "tenant",
+                    message: "Benchling tenant (e.g., 'acme' for acme.benchling.com):",
+                    default: config.benchling?.tenant || "",
+                    filter: (value) => value.trim(),
+                    validate: (input) => input.trim().length > 0 || "Tenant is required",
+                },
+            ]);
+            const candidateTenant = tenantAnswer.tenant.trim();
+            const tenantValidation = await validateBenchlingTenant(candidateTenant);
+            if (tenantValidation.isValid) {
+                benchlingTenant = candidateTenant;
+                if (tenantValidation.warnings && tenantValidation.warnings.length > 0) {
+                    console.warn("");
+                    console.warn("⚠ Tenant validation warnings:");
+                    tenantValidation.warnings.forEach((warning) => console.warn(`  - ${warning}`));
+                    console.warn("");
+                }
+            }
+            else {
+                console.error("\n❌ Benchling tenant validation failed:");
+                tenantValidation.errors.forEach((err) => console.error(`  - ${err}`));
+                console.log("");
+            }
+        }
+    }
+    let manifestPath = (0, path_1.join)(process.cwd(), MANIFEST_FILENAME);
+    if (!nonInteractive) {
+        const manifestContent = (0, manifest_1.generateBenchlingManifest)({
+            catalogDomain: config.quilt?.catalog,
+            version: pkg.version,
+        });
+        let shouldWriteManifest = true;
+        if ((0, fs_1.existsSync)(manifestPath)) {
+            const { overwrite } = await inquirer_1.default.prompt([
+                {
+                    type: "confirm",
+                    name: "overwrite",
+                    message: `A manifest already exists at ${manifestPath}. Overwrite it?`,
+                    default: false,
+                },
+            ]);
+            shouldWriteManifest = overwrite;
+            if (!overwrite) {
+                console.log(`\nUsing existing manifest: ${manifestPath}`);
+            }
+        }
+        if (shouldWriteManifest) {
+            (0, fs_1.writeFileSync)(manifestPath, manifestContent, "utf-8");
+            console.log(`\n✓ Generated app manifest: ${manifestPath}`);
+        }
+        const manifestAppName = config.quilt?.catalog && config.quilt.catalog.length > 0
+            ? config.quilt.catalog.replace(/[.:]/g, "-")
+            : "Quilt Integration";
+        const instructions = chalk_1.default.bold("Create your Benchling app:\n\n") +
+            `1. Open ${chalk_1.default.cyan(`https://${benchlingTenant}.benchling.com/admin/apps`)}\n` +
+            "2. Click 'Create New App'\n" +
+            `3. Upload the manifest: ${chalk_1.default.cyan(manifestPath)}\n` +
+            "4. Create OAuth credentials and copy the Client ID / Secret\n" +
+            "5. Install the app (leave webhook URL blank for now)\n" +
+            "6. Copy the App Definition ID from the overview page\n";
+        console.log();
+        console.log((0, boxen_1.default)(instructions, {
+            padding: 1,
+            borderColor: "blue",
+            borderStyle: "round",
+        }));
+        console.log();
+        const { ready } = await inquirer_1.default.prompt([
+            {
+                type: "confirm",
+                name: "ready",
+                message: "Have you created and installed the Benchling app?",
+                default: true,
+            },
+        ]);
+        if (!ready) {
+            console.log("\n⏸  Setup paused. Re-run when ready:\n");
+            console.log(`  ${chalk_1.default.cyan("npx @quiltdata/benchling-webhook setup")}\n`);
+            process.exit(0);
+        }
+        console.log(`Using manifest app name: ${manifestAppName}\n`);
+    }
+    let benchlingClientId = config.benchling?.clientId?.trim();
+    let benchlingClientSecret = config.benchling?.clientSecret?.trim();
+    let benchlingAppDefinitionId = config.benchling?.appDefinitionId?.trim();
+    let benchlingTestEntryId = config.benchling?.testEntryId?.trim();
+    if (nonInteractive) {
+        if (!benchlingClientId || !benchlingClientSecret || !benchlingAppDefinitionId) {
+            throw new Error("Non-interactive mode requires Benchling clientId, clientSecret, and appDefinitionId to be configured");
+        }
+    }
+    else {
+        let credentialsValid = false;
+        while (!credentialsValid) {
+            const credentialAnswers = await inquirer_1.default.prompt([
+                {
+                    type: "input",
+                    name: "clientId",
+                    message: "Benchling OAuth Client ID:",
+                    default: benchlingClientId || "",
+                    filter: (value) => value.trim(),
+                    validate: (input) => input.trim().length > 0 || "Client ID is required",
+                },
+                {
+                    type: "password",
+                    name: "clientSecret",
+                    message: benchlingClientSecret
+                        ? "Benchling OAuth Client Secret (press Enter to keep existing):"
+                        : "Benchling OAuth Client Secret:",
+                },
+                {
+                    type: "input",
+                    name: "appDefinitionId",
+                    message: "Benchling App Definition ID:",
+                    default: benchlingAppDefinitionId || "",
+                    filter: (value) => value.trim(),
+                    validate: (input) => input.trim().length > 0 || "App Definition ID is required",
+                },
+                {
+                    type: "input",
+                    name: "testEntryId",
+                    message: "Benchling Test Entry ID (optional):",
+                    default: benchlingTestEntryId || "",
+                    filter: (value) => value.trim(),
+                },
+            ]);
+            const candidateSecret = credentialAnswers.clientSecret.trim().length === 0 && benchlingClientSecret
+                ? benchlingClientSecret
+                : credentialAnswers.clientSecret.trim();
+            if (!candidateSecret) {
+                console.error("\n❌ Benchling OAuth client secret is required\n");
+                continue;
+            }
+            const spinner = (0, ora_1.default)("Validating Benchling credentials...").start();
+            const validation = await validateBenchlingCredentials(benchlingTenant, credentialAnswers.clientId.trim(), candidateSecret);
+            if (validation.isValid) {
+                spinner.succeed("Benchling credentials validated");
+                if (validation.warnings && validation.warnings.length > 0) {
+                    console.warn("\n⚠ Credential validation warnings:");
+                    validation.warnings.forEach((warn) => console.warn(`  - ${warn}`));
+                    console.warn("");
+                }
+                benchlingClientId = credentialAnswers.clientId.trim();
+                benchlingClientSecret = candidateSecret;
+                benchlingAppDefinitionId = credentialAnswers.appDefinitionId.trim();
+                benchlingTestEntryId = credentialAnswers.testEntryId || undefined;
+                credentialsValid = true;
+            }
+            else {
+                spinner.fail("Benchling credential validation failed");
+                console.error("");
+                validation.errors.forEach((err) => console.error(`  - ${err}`));
+                console.error("");
+                const { retry } = await inquirer_1.default.prompt([
+                    {
+                        type: "confirm",
+                        name: "retry",
+                        message: "Credentials invalid. Try again?",
+                        default: true,
+                    },
+                ]);
+                if (!retry) {
+                    throw new Error("Setup aborted due to invalid Benchling credentials");
+                }
+            }
+        }
+    }
+    config.benchling = {
+        tenant: benchlingTenant,
+        clientId: benchlingClientId,
+        clientSecret: benchlingClientSecret,
+        appDefinitionId: benchlingAppDefinitionId,
+    };
+    if (benchlingTestEntryId && benchlingTestEntryId.length > 0) {
+        config.benchling.testEntryId = benchlingTestEntryId;
+    }
+    // Prompt for package configuration
+    console.log("\nPackage Storage Configuration\n");
+    const packageAnswers = await inquirer_1.default.prompt([
+        {
+            type: "input",
+            name: "bucket",
+            message: "Package S3 Bucket:",
+            default: config.packages?.bucket || config.quilt?.bucket,
+            validate: (input) => input.trim().length > 0 || "Bucket name is required",
+        },
+        {
+            type: "input",
+            name: "prefix",
+            message: "Package S3 prefix:",
+            default: config.packages?.prefix || "benchling",
+        },
+        {
+            type: "input",
+            name: "metadataKey",
+            message: "Package metadata key:",
+            default: config.packages?.metadataKey || "experiment_id",
+        },
+    ]);
+    config.packages = {
+        bucket: packageAnswers.bucket,
+        prefix: packageAnswers.prefix,
+        metadataKey: packageAnswers.metadataKey,
+    };
+    // Prompt for deployment configuration
+    console.log("\nDeployment Defaults\n");
+    const defaultAccount = config.deployment?.account || getAccountFromStackArn(config.quilt?.stackArn);
+    const deploymentAnswers = await inquirer_1.default.prompt([
+        {
+            type: "input",
+            name: "account",
+            message: "AWS Account ID:",
+            default: defaultAccount || "",
+            filter: (value) => value.trim(),
+            validate: (input) => input.trim().length === 0 || /^[0-9]{12}$/.test(input.trim()) || "Account ID must be a 12 digit number",
+        },
+        {
+            type: "input",
+            name: "region",
+            message: "AWS Deployment Region:",
+            default: config.deployment?.region || config.quilt?.region || "us-east-1",
+        },
+        {
+            type: "input",
+            name: "imageTag",
+            message: "Docker image tag:",
+            default: config.deployment?.imageTag || "latest",
+        },
+    ]);
+    config.deployment = {
+        ...(deploymentAnswers.account ? { account: deploymentAnswers.account } : {}),
+        region: deploymentAnswers.region,
+        imageTag: deploymentAnswers.imageTag,
+    };
+    // Optional: Logging configuration
+    console.log("\nSecurity and Logging Options\n");
+    const optionalAnswers = await inquirer_1.default.prompt([
+        {
+            type: "list",
+            name: "logLevel",
+            message: "Log level:",
+            choices: ["DEBUG", "INFO", "WARNING", "ERROR"],
+            default: config.logging?.level || "INFO",
+        },
         {
             type: "confirm",
-            name: "shouldDeploy",
-            message: "Would you like to deploy to AWS now?",
-            default: true,
+            name: "enableVerification",
+            message: "Enable webhook signature verification:",
+            default: config.security?.enableVerification !== false,
+        },
+        {
+            type: "input",
+            name: "webhookAllowList",
+            message: "Webhook IP allowlist (comma-separated, empty for none):",
+            default: config.security?.webhookAllowList || "",
         },
     ]);
-    if (shouldDeploy) {
-        console.log(chalk_1.default.cyan("\n📦 Starting deployment...\n"));
-        const { deployCommand } = await Promise.resolve().then(() => __importStar(require("./deploy")));
-        await deployCommand({});
-        console.log(chalk_1.default.green.bold("\n✓ Deployment complete!\n"));
-        console.log("Next steps:");
-        console.log(chalk_1.default.cyan("  • Set webhook URL in Benchling app settings"));
-        console.log(chalk_1.default.cyan("  • Install the app in your Benchling tenant"));
-        console.log(chalk_1.default.cyan("  • Test integration: npx @quiltdata/benchling-webhook test"));
+    config.logging = {
+        level: optionalAnswers.logLevel,
+    };
+    config.security = {
+        enableVerification: optionalAnswers.enableVerification,
+        webhookAllowList: optionalAnswers.webhookAllowList,
+    };
+    // Add metadata
+    const now = new Date().toISOString();
+    config._metadata = {
+        version: pkg.version,
+        createdAt: config._metadata?.createdAt || now,
+        updatedAt: now,
+        source: "wizard",
+    };
+    // Add inheritance marker if specified
+    if (inheritFrom) {
+        config._inherits = inheritFrom;
+    }
+    return config;
+}
+/**
+ * Main install wizard function
+ *
+ * Orchestrates the complete configuration workflow:
+ * 1. Load existing configuration (if any)
+ * 2. Infer Quilt configuration from AWS
+ * 3. Run interactive prompts for missing fields
+ * 4. Validate configuration
+ * 5. Save to XDG config directory
+ */
+async function runInstallWizard(options = {}) {
+    const { profile = "default", inheritFrom, nonInteractive = false, skipValidation = false, skipSecretsSync = false, skipDeployment = false, deployStage = "prod", awsProfile, awsRegion = "us-east-1", } = options;
+    const xdg = new xdg_config_1.XDGConfig();
+    console.log("\n╔═══════════════════════════════════════════════════════════╗");
+    const headerLine = `║   Benchling Webhook Setup (v${pkg.version})`;
+    console.log(`${headerLine.padEnd(59, " ")}║`);
+    console.log("╚═══════════════════════════════════════════════════════════╝\n");
+    // Step 1: Load existing configuration (if profile exists)
+    let existingConfig;
+    if (xdg.profileExists(profile)) {
+        console.log(`Loading existing configuration for profile: ${profile}\n`);
+        try {
+            existingConfig = inheritFrom
+                ? xdg.readProfileWithInheritance(profile, inheritFrom)
+                : xdg.readProfile(profile);
+        }
+        catch (error) {
+            console.warn(`Warning: Could not load existing config: ${error.message}`);
+        }
+    }
+    else if (inheritFrom) {
+        console.log(`Creating new profile '${profile}' inheriting from '${inheritFrom}'\n`);
+        try {
+            existingConfig = xdg.readProfile(inheritFrom);
+        }
+        catch (error) {
+            throw new Error(`Base profile '${inheritFrom}' not found: ${error.message}`);
+        }
+    }
+    // Step 2: Infer Quilt configuration (unless inheriting from another profile)
+    let quiltConfig = existingConfig?.quilt || {};
+    if (!inheritFrom || !existingConfig?.quilt) {
+        console.log("Step 1: Inferring Quilt configuration from AWS...\n");
+        try {
+            const inferenceResult = await (0, infer_quilt_config_1.inferQuiltConfig)({
+                region: awsRegion,
+                profile: awsProfile,
+                interactive: !nonInteractive,
+            });
+            // Map InferenceResult to QuiltConfig fields
+            if (inferenceResult.quiltStackArn) {
+                quiltConfig.stackArn = inferenceResult.quiltStackArn;
+            }
+            if (inferenceResult.catalogUrl) {
+                // Strip protocol and trailing slash to store only domain
+                quiltConfig.catalog = inferenceResult.catalogUrl.replace(/^https?:\/\//, "").replace(/\/$/, "");
+            }
+            if (inferenceResult.quiltUserBucket) {
+                quiltConfig.bucket = inferenceResult.quiltUserBucket;
+            }
+            if (inferenceResult.quiltDatabase) {
+                quiltConfig.database = inferenceResult.quiltDatabase;
+            }
+            if (inferenceResult.queueArn) {
+                const queueArn = inferenceResult.queueArn;
+                if (queueArn.startsWith("arn:aws:sqs:") || !quiltConfig.queueArn) {
+                    quiltConfig.queueArn = queueArn;
+                }
+            }
+            if (inferenceResult.quiltRegion) {
+                quiltConfig.region = inferenceResult.quiltRegion;
+            }
+            console.log("✓ Quilt configuration inferred\n");
+        }
+        catch (error) {
+            console.error(`Failed to infer Quilt configuration: ${error.message}`);
+            if (nonInteractive) {
+                throw error;
+            }
+            const { continueManually } = await inquirer_1.default.prompt([
+                {
+                    type: "confirm",
+                    name: "continueManually",
+                    message: "Continue and enter Quilt configuration manually?",
+                    default: true,
+                },
+            ]);
+            if (!continueManually) {
+                throw new Error("Setup aborted by user");
+            }
+        }
+    }
+    // Merge inferred Quilt config with existing config
+    const partialConfig = {
+        ...existingConfig,
+        quilt: {
+            ...existingConfig?.quilt,
+            ...quiltConfig,
+        },
+    };
+    // Step 3: Run interactive wizard for remaining configuration
+    let config = await runConfigWizard({
+        existingConfig: partialConfig,
+        nonInteractive,
+        inheritFrom,
+    });
+    // Step 4: Validate configuration
+    if (!skipValidation) {
+        console.log("\nValidating configuration...\n");
+        const validation = await validateConfig(config, {
+            skipValidation,
+            awsProfile,
+        });
+        if (!validation.isValid) {
+            console.error("\n❌ Configuration validation failed:");
+            validation.errors.forEach((err) => console.error(`  - ${err}`));
+            if (nonInteractive) {
+                throw new Error("Configuration validation failed");
+            }
+            const { proceed } = await inquirer_1.default.prompt([
+                {
+                    type: "confirm",
+                    name: "proceed",
+                    message: "Save configuration anyway?",
+                    default: false,
+                },
+            ]);
+            if (!proceed) {
+                throw new Error("Setup aborted by user");
+            }
+        }
+        else {
+            console.log("✓ Configuration validated successfully\n");
+        }
+        if (validation.warnings && validation.warnings.length > 0) {
+            console.warn("\n⚠ Warnings:");
+            validation.warnings.forEach((warn) => console.warn(`  - ${warn}`));
+            console.log("");
+        }
+    }
+    // Step 5: Persist configuration locally
+    console.log(`Saving configuration to profile: ${profile}...\n`);
+    try {
+        xdg.writeProfile(profile, config);
+        console.log(chalk_1.default.green(`✓ Configuration saved: ~/.config/benchling-webhook/${profile}/config.json\n`));
+    }
+    catch (error) {
+        throw new Error(`Failed to save configuration: ${error.message}`);
+    }
+    // Step 6: Sync secrets and deploy (unless skipped)
+    console.log(chalk_1.default.bold("Step 3: Deploy Stack and Return Webhook URL\n"));
+    if (skipSecretsSync) {
+        console.log(chalk_1.default.yellow("Skipping secrets sync (--skip-secrets-sync)."));
+        console.log(chalk_1.default.yellow(`Run \`npm run setup:sync-secrets -- --profile ${profile}\` when ready.\n`));
     }
     else {
-        console.log("\nNext steps:");
-        console.log(chalk_1.default.cyan("  • Run deployment: npx @quiltdata/benchling-webhook deploy"));
-        console.log(chalk_1.default.cyan("  • Test integration: npx @quiltdata/benchling-webhook test"));
+        console.log("Syncing secrets to AWS Secrets Manager...\n");
+        try {
+            await (0, sync_secrets_1.syncSecretsToAWS)({
+                profile,
+                awsProfile,
+                region: config.deployment.region,
+                force: true,
+            });
+            console.log(chalk_1.default.green("\n✓ Secrets synced to AWS Secrets Manager\n"));
+            // Reload config to capture secret ARN written by sync
+            config = xdg.readProfile(profile);
+        }
+        catch (error) {
+            throw new Error(`Secrets sync failed: ${error.message}`);
+        }
     }
-    console.log(chalk_1.default.dim("\nFor more information: https://github.com/quiltdata/benchling-webhook\n"));
+    if (skipDeployment) {
+        console.log(chalk_1.default.yellow("Skipping deployment (--skip-deployment)."));
+        console.log(chalk_1.default.yellow(`Run \`npm run deploy -- --profile ${profile} --stage ${deployStage}\` to deploy later.\n`));
+        return config;
+    }
+    if (!nonInteractive) {
+        console.log(`Deploy target: profile=${chalk_1.default.cyan(profile)}, stage=${chalk_1.default.cyan(deployStage)}, region=${chalk_1.default.cyan(config.deployment.region)}\n`);
+        const { confirmDeploy } = await inquirer_1.default.prompt([
+            {
+                type: "confirm",
+                name: "confirmDeploy",
+                message: "Deploy AWS infrastructure now? (takes ~5-10 minutes)",
+                default: true,
+            },
+        ]);
+        if (!confirmDeploy) {
+            console.log(chalk_1.default.yellow("\nDeployment skipped by user."));
+            console.log(chalk_1.default.yellow(`Re-run with \`npm run deploy -- --profile ${profile} --stage ${deployStage}\` when ready.\n`));
+            return config;
+        }
+    }
+    console.log("Deploying AWS infrastructure. This can take several minutes...\n");
+    await (0, deploy_1.deployCommand)({
+        profile,
+        stage: deployStage,
+        requireApproval: "never",
+        yes: true,
+    });
+    return config;
+}
+// =============================================================================
+// CLI COMMAND EXPORT
+// =============================================================================
+/**
+ * Setup wizard command handler
+ *
+ * @param options - Wizard options
+ * @returns Promise that resolves when wizard completes
+ */
+async function setupWizardCommand(options = {}) {
+    await runInstallWizard(options);
 }
 //# sourceMappingURL=setup-wizard.js.map