@quiltdata/benchling-webhook 0.4.13 → 0.5.0-20251029T180511Z

package/dist/bin/commands/init.js

@@ -0,0 +1,155 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.initCommand = initCommand;
+const fs_1 = require("fs");
+const path_1 = require("path");
+const chalk_1 = __importDefault(require("chalk"));
+const ora_1 = __importDefault(require("ora"));
+const boxen_1 = __importDefault(require("boxen"));
+const enquirer_1 = require("enquirer");
+const benchling_webhook_1 = require("../benchling-webhook");
+async function initCommand(options) {
+    console.log((0, boxen_1.default)(chalk_1.default.bold("Benchling Webhook Setup"), {
+        padding: 1,
+        borderColor: "cyan",
+        borderStyle: "round",
+    }));
+    console.log();
+    console.log("Let's configure your deployment. You'll need:");
+    console.log("  • Access to your Quilt catalog");
+    console.log("  • An S3 bucket for storing data");
+    console.log("  • Benchling API credentials");
+    console.log();
+    console.log(chalk_1.default.dim("Press Ctrl+C at any time to cancel."));
+    console.log();
+    // Check if output file exists
+    const outputPath = (0, path_1.resolve)(options.output || ".env");
+    if ((0, fs_1.existsSync)(outputPath) && !options.force) {
+        console.error(chalk_1.default.yellow(`⚠️  File already exists: ${outputPath}`));
+        console.error();
+        const response = await (0, enquirer_1.prompt)({
+            type: "confirm",
+            name: "overwrite",
+            message: "Overwrite existing file?",
+            initial: false,
+        });
+        if (!response.overwrite) {
+            console.log(chalk_1.default.yellow("Setup cancelled"));
+            process.exit(0);
+        }
+        console.log();
+    }
+    // Prompt for required values
+    const answers = await (0, enquirer_1.prompt)([
+        {
+            type: "input",
+            name: "catalog",
+            message: "Quilt catalog URL (domain only):",
+            initial: "quilt-catalog.company.com",
+            validate: (value) => /^[a-z0-9.-]+\.[a-z]{2,}$/i.test(value) || "Please enter a valid domain name",
+        },
+        {
+            type: "input",
+            name: "bucket",
+            message: "S3 data bucket name:",
+            initial: "my-data-bucket",
+            validate: (value) => /^[a-z0-9.-]{3,63}$/.test(value) || "Please enter a valid S3 bucket name",
+        },
+        {
+            type: "input",
+            name: "tenant",
+            message: "Benchling tenant (XXX if you login to XXX.benchling.com):",
+            validate: (value) => value.trim().length > 0 || "Tenant is required",
+        },
+        {
+            type: "input",
+            name: "clientId",
+            message: "Benchling OAuth client ID:",
+            validate: (value) => value.trim().length > 0 || "Client ID is required",
+        },
+        {
+            type: "password",
+            name: "clientSecret",
+            message: "Benchling OAuth client secret:",
+            validate: (value) => value.trim().length > 0 || "Client secret is required",
+        },
+        {
+            type: "input",
+            name: "appId",
+            message: "Benchling app definition ID:",
+            validate: (value) => value.trim().length > 0 || "App definition ID is required",
+        },
+    ]);
+    // Build .env content
+    const envLines = [];
+    envLines.push("# ==============================================================================");
+    envLines.push("# Benchling Webhook Configuration");
+    envLines.push("# ==============================================================================");
+    envLines.push("# Generated by: npx @quiltdata/benchling-webhook init");
+    envLines.push("# Date: " + new Date().toISOString());
+    envLines.push("# ==============================================================================");
+    envLines.push("");
+    envLines.push("# Quilt Configuration");
+    envLines.push(`QUILT_CATALOG=${answers.catalog}`);
+    envLines.push(`QUILT_USER_BUCKET=${answers.bucket}`);
+    envLines.push("");
+    envLines.push("# Benchling Configuration");
+    envLines.push(`BENCHLING_TENANT=${answers.tenant}`);
+    envLines.push(`BENCHLING_CLIENT_ID=${answers.clientId}`);
+    envLines.push(`BENCHLING_CLIENT_SECRET=${answers.clientSecret}`);
+    envLines.push(`BENCHLING_APP_DEFINITION_ID=${answers.appId}`);
+    envLines.push("");
+    // Attempt inference if requested
+    let inferredVars = {};
+    if (options.infer !== false) {
+        console.log();
+        const spinner = (0, ora_1.default)("Inferring additional configuration from catalog...").start();
+        const inferenceResult = await (0, benchling_webhook_1.inferConfiguration)(answers.catalog);
+        if (inferenceResult.success) {
+            inferredVars = inferenceResult.inferredVars;
+            spinner.succeed("Successfully inferred additional configuration");
+            if (inferredVars.CDK_DEFAULT_ACCOUNT) {
+                envLines.push("# AWS Configuration (inferred)");
+                envLines.push(`CDK_DEFAULT_ACCOUNT=${inferredVars.CDK_DEFAULT_ACCOUNT}`);
+                envLines.push(`CDK_DEFAULT_REGION=${inferredVars.CDK_DEFAULT_REGION}`);
+                envLines.push("");
+            }
+            if (inferredVars.QUEUE_NAME) {
+                envLines.push("# SQS Configuration (inferred)");
+                envLines.push(`QUEUE_NAME=${inferredVars.QUEUE_NAME}`);
+                envLines.push(`SQS_QUEUE_URL=${inferredVars.SQS_QUEUE_URL}`);
+                envLines.push("");
+            }
+            if (inferredVars.QUILT_DATABASE) {
+                envLines.push("# Quilt Database (inferred)");
+                envLines.push(`QUILT_DATABASE=${inferredVars.QUILT_DATABASE}`);
+                envLines.push("");
+            }
+        }
+        else {
+            spinner.warn(`Could not infer additional configuration: ${inferenceResult.error}`);
+        }
+    }
+    // Add optional configuration section
+    if (!options.minimal) {
+        envLines.push("# Optional Configuration");
+        envLines.push("# PKG_PREFIX=benchling");
+        envLines.push("# LOG_LEVEL=INFO");
+        envLines.push("# ENABLE_WEBHOOK_VERIFICATION=true");
+        envLines.push("");
+    }
+    // Write file
+    (0, fs_1.writeFileSync)(outputPath, envLines.join("\n"));
+    console.log();
+    console.log((0, boxen_1.default)(`${chalk_1.default.green.bold("✓ Configuration saved!")}\n\n` +
+        `File: ${chalk_1.default.cyan(outputPath)}\n\n` +
+        `${chalk_1.default.bold("Next steps:")}\n` +
+        `  1. Review ${outputPath} and verify all values\n` +
+        `  2. Run: ${chalk_1.default.cyan("npx @quiltdata/benchling-webhook deploy")}\n` +
+        "  3. Configure your Benchling app\n\n" +
+        `${chalk_1.default.dim("For help: npx @quiltdata/benchling-webhook --help")}`, { padding: 1, borderColor: "green", borderStyle: "round" }));
+}
+//# sourceMappingURL=init.js.map

package/dist/bin/commands/init.js.map

@@ -0,0 +1 @@
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package/dist/bin/commands/validate.d.ts

@@ -0,0 +1,5 @@
+import { type ConfigOptions } from "../../lib/utils/config";
+export declare function validateCommand(options: ConfigOptions & {
+    verbose?: boolean;
+}): Promise<void>;
+//# sourceMappingURL=validate.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/bin/commands/validate.js

@@ -0,0 +1,135 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.validateCommand = validateCommand;
+const chalk_1 = __importDefault(require("chalk"));
+const ora_1 = __importDefault(require("ora"));
+const boxen_1 = __importDefault(require("boxen"));
+const child_process_1 = require("child_process");
+const config_1 = require("../../lib/utils/config");
+const benchling_webhook_1 = require("../benchling-webhook");
+async function validateCommand(options) {
+    console.log((0, boxen_1.default)(chalk_1.default.bold("Configuration Validation"), {
+        padding: 1,
+        borderColor: "yellow",
+        borderStyle: "round",
+    }));
+    console.log();
+    // 1. Load configuration
+    const spinner = (0, ora_1.default)("Loading configuration...").start();
+    let config = (0, config_1.loadConfigSync)(options);
+    spinner.succeed(`Configuration loaded from: ${options.envFile || ".env"}`);
+    // 2. Attempt inference
+    if (config.quiltCatalog) {
+        spinner.start("Inferring additional configuration from catalog...");
+        const inferenceResult = await (0, benchling_webhook_1.inferConfiguration)(config.quiltCatalog);
+        if (inferenceResult.success) {
+            config = (0, config_1.mergeInferredConfig)(config, inferenceResult.inferredVars);
+            spinner.succeed("Configuration inferred from catalog");
+        }
+        else {
+            spinner.warn(`Could not infer configuration: ${inferenceResult.error}`);
+        }
+    }
+    // 3. Validate
+    spinner.start("Validating configuration...");
+    const validation = (0, config_1.validateConfig)(config);
+    if (validation.valid) {
+        spinner.succeed("Configuration is valid");
+    }
+    else {
+        spinner.fail("Configuration validation failed");
+    }
+    // 4. Display results
+    console.log();
+    if (options.verbose || !validation.valid) {
+        console.log(chalk_1.default.bold("Configuration Summary:"));
+        console.log(chalk_1.default.gray("─".repeat(80)));
+        console.log();
+        // Required user values
+        console.log(chalk_1.default.bold("Required user values:"));
+        const userFields = [
+            "quiltCatalog",
+            "quiltUserBucket",
+            "benchlingTenant",
+            "benchlingClientId",
+            "benchlingClientSecret",
+            "benchlingAppDefinitionId",
+        ];
+        for (const field of userFields) {
+            const value = config[field];
+            const status = value ? chalk_1.default.green("✓") : chalk_1.default.red("✗");
+            const display = value || chalk_1.default.gray("(not set)");
+            console.log(`  ${status} ${field}: ${display}`);
+        }
+        console.log();
+        // Inferred values
+        console.log(chalk_1.default.bold("Inferred values:"));
+        const inferredFields = [
+            "cdkAccount",
+            "cdkRegion",
+            "queueName",
+            "sqsQueueUrl",
+            "quiltDatabase",
+        ];
+        for (const field of inferredFields) {
+            const value = config[field];
+            const status = value ? chalk_1.default.green("✓") : chalk_1.default.red("✗");
+            const display = value || chalk_1.default.gray("(could not infer)");
+            console.log(`  ${status} ${field}: ${display}`);
+        }
+        console.log();
+    }
+    // 5. Check AWS credentials
+    spinner.start("Checking AWS credentials...");
+    try {
+        const accountId = (0, child_process_1.execSync)("aws sts get-caller-identity --query Account --output text", {
+            encoding: "utf-8",
+        }).trim();
+        spinner.succeed(`AWS credentials configured (account: ${accountId})`);
+    }
+    catch {
+        spinner.fail("AWS credentials not configured");
+        console.log();
+        console.log(chalk_1.default.yellow("To configure AWS credentials, run:"));
+        console.log(chalk_1.default.cyan("  aws configure"));
+        console.log();
+    }
+    // 6. Check CDK bootstrap
+    if (config.cdkAccount && config.cdkRegion) {
+        spinner.start("Checking CDK bootstrap status...");
+        const bootstrapStatus = await (0, benchling_webhook_1.checkCdkBootstrap)(config.cdkAccount, config.cdkRegion);
+        if (bootstrapStatus.bootstrapped) {
+            spinner.succeed(`CDK is bootstrapped (${bootstrapStatus.status})`);
+        }
+        else {
+            spinner.fail("CDK is not bootstrapped");
+            console.log();
+            console.log(chalk_1.default.yellow("To bootstrap CDK, run:"));
+            console.log(chalk_1.default.cyan(`  ${bootstrapStatus.command}`));
+            console.log();
+        }
+    }
+    // 7. Final result
+    console.log();
+    console.log(chalk_1.default.gray("─".repeat(80)));
+    if (validation.valid) {
+        console.log();
+        console.log((0, boxen_1.default)(`${chalk_1.default.green.bold("✓ Configuration is valid!")}\n\n` +
+            "Ready to deploy.\n\n" +
+            `Run: ${chalk_1.default.cyan("npx @quiltdata/benchling-webhook deploy")}`, { padding: 1, borderColor: "green", borderStyle: "round" }));
+    }
+    else {
+        console.log();
+        console.error(chalk_1.default.red.bold("❌ Configuration is invalid\n"));
+        console.error((0, config_1.formatValidationErrors)(validation));
+        console.log(chalk_1.default.yellow("To fix this:"));
+        console.log("  1. Run: " + chalk_1.default.cyan("npx @quiltdata/benchling-webhook init"));
+        console.log("  2. Or edit your .env file to add missing values");
+        console.log();
+        process.exit(1);
+    }
+}
+//# sourceMappingURL=validate.js.map

package/dist/bin/commands/validate.js.map

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package/dist/bin/get-env.js

@@ -0,0 +1,180 @@
+#!/usr/bin/env node
+/**
+ * Get environment configuration from a Quilt catalog's config.json
+ *
+ * This script fetches config.json from a Quilt catalog URL and attempts to:
+ * 1. Parse the configuration
+ * 2. Query AWS CloudFormation to find the stack using resource identifiers
+ * 3. Extract stack outputs and parameters
+ * 4. Generate environment variables for .env
+ *
+ * Usage:
+ *   node bin/get-env.js https://quilt-catalog.yourcompany.com
+ *   node bin/get-env.js https://quilt-catalog.yourcompany.com --write
+ */
+
+const fs = require("fs");
+const path = require("path");
+
+// Import utility functions from lib/utils
+const { inferStackConfig } = require("../lib/utils/stack-inference");
+
+// Parse command line arguments (only when run directly)
+let args, catalogUrl, outputFile, writeFile;
+if (require.main === module) {
+    args = process.argv.slice(2);
+    catalogUrl = args.find((arg) => !arg.startsWith("--"));
+    outputFile = args.find((arg) => arg.startsWith("--output="))?.split("=")[1];
+    writeFile = args.includes("--write");
+
+    if (!catalogUrl || args.includes("--help") || args.includes("-h")) {
+        printHelp();
+        process.exit(catalogUrl ? 0 : 1);
+    }
+}
+
+// CLI-specific functions moved to lib/utils/stack-inference.ts
+// Re-export for backward compatibility if needed
+
+/**
+ * Format environment variables for output
+ */
+function formatEnvVars(vars) {
+    const lines = [];
+
+    lines.push("# ==============================================================================");
+    lines.push("# INFERRED CONFIGURATION");
+    lines.push("# ==============================================================================");
+    lines.push("# Generated by: bin/get-env.js");
+    lines.push("# Date: " + new Date().toISOString());
+    lines.push("#");
+    lines.push("# ⚠️  IMPORTANT: Review and verify all values before using!");
+    lines.push("#    Some values may need manual verification or completion.");
+    lines.push("# ==============================================================================");
+    lines.push("");
+
+    for (const [key, value] of Object.entries(vars)) {
+        if (key.startsWith("#")) {
+            lines.push(`${key}: ${value}`);
+        } else {
+            lines.push(`${key}=${value}`);
+        }
+    }
+
+    lines.push("");
+    lines.push("# ==============================================================================");
+    lines.push("# REQUIRED VALUES NOT INFERRED - Must be filled manually");
+    lines.push("# ==============================================================================");
+    lines.push("PREFIX=benchling-webhook");
+    lines.push("BENCHLING_TENANT=your-tenant");
+    lines.push("BENCHLING_CLIENT_ID=your-client-id");
+    lines.push("BENCHLING_CLIENT_SECRET=your-client-secret");
+    lines.push("BENCHLING_APP=benchling-webhook");
+    lines.push("BENCHLING_API_KEY=your-api-key");
+    lines.push("BENCHLING_APP_DEFINITION_ID=appdef_your_id_here");
+    lines.push("ENABLE_WEBHOOK_VERIFICATION=true");
+    lines.push("BENCHLING_TEST_ENTRY=etr_123456789");
+    lines.push("");
+
+    return lines.join("\n");
+}
+
+/**
+ * Print help
+ */
+function printHelp() {
+    console.log("Usage: node bin/get-env.js <catalog-url> [options]");
+    console.log("");
+    console.log("Arguments:");
+    console.log("  catalog-url    URL of Quilt catalog (e.g., https://quilt-catalog.yourcompany.com)");
+    console.log("");
+    console.log("Options:");
+    console.log("  --output=FILE  Write output to FILE instead of stdout");
+    console.log("  --write        Write to env.inferred by default (without dot - user-visible)");
+    console.log("  --help, -h     Show this help message");
+    console.log("");
+    console.log("Examples:");
+    console.log("  node bin/get-env.js https://nightly.quilttest.com");
+    console.log("  node bin/get-env.js https://nightly.quilttest.com --write");
+    console.log("  node bin/get-env.js https://nightly.quilttest.com --output=env.staging");
+    console.log("");
+    console.log("Description:");
+    console.log("  This script fetches config.json from a Quilt catalog and infers");
+    console.log("  environment variables needed for benchling-webhook deployment by:");
+    console.log("  1. Parsing the catalog configuration");
+    console.log("  2. Querying AWS CloudFormation to find the associated stack");
+    console.log("  3. Extracting stack outputs and parameters");
+    console.log("  4. Generating environment variable assignments");
+    console.log("");
+    console.log("Requirements:");
+    console.log("  - AWS CLI installed and configured");
+    console.log("  - AWS credentials with CloudFormation read permissions");
+    console.log("  - Network access to the catalog URL");
+}
+
+/**
+ * Main execution
+ */
+async function main() {
+    try {
+        const result = await inferStackConfig(catalogUrl);
+
+        // Format output
+        const output = formatEnvVars(result.inferredVars);
+
+        // Print summary
+        console.log("=".repeat(80));
+        console.log("INFERRED CONFIGURATION");
+        console.log("=".repeat(80));
+        console.log("");
+        console.log(output);
+        console.log("");
+
+        // Write to file if requested
+        const targetFile = outputFile || (writeFile ? "env.inferred" : null);
+        if (targetFile) {
+            const fullPath = path.resolve(targetFile);
+
+            // Check if .env already exists and warn before proceeding
+            const envPath = path.resolve(".env");
+            if (fs.existsSync(envPath)) {
+                console.log("⚠️  NOTICE: A .env file already exists!");
+                console.log(`   Writing to ${targetFile} instead to avoid overwriting your configuration.`);
+                console.log("");
+            }
+
+            fs.writeFileSync(fullPath, output);
+            console.log("=".repeat(80));
+            console.log(`✓ Configuration written to: ${fullPath}`);
+            console.log("=".repeat(80));
+            console.log("");
+            console.log("Next steps:");
+            console.log("  1. Review the generated file and verify all values");
+            console.log("  2. Fill in the REQUIRED VALUES section with your Benchling credentials");
+            if (fs.existsSync(envPath)) {
+                console.log("  3. Carefully merge with your existing .env file (DO NOT overwrite!)");
+                console.log("     Compare: diff .env env.inferred");
+            } else {
+                console.log("  3. Copy to .env when ready: cp env.inferred .env");
+            }
+            console.log("");
+        } else {
+            console.log("=".repeat(80));
+            console.log("To save this configuration, run:");
+            console.log(`  node bin/get-env.js ${catalogUrl} --write`);
+            console.log("=".repeat(80));
+            console.log("");
+        }
+
+    } catch (error) {
+        console.error("Error:", error.message);
+        process.exit(1);
+    }
+}
+
+if (require.main === module) {
+    main();
+}
+
+// For backward compatibility, re-export from the new location
+module.exports = require("../lib/utils/stack-inference");