@quiltdata/benchling-webhook 0.7.7 → 0.7.8-20251115T063729Z

package/dist/lib/wizard/phase2-stack-query.js

@@ -0,0 +1,99 @@
+"use strict";
+/**
+ * Phase 2: Stack Query
+ *
+ * Queries CloudFormation stack for the confirmed catalog and extracts
+ * all available parameters including BenchlingSecret ARN.
+ *
+ * @module wizard/phase2-stack-query
+ */
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.runStackQuery = runStackQuery;
+const chalk_1 = __importDefault(require("chalk"));
+const infer_quilt_config_1 = require("../../bin/commands/infer-quilt-config");
+/**
+ * Phase 2: Stack Query
+ *
+ * Responsibilities:
+ * - Query CloudFormation stack for the confirmed catalog
+ * - Extract ALL available parameters from stack
+ * - Handle stack query failures gracefully
+ * - Return stack configuration
+ *
+ * @param catalogDns - Confirmed catalog DNS name
+ * @param options - Stack query options
+ * @returns Stack query result
+ */
+async function runStackQuery(catalogDns, options = {}) {
+    const { awsProfile, awsRegion, yes = false } = options;
+    console.log(`Querying CloudFormation stack for catalog: ${catalogDns}...\n`);
+    try {
+        // Use inferQuiltConfig with the confirmed catalog - this will skip quilt3 check
+        const inferenceResult = await (0, infer_quilt_config_1.inferQuiltConfig)({
+            region: awsRegion,
+            profile: awsProfile,
+            interactive: false, // Don't prompt - we already have the catalog
+            yes: true, // Auto-confirm - we already got user's catalog choice
+            catalogDns: catalogDns, // Pass the confirmed catalog
+        });
+        // Verify the inferred catalog matches our confirmed catalog
+        const normalizedInferred = inferenceResult.catalog?.replace(/^https?:\/\//, "").replace(/\/$/, "");
+        const normalizedConfirmed = catalogDns.replace(/^https?:\/\//, "").replace(/\/$/, "");
+        if (normalizedInferred !== normalizedConfirmed) {
+            console.log(chalk_1.default.yellow(`Warning: Inferred catalog (${normalizedInferred}) does not match confirmed catalog (${normalizedConfirmed})`));
+        }
+        // Extract data from inference result
+        if (!inferenceResult.stackArn) {
+            throw new Error(`No CloudFormation stack found for catalog: ${catalogDns}`);
+        }
+        const stackArn = inferenceResult.stackArn;
+        const database = inferenceResult.database || "quilt_catalog";
+        const queueUrl = inferenceResult.queueUrl || "";
+        const region = inferenceResult.region || awsRegion || "us-east-1";
+        const account = inferenceResult.account || "";
+        const benchlingSecretArn = inferenceResult.benchlingSecretArn;
+        // Log what we found
+        console.log(chalk_1.default.green("✓ Stack query succeeded\n"));
+        console.log(chalk_1.default.dim(`Stack ARN: ${stackArn}`));
+        console.log(chalk_1.default.dim(`Database: ${database}`));
+        console.log(chalk_1.default.dim(`Queue URL: ${queueUrl}`));
+        console.log(chalk_1.default.dim(`Region: ${region}`));
+        console.log(chalk_1.default.dim(`Account: ${account}`));
+        if (benchlingSecretArn) {
+            console.log(chalk_1.default.dim(`BenchlingSecret: ${benchlingSecretArn}`));
+        }
+        else {
+            console.log(chalk_1.default.dim("BenchlingSecret: Not found in stack"));
+        }
+        console.log("");
+        return {
+            stackArn,
+            catalog: normalizedConfirmed,
+            database,
+            queueUrl,
+            region,
+            account,
+            benchlingSecretArn,
+            stackQuerySucceeded: true,
+        };
+    }
+    catch (error) {
+        const errorMessage = error.message;
+        console.error(chalk_1.default.red(`Stack query failed: ${errorMessage}\n`));
+        // Return partial data for graceful degradation
+        return {
+            stackArn: "",
+            catalog: catalogDns,
+            database: "quilt_catalog",
+            queueUrl: "",
+            region: awsRegion || "us-east-1",
+            account: "",
+            benchlingSecretArn: undefined,
+            stackQuerySucceeded: false,
+        };
+    }
+}
+//# sourceMappingURL=phase2-stack-query.js.map

package/dist/lib/wizard/phase2-stack-query.js.map

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package/dist/lib/wizard/phase3-parameter-collection.d.ts

@@ -0,0 +1,24 @@
+/**
+ * Phase 3: Parameter Collection
+ *
+ * Collects all required parameters from the user, using stack query results
+ * as defaults to avoid re-prompting.
+ *
+ * @module wizard/phase3-parameter-collection
+ */
+import { ParameterCollectionInput, ParameterCollectionResult } from "./types";
+/**
+ * Phase 3: Parameter Collection
+ *
+ * Responsibilities:
+ * - Collect Benchling credentials
+ * - Collect package settings
+ * - Collect deployment configuration
+ * - Use stack query results as defaults (don't re-prompt)
+ * - Return complete configuration
+ *
+ * @param input - Parameter collection input
+ * @returns Parameter collection result
+ */
+export declare function runParameterCollection(input: ParameterCollectionInput): Promise<ParameterCollectionResult>;
+//# sourceMappingURL=phase3-parameter-collection.d.ts.map

package/dist/lib/wizard/phase3-parameter-collection.d.ts.map

@@ -0,0 +1 @@
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package/dist/lib/wizard/phase3-parameter-collection.js

@@ -0,0 +1,399 @@
+"use strict";
+/**
+ * Phase 3: Parameter Collection
+ *
+ * Collects all required parameters from the user, using stack query results
+ * as defaults to avoid re-prompting.
+ *
+ * @module wizard/phase3-parameter-collection
+ */
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.runParameterCollection = runParameterCollection;
+const inquirer_1 = __importDefault(require("inquirer"));
+const chalk_1 = __importDefault(require("chalk"));
+const manifest_1 = require("../../bin/commands/manifest");
+/**
+ * Phase 3: Parameter Collection
+ *
+ * Responsibilities:
+ * - Collect Benchling credentials
+ * - Collect package settings
+ * - Collect deployment configuration
+ * - Use stack query results as defaults (don't re-prompt)
+ * - Return complete configuration
+ *
+ * @param input - Parameter collection input
+ * @returns Parameter collection result
+ */
+async function runParameterCollection(input) {
+    const { stackQuery, existingConfig, yes = false } = input;
+    // =========================================================================
+    // Benchling Configuration
+    // =========================================================================
+    console.log(chalk_1.default.cyan("Benchling Configuration:"));
+    // Tenant
+    let tenant;
+    if (input.benchlingTenant) {
+        tenant = input.benchlingTenant;
+        console.log(`  Tenant: ${tenant} (from CLI)`);
+    }
+    else if (yes) {
+        // In non-interactive mode, use existing config or error
+        if (existingConfig?.benchling?.tenant) {
+            tenant = existingConfig.benchling.tenant;
+            console.log(`  Tenant: ${tenant} (from existing config)`);
+        }
+        else {
+            throw new Error("--benchling-tenant is required in non-interactive mode");
+        }
+    }
+    else {
+        // Always show prompt with default from existing config
+        const tenantAnswer = await inquirer_1.default.prompt([
+            {
+                type: "input",
+                name: "tenant",
+                message: "Benchling Tenant:",
+                default: existingConfig?.benchling?.tenant || "",
+                validate: (value) => value.trim().length > 0 || "Tenant is required",
+            },
+        ]);
+        tenant = tenantAnswer.tenant;
+    }
+    // Check if we have existing app - offer to reuse or create new
+    let shouldReuseApp = true; // Default to reusing existing app
+    const catalogChanged = existingConfig?.quilt?.catalog && existingConfig.quilt.catalog !== stackQuery.catalog;
+    if (existingConfig?.benchling?.appDefinitionId && !yes) {
+        // Show catalog change warning if applicable
+        if (catalogChanged) {
+            console.log("\n" + chalk_1.default.yellow(`Catalog changed from ${existingConfig.quilt.catalog} to ${stackQuery.catalog}`));
+        }
+        // Always ask if user wants to reuse existing app or create new one
+        const { reuseApp } = await inquirer_1.default.prompt([
+            {
+                type: "list",
+                name: "reuseApp",
+                message: "Benchling app configuration:",
+                choices: [
+                    {
+                        name: `Use existing app (${existingConfig.benchling.appDefinitionId})`,
+                        value: true,
+                    },
+                    {
+                        name: "Create new app for this catalog",
+                        value: false,
+                    },
+                ],
+                default: true,
+            },
+        ]);
+        shouldReuseApp = reuseApp;
+        if (!shouldReuseApp) {
+            console.log(chalk_1.default.dim("Will prompt for new app credentials\n"));
+        }
+    }
+    // App Definition ID
+    let appDefinitionId;
+    let hasAppDefId = false;
+    if (input.benchlingAppDefinitionId) {
+        appDefinitionId = input.benchlingAppDefinitionId;
+        hasAppDefId = true;
+        console.log(`  App Definition ID: ${appDefinitionId} (from CLI)`);
+    }
+    else if (yes) {
+        // In non-interactive mode, use existing config or error
+        if (existingConfig?.benchling?.appDefinitionId && shouldReuseApp) {
+            appDefinitionId = existingConfig.benchling.appDefinitionId;
+            hasAppDefId = true;
+            console.log(`  App Definition ID: ${appDefinitionId} (from existing config)`);
+        }
+        else {
+            throw new Error("--benchling-app-definition-id is required in non-interactive mode");
+        }
+    }
+    else if (existingConfig?.benchling?.appDefinitionId && shouldReuseApp) {
+        // Have existing app ID and user chose to reuse - show prompt with default
+        const appDefAnswer = await inquirer_1.default.prompt([
+            {
+                type: "input",
+                name: "appDefinitionId",
+                message: "Benchling App Definition ID:",
+                default: existingConfig.benchling.appDefinitionId,
+                validate: (value) => value.trim().length > 0 || "App definition ID is required",
+            },
+        ]);
+        appDefinitionId = appDefAnswer.appDefinitionId;
+        hasAppDefId = true;
+    }
+    else if (!shouldReuseApp) {
+        // User explicitly chose to create new app - skip to manifest generation
+        hasAppDefId = false;
+    }
+    else {
+        // No existing app ID and no choice made - ask if they have one
+        const hasAppDefIdAnswer = await inquirer_1.default.prompt([
+            {
+                type: "confirm",
+                name: "hasIt",
+                message: "Do you have a Benchling App Definition ID for this app?",
+                default: false,
+            },
+        ]);
+        hasAppDefId = hasAppDefIdAnswer.hasIt;
+        if (hasAppDefId) {
+            // Prompt for it
+            const appDefAnswer = await inquirer_1.default.prompt([
+                {
+                    type: "input",
+                    name: "appDefinitionId",
+                    message: "Benchling App Definition ID:",
+                    validate: (value) => value.trim().length > 0 || "App definition ID is required",
+                },
+            ]);
+            appDefinitionId = appDefAnswer.appDefinitionId;
+        }
+    }
+    if (!hasAppDefId) {
+        // They don't have it - create manifest and guide them
+        console.log("\n" + chalk_1.default.blue("Creating app manifest...") + "\n");
+        await (0, manifest_1.manifestCommand)({
+            catalog: stackQuery.catalog,
+            output: "app-manifest.yaml",
+        });
+        console.log("\n" + chalk_1.default.yellow("After you have installed the app in Benchling and have the App Definition ID, you can continue.") + "\n");
+        // Now ask for the app definition ID
+        const appDefAnswer = await inquirer_1.default.prompt([
+            {
+                type: "input",
+                name: "appDefinitionId",
+                message: "Benchling App Definition ID:",
+                validate: (value) => value.trim().length > 0 || "App definition ID is required to continue",
+            },
+        ]);
+        appDefinitionId = appDefAnswer.appDefinitionId;
+    }
+    // Validation: Exit if no app definition ID
+    if (!appDefinitionId || appDefinitionId.trim().length === 0) {
+        console.log("\n" + chalk_1.default.red("Setup cannot continue without an App Definition ID."));
+        console.log(chalk_1.default.yellow("Please install the app in Benchling first, then run setup again.\n"));
+        process.exit(0);
+    }
+    // OAuth Credentials
+    let clientId;
+    let clientSecret;
+    if (input.benchlingClientId && input.benchlingClientSecret) {
+        clientId = input.benchlingClientId;
+        clientSecret = input.benchlingClientSecret;
+        console.log(`  Client ID: ${clientId.substring(0, 8)}... (from CLI)`);
+        console.log("  Client Secret: ******** (from CLI)");
+    }
+    else if (yes) {
+        // In non-interactive mode, use existing config or error
+        if (existingConfig?.benchling?.clientId && existingConfig?.benchling?.clientSecret && shouldReuseApp) {
+            clientId = existingConfig.benchling.clientId;
+            clientSecret = existingConfig.benchling.clientSecret;
+            console.log(`  Client ID: ${clientId.substring(0, 8)}... (from existing config)`);
+            console.log("  Client Secret: ******** (from existing config)");
+        }
+        else {
+            throw new Error("--benchling-client-id and --benchling-client-secret are required in non-interactive mode");
+        }
+    }
+    else {
+        // Always show prompts with defaults from existing config (only if reusing app)
+        const hasExistingCreds = shouldReuseApp && existingConfig?.benchling?.clientId && existingConfig?.benchling?.clientSecret;
+        const credentialAnswers = await inquirer_1.default.prompt([
+            {
+                type: "input",
+                name: "clientId",
+                message: "Benchling OAuth Client ID:",
+                default: hasExistingCreds ? existingConfig?.benchling?.clientId : "",
+                validate: (value) => value.trim().length > 0 || "Client ID is required",
+            },
+            {
+                type: "password",
+                name: "clientSecret",
+                message: "Benchling OAuth Client Secret" +
+                    (hasExistingCreds ? " (press Enter to keep existing):" : ":"),
+                default: hasExistingCreds ? existingConfig?.benchling?.clientSecret : "",
+                validate: (value) => {
+                    // Allow empty input if we have existing credentials (will use default)
+                    if (hasExistingCreds && value.trim().length === 0) {
+                        return true;
+                    }
+                    return value.trim().length > 0 || "Client secret is required";
+                },
+            },
+        ]);
+        clientId = credentialAnswers.clientId;
+        // If user pressed Enter with empty input and we have existing creds, use the existing secret
+        clientSecret = credentialAnswers.clientSecret.trim() === "" && hasExistingCreds
+            ? existingConfig.benchling.clientSecret
+            : credentialAnswers.clientSecret;
+    }
+    // Test Entry ID (optional) - can be reused even when creating new app
+    let testEntryId;
+    if (input.benchlingTestEntryId) {
+        testEntryId = input.benchlingTestEntryId;
+        console.log(`  Test Entry ID: ${testEntryId} (from CLI)`);
+    }
+    else if (yes) {
+        // In non-interactive mode, use existing config if available
+        testEntryId = existingConfig?.benchling?.testEntryId;
+        if (testEntryId) {
+            console.log(`  Test Entry ID: ${testEntryId} (from existing config)`);
+        }
+    }
+    else {
+        // Always show prompt with default from existing config (even for new apps)
+        const existingTestEntryId = existingConfig?.benchling?.testEntryId;
+        const testEntryAnswer = await inquirer_1.default.prompt([
+            {
+                type: "input",
+                name: "testEntryId",
+                message: "Benchling Test Entry ID (optional)" +
+                    (existingTestEntryId ? " (press Enter to keep existing):" : ":"),
+                default: existingTestEntryId || "",
+            },
+        ]);
+        // Accept both empty (to keep existing) and new values
+        if (testEntryAnswer.testEntryId && testEntryAnswer.testEntryId.trim() !== "") {
+            testEntryId = testEntryAnswer.testEntryId.trim();
+        }
+        else if (existingTestEntryId) {
+            // User pressed Enter with existing value - keep it
+            testEntryId = existingTestEntryId;
+        }
+    }
+    // =========================================================================
+    // Package Configuration
+    // =========================================================================
+    console.log("\n" + chalk_1.default.cyan("Package Configuration:"));
+    let bucket;
+    let prefix;
+    let metadataKey;
+    if (input.userBucket && input.pkgPrefix && input.pkgKey) {
+        bucket = input.userBucket;
+        prefix = input.pkgPrefix;
+        metadataKey = input.pkgKey;
+        console.log(`  Bucket: ${bucket} (from CLI)`);
+        console.log(`  Prefix: ${prefix} (from CLI)`);
+        console.log(`  Metadata Key: ${metadataKey} (from CLI)`);
+    }
+    else if (yes) {
+        // In non-interactive mode, use CLI args or existing config or error
+        bucket = input.userBucket || existingConfig?.packages?.bucket || "";
+        prefix = input.pkgPrefix || existingConfig?.packages?.prefix || "benchling";
+        metadataKey = input.pkgKey || existingConfig?.packages?.metadataKey || "experiment_id";
+        if (!bucket) {
+            throw new Error("--user-bucket is required in non-interactive mode");
+        }
+        console.log(`  Bucket: ${bucket} (from ${input.userBucket ? 'CLI' : 'existing config'})`);
+        console.log(`  Prefix: ${prefix} (from ${input.pkgPrefix ? 'CLI' : existingConfig?.packages?.prefix ? 'existing config' : 'default'})`);
+        console.log(`  Metadata Key: ${metadataKey} (from ${input.pkgKey ? 'CLI' : existingConfig?.packages?.metadataKey ? 'existing config' : 'default'})`);
+    }
+    else {
+        // Always show prompts with defaults from existing config
+        const packageAnswers = await inquirer_1.default.prompt([
+            {
+                type: "input",
+                name: "bucket",
+                message: "Package S3 Bucket:",
+                default: existingConfig?.packages?.bucket || "",
+                validate: (value) => value.trim().length > 0 || "Bucket name is required",
+            },
+            {
+                type: "input",
+                name: "prefix",
+                message: "Package S3 prefix:",
+                default: existingConfig?.packages?.prefix || "benchling",
+            },
+            {
+                type: "input",
+                name: "metadataKey",
+                message: "Package metadata key:",
+                default: existingConfig?.packages?.metadataKey || "experiment_id",
+            },
+        ]);
+        bucket = packageAnswers.bucket;
+        prefix = packageAnswers.prefix;
+        metadataKey = packageAnswers.metadataKey;
+    }
+    // =========================================================================
+    // Deployment Configuration
+    // =========================================================================
+    console.log("\n" + chalk_1.default.cyan("Deployment Configuration:"));
+    const region = stackQuery.region;
+    const account = stackQuery.account;
+    console.log(`  Region: ${region} (from stack)`);
+    console.log(`  Account: ${account} (from stack)`);
+    // =========================================================================
+    // Optional Configuration
+    // =========================================================================
+    console.log("\n" + chalk_1.default.cyan("Optional Configuration:"));
+    let logLevel;
+    let webhookAllowList;
+    if (input.logLevel && input.webhookAllowList !== undefined) {
+        logLevel = input.logLevel;
+        webhookAllowList = input.webhookAllowList;
+        console.log(`  Log Level: ${logLevel} (from CLI)`);
+        console.log(`  Webhook Allow List: ${webhookAllowList || "(none)"} (from CLI)`);
+    }
+    else if (yes) {
+        // In non-interactive mode, use CLI args or existing config or defaults
+        logLevel = input.logLevel || existingConfig?.logging?.level || "INFO";
+        webhookAllowList = input.webhookAllowList ?? existingConfig?.security?.webhookAllowList ?? "";
+        console.log(`  Log Level: ${logLevel} (from ${input.logLevel ? 'CLI' : existingConfig?.logging?.level ? 'existing config' : 'default'})`);
+        console.log(`  Webhook Allow List: ${webhookAllowList || "(none)"} (from ${input.webhookAllowList !== undefined ? 'CLI' : existingConfig?.security?.webhookAllowList ? 'existing config' : 'default'})`);
+    }
+    else {
+        // Always show prompts with defaults from existing config
+        const optionalAnswers = await inquirer_1.default.prompt([
+            {
+                type: "list",
+                name: "logLevel",
+                message: "Log level:",
+                choices: ["DEBUG", "INFO", "WARNING", "ERROR"],
+                default: existingConfig?.logging?.level || "INFO",
+            },
+            {
+                type: "input",
+                name: "webhookAllowList",
+                message: "Webhook IP allowlist (comma-separated, empty for none):",
+                default: existingConfig?.security?.webhookAllowList || "",
+            },
+        ]);
+        logLevel = optionalAnswers.logLevel;
+        webhookAllowList = optionalAnswers.webhookAllowList;
+    }
+    console.log(""); // Empty line for spacing
+    return {
+        benchling: {
+            tenant,
+            clientId,
+            clientSecret,
+            appDefinitionId,
+            testEntryId,
+        },
+        packages: {
+            bucket,
+            prefix,
+            metadataKey,
+        },
+        deployment: {
+            region,
+            account,
+        },
+        logging: {
+            level: logLevel,
+        },
+        security: {
+            enableVerification: true,
+            webhookAllowList,
+        },
+    };
+}
+//# sourceMappingURL=phase3-parameter-collection.js.map

package/dist/lib/wizard/phase3-parameter-collection.js.map

@@ -0,0 +1 @@
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package/dist/lib/wizard/phase4-validation.d.ts

@@ -0,0 +1,22 @@
+/**
+ * Phase 4: Validation
+ *
+ * Validates all collected parameters before proceeding to mode decision.
+ *
+ * @module wizard/phase4-validation
+ */
+import { ValidationInput, ValidationResult } from "./types";
+/**
+ * Phase 4: Validation
+ *
+ * Responsibilities:
+ * - Validate Benchling credentials (OAuth test)
+ * - Validate S3 bucket access
+ * - Validate app definition ID exists
+ * - Return validation result with errors
+ *
+ * @param input - Validation input
+ * @returns Validation result
+ */
+export declare function runValidation(input: ValidationInput): Promise<ValidationResult>;
+//# sourceMappingURL=phase4-validation.d.ts.map

package/dist/lib/wizard/phase4-validation.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"phase4-validation.d.ts","sourceRoot":"","sources":["../../../lib/wizard/phase4-validation.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAMH,OAAO,EAAE,eAAe,EAAE,gBAAgB,EAAE,MAAM,SAAS,CAAC;AAsO5D;;;;;;;;;;;GAWG;AACH,wBAAsB,aAAa,CAAC,KAAK,EAAE,eAAe,GAAG,OAAO,CAAC,gBAAgB,CAAC,CA4DrF"}