@quiltdata/benchling-webhook 0.7.7 → 0.7.9

package/dist/lib/utils/config.js

@@ -1,15 +1,16 @@
 "use strict";
+/**
+ * Configuration Utilities
+ *
+ * Legacy configuration types and utility functions.
+ * Most configuration loading now happens via XDG profiles (see lib/xdg-config.ts).
+ */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getQuilt3Catalog = getQuilt3Catalog;
-exports.loadDotenv = loadDotenv;
 exports.processBenchlingSecretsInput = processBenchlingSecretsInput;
 exports.maskArn = maskArn;
-exports.loadConfigSync = loadConfigSync;
-exports.mergeInferredConfig = mergeInferredConfig;
 exports.validateConfig = validateConfig;
 exports.formatValidationErrors = formatValidationErrors;
-const dotenv_1 = require("dotenv");
-const dotenv_expand_1 = require("dotenv-expand");
 const fs_1 = require("fs");
 const path_1 = require("path");
 const child_process_1 = require("child_process");
@@ -34,24 +35,6 @@ function getQuilt3Catalog() {
     }
     return undefined;
 }
-/**
- * Load .env file and expand variables
- */
-function loadDotenv(filePath) {
-    const resolvedPath = (0, path_1.resolve)(filePath);
-    if (!(0, fs_1.existsSync)(resolvedPath)) {
-        return {};
-    }
-    const result = (0, dotenv_1.config)({ path: resolvedPath });
-    if (result.error) {
-        throw new Error(`Failed to load ${filePath}: ${result.error.message}`);
-    }
-    // Expand variables like ${VAR}
-    if (result.parsed) {
-        (0, dotenv_expand_1.expand)(result);
-    }
-    return result.parsed || {};
-}
 /**
  * Process benchling-secrets parameter, handling @file.json syntax
  *
@@ -130,71 +113,6 @@ function maskArn(arn) {
     // Return as-is if pattern doesn't match
     return arn;
 }
-/**
- * Load configuration from multiple sources with priority:
- * 1. CLI options (highest)
- * 2. Environment variables
- * 3. .env file
- * 4. quilt3 config (for catalog only)
- * 5. Inferred values (will be added separately)
- */
-function loadConfigSync(options = {}) {
-    // 1. Load .env file
-    const envFile = options.envFile || ".env";
-    const dotenvVars = (0, fs_1.existsSync)(envFile) ? loadDotenv(envFile) : {};
-    // 2. Merge with process.env
-    const envVars = { ...dotenvVars, ...process.env };
-    // 3. Try to get catalog from quilt3 config as fallback
-    const quilt3Catalog = getQuilt3Catalog();
-    // 4. Build config with CLI options taking priority
-    const config = {
-        // Quilt
-        quiltCatalog: options.catalog || envVars.QUILT_CATALOG || quilt3Catalog,
-        quiltUserBucket: options.bucket || envVars.QUILT_USER_BUCKET,
-        quiltDatabase: envVars.QUILT_DATABASE,
-        // Benchling
-        benchlingTenant: options.tenant || envVars.BENCHLING_TENANT,
-        benchlingClientId: options.clientId || envVars.BENCHLING_CLIENT_ID,
-        benchlingClientSecret: options.clientSecret || envVars.BENCHLING_CLIENT_SECRET,
-        benchlingAppDefinitionId: options.appId || envVars.BENCHLING_APP_DEFINITION_ID,
-        // Unified secrets (priority: CLI > env > .env)
-        // Process file input syntax (@file.json) if present
-        benchlingSecrets: (() => {
-            const rawSecrets = options.benchlingSecrets || envVars.BENCHLING_SECRETS;
-            return rawSecrets ? processBenchlingSecretsInput(rawSecrets) : undefined;
-        })(),
-        // AWS
-        cdkAccount: envVars.CDK_DEFAULT_ACCOUNT,
-        cdkRegion: options.region || envVars.CDK_DEFAULT_REGION || envVars.AWS_REGION,
-        awsProfile: options.profile || envVars.AWS_PROFILE,
-        // SQS
-        queueUrl: envVars.QUEUE_URL,
-        // Optional
-        pkgPrefix: envVars.PKG_PREFIX || "benchling",
-        pkgKey: envVars.PKG_KEY || "experiment_id",
-        logLevel: envVars.LOG_LEVEL || "INFO",
-        webhookAllowList: envVars.WEBHOOK_ALLOW_LIST,
-        enableWebhookVerification: envVars.ENABLE_WEBHOOK_VERIFICATION ?? "true",
-        createEcrRepository: envVars.CREATE_ECR_REPOSITORY,
-        ecrRepositoryName: envVars.ECR_REPOSITORY_NAME || "quiltdata/benchling",
-        imageTag: options.imageTag || envVars.IMAGE_TAG || "latest",
-    };
-    // Remove undefined values
-    return Object.fromEntries(Object.entries(config).filter(([, v]) => v !== undefined));
-}
-/**
- * Merge inferred configuration with loaded config
- */
-function mergeInferredConfig(config, inferredVars) {
-    // Only use inferred values if not already set
-    return {
-        cdkAccount: config.cdkAccount || inferredVars.CDK_DEFAULT_ACCOUNT,
-        cdkRegion: config.cdkRegion || inferredVars.CDK_DEFAULT_REGION,
-        queueUrl: config.queueUrl || inferredVars.QUEUE_URL,
-        quiltDatabase: config.quiltDatabase || inferredVars.QUILT_DATABASE,
-        ...config, // User values always take precedence
-    };
-}
 /**
  * Validate configuration and return detailed errors
  */

package/dist/lib/utils/config.js.map

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package/dist/lib/utils/stack-parameter-update.d.ts

@@ -0,0 +1,37 @@
+/**
+ * CloudFormation stack parameter update utility
+ *
+ * Provides safe parameter updates with UsePreviousValue for all other parameters
+ *
+ * @module utils/stack-parameter-update
+ */
+export interface StackParameterUpdateOptions {
+    stackArn: string;
+    region: string;
+    parameterKey: string;
+    parameterValue: string;
+    awsProfile?: string;
+}
+export interface StackParameterUpdateResult {
+    success: boolean;
+    stackId?: string;
+    error?: string;
+}
+/**
+ * Updates a single CloudFormation stack parameter while preserving all others
+ *
+ * @param options - Update options
+ * @returns Update result
+ */
+export declare function updateStackParameter(options: StackParameterUpdateOptions): Promise<StackParameterUpdateResult>;
+/**
+ * Gets current value of a stack parameter
+ *
+ * @param stackArn - Stack ARN
+ * @param region - AWS region
+ * @param parameterKey - Parameter key to query
+ * @param awsProfile - Optional AWS profile
+ * @returns Parameter value or undefined if not found
+ */
+export declare function getStackParameter(stackArn: string, region: string, parameterKey: string, awsProfile?: string): Promise<string | undefined>;
+//# sourceMappingURL=stack-parameter-update.d.ts.map

package/dist/lib/utils/stack-parameter-update.d.ts.map

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+{"version":3,"file":"stack-parameter-update.d.ts","sourceRoot":"","sources":["../../../lib/utils/stack-parameter-update.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAMH,MAAM,WAAW,2BAA2B;IACxC,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,YAAY,EAAE,MAAM,CAAC;IACrB,cAAc,EAAE,MAAM,CAAC;IACvB,UAAU,CAAC,EAAE,MAAM,CAAC;CACvB;AAED,MAAM,WAAW,0BAA0B;IACvC,OAAO,EAAE,OAAO,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;CAClB;AAED;;;;;GAKG;AACH,wBAAsB,oBAAoB,CACtC,OAAO,EAAE,2BAA2B,GACrC,OAAO,CAAC,0BAA0B,CAAC,CA0ErC;AAED;;;;;;;;GAQG;AACH,wBAAsB,iBAAiB,CACnC,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,MAAM,EACpB,UAAU,CAAC,EAAE,MAAM,GACpB,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CA8B7B"}

package/dist/lib/utils/stack-parameter-update.js

@@ -0,0 +1,129 @@
+"use strict";
+/**
+ * CloudFormation stack parameter update utility
+ *
+ * Provides safe parameter updates with UsePreviousValue for all other parameters
+ *
+ * @module utils/stack-parameter-update
+ */
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.updateStackParameter = updateStackParameter;
+exports.getStackParameter = getStackParameter;
+const client_cloudformation_1 = require("@aws-sdk/client-cloudformation");
+const credential_providers_1 = require("@aws-sdk/credential-providers");
+const chalk_1 = __importDefault(require("chalk"));
+/**
+ * Updates a single CloudFormation stack parameter while preserving all others
+ *
+ * @param options - Update options
+ * @returns Update result
+ */
+async function updateStackParameter(options) {
+    const { stackArn, region, parameterKey, parameterValue, awsProfile } = options;
+    try {
+        // Extract stack name from ARN
+        // ARN format: arn:aws:cloudformation:REGION:ACCOUNT:stack/STACK_NAME/STACK_ID
+        const stackNameMatch = stackArn.match(/stack\/([^\/]+)\//);
+        if (!stackNameMatch) {
+            throw new Error(`Invalid stack ARN format: ${stackArn}`);
+        }
+        const stackName = stackNameMatch[1];
+        // Configure AWS SDK client
+        const clientConfig = { region };
+        if (awsProfile) {
+            clientConfig.credentials = (0, credential_providers_1.fromIni)({ profile: awsProfile });
+        }
+        const client = new client_cloudformation_1.CloudFormationClient(clientConfig);
+        // Get current stack parameters
+        const describeCommand = new client_cloudformation_1.DescribeStacksCommand({
+            StackName: stackName,
+        });
+        const describeResponse = await client.send(describeCommand);
+        const stack = describeResponse.Stacks?.[0];
+        if (!stack) {
+            throw new Error(`Stack not found: ${stackName}`);
+        }
+        const currentParameters = stack.Parameters || [];
+        // Build parameter list: update target parameter, preserve all others
+        const parameters = currentParameters.map((param) => {
+            if (param.ParameterKey === parameterKey) {
+                return {
+                    ParameterKey: parameterKey,
+                    ParameterValue: parameterValue,
+                };
+            }
+            else {
+                return {
+                    ParameterKey: param.ParameterKey,
+                    UsePreviousValue: true,
+                };
+            }
+        });
+        // Update stack
+        const updateCommand = new client_cloudformation_1.UpdateStackCommand({
+            StackName: stackName,
+            Parameters: parameters,
+            UsePreviousTemplate: true, // CRITICAL: Don't change template
+            Capabilities: stack.Capabilities, // Preserve capabilities
+        });
+        const updateResponse = await client.send(updateCommand);
+        return {
+            success: true,
+            stackId: updateResponse.StackId,
+        };
+    }
+    catch (error) {
+        const err = error;
+        // CloudFormation returns specific error if no updates are needed
+        if (err.message?.includes("No updates are to be performed")) {
+            return {
+                success: true, // Not really an error
+            };
+        }
+        return {
+            success: false,
+            error: err.message,
+        };
+    }
+}
+/**
+ * Gets current value of a stack parameter
+ *
+ * @param stackArn - Stack ARN
+ * @param region - AWS region
+ * @param parameterKey - Parameter key to query
+ * @param awsProfile - Optional AWS profile
+ * @returns Parameter value or undefined if not found
+ */
+async function getStackParameter(stackArn, region, parameterKey, awsProfile) {
+    try {
+        const stackNameMatch = stackArn.match(/stack\/([^\/]+)\//);
+        if (!stackNameMatch) {
+            throw new Error(`Invalid stack ARN format: ${stackArn}`);
+        }
+        const stackName = stackNameMatch[1];
+        const clientConfig = { region };
+        if (awsProfile) {
+            clientConfig.credentials = (0, credential_providers_1.fromIni)({ profile: awsProfile });
+        }
+        const client = new client_cloudformation_1.CloudFormationClient(clientConfig);
+        const describeCommand = new client_cloudformation_1.DescribeStacksCommand({
+            StackName: stackName,
+        });
+        const describeResponse = await client.send(describeCommand);
+        const stack = describeResponse.Stacks?.[0];
+        if (!stack) {
+            return undefined;
+        }
+        const param = stack.Parameters?.find((p) => p.ParameterKey === parameterKey);
+        return param?.ParameterValue;
+    }
+    catch (error) {
+        console.warn(chalk_1.default.yellow(`Warning: Could not get parameter ${parameterKey}: ${error.message}`));
+        return undefined;
+    }
+}
+//# sourceMappingURL=stack-parameter-update.js.map

package/dist/lib/utils/stack-parameter-update.js.map

@@ -0,0 +1 @@
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package/dist/lib/wizard/phase1-catalog-discovery.d.ts

@@ -0,0 +1,41 @@
+/**
+ * Phase 1: Catalog Discovery
+ *
+ * Detects and confirms the Quilt catalog DNS name.
+ * Does NOT query AWS - only reads local quilt3 config.
+ *
+ * @module wizard/phase1-catalog-discovery
+ */
+import { CatalogDiscoveryResult } from "./types";
+/**
+ * Phase 1 options
+ */
+export interface CatalogDiscoveryOptions {
+    /** Non-interactive mode (skip prompts) */
+    yes?: boolean;
+    /** Catalog URL provided via CLI */
+    catalogUrl?: string;
+    /** Existing catalog from loaded profile (takes precedence over detection) */
+    existingCatalog?: string;
+}
+/**
+ * Phase 1: Catalog Discovery
+ *
+ * Responsibilities:
+ * - Check existing config first (highest priority)
+ * - Read quilt3 CLI config as fallback
+ * - Ask user to confirm detected catalog
+ * - If not confirmed, prompt for manual entry
+ * - Return confirmed catalog DNS
+ *
+ * Priority order:
+ * 1. CLI argument (--catalog-url)
+ * 2. Existing profile config
+ * 3. quilt3 CLI detection
+ * 4. Manual entry prompt
+ *
+ * @param options - Catalog discovery options
+ * @returns Catalog discovery result
+ */
+export declare function runCatalogDiscovery(options: CatalogDiscoveryOptions): Promise<CatalogDiscoveryResult>;
+//# sourceMappingURL=phase1-catalog-discovery.d.ts.map

package/dist/lib/wizard/phase1-catalog-discovery.d.ts.map

@@ -0,0 +1 @@
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package/dist/lib/wizard/phase1-catalog-discovery.js

@@ -0,0 +1,206 @@
+"use strict";
+/**
+ * Phase 1: Catalog Discovery
+ *
+ * Detects and confirms the Quilt catalog DNS name.
+ * Does NOT query AWS - only reads local quilt3 config.
+ *
+ * @module wizard/phase1-catalog-discovery
+ */
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.runCatalogDiscovery = runCatalogDiscovery;
+const child_process_1 = require("child_process");
+const inquirer_1 = __importDefault(require("inquirer"));
+const chalk_1 = __importDefault(require("chalk"));
+/**
+ * Attempts to detect catalog from quilt3 CLI config
+ *
+ * @returns Catalog URL from quilt3 config, or null if not found
+ */
+function detectQuilt3Catalog() {
+    try {
+        const output = (0, child_process_1.execSync)("quilt3 config", {
+            encoding: "utf-8",
+            stdio: ["pipe", "pipe", "ignore"],
+        });
+        const catalogUrl = output.trim();
+        if (catalogUrl && catalogUrl.startsWith("http")) {
+            return catalogUrl;
+        }
+        return null;
+    }
+    catch {
+        // quilt3 command not available or failed
+        return null;
+    }
+}
+/**
+ * Normalizes catalog URL to DNS format (removes protocol, trailing slash)
+ *
+ * @param catalogUrl - Raw catalog URL
+ * @returns Normalized DNS name
+ */
+function normalizeCatalogDns(catalogUrl) {
+    return catalogUrl.replace(/^https?:\/\//, "").replace(/\/$/, "");
+}
+/**
+ * Validates catalog DNS format
+ *
+ * @param catalogDns - Catalog DNS to validate
+ * @returns True if valid, error message otherwise
+ */
+function validateCatalogDns(catalogDns) {
+    const trimmed = catalogDns.trim();
+    if (trimmed.length === 0) {
+        return "Catalog DNS name is required";
+    }
+    // Basic DNS validation (allow alphanumeric, dots, hyphens)
+    if (!/^[a-zA-Z0-9.-]+$/.test(trimmed)) {
+        return "Invalid DNS name format";
+    }
+    return true;
+}
+/**
+ * Phase 1: Catalog Discovery
+ *
+ * Responsibilities:
+ * - Check existing config first (highest priority)
+ * - Read quilt3 CLI config as fallback
+ * - Ask user to confirm detected catalog
+ * - If not confirmed, prompt for manual entry
+ * - Return confirmed catalog DNS
+ *
+ * Priority order:
+ * 1. CLI argument (--catalog-url)
+ * 2. Existing profile config
+ * 3. quilt3 CLI detection
+ * 4. Manual entry prompt
+ *
+ * @param options - Catalog discovery options
+ * @returns Catalog discovery result
+ */
+async function runCatalogDiscovery(options) {
+    const { yes = false, catalogUrl: cliCatalogUrl, existingCatalog } = options;
+    // If catalog provided via CLI, use it directly
+    if (cliCatalogUrl) {
+        const catalogDns = normalizeCatalogDns(cliCatalogUrl);
+        console.log(chalk_1.default.blue(`Using catalog from CLI: ${catalogDns}\n`));
+        return {
+            catalogDns,
+            wasManuallyEntered: true,
+        };
+    }
+    // If existing config has a catalog, prioritize it over detection
+    if (existingCatalog) {
+        const catalogDns = normalizeCatalogDns(existingCatalog);
+        console.log(chalk_1.default.blue(`Using catalog from existing profile: ${catalogDns}\n`));
+        // In --yes mode, use existing catalog automatically
+        if (yes) {
+            return {
+                catalogDns,
+                wasManuallyEntered: false,
+                detectedCatalog: catalogDns,
+            };
+        }
+        // Ask user to confirm existing catalog
+        const { isCorrect } = await inquirer_1.default.prompt([
+            {
+                type: "confirm",
+                name: "isCorrect",
+                message: `Is ${catalogDns} the correct catalog?`,
+                default: true,
+            },
+        ]);
+        if (isCorrect) {
+            return {
+                catalogDns,
+                wasManuallyEntered: false,
+                detectedCatalog: catalogDns,
+            };
+        }
+        // User declined, ask for manual entry
+        const { manualCatalog } = await inquirer_1.default.prompt([
+            {
+                type: "input",
+                name: "manualCatalog",
+                message: "Enter catalog DNS name:",
+                validate: validateCatalogDns,
+                filter: normalizeCatalogDns,
+            },
+        ]);
+        return {
+            catalogDns: manualCatalog,
+            wasManuallyEntered: true,
+            detectedCatalog: catalogDns,
+        };
+    }
+    // Try to detect catalog from quilt3 CLI
+    const detectedCatalog = detectQuilt3Catalog();
+    if (detectedCatalog) {
+        const catalogDns = normalizeCatalogDns(detectedCatalog);
+        console.log(chalk_1.default.blue(`Detected catalog: ${catalogDns}\n`));
+        // In --yes mode, use detected catalog automatically
+        if (yes) {
+            return {
+                catalogDns,
+                wasManuallyEntered: false,
+                detectedCatalog: catalogDns,
+            };
+        }
+        // Ask user to confirm
+        const { isCorrect } = await inquirer_1.default.prompt([
+            {
+                type: "confirm",
+                name: "isCorrect",
+                message: `Is ${catalogDns} the correct catalog?`,
+                default: true,
+            },
+        ]);
+        if (isCorrect) {
+            return {
+                catalogDns,
+                wasManuallyEntered: false,
+                detectedCatalog: catalogDns,
+            };
+        }
+        // User declined, ask for manual entry
+        const { manualCatalog } = await inquirer_1.default.prompt([
+            {
+                type: "input",
+                name: "manualCatalog",
+                message: "Enter catalog DNS name:",
+                validate: validateCatalogDns,
+                filter: normalizeCatalogDns,
+            },
+        ]);
+        return {
+            catalogDns: manualCatalog,
+            wasManuallyEntered: true,
+            detectedCatalog: catalogDns,
+        };
+    }
+    // No catalog detected
+    console.log(chalk_1.default.yellow("No quilt3 CLI configuration detected.\n"));
+    if (yes) {
+        throw new Error("No catalog detected and --yes flag prevents interactive prompt. " +
+            "Provide catalog URL via --catalog-url argument.");
+    }
+    // Prompt for manual entry
+    const { manualCatalog } = await inquirer_1.default.prompt([
+        {
+            type: "input",
+            name: "manualCatalog",
+            message: "Enter Quilt Catalog DNS name (e.g., open.quiltdata.com):",
+            validate: validateCatalogDns,
+            filter: normalizeCatalogDns,
+        },
+    ]);
+    return {
+        catalogDns: manualCatalog,
+        wasManuallyEntered: true,
+    };
+}
+//# sourceMappingURL=phase1-catalog-discovery.js.map

package/dist/lib/wizard/phase1-catalog-discovery.js.map

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package/dist/lib/wizard/phase2-stack-query.d.ts

@@ -0,0 +1,35 @@
+/**
+ * Phase 2: Stack Query
+ *
+ * Queries CloudFormation stack for the confirmed catalog and extracts
+ * all available parameters including BenchlingSecret ARN.
+ *
+ * @module wizard/phase2-stack-query
+ */
+import { StackQueryResult } from "./types";
+/**
+ * Phase 2 options
+ */
+export interface StackQueryOptions {
+    /** AWS profile to use for querying */
+    awsProfile?: string;
+    /** AWS region to search in */
+    awsRegion?: string;
+    /** Non-interactive mode */
+    yes?: boolean;
+}
+/**
+ * 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
+ */
+export declare function runStackQuery(catalogDns: string, options?: StackQueryOptions): Promise<StackQueryResult>;
+//# sourceMappingURL=phase2-stack-query.d.ts.map

package/dist/lib/wizard/phase2-stack-query.d.ts.map

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