@quiltdata/benchling-webhook 0.4.13 → 0.5.0

package/dist/lib/utils/config.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../../../lib/utils/config.ts"],"names":[],"mappings":"AAKA,MAAM,WAAW,MAAM;IAErB,YAAY,EAAE,MAAM,CAAC;IACrB,eAAe,EAAE,MAAM,CAAC;IACxB,aAAa,EAAE,MAAM,CAAC;IAGtB,eAAe,EAAE,MAAM,CAAC;IACxB,iBAAiB,EAAE,MAAM,CAAC;IAC1B,qBAAqB,EAAE,MAAM,CAAC;IAC9B,wBAAwB,CAAC,EAAE,MAAM,CAAC;IAGlC,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,MAAM,CAAC;IAClB,UAAU,CAAC,EAAE,MAAM,CAAC;IAGpB,SAAS,EAAE,MAAM,CAAC;IAClB,WAAW,EAAE,MAAM,CAAC;IAGpB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,yBAAyB,CAAC,EAAE,MAAM,CAAC;IACnC,mBAAmB,CAAC,EAAE,MAAM,CAAC;IAC7B,iBAAiB,CAAC,EAAE,MAAM,CAAC;CAC5B;AAED,MAAM,WAAW,aAAa;IAC5B,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,gBAAgB;IAC/B,KAAK,EAAE,OAAO,CAAC;IACf,MAAM,EAAE,eAAe,EAAE,CAAC;IAC1B,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,MAAM,WAAW,eAAe;IAC9B,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,MAAM,CAAC;IAChB,QAAQ,EAAE,OAAO,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED;;GAEG;AACH,wBAAgB,UAAU,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAmBnE;AAED;;;;;;GAMG;AACH,wBAAgB,cAAc,CAAC,OAAO,GAAE,aAAkB,GAAG,OAAO,CAAC,MAAM,CAAC,CA4C3E;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAC/B,MAAM,EAAE,OAAO,CAAC,MAAM,CAAC,EACvB,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GACrC,OAAO,CAAC,MAAM,CAAC,CAUjB;AAED;;GAEG;AACH,wBAAgB,cAAc,CAAC,MAAM,EAAE,OAAO,CAAC,MAAM,CAAC,GAAG,gBAAgB,CAyExE;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,MAAM,EAAE,gBAAgB,GAAG,MAAM,CA0CvE"}

package/dist/lib/utils/config.js

@@ -0,0 +1,195 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.loadDotenv = loadDotenv;
+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");
+/**
+ * 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 || {};
+}
+/**
+ * Load configuration from multiple sources with priority:
+ * 1. CLI options (highest)
+ * 2. Environment variables
+ * 3. .env file
+ * 4. 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. Build config with CLI options taking priority
+    const config = {
+        // Quilt
+        quiltCatalog: options.catalog || envVars.QUILT_CATALOG,
+        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,
+        // AWS
+        cdkAccount: envVars.CDK_DEFAULT_ACCOUNT,
+        cdkRegion: options.region || envVars.CDK_DEFAULT_REGION || envVars.AWS_REGION,
+        awsProfile: options.profile || envVars.AWS_PROFILE,
+        // SQS
+        queueName: envVars.QUEUE_NAME,
+        sqsQueueUrl: envVars.SQS_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",
+    };
+    // 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,
+        queueName: config.queueName || inferredVars.QUEUE_NAME,
+        sqsQueueUrl: config.sqsQueueUrl || inferredVars.SQS_QUEUE_URL,
+        quiltDatabase: config.quiltDatabase || inferredVars.QUILT_DATABASE,
+        ...config, // User values always take precedence
+    };
+}
+/**
+ * Validate configuration and return detailed errors
+ */
+function validateConfig(config) {
+    const errors = [];
+    const warnings = [];
+    // Required user-provided values
+    const requiredUserFields = [
+        ["quiltCatalog", "Quilt catalog URL", "Your Quilt catalog domain (e.g., quilt-catalog.company.com)"],
+        ["quiltUserBucket", "S3 bucket for data", "The S3 bucket where you want to store Benchling exports"],
+        ["benchlingTenant", "Benchling tenant", "Your Benchling tenant name (use XXX if you login to XXX.benchling.com)"],
+        ["benchlingClientId", "Benchling OAuth client ID", "OAuth client ID from your Benchling app"],
+        ["benchlingClientSecret", "Benchling OAuth client secret", "OAuth client secret from your Benchling app"],
+    ];
+    for (const [field, message, helpText] of requiredUserFields) {
+        if (!config[field]) {
+            errors.push({
+                field: field,
+                message,
+                canInfer: false,
+                helpText,
+            });
+        }
+    }
+    // Conditional requirement for app definition ID
+    if (config.enableWebhookVerification !== "false" && !config.benchlingAppDefinitionId) {
+        errors.push({
+            field: "benchlingAppDefinitionId",
+            message: "Benchling app definition ID",
+            canInfer: false,
+            helpText: "Required when webhook verification is enabled (ENABLE_WEBHOOK_VERIFICATION=true). Set ENABLE_WEBHOOK_VERIFICATION=false to skip this.",
+        });
+    }
+    // Required inferred values
+    const requiredInferredFields = [
+        ["cdkAccount", "AWS account ID"],
+        ["cdkRegion", "AWS region"],
+        ["queueName", "SQS queue name"],
+        ["sqsQueueUrl", "SQS queue URL"],
+        ["quiltDatabase", "Quilt database name"],
+    ];
+    for (const [field, message] of requiredInferredFields) {
+        if (!config[field]) {
+            errors.push({
+                field: field,
+                message,
+                canInfer: true,
+                helpText: "This value should be automatically inferred from your Quilt catalog configuration",
+            });
+        }
+    }
+    // Validation rules for existing values
+    if (config.quiltCatalog && !/^[a-z0-9.-]+\.[a-z]{2,}$/i.test(config.quiltCatalog)) {
+        warnings.push("QUILT_CATALOG should be a domain name without protocol (e.g., catalog.company.com, not https://catalog.company.com)");
+    }
+    if (config.quiltUserBucket && !/^[a-z0-9.-]{3,63}$/.test(config.quiltUserBucket)) {
+        warnings.push("QUILT_USER_BUCKET does not look like a valid S3 bucket name");
+    }
+    // Security warnings
+    if (config.enableWebhookVerification === "false") {
+        warnings.push("Webhook verification is disabled - this is NOT recommended for production use");
+    }
+    return {
+        valid: errors.length === 0,
+        errors,
+        warnings,
+    };
+}
+/**
+ * Format validation errors for CLI display
+ */
+function formatValidationErrors(result) {
+    const lines = [];
+    if (result.errors.length > 0) {
+        lines.push("Missing required configuration:");
+        lines.push("");
+        const userErrors = result.errors.filter(e => !e.canInfer);
+        const inferErrors = result.errors.filter(e => e.canInfer);
+        if (userErrors.length > 0) {
+            lines.push("Values you must provide:");
+            for (const error of userErrors) {
+                lines.push(`  • ${error.message}`);
+                if (error.helpText) {
+                    lines.push(`    ${error.helpText}`);
+                }
+            }
+            lines.push("");
+        }
+        if (inferErrors.length > 0) {
+            lines.push("Values that could not be inferred:");
+            for (const error of inferErrors) {
+                lines.push(`  • ${error.message}`);
+                if (error.helpText) {
+                    lines.push(`    ${error.helpText}`);
+                }
+            }
+            lines.push("");
+        }
+    }
+    if (result.warnings.length > 0) {
+        lines.push("Warnings:");
+        for (const warning of result.warnings) {
+            lines.push(`  ⚠ ${warning}`);
+        }
+        lines.push("");
+    }
+    return lines.join("\n");
+}
+//# sourceMappingURL=config.js.map

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package/dist/lib/utils/stack-inference.d.ts

@@ -0,0 +1,73 @@
+/**
+ * Stack inference utilities for discovering CloudFormation stacks
+ * and extracting configuration from Quilt catalogs
+ */
+export interface QuiltCatalogConfig {
+    region: string;
+    apiGatewayEndpoint: string;
+    analyticsBucket: string;
+    serviceBucket: string;
+    stackVersion?: string;
+    [key: string]: unknown;
+}
+export interface StackDetails {
+    outputs: Array<{
+        OutputKey: string;
+        OutputValue: string;
+    }>;
+    parameters: Array<{
+        ParameterKey: string;
+        ParameterValue: string;
+    }>;
+}
+export interface InferredStackInfo {
+    config: QuiltCatalogConfig;
+    stackName: string | null;
+    stackDetails: StackDetails;
+    inferredVars: Record<string, string>;
+}
+/**
+ * Fetch JSON from a URL using native Node.js modules
+ */
+export declare function fetchJson(url: string): Promise<unknown>;
+/**
+ * Extract bucket name from S3 ARN or bucket name string
+ */
+export declare function extractBucketName(bucketString: string): string;
+/**
+ * Try to find CloudFormation stack by searching for resource
+ */
+export declare function findStackByResource(region: string, resourceId: string): string | null;
+/**
+ * Search for stacks by name pattern
+ */
+export declare function searchStacksByPattern(region: string, pattern: string): string[];
+/**
+ * Get stack outputs and parameters
+ */
+export declare function getStackDetails(region: string, stackName: string): StackDetails;
+/**
+ * Get AWS account ID
+ */
+export declare function getAwsAccountId(): string | null;
+/**
+ * Extract API Gateway ID from endpoint URL
+ */
+export declare function extractApiGatewayId(endpoint: string): string | null;
+/**
+ * Extract stack name prefix from bucket names
+ */
+export declare function inferStackPrefix(analyticsBucket?: string, serviceBucket?: string): string;
+/**
+ * Find CloudFormation stack using multiple search strategies
+ */
+export declare function findStack(region: string, apiGatewayId: string | null, analyticsBucket: string, serviceBucket: string, stackPrefix: string, verbose?: boolean): string | null;
+/**
+ * Build inferred configuration from stack details
+ */
+export declare function buildInferredConfig(config: QuiltCatalogConfig, stackName: string | null, stackDetails: StackDetails, region: string, accountId: string | null, catalogDomain: string): Record<string, string>;
+/**
+ * Parse config.json and infer stack information
+ */
+export declare function inferStackConfig(catalogUrl: string, verbose?: boolean): Promise<InferredStackInfo>;
+//# sourceMappingURL=stack-inference.d.ts.map

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