@quiltdata/benchling-webhook 0.5.4 → 0.6.0

package/dist/bin/config-profiles.js

@@ -0,0 +1,272 @@
+#!/usr/bin/env node
+"use strict";
+/**
+ * Configuration Profile Management CLI
+ *
+ * Provides commands for creating, listing, and managing configuration profiles.
+ * Supports AWS profile integration and profile validation.
+ *
+ * Usage:
+ *   npx ts-node bin/config-profiles.ts list
+ *   npx ts-node bin/config-profiles.ts create <profile-name>
+ *   npx ts-node bin/config-profiles.ts show <profile-name>
+ *   npx ts-node bin/config-profiles.ts validate <profile-name>
+ *
+ * @module bin/config-profiles
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ProfileManager = void 0;
+const xdg_config_1 = require("../lib/xdg-config");
+const commander_1 = require("commander");
+/**
+ * Profile Manager
+ *
+ * Manages configuration profiles with validation and AWS integration.
+ */
+class ProfileManager {
+    constructor() {
+        this.xdgConfig = new xdg_config_1.XDGConfig();
+    }
+    /**
+     * Lists all available profiles
+     */
+    listProfiles() {
+        console.log("Available configuration profiles:\n");
+        const profiles = this.xdgConfig.listProfiles();
+        if (profiles.length === 0) {
+            console.log("  No profiles found.");
+            console.log("\n  Run 'config-profiles create <name>' to create a new profile.");
+            return;
+        }
+        profiles.forEach((profileName) => {
+            const exists = this.xdgConfig.profileExists(profileName);
+            const status = exists ? "✓" : "✗";
+            const marker = profileName === "default" ? " (default)" : "";
+            console.log(`  ${status} ${profileName}${marker}`);
+            // Show configuration status
+            if (exists) {
+                const profile = this.xdgConfig.loadProfile(profileName);
+                const hasUser = profile.user ? "user" : "";
+                const hasDerived = profile.derived ? "derived" : "";
+                const hasDeploy = profile.deploy ? "deploy" : "";
+                const configs = [hasUser, hasDerived, hasDeploy].filter(Boolean).join(", ");
+                if (configs) {
+                    console.log(`    Configs: ${configs}`);
+                }
+            }
+        });
+        console.log();
+    }
+    /**
+     * Creates a new profile
+     *
+     * @param profileName - Name of the profile to create
+     * @param options - Creation options
+     */
+    createProfile(profileName, options = {}) {
+        console.log(`Creating profile: ${profileName}\n`);
+        // Check if profile already exists
+        if (this.xdgConfig.profileExists(profileName)) {
+            console.error(`Error: Profile '${profileName}' already exists.`);
+            process.exit(1);
+        }
+        // Ensure directories exist
+        this.xdgConfig.ensureProfileDirectories(profileName);
+        // Create initial user configuration
+        const userConfig = {
+            awsProfile: options.awsProfile,
+            _metadata: {
+                savedAt: new Date().toISOString(),
+                source: "cli",
+                version: "0.6.0",
+            },
+        };
+        // Write user configuration
+        this.xdgConfig.writeProfileConfig("user", userConfig, profileName);
+        const paths = this.xdgConfig.getProfilePaths(profileName);
+        console.log(`Profile '${profileName}' created successfully!`);
+        console.log("\nConfiguration files:");
+        console.log(`  User config:   ${paths.userConfig}`);
+        console.log(`  Derived config: ${paths.derivedConfig}`);
+        console.log(`  Deploy config:  ${paths.deployConfig}`);
+        console.log();
+    }
+    /**
+     * Shows detailed information about a profile
+     *
+     * @param profileName - Name of the profile to show
+     */
+    showProfile(profileName) {
+        if (!this.xdgConfig.profileExists(profileName)) {
+            console.error(`Error: Profile '${profileName}' does not exist.`);
+            process.exit(1);
+        }
+        console.log(`Profile: ${profileName}\n`);
+        const profile = this.xdgConfig.loadProfile(profileName);
+        const paths = this.xdgConfig.getProfilePaths(profileName);
+        // Show paths
+        console.log("Configuration files:");
+        console.log(`  User config:   ${paths.userConfig}`);
+        console.log(`  Derived config: ${paths.derivedConfig}`);
+        console.log(`  Deploy config:  ${paths.deployConfig}`);
+        console.log();
+        // Show user configuration
+        if (profile.user) {
+            console.log("User Configuration:");
+            this.printConfig(profile.user);
+            console.log();
+        }
+        // Show derived configuration
+        if (profile.derived) {
+            console.log("Derived Configuration:");
+            this.printConfig(profile.derived);
+            console.log();
+        }
+        // Show deployment configuration
+        if (profile.deploy) {
+            console.log("Deployment Configuration:");
+            this.printConfig(profile.deploy);
+            console.log();
+        }
+    }
+    /**
+     * Validates a profile configuration
+     *
+     * @param profileName - Name of the profile to validate
+     */
+    validateProfile(profileName) {
+        console.log(`Validating profile: ${profileName}\n`);
+        if (!this.xdgConfig.profileExists(profileName)) {
+            console.error(`Error: Profile '${profileName}' does not exist.`);
+            process.exit(1);
+        }
+        const profile = this.xdgConfig.loadProfile(profileName);
+        const errors = [];
+        const warnings = [];
+        // Validate user configuration
+        if (!profile.user) {
+            errors.push("Missing user configuration");
+        }
+        else {
+            // Check required fields
+            const required = [
+                "benchlingTenant",
+                "benchlingClientId",
+                "quiltCatalog",
+                "quiltUserBucket",
+            ];
+            required.forEach((field) => {
+                if (!profile.user[field]) {
+                    errors.push(`Missing required field in user config: ${field}`);
+                }
+            });
+            // Check AWS profile
+            if (!profile.user.awsProfile) {
+                warnings.push("No AWS profile specified");
+            }
+        }
+        // Validate derived configuration
+        if (profile.derived) {
+            if (!profile.derived.catalogUrl) {
+                warnings.push("Derived config missing catalogUrl");
+            }
+        }
+        else {
+            warnings.push("No derived configuration found");
+        }
+        // Report results
+        if (errors.length === 0 && warnings.length === 0) {
+            console.log("✓ Profile validation passed!");
+            return;
+        }
+        if (errors.length > 0) {
+            console.log("Errors:");
+            errors.forEach((error) => console.log(`  ✗ ${error}`));
+            console.log();
+        }
+        if (warnings.length > 0) {
+            console.log("Warnings:");
+            warnings.forEach((warning) => console.log(`  ⚠ ${warning}`));
+            console.log();
+        }
+        if (errors.length > 0) {
+            process.exit(1);
+        }
+    }
+    /**
+     * Prints configuration object in a readable format
+     *
+     * @param config - Configuration object to print
+     */
+    printConfig(config) {
+        const entries = Object.entries(config).filter(([key]) => key !== "_metadata");
+        if (entries.length === 0) {
+            console.log("  (empty)");
+            return;
+        }
+        entries.forEach(([key, value]) => {
+            if (key.toLowerCase().includes("secret") && typeof value === "string") {
+                // Mask secrets
+                console.log(`  ${key}: ${value.substring(0, 4)}****`);
+            }
+            else if (typeof value === "object") {
+                console.log(`  ${key}: ${JSON.stringify(value, null, 2)}`);
+            }
+            else {
+                console.log(`  ${key}: ${value}`);
+            }
+        });
+    }
+}
+exports.ProfileManager = ProfileManager;
+/**
+ * Main CLI program
+ */
+function main() {
+    const program = new commander_1.Command();
+    const manager = new ProfileManager();
+    program
+        .name("config-profiles")
+        .description("Configuration Profile Management for Benchling Webhook")
+        .version("0.6.0");
+    // List command
+    program
+        .command("list")
+        .description("List all available configuration profiles")
+        .action(() => {
+        manager.listProfiles();
+    });
+    // Create command
+    program
+        .command("create <profile-name>")
+        .description("Create a new configuration profile")
+        .option("--aws-profile <profile>", "AWS profile to associate with this configuration")
+        .option("--description <text>", "Profile description")
+        .action((profileName, options) => {
+        manager.createProfile(profileName, options);
+    });
+    // Show command
+    program
+        .command("show <profile-name>")
+        .description("Show detailed information about a profile")
+        .action((profileName) => {
+        manager.showProfile(profileName);
+    });
+    // Validate command
+    program
+        .command("validate <profile-name>")
+        .description("Validate a profile configuration")
+        .action((profileName) => {
+        manager.validateProfile(profileName);
+    });
+    program.parse(process.argv);
+    // Show help if no command provided
+    if (!process.argv.slice(2).length) {
+        program.outputHelp();
+    }
+}
+// Run CLI
+if (require.main === module) {
+    main();
+}
+//# sourceMappingURL=config-profiles.js.map

package/dist/bin/config-profiles.js.map

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package/dist/bin/create-secret.d.ts

@@ -0,0 +1,25 @@
+#!/usr/bin/env ts-node
+/**
+ * Create or update Benchling webhook secret in AWS Secrets Manager
+ *
+ * Usage:
+ *   npm run config
+ *   npm run config -- --secret-name benchling-webhook-dev --region us-east-1
+ *   npm run config -- --secret-name benchling-webhook-prod --region us-east-1 --env-file .env.prod
+ *
+ * Default secret name: @quiltdata/benchling-webhook (package name)
+ *
+ * Required parameters (from .env file or environment):
+ *   BENCHLING_TENANT
+ *   BENCHLING_CLIENT_ID
+ *   BENCHLING_CLIENT_SECRET
+ *   BENCHLING_APP_DEFINITION_ID
+ *   BENCHLING_PKG_PREFIX
+ *   BENCHLING_PKG_KEY
+ *   BENCHLING_USER_BUCKET
+ *   BENCHLING_LOG_LEVEL
+ *   BENCHLING_ENABLE_WEBHOOK_VERIFICATION
+ *   BENCHLING_WEBHOOK_ALLOW_LIST
+ */
+export {};
+//# sourceMappingURL=create-secret.d.ts.map

package/dist/bin/create-secret.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"create-secret.d.ts","sourceRoot":"","sources":["../../bin/create-secret.ts"],"names":[],"mappings":";AAEA;;;;;;;;;;;;;;;;;;;;;GAqBG"}

package/dist/bin/create-secret.js

@@ -0,0 +1,239 @@
+#!/usr/bin/env ts-node
+"use strict";
+/**
+ * Create or update Benchling webhook secret in AWS Secrets Manager
+ *
+ * Usage:
+ *   npm run config
+ *   npm run config -- --secret-name benchling-webhook-dev --region us-east-1
+ *   npm run config -- --secret-name benchling-webhook-prod --region us-east-1 --env-file .env.prod
+ *
+ * Default secret name: @quiltdata/benchling-webhook (package name)
+ *
+ * Required parameters (from .env file or environment):
+ *   BENCHLING_TENANT
+ *   BENCHLING_CLIENT_ID
+ *   BENCHLING_CLIENT_SECRET
+ *   BENCHLING_APP_DEFINITION_ID
+ *   BENCHLING_PKG_PREFIX
+ *   BENCHLING_PKG_KEY
+ *   BENCHLING_USER_BUCKET
+ *   BENCHLING_LOG_LEVEL
+ *   BENCHLING_ENABLE_WEBHOOK_VERIFICATION
+ *   BENCHLING_WEBHOOK_ALLOW_LIST
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const commander_1 = require("commander");
+const dotenv_1 = require("dotenv");
+const dotenv_expand_1 = require("dotenv-expand");
+const client_secrets_manager_1 = require("@aws-sdk/client-secrets-manager");
+const fs = __importStar(require("fs"));
+const chalk_1 = __importDefault(require("chalk"));
+const REQUIRED_PARAMS = [
+    "BENCHLING_TENANT",
+    "BENCHLING_CLIENT_ID",
+    "BENCHLING_CLIENT_SECRET",
+    "BENCHLING_APP_DEFINITION_ID",
+    "BENCHLING_PKG_PREFIX",
+    "BENCHLING_PKG_KEY",
+    "BENCHLING_USER_BUCKET",
+    "BENCHLING_LOG_LEVEL",
+    "BENCHLING_ENABLE_WEBHOOK_VERIFICATION",
+    "BENCHLING_WEBHOOK_ALLOW_LIST",
+];
+const VALID_LOG_LEVELS = ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"];
+function loadEnvFile(envFile) {
+    const envPath = envFile || ".env";
+    if (!fs.existsSync(envPath)) {
+        console.log(chalk_1.default.yellow(`ℹ️  No .env file found at ${envPath}, using environment variables only`));
+        return;
+    }
+    console.log(chalk_1.default.blue(`📄 Loading environment from ${envPath}`));
+    const myEnv = (0, dotenv_1.config)({ path: envPath });
+    (0, dotenv_expand_1.expand)(myEnv);
+}
+function validateParameters(params) {
+    // WEBHOOK_ALLOW_LIST can be empty string (no restrictions)
+    // All others must be non-empty
+    const missing = REQUIRED_PARAMS.filter(param => {
+        if (param === "BENCHLING_WEBHOOK_ALLOW_LIST") {
+            return params[param] === undefined; // Only fail if undefined, not empty string
+        }
+        return !params[param];
+    });
+    if (missing.length > 0) {
+        console.error(chalk_1.default.red(`❌ Missing required parameters: ${missing.join(", ")}`));
+        console.log(chalk_1.default.yellow("\nExpected parameters (from .env or environment):"));
+        REQUIRED_PARAMS.forEach(param => {
+            const value = params[param];
+            const status = value !== undefined ? "✓" : "✗";
+            console.log(chalk_1.default.yellow(`  ${param}=${status}`));
+        });
+        process.exit(1);
+    }
+    // Validate log level
+    const logLevel = params.BENCHLING_LOG_LEVEL.toUpperCase();
+    if (!VALID_LOG_LEVELS.includes(logLevel)) {
+        console.error(chalk_1.default.red(`❌ Invalid log level: ${params.BENCHLING_LOG_LEVEL}`));
+        console.log(chalk_1.default.yellow(`Valid levels: ${VALID_LOG_LEVELS.join(", ")}`));
+        process.exit(1);
+    }
+    // Validate boolean
+    const verification = params.BENCHLING_ENABLE_WEBHOOK_VERIFICATION.toLowerCase();
+    if (!["true", "false", "1", "0"].includes(verification)) {
+        console.error(chalk_1.default.red(`❌ Invalid boolean value for BENCHLING_ENABLE_WEBHOOK_VERIFICATION: ${params.BENCHLING_ENABLE_WEBHOOK_VERIFICATION}`));
+        console.log(chalk_1.default.yellow("Valid values: true, false, 1, 0"));
+        process.exit(1);
+    }
+    // Build secret data (convert SCREAMING_SNAKE_CASE to snake_case)
+    return {
+        tenant: params.BENCHLING_TENANT,
+        client_id: params.BENCHLING_CLIENT_ID,
+        client_secret: params.BENCHLING_CLIENT_SECRET,
+        app_definition_id: params.BENCHLING_APP_DEFINITION_ID,
+        pkg_prefix: params.BENCHLING_PKG_PREFIX,
+        pkg_key: params.BENCHLING_PKG_KEY,
+        user_bucket: params.BENCHLING_USER_BUCKET,
+        log_level: logLevel,
+        enable_webhook_verification: verification,
+        webhook_allow_list: params.BENCHLING_WEBHOOK_ALLOW_LIST,
+    };
+}
+async function secretExists(client, secretName) {
+    try {
+        await client.send(new client_secrets_manager_1.DescribeSecretCommand({ SecretId: secretName }));
+        return true;
+    }
+    catch (error) {
+        if (error instanceof client_secrets_manager_1.ResourceNotFoundException) {
+            return false;
+        }
+        throw error;
+    }
+}
+async function createOrUpdateSecret(secretName, region, secretData, dryRun) {
+    const client = new client_secrets_manager_1.SecretsManagerClient({ region });
+    const secretString = JSON.stringify(secretData, null, 2);
+    if (dryRun) {
+        console.log(chalk_1.default.blue("\n🔍 DRY RUN MODE - No changes will be made\n"));
+        console.log(chalk_1.default.cyan("Secret Name:"), secretName);
+        console.log(chalk_1.default.cyan("Region:"), region);
+        console.log(chalk_1.default.cyan("Secret Content:"));
+        console.log(chalk_1.default.gray(secretString));
+        return;
+    }
+    const exists = await secretExists(client, secretName);
+    if (exists) {
+        console.log(chalk_1.default.blue(`📝 Updating existing secret: ${secretName}`));
+        await client.send(new client_secrets_manager_1.UpdateSecretCommand({
+            SecretId: secretName,
+            SecretString: secretString,
+        }));
+        console.log(chalk_1.default.green("✅ Secret updated successfully"));
+    }
+    else {
+        console.log(chalk_1.default.blue(`🆕 Creating new secret: ${secretName}`));
+        const result = await client.send(new client_secrets_manager_1.CreateSecretCommand({
+            Name: secretName,
+            Description: "Benchling webhook runtime configuration (10 parameters)",
+            SecretString: secretString,
+        }));
+        console.log(chalk_1.default.green("✅ Secret created successfully"));
+        console.log(chalk_1.default.cyan(`ARN: ${result.ARN}`));
+    }
+    console.log(chalk_1.default.green(`\n✨ Secret ${exists ? "updated" : "created"}: ${secretName}`));
+    console.log(chalk_1.default.yellow("\nTo use this secret in deployment:"));
+    console.log(chalk_1.default.gray("  npm run cli -- deploy \\"));
+    console.log(chalk_1.default.gray("    --quilt-stack-arn <your-quilt-stack-arn> \\"));
+    console.log(chalk_1.default.gray(`    --benchling-secret ${secretName}`));
+}
+async function main() {
+    const program = new commander_1.Command();
+    program
+        .name("npm run config")
+        .description("Create or update Benchling webhook secret in AWS Secrets Manager")
+        .option("-s, --secret-name <name>", "Secret name (defaults to package name)", "@quiltdata/benchling-webhook")
+        .option("-r, --region <region>", "AWS region", "us-east-1")
+        .option("-e, --env-file <path>", ".env file path", ".env")
+        .option("-d, --dry-run", "Show what would be created without making changes", false)
+        .parse(process.argv);
+    const options = program.opts();
+    console.log(chalk_1.default.bold.blue("\n🔐 Benchling Webhook Secret Configuration\n"));
+    // Load environment
+    loadEnvFile(options.envFile);
+    // Gather parameters from environment
+    const params = {};
+    REQUIRED_PARAMS.forEach(param => {
+        const value = process.env[param];
+        // Special handling for WEBHOOK_ALLOW_LIST - allow empty string
+        if (param === "BENCHLING_WEBHOOK_ALLOW_LIST" && value === undefined) {
+            params[param] = ""; // Default to empty string for allowlist
+        }
+        else {
+            params[param] = value || "";
+        }
+    });
+    // Validate and build secret data
+    const secretData = validateParameters(params);
+    console.log(chalk_1.default.green("\n✓ All parameters validated"));
+    console.log(chalk_1.default.blue("\nParameters to be stored in secret:"));
+    console.log(chalk_1.default.gray(`  tenant: ${secretData.tenant}`));
+    console.log(chalk_1.default.gray(`  client_id: ${secretData.client_id.substring(0, 4)}***`));
+    console.log(chalk_1.default.gray("  client_secret: ***"));
+    console.log(chalk_1.default.gray(`  app_definition_id: ${secretData.app_definition_id}`));
+    console.log(chalk_1.default.gray(`  pkg_prefix: ${secretData.pkg_prefix}`));
+    console.log(chalk_1.default.gray(`  pkg_key: ${secretData.pkg_key}`));
+    console.log(chalk_1.default.gray(`  user_bucket: ${secretData.user_bucket}`));
+    console.log(chalk_1.default.gray(`  log_level: ${secretData.log_level}`));
+    console.log(chalk_1.default.gray(`  enable_webhook_verification: ${secretData.enable_webhook_verification}`));
+    console.log(chalk_1.default.gray(`  webhook_allow_list: ${secretData.webhook_allow_list || "(empty)"}`));
+    // Create or update secret
+    await createOrUpdateSecret(options.secretName, options.region, secretData, options.dryRun);
+}
+main().catch(error => {
+    console.error(chalk_1.default.red(`\n❌ Error: ${error.message}`));
+    if (error.code === "ResourceNotFoundException") {
+        console.log(chalk_1.default.yellow("\nMake sure the AWS region is correct and you have necessary permissions."));
+    }
+    else if (error.name === "CredentialsProviderError") {
+        console.log(chalk_1.default.yellow("\nAWS credentials not found. Please configure AWS CLI or set environment variables."));
+    }
+    process.exit(1);
+});
+//# sourceMappingURL=create-secret.js.map

package/dist/bin/create-secret.js.map

@@ -0,0 +1 @@
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package/dist/lib/benchling-auth-validator.d.ts

@@ -0,0 +1,65 @@
+/**
+ * Benchling credentials for authentication
+ */
+export interface BenchlingCredentials {
+    tenant: string;
+    clientId: string;
+    clientSecret: string;
+}
+/**
+ * Validation result from Benchling authentication
+ */
+export interface ValidationResult {
+    isValid: boolean;
+    hasRequiredPermissions?: boolean;
+    errors: string[];
+    warnings?: string[];
+}
+/**
+ * Benchling authentication validator
+ *
+ * Validates Benchling credentials by attempting OAuth authentication
+ * and checking required permissions.
+ */
+export declare class BenchlingAuthValidator {
+    /**
+     * Required OAuth scopes for the webhook integration
+     */
+    private static readonly REQUIRED_SCOPES;
+    /**
+     * Validate Benchling credentials
+     *
+     * @param credentials - Benchling credentials to validate
+     * @returns Validation result with errors and warnings
+     */
+    static validate(credentials: BenchlingCredentials): Promise<ValidationResult>;
+    /**
+     * Validate tenant format
+     *
+     * @param tenant - Benchling tenant name
+     * @returns True if tenant format is valid
+     */
+    static validateTenant(tenant: string): Promise<boolean>;
+    /**
+     * Validate credentials completeness
+     *
+     * @param credentials - Credentials to validate
+     * @returns True if all required fields are present
+     */
+    static validateCredentials(credentials: BenchlingCredentials): boolean;
+    /**
+     * Authenticate with Benchling OAuth API
+     *
+     * @param credentials - Benchling credentials
+     * @returns Token response from Benchling
+     */
+    private static authenticate;
+    /**
+     * Check if OAuth scopes include required permissions
+     *
+     * @param scope - OAuth scope string
+     * @returns True if all required scopes are present
+     */
+    private static checkPermissions;
+}
+//# sourceMappingURL=benchling-auth-validator.d.ts.map

package/dist/lib/benchling-auth-validator.d.ts.map

@@ -0,0 +1 @@
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