@grafema/cli 0.2.5-beta → 0.2.6-beta

package/README.md

@@ -2,6 +2,8 @@
 
 > Grafema command-line interface for building and querying the code graph.
 
+**Warning: This package is in beta stage and the API may change between minor versions.**
+
 ## Quick Start
 
 ```bash
@@ -59,15 +61,25 @@ npx @grafema/cli check --list-categories
 npx @grafema/cli doctor                # Validate local setup
 ```
 
+### Server management
+
+```bash
+npx @grafema/cli server start          # Start RFDB server
+npx @grafema/cli server stop           # Stop RFDB server
+npx @grafema/cli server status         # Check server status
+```
+
 ### Misc
 
 ```bash
 npx @grafema/cli coverage               # Coverage stats
 npx @grafema/cli impact                 # Impact analysis
 npx @grafema/cli explore                # Interactive explorer (TUI)
+npx @grafema/cli analyze --log-file analysis.log  # Log to file
 ```
 
 ## Notes
 
 - All commands accept `--project <path>` to point at a specific repo.
 - `npx @grafema/cli` works without global install and is preferred for docs/examples.
+- Unknown Datalog predicates in `--raw` queries will show a warning with suggestions.

package/dist/cli.js

@@ -15,7 +15,7 @@ import { lsCommand } from './commands/ls.js';
 import { getCommand } from './commands/get.js';
 import { traceCommand } from './commands/trace.js';
 import { impactCommand } from './commands/impact.js';
-import { exploreCommand } from './commands/explore.js';
+import { contextCommand } from './commands/context.js';
 import { statsCommand } from './commands/stats.js';
 import { checkCommand } from './commands/check.js';
 import { serverCommand } from './commands/server.js';
@@ -23,6 +23,8 @@ import { coverageCommand } from './commands/coverage.js';
 import { doctorCommand } from './commands/doctor.js';
 import { schemaCommand } from './commands/schema.js';
 import { explainCommand } from './commands/explain.js';
+import { fileCommand } from './commands/file.js';
+import { setupSkillCommand } from './commands/setup-skill.js';
 // Read version from package.json
 const __dirname = dirname(fileURLToPath(import.meta.url));
 const pkg = JSON.parse(readFileSync(join(__dirname, '..', 'package.json'), 'utf-8'));
@@ -36,12 +38,12 @@ program.addCommand(initCommand);
 program.addCommand(analyzeCommand);
 program.addCommand(overviewCommand);
 program.addCommand(queryCommand);
+program.addCommand(contextCommand);
 program.addCommand(typesCommand);
 program.addCommand(lsCommand);
 program.addCommand(getCommand);
 program.addCommand(traceCommand);
 program.addCommand(impactCommand);
-program.addCommand(exploreCommand);
 program.addCommand(statsCommand); // Keep for backwards compat
 program.addCommand(coverageCommand);
 program.addCommand(checkCommand);
@@ -49,5 +51,7 @@ program.addCommand(serverCommand);
 program.addCommand(doctorCommand);
 program.addCommand(schemaCommand);
 program.addCommand(explainCommand);
+program.addCommand(fileCommand);
+program.addCommand(setupSkillCommand);
 program.parse();
 //# sourceMappingURL=cli.js.map

package/dist/cli.js.map

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package/dist/commands/analyze.d.ts

@@ -1,15 +1,8 @@
 /**
- * Analyze command - Run project analysis via Orchestrator
+ * Analyze command — Run project analysis via Orchestrator.
+ *
+ * Command definition only. Execution logic is in analyzeAction.ts.
  */
 import { Command } from 'commander';
-export interface NodeEdgeCountBackend {
-    nodeCount: () => Promise<number>;
-    edgeCount: () => Promise<number>;
-}
-export declare function fetchNodeEdgeCounts(backend: NodeEdgeCountBackend): Promise<{
-    nodeCount: number;
-    edgeCount: number;
-}>;
-export declare function exitWithCode(code: number, exitFn?: (code: number) => void): void;
 export declare const analyzeCommand: Command;
 //# sourceMappingURL=analyze.d.ts.map

package/dist/commands/analyze.d.ts.map

@@ -1 +1 @@
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package/dist/commands/analyze.js

@@ -1,149 +1,10 @@
 /**
- * Analyze command - Run project analysis via Orchestrator
- */
-import { Command } from 'commander';
-import { resolve, join } from 'path';
-import { existsSync, mkdirSync, readdirSync } from 'fs';
-import { pathToFileURL } from 'url';
-import { Orchestrator, RFDBServerBackend, DiagnosticReporter, DiagnosticWriter, createLogger, loadConfig, StrictModeFailure, 
-// Discovery
-SimpleProjectDiscovery, MonorepoServiceDiscovery, WorkspaceDiscovery, 
-// Indexing
-JSModuleIndexer, RustModuleIndexer, 
-// Analysis
-JSASTAnalyzer, ExpressRouteAnalyzer, ExpressResponseAnalyzer, SocketIOAnalyzer, DatabaseAnalyzer, FetchAnalyzer, ServiceLayerAnalyzer, ReactAnalyzer, RustAnalyzer, 
-// Enrichment
-MethodCallResolver, ArgumentParameterLinker, AliasTracker, ValueDomainAnalyzer, MountPointResolver, ExpressHandlerLinker, PrefixEvaluator, InstanceOfResolver, ImportExportLinker, FunctionCallResolver, HTTPConnectionEnricher, RustFFIEnricher, RejectionPropagationEnricher, 
-// Validation
-CallResolverValidator, EvalBanValidator, SQLInjectionValidator, ShadowingDetector, GraphConnectivityValidator, DataFlowValidator, TypeScriptDeadCodeValidator, BrokenImportValidator, } from '@grafema/core';
-import { ProgressRenderer } from '../utils/progressRenderer.js';
-export async function fetchNodeEdgeCounts(backend) {
-    const [nodeCount, edgeCount] = await Promise.all([backend.nodeCount(), backend.edgeCount()]);
-    return { nodeCount, edgeCount };
-}
-export function exitWithCode(code, exitFn = process.exit) {
-    exitFn(code);
-}
-const BUILTIN_PLUGINS = {
-    // Discovery
-    SimpleProjectDiscovery: () => new SimpleProjectDiscovery(),
-    MonorepoServiceDiscovery: () => new MonorepoServiceDiscovery(),
-    WorkspaceDiscovery: () => new WorkspaceDiscovery(),
-    // Indexing
-    JSModuleIndexer: () => new JSModuleIndexer(),
-    RustModuleIndexer: () => new RustModuleIndexer(),
-    // Analysis
-    JSASTAnalyzer: () => new JSASTAnalyzer(),
-    ExpressRouteAnalyzer: () => new ExpressRouteAnalyzer(),
-    ExpressResponseAnalyzer: () => new ExpressResponseAnalyzer(),
-    SocketIOAnalyzer: () => new SocketIOAnalyzer(),
-    DatabaseAnalyzer: () => new DatabaseAnalyzer(),
-    FetchAnalyzer: () => new FetchAnalyzer(),
-    ServiceLayerAnalyzer: () => new ServiceLayerAnalyzer(),
-    ReactAnalyzer: () => new ReactAnalyzer(),
-    RustAnalyzer: () => new RustAnalyzer(),
-    // Enrichment
-    MethodCallResolver: () => new MethodCallResolver(),
-    ArgumentParameterLinker: () => new ArgumentParameterLinker(),
-    AliasTracker: () => new AliasTracker(),
-    ValueDomainAnalyzer: () => new ValueDomainAnalyzer(),
-    MountPointResolver: () => new MountPointResolver(),
-    ExpressHandlerLinker: () => new ExpressHandlerLinker(),
-    PrefixEvaluator: () => new PrefixEvaluator(),
-    InstanceOfResolver: () => new InstanceOfResolver(),
-    ImportExportLinker: () => new ImportExportLinker(),
-    FunctionCallResolver: () => new FunctionCallResolver(),
-    HTTPConnectionEnricher: () => new HTTPConnectionEnricher(),
-    RustFFIEnricher: () => new RustFFIEnricher(),
-    RejectionPropagationEnricher: () => new RejectionPropagationEnricher(),
-    // Validation
-    CallResolverValidator: () => new CallResolverValidator(),
-    EvalBanValidator: () => new EvalBanValidator(),
-    SQLInjectionValidator: () => new SQLInjectionValidator(),
-    ShadowingDetector: () => new ShadowingDetector(),
-    GraphConnectivityValidator: () => new GraphConnectivityValidator(),
-    DataFlowValidator: () => new DataFlowValidator(),
-    TypeScriptDeadCodeValidator: () => new TypeScriptDeadCodeValidator(),
-    BrokenImportValidator: () => new BrokenImportValidator(),
-};
-/**
- * Load custom plugins from .grafema/plugins/ directory
- */
-async function loadCustomPlugins(projectPath, log) {
-    const pluginsDir = join(projectPath, '.grafema', 'plugins');
-    if (!existsSync(pluginsDir)) {
-        return {};
-    }
-    const customPlugins = {};
-    try {
-        const files = readdirSync(pluginsDir).filter((f) => f.endsWith('.js') || f.endsWith('.mjs') || f.endsWith('.cjs'));
-        for (const file of files) {
-            try {
-                const pluginPath = join(pluginsDir, file);
-                const pluginUrl = pathToFileURL(pluginPath).href;
-                const module = await import(pluginUrl);
-                const PluginClass = module.default || module[file.replace(/\.[cm]?js$/, '')];
-                if (PluginClass && typeof PluginClass === 'function') {
-                    const pluginName = PluginClass.name || file.replace(/\.[cm]?js$/, '');
-                    customPlugins[pluginName] = () => {
-                        const instance = new PluginClass();
-                        instance.config.sourceFile = pluginPath;
-                        return instance;
-                    };
-                    log(`Loaded custom plugin: ${pluginName}`);
-                }
-            }
-            catch (err) {
-                const message = err instanceof Error ? err.message : String(err);
-                console.warn(`Failed to load plugin ${file}: ${message}`);
-            }
-        }
-    }
-    catch (err) {
-        const message = err instanceof Error ? err.message : String(err);
-        console.warn(`Error loading custom plugins: ${message}`);
-    }
-    return customPlugins;
-}
-function createPlugins(config, customPlugins = {}, verbose = false) {
-    const plugins = [];
-    const phases = ['discovery', 'indexing', 'analysis', 'enrichment', 'validation'];
-    for (const phase of phases) {
-        const names = config[phase] || [];
-        for (const name of names) {
-            // Check built-in first, then custom
-            const factory = BUILTIN_PLUGINS[name] || customPlugins[name];
-            if (factory) {
-                plugins.push(factory());
-            }
-            else if (verbose) {
-                // Only show plugin warning in verbose mode
-                console.warn(`Plugin not found: ${name} (skipping). Check .grafema/config.yaml or add to .grafema/plugins/`);
-            }
-        }
-    }
-    return plugins;
-}
-/**
- * Determine log level from CLI options.
- * Priority: --log-level > --quiet > --verbose > default ('silent')
+ * Analyze command — Run project analysis via Orchestrator.
  *
- * By default, logs are silent to allow clean progress UI.
- * Use --verbose to see detailed logs (disables interactive progress).
+ * Command definition only. Execution logic is in analyzeAction.ts.
  */
-function getLogLevel(options) {
-    if (options.logLevel) {
-        const validLevels = ['silent', 'errors', 'warnings', 'info', 'debug'];
-        if (validLevels.includes(options.logLevel)) {
-            return options.logLevel;
-        }
-    }
-    if (options.quiet)
-        return 'silent';
-    if (options.verbose)
-        return 'info'; // --verbose shows logs instead of progress UI
-    return 'silent'; // Default: silent logs, clean progress UI
-}
+import { Command } from 'commander';
+import { analyzeAction } from './analyzeAction.js';
 export const analyzeCommand = new Command('analyze')
     .description('Run project analysis')
     .argument('[path]', 'Project path to analyze', '.')
@@ -171,208 +32,5 @@ Examples:
 
 Note: Start the server first with: grafema server start
 `)
-    .action(async (path, options) => {
-    const projectPath = resolve(path);
-    const grafemaDir = join(projectPath, '.grafema');
-    const dbPath = join(grafemaDir, 'graph.rfdb');
-    if (!existsSync(grafemaDir)) {
-        mkdirSync(grafemaDir, { recursive: true });
-    }
-    // Two log levels for CLI output:
-    // - info: important results (shows unless --quiet)
-    // - debug: verbose details (shows only with --verbose)
-    const info = options.quiet ? () => { } : console.log;
-    const debug = options.verbose ? console.log : () => { };
-    // Create logger based on CLI flags
-    const logLevel = getLogLevel(options);
-    const logFile = options.logFile ? resolve(options.logFile) : undefined;
-    const logger = createLogger(logLevel, logFile ? { logFile } : undefined);
-    if (logFile) {
-        debug(`Log file: ${logFile}`);
-    }
-    debug(`Analyzing project: ${projectPath}`);
-    // Connect to RFDB server
-    // Default: require explicit `grafema server start`
-    // Use --auto-start for CI or backwards compatibility
-    // In normal mode (not verbose), suppress backend logs for clean progress UI
-    const backend = new RFDBServerBackend({
-        dbPath,
-        autoStart: options.autoStart ?? false,
-        silent: !options.verbose // Silent in normal mode (show progress), verbose shows logs
-    });
-    try {
-        await backend.connect();
-    }
-    catch (err) {
-        if (!options.autoStart && err instanceof Error && err.message.includes('not running')) {
-            console.error('');
-            console.error('RFDB server is not running.');
-            console.error('');
-            console.error('Start the server first:');
-            console.error('  grafema server start');
-            console.error('');
-            console.error('Or use --auto-start flag:');
-            console.error('  grafema analyze --auto-start');
-            console.error('');
-            process.exit(1);
-        }
-        throw err;
-    }
-    if (options.clear) {
-        debug('Clearing existing database...');
-        await backend.clear();
-    }
-    const config = loadConfig(projectPath, logger);
-    // Extract services from config (REG-174)
-    if (config.services.length > 0) {
-        debug(`Loaded ${config.services.length} service(s) from config`);
-        for (const svc of config.services) {
-            const entry = svc.entryPoint ? ` (entry: ${svc.entryPoint})` : '';
-            debug(`  - ${svc.name}: ${svc.path}${entry}`);
-        }
-    }
-    // Load custom plugins from .grafema/plugins/
-    const customPlugins = await loadCustomPlugins(projectPath, debug);
-    const plugins = createPlugins(config.plugins, customPlugins, options.verbose);
-    debug(`Loaded ${plugins.length} plugins`);
-    // Resolve strict mode: CLI flag overrides config
-    const strictMode = options.strict ?? config.strict ?? false;
-    if (strictMode) {
-        debug('Strict mode enabled - analysis will fail on unresolved references');
-    }
-    const startTime = Date.now();
-    // Create progress renderer for CLI output
-    // In quiet mode, use a no-op renderer (skip rendering)
-    // In verbose mode, use non-interactive (newlines per update)
-    // In normal mode, use interactive (spinner with line overwrite)
-    const renderer = options.quiet
-        ? null
-        : new ProgressRenderer({
-            isInteractive: !options.verbose && process.stdout.isTTY,
-        });
-    // Poll graph stats periodically to show node/edge counts in progress
-    let statsInterval = null;
-    if (renderer && !options.quiet) {
-        statsInterval = setInterval(async () => {
-            try {
-                const stats = await fetchNodeEdgeCounts(backend);
-                renderer.setStats(stats.nodeCount, stats.edgeCount);
-            }
-            catch {
-                // Ignore stats errors during analysis
-            }
-        }, 500); // Poll every 500ms
-        statsInterval.unref?.();
-    }
-    const orchestrator = new Orchestrator({
-        graph: backend,
-        plugins,
-        serviceFilter: options.service || null,
-        entrypoint: options.entrypoint,
-        forceAnalysis: options.clear || false,
-        logger,
-        services: config.services.length > 0 ? config.services : undefined, // Pass config services (REG-174)
-        strictMode, // REG-330: Pass strict mode flag
-        onProgress: (progress) => {
-            renderer?.update(progress);
-        },
-    });
-    let exitCode = 0;
-    try {
-        await orchestrator.run(projectPath);
-        await backend.flush();
-        const elapsedSeconds = (Date.now() - startTime) / 1000;
-        const stats = await fetchNodeEdgeCounts(backend);
-        // Clear progress line in interactive mode, then show results
-        if (renderer && process.stdout.isTTY) {
-            process.stdout.write('\r\x1b[K'); // Clear line
-        }
-        info('');
-        info(renderer ? renderer.finish(elapsedSeconds) : `Analysis complete in ${elapsedSeconds.toFixed(2)}s`);
-        info(`  Nodes: ${stats.nodeCount}`);
-        info(`  Edges: ${stats.edgeCount}`);
-        // Get diagnostics and report summary
-        const diagnostics = orchestrator.getDiagnostics();
-        const reporter = new DiagnosticReporter(diagnostics);
-        // Print summary if there are any issues
-        if (diagnostics.count() > 0) {
-            info('');
-            info(reporter.categorizedSummary());
-            // In verbose mode, print full report
-            if (options.verbose) {
-                debug('');
-                debug(reporter.report({ format: 'text', includeSummary: false }));
-            }
-        }
-        // Always write diagnostics.log (required for `grafema check` command)
-        const writer = new DiagnosticWriter();
-        await writer.write(diagnostics, grafemaDir);
-        if (options.debug) {
-            debug(`Diagnostics written to ${writer.getLogPath(grafemaDir)}`);
-        }
-        // Determine exit code based on severity
-        if (diagnostics.hasFatal()) {
-            exitCode = 1;
-        }
-        else if (diagnostics.hasErrors()) {
-            exitCode = 2; // Completed with errors
-        }
-        else {
-            exitCode = 0; // Success (maybe warnings)
-        }
-    }
-    catch (e) {
-        const diagnostics = orchestrator.getDiagnostics();
-        const reporter = new DiagnosticReporter(diagnostics);
-        // Clear progress line in interactive mode
-        if (renderer && process.stdout.isTTY) {
-            process.stdout.write('\r\x1b[K');
-        }
-        // Check if this is a strict mode failure (REG-332: structured output)
-        if (e instanceof StrictModeFailure) {
-            // Format ONLY from diagnostics, not from error.message
-            console.error('');
-            console.error(`✗ Strict mode: ${e.count} unresolved reference(s) found during ENRICHMENT.`);
-            console.error('');
-            console.error(reporter.formatStrict(e.diagnostics, {
-                verbose: options.verbose,
-                suppressedCount: e.suppressedCount, // REG-332
-            }));
-            console.error('');
-            console.error('Run without --strict for graceful degradation, or fix the underlying issues.');
-        }
-        else {
-            // Generic error handling (non-strict)
-            const error = e instanceof Error ? e : new Error(String(e));
-            console.error('');
-            console.error(`✗ Analysis failed: ${error.message}`);
-            console.error('');
-            console.error('→ Run with --debug for detailed diagnostics');
-            if (diagnostics.count() > 0) {
-                console.error('');
-                console.error(reporter.report({ format: 'text', includeSummary: true }));
-            }
-        }
-        // Write diagnostics.log in debug mode even on failure
-        if (options.debug) {
-            const writer = new DiagnosticWriter();
-            await writer.write(diagnostics, grafemaDir);
-            console.error(`Diagnostics written to ${writer.getLogPath(grafemaDir)}`);
-        }
-        exitCode = 1;
-    }
-    finally {
-        // Stop stats polling
-        if (statsInterval) {
-            clearInterval(statsInterval);
-            statsInterval = null;
-        }
-        if (backend.connected) {
-            await backend.close();
-        }
-        // Exit with appropriate code
-        // 0 = success, 1 = fatal, 2 = errors
-        exitWithCode(exitCode);
-    }
-});
+    .action(analyzeAction);
 //# sourceMappingURL=analyze.js.map

package/dist/commands/analyze.js.map

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+{"version":3,"file":"analyze.js","sourceRoot":"","sources":["../../src/commands/analyze.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAC;AAGnD,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,OAAO,CAAC,SAAS,CAAC;KACjD,WAAW,CAAC,sBAAsB,CAAC;KACnC,QAAQ,CAAC,QAAQ,EAAE,yBAAyB,EAAE,GAAG,CAAC;KAClD,MAAM,CAAC,sBAAsB,EAAE,iCAAiC,CAAC;KACjE,MAAM,CAAC,yBAAyB,EAAE,+CAA+C,CAAC;KAClF,MAAM,CAAC,aAAa,EAAE,yCAAyC,CAAC;KAChE,MAAM,CAAC,aAAa,EAAE,0BAA0B,CAAC;KACjD,MAAM,CAAC,eAAe,EAAE,sBAAsB,CAAC;KAC/C,MAAM,CAAC,SAAS,EAAE,4CAA4C,CAAC;KAC/D,MAAM,CAAC,qBAAqB,EAAE,uDAAuD,CAAC;KACtF,MAAM,CAAC,mBAAmB,EAAE,gCAAgC,CAAC;KAC7D,MAAM,CAAC,UAAU,EAAE,oDAAoD,CAAC;KACxE,MAAM,CAAC,cAAc,EAAE,uCAAuC,CAAC;KAC/D,WAAW,CAAC,OAAO,EAAE;;;;;;;;;;;;;CAavB,CAAC;KACC,MAAM,CAAC,aAAa,CAAC,CAAC"}

package/dist/commands/analyzeAction.d.ts

@@ -0,0 +1,28 @@
+/**
+ * Analyze command action — connects to RFDB, loads plugins, runs Orchestrator.
+ *
+ * Extracted from analyze.ts (REG-435) to keep command definition separate
+ * from execution logic.
+ */
+export interface NodeEdgeCountBackend {
+    nodeCount: () => Promise<number>;
+    edgeCount: () => Promise<number>;
+}
+export declare function fetchNodeEdgeCounts(backend: NodeEdgeCountBackend): Promise<{
+    nodeCount: number;
+    edgeCount: number;
+}>;
+export declare function exitWithCode(code: number, exitFn?: (code: number) => void): void;
+export declare function analyzeAction(path: string, options: {
+    service?: string;
+    entrypoint?: string;
+    clear?: boolean;
+    quiet?: boolean;
+    verbose?: boolean;
+    debug?: boolean;
+    logLevel?: string;
+    logFile?: string;
+    strict?: boolean;
+    autoStart?: boolean;
+}): Promise<void>;
+//# sourceMappingURL=analyzeAction.d.ts.map

package/dist/commands/analyzeAction.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"analyzeAction.d.ts","sourceRoot":"","sources":["../../src/commands/analyzeAction.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAiBH,MAAM,WAAW,oBAAoB;IACnC,SAAS,EAAE,MAAM,OAAO,CAAC,MAAM,CAAC,CAAC;IACjC,SAAS,EAAE,MAAM,OAAO,CAAC,MAAM,CAAC,CAAC;CAClC;AAED,wBAAsB,mBAAmB,CAAC,OAAO,EAAE,oBAAoB,GAAG,OAAO,CAAC;IAAE,SAAS,EAAE,MAAM,CAAC;IAAC,SAAS,EAAE,MAAM,CAAA;CAAE,CAAC,CAG1H;AAED,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,GAAE,CAAC,IAAI,EAAE,MAAM,KAAK,IAAmB,GAAG,IAAI,CAE9F;AAqBD,wBAAsB,aAAa,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE;IAAE,OAAO,CAAC,EAAE,MAAM,CAAC;IAAC,UAAU,CAAC,EAAE,MAAM,CAAC;IAAC,KAAK,CAAC,EAAE,OAAO,CAAC;IAAC,KAAK,CAAC,EAAE,OAAO,CAAC;IAAC,OAAO,CAAC,EAAE,OAAO,CAAC;IAAC,KAAK,CAAC,EAAE,OAAO,CAAC;IAAC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAAC,OAAO,CAAC,EAAE,MAAM,CAAC;IAAC,MAAM,CAAC,EAAE,OAAO,CAAC;IAAC,SAAS,CAAC,EAAE,OAAO,CAAA;CAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAoOrQ"}