@monoes/monograph 1.0.0 → 1.2.0

package/dist/src/pipeline/phases/scope-resolution.js

@@ -0,0 +1,372 @@
+import { readFileSync } from 'fs';
+import { join, extname } from 'path';
+import { makeId } from '../../types.js';
+// ── JS/TS keywords to skip for direct calls ───────────────────────────────────
+const JS_KEYWORDS = new Set([
+    'if', 'for', 'while', 'switch', 'return', 'function', 'class', 'new', 'typeof',
+    'await', 'catch', 'throw', 'delete', 'void', 'instanceof', 'in', 'of',
+    'import', 'export', 'yield', 'async', 'super', 'this', 'const', 'let', 'var',
+    'try', 'finally', 'break', 'continue', 'debugger', 'with', 'do',
+]);
+const PY_KEYWORDS = new Set([
+    'if', 'for', 'while', 'with', 'return', 'def', 'class', 'import', 'from',
+    'raise', 'yield', 'lambda', 'await', 'async', 'del', 'pass', 'assert',
+    'except', 'elif', 'else', 'not', 'and', 'or', 'in', 'is', 'print',
+]);
+const GO_KEYWORDS = new Set([
+    'if', 'for', 'range', 'return', 'func', 'type', 'var', 'const', 'import', 'package',
+    'go', 'defer', 'select', 'case', 'default', 'break', 'continue', 'goto', 'fallthrough',
+    'chan', 'map', 'struct', 'interface', 'make', 'new', 'len', 'cap', 'append', 'delete',
+    'panic', 'recover', 'close', 'switch', 'else',
+]);
+const JAVA_KEYWORDS = new Set([
+    'if', 'for', 'while', 'do', 'switch', 'case', 'return', 'class', 'interface', 'enum',
+    'new', 'extends', 'implements', 'import', 'package', 'throw', 'throws', 'catch', 'try',
+    'finally', 'static', 'final', 'abstract', 'public', 'private', 'protected', 'void',
+    'break', 'continue', 'default', 'else', 'instanceof', 'this', 'super',
+]);
+const RUST_KEYWORDS = new Set([
+    'if', 'let', 'for', 'while', 'loop', 'match', 'return', 'fn', 'struct', 'enum', 'trait',
+    'impl', 'use', 'mod', 'pub', 'super', 'self', 'type', 'where', 'in', 'as', 'mut',
+    'ref', 'move', 'async', 'await', 'dyn', 'extern', 'crate', 'static', 'const', 'unsafe',
+    'break', 'continue', 'else',
+]);
+// ── Supported extensions ──────────────────────────────────────────────────────
+const TS_JS_EXTS = new Set(['.ts', '.tsx', '.js', '.jsx']);
+const PY_EXTS = new Set(['.py']);
+const GO_EXTS = new Set(['.go']);
+const JAVA_EXTS = new Set(['.java']);
+const RUST_EXTS = new Set(['.rs']);
+function isSupportedExt(ext) {
+    return TS_JS_EXTS.has(ext) || PY_EXTS.has(ext) || GO_EXTS.has(ext) || JAVA_EXTS.has(ext) || RUST_EXTS.has(ext);
+}
+// ── Language-specific extractors ──────────────────────────────────────────────
+export function extractGoCallSites(source, filePath, fileNodeId) {
+    const sites = [];
+    const methodPattern = /(\w+)\.(\w+)\s*\(/g;
+    let m;
+    while ((m = methodPattern.exec(source)) !== null) {
+        sites.push({ callerFileNodeId: fileNodeId, callerFilePath: filePath, calleeRaw: `${m[1]}.${m[2]}`, form: 'method', receiverName: m[1], methodName: m[2] });
+    }
+    const directPattern = /(?<![.[\w])([A-Za-z_][\w]*)\s*\(/g;
+    while ((m = directPattern.exec(source)) !== null) {
+        const name = m[1];
+        if (GO_KEYWORDS.has(name))
+            continue;
+        sites.push({ callerFileNodeId: fileNodeId, callerFilePath: filePath, calleeRaw: name, form: 'direct' });
+    }
+    return sites;
+}
+export function extractJavaCallSites(source, filePath, fileNodeId) {
+    const sites = [];
+    const methodPattern = /(\w+)\.(\w+)\s*\(/g;
+    let m;
+    while ((m = methodPattern.exec(source)) !== null) {
+        sites.push({ callerFileNodeId: fileNodeId, callerFilePath: filePath, calleeRaw: `${m[1]}.${m[2]}`, form: 'method', receiverName: m[1], methodName: m[2] });
+    }
+    const directPattern = /(?<![.[\w])([A-Za-z_$][\w$]*)\s*\(/g;
+    while ((m = directPattern.exec(source)) !== null) {
+        const name = m[1];
+        if (JAVA_KEYWORDS.has(name))
+            continue;
+        sites.push({ callerFileNodeId: fileNodeId, callerFilePath: filePath, calleeRaw: name, form: 'direct' });
+    }
+    return sites;
+}
+export function extractRustCallSites(source, filePath, fileNodeId) {
+    const sites = [];
+    const methodPattern = /(\w+)\.(\w+)\s*\(/g;
+    let m;
+    while ((m = methodPattern.exec(source)) !== null) {
+        sites.push({ callerFileNodeId: fileNodeId, callerFilePath: filePath, calleeRaw: `${m[1]}.${m[2]}`, form: 'method', receiverName: m[1], methodName: m[2] });
+    }
+    const directPattern = /(?<![.[\w])([A-Za-z_][\w]*)\s*\(/g;
+    while ((m = directPattern.exec(source)) !== null) {
+        const name = m[1];
+        if (RUST_KEYWORDS.has(name))
+            continue;
+        sites.push({ callerFileNodeId: fileNodeId, callerFilePath: filePath, calleeRaw: name, form: 'direct' });
+    }
+    return sites;
+}
+// ── Stage 1 + 2: Extract and classify call sites ──────────────────────────────
+function extractCallSites(source, filePath, fileNodeId, ext) {
+    const sites = [];
+    if (TS_JS_EXTS.has(ext)) {
+        // Method calls: word.word(
+        const methodPattern = /(\w+)\.(\w+)\s*\(/g;
+        let m;
+        while ((m = methodPattern.exec(source)) !== null) {
+            sites.push({
+                callerFileNodeId: fileNodeId,
+                callerFilePath: filePath,
+                calleeRaw: `${m[1]}.${m[2]}`,
+                form: 'method',
+                receiverName: m[1],
+                methodName: m[2],
+            });
+        }
+        // Direct calls: word( not preceded by . or word char
+        const directPattern = /(?<![.[\w])([A-Za-z_$][\w$]*)\s*\(/g;
+        while ((m = directPattern.exec(source)) !== null) {
+            const name = m[1];
+            if (JS_KEYWORDS.has(name))
+                continue;
+            sites.push({
+                callerFileNodeId: fileNodeId,
+                callerFilePath: filePath,
+                calleeRaw: name,
+                form: 'direct',
+                methodName: name,
+            });
+        }
+        // Dynamic calls: obj[key]( → mark as dynamic
+        const dynamicPattern = /\w+\s*\[[\w'"` ]+\]\s*\(/g;
+        while ((m = dynamicPattern.exec(source)) !== null) {
+            sites.push({
+                callerFileNodeId: fileNodeId,
+                callerFilePath: filePath,
+                calleeRaw: m[0],
+                form: 'dynamic',
+            });
+        }
+    }
+    else if (PY_EXTS.has(ext)) {
+        // Method calls: self.method( or obj.method(
+        const methodPattern = /(\w+)\.(\w+)\s*\(/g;
+        let m;
+        while ((m = methodPattern.exec(source)) !== null) {
+            sites.push({
+                callerFileNodeId: fileNodeId,
+                callerFilePath: filePath,
+                calleeRaw: `${m[1]}.${m[2]}`,
+                form: 'method',
+                receiverName: m[1],
+                methodName: m[2],
+            });
+        }
+        // Direct calls: word( not preceded by . or word char
+        const directPattern = /(?<![.[\w])([A-Za-z_][\w]*)\s*\(/g;
+        while ((m = directPattern.exec(source)) !== null) {
+            const name = m[1];
+            if (PY_KEYWORDS.has(name))
+                continue;
+            sites.push({
+                callerFileNodeId: fileNodeId,
+                callerFilePath: filePath,
+                calleeRaw: name,
+                form: 'direct',
+                methodName: name,
+            });
+        }
+    }
+    else if (GO_EXTS.has(ext)) {
+        return extractGoCallSites(source, filePath, fileNodeId);
+    }
+    else if (JAVA_EXTS.has(ext)) {
+        return extractJavaCallSites(source, filePath, fileNodeId);
+    }
+    else if (RUST_EXTS.has(ext)) {
+        return extractRustCallSites(source, filePath, fileNodeId);
+    }
+    return sites;
+}
+// ── Stage 3: Build import map from DB ─────────────────────────────────────────
+/** Returns a map of imported name → source file path for a given file node */
+function buildImportMap(ctx, fileNodeId, symbolNodes) {
+    const importMap = new Map();
+    if (!ctx.db)
+        return importMap;
+    // Get IMPORTS edges for this file to find which modules it imports
+    const importsRows = ctx.db
+        .prepare(`SELECT target_id FROM edges WHERE source_id = ? AND relation = 'IMPORTS'`)
+        .all(fileNodeId);
+    for (const row of importsRows) {
+        const targetId = row.target_id;
+        // Find a File node that matches the resolved target
+        const fileNode = symbolNodes.find(n => n.label === 'File' && (n.id === targetId ||
+            makeId(n.filePath?.replace(/\//g, '_') ?? '', 'file') === targetId));
+        if (fileNode?.filePath) {
+            // Extract the module name from the last path segment without extension
+            const parts = fileNode.filePath.split('/');
+            const baseName = parts[parts.length - 1].replace(/\.\w+$/, '');
+            importMap.set(baseName, fileNode.filePath);
+            importMap.set(fileNode.filePath, fileNode.filePath);
+        }
+    }
+    return importMap;
+}
+// ── Stage 4 + 5: Resolve target node ─────────────────────────────────────────
+function resolveTarget(ctx, site, callerFilePath, importMap) {
+    if (!ctx.db)
+        return null;
+    const methodName = site.methodName;
+    if (!methodName)
+        return null;
+    let candidateFilePaths = [];
+    if (site.form === 'method' && site.receiverName) {
+        // Stage 3: Infer receiver type — look up receiver in import map
+        const receiverPath = importMap.get(site.receiverName);
+        if (receiverPath) {
+            candidateFilePaths = [receiverPath];
+        }
+        else {
+            // Receiver not imported — look in same file only
+            candidateFilePaths = [callerFilePath];
+        }
+    }
+    else if (site.form === 'direct') {
+        // Direct call: same file first, then all imported files
+        candidateFilePaths = [callerFilePath, ...importMap.values()];
+    }
+    else {
+        return null;
+    }
+    // Stage 5: Query nodes table for matching function/method/constructor
+    for (const fp of candidateFilePaths) {
+        const rows = ctx.db
+            .prepare(`
+        SELECT id FROM nodes
+        WHERE name = ?
+          AND label IN ('Function', 'Method', 'Constructor')
+          AND file_path = ?
+        LIMIT 2
+      `)
+            .all(methodName, fp);
+        if (rows.length === 1) {
+            return { targetId: rows[0].id };
+        }
+        // If > 1 match, it's ambiguous — skip this candidate file
+    }
+    return null;
+}
+// ── Stage 6: Emit edge ────────────────────────────────────────────────────────
+function emitEdge(ctx, sourceId, targetId) {
+    if (!ctx.db)
+        return 'skipped';
+    if (sourceId === targetId)
+        return 'skipped';
+    const RESOLVED_CONFIDENCE_SCORE = 0.75;
+    // Check if a CALLS edge already exists
+    const existing = ctx.db
+        .prepare(`
+      SELECT id, confidence_score FROM edges
+      WHERE source_id = ? AND target_id = ? AND relation = 'CALLS'
+    `)
+        .get(sourceId, targetId);
+    if (existing) {
+        const newScore = Math.max(existing.confidence_score, RESOLVED_CONFIDENCE_SCORE);
+        if (newScore > existing.confidence_score) {
+            ctx.db
+                .prepare(`
+          UPDATE edges
+          SET confidence_score = ?, confidence = 'EXTRACTED'
+          WHERE id = ?
+        `)
+                .run(newScore, existing.id);
+        }
+        return 'upgraded';
+    }
+    // Insert new CALLS edge
+    const edgeId = makeId(sourceId, targetId, 'calls_resolved');
+    try {
+        ctx.db
+            .prepare(`
+        INSERT OR IGNORE INTO edges (id, source_id, target_id, relation, confidence, confidence_score)
+        VALUES (?, ?, ?, 'CALLS', 'EXTRACTED', ?)
+      `)
+            .run(edgeId, sourceId, targetId, RESOLVED_CONFIDENCE_SCORE);
+        return 'inserted';
+    }
+    catch {
+        return 'skipped';
+    }
+}
+// ── Phase definition ──────────────────────────────────────────────────────────
+export const scopeResolutionPhase = {
+    name: 'scope-resolution',
+    deps: ['parse', 'cross-file'],
+    async execute(ctx, deps) {
+        const { symbolNodes } = deps.get('parse');
+        let resolvedEdges = 0;
+        let skippedDynamic = 0;
+        let ambiguous = 0;
+        // Build a map from file_path → file node id using the parse output
+        const fileNodesByPath = new Map();
+        for (const node of symbolNodes) {
+            if (node.label === 'File' && node.filePath) {
+                fileNodesByPath.set(node.filePath, node);
+            }
+        }
+        // Also look up File nodes from the DB (includes nodes created by structure phase)
+        if (ctx.db) {
+            const dbFileNodes = ctx.db
+                .prepare(`SELECT id, file_path FROM nodes WHERE label = 'File'`)
+                .all();
+            for (const row of dbFileNodes) {
+                if (row.file_path && !fileNodesByPath.has(row.file_path)) {
+                    fileNodesByPath.set(row.file_path, {
+                        id: row.id,
+                        label: 'File',
+                        name: row.file_path.split('/').pop() ?? row.file_path,
+                        normLabel: '',
+                        filePath: row.file_path,
+                        isExported: false,
+                    });
+                }
+            }
+        }
+        for (const [filePath, fileNode] of fileNodesByPath) {
+            const ext = extname(filePath).toLowerCase();
+            if (!isSupportedExt(ext))
+                continue;
+            // Read file source
+            let source;
+            try {
+                source = readFileSync(join(ctx.repoPath, filePath), 'utf-8');
+            }
+            catch {
+                continue;
+            }
+            // Stage 1+2: Extract call sites
+            const callSites = extractCallSites(source, filePath, fileNode.id, ext);
+            // Stage 3: Build import map for this file
+            const importMap = buildImportMap(ctx, fileNode.id, symbolNodes);
+            for (const site of callSites) {
+                if (site.form === 'dynamic') {
+                    skippedDynamic++;
+                    continue;
+                }
+                // Stage 4+5: Resolve target
+                const resolved = resolveTarget(ctx, site, filePath, importMap);
+                if (!resolved) {
+                    // Could not resolve — treat as ambiguous if we had candidates
+                    // (method calls with unresolvable receivers are simply skipped)
+                    continue;
+                }
+                // Check if the resolved target is actually in multiple places (ambiguity check)
+                if (ctx.db && site.methodName) {
+                    const totalMatches = ctx.db
+                        .prepare(`
+              SELECT COUNT(*) as cnt FROM nodes
+              WHERE name = ?
+                AND label IN ('Function', 'Method', 'Constructor')
+            `)
+                        .get(site.methodName);
+                    if (totalMatches.cnt > 1) {
+                        ambiguous++;
+                        // Still emit if we found exactly one in the candidate file — this is per-file ambiguity
+                        // The resolve already picked one candidate, so proceed
+                    }
+                }
+                // Stage 6: Emit edge (source is the file node of the caller)
+                const result = emitEdge(ctx, site.callerFileNodeId, resolved.targetId);
+                if (result === 'inserted' || result === 'upgraded') {
+                    resolvedEdges++;
+                }
+            }
+        }
+        return { resolvedEdges, skippedDynamic, ambiguous };
+    },
+};
+//# sourceMappingURL=scope-resolution.js.map

package/dist/src/pipeline/phases/scope-resolution.js.map

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package/dist/src/pipeline/phases/suggest.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"suggest.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/suggest.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAmB,MAAM,aAAa,CAAC;AAClE,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,gBAAgB,CAAC;AAIxD,MAAM,WAAW,aAAa;IAC5B,SAAS,EAAE,iBAAiB,EAAE,CAAC;CAChC;AAED,eAAO,MAAM,YAAY,EAAE,aAAa,CAAC,aAAa,CA6DrD,CAAC"}
+{"version":3,"file":"suggest.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/suggest.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAmB,MAAM,aAAa,CAAC;AAClE,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,gBAAgB,CAAC;AAIxD,MAAM,WAAW,aAAa;IAC5B,SAAS,EAAE,iBAAiB,EAAE,CAAC;CAChC;AAED,eAAO,MAAM,YAAY,EAAE,aAAa,CAAC,aAAa,CAiFrD,CAAC"}

package/dist/src/pipeline/phases/suggest.js

@@ -17,7 +17,9 @@ export const suggestPhase = {
             const srcComm = memberships.get(edge.sourceId);
             const tgtComm = memberships.get(edge.targetId);
             if (srcComm !== undefined && tgtComm !== undefined && srcComm !== tgtComm) {
-                for (const [nid, comm] of [[edge.sourceId, srcComm], [edge.targetId, tgtComm]]) {
+                // Record the NEIGHBOR's community for each endpoint so a node accumulates
+                // the communities it bridges TO, enabling comms.size >= 2 to fire correctly.
+                for (const [nid, comm] of [[edge.sourceId, tgtComm], [edge.targetId, srcComm]]) {
                     const s = nodeCommSet.get(nid) ?? new Set();
                     s.add(comm);
                     nodeCommSet.set(nid, s);
@@ -49,8 +51,24 @@ export const suggestPhase = {
         if (isolated.length > 0) {
             questions.push({ type: 'isolated_nodes', nodes: isolated.slice(0, 10), reason: 'No edges found' });
         }
+        // Signal 5: no_signal — AMBIGUOUS edges with very low confidence
+        for (const edge of allEdges) {
+            if (edge.confidence === 'AMBIGUOUS' && (edge.confidenceScore ?? 1) < 0.2) {
+                questions.push({ type: 'no_signal', edge, reason: 'Very low confidence — no supporting evidence found' });
+            }
+        }
+        // Signal 6: thin_community — communities with fewer than 3 members
+        const commMemberCount = new Map();
+        for (const [, commId] of memberships) {
+            commMemberCount.set(commId, (commMemberCount.get(commId) ?? 0) + 1);
+        }
+        for (const [commId, count] of commMemberCount) {
+            if (count < 3) {
+                questions.push({ type: 'thin_community', communityId: commId, memberCount: count, reason: `Community has only ${count} members — may need merging` });
+            }
+        }
         const PRIORITY = {
-            bridge_node: 5, ambiguous_edge: 4, verify_inferred: 3, low_cohesion: 2, isolated_nodes: 1
+            bridge_node: 5, ambiguous_edge: 4, verify_inferred: 3, no_signal: 3, low_cohesion: 2, thin_community: 2, isolated_nodes: 1
         };
         questions.sort((a, b) => (PRIORITY[b.type] ?? 0) - (PRIORITY[a.type] ?? 0));
         return { questions };

package/dist/src/pipeline/phases/suggest.js.map

@@ -1 +1 @@
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package/dist/src/pipeline/phases/surprises.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"surprises.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/surprises.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAmB,MAAM,aAAa,CAAC;AAClE,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AAa3D,MAAM,WAAW,eAAe;IAC9B,SAAS,EAAE,oBAAoB,EAAE,CAAC;CACnC;AAED,eAAO,MAAM,cAAc,EAAE,aAAa,CAAC,eAAe,CAmDzD,CAAC"}
+{"version":3,"file":"surprises.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/surprises.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAmB,MAAM,aAAa,CAAC;AAClE,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AAc3D,MAAM,WAAW,eAAe;IAC9B,SAAS,EAAE,oBAAoB,EAAE,CAAC;CACnC;AAED,eAAO,MAAM,cAAc,EAAE,aAAa,CAAC,eAAe,CA+DzD,CAAC"}

package/dist/src/pipeline/phases/surprises.js

@@ -1,3 +1,4 @@
+import { classifyFile } from '../../analysis/file-classifier.js';
 const WEIGHTS = {
     confidence: 0.30,
     crossType: 0.20,
@@ -17,7 +18,7 @@ export const surprisesPhase = {
         const inDeg = new Map();
         for (const e of edges)
             inDeg.set(e.targetId, (inDeg.get(e.targetId) ?? 0) + 1);
-        const maxDeg = Math.max(...inDeg.values(), 1);
+        const maxDeg = [...inDeg.values()].reduce((a, b) => Math.max(a, b), 1);
         const peripheralThreshold = maxDeg * 0.1;
         const surprises = edges
             .filter(e => e.confidence !== 'EXTRACTED')
@@ -40,6 +41,17 @@ export const surprisesPhase = {
                 score += WEIGHTS.crossCommunity;
                 reasons.push('cross-community');
             }
+            // Cross-filetype bonus: CODE↔DOCUMENT/PAPER edges get extra weight
+            const srcFilePath = symbolNodes.find(n => n.id === e.sourceId)?.filePath;
+            const tgtFilePath = symbolNodes.find(n => n.id === e.targetId)?.filePath;
+            if (srcFilePath && tgtFilePath) {
+                const srcFileType = classifyFile(srcFilePath);
+                const tgtFileType = classifyFile(tgtFilePath);
+                if (srcFileType !== tgtFileType) {
+                    score += WEIGHTS.crossRepo; // reuse unused crossRepo weight (0.15)
+                    reasons.push(`cross-filetype (${srcFileType}→${tgtFileType})`);
+                }
+            }
             if ((inDeg.get(e.targetId) ?? 0) < peripheralThreshold) {
                 score += WEIGHTS.peripheral;
                 reasons.push('peripheral target');

package/dist/src/pipeline/phases/surprises.js.map

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package/dist/src/pipeline/phases/tools.d.ts

@@ -0,0 +1,13 @@
+import type { PipelinePhase } from '../types.js';
+export interface ToolDef {
+    name: string;
+    filePath: string;
+    description?: string;
+    handlerNodeId?: string;
+    toolNodeId: string;
+}
+export interface ToolsOutput {
+    toolDefs: ToolDef[];
+}
+export declare const toolsPhase: PipelinePhase<ToolsOutput>;
+//# sourceMappingURL=tools.d.ts.map

package/dist/src/pipeline/phases/tools.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"tools.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/tools.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAajD,MAAM,WAAW,OAAO;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,MAAM,CAAC;IACjB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,WAAW;IAC1B,QAAQ,EAAE,OAAO,EAAE,CAAC;CACrB;AAeD,eAAO,MAAM,UAAU,EAAE,aAAa,CAAC,WAAW,CA+GjD,CAAC"}