@monoes/monomindcli 1.10.54 → 1.10.55

package/bundled-graph/dist/src/extract/languages/typescript.js

@@ -1,295 +0,0 @@
-import { basename } from 'path';
-import { tryLoadParser, walk, } from '../tree-sitter-runner.js';
-// ---- helpers ----
-function nodeName(node) {
-    // Most declaration nodes expose "name" as a named field
-    const nameNode = node.childForFieldName('name');
-    return nameNode?.text ?? '';
-}
-function loc(node) {
-    return `L${node.startPosition.row + 1}`;
-}
-// ---- tree-sitter extraction ----
-const CLASS_TYPES = new Set([
-    'class_declaration',
-    'abstract_class_declaration',
-]);
-const FUNCTION_TYPES = new Set([
-    'function_declaration',
-    'generator_function_declaration',
-]);
-function extractWithTreeSitter(filePath, content, language) {
-    const nodes = [];
-    const edges = [];
-    const errors = [];
-    const parser = tryLoadParser(language);
-    if (!parser) {
-        return { nodes, edges, filesProcessed: 1, fromCache: 0, errors };
-    }
-    let tree;
-    try {
-        tree = parser.parse(content);
-    }
-    catch (err) {
-        errors.push(`tree-sitter parse error in ${filePath}: ${String(err)}`);
-        return { nodes, edges, filesProcessed: 1, fromCache: 0, errors };
-    }
-    // Track current class/method context for call-edge attribution
-    const classStack = [];
-    const methodStack = [];
-    const addNode = (name, n) => {
-        if (!name)
-            return;
-        nodes.push({
-            id: name,
-            label: name,
-            fileType: 'code',
-            sourceFile: filePath,
-            sourceLocation: loc(n),
-        });
-    };
-    walk(tree.rootNode, (n) => {
-        // ---- classes ----
-        if (CLASS_TYPES.has(n.type)) {
-            const name = nodeName(n);
-            addNode(name, n);
-            if (name)
-                classStack.push(name);
-            // heritage: extends / implements
-            for (const child of n.children) {
-                if (child.type === 'class_heritage') {
-                    for (const clause of child.children) {
-                        if (clause.type !== 'extends_clause' && clause.type !== 'implements_clause')
-                            continue;
-                        const relation = clause.type === 'extends_clause' ? 'extends' : 'implements';
-                        // Each type_identifier inside the clause is a target
-                        for (const target of clause.children) {
-                            if (target.type === 'type_identifier' ||
-                                target.type === 'identifier') {
-                                edges.push({
-                                    source: name,
-                                    target: target.text,
-                                    relation,
-                                    confidence: 'EXTRACTED',
-                                    sourceFile: filePath,
-                                    sourceLocation: loc(clause),
-                                });
-                            }
-                        }
-                    }
-                }
-            }
-            return;
-        }
-        // ---- functions (top-level) ----
-        if (FUNCTION_TYPES.has(n.type)) {
-            const name = nodeName(n);
-            addNode(name, n);
-            if (name)
-                methodStack.push(name);
-            return;
-        }
-        // ---- method definitions (inside class body) ----
-        if (n.type === 'method_definition' || n.type === 'public_field_definition') {
-            const name = nodeName(n);
-            // Qualify name with class if available
-            const qualifiedName = classStack.length > 0 ? `${classStack[classStack.length - 1]}.${name}` : name;
-            addNode(qualifiedName, n);
-            if (qualifiedName)
-                methodStack.push(qualifiedName);
-            return;
-        }
-        // ---- interfaces ----
-        if (n.type === 'interface_declaration') {
-            const name = nodeName(n);
-            addNode(name, n);
-            // interface X extends Y
-            for (const child of n.children) {
-                if (child.type === 'extends_type_clause' || child.type === 'extends_clause') {
-                    for (const target of child.children) {
-                        if (target.type === 'type_identifier' || target.type === 'identifier') {
-                            edges.push({
-                                source: name,
-                                target: target.text,
-                                relation: 'extends',
-                                confidence: 'EXTRACTED',
-                                sourceFile: filePath,
-                                sourceLocation: loc(child),
-                            });
-                        }
-                    }
-                }
-            }
-            return;
-        }
-        // ---- type aliases ----
-        if (n.type === 'type_alias_declaration') {
-            const name = nodeName(n);
-            addNode(name, n);
-            return;
-        }
-        // ---- import statements ----
-        if (n.type === 'import_statement') {
-            // Extract the module specifier
-            const moduleSpecifier = n.childForFieldName('source');
-            const moduleText = moduleSpecifier
-                ? moduleSpecifier.text.replace(/^['"]|['"]$/g, '')
-                : '';
-            // Extract named specifiers: import { A, B } from '...'
-            for (const child of n.children) {
-                if (child.type === 'named_imports' || child.type === 'import_clause') {
-                    for (const spec of child.children) {
-                        if (spec.type === 'import_specifier') {
-                            const importedName = spec.childForFieldName('name')?.text ?? spec.text;
-                            if (importedName) {
-                                edges.push({
-                                    source: filePath,
-                                    target: importedName,
-                                    relation: 'imports',
-                                    confidence: 'EXTRACTED',
-                                    sourceFile: filePath,
-                                    sourceLocation: loc(n),
-                                });
-                            }
-                        }
-                    }
-                }
-                // Default import: import X from '...'
-                if (child.type === 'import_clause') {
-                    const defaultId = child.childForFieldName('name') ?? (child.children.find(c => c.type === 'identifier') ?? null);
-                    if (defaultId) {
-                        edges.push({
-                            source: filePath,
-                            target: defaultId.text,
-                            relation: 'imports',
-                            confidence: 'EXTRACTED',
-                            sourceFile: filePath,
-                            sourceLocation: loc(n),
-                        });
-                    }
-                }
-            }
-            // Always emit a file-level import edge to the module path
-            if (moduleText) {
-                edges.push({
-                    source: basename(filePath),
-                    target: moduleText,
-                    relation: 'imports',
-                    confidence: 'EXTRACTED',
-                    sourceFile: filePath,
-                    sourceLocation: loc(n),
-                });
-            }
-            return;
-        }
-        // ---- call expressions ----
-        if (n.type === 'call_expression') {
-            const fnNode = n.childForFieldName('function');
-            if (!fnNode)
-                return;
-            // Resolve callee name (may be `a.b()` or plain `foo()`)
-            let calleeName;
-            if (fnNode.type === 'member_expression') {
-                calleeName = fnNode.text;
-            }
-            else {
-                calleeName = fnNode.text;
-            }
-            // Attribute to deepest known method context
-            const caller = methodStack[methodStack.length - 1] ??
-                classStack[classStack.length - 1] ??
-                basename(filePath);
-            if (calleeName && caller && calleeName !== caller) {
-                edges.push({
-                    source: caller,
-                    target: calleeName,
-                    relation: 'calls',
-                    confidence: 'INFERRED',
-                    confidenceScore: 0.8,
-                    sourceFile: filePath,
-                    sourceLocation: loc(n),
-                });
-            }
-        }
-    });
-    return { nodes, edges, filesProcessed: 1, fromCache: 0, errors };
-}
-// ---- regex fallback ----
-function extractWithRegex(filePath, content) {
-    const nodes = [];
-    const edges = [];
-    const lines = content.split('\n');
-    lines.forEach((line, idx) => {
-        const location = `L${idx + 1}`;
-        // class
-        const classMatch = line.match(/^(export\s+)?(abstract\s+)?class\s+(\w+)/);
-        if (classMatch) {
-            const name = classMatch[3];
-            nodes.push({ id: name, label: name, fileType: 'code', sourceFile: filePath, sourceLocation: location });
-            // extends
-            const extendsMatch = line.match(/\bextends\s+(\w+)/);
-            if (extendsMatch) {
-                edges.push({ source: name, target: extendsMatch[1], relation: 'extends', confidence: 'EXTRACTED', sourceFile: filePath, sourceLocation: location });
-            }
-            // implements
-            const implementsMatch = line.match(/\bimplements\s+([\w,\s]+)/);
-            if (implementsMatch) {
-                for (const impl of implementsMatch[1].split(',')) {
-                    const implName = impl.trim().split(/\s/)[0];
-                    if (implName) {
-                        edges.push({ source: name, target: implName, relation: 'implements', confidence: 'EXTRACTED', sourceFile: filePath, sourceLocation: location });
-                    }
-                }
-            }
-        }
-        // interface
-        const ifaceMatch = line.match(/^(export\s+)?interface\s+(\w+)/);
-        if (ifaceMatch) {
-            const name = ifaceMatch[2];
-            nodes.push({ id: name, label: name, fileType: 'code', sourceFile: filePath, sourceLocation: location });
-        }
-        // type alias
-        const typeMatch = line.match(/^(export\s+)?type\s+(\w+)\s*=/);
-        if (typeMatch) {
-            const name = typeMatch[2];
-            nodes.push({ id: name, label: name, fileType: 'code', sourceFile: filePath, sourceLocation: location });
-        }
-        // function
-        const funcMatch = line.match(/^(export\s+)?(default\s+)?(async\s+)?function\s+(\w+)/);
-        if (funcMatch) {
-            const name = funcMatch[4];
-            nodes.push({ id: name, label: name, fileType: 'code', sourceFile: filePath, sourceLocation: location });
-        }
-        // import
-        const importMatch = line.match(/^import\s+.*from\s+['"]([^'"]+)['"]/);
-        if (importMatch) {
-            edges.push({ source: basename(filePath), target: importMatch[1], relation: 'imports', confidence: 'EXTRACTED', sourceFile: filePath, sourceLocation: location });
-            // Named specifiers
-            const namedMatch = line.match(/\{([^}]+)\}/);
-            if (namedMatch) {
-                for (const spec of namedMatch[1].split(',')) {
-                    const specName = spec.trim().split(/\s+as\s+/)[0].trim();
-                    if (specName) {
-                        edges.push({ source: filePath, target: specName, relation: 'imports', confidence: 'EXTRACTED', sourceFile: filePath, sourceLocation: location });
-                    }
-                }
-            }
-        }
-    });
-    return { nodes, edges, filesProcessed: 1, fromCache: 0, errors: [] };
-}
-// ---- extractor implementation ----
-export const typescriptExtractor = {
-    language: 'typescript',
-    extensions: ['.ts', '.tsx', '.js', '.jsx', '.mjs', '.cjs'],
-    extract(filePath, content) {
-        const lang = filePath.endsWith('.tsx') || filePath.endsWith('.jsx') ? 'tsx' : 'typescript';
-        const tsResult = extractWithTreeSitter(filePath, content, lang);
-        if (tsResult.nodes.length > 0 || tsResult.edges.length > 0 || tsResult.errors.length > 0) {
-            return tsResult;
-        }
-        // tree-sitter not available or produced nothing — fall back to regex
-        return extractWithRegex(filePath, content);
-    },
-};
-//# sourceMappingURL=typescript.js.map

package/bundled-graph/dist/src/extract/languages/typescript.js.map

@@ -1 +0,0 @@
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package/bundled-graph/dist/src/extract/semantic.d.ts

@@ -1,38 +0,0 @@
-/**
- * Semantic extraction via the Anthropic Claude API.
- *
- * Mirrors graphify's skill.md Step B1-B3 pipeline:
- * - Groups files into chunks of ~20
- * - Sends each chunk to Claude with the graphify extraction prompt
- * - Merges results into a single ExtractionResult
- *
- * Gracefully returns empty results if ANTHROPIC_API_KEY is not set
- * or the API call fails.
- */
-import type { ExtractionResult } from '../types.js';
-export interface SemanticFile {
-    path: string;
-    relPath: string;
-    content: string;
-}
-export interface SemanticOptions {
-    apiKey?: string;
-    model?: string;
-    chunkSize?: number;
-    mode?: 'fast' | 'deep';
-    maxTokens?: number;
-    timeBudget?: number;
-    targetChunkTokens?: number;
-}
-/**
- * Run semantic extraction on a set of files using the Anthropic Claude API.
- *
- * Returns an empty ExtractionResult (not an error) when:
- * - No API key is available
- * - The API call fails
- *
- * Only document/paper files benefit from semantic extraction.
- * Code files may be included but the prompt instructs Claude not to re-extract imports.
- */
-export declare function extractSemantic(files: SemanticFile[], options?: SemanticOptions): Promise<ExtractionResult>;
-//# sourceMappingURL=semantic.d.ts.map

package/bundled-graph/dist/src/extract/semantic.d.ts.map

@@ -1 +0,0 @@
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package/bundled-graph/dist/src/extract/semantic.js

@@ -1,242 +0,0 @@
-// ---------------------------------------------------------------------------
-// Prompt template (mirrors graphify skill.md lines 253-303)
-// ---------------------------------------------------------------------------
-function buildPrompt(files, mode, chunkNum, totalChunks) {
-    const deepInstructions = mode === 'deep'
-        ? '\nDEEP MODE: be aggressive with INFERRED edges - indirect deps, shared assumptions, latent couplings. Mark uncertain ones AMBIGUOUS instead of omitting.\n'
-        : '';
-    const fileList = files
-        .map((f) => `--- file: ${f.relPath} ---\n${f.content.slice(0, 6000)}\n---`)
-        .join('\n\n');
-    return `You are a graphify extraction subagent. Read the files listed and extract a knowledge graph fragment.
-Output ONLY valid JSON matching the schema below - no explanation, no markdown fences, no preamble.
-
-Files (chunk ${chunkNum} of ${totalChunks}):
-${fileList}
-
-Rules:
-- EXTRACTED: relationship explicit in source (import, call, citation, "see §3.2")
-- INFERRED: reasonable inference (shared data structure, implied dependency)
-- AMBIGUOUS: uncertain - flag for review, do not omit
-
-Code files: focus on semantic edges AST cannot find (call relationships, shared data, arch patterns).
-  Do not re-extract imports - AST already has those.
-Doc/paper files: extract named concepts, entities, citations. Also extract rationale — sections that explain WHY a decision was made, trade-offs chosen, or design intent. These become nodes with "rationale_for" edges pointing to the concept they explain.
-${deepInstructions}
-Semantic similarity: if two concepts in this chunk solve the same problem or represent the same idea without any structural link, add a "semantically_similar_to" edge marked INFERRED with a confidence_score reflecting how similar they are (0.6-0.95). Only add these when the similarity is genuinely non-obvious and cross-cutting.
-
-Hyperedges: if 3 or more nodes clearly participate together in a shared concept, flow, or pattern not captured by pairwise edges, add a hyperedge to the "hyperedges" array. Use sparingly — maximum 3 hyperedges per chunk.
-
-If a file has YAML frontmatter (--- ... ---), copy source_url, captured_at, author, contributor onto every node from that file.
-
-confidence_score is REQUIRED on every edge:
-- EXTRACTED edges: confidence_score = 1.0 always
-- INFERRED edges: Direct structural evidence: 0.8-0.9. Reasonable with uncertainty: 0.6-0.7. Weak/speculative: 0.4-0.5.
-- AMBIGUOUS edges: 0.1-0.3
-
-Output exactly this JSON (no other text):
-{"nodes":[{"id":"filestem_entityname","label":"Human Readable Name","file_type":"code|document|paper|image","source_file":"relative/path","source_location":null,"source_url":null,"captured_at":null,"author":null,"contributor":null}],"edges":[{"source":"node_id","target":"node_id","relation":"calls|implements|references|cites|conceptually_related_to|shares_data_with|semantically_similar_to|rationale_for","confidence":"EXTRACTED|INFERRED|AMBIGUOUS","confidence_score":1.0,"source_file":"relative/path","source_location":null,"weight":1.0}],"hyperedges":[{"id":"snake_case_id","label":"Human Readable Label","nodes":["node_id1","node_id2","node_id3"],"relation":"participate_in|implement|form","confidence":"EXTRACTED|INFERRED","confidence_score":0.75,"source_file":"relative/path"}],"input_tokens":0,"output_tokens":0}`;
-}
-async function callClaude(prompt, apiKey, model, maxTokens) {
-    const response = await fetch('https://api.anthropic.com/v1/messages', {
-        method: 'POST',
-        headers: {
-            'Content-Type': 'application/json',
-            'x-api-key': apiKey,
-            'anthropic-version': '2023-06-01',
-        },
-        body: JSON.stringify({
-            model,
-            max_tokens: maxTokens,
-            messages: [{ role: 'user', content: prompt }],
-        }),
-    });
-    if (!response.ok) {
-        const body = await response.text();
-        throw new Error(`Anthropic API error ${response.status}: ${body}`);
-    }
-    const msg = (await response.json());
-    const text = msg.content.find((c) => c.type === 'text')?.text ?? '';
-    return {
-        text,
-        inputTokens: msg.usage?.input_tokens ?? 0,
-        outputTokens: msg.usage?.output_tokens ?? 0,
-    };
-}
-function parseChunkResult(text, chunkFiles) {
-    // Strip markdown fences if model added them despite instructions
-    const cleaned = text.replace(/^```json\s*/i, '').replace(/\s*```\s*$/, '').trim();
-    let raw;
-    try {
-        raw = JSON.parse(cleaned);
-    }
-    catch {
-        return { nodes: [], edges: [], hyperedges: [], inputTokens: 0, outputTokens: 0 };
-    }
-    const fileSet = new Set(chunkFiles.map((f) => f.relPath));
-    const nodes = (raw.nodes ?? [])
-        .filter((n) => typeof n === 'object' && n !== null)
-        .map((n) => ({
-        id: String(n['id'] ?? ''),
-        label: String(n['label'] ?? n['id'] ?? ''),
-        fileType: n['file_type'] ?? 'document',
-        sourceFile: String(n['source_file'] ?? ''),
-        sourceLocation: n['source_location'] ?? undefined,
-        // Extra metadata from YAML frontmatter
-        ...(n['source_url'] ? { sourceUrl: n['source_url'] } : {}),
-        ...(n['captured_at'] ? { capturedAt: n['captured_at'] } : {}),
-        ...(n['author'] ? { author: n['author'] } : {}),
-    }))
-        .filter((n) => n.id && fileSet.has(n.sourceFile));
-    const edges = (raw.edges ?? [])
-        .filter((e) => typeof e === 'object' && e !== null)
-        .map((e) => ({
-        source: String(e['source'] ?? ''),
-        target: String(e['target'] ?? ''),
-        relation: String(e['relation'] ?? 'references'),
-        confidence: e['confidence'] ?? 'INFERRED',
-        confidenceScore: typeof e['confidence_score'] === 'number' ? e['confidence_score'] : 0.7,
-        sourceFile: e['source_file'] ?? undefined,
-        weight: typeof e['weight'] === 'number' ? e['weight'] : 1.0,
-    }))
-        .filter((e) => e.source && e.target);
-    const hyperedges = (raw.hyperedges ?? [])
-        .filter((h) => typeof h === 'object' && h !== null)
-        .map((h) => ({
-        label: String(h['label'] ?? h['id'] ?? ''),
-        nodes: Array.isArray(h['nodes']) ? h['nodes'] : [],
-        confidence: h['confidence'] ?? 'INFERRED',
-        confidenceScore: typeof h['confidence_score'] === 'number' ? h['confidence_score'] : 0.7,
-    }))
-        .filter((h) => h.label && h.nodes.length >= 2);
-    return {
-        nodes,
-        edges,
-        hyperedges,
-        inputTokens: raw.input_tokens ?? 0,
-        outputTokens: raw.output_tokens ?? 0,
-    };
-}
-// ---------------------------------------------------------------------------
-// Best-Fit Decreasing (BFD) chunk packing — from autoresearch experiment loop
-//
-// Instead of slicing files into equal-sized groups, BFD estimates the token
-// count of each file, sorts descending, and packs into bins that stay under
-// targetTokens.  This mirrors the document-packing dataloader in autoresearch
-// (best-fit + zero-waste) and produces denser, fairer prompts than fixed chunks.
-// ---------------------------------------------------------------------------
-/**
- * Pack `files` into chunks using First-Fit Decreasing bin packing.
- *
- * Each file's token estimate = min(content.length / 4, 1500)
- * (the prompt already truncates each file to 6000 chars = ~1500 tokens).
- *
- * @param files         - Files to pack
- * @param targetTokens  - Soft upper bound on tokens per chunk (default 30 000)
- * @returns             - Array of chunks; each chunk is an array of files
- */
-function packChunksBFD(files, targetTokens) {
-    // Estimate tokens per file — capped at the 6 000-char prompt truncation limit
-    const sized = files.map((f) => ({
-        file: f,
-        tokens: Math.min(Math.ceil(f.content.length / 4), 1500),
-    }));
-    // Sort descending so large files get placed first (First Fit Decreasing)
-    sized.sort((a, b) => b.tokens - a.tokens);
-    const bins = [];
-    for (const item of sized) {
-        let placed = false;
-        for (const bin of bins) {
-            if (bin.tokens + item.tokens <= targetTokens) {
-                bin.files.push(item.file);
-                bin.tokens += item.tokens;
-                placed = true;
-                break;
-            }
-        }
-        if (!placed) {
-            // File is too large (or bins are all full) — open a new bin
-            bins.push({ files: [item.file], tokens: item.tokens });
-        }
-    }
-    return bins.map((b) => b.files);
-}
-// ---------------------------------------------------------------------------
-// Main export
-// ---------------------------------------------------------------------------
-/**
- * Run semantic extraction on a set of files using the Anthropic Claude API.
- *
- * Returns an empty ExtractionResult (not an error) when:
- * - No API key is available
- * - The API call fails
- *
- * Only document/paper files benefit from semantic extraction.
- * Code files may be included but the prompt instructs Claude not to re-extract imports.
- */
-export async function extractSemantic(files, options = {}) {
-    const apiKey = options.apiKey ?? process.env['ANTHROPIC_API_KEY'] ?? '';
-    if (!apiKey) {
-        return { nodes: [], edges: [], hyperedges: [], filesProcessed: 0, fromCache: 0, errors: ['ANTHROPIC_API_KEY not set — semantic extraction skipped'] };
-    }
-    const model = options.model ?? 'claude-haiku-4-5-20251001';
-    const mode = options.mode ?? 'fast';
-    const maxTokens = options.maxTokens ?? 8192;
-    // BFD packing — targetChunkTokens defaults to 30 000 (~20 avg files × 1500 tok each).
-    // Fallback to legacy chunkSize if targetChunkTokens is not set and chunkSize was specified,
-    // so callers that relied on chunkSize still get predictable behaviour.
-    const targetChunkTokens = options.targetChunkTokens
-        ?? (options.chunkSize ? options.chunkSize * 1500 : 30_000);
-    // Time budget — undefined = no limit (run all chunks)
-    const deadline = options.timeBudget ? Date.now() + options.timeBudget : Infinity;
-    const allNodes = [];
-    const allEdges = [];
-    const allHyperedges = [];
-    const errors = [];
-    let totalInput = 0;
-    let totalOutput = 0;
-    // Pack files into token-aware chunks using BFD (replaces fixed equal-size slicing)
-    const chunks = packChunksBFD(files, targetChunkTokens);
-    for (let i = 0; i < chunks.length; i++) {
-        // Time budget enforcement — mirrors autoresearch's 5-min wall-clock limit
-        if (Date.now() > deadline) {
-            errors.push(`Time budget (${options.timeBudget}ms) exceeded after chunk ${i}/${chunks.length} — partial results returned`);
-            break;
-        }
-        const chunk = chunks[i];
-        const prompt = buildPrompt(chunk, mode, i + 1, chunks.length);
-        try {
-            const { text, inputTokens, outputTokens } = await callClaude(prompt, apiKey, model, maxTokens);
-            totalInput += inputTokens;
-            totalOutput += outputTokens;
-            const parsed = parseChunkResult(text, chunk);
-            allNodes.push(...parsed.nodes);
-            allEdges.push(...parsed.edges);
-            allHyperedges.push(...parsed.hyperedges);
-        }
-        catch (err) {
-            errors.push(`Chunk ${i + 1}/${chunks.length} failed: ${err instanceof Error ? err.message : String(err)}`);
-        }
-    }
-    // Deduplicate nodes by id
-    const seenNodeIds = new Set();
-    const dedupedNodes = allNodes.filter((n) => {
-        if (seenNodeIds.has(n.id))
-            return false;
-        seenNodeIds.add(n.id);
-        return true;
-    });
-    // Attach token totals as extra fields for report generation
-    const result = {
-        nodes: dedupedNodes,
-        edges: allEdges,
-        hyperedges: allHyperedges,
-        filesProcessed: files.length,
-        fromCache: 0,
-        errors,
-        inputTokens: totalInput,
-        outputTokens: totalOutput,
-    };
-    return result;
-}
-//# sourceMappingURL=semantic.js.map

package/bundled-graph/dist/src/extract/semantic.js.map

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