@monoes/monograph 1.1.0 → 1.2.0

package/dist/src/graph/shingle-filter.js

@@ -0,0 +1,130 @@
+/**
+ * Generate k-shingles (k-grams) from a token array.
+ * Each shingle is the concatenation of k consecutive tokens joined by a space.
+ */
+function kShingles(tokens, k) {
+    if (tokens.length < k)
+        return [tokens.join(' ')];
+    const shingles = [];
+    for (let i = 0; i <= tokens.length - k; i++) {
+        shingles.push(tokens.slice(i, i + k).join(' '));
+    }
+    return shingles;
+}
+/**
+ * Simple string hash that produces a non-negative 32-bit integer.
+ * Uses a djb2-style hash.
+ */
+function hashString(s) {
+    let h = 5381;
+    for (let i = 0; i < s.length; i++) {
+        h = ((h << 5) + h) ^ s.charCodeAt(i);
+        h = h >>> 0; // keep unsigned 32-bit
+    }
+    return h;
+}
+/**
+ * Compute a MinHash signature for a set of shingles using
+ * numHashes linear hash functions: h_i(x) = (a_i * x + b_i) % prime
+ */
+function minHashSignature(shingles, numHashes) {
+    const PRIME = 4294967311; // first prime > 2^32
+    const sig = new Uint32Array(numHashes).fill(0xffffffff);
+    // Deterministic seeds derived from hash index
+    for (const shingle of shingles) {
+        const x = hashString(shingle);
+        for (let i = 0; i < numHashes; i++) {
+            // Deterministic a, b per hash function — use index-based seeds
+            const a = ((i * 2654435761 + 0x9e3779b9) >>> 0);
+            const b = ((i * 2246822519 + 0x85ebca6b) >>> 0);
+            // Linear hash modulo prime (BigInt for correctness)
+            const hashVal = Number((BigInt(a) * BigInt(x) + BigInt(b)) % BigInt(PRIME)) >>> 0;
+            if (hashVal < sig[i]) {
+                sig[i] = hashVal;
+            }
+        }
+    }
+    return sig;
+}
+export function createShingleFilter(k = 5, numHashes = 128) {
+    // Each entry: { sig: Uint32Array }
+    const index = new Map();
+    // LSH: split numHashes into bands of rows
+    // Standard LSH: numBands * numRows = numHashes, threshold ≈ (1/numBands)^(1/numRows)
+    // We target threshold ~0.5: solve (1/b)^(1/r) = 0.5 with b*r = numHashes
+    // A reasonable split is sqrt(numHashes) bands of sqrt(numHashes) rows each.
+    const numBands = Math.round(Math.sqrt(numHashes));
+    const numRows = Math.floor(numHashes / numBands);
+    function getBandKey(id, band, sig) {
+        const parts = [];
+        for (let r = 0; r < numRows; r++) {
+            const idx = band * numRows + r;
+            if (idx < numHashes)
+                parts.push(sig[idx]);
+        }
+        return `b${band}:${parts.join(',')}`;
+    }
+    // Band bucket → list of candidate IDs
+    const bandBuckets = new Map();
+    return {
+        add(id, tokens) {
+            const shingles = kShingles(tokens, k);
+            const sig = minHashSignature(shingles, numHashes);
+            index.set(id, sig);
+            // Insert into LSH band buckets
+            for (let band = 0; band < numBands; band++) {
+                const key = getBandKey(id, band, sig);
+                const bucket = bandBuckets.get(key);
+                if (bucket) {
+                    bucket.push(id);
+                }
+                else {
+                    bandBuckets.set(key, [id]);
+                }
+            }
+        },
+        candidates(tokens, topK = 10) {
+            const shingles = kShingles(tokens, k);
+            const querySig = minHashSignature(shingles, numHashes);
+            // Collect candidate IDs via LSH band matching
+            const candidateScores = new Map();
+            for (let band = 0; band < numBands; band++) {
+                const key = getBandKey('__query__', band, querySig);
+                // Manually compute the key for the query signature
+                const parts = [];
+                for (let r = 0; r < numRows; r++) {
+                    const idx = band * numRows + r;
+                    if (idx < numHashes)
+                        parts.push(querySig[idx]);
+                }
+                const queryKey = `b${band}:${parts.join(',')}`;
+                const bucket = bandBuckets.get(queryKey);
+                if (bucket) {
+                    for (const id of bucket) {
+                        candidateScores.set(id, (candidateScores.get(id) ?? 0) + 1);
+                    }
+                }
+            }
+            if (candidateScores.size === 0)
+                return [];
+            // Compute Jaccard estimate from signature agreement for ranked results
+            const ranked = [...candidateScores.keys()].map(id => {
+                const sig = index.get(id);
+                let matches = 0;
+                for (let i = 0; i < numHashes; i++) {
+                    if (sig[i] === querySig[i])
+                        matches++;
+                }
+                const jaccardEst = matches / numHashes;
+                return { id, jaccardEst };
+            });
+            // Filter by estimated Jaccard > 0.5 and return topK
+            return ranked
+                .filter(r => r.jaccardEst > 0.5)
+                .sort((a, b) => b.jaccardEst - a.jaccardEst)
+                .slice(0, topK)
+                .map(r => r.id);
+        },
+    };
+}
+//# sourceMappingURL=shingle-filter.js.map

package/dist/src/graph/shingle-filter.js.map

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package/dist/src/graph/statistics.d.ts

@@ -0,0 +1,26 @@
+import type { MonographDb } from '../storage/db.js';
+/**
+ * Graph density: ratio of actual edges to maximum possible directed edges.
+ * For a directed graph with n nodes: max = n * (n - 1).
+ * Ignores self-loops.
+ */
+export declare function graphDensity(db: MonographDb): number;
+/**
+ * Average local clustering coefficient across all nodes.
+ * For a directed graph, the local clustering coefficient of node v is:
+ *   (triangles through v) / (directed_pairs through v)
+ * where directed_pairs = k_in * k_out - mutual_pairs
+ * We use the undirected approximation: treat edges as undirected, count triangles.
+ */
+export declare function clusteringCoefficient(db: MonographDb): number;
+/**
+ * Average shortest path length across all reachable node pairs (i, j) where i ≠ j.
+ * Computed using BFS from each node. Unreachable pairs are excluded from the average.
+ */
+export declare function averagePathLength(db: MonographDb): number;
+/**
+ * Graph diameter: the maximum shortest path length across all reachable node pairs.
+ * Returns 0 for empty or single-node graphs.
+ */
+export declare function graphDiameter(db: MonographDb): number;
+//# sourceMappingURL=statistics.d.ts.map

package/dist/src/graph/statistics.d.ts.map

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package/dist/src/graph/statistics.js

@@ -0,0 +1,121 @@
+import { bfsFromNode } from 'graphology-traversal/bfs.js';
+import { loadGraphFromDb } from './loader.js';
+/**
+ * Graph density: ratio of actual edges to maximum possible directed edges.
+ * For a directed graph with n nodes: max = n * (n - 1).
+ * Ignores self-loops.
+ */
+export function graphDensity(db) {
+    const graph = loadGraphFromDb(db);
+    const n = graph.order;
+    if (n < 2)
+        return 0;
+    const maxEdges = n * (n - 1);
+    // Use simple directed edge count (deduplicate multi-edges for density)
+    const seen = new Set();
+    graph.forEachEdge((_, _attr, src, tgt) => {
+        if (src !== tgt)
+            seen.add(`${src}→${tgt}`);
+    });
+    return seen.size / maxEdges;
+}
+/**
+ * Average local clustering coefficient across all nodes.
+ * For a directed graph, the local clustering coefficient of node v is:
+ *   (triangles through v) / (directed_pairs through v)
+ * where directed_pairs = k_in * k_out - mutual_pairs
+ * We use the undirected approximation: treat edges as undirected, count triangles.
+ */
+export function clusteringCoefficient(db) {
+    const graph = loadGraphFromDb(db);
+    if (graph.order === 0)
+        return 0;
+    // Build undirected adjacency sets
+    const neighbors = new Map();
+    graph.forEachNode(node => neighbors.set(node, new Set()));
+    graph.forEachEdge((_, _attr, src, tgt) => {
+        if (src !== tgt) {
+            neighbors.get(src).add(tgt);
+            neighbors.get(tgt).add(src);
+        }
+    });
+    let totalCoeff = 0;
+    let countWithNeighbors = 0;
+    for (const [node, nbrs] of neighbors) {
+        const k = nbrs.size;
+        if (k < 2)
+            continue;
+        let triangles = 0;
+        const nbList = [...nbrs];
+        for (let i = 0; i < nbList.length; i++) {
+            for (let j = i + 1; j < nbList.length; j++) {
+                if (neighbors.get(nbList[i])?.has(nbList[j])) {
+                    triangles++;
+                }
+            }
+        }
+        const possible = (k * (k - 1)) / 2;
+        totalCoeff += triangles / possible;
+        countWithNeighbors++;
+    }
+    if (countWithNeighbors === 0)
+        return 0;
+    return totalCoeff / countWithNeighbors;
+}
+/**
+ * Average shortest path length across all reachable node pairs (i, j) where i ≠ j.
+ * Computed using BFS from each node. Unreachable pairs are excluded from the average.
+ */
+export function averagePathLength(db) {
+    const graph = loadGraphFromDb(db);
+    const nodes = graph.nodes();
+    if (nodes.length < 2)
+        return 0;
+    let totalLength = 0;
+    let reachablePairs = 0;
+    for (const source of nodes) {
+        const distances = new Map();
+        distances.set(source, 0);
+        bfsFromNode(graph, source, (node, _attr, depth) => {
+            if (node !== source) {
+                distances.set(node, depth);
+            }
+        });
+        for (const [target, dist] of distances) {
+            if (target !== source && dist > 0) {
+                totalLength += dist;
+                reachablePairs++;
+            }
+        }
+    }
+    if (reachablePairs === 0)
+        return 0;
+    return totalLength / reachablePairs;
+}
+/**
+ * Graph diameter: the maximum shortest path length across all reachable node pairs.
+ * Returns 0 for empty or single-node graphs.
+ */
+export function graphDiameter(db) {
+    const graph = loadGraphFromDb(db);
+    const nodes = graph.nodes();
+    if (nodes.length < 2)
+        return 0;
+    let maxDist = 0;
+    for (const source of nodes) {
+        const distances = new Map();
+        distances.set(source, 0);
+        bfsFromNode(graph, source, (node, _attr, depth) => {
+            if (node !== source) {
+                distances.set(node, depth);
+            }
+        });
+        for (const [target, dist] of distances) {
+            if (target !== source && dist > maxDist) {
+                maxDist = dist;
+            }
+        }
+    }
+    return maxDist;
+}
+//# sourceMappingURL=statistics.js.map

package/dist/src/graph/statistics.js.map

@@ -0,0 +1 @@
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package/dist/src/graph/stats.d.ts

@@ -0,0 +1,38 @@
+import type Database from 'better-sqlite3';
+export type RiskBin = 'low' | 'medium' | 'high' | 'critical';
+export interface RiskProfile {
+    low: number;
+    medium: number;
+    high: number;
+    critical: number;
+    lowPct: number;
+    mediumPct: number;
+    highPct: number;
+    criticalPct: number;
+}
+export interface CouplingProfile {
+    p50FanIn: number;
+    p75FanIn: number;
+    p90FanIn: number;
+    p95FanIn: number;
+    couplingHighPct: number;
+    fanInProfile: RiskProfile;
+    fanOutProfile: RiskProfile;
+    totalFiles: number;
+}
+export interface GraphStatsSummary {
+    nodeCount: number;
+    edgeCount: number;
+    communityCount: number;
+    fileCount: number;
+    couplingProfile: CouplingProfile;
+}
+/**
+ * Compute full coupling profile from SQLite.
+ */
+export declare function computeCouplingProfile(db: Database.Database): CouplingProfile;
+/**
+ * Quick stats summary (extends existing stats from monograph_stats MCP tool).
+ */
+export declare function computeGraphStats(db: Database.Database): GraphStatsSummary;
+//# sourceMappingURL=stats.d.ts.map

package/dist/src/graph/stats.d.ts.map

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package/dist/src/graph/stats.js

@@ -0,0 +1,74 @@
+function percentile(sorted, p) {
+    if (sorted.length === 0)
+        return 0;
+    const idx = Math.floor((p / 100) * sorted.length);
+    return sorted[Math.min(idx, sorted.length - 1)];
+}
+function buildRiskProfile(values) {
+    const total = values.length;
+    let low = 0, medium = 0, high = 0, critical = 0;
+    for (const v of values) {
+        if (v < 5)
+            low++;
+        else if (v <= 15)
+            medium++;
+        else if (v <= 30)
+            high++;
+        else
+            critical++;
+    }
+    const pct = (n) => total > 0 ? Math.round((n / total) * 100) : 0;
+    return {
+        low,
+        medium,
+        high,
+        critical,
+        lowPct: pct(low),
+        mediumPct: pct(medium),
+        highPct: pct(high),
+        criticalPct: pct(critical),
+    };
+}
+/**
+ * Compute full coupling profile from SQLite.
+ */
+export function computeCouplingProfile(db) {
+    const fanInRows = db.prepare('SELECT target_id, COUNT(*) as c FROM edges GROUP BY target_id').all();
+    const fanOutRows = db.prepare('SELECT source_id, COUNT(*) as c FROM edges GROUP BY source_id').all();
+    const totalFiles = db.prepare("SELECT COUNT(*) as n FROM nodes WHERE label = 'File'").get().n;
+    const fanInValues = fanInRows.map(r => r.c).sort((a, b) => a - b);
+    const fanOutValues = fanOutRows.map(r => r.c).sort((a, b) => a - b);
+    const p95FanIn = percentile(fanInValues, 95);
+    const couplingHighCount = fanInValues.filter(v => v > p95FanIn).length;
+    const couplingHighPct = fanInValues.length > 0
+        ? Math.round((couplingHighCount / fanInValues.length) * 100)
+        : 0;
+    return {
+        p50FanIn: percentile(fanInValues, 50),
+        p75FanIn: percentile(fanInValues, 75),
+        p90FanIn: percentile(fanInValues, 90),
+        p95FanIn,
+        couplingHighPct,
+        fanInProfile: buildRiskProfile(fanInValues),
+        fanOutProfile: buildRiskProfile(fanOutValues),
+        totalFiles,
+    };
+}
+/**
+ * Quick stats summary (extends existing stats from monograph_stats MCP tool).
+ */
+export function computeGraphStats(db) {
+    const nodeCount = db.prepare('SELECT COUNT(*) as n FROM nodes').get().n;
+    const edgeCount = db.prepare('SELECT COUNT(*) as n FROM edges').get().n;
+    const communityCount = db.prepare("SELECT COUNT(DISTINCT community_id) as n FROM nodes WHERE community_id IS NOT NULL").get().n;
+    const fileCount = db.prepare("SELECT COUNT(*) as n FROM nodes WHERE label = 'File'").get().n;
+    const couplingProfile = computeCouplingProfile(db);
+    return {
+        nodeCount,
+        edgeCount,
+        communityCount,
+        fileCount,
+        couplingProfile,
+    };
+}
+//# sourceMappingURL=stats.js.map

package/dist/src/graph/stats.js.map

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package/dist/src/graph/subgraph.d.ts

@@ -0,0 +1,8 @@
+import type { MonographNode, MonographEdge } from '../types.js';
+import type { MonographDb } from '../storage/db.js';
+export interface InducedSubgraph {
+    nodes: MonographNode[];
+    edges: MonographEdge[];
+}
+export declare function extractInducedSubgraph(db: MonographDb, nodeIds: string[]): InducedSubgraph;
+//# sourceMappingURL=subgraph.d.ts.map

package/dist/src/graph/subgraph.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/graph/subgraph.js

@@ -0,0 +1,59 @@
+/**
+ * Extract the induced subgraph for the given set of node ids.
+ *
+ * The induced subgraph contains:
+ * - Only the nodes whose ids are in `nodeIds` (and exist in the DB)
+ * - Only the edges where both source and target are in `nodeIds`
+ *
+ * @param db - The MonographDb instance
+ * @param nodeIds - The subset of node ids to include
+ * @returns An object with `nodes` and `edges` arrays
+ */
+// SQLite SQLITE_MAX_VARIABLE_NUMBER limit (32766). Edge query binds nodeIds once
+// (source_id IN chunk), then filters target in-memory — full limit available per chunk.
+const SQLITE_VAR_LIMIT = 32766;
+export function extractInducedSubgraph(db, nodeIds) {
+    if (nodeIds.length === 0)
+        return { nodes: [], edges: [] };
+    // Chunk helper to stay within SQLITE_MAX_VARIABLE_NUMBER
+    function queryChunked(ids, chunkSize, query) {
+        const results = [];
+        for (let i = 0; i < ids.length; i += chunkSize) {
+            const chunk = ids.slice(i, i + chunkSize);
+            const ph = chunk.map(() => '?').join(',');
+            results.push(...query(ph, chunk));
+        }
+        return results;
+    }
+    const rawNodes = queryChunked(nodeIds, SQLITE_VAR_LIMIT, (ph, chunk) => db.prepare(`SELECT id, label, name, file_path, start_line, end_line, community_id, is_exported, language, properties
+       FROM nodes WHERE id IN (${ph})`).all(...chunk));
+    // For edges: query by source_id chunks (1 bind per row), then filter target in-memory.
+    // Querying by both source+target would miss cross-chunk edges and requires 2× bind slots.
+    const nodeSet = new Set(nodeIds);
+    const rawEdges = queryChunked(nodeIds, SQLITE_VAR_LIMIT, (ph, chunk) => db.prepare(`SELECT id, source_id, target_id, relation, confidence, confidence_score, reason, evidence
+       FROM edges WHERE source_id IN (${ph})`).all(...chunk).filter(e => nodeSet.has(e.target_id)));
+    const nodes = rawNodes.map(n => ({
+        id: n.id,
+        label: n.label,
+        name: n.name,
+        normLabel: (n.norm_label ?? n.name ?? '').toLowerCase(),
+        filePath: n.file_path ?? undefined,
+        startLine: n.start_line ?? undefined,
+        endLine: n.end_line ?? undefined,
+        communityId: n.community_id ?? undefined,
+        isExported: n.is_exported === 1,
+        language: n.language ?? undefined,
+        properties: n.properties ? JSON.parse(n.properties) : undefined,
+    }));
+    const edges = rawEdges.map(e => ({
+        id: e.id,
+        sourceId: e.source_id,
+        targetId: e.target_id,
+        relation: e.relation,
+        confidence: e.confidence,
+        confidenceScore: e.confidence_score,
+        reason: e.reason ?? undefined,
+    }));
+    return { nodes, edges };
+}
+//# sourceMappingURL=subgraph.js.map

package/dist/src/graph/subgraph.js.map

@@ -0,0 +1 @@
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package/dist/src/graph/topo-sort.d.ts

@@ -0,0 +1,21 @@
+import type { MonographDb } from '../storage/db.js';
+export interface TopoSortResult {
+    /** Groups of nodes that can be processed independently at each level.
+     *  Level 0 = leaves (nodes with no outgoing IMPORTS edges on the reverse graph).
+     *  Higher levels depend on previous levels. Cycle nodes are appended last. */
+    levels: string[][];
+    /** Number of nodes that are part of a cycle and could not be sorted. */
+    cycleCount: number;
+}
+/**
+ * Topological level sort using Kahn's algorithm on the *reverse* import graph.
+ *
+ * In the reverse graph, an edge A→B in the original (A imports B) becomes B→A.
+ * Files with no incoming edges on the reverse graph (i.e., no one imports them)
+ * are leaves and appear in level 0.
+ *
+ * @param db - The MonographDb instance
+ * @returns Object with `levels` (array of independent groups, leaf-first) and `cycleCount`.
+ */
+export declare function topologicalLevelSort(db: MonographDb): TopoSortResult;
+//# sourceMappingURL=topo-sort.d.ts.map

package/dist/src/graph/topo-sort.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/graph/topo-sort.js

@@ -0,0 +1,67 @@
+/**
+ * Topological level sort using Kahn's algorithm on the *reverse* import graph.
+ *
+ * In the reverse graph, an edge A→B in the original (A imports B) becomes B→A.
+ * Files with no incoming edges on the reverse graph (i.e., no one imports them)
+ * are leaves and appear in level 0.
+ *
+ * @param db - The MonographDb instance
+ * @returns Object with `levels` (array of independent groups, leaf-first) and `cycleCount`.
+ */
+export function topologicalLevelSort(db) {
+    const nodeRows = db.prepare('SELECT id FROM nodes').all();
+    const edgeRows = db.prepare('SELECT source_id, target_id FROM edges').all();
+    if (nodeRows.length === 0)
+        return { levels: [], cycleCount: 0 };
+    const nodes = nodeRows.map(r => r.id);
+    // Build reverse graph: original edge src→tgt becomes tgt→src in reverse
+    // In-degree in the reverse graph = number of nodes that tgt imports (out-degree in original)
+    const reverseAdj = new Map();
+    const inDegree = new Map();
+    for (const n of nodes) {
+        reverseAdj.set(n, []);
+        inDegree.set(n, 0);
+    }
+    for (const { source_id: src, target_id: tgt } of edgeRows) {
+        if (src === tgt)
+            continue; // skip self-loops
+        if (!reverseAdj.has(tgt) || !reverseAdj.has(src))
+            continue;
+        reverseAdj.get(tgt).push(src);
+        inDegree.set(src, (inDegree.get(src) ?? 0) + 1);
+    }
+    // Kahn's BFS on the reverse graph
+    const queue = [];
+    for (const [node, deg] of inDegree) {
+        if (deg === 0)
+            queue.push(node);
+    }
+    const levels = [];
+    const visited = new Set();
+    while (queue.length > 0) {
+        // All nodes currently at in-degree 0 form one level
+        const level = [...queue];
+        queue.length = 0;
+        levels.push(level);
+        for (const node of level) {
+            visited.add(node);
+            for (const neighbor of reverseAdj.get(node) ?? []) {
+                if (visited.has(neighbor))
+                    continue;
+                const newDeg = (inDegree.get(neighbor) ?? 0) - 1;
+                inDegree.set(neighbor, newDeg);
+                if (newDeg === 0)
+                    queue.push(neighbor);
+            }
+        }
+    }
+    // Remaining unvisited nodes are in cycles
+    const cycleNodes = nodes.filter(n => !visited.has(n));
+    let cycleCount = 0;
+    if (cycleNodes.length > 0) {
+        cycleCount = cycleNodes.length;
+        levels.push(cycleNodes);
+    }
+    return { levels, cycleCount };
+}
+//# sourceMappingURL=topo-sort.js.map

package/dist/src/graph/topo-sort.js.map

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package/dist/src/graph/wcc.d.ts

@@ -0,0 +1,13 @@
+import type { MonographDb } from '../storage/db.js';
+/**
+ * Find all weakly connected components (WCCs) of the graph.
+ *
+ * Treats the directed graph as undirected: an edge A→B connects A and B
+ * regardless of direction. Uses union-find (disjoint-set) for O(α·n) performance.
+ *
+ * @param db - The MonographDb instance
+ * @returns Array of components; each component is an array of node ids.
+ *          Sorted so the largest component comes first.
+ */
+export declare function weaklyConnectedComponents(db: MonographDb): string[][];
+//# sourceMappingURL=wcc.d.ts.map

package/dist/src/graph/wcc.d.ts.map

@@ -0,0 +1 @@
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