@monoes/monograph 1.1.0 → 1.2.1

package/dist/src/graph/node-search.d.ts.map

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

@@ -0,0 +1,128 @@
+// ── Row → node mapper (mirrors subgraph.ts) ───────────────────────────────────
+function rowToNode(r) {
+    return {
+        id: r.id,
+        label: r.label,
+        name: r.name,
+        normLabel: r.norm_label ?? r.name.toLowerCase(),
+        filePath: r.file_path ?? undefined,
+        startLine: r.start_line ?? undefined,
+        endLine: r.end_line ?? undefined,
+        communityId: r.community_id ?? undefined,
+        isExported: r.is_exported === 1,
+        language: r.language ?? undefined,
+        properties: r.properties ? JSON.parse(r.properties) : undefined,
+    };
+}
+// ── Prepared statement cache ───────────────────────────────────────────────────
+// Keyed by a fingerprint of which conditions are active (not by param values),
+// so the same query shape reuses the compiled statement across calls.
+// WeakMap ensures the cache is garbage-collected when the DB object is released.
+const stmtCache = new WeakMap();
+function getCachedStmt(db, key, buildSql) {
+    let dbCache = stmtCache.get(db);
+    if (!dbCache) {
+        dbCache = new Map();
+        stmtCache.set(db, dbCache);
+    }
+    let stmt = dbCache.get(key);
+    if (!stmt) {
+        stmt = db.prepare(buildSql());
+        dbCache.set(key, stmt);
+    }
+    return stmt;
+}
+// ── DB-backed search ───────────────────────────────────────────────────────────
+/**
+ * Search nodes by structured property criteria.
+ * All supplied criteria are combined with AND.
+ *
+ * Prepared statements are cached per-DB keyed by the active condition set so
+ * repeated calls with the same filter shape reuse the compiled statement.
+ */
+export function searchNodesByProperty(db, options = {}) {
+    const conditions = [];
+    const params = [];
+    // fingerprint encodes which conditions are active (not their values)
+    const fingerprint = [];
+    if (options.label) {
+        conditions.push('label = ?');
+        params.push(options.label);
+        fingerprint.push('lbl');
+    }
+    if (options.language) {
+        conditions.push('LOWER(language) = LOWER(?)');
+        params.push(options.language);
+        fingerprint.push('lang');
+    }
+    if (options.fileExtension !== undefined) {
+        // Normalise: ensure leading dot
+        const ext = options.fileExtension.startsWith('.')
+            ? options.fileExtension
+            : `.${options.fileExtension}`;
+        conditions.push("file_path LIKE ?");
+        params.push(`%${ext}`);
+        fingerprint.push('ext');
+    }
+    if (options.filePath !== undefined) {
+        conditions.push("LOWER(file_path) LIKE LOWER(?)");
+        params.push(`%${options.filePath}%`);
+        fingerprint.push('fp');
+    }
+    if (options.isExported !== undefined) {
+        conditions.push('is_exported = ?');
+        params.push(options.isExported ? 1 : 0);
+        fingerprint.push('exp');
+    }
+    if (options.communityId !== undefined) {
+        conditions.push('community_id = ?');
+        params.push(options.communityId);
+        fingerprint.push('com');
+    }
+    const hasLimit = options.limit !== undefined;
+    if (hasLimit)
+        fingerprint.push('lim');
+    const where = conditions.length > 0 ? `WHERE ${conditions.join(' AND ')}` : '';
+    const limitClause = hasLimit ? `LIMIT ${Number(options.limit)}` : '';
+    const cacheKey = fingerprint.join(':') || 'all';
+    const stmt = getCachedStmt(db, cacheKey, () => `SELECT id, label, name, norm_label, file_path, start_line, end_line,
+                      community_id, is_exported, language, properties
+               FROM nodes ${where} ${limitClause}`);
+    const rows = stmt.all(...params);
+    return rows.map(rowToNode);
+}
+// ── In-memory search ───────────────────────────────────────────────────────────
+/**
+ * Filter an already-loaded array of nodes in memory.
+ */
+export function searchNodesInMemory(nodes, options = {}) {
+    let result = nodes;
+    if (options.label) {
+        result = result.filter(n => n.label === options.label);
+    }
+    if (options.language) {
+        const lang = options.language.toLowerCase();
+        result = result.filter(n => n.language?.toLowerCase() === lang);
+    }
+    if (options.fileExtension !== undefined) {
+        const ext = options.fileExtension.startsWith('.')
+            ? options.fileExtension.toLowerCase()
+            : `.${options.fileExtension.toLowerCase()}`;
+        result = result.filter(n => n.filePath?.toLowerCase().endsWith(ext));
+    }
+    if (options.filePath !== undefined) {
+        const fp = options.filePath.toLowerCase();
+        result = result.filter(n => n.filePath?.toLowerCase().includes(fp));
+    }
+    if (options.isExported !== undefined) {
+        result = result.filter(n => n.isExported === options.isExported);
+    }
+    if (options.communityId !== undefined) {
+        result = result.filter(n => n.communityId === options.communityId);
+    }
+    if (options.limit !== undefined) {
+        result = result.slice(0, options.limit);
+    }
+    return result;
+}
+//# sourceMappingURL=node-search.js.map

package/dist/src/graph/node-search.js.map

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package/dist/src/graph/node-types.d.ts

@@ -0,0 +1,42 @@
+export type ReferenceKind = 'Value' | 'Type' | 'Namespace' | 'Unknown';
+export interface ExportSymbol {
+    name: string;
+    isType: boolean;
+    isReExport: boolean;
+    line?: number;
+}
+export interface ReExportEdge {
+    fromFile: string;
+    toFile: string;
+    symbol?: string;
+    isNamespace: boolean;
+}
+export interface SymbolReference {
+    name: string;
+    kind: ReferenceKind;
+    fromFile: string;
+    line?: number;
+}
+export declare const ModuleNodeFlags: {
+    readonly ENTRY_POINT: 1;
+    readonly REACHABLE: 2;
+    readonly RUNTIME_REACHABLE: 4;
+    readonly TEST_REACHABLE: 8;
+    readonly CJS_EXPORTS: 16;
+};
+export interface ModuleNode {
+    fileId: number;
+    filePath: string;
+    flags: number;
+    exports: ExportSymbol[];
+    reExports: ReExportEdge[];
+    references: SymbolReference[];
+}
+export declare function isEntryPoint(node: ModuleNode): boolean;
+export declare function isReachable(node: ModuleNode): boolean;
+export declare function isRuntimeReachable(node: ModuleNode): boolean;
+export declare function isTestReachable(node: ModuleNode): boolean;
+export declare function hasCjsExports(node: ModuleNode): boolean;
+export declare function setFlag(node: ModuleNode, flag: number): void;
+export declare function clearFlag(node: ModuleNode, flag: number): void;
+//# sourceMappingURL=node-types.d.ts.map

package/dist/src/graph/node-types.d.ts.map

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

@@ -0,0 +1,29 @@
+export const ModuleNodeFlags = {
+    ENTRY_POINT: 1,
+    REACHABLE: 2,
+    RUNTIME_REACHABLE: 4,
+    TEST_REACHABLE: 8,
+    CJS_EXPORTS: 16,
+};
+export function isEntryPoint(node) {
+    return (node.flags & ModuleNodeFlags.ENTRY_POINT) !== 0;
+}
+export function isReachable(node) {
+    return (node.flags & ModuleNodeFlags.REACHABLE) !== 0;
+}
+export function isRuntimeReachable(node) {
+    return (node.flags & ModuleNodeFlags.RUNTIME_REACHABLE) !== 0;
+}
+export function isTestReachable(node) {
+    return (node.flags & ModuleNodeFlags.TEST_REACHABLE) !== 0;
+}
+export function hasCjsExports(node) {
+    return (node.flags & ModuleNodeFlags.CJS_EXPORTS) !== 0;
+}
+export function setFlag(node, flag) {
+    node.flags |= flag;
+}
+export function clearFlag(node, flag) {
+    node.flags &= ~flag;
+}
+//# sourceMappingURL=node-types.js.map

package/dist/src/graph/node-types.js.map

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package/dist/src/graph/normalize-id.d.ts

@@ -0,0 +1,57 @@
+/**
+ * Normalized-ID edge reconciliation.
+ *
+ * Mirrors graphify's `_normalize_id` / `norm_to_id` logic:
+ * when an LLM-generated edge endpoint ID does not exactly match any node ID
+ * in the graph, we try a normalized form (lowercase, non-alphanumeric → '_').
+ * This lets edges survive across minor casing / punctuation mismatches between
+ * the AST extractor and the LLM.
+ */
+/**
+ * Normalise an ID string the same way graphify's `_normalize_id` does.
+ *
+ * Replaces all runs of non-alphanumeric characters with a single underscore,
+ * strips leading/trailing underscores, and lowercases the result.
+ *
+ * @example
+ * normalizeId('Session_ValidateToken') // 'session_validatetoken'
+ * normalizeId('My-Class::method')      // 'my_class_method'
+ */
+export declare function normalizeId(id: string): string;
+/**
+ * Build a Map from normalised id → canonical id from a set of known node ids.
+ * Used during edge reconciliation to remap mismatched endpoints.
+ *
+ * @param nodeIds - The authoritative set of node ids.
+ * @returns Map of `normalizeId(id)` → original `id`.
+ */
+export declare function buildNormToIdMap(nodeIds: Iterable<string>): Map<string, string>;
+export interface RawEdge {
+    source: string;
+    target: string;
+    [key: string]: unknown;
+}
+export interface ReconciliationResult {
+    /** Edges whose endpoints were resolved (possibly with normalization). */
+    resolved: RawEdge[];
+    /** Edges that could not be matched even after normalization. */
+    dangling: RawEdge[];
+    /** Number of edges that required normalization to resolve. */
+    remappedCount: number;
+}
+/**
+ * Reconcile a list of raw edges against a known set of node ids.
+ *
+ * For each edge:
+ * 1. If both endpoints are in `nodeIds` → resolved as-is.
+ * 2. If an endpoint is missing, try `normalizeId(endpoint)` lookup.
+ * 3. If still missing → moved to `dangling` (not added to the graph).
+ *
+ * Mutates `source`/`target` fields on resolved edges in-place when remapping.
+ */
+export declare function reconcileEdges(edges: RawEdge[], nodeIds: Set<string>): ReconciliationResult;
+/**
+ * Format a ReconciliationResult as structured text for LLM consumption.
+ */
+export declare function formatReconciliationResult(result: ReconciliationResult): string;
+//# sourceMappingURL=normalize-id.d.ts.map

package/dist/src/graph/normalize-id.d.ts.map

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package/dist/src/graph/normalize-id.js

@@ -0,0 +1,109 @@
+/**
+ * Normalized-ID edge reconciliation.
+ *
+ * Mirrors graphify's `_normalize_id` / `norm_to_id` logic:
+ * when an LLM-generated edge endpoint ID does not exactly match any node ID
+ * in the graph, we try a normalized form (lowercase, non-alphanumeric → '_').
+ * This lets edges survive across minor casing / punctuation mismatches between
+ * the AST extractor and the LLM.
+ */
+// ── Core normaliser ────────────────────────────────────────────────────────────
+/**
+ * Normalise an ID string the same way graphify's `_normalize_id` does.
+ *
+ * Replaces all runs of non-alphanumeric characters with a single underscore,
+ * strips leading/trailing underscores, and lowercases the result.
+ *
+ * @example
+ * normalizeId('Session_ValidateToken') // 'session_validatetoken'
+ * normalizeId('My-Class::method')      // 'my_class_method'
+ */
+export function normalizeId(id) {
+    return id
+        .replace(/[^a-zA-Z0-9]+/g, '_')
+        .replace(/^_+|_+$/g, '')
+        .toLowerCase();
+}
+// ── Lookup map builder ─────────────────────────────────────────────────────────
+/**
+ * Build a Map from normalised id → canonical id from a set of known node ids.
+ * Used during edge reconciliation to remap mismatched endpoints.
+ *
+ * @param nodeIds - The authoritative set of node ids.
+ * @returns Map of `normalizeId(id)` → original `id`.
+ */
+export function buildNormToIdMap(nodeIds) {
+    const map = new Map();
+    for (const id of nodeIds) {
+        map.set(normalizeId(id), id);
+    }
+    return map;
+}
+/**
+ * Reconcile a list of raw edges against a known set of node ids.
+ *
+ * For each edge:
+ * 1. If both endpoints are in `nodeIds` → resolved as-is.
+ * 2. If an endpoint is missing, try `normalizeId(endpoint)` lookup.
+ * 3. If still missing → moved to `dangling` (not added to the graph).
+ *
+ * Mutates `source`/`target` fields on resolved edges in-place when remapping.
+ */
+export function reconcileEdges(edges, nodeIds) {
+    const normToId = buildNormToIdMap(nodeIds);
+    const resolved = [];
+    const dangling = [];
+    let remappedCount = 0;
+    for (const edge of edges) {
+        let src = edge.source;
+        let tgt = edge.target;
+        let remapped = false;
+        if (!nodeIds.has(src)) {
+            // Cache normalizeId result to avoid calling it twice for the same string
+            const canonical = normToId.get(normalizeId(src));
+            if (canonical !== undefined) {
+                src = canonical;
+                remapped = true;
+            }
+        }
+        if (!nodeIds.has(tgt)) {
+            const canonical = normToId.get(normalizeId(tgt));
+            if (canonical !== undefined) {
+                tgt = canonical;
+                remapped = true;
+            }
+        }
+        if (nodeIds.has(src) && nodeIds.has(tgt)) {
+            resolved.push({ ...edge, source: src, target: tgt });
+            if (remapped)
+                remappedCount++;
+        }
+        else {
+            dangling.push(edge);
+        }
+    }
+    return { resolved, dangling, remappedCount };
+}
+/**
+ * Format a ReconciliationResult as structured text for LLM consumption.
+ */
+export function formatReconciliationResult(result) {
+    const total = result.resolved.length + result.dangling.length;
+    const lines = [
+        `Edge reconciliation: ${result.resolved.length}/${total} resolved, ${result.remappedCount} remapped, ${result.dangling.length} dangling`,
+    ];
+    if (result.dangling.length > 0) {
+        lines.push('');
+        lines.push('Dangling edges (unresolvable endpoints):');
+        const limit = Math.min(result.dangling.length, 20);
+        for (let i = 0; i < limit; i++) {
+            const e = result.dangling[i];
+            lines.push(`  ${e.source} -> ${e.target}`);
+        }
+        if (result.dangling.length > limit) {
+            lines.push(`  ... and ${result.dangling.length - limit} more`);
+        }
+    }
+    return lines.join('\n');
+}
+//# sourceMappingURL=normalize-id.js.map

package/dist/src/graph/normalize-id.js.map

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

@@ -0,0 +1,29 @@
+import type { MonographDb } from '../storage/db.js';
+export interface PageRankOptions {
+    /** Damping factor (probability of following an edge). Default: 0.85 */
+    dampingFactor?: number;
+    /** Maximum number of power-iteration steps. Default: 100 */
+    maxIterations?: number;
+    /** Convergence threshold (L1 norm delta). Default: 1e-6 */
+    tolerance?: number;
+}
+/**
+ * Evict cached statements and results for a given DB instance (call after writes).
+ */
+export declare function invalidatePageRankCache(db: MonographDb): void;
+/**
+ * Compute PageRank scores for all nodes using power iteration.
+ *
+ * Each node's score is initialized to 1/N (so scores sum to 1).
+ * After convergence the scores still sum to ~1 (standard normalized PageRank).
+ * Dangling nodes (out-degree 0) distribute their rank equally to all nodes.
+ *
+ * Results are cached for 5 seconds when the graph's node+edge counts are
+ * unchanged, making repeated calls (e.g. during context preloading) free.
+ *
+ * @param db - The MonographDb instance
+ * @param options - Optional tuning parameters
+ * @returns Map of nodeId → PageRank score
+ */
+export declare function pageRank(db: MonographDb, options?: PageRankOptions): Map<string, number>;
+//# sourceMappingURL=pagerank.d.ts.map

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

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

@@ -0,0 +1,116 @@
+const _stmtCache = new Map();
+function getStmts(db) {
+    const key = db.name ?? '__default__';
+    let cache = _stmtCache.get(key);
+    if (!cache) {
+        cache = {
+            selectNodes: db.prepare('SELECT id FROM nodes'),
+            selectEdges: db.prepare('SELECT source_id, target_id FROM edges'),
+        };
+        _stmtCache.set(key, cache);
+    }
+    return cache;
+}
+// ---------------------------------------------------------------------------
+// Result cache — avoids re-running power iteration when the graph hasn't
+// changed. Keyed by (dbName, nodeCount, edgeCount) with a 5-second TTL.
+// ---------------------------------------------------------------------------
+const PAGERANK_CACHE_TTL_MS = 5_000;
+const _resultCache = new Map();
+function resultCacheKey(db, nodeCount, edgeCount) {
+    const name = db.name ?? '__default__';
+    return `${name}:${nodeCount}:${edgeCount}`;
+}
+/**
+ * Evict cached statements and results for a given DB instance (call after writes).
+ */
+export function invalidatePageRankCache(db) {
+    const key = db.name ?? '__default__';
+    _stmtCache.delete(key);
+    // Purge all result-cache entries for this DB (they have the name as prefix)
+    for (const k of _resultCache.keys()) {
+        if (k.startsWith(`${key}:`))
+            _resultCache.delete(k);
+    }
+}
+/**
+ * Compute PageRank scores for all nodes using power iteration.
+ *
+ * Each node's score is initialized to 1/N (so scores sum to 1).
+ * After convergence the scores still sum to ~1 (standard normalized PageRank).
+ * Dangling nodes (out-degree 0) distribute their rank equally to all nodes.
+ *
+ * Results are cached for 5 seconds when the graph's node+edge counts are
+ * unchanged, making repeated calls (e.g. during context preloading) free.
+ *
+ * @param db - The MonographDb instance
+ * @param options - Optional tuning parameters
+ * @returns Map of nodeId → PageRank score
+ */
+export function pageRank(db, options = {}) {
+    const { dampingFactor = 0.85, maxIterations = 100, tolerance = 1e-6 } = options;
+    const stmts = getStmts(db);
+    const nodeRows = stmts.selectNodes.all();
+    const edgeRows = stmts.selectEdges.all();
+    if (nodeRows.length === 0)
+        return new Map();
+    // Check result cache before running power iteration
+    const cacheKey = resultCacheKey(db, nodeRows.length, edgeRows.length);
+    const now = Date.now();
+    const cached = _resultCache.get(cacheKey);
+    if (cached && now < cached.expiresAt)
+        return cached.result;
+    const nodes = nodeRows.map(r => r.id);
+    const n = nodes.length;
+    const nodeIndex = new Map();
+    nodes.forEach((id, i) => nodeIndex.set(id, i));
+    // Build adjacency: outEdges[i] = list of target indices
+    const outEdges = nodes.map(() => []);
+    const inEdges = nodes.map(() => []);
+    for (const { source_id: src, target_id: tgt } of edgeRows) {
+        if (src === tgt)
+            continue;
+        const si = nodeIndex.get(src);
+        const ti = nodeIndex.get(tgt);
+        if (si === undefined || ti === undefined)
+            continue;
+        outEdges[si].push(ti);
+        inEdges[ti].push(si);
+    }
+    // Power iteration — initialize to uniform 1/N so scores sum to 1
+    let scores = new Float64Array(n).fill(1 / n);
+    const dangling1OverN = (1 - dampingFactor) / n;
+    for (let iter = 0; iter < maxIterations; iter++) {
+        const newScores = new Float64Array(n);
+        // Collect dangling node contribution
+        let danglingSum = 0;
+        for (let i = 0; i < n; i++) {
+            if (outEdges[i].length === 0)
+                danglingSum += scores[i];
+        }
+        const danglingContrib = (dampingFactor * danglingSum) / n;
+        for (let i = 0; i < n; i++) {
+            let incoming = 0;
+            for (const j of inEdges[i]) {
+                incoming += scores[j] / outEdges[j].length;
+            }
+            newScores[i] = dangling1OverN + dampingFactor * incoming + danglingContrib;
+        }
+        // Check convergence
+        let delta = 0;
+        for (let i = 0; i < n; i++) {
+            delta += Math.abs(newScores[i] - scores[i]);
+        }
+        scores = newScores;
+        if (delta < tolerance)
+            break;
+    }
+    const result = new Map();
+    for (let i = 0; i < n; i++) {
+        result.set(nodes[i], scores[i]);
+    }
+    // Store in result cache
+    _resultCache.set(cacheKey, { result, expiresAt: now + PAGERANK_CACHE_TTL_MS });
+    return result;
+}
+//# sourceMappingURL=pagerank.js.map

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

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

@@ -0,0 +1,40 @@
+import type { MonographDb } from '../storage/db.js';
+export interface PruneResult {
+    danglingEdgesRemoved: number;
+    orphanNodesRemoved: number;
+    staleFileNodesRemoved: number;
+}
+/**
+ * Remove edges whose source or target node does not exist in the nodes table.
+ *
+ * @param db - The MonographDb instance (better-sqlite3 Database)
+ * @returns The number of dangling edges pruned
+ */
+export declare function pruneDanglingEdges(db: MonographDb): number;
+/**
+ * Remove non-File nodes that have no incoming or outgoing edges.
+ * Leaves File nodes in place so they can still be queried even if isolated.
+ *
+ * @param db - The MonographDb instance
+ * @returns Number of orphan nodes removed
+ */
+export declare function pruneOrphanNodes(db: MonographDb): number;
+/**
+ * Remove File nodes whose file_path no longer exists on disk.
+ * Also cascades to remove any edges connected to those nodes (via pruneDanglingEdges).
+ *
+ * @param db - The MonographDb instance
+ * @param existingPaths - Set of file paths that currently exist on disk
+ * @returns Number of stale File nodes removed (call pruneDanglingEdges after to clean edges)
+ */
+export declare function pruneStaleFileNodes(db: MonographDb, existingPaths: Set<string>): number;
+/**
+ * Run a full prune pass: dangling edges → orphan nodes → stale file nodes.
+ * Optionally pass existingPaths to also remove deleted-file nodes.
+ */
+export declare function pruneAll(db: MonographDb, existingPaths?: Set<string>): PruneResult;
+/**
+ * Format a PruneResult as structured text for LLM consumption.
+ */
+export declare function formatPruneResult(result: PruneResult): string;
+//# sourceMappingURL=prune.d.ts.map

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

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