code-auditor-mcp 3.1.0 → 3.4.0

package/dist/graph/callGraph.js

@@ -0,0 +1,484 @@
+/**
+ * Spec 14 R1, R2 — Call Graph Construction, Centrality, and Risk Ranking
+ *
+ * Builds a weighted call graph from the `function_calls` table, computes
+ * PageRank and betweenness centrality, and produces a risk ranking.
+ *
+ * All advisory — zero violations. Reports and annotations only.
+ */
+// ── R1 — Call graph construction ───────────────────────────────────────
+/**
+ * Build a weighted call graph from the `function_calls` table.
+ *
+ * Resolves `callee_name` TEXT → `functions.id` via name join. Edge weight
+ * is the count of call sites between the same (caller, callee) pair.
+ */
+export function buildCallGraph(db) {
+    const adjacency = new Map();
+    const nodeIds = new Set();
+    const nodeNames = new Map();
+    const nodePaths = new Map();
+    // Collect all function IDs, names, file paths
+    const allFns = db.prepare('SELECT id, name, file_path FROM functions').all();
+    for (const fn of allFns) {
+        nodeIds.add(fn.id);
+        nodeNames.set(fn.id, fn.name);
+        nodePaths.set(fn.id, fn.file_path);
+    }
+    // Build call graph: group by (caller_id, resolved_callee_id), weight = count
+    const callRows = db.prepare(`
+    SELECT
+      fc.caller_id,
+      fc.callee_name,
+      f.id AS callee_id
+    FROM function_calls fc
+    LEFT JOIN functions f ON f.name = fc.callee_name
+  `).all();
+    let unresolvedCount = 0;
+    const totalCalls = callRows.length;
+    // Group edge weights: key = "caller_id→callee_id", count occurrences
+    const edgeWeights = new Map();
+    for (const row of callRows) {
+        const callerId = row.caller_id;
+        const calleeId = row.callee_id;
+        if (calleeId === null || calleeId === undefined) {
+            unresolvedCount++;
+            // Still add to node set for completeness
+            if (!nodeIds.has(callerId)) {
+                nodeIds.add(callerId);
+            }
+            continue;
+        }
+        // Ensure both nodes are in the graph
+        if (!adjacency.has(callerId)) {
+            adjacency.set(callerId, new Map());
+        }
+        if (!adjacency.has(calleeId)) {
+            adjacency.set(calleeId, new Map());
+        }
+        const key = `${callerId}→${calleeId}`;
+        edgeWeights.set(key, (edgeWeights.get(key) ?? 0) + 1);
+    }
+    // Apply edge weights to adjacency
+    for (const [key, weight] of edgeWeights) {
+        const [callerStr, calleeStr] = key.split('→');
+        const callerId = parseInt(callerStr, 10);
+        const calleeId = parseInt(calleeStr, 10);
+        adjacency.get(callerId).set(calleeId, weight);
+    }
+    const unresolvedShare = totalCalls > 0 ? unresolvedCount / totalCalls : 0;
+    return {
+        graph: { adjacency, nodeIds, nodeNames, nodePaths },
+        unresolvedCount,
+        unresolvedShare,
+    };
+}
+/**
+ * Build a call graph from the persistent `graph_cache` table (fast path).
+ */
+export function buildCallGraphFromCache(db) {
+    const adjacency = new Map();
+    const nodeIds = new Set();
+    const nodeNames = new Map();
+    const nodePaths = new Map();
+    const allFns = db.prepare('SELECT id, name, file_path FROM functions').all();
+    for (const fn of allFns) {
+        nodeIds.add(fn.id);
+        nodeNames.set(fn.id, fn.name);
+        nodePaths.set(fn.id, fn.file_path);
+    }
+    const rows = db.prepare(`SELECT node_key, neighbor_key, weight FROM graph_cache WHERE graph_type = 'call'`).all();
+    for (const row of rows) {
+        const callerId = parseInt(row.node_key, 10);
+        const calleeId = parseInt(row.neighbor_key, 10);
+        if (!adjacency.has(callerId))
+            adjacency.set(callerId, new Map());
+        if (!adjacency.has(calleeId))
+            adjacency.set(calleeId, new Map());
+        adjacency.get(callerId).set(calleeId, row.weight);
+    }
+    // Unresolved: count function_calls where callee_name doesn't match any function
+    const resolvedRow = db.prepare(`
+    SELECT COUNT(*) as cnt FROM function_calls fc
+    JOIN functions f ON f.name = fc.callee_name
+  `).get();
+    const totalRow = db.prepare('SELECT COUNT(*) as cnt FROM function_calls').get();
+    const unresolvedCount = totalRow.cnt - resolvedRow.cnt;
+    const unresolvedShare = totalRow.cnt > 0 ? unresolvedCount / totalRow.cnt : 0;
+    return {
+        graph: { adjacency, nodeIds, nodeNames, nodePaths },
+        unresolvedCount,
+        unresolvedShare,
+    };
+}
+/**
+ * Populate `graph_cache` with call and import graph edges.
+ * Called after a full sync or scoped sync.
+ */
+export function populateCallGraphCache(db) {
+    const txn = db.transaction(() => {
+        // Clear existing call cache
+        db.prepare("DELETE FROM graph_cache WHERE graph_type = 'call'").run();
+        const stmt = db.prepare(`INSERT OR REPLACE INTO graph_cache (graph_type, node_key, neighbor_key, weight)
+       VALUES ('call', ?, ?, ?)`);
+        // Aggregate call edges with weights
+        const rows = db.prepare(`
+      SELECT
+        fc.caller_id,
+        f.id AS callee_id,
+        COUNT(*) AS weight
+      FROM function_calls fc
+      JOIN functions f ON f.name = fc.callee_name
+      GROUP BY fc.caller_id, f.id
+    `).all();
+        for (const row of rows) {
+            stmt.run(String(row.caller_id), String(row.callee_id), row.weight);
+        }
+    });
+    txn();
+}
+// ── R2 — PageRank ──────────────────────────────────────────────────────
+/**
+ * Compute PageRank on a weighted directed graph.
+ *
+ * Standard iterative algorithm: damping factor 0.85, convergence 1e-6,
+ * max 100 iterations.
+ */
+export function computePageRank(adjacency, nodeIds, damping = 0.85, convergence = 1e-6) {
+    const N = nodeIds.size;
+    const nodes = [...nodeIds];
+    const nodeIndex = new Map();
+    for (let i = 0; i < nodes.length; i++) {
+        nodeIndex.set(nodes[i], i);
+    }
+    // Initialize scores to 1/N
+    let scores = new Float64Array(N);
+    for (let i = 0; i < N; i++)
+        scores[i] = 1.0 / N;
+    // Pre-compute outbound weights for each node
+    const outSum = new Float64Array(N);
+    for (const [nodeId, neighbors] of adjacency) {
+        const idx = nodeIndex.get(nodeId);
+        if (idx === undefined)
+            continue;
+        let total = 0;
+        for (const weight of neighbors.values()) {
+            total += weight;
+        }
+        outSum[idx] = total;
+    }
+    for (let iter = 0; iter < 100; iter++) {
+        const newScores = new Float64Array(N);
+        newScores.fill((1 - damping) / N);
+        for (const [callerId, neighbors] of adjacency) {
+            const callerIdx = nodeIndex.get(callerId);
+            if (callerIdx === undefined)
+                continue;
+            const callerOut = outSum[callerIdx];
+            if (callerOut === 0)
+                continue;
+            const contribution = (damping * scores[callerIdx]) / callerOut;
+            for (const [calleeId, weight] of neighbors) {
+                const calleeIdx = nodeIndex.get(calleeId);
+                if (calleeIdx === undefined)
+                    continue;
+                newScores[calleeIdx] += contribution * weight;
+            }
+        }
+        // Handle dangling nodes (no outbound edges)
+        let danglingSum = 0;
+        for (let i = 0; i < N; i++) {
+            if (outSum[i] === 0) {
+                danglingSum += scores[i];
+            }
+        }
+        if (danglingSum > 0) {
+            const distrib = (damping * danglingSum) / N;
+            for (let i = 0; i < N; i++) {
+                newScores[i] += distrib;
+            }
+        }
+        // Check convergence
+        let maxDiff = 0;
+        for (let i = 0; i < N; i++) {
+            const diff = Math.abs(newScores[i] - scores[i]);
+            if (diff > maxDiff)
+                maxDiff = diff;
+        }
+        scores = newScores;
+        if (maxDiff < convergence)
+            break;
+    }
+    // Convert back to Map<nodeId, score>
+    const result = new Map();
+    for (let i = 0; i < nodes.length; i++) {
+        result.set(nodes[i], scores[i]);
+    }
+    return result;
+}
+// ── R2 — Betweenness Centrality ─────────────────────────────────────────
+const BETWEENNESS_EXACT_NODE_CAP = 2000;
+const BETWEENNESS_PIVOT_COUNT = 200;
+/**
+ * Compute Brandes betweenness centrality.
+ *
+ * When `nodeCount <= 2000`, uses exact Brandes.
+ * Above that, uses Brandes-Pich pivot sampling with `BETWEENNESS_PIVOT_COUNT` pivots.
+ * Returns scores and the number of pivots sampled (0 = exact).
+ */
+export function computeBetweenness(adjacency, nodeIds) {
+    const N = nodeIds.size;
+    const nodes = [...nodeIds];
+    const nodeIndex = new Map();
+    for (let i = 0; i < nodes.length; i++) {
+        nodeIndex.set(nodes[i], i);
+    }
+    if (N <= BETWEENNESS_EXACT_NODE_CAP) {
+        return { scores: brandesExact(adjacency, nodes, nodeIndex), pivotCount: 0 };
+    }
+    // Brandes-Pich pivot sampling
+    const pivotCount = Math.min(BETWEENNESS_PIVOT_COUNT, N);
+    // Deterministic pivot selection: evenly spaced indices
+    const pivots = [];
+    const step = Math.floor(N / pivotCount);
+    for (let i = 0; i < pivotCount; i++) {
+        pivots.push(nodes[Math.min(i * step, N - 1)]);
+    }
+    return { scores: brandesSampled(adjacency, nodes, nodeIndex, pivots), pivotCount };
+}
+/**
+ * Exact Brandes betweenness on all nodes.
+ */
+function brandesExact(adjacency, nodes, nodeIndex) {
+    const N = nodes.length;
+    const bc = new Float64Array(N);
+    for (const s of nodes) {
+        const { stack, pred, sigma, dist, delta } = brandesBfs(adjacency, nodeIndex, N, s);
+        // Accumulate dependencies (reverse BFS order)
+        while (stack.length > 0) {
+            const w = stack.pop();
+            const wIdx = nodeIndex.get(w);
+            for (const v of pred[wIdx]) {
+                const vIdx = nodeIndex.get(v);
+                const weight = sigma[vIdx] / sigma[wIdx];
+                delta[vIdx] += weight * (1 + delta[wIdx]);
+            }
+            if (w !== s) {
+                bc[wIdx] += delta[wIdx];
+            }
+        }
+    }
+    // Undirected normalization: divide by 2
+    // (Brandes for undirected graphs divides by (N-1)(N-2) but we work
+    // with a directed call graph, so no normalization is standard.)
+    const result = new Map();
+    for (let i = 0; i < N; i++) {
+        result.set(nodes[i], bc[i]);
+    }
+    return result;
+}
+/**
+ * Sampled Brandes-Pich: run exact Brandes from pivot nodes, extrapolate.
+ */
+function brandesSampled(adjacency, nodes, nodeIndex, pivots) {
+    const N = nodes.length;
+    const bc = new Float64Array(N);
+    for (const s of pivots) {
+        const { stack, pred, sigma, dist, delta } = brandesBfs(adjacency, nodeIndex, N, s);
+        while (stack.length > 0) {
+            const w = stack.pop();
+            const wIdx = nodeIndex.get(w);
+            for (const v of pred[wIdx]) {
+                const vIdx = nodeIndex.get(v);
+                const weight = sigma[vIdx] / sigma[wIdx];
+                delta[vIdx] += weight * (1 + delta[wIdx]);
+            }
+            if (w !== s) {
+                bc[wIdx] += delta[wIdx];
+            }
+        }
+    }
+    // Scale: multiply by N / pivotCount to estimate the full values
+    const scale = N / pivots.length;
+    const result = new Map();
+    for (let i = 0; i < N; i++) {
+        result.set(nodes[i], bc[i] * scale);
+    }
+    return result;
+}
+/**
+ * Brandes single-source BFS helper.
+ * Returns predecessors, sigma (shortest-path counts), distances, deltas, and BFS stack.
+ */
+function brandesBfs(adjacency, nodeIndex, N, source) {
+    const stack = [];
+    const pred = Array.from({ length: N }, () => []);
+    const sigma = new Float64Array(N);
+    const dist = new Int32Array(N);
+    const delta = new Float64Array(N);
+    dist.fill(-1);
+    const sIdx = nodeIndex.get(source);
+    dist[sIdx] = 0;
+    sigma[sIdx] = 1;
+    const queue = [source];
+    while (queue.length > 0) {
+        const v = queue.shift();
+        const vIdx = nodeIndex.get(v);
+        stack.push(v);
+        const neighbors = adjacency.get(v);
+        if (!neighbors)
+            continue;
+        for (const [w, _weight] of neighbors) {
+            const wIdx = nodeIndex.get(w);
+            if (wIdx === undefined)
+                continue;
+            // First visit
+            if (dist[wIdx] < 0) {
+                dist[wIdx] = dist[vIdx] + 1;
+                queue.push(w);
+            }
+            // Edge lies on a shortest path
+            if (dist[wIdx] === dist[vIdx] + 1) {
+                sigma[wIdx] += sigma[vIdx];
+                pred[wIdx].push(v);
+            }
+        }
+    }
+    return { stack, pred, sigma, dist, delta };
+}
+// ── R2 — Risk ranking ───────────────────────────────────────────────────
+/**
+ * Detect whether a function is untested by checking if any transitive caller
+ * (depth ≤ 2) resides in a file matching test globs.
+ */
+function detectUntested(db, functionId, adjacency) {
+    // Perform a 2-hop BFS in the callers direction (who calls this function)
+    const visited = new Set();
+    const queue = [{ id: functionId, depth: 0 }];
+    visited.add(functionId);
+    // Build reverse adjacency (callee → callers) from forward adjacency
+    const reverseAdj = new Map();
+    for (const [callerId, neighbors] of adjacency) {
+        for (const calleeId of neighbors.keys()) {
+            if (!reverseAdj.has(calleeId)) {
+                reverseAdj.set(calleeId, new Set());
+            }
+            reverseAdj.get(calleeId).add(callerId);
+        }
+    }
+    while (queue.length > 0) {
+        const current = queue.shift();
+        if (current.depth > 2)
+            continue;
+        // Check if this caller's file matches test patterns
+        if (current.depth > 0) {
+            const fileRow = db.prepare('SELECT file_path FROM functions WHERE id = ?').get(current.id);
+            if (fileRow && isTestFile(fileRow.file_path)) {
+                return false; // Found a test — NOT untested
+            }
+        }
+        // Follow reverse edges (who calls this node)
+        const callers = reverseAdj.get(current.id);
+        if (callers) {
+            for (const callerId of callers) {
+                if (!visited.has(callerId)) {
+                    visited.add(callerId);
+                    queue.push({ id: callerId, depth: current.depth + 1 });
+                }
+            }
+        }
+    }
+    return true; // No test caller found — untested
+}
+function isTestFile(filePath) {
+    return (filePath.includes('.test.') ||
+        filePath.includes('.spec.') ||
+        filePath.includes('__tests__') ||
+        filePath.includes('/test/') ||
+        filePath.includes('/tests/'));
+}
+/**
+ * Compute a risk score for every function.
+ *
+ * risk = max(pageRank percentile, betweenness percentile)
+ *      × complexity percentile
+ *      × (1 + untested)  — where untested = 1 if true, 0 otherwise
+ */
+export function computeRisk(db, adjacency, nodeIds, nodeNames, nodePaths) {
+    const pageRank = computePageRank(adjacency, nodeIds);
+    const { scores: betweenness } = computeBetweenness(adjacency, nodeIds);
+    const nodes = [...nodeIds];
+    const N = nodes.length;
+    if (N === 0)
+        return [];
+    // Sort nodes by each metric to compute percentiles
+    const prSorted = nodes.map(id => ({ id, score: pageRank.get(id) ?? 0 })).sort((a, b) => a.score - b.score);
+    const bwSorted = nodes.map(id => ({ id, score: betweenness.get(id) ?? 0 })).sort((a, b) => a.score - b.score);
+    const prPercentile = new Map();
+    const bwPercentile = new Map();
+    for (let i = 0; i < N; i++) {
+        prPercentile.set(prSorted[i].id, i / (N - 1));
+        bwPercentile.set(bwSorted[i].id, i / (N - 1));
+    }
+    // Get complexity from DB
+    const complexityRows = db.prepare('SELECT id, complexity, name, file_path FROM functions WHERE id IN (' +
+        nodes.map(() => '?').join(',') + ')').all(...nodes);
+    const complexityMap = new Map();
+    for (const row of complexityRows) {
+        complexityMap.set(row.id, row.complexity ?? 0);
+    }
+    // Complexity percentile
+    const cxSorted = complexityRows
+        .map(r => ({ id: r.id, cx: r.complexity ?? 0 }))
+        .sort((a, b) => a.cx - b.cx);
+    const cxPercentile = new Map();
+    for (let i = 0; i < cxSorted.length; i++) {
+        cxPercentile.set(cxSorted[i].id, i / (Math.max(cxSorted.length - 1, 1)));
+    }
+    // Build risk entries
+    const entries = [];
+    for (const nodeId of nodes) {
+        // Skip unresolved externals (IDs that appear only as callees but aren't in functions table)
+        const name = nodeNames.get(nodeId);
+        const filePath = nodePaths.get(nodeId);
+        if (!name || !filePath)
+            continue;
+        const pr = prPercentile.get(nodeId) ?? 0;
+        const bw = bwPercentile.get(nodeId) ?? 0;
+        const cx = cxPercentile.get(nodeId) ?? 0;
+        const untested = detectUntested(db, nodeId, adjacency);
+        const risk = Math.max(pr, bw) * cx * (1 + (untested ? 1 : 0));
+        entries.push({
+            functionName: name,
+            filePath,
+            pageRankPercentile: pr,
+            betweennessPercentile: bw,
+            complexityPercentile: cx,
+            untested,
+            riskScore: risk,
+        });
+    }
+    // Sort by risk descending
+    entries.sort((a, b) => b.riskScore - a.riskScore);
+    return entries;
+}
+// ── Graph statistics ────────────────────────────────────────────────────
+export function getGraphStats(db) {
+    const callRows = db.prepare(`SELECT COUNT(*) as cnt FROM graph_cache WHERE graph_type = 'call'`).get();
+    const importRows = db.prepare(`SELECT COUNT(*) as cnt FROM graph_cache WHERE graph_type = 'import'`).get();
+    const callNodes = db.prepare("SELECT COUNT(DISTINCT node_key) as cnt FROM graph_cache WHERE graph_type = 'call'").get().cnt;
+    const importNodes = db.prepare("SELECT COUNT(DISTINCT node_key) as cnt FROM graph_cache WHERE graph_type = 'import'").get().cnt;
+    const totalCalls = db.prepare('SELECT COUNT(*) as cnt FROM function_calls').get().cnt;
+    const resolvedCalls = db.prepare('SELECT COUNT(*) as cnt FROM function_calls fc JOIN functions f ON f.name = fc.callee_name').get().cnt;
+    const unresolvedCalls = totalCalls - resolvedCalls;
+    const unresolvedShare = totalCalls > 0 ? unresolvedCalls / totalCalls : 0;
+    return {
+        callNodes,
+        callEdges: callRows.cnt,
+        unresolvedCalls,
+        unresolvedShare,
+        importNodes,
+        importEdges: importRows.cnt,
+    };
+}
+//# sourceMappingURL=callGraph.js.map

package/dist/graph/callGraph.js.map

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package/dist/graph/importGraph.d.ts

@@ -0,0 +1,91 @@
+/**
+ * Spec 14 R3, R4 — Import Graph, Community Detection, and Martin Metrics
+ *
+ * Builds a file-level import graph from `function_dependencies`, runs Louvain
+ * community detection, computes directory purity vs community structure, and
+ * calculates Martin instability/abstractness metrics.
+ *
+ * IMPORTANT (R4 abstractness gate): The `functions` entity_type column stores
+ * only 'function' and 'component' — NOT type/interface declarations. Abstractness (A)
+ * is computed from `is_exported` rows using a per-file AST scan for export type/interface
+ * declarations. Without this, A = 0 everywhere (dead path).
+ *
+ * All advisory — zero violations. Reports and annotations only.
+ */
+import type Database from 'better-sqlite3';
+import type { DirectoryPurity, MartinEntry } from '../types.js';
+export interface ImportGraph {
+    /** Adjacency: filePath → (neighborFilePath → edgeWeight) */
+    adjacency: Map<string, Map<string, number>>;
+    /** Set of all file paths in the graph */
+    filePaths: Set<string>;
+}
+export interface CommunityResult {
+    /** filePath → community ID */
+    communities: Map<string, number>;
+    /** Number of communities detected */
+    communityCount: number;
+    /** Final modularity score */
+    modularity: number;
+}
+export interface PurityResult {
+    directoryPurities: DirectoryPurity[];
+    splitCandidates: Array<{
+        directory: string;
+        communities: number[];
+        fileCounts: number[];
+    }>;
+    mergeCandidates: Array<{
+        directories: string[];
+        community: number;
+        fileCount: number;
+    }>;
+    agreementScore: number;
+}
+/**
+ * Build a file-level import graph by aggregating `function_dependencies`
+ * joined with `functions.file_path`.
+ *
+ * Edge weight = count of distinct dependency symbols between a file pair.
+ */
+export declare function buildImportGraph(db: Database.Database): ImportGraph;
+/**
+ * Populate `graph_cache` with import graph edges.
+ */
+export declare function populateImportGraphCache(db: Database.Database): void;
+/**
+ * Build an import graph from the persistent `graph_cache` table (fast path).
+ */
+export declare function buildImportGraphFromCache(db: Database.Database): ImportGraph;
+/**
+ * Louvain community detection on weighted undirected graph.
+ *
+ * Standard two-phase algorithm:
+ * Phase 1: Greedy modularity optimization (move nodes between communities)
+ * Phase 2: Community aggregation (build super-graph)
+ * Repeat until modularity gain < threshold.
+ */
+export declare function detectCommunities(adjacency: Map<string, Map<string, number>>, filePaths: Set<string>): CommunityResult;
+/**
+ * Compute directory purity against detected communities.
+ *
+ * For each directory, compute: share of its files in the plurality community.
+ * Detects split candidates (directories spanning ≥2 communities) and
+ * merge candidates (one community dominating ≥2 directories).
+ */
+export declare function computeDirectoryPurity(communities: Map<string, number>, filePaths: Set<string>): PurityResult;
+/**
+ * Compute Martin metrics per directory (treated as package).
+ *
+ * Ce = efferent couplings: distinct directories this directory imports from
+ * Ca = afferent couplings: distinct directories that import this directory
+ * I  = Ce / (Ca + Ce) — instability (0 if both zero)
+ * A  = abstractness: exported type/interface declarations ÷ total exported symbols
+ * D  = |A + I − 1| — distance from main sequence
+ *
+ * IMPORTANT: Abstractness computation uses an AST scan for export type/interface
+ * declarations because the `functions` table does not index type/interface entities.
+ * Uses a lightweight file-content scan.
+ */
+export declare function computeMartinMetrics(db: Database.Database, importGraph: ImportGraph): MartinEntry[];
+//# sourceMappingURL=importGraph.d.ts.map

package/dist/graph/importGraph.d.ts.map

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