kirograph 0.16.1 → 0.19.0

package/dist/security/vuln/client.js

@@ -0,0 +1,355 @@
+"use strict";
+var __defProp = Object.defineProperty;
+var __getOwnPropDesc = Object.getOwnPropertyDescriptor;
+var __getOwnPropNames = Object.getOwnPropertyNames;
+var __hasOwnProp = Object.prototype.hasOwnProperty;
+var __export = (target, all) => {
+  for (var name in all)
+    __defProp(target, name, { get: all[name], enumerable: true });
+};
+var __copyProps = (to, from, except, desc) => {
+  if (from && typeof from === "object" || typeof from === "function") {
+    for (let key of __getOwnPropNames(from))
+      if (!__hasOwnProp.call(to, key) && key !== except)
+        __defProp(to, key, { get: () => from[key], enumerable: !(desc = __getOwnPropDesc(from, key)) || desc.enumerable });
+  }
+  return to;
+};
+var __toCommonJS = (mod) => __copyProps(__defProp({}, "__esModule", { value: true }), mod);
+var client_exports = {};
+__export(client_exports, {
+  VulnerabilityDatabaseClient: () => VulnerabilityDatabaseClient,
+  computeRiskScore: () => computeRiskScore
+});
+module.exports = __toCommonJS(client_exports);
+var import_errors = require("../../errors");
+var import_epss_client = require("./epss-client");
+const BATCH_CHUNK_SIZE = 1e3;
+function computeRiskScore(cvss, epss, verdict, staleness) {
+  const cvssNormalized = (cvss ?? 5) / 10;
+  const epssValue = epss ?? 0;
+  let reachabilityFactor;
+  if (verdict === "affected") {
+    reachabilityFactor = 1;
+  } else if (verdict === "under_investigation") {
+    reachabilityFactor = 0.5;
+  } else if (verdict === "not_affected") {
+    reachabilityFactor = 0.1;
+  } else {
+    reachabilityFactor = 0.3;
+  }
+  const stalenessBonus = 1 + (staleness ?? 0) * 0.2;
+  const raw = reachabilityFactor * (0.4 * cvssNormalized + 0.6 * epssValue) * stalenessBonus;
+  return Math.min(raw * 10, 10);
+}
+class VulnerabilityDatabaseClient {
+  constructor(adapters, db, timeoutMs = 3e4) {
+    this.adapters = adapters;
+    this.db = db;
+    this.timeoutMs = timeoutMs;
+  }
+  /**
+   * Enrich all Dependency_Nodes with vulnerability data.
+   *
+   * Uses batch queries (up to 1000 per HTTP request) when the adapter supports
+   * `queryBatch`. Falls back to sequential single queries per dependency if batch
+   * is unavailable or fails. Results are deduplicated by CVE ID across adapters.
+   */
+  async enrichAll() {
+    const rawDb = this.db.getRawDb();
+    const result = {
+      vulnerabilitiesFound: 0,
+      dependenciesChecked: 0,
+      errors: [],
+      staleNodes: []
+    };
+    const depRows = rawDb.all(
+      `SELECT node_id, ecosystem, package_name, resolved_version, declared_constraint
+       FROM sec_dependencies`
+    );
+    const queryableDeps = depRows.filter((d) => d.resolved_version || d.declared_constraint);
+    for (const adapter of this.adapters) {
+      if (adapter.queryBatch) {
+        await this.enrichAllBatch(adapter, queryableDeps, result);
+      } else {
+        await this.enrichAllSequential(adapter, queryableDeps, result);
+      }
+    }
+    const now = Date.now();
+    for (const dep of queryableDeps) {
+      rawDb.run(
+        `UPDATE sec_dependencies SET last_vuln_check = ? WHERE node_id = ?`,
+        [now, dep.node_id]
+      );
+    }
+    result.dependenciesChecked = queryableDeps.length;
+    await this.enrichEpss(rawDb);
+    await this.computeRiskScores(rawDb);
+    return result;
+  }
+  /**
+   * Fetch EPSS scores for all stored vulnerabilities and update the database.
+   */
+  async enrichEpss(rawDb) {
+    try {
+      const cveRows = rawDb.all(
+        `SELECT cve_id FROM sec_vulnerabilities`
+      );
+      if (cveRows.length === 0) {
+        return;
+      }
+      const cveIds = cveRows.map((r) => r.cve_id);
+      const epssClient = new import_epss_client.EpssClient();
+      const scores = await epssClient.fetchScores(cveIds);
+      if (scores.size === 0) {
+        return;
+      }
+      const fetchedAt = Date.now();
+      for (const [cveId, { score, percentile }] of scores) {
+        rawDb.run(
+          `UPDATE sec_vulnerabilities SET epss_score = ?, epss_percentile = ?, epss_fetched_at = ? WHERE cve_id = ?`,
+          [score, percentile, fetchedAt, cveId]
+        );
+      }
+    } catch (error) {
+      const msg = error instanceof Error ? error.message : String(error);
+      (0, import_errors.logWarn)(`[sec:epss] EPSS enrichment failed (non-critical): ${msg}`);
+    }
+  }
+  /**
+   * Compute and persist combined risk scores for all stored vulnerabilities.
+   * Called after EPSS enrichment so epss_score values are up to date.
+   */
+  async computeRiskScores(rawDb) {
+    const rows = rawDb.all(`
+      SELECT v.node_id, v.severity_score, v.epss_score,
+             r.verdict,
+             d.staleness_score
+      FROM sec_vulnerabilities v
+      LEFT JOIN edges e ON e.target = v.node_id AND e.kind = 'has_vulnerability'
+      LEFT JOIN sec_dependencies d ON d.node_id = e.source
+      LEFT JOIN sec_reachability r ON r.vulnerability_node_id = v.node_id
+    `);
+    for (const row of rows) {
+      const score = computeRiskScore(row.severity_score, row.epss_score, row.verdict, row.staleness_score);
+      rawDb.run(`UPDATE sec_vulnerabilities SET risk_score = ? WHERE node_id = ?`, [score, row.node_id]);
+    }
+  }
+  /**
+   * Batch enrichment path: groups deps into chunks of BATCH_CHUNK_SIZE and sends
+   * one HTTP request per chunk. Falls back to sequential on batch failure.
+   */
+  async enrichAllBatch(adapter, deps, result) {
+    const rawDb = this.db.getRawDb();
+    for (let i = 0; i < deps.length; i += BATCH_CHUNK_SIZE) {
+      const chunk = deps.slice(i, i + BATCH_CHUNK_SIZE);
+      const queries = chunk.map((dep) => ({
+        ecosystem: dep.ecosystem,
+        packageName: dep.package_name,
+        version: dep.resolved_version || dep.declared_constraint
+      }));
+      let batchResults;
+      try {
+        const controller = new AbortController();
+        const timeout = setTimeout(() => controller.abort(), this.timeoutMs);
+        try {
+          batchResults = await adapter.queryBatch(queries, controller.signal);
+        } finally {
+          clearTimeout(timeout);
+        }
+      } catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        (0, import_errors.logWarn)(`[sec:vuln] ${adapter.name} batch query failed (${msg}), falling back to sequential for chunk of ${chunk.length}`);
+        await this.enrichAllSequential(adapter, chunk, result);
+        continue;
+      }
+      for (let j = 0; j < chunk.length; j++) {
+        const dep = chunk[j];
+        const cveRecords = batchResults[j] ?? [];
+        const uniqueCves = this.deduplicateByCveId(cveRecords);
+        for (const cve of uniqueCves) {
+          this.upsertVulnerabilityNode(rawDb, cve, dep.node_id);
+          result.vulnerabilitiesFound++;
+        }
+      }
+    }
+  }
+  /**
+   * Sequential enrichment path: queries one dependency at a time.
+   * Used when the adapter does not support queryBatch, or as a fallback.
+   */
+  async enrichAllSequential(adapter, deps, result) {
+    const rawDb = this.db.getRawDb();
+    for (const dep of deps) {
+      const version = dep.resolved_version || dep.declared_constraint;
+      const cveRecords = await this.queryAdaptersForDependency(dep, version, result, [adapter]);
+      const uniqueCves = this.deduplicateByCveId(cveRecords);
+      for (const cve of uniqueCves) {
+        this.upsertVulnerabilityNode(rawDb, cve, dep.node_id);
+        result.vulnerabilitiesFound++;
+      }
+    }
+  }
+  /**
+   * Enrich a single Dependency_Node with vulnerability data.
+   *
+   * @param dependencyNodeId - The node ID of the dependency to enrich
+   * @returns Array of CVE records found for this dependency
+   */
+  async enrichOne(dependencyNodeId) {
+    const rawDb = this.db.getRawDb();
+    const dep = rawDb.get(
+      `SELECT node_id, ecosystem, package_name, resolved_version, declared_constraint
+       FROM sec_dependencies WHERE node_id = ?`,
+      [dependencyNodeId]
+    );
+    if (!dep) {
+      return [];
+    }
+    const version = dep.resolved_version || dep.declared_constraint;
+    if (!version) {
+      return [];
+    }
+    const enrichResult = {
+      vulnerabilitiesFound: 0,
+      dependenciesChecked: 0,
+      errors: [],
+      staleNodes: []
+    };
+    const cveRecords = await this.queryAdaptersForDependency(
+      dep,
+      version,
+      enrichResult
+    );
+    const uniqueCves = this.deduplicateByCveId(cveRecords);
+    for (const cve of uniqueCves) {
+      this.upsertVulnerabilityNode(rawDb, cve, dep.node_id);
+    }
+    const now = Date.now();
+    rawDb.run(
+      `UPDATE sec_dependencies SET last_vuln_check = ? WHERE node_id = ?`,
+      [now, dep.node_id]
+    );
+    return uniqueCves;
+  }
+  /**
+   * Query a set of adapters for a single dependency.
+   * Handles timeouts and unreachable databases gracefully.
+   * Defaults to all configured adapters when adapterList is omitted.
+   */
+  async queryAdaptersForDependency(dep, version, result, adapterList = this.adapters) {
+    const allRecords = [];
+    for (const adapter of adapterList) {
+      try {
+        const controller = new AbortController();
+        const timeout = setTimeout(() => controller.abort(), this.timeoutMs);
+        try {
+          const records = await adapter.query(
+            dep.ecosystem,
+            dep.package_name,
+            version,
+            controller.signal
+          );
+          allRecords.push(...records);
+        } finally {
+          clearTimeout(timeout);
+        }
+      } catch (error) {
+        const errorMessage = error instanceof Error ? error.message : String(error);
+        (0, import_errors.logError)(
+          `[sec:vuln] Failed to query ${adapter.name} for ${dep.package_name}@${version}: ${errorMessage}`
+        );
+        result.errors.push({
+          dependency: dep.package_name,
+          database: adapter.name,
+          error: errorMessage
+        });
+        this.markDependencyStale(dep.node_id, result);
+      }
+    }
+    return allRecords;
+  }
+  /**
+   * Mark a dependency node as having stale vulnerability data.
+   * Retains cached data but sets the stale flag with timestamp.
+   */
+  markDependencyStale(nodeId, result) {
+    const rawDb = this.db.getRawDb();
+    const now = Date.now();
+    rawDb.run(
+      `UPDATE sec_dependencies
+       SET vuln_data_stale = 1, vuln_data_stale_since = ?
+       WHERE node_id = ?`,
+      [now, nodeId]
+    );
+    if (!result.staleNodes.includes(nodeId)) {
+      result.staleNodes.push(nodeId);
+    }
+    (0, import_errors.logWarn)(
+      `[sec:vuln] Vulnerability data marked stale for dependency node ${nodeId}`
+    );
+  }
+  /**
+   * Deduplicate CVE records by their ID.
+   * When the same CVE is reported by multiple databases, keep the first occurrence.
+   */
+  deduplicateByCveId(records) {
+    const seen = /* @__PURE__ */ new Map();
+    for (const record of records) {
+      if (!seen.has(record.id)) {
+        seen.set(record.id, record);
+      }
+    }
+    return [...seen.values()];
+  }
+  /**
+   * Create or update a Vulnerability_Node and link it to the affected dependency.
+   *
+   * - Creates a node in `nodes` table with kind='vulnerability', ID format `vuln:<cve_id>`
+   * - Inserts a row in `sec_vulnerabilities` with CVE metadata
+   * - Creates a `has_vulnerability` edge from the Dependency_Node to the Vulnerability_Node
+   */
+  upsertVulnerabilityNode(rawDb, cve, dependencyNodeId) {
+    const vulnNodeId = `vuln:${cve.id}`;
+    const now = Date.now();
+    const summary = cve.summary.length > 500 ? cve.summary.slice(0, 500) : cve.summary;
+    const sourceDatabase = this.adapters.length > 0 ? this.adapters[0].name : "unknown";
+    rawDb.run(
+      `INSERT OR REPLACE INTO nodes
+        (id, kind, name, qualified_name, file_path, language,
+         start_line, end_line, start_column, end_column,
+         is_exported, is_async, is_static, is_abstract, updated_at)
+       VALUES (?, 'vulnerability', ?, ?, '', 'unknown', 0, 0, 0, 0, 0, 0, 0, 0, ?)`,
+      [vulnNodeId, cve.id, cve.id, now]
+    );
+    const affectedRangesJson = JSON.stringify(cve.affectedVersionRanges);
+    rawDb.run(
+      `INSERT OR REPLACE INTO sec_vulnerabilities
+        (node_id, cve_id, severity_score, affected_ranges, fixed_version, summary, source_database)
+       VALUES (?, ?, ?, ?, ?, ?, ?)`,
+      [
+        vulnNodeId,
+        cve.id,
+        cve.severity,
+        affectedRangesJson,
+        cve.fixedVersion ?? null,
+        summary,
+        sourceDatabase
+      ]
+    );
+    const edge = {
+      source: dependencyNodeId,
+      target: vulnNodeId,
+      kind: "has_vulnerability",
+      confidence: "extracted",
+      confidenceScore: 1
+    };
+    this.db.insertEdge(edge);
+  }
+}
+// Annotate the CommonJS export names for ESM import in node:
+0 && (module.exports = {
+  VulnerabilityDatabaseClient,
+  computeRiskScore
+});
+//# sourceMappingURL=client.js.map

package/dist/security/vuln/client.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../../src/security/vuln/client.ts"],
+  "sourcesContent": ["/**\n * VulnerabilityDatabaseClient\n *\n * Orchestrates vulnerability enrichment by querying configured databases,\n * merging and deduplicating results by CVE identifier, creating Vulnerability_Nodes\n * linked to affected Dependency_Nodes, and handling unreachable databases gracefully.\n *\n * Requirements: 3.1, 3.2, 3.3, 3.4, 3.5, 3.7\n */\n\nimport type { GraphDatabase } from '../../db/database';\nimport type { Edge } from '../../types';\nimport type { CVERecord, EnrichmentResult } from '../types';\nimport type { VulnDatabaseAdapter, BatchQuery } from './types';\nimport { logError, logWarn } from '../../errors';\nimport { EpssClient } from './epss-client';\n\nconst BATCH_CHUNK_SIZE = 1000;\n\n/**\n * Compute a combined risk score (0.0\u201310.0) for a vulnerability.\n *\n * Formula:\n *   risk = reachability_factor \u00D7 (0.4 \u00D7 cvss_normalized + 0.6 \u00D7 epss) \u00D7 staleness_bonus\n *   scaled to 0\u201310: min(risk \u00D7 10, 10.0)\n *\n * @param cvss        - CVSS base score (0.0\u201310.0), null treated as 5.0\n * @param epss        - EPSS exploitation probability (0.0\u20131.0), null treated as 0.0\n * @param verdict     - Reachability verdict or null/undefined\n * @param staleness   - Dependency staleness score (0.0\u20131.0), null treated as 0.0\n */\nexport function computeRiskScore(\n  cvss: number | null | undefined,\n  epss: number | null | undefined,\n  verdict: string | null | undefined,\n  staleness: number | null | undefined,\n): number {\n  const cvssNormalized = (cvss ?? 5.0) / 10.0;\n  const epssValue = epss ?? 0.0;\n\n  let reachabilityFactor: number;\n  if (verdict === 'affected') {\n    reachabilityFactor = 1.0;\n  } else if (verdict === 'under_investigation') {\n    reachabilityFactor = 0.5;\n  } else if (verdict === 'not_affected') {\n    reachabilityFactor = 0.1;\n  } else {\n    // no verdict\n    reachabilityFactor = 0.3;\n  }\n\n  const stalenessBonus = 1.0 + ((staleness ?? 0) * 0.2);\n\n  const raw = reachabilityFactor * (0.4 * cvssNormalized + 0.6 * epssValue) * stalenessBonus;\n  return Math.min(raw * 10, 10.0);\n}\n\n/**\n * Dependency row from sec_dependencies table.\n */\ninterface DependencyRow {\n  node_id: string;\n  ecosystem: string;\n  package_name: string;\n  resolved_version: string | null;\n  declared_constraint: string;\n}\n\nexport class VulnerabilityDatabaseClient {\n  private readonly adapters: VulnDatabaseAdapter[];\n  private readonly db: GraphDatabase;\n  private readonly timeoutMs: number;\n\n  constructor(\n    adapters: VulnDatabaseAdapter[],\n    db: GraphDatabase,\n    timeoutMs: number = 30000,\n  ) {\n    this.adapters = adapters;\n    this.db = db;\n    this.timeoutMs = timeoutMs;\n  }\n\n  /**\n   * Enrich all Dependency_Nodes with vulnerability data.\n   *\n   * Uses batch queries (up to 1000 per HTTP request) when the adapter supports\n   * `queryBatch`. Falls back to sequential single queries per dependency if batch\n   * is unavailable or fails. Results are deduplicated by CVE ID across adapters.\n   */\n  async enrichAll(): Promise<EnrichmentResult> {\n    const rawDb = this.db.getRawDb();\n    const result: EnrichmentResult = {\n      vulnerabilitiesFound: 0,\n      dependenciesChecked: 0,\n      errors: [],\n      staleNodes: [],\n    };\n\n    const depRows: DependencyRow[] = rawDb.all(\n      `SELECT node_id, ecosystem, package_name, resolved_version, declared_constraint\n       FROM sec_dependencies`,\n    );\n\n    // Filter out deps with no usable version\n    const queryableDeps = depRows.filter(d => d.resolved_version || d.declared_constraint);\n\n    for (const adapter of this.adapters) {\n      if (adapter.queryBatch) {\n        await this.enrichAllBatch(adapter, queryableDeps, result);\n      } else {\n        await this.enrichAllSequential(adapter, queryableDeps, result);\n      }\n    }\n\n    // Record lastVulnCheck for all queried deps (do once, after all adapters)\n    const now = Date.now();\n    for (const dep of queryableDeps) {\n      rawDb.run(\n        `UPDATE sec_dependencies SET last_vuln_check = ? WHERE node_id = ?`,\n        [now, dep.node_id],\n      );\n    }\n    result.dependenciesChecked = queryableDeps.length;\n\n    // Enrich stored vulnerabilities with EPSS scores\n    await this.enrichEpss(rawDb);\n\n    // Compute combined risk scores after all enrichment is done\n    await this.computeRiskScores(rawDb);\n\n    return result;\n  }\n\n  /**\n   * Fetch EPSS scores for all stored vulnerabilities and update the database.\n   */\n  private async enrichEpss(rawDb: any): Promise<void> {\n    try {\n      const cveRows: Array<{ cve_id: string }> = rawDb.all(\n        `SELECT cve_id FROM sec_vulnerabilities`,\n      );\n\n      if (cveRows.length === 0) {\n        return;\n      }\n\n      const cveIds = cveRows.map(r => r.cve_id);\n      const epssClient = new EpssClient();\n      const scores = await epssClient.fetchScores(cveIds);\n\n      if (scores.size === 0) {\n        return;\n      }\n\n      const fetchedAt = Date.now();\n      for (const [cveId, { score, percentile }] of scores) {\n        rawDb.run(\n          `UPDATE sec_vulnerabilities SET epss_score = ?, epss_percentile = ?, epss_fetched_at = ? WHERE cve_id = ?`,\n          [score, percentile, fetchedAt, cveId],\n        );\n      }\n    } catch (error: unknown) {\n      const msg = error instanceof Error ? error.message : String(error);\n      logWarn(`[sec:epss] EPSS enrichment failed (non-critical): ${msg}`);\n    }\n  }\n\n  /**\n   * Compute and persist combined risk scores for all stored vulnerabilities.\n   * Called after EPSS enrichment so epss_score values are up to date.\n   */\n  private async computeRiskScores(rawDb: any): Promise<void> {\n    const rows: Array<{\n      node_id: string;\n      severity_score: number | null;\n      epss_score: number | null;\n      verdict: string | null;\n      staleness_score: number | null;\n    }> = rawDb.all(`\n      SELECT v.node_id, v.severity_score, v.epss_score,\n             r.verdict,\n             d.staleness_score\n      FROM sec_vulnerabilities v\n      LEFT JOIN edges e ON e.target = v.node_id AND e.kind = 'has_vulnerability'\n      LEFT JOIN sec_dependencies d ON d.node_id = e.source\n      LEFT JOIN sec_reachability r ON r.vulnerability_node_id = v.node_id\n    `);\n    for (const row of rows) {\n      const score = computeRiskScore(row.severity_score, row.epss_score, row.verdict, row.staleness_score);\n      rawDb.run(`UPDATE sec_vulnerabilities SET risk_score = ? WHERE node_id = ?`, [score, row.node_id]);\n    }\n  }\n\n  /**\n   * Batch enrichment path: groups deps into chunks of BATCH_CHUNK_SIZE and sends\n   * one HTTP request per chunk. Falls back to sequential on batch failure.\n   */\n  private async enrichAllBatch(\n    adapter: VulnDatabaseAdapter & Required<Pick<VulnDatabaseAdapter, 'queryBatch'>>,\n    deps: DependencyRow[],\n    result: EnrichmentResult,\n  ): Promise<void> {\n    const rawDb = this.db.getRawDb();\n\n    for (let i = 0; i < deps.length; i += BATCH_CHUNK_SIZE) {\n      const chunk = deps.slice(i, i + BATCH_CHUNK_SIZE);\n      const queries: BatchQuery[] = chunk.map(dep => ({\n        ecosystem: dep.ecosystem,\n        packageName: dep.package_name,\n        version: dep.resolved_version || dep.declared_constraint,\n      }));\n\n      let batchResults: Array<CVERecord[]>;\n      try {\n        const controller = new AbortController();\n        const timeout = setTimeout(() => controller.abort(), this.timeoutMs);\n        try {\n          batchResults = await adapter.queryBatch(queries, controller.signal);\n        } finally {\n          clearTimeout(timeout);\n        }\n      } catch (error: unknown) {\n        // Batch failed \u2014 fall back to sequential for this chunk\n        const msg = error instanceof Error ? error.message : String(error);\n        logWarn(`[sec:vuln] ${adapter.name} batch query failed (${msg}), falling back to sequential for chunk of ${chunk.length}`);\n        await this.enrichAllSequential(adapter, chunk, result);\n        continue;\n      }\n\n      for (let j = 0; j < chunk.length; j++) {\n        const dep = chunk[j]!;\n        const cveRecords = batchResults[j] ?? 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