ocr-provenance-mcp 1.0.0

package/dist/utils/validation.d.ts.map

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package/dist/utils/validation.js

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+/**
+ * OCR Provenance MCP System - Zod Validation Schemas
+ *
+ * This module provides comprehensive input validation for all MCP tool inputs.
+ * Each schema includes:
+ * - Type validation
+ * - Constraint validation (min/max, patterns, etc.)
+ * - Descriptive error messages
+ * - Default values where appropriate
+ *
+ * @module utils/validation
+ */
+import { z } from 'zod';
+import * as path from 'path';
+import { homedir } from 'os';
+// ═══════════════════════════════════════════════════════════════════════════════
+// CUSTOM ERROR CLASS
+// ═══════════════════════════════════════════════════════════════════════════════
+/**
+ * Custom validation error with descriptive message
+ */
+export class ValidationError extends Error {
+    constructor(message) {
+        super(message);
+        this.name = 'ValidationError';
+    }
+}
+// ═══════════════════════════════════════════════════════════════════════════════
+// HELPER FUNCTIONS
+// ═══════════════════════════════════════════════════════════════════════════════
+/**
+ * Validate input against schema and throw descriptive error if invalid
+ *
+ * @param schema - Zod schema to validate against
+ * @param input - Input value to validate
+ * @returns Validated and typed input data
+ * @throws ValidationError with descriptive message if validation fails
+ */
+export function validateInput(schema, input) {
+    const result = schema.safeParse(input);
+    if (!result.success) {
+        const errors = result.error.errors.map((e) => {
+            const path = e.path.length > 0 ? `${e.path.join('.')}: ` : '';
+            return `${path}${e.message}`;
+        });
+        throw new ValidationError(errors.join('; '));
+    }
+    return result.data;
+}
+// ═══════════════════════════════════════════════════════════════════════════════
+// SHARED ENUMS AND BASE SCHEMAS
+// ═══════════════════════════════════════════════════════════════════════════════
+/**
+ * OCR processing mode enum
+ */
+export const OCRMode = z.enum(['fast', 'balanced', 'accurate']);
+/**
+ * Item type for provenance lookups
+ */
+export const ItemType = z.enum([
+    'document',
+    'ocr_result',
+    'chunk',
+    'embedding',
+    'image',
+    'comparison',
+    'clustering',
+    'form_fill',
+    'extraction',
+    'auto',
+]);
+/**
+ * Export format for provenance data
+ */
+export const ExportFormat = z.enum(['json', 'w3c-prov', 'csv']);
+/**
+ * Export scope for provenance exports
+ */
+export const ExportScope = z.enum(['document', 'database']);
+/**
+ * Configuration keys that can be set
+ */
+export const ConfigKey = z.enum([
+    'datalab_default_mode',
+    'datalab_max_concurrent',
+    'embedding_batch_size',
+    'embedding_device',
+    'chunk_size',
+    'chunk_overlap_percent',
+    'max_chunk_size',
+    'auto_cluster_enabled',
+    'auto_cluster_threshold',
+    'auto_cluster_algorithm',
+]);
+// ═══════════════════════════════════════════════════════════════════════════════
+// DATABASE MANAGEMENT SCHEMAS
+// ═══════════════════════════════════════════════════════════════════════════════
+/**
+ * Schema for creating a new database
+ */
+export const DatabaseCreateInput = z.object({
+    name: z
+        .string()
+        .min(1, 'Database name is required')
+        .max(64, 'Database name must be 64 characters or less')
+        .regex(/^[a-zA-Z0-9_-]+$/, 'Database name must contain only alphanumeric characters, underscores, and hyphens'),
+    description: z.string().max(500, 'Description must be 500 characters or less').optional(),
+    storage_path: z.string().optional(),
+});
+/**
+ * Schema for listing databases
+ */
+export const DatabaseListInput = z.object({
+    include_stats: z.boolean().default(false),
+});
+/**
+ * Schema for selecting a database
+ */
+export const DatabaseSelectInput = z.object({
+    database_name: z.string().min(1, 'Database name is required'),
+});
+/**
+ * Schema for getting database statistics
+ */
+export const DatabaseStatsInput = z.object({
+    database_name: z.string().optional(),
+});
+/**
+ * Schema for deleting a database
+ */
+export const DatabaseDeleteInput = z.object({
+    database_name: z.string().min(1, 'Database name is required'),
+    confirm: z.literal(true, {
+        errorMap: () => ({ message: 'Confirm must be true to delete database' }),
+    }),
+});
+// ═══════════════════════════════════════════════════════════════════════════════
+// DOCUMENT INGESTION SCHEMAS
+// ═══════════════════════════════════════════════════════════════════════════════
+/**
+ * Default supported file types for ingestion
+ */
+export const DEFAULT_FILE_TYPES = [
+    // Documents
+    'pdf',
+    'docx',
+    'doc',
+    'pptx',
+    'ppt',
+    'xlsx',
+    'xls',
+    // Images
+    'png',
+    'jpg',
+    'jpeg',
+    'tiff',
+    'tif',
+    'bmp',
+    'gif',
+    'webp',
+    // Text
+    'txt',
+    'csv',
+    'md',
+];
+/**
+ * Schema for ingesting a directory
+ */
+export const IngestDirectoryInput = z.object({
+    directory_path: z.string().min(1, 'Directory path is required'),
+    recursive: z.boolean().default(true),
+    file_types: z.array(z.string()).optional().default(DEFAULT_FILE_TYPES),
+});
+/**
+ * Schema for ingesting specific files
+ */
+export const IngestFilesInput = z.object({
+    file_paths: z
+        .array(z.string().min(1, 'File path cannot be empty'))
+        .min(1, 'At least one file path is required'),
+});
+/**
+ * Schema for processing pending documents
+ */
+export const ProcessPendingInput = z.object({
+    max_concurrent: z.number().int().min(1).max(10).default(3),
+    ocr_mode: OCRMode.optional(),
+    // Datalab API parameters
+    max_pages: z
+        .number()
+        .int()
+        .min(1)
+        .max(7000)
+        .optional()
+        .describe('Maximum pages to process per document (Datalab limit: 7000)'),
+    page_range: z
+        .string()
+        .regex(/^[0-9,\-\s]+$/)
+        .optional()
+        .describe('Specific pages to process, 0-indexed (e.g., "0-5,10")'),
+    skip_cache: z.boolean().optional().describe('Force reprocessing, skip Datalab cache'),
+    disable_image_extraction: z
+        .boolean()
+        .optional()
+        .describe('Skip image extraction for text-only processing'),
+    extras: z
+        .array(z.enum([
+        'track_changes',
+        'chart_understanding',
+        'extract_links',
+        'table_row_bboxes',
+        'infographic',
+        'new_block_types',
+    ]))
+        .optional()
+        .describe('Extra Datalab features to enable'),
+    page_schema: z
+        .string()
+        .optional()
+        .describe('JSON schema string for structured data extraction per page'),
+    additional_config: z
+        .record(z.unknown())
+        .optional()
+        .describe('Additional Datalab config: keep_pageheader_in_output, keep_pagefooter_in_output, keep_spreadsheet_formatting'),
+});
+/**
+ * Schema for checking OCR status
+ */
+export const OCRStatusInput = z.object({
+    document_id: z.string().optional(),
+    status_filter: z.enum(['pending', 'processing', 'complete', 'failed', 'all']).default('all'),
+});
+// ═══════════════════════════════════════════════════════════════════════════════
+// SEARCH SCHEMAS
+// ═══════════════════════════════════════════════════════════════════════════════
+/**
+ * Metadata filter for filtering search results by document metadata
+ */
+export const MetadataFilter = z
+    .object({
+    doc_title: z.string().optional(),
+    doc_author: z.string().optional(),
+    doc_subject: z.string().optional(),
+})
+    .optional();
+/**
+ * Page range filter for chunk-level filtering
+ */
+export const PageRangeFilter = z
+    .object({
+    min_page: z.number().int().min(1).optional(),
+    max_page: z.number().int().min(1).optional(),
+})
+    .optional();
+/**
+ * Search filters sub-object schema.
+ * Groups all filter parameters into a single `filters` object to reduce
+ * the top-level parameter count and improve schema clarity.
+ */
+export const SearchFilters = z.object({
+    document_filter: z.array(z.string()).optional()
+        .describe('Restrict results to specific document IDs'),
+    metadata_filter: MetadataFilter
+        .describe('Filter by document metadata (doc_title, doc_author, doc_subject)'),
+    cluster_id: z.string().optional()
+        .describe('Filter results to documents in this cluster'),
+    content_type_filter: z
+        .array(z.string())
+        .optional()
+        .describe('Filter by chunk content types (e.g., ["table", "code", "heading"])'),
+    section_path_filter: z
+        .string()
+        .optional()
+        .describe('Filter by section path prefix (e.g., "Section 3" matches "Section 3 > 3.1 > Definitions")'),
+    heading_filter: z
+        .string()
+        .optional()
+        .describe('Filter by heading context text (LIKE match)'),
+    page_range_filter: PageRangeFilter.describe('Filter results to specific page range'),
+    is_atomic_filter: z.boolean().optional()
+        .describe('When true, return only atomic chunks (complete tables, figures, code blocks). When false, exclude atomic chunks.'),
+    heading_level_filter: z.object({
+        min_level: z.number().int().min(1).max(6).optional(),
+        max_level: z.number().int().min(1).max(6).optional(),
+    }).optional().describe('Filter by heading level (1=h1 top-level, 6=h6 deepest)'),
+    min_page_count: z.number().int().min(1).optional()
+        .describe('Only include results from documents with at least this many pages'),
+    max_page_count: z.number().int().min(1).optional()
+        .describe('Only include results from documents with at most this many pages'),
+    table_columns_contain: z.string().optional()
+        .describe('Filter to table chunks whose column headers contain this text (case-insensitive match on stored table_columns in processing_params)'),
+    min_quality_score: z
+        .number()
+        .min(0.01)
+        .max(5)
+        .optional()
+        .describe('Minimum OCR quality score (0.01-5). Filters to documents with quality >= threshold. Use 0.01 for "all scored documents".'),
+}).optional().default({});
+/**
+ * Unified search schema - single schema for keyword, semantic, and hybrid search.
+ * Mode parameter selects the search strategy. Defaults that are always-on are
+ * hardcoded in the handler (quality_boost, expand_query, exclude_duplicate_chunks,
+ * exclude headers/footers, include cluster context).
+ *
+ * Filter parameters are grouped under `filters` to reduce top-level parameter count.
+ */
+export const SearchUnifiedInput = z.object({
+    // ── Core parameters ─────────────────────────────────────────────────────
+    query: z.string().min(1, 'Query is required').max(1000, 'Query must be 1000 characters or less'),
+    mode: z.enum(['keyword', 'semantic', 'hybrid']).default('hybrid')
+        .describe('Search mode: keyword (BM25), semantic (vector), or hybrid (BM25+semantic fusion). Default: hybrid.'),
+    limit: z.number().int().min(1).max(100).default(10),
+    include_provenance: z.boolean().default(false),
+    rerank: z
+        .boolean()
+        .default(false)
+        .describe('Re-rank results using local cross-encoder model for contextual relevance scoring'),
+    include_context_chunks: z.number().int().min(0).max(3).default(0)
+        .describe('Number of neighboring chunks to include before and after each result (0=none, max 3). Adds context_before and context_after arrays.'),
+    group_by_document: z.boolean().default(false)
+        .describe('Group results by source document with document-level statistics'),
+    // ── Filters (grouped) ──────────────────────────────────────────────────
+    filters: SearchFilters,
+    // ── Keyword-mode specific ───────────────────────────────────────────────
+    phrase_search: z.boolean().default(false)
+        .describe('(keyword mode) Treat query as exact phrase'),
+    include_highlight: z.boolean().default(true)
+        .describe('(keyword mode) Include highlighted snippets'),
+    // ── Semantic-mode specific ──────────────────────────────────────────────
+    similarity_threshold: z.number().min(0).max(1).default(0.7)
+        .describe('(semantic mode) Minimum similarity score (0-1)'),
+    // ── Hybrid-mode specific ────────────────────────────────────────────────
+    bm25_weight: z.number().min(0).max(2).default(1.0)
+        .describe('(hybrid mode) BM25 result weight'),
+    semantic_weight: z.number().min(0).max(2).default(1.0)
+        .describe('(hybrid mode) Semantic result weight'),
+    rrf_k: z.number().int().min(1).max(100).default(60)
+        .describe('(hybrid mode) RRF smoothing constant'),
+    auto_route: z.boolean().default(true)
+        .describe('(hybrid mode) Auto-adjust BM25/semantic weights based on query classification'),
+    // ── V7 Intelligence Optimization ──────────────────────────────────────
+    compact: z.boolean().default(false)
+        .describe('When true, return only essential fields per result (document_id, chunk_id, original_text, source_file_name, page_number, score, result_type) for ~77% token reduction'),
+    include_provenance_summary: z.boolean().default(false)
+        .describe('When true, add a one-line provenance_summary string to each result showing the data lineage chain'),
+});
+/**
+ * Schema for FTS5 index management
+ */
+export const FTSManageInput = z.object({
+    action: z.enum(['rebuild', 'status']),
+});
+// ═══════════════════════════════════════════════════════════════════════════════
+// DOCUMENT MANAGEMENT SCHEMAS
+// ═══════════════════════════════════════════════════════════════════════════════
+/**
+ * Schema for listing documents
+ */
+export const DocumentListInput = z.object({
+    status_filter: z.enum(['pending', 'processing', 'complete', 'failed']).optional(),
+    limit: z.number().int().min(1).max(1000).default(50),
+    offset: z.number().int().min(0).default(0),
+    created_after: z.string().datetime().optional()
+        .describe('Filter documents created after this ISO 8601 timestamp'),
+    created_before: z.string().datetime().optional()
+        .describe('Filter documents created before this ISO 8601 timestamp'),
+    file_type: z.string().optional()
+        .describe('Filter by file type (e.g., "pdf", "docx")'),
+});
+/**
+ * Schema for getting a specific document
+ */
+export const DocumentGetInput = z.object({
+    document_id: z.string().min(1, 'Document ID is required'),
+    include_text: z.boolean().default(false),
+    include_chunks: z.boolean().default(false),
+    include_blocks: z.boolean().default(false),
+    include_full_provenance: z.boolean().default(false),
+});
+/**
+ * Schema for deleting a document
+ */
+export const DocumentDeleteInput = z.object({
+    document_id: z.string().min(1, 'Document ID is required'),
+    confirm: z.literal(true, {
+        errorMap: () => ({ message: 'Confirm must be true to delete document' }),
+    }),
+});
+/**
+ * Schema for retrying failed documents
+ */
+export const RetryFailedInput = z.object({
+    document_id: z.string().min(1).optional(),
+});
+// ═══════════════════════════════════════════════════════════════════════════════
+// PROVENANCE SCHEMAS
+// ═══════════════════════════════════════════════════════════════════════════════
+/**
+ * Schema for getting provenance information
+ */
+export const ProvenanceGetInput = z.object({
+    item_id: z.string().min(1, 'Item ID is required'),
+    item_type: ItemType.default('auto'),
+});
+/**
+ * Schema for verifying provenance integrity
+ */
+export const ProvenanceVerifyInput = z.object({
+    item_id: z.string().min(1, 'Item ID is required'),
+    verify_content: z.boolean().default(true),
+    verify_chain: z.boolean().default(true),
+});
+/**
+ * Schema for exporting provenance data
+ */
+export const ProvenanceExportInput = z
+    .object({
+    scope: ExportScope,
+    document_id: z.string().optional(),
+    format: ExportFormat.default('json'),
+})
+    .refine((data) => data.scope !== 'document' || data.document_id !== undefined, {
+    message: 'document_id is required when scope is "document"',
+    path: ['document_id'],
+});
+// ═══════════════════════════════════════════════════════════════════════════════
+// CONFIG SCHEMAS
+// ═══════════════════════════════════════════════════════════════════════════════
+/**
+ * Schema for getting configuration
+ */
+export const ConfigGetInput = z.object({
+    key: ConfigKey.optional(),
+});
+/**
+ * Schema for setting configuration
+ */
+export const ConfigSetInput = z.object({
+    key: ConfigKey,
+    value: z.union([z.string(), z.number(), z.boolean()]),
+});
+// ═══════════════════════════════════════════════════════════════════════════════
+// PATH SANITIZATION
+// ═══════════════════════════════════════════════════════════════════════════════
+/**
+ * Build the default set of allowed base directories.
+ *
+ * SEC-002: Paths MUST always be validated against allowed directories.
+ * The default set covers all directories the system legitimately needs:
+ *   - The storage path (database location) from server config
+ *   - The user's home directory (documents live here)
+ *   - /tmp for temporary files
+ *   - The current working directory (project root)
+ *
+ * This function is called lazily so it picks up the current config at call time.
+ */
+function getDefaultAllowedBaseDirs() {
+    // Inline the default storage path computation to avoid circular dependency and
+    // module resolution failures (M-8: createRequire fails during vitest because
+    // it resolves .js from src/ where only .ts files exist). This matches the
+    // value in src/services/storage/database/helpers.ts DEFAULT_STORAGE_PATH.
+    const storagePath = process.env.OCR_PROVENANCE_DATABASES_PATH
+        || path.join(homedir(), '.ocr-provenance', 'databases');
+    const dirs = [
+        path.resolve(storagePath),
+        path.resolve(homedir()),
+        path.resolve('/tmp'),
+        path.resolve(process.cwd()),
+    ];
+    // OCR_PROVENANCE_ALLOWED_DIRS: comma-separated list of additional allowed directories.
+    // Used in Docker to allow read-only host mounts (e.g., /host).
+    const extraDirs = process.env.OCR_PROVENANCE_ALLOWED_DIRS;
+    if (extraDirs) {
+        for (const d of extraDirs.split(',')) {
+            const trimmed = d.trim();
+            if (trimmed) {
+                dirs.push(path.resolve(trimmed));
+            }
+        }
+    }
+    return dirs;
+}
+/**
+ * Sanitize a file path to prevent directory traversal attacks.
+ *
+ * SEC-002 ENFORCEMENT: Paths are ALWAYS validated against allowed directories.
+ * When no allowedBaseDirs are provided, a default set is used that covers
+ * the storage path, home directory, /tmp, and the current working directory.
+ *
+ * - Rejects null bytes
+ * - Resolves the path fully via path.resolve() to eliminate '..' segments
+ * - Verifies the resolved path starts with one of the allowed base directories
+ *
+ * @param filePath - The file path to sanitize
+ * @param allowedBaseDirs - Optional array of allowed base directories. When omitted,
+ *   defaults to [storagePath, homedir, /tmp, cwd] per SEC-002.
+ * @returns The resolved, safe path
+ * @throws ValidationError if the path contains null bytes or escapes allowed directories
+ */
+export function sanitizePath(filePath, allowedBaseDirs) {
+    if (filePath.includes('\0')) {
+        throw new ValidationError('Path contains null bytes');
+    }
+    const resolved = path.resolve(filePath);
+    // SEC-002: ALWAYS enforce path restrictions. Use defaults when none provided.
+    const baseDirs = (allowedBaseDirs && allowedBaseDirs.length > 0)
+        ? allowedBaseDirs
+        : getDefaultAllowedBaseDirs();
+    const resolvedBases = baseDirs.map((d) => path.resolve(d));
+    const withinAllowed = resolvedBases.some((base) => resolved === base || resolved.startsWith(base + path.sep));
+    if (!withinAllowed) {
+        throw new ValidationError(`Path "${resolved}" is outside allowed directories: ${resolvedBases.join(', ')}`);
+    }
+    return resolved;
+}
+// ═══════════════════════════════════════════════════════════════════════════════
+// SQL ESCAPING
+// ═══════════════════════════════════════════════════════════════════════════════
+/**
+ * Escape special characters for safe use in SQL LIKE clauses.
+ * Escapes '%', '_', and '\' characters.
+ *
+ * @param pattern - The raw string to escape
+ * @returns The escaped string safe for LIKE clause usage
+ */
+export function escapeLikePattern(pattern) {
+    return pattern.replace(/\\/g, '\\\\').replace(/%/g, '\\%').replace(/_/g, '\\_');
+}
+//# sourceMappingURL=validation.js.map

package/dist/utils/validation.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -0,0 +1,96 @@
+{
+  "name": "ocr-provenance-mcp",
+  "version": "1.0.0",
+  "description": "MCP server for document OCR processing, semantic search, document comparison, clustering, and provenance tracking",
+  "type": "module",
+  "main": "dist/index.js",
+  "exports": {
+    ".": "./dist/index.js"
+  },
+  "bin": {
+    "ocr-provenance-mcp": "dist/bin.js",
+    "ocr-provenance-mcp-http": "dist/bin-http.js",
+    "ocr-provenance-mcp-setup": "dist/bin-setup.js"
+  },
+  "files": [
+    "dist",
+    "python",
+    "!python/__pycache__",
+    "README.md",
+    "LICENSE",
+    ".env.example"
+  ],
+  "license": "SEE LICENSE IN LICENSE",
+  "author": "Chris Royse",
+  "homepage": "https://github.com/ChrisRoyse/OCR-Provenance#readme",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/ChrisRoyse/OCR-Provenance.git"
+  },
+  "bugs": {
+    "url": "https://github.com/ChrisRoyse/OCR-Provenance/issues"
+  },
+  "keywords": [
+    "mcp",
+    "ocr",
+    "provenance",
+    "semantic-search",
+    "document-clustering",
+    "sqlite",
+    "vector-search",
+    "claude",
+    "model-context-protocol"
+  ],
+  "scripts": {
+    "build": "tsc",
+    "build:fast": "tsc --noCheck",
+    "start": "node --max-semi-space-size=64 dist/index.js",
+    "start:http": "MCP_TRANSPORT=http node --max-semi-space-size=64 dist/bin-http.js",
+    "start:docker": "node --max-semi-space-size=64 dist/bin-http.js",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "test:unit": "vitest run tests/unit",
+    "test:integration": "vitest run tests/integration",
+    "test:manual": "vitest run --config vitest.config.all.ts tests/manual/",
+    "test:gpu": "vitest run tests/unit/embedding tests/gpu",
+    "test:all": "vitest run --config vitest.config.all.ts",
+    "lint": "eslint src/ tests/",
+    "lint:fix": "eslint src/ tests/ --fix",
+    "format": "prettier --write \"src/**/*.ts\" \"tests/**/*.ts\"",
+    "format:check": "prettier --check \"src/**/*.ts\" \"tests/**/*.ts\"",
+    "typecheck": "tsc --noEmit --skipLibCheck",
+    "lint:py": "cd python && ruff check . && ruff format --check .",
+    "lint:py:fix": "cd python && ruff check --fix . && ruff format .",
+    "lint:all": "npm run lint && npm run format:check && npm run lint:py",
+    "lint:all:fix": "npm run lint:fix && npm run format && npm run lint:py:fix",
+    "check": "npm run typecheck && npm run lint:all && npm run test"
+  },
+  "dependencies": {
+    "@google/genai": "^1.41.0",
+    "@modelcontextprotocol/sdk": "^1.0.0",
+    "better-sqlite3": "^11.0.0",
+    "diff": "^8.0.3",
+    "dotenv": "^17.2.3",
+    "python-shell": "^5.0.0",
+    "sqlite-vec": "0.1.7-alpha.2",
+    "uuid": "^10.0.0",
+    "zod": "^3.25.0"
+  },
+  "devDependencies": {
+    "@eslint/js": "^9.0.0",
+    "@types/better-sqlite3": "^7.0.0",
+    "@types/node": "^20.0.0",
+    "@types/uuid": "^10.0.0",
+    "@typescript-eslint/eslint-plugin": "^8.0.0",
+    "@typescript-eslint/parser": "^8.0.0",
+    "eslint": "^9.0.0",
+    "globals": "^15.0.0",
+    "prettier": "^3.3.0",
+    "typescript": "^5.5.0",
+    "typescript-eslint": "^8.0.0",
+    "vitest": "^2.0.0"
+  },
+  "engines": {
+    "node": ">=20.0.0"
+  }
+}