ocr-provenance-mcp 1.0.0

package/dist/services/storage/database/types.d.ts

@@ -0,0 +1,286 @@
+/**
+ * Type definitions for DatabaseService
+ *
+ * Contains all interfaces, enums, and row types used by the database service.
+ */
+import { DocumentStatus } from '../../../models/document.js';
+/**
+ * Database information interface
+ */
+export interface DatabaseInfo {
+    name: string;
+    path: string;
+    size_bytes: number;
+    created_at: string;
+    last_modified_at: string;
+    total_documents: number;
+    total_ocr_results: number;
+    total_chunks: number;
+    total_embeddings: number;
+}
+/**
+ * Database statistics interface
+ */
+export interface DatabaseStats {
+    name: string;
+    total_documents: number;
+    documents_by_status: {
+        pending: number;
+        processing: number;
+        complete: number;
+        failed: number;
+    };
+    total_ocr_results: number;
+    total_chunks: number;
+    chunks_by_embedding_status: {
+        pending: number;
+        complete: number;
+        failed: number;
+    };
+    total_embeddings: number;
+    total_images: number;
+    total_extractions: number;
+    total_form_fills: number;
+    total_comparisons: number;
+    total_clusters: number;
+    total_provenance: number;
+    storage_size_bytes: number;
+    avg_chunks_per_document: number;
+    avg_embeddings_per_chunk: number;
+    ocr_quality: {
+        avg: number | null;
+        min: number | null;
+        max: number | null;
+        scored_count: number;
+    };
+    costs: {
+        total_ocr_cost_cents: number;
+        total_form_fill_cost_cents: number;
+        total_cost_cents: number;
+    };
+}
+/**
+ * Document list options
+ */
+export interface ListDocumentsOptions {
+    status?: DocumentStatus;
+    limit?: number;
+    offset?: number;
+    /** Cursor for cursor-based pagination (base64url-encoded created_at + id) */
+    cursor?: string;
+}
+/**
+ * Error codes for database operations
+ */
+export declare enum DatabaseErrorCode {
+    DATABASE_NOT_FOUND = "DATABASE_NOT_FOUND",
+    DATABASE_ALREADY_EXISTS = "DATABASE_ALREADY_EXISTS",
+    DATABASE_LOCKED = "DATABASE_LOCKED",
+    DOCUMENT_NOT_FOUND = "DOCUMENT_NOT_FOUND",
+    OCR_RESULT_NOT_FOUND = "OCR_RESULT_NOT_FOUND",
+    CHUNK_NOT_FOUND = "CHUNK_NOT_FOUND",
+    EMBEDDING_NOT_FOUND = "EMBEDDING_NOT_FOUND",
+    IMAGE_NOT_FOUND = "IMAGE_NOT_FOUND",
+    PROVENANCE_NOT_FOUND = "PROVENANCE_NOT_FOUND",
+    FOREIGN_KEY_VIOLATION = "FOREIGN_KEY_VIOLATION",
+    SCHEMA_MISMATCH = "SCHEMA_MISMATCH",
+    EXTENSION_LOAD_FAILED = "EXTENSION_LOAD_FAILED",
+    PERMISSION_DENIED = "PERMISSION_DENIED",
+    INVALID_NAME = "INVALID_NAME"
+}
+/**
+ * Custom error class for database operations
+ */
+export declare class DatabaseError extends Error {
+    readonly code: DatabaseErrorCode;
+    readonly cause?: unknown | undefined;
+    constructor(message: string, code: DatabaseErrorCode, cause?: unknown | undefined);
+}
+/**
+ * Database row type for metadata
+ */
+export interface MetadataRow {
+    database_name: string;
+    database_version: string;
+    created_at: string;
+    last_modified_at: string;
+    total_documents: number;
+    total_ocr_results: number;
+    total_chunks: number;
+    total_embeddings: number;
+}
+/**
+ * Database row type for documents
+ */
+export interface DocumentRow {
+    id: string;
+    file_path: string;
+    file_name: string;
+    file_hash: string;
+    file_size: number;
+    file_type: string;
+    status: string;
+    page_count: number | null;
+    provenance_id: string;
+    created_at: string;
+    modified_at: string | null;
+    ocr_completed_at: string | null;
+    error_message: string | null;
+    doc_title: string | null;
+    doc_author: string | null;
+    doc_subject: string | null;
+    datalab_file_id: string | null;
+}
+/**
+ * Database row type for OCR results
+ */
+export interface OCRResultRow {
+    id: string;
+    provenance_id: string;
+    document_id: string;
+    extracted_text: string;
+    text_length: number;
+    datalab_request_id: string;
+    datalab_mode: string;
+    parse_quality_score: number | null;
+    page_count: number;
+    cost_cents: number | null;
+    content_hash: string;
+    processing_started_at: string;
+    processing_completed_at: string;
+    processing_duration_ms: number;
+    json_blocks: string | null;
+    extras_json: string | null;
+}
+/**
+ * Database row type for chunks
+ */
+export interface ChunkRow {
+    id: string;
+    document_id: string;
+    ocr_result_id: string;
+    text: string;
+    text_hash: string;
+    chunk_index: number;
+    character_start: number;
+    character_end: number;
+    page_number: number | null;
+    page_range: string | null;
+    overlap_previous: number;
+    overlap_next: number;
+    provenance_id: string;
+    created_at: string;
+    embedding_status: string;
+    embedded_at: string | null;
+    ocr_quality_score: number | null;
+    heading_context: string | null;
+    heading_level: number | null;
+    section_path: string | null;
+    content_types: string | null;
+    is_atomic: number;
+    chunking_strategy: string;
+}
+/**
+ * Database row type for embeddings (without vector)
+ * chunk_id is for text embeddings, image_id is for VLM description embeddings,
+ * extraction_id is for extraction embeddings.
+ * At least one of chunk_id, image_id, or extraction_id must be set.
+ */
+export interface EmbeddingRow {
+    id: string;
+    chunk_id: string | null;
+    image_id: string | null;
+    extraction_id: string | null;
+    document_id: string;
+    original_text: string;
+    original_text_length: number;
+    source_file_path: string;
+    source_file_name: string;
+    source_file_hash: string;
+    page_number: number | null;
+    page_range: string | null;
+    character_start: number;
+    character_end: number;
+    chunk_index: number;
+    total_chunks: number;
+    model_name: string;
+    model_version: string;
+    task_type: string;
+    inference_mode: string;
+    gpu_device: string | null;
+    provenance_id: string;
+    content_hash: string;
+    created_at: string;
+    generation_duration_ms: number | null;
+}
+/**
+ * Database row type for provenance
+ */
+export interface ProvenanceRow {
+    id: string;
+    type: string;
+    created_at: string;
+    processed_at: string;
+    source_file_created_at: string | null;
+    source_file_modified_at: string | null;
+    source_type: string;
+    source_path: string | null;
+    source_id: string | null;
+    root_document_id: string;
+    location: string | null;
+    content_hash: string;
+    input_hash: string | null;
+    file_hash: string | null;
+    processor: string;
+    processor_version: string;
+    processing_params: string;
+    processing_duration_ms: number | null;
+    processing_quality_score: number | null;
+    parent_id: string | null;
+    parent_ids: string;
+    chain_depth: number;
+    chain_path: string | null;
+}
+/**
+ * Database row type for images
+ */
+export interface ImageRow {
+    id: string;
+    document_id: string;
+    ocr_result_id: string;
+    page_number: number;
+    bbox_x: number;
+    bbox_y: number;
+    bbox_width: number;
+    bbox_height: number;
+    image_index: number;
+    format: string;
+    width: number;
+    height: number;
+    extracted_path: string | null;
+    file_size: number | null;
+    vlm_status: string;
+    vlm_description: string | null;
+    vlm_structured_data: string | null;
+    vlm_embedding_id: string | null;
+    vlm_model: string | null;
+    vlm_confidence: number | null;
+    vlm_processed_at: string | null;
+    vlm_tokens_used: number | null;
+    context_text: string | null;
+    provenance_id: string | null;
+    created_at: string;
+    error_message: string | null;
+    block_type: string | null;
+    is_header_footer: number;
+    content_hash: string | null;
+}
+/**
+ * Options for listing images
+ */
+export interface ListImagesOptions {
+    vlmStatus?: 'pending' | 'processing' | 'complete' | 'failed';
+    limit?: number;
+    offset?: number;
+}
+//# sourceMappingURL=types.d.ts.map

package/dist/services/storage/database/types.d.ts.map

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package/dist/services/storage/database/types.js

@@ -0,0 +1,39 @@
+/**
+ * Type definitions for DatabaseService
+ *
+ * Contains all interfaces, enums, and row types used by the database service.
+ */
+/**
+ * Error codes for database operations
+ */
+export var DatabaseErrorCode;
+(function (DatabaseErrorCode) {
+    DatabaseErrorCode["DATABASE_NOT_FOUND"] = "DATABASE_NOT_FOUND";
+    DatabaseErrorCode["DATABASE_ALREADY_EXISTS"] = "DATABASE_ALREADY_EXISTS";
+    DatabaseErrorCode["DATABASE_LOCKED"] = "DATABASE_LOCKED";
+    DatabaseErrorCode["DOCUMENT_NOT_FOUND"] = "DOCUMENT_NOT_FOUND";
+    DatabaseErrorCode["OCR_RESULT_NOT_FOUND"] = "OCR_RESULT_NOT_FOUND";
+    DatabaseErrorCode["CHUNK_NOT_FOUND"] = "CHUNK_NOT_FOUND";
+    DatabaseErrorCode["EMBEDDING_NOT_FOUND"] = "EMBEDDING_NOT_FOUND";
+    DatabaseErrorCode["IMAGE_NOT_FOUND"] = "IMAGE_NOT_FOUND";
+    DatabaseErrorCode["PROVENANCE_NOT_FOUND"] = "PROVENANCE_NOT_FOUND";
+    DatabaseErrorCode["FOREIGN_KEY_VIOLATION"] = "FOREIGN_KEY_VIOLATION";
+    DatabaseErrorCode["SCHEMA_MISMATCH"] = "SCHEMA_MISMATCH";
+    DatabaseErrorCode["EXTENSION_LOAD_FAILED"] = "EXTENSION_LOAD_FAILED";
+    DatabaseErrorCode["PERMISSION_DENIED"] = "PERMISSION_DENIED";
+    DatabaseErrorCode["INVALID_NAME"] = "INVALID_NAME";
+})(DatabaseErrorCode || (DatabaseErrorCode = {}));
+/**
+ * Custom error class for database operations
+ */
+export class DatabaseError extends Error {
+    code;
+    cause;
+    constructor(message, code, cause) {
+        super(message);
+        this.code = code;
+        this.cause = cause;
+        this.name = 'DatabaseError';
+    }
+}
+//# sourceMappingURL=types.js.map

package/dist/services/storage/database/types.js.map

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package/dist/services/storage/database/upload-operations.d.ts

@@ -0,0 +1,71 @@
+/**
+ * Upload operations for DatabaseService
+ *
+ * Handles all CRUD operations for uploaded_files table
+ * tracking Datalab cloud file uploads.
+ */
+import Database from 'better-sqlite3';
+import { UploadedFile } from '../../../models/uploaded-file.js';
+/**
+ * Insert an uploaded file record
+ *
+ * @param db - Database connection
+ * @param data - Uploaded file data
+ * @returns string - The uploaded file ID
+ */
+export declare function insertUploadedFile(db: Database.Database, data: UploadedFile): UploadedFile;
+/**
+ * Get an uploaded file by ID
+ *
+ * @param db - Database connection
+ * @param id - Uploaded file ID
+ * @returns UploadedFile | null
+ */
+export declare function getUploadedFile(db: Database.Database, id: string): UploadedFile | null;
+/**
+ * Get an uploaded file by file hash (for deduplication)
+ *
+ * @param db - Database connection
+ * @param fileHash - SHA-256 hash of the file
+ * @returns UploadedFile | null - The first matching upload or null
+ */
+export declare function getUploadedFileByHash(db: Database.Database, fileHash: string): UploadedFile | null;
+/**
+ * List uploaded files with optional filtering
+ *
+ * @param db - Database connection
+ * @param options - Optional filter options (status, limit, offset)
+ * @returns UploadedFile[] - Array of uploaded files
+ */
+export declare function listUploadedFiles(db: Database.Database, options?: {
+    status?: string;
+    limit?: number;
+    offset?: number;
+}): UploadedFile[];
+/**
+ * Update uploaded file status
+ *
+ * @param db - Database connection
+ * @param id - Uploaded file ID
+ * @param status - New upload status
+ * @param errorMessage - Optional error message (for 'failed' status)
+ */
+export declare function updateUploadedFileStatus(db: Database.Database, id: string, status: 'pending' | 'uploading' | 'confirming' | 'complete' | 'failed', errorMessage?: string): void;
+/**
+ * Update uploaded file with Datalab file ID and reference after successful upload
+ *
+ * @param db - Database connection
+ * @param id - Uploaded file ID
+ * @param datalabFileId - Datalab cloud file ID
+ * @param datalabReference - Datalab reference string
+ */
+export declare function updateUploadedFileDatalabInfo(db: Database.Database, id: string, datalabFileId: string, datalabReference: string | null): void;
+/**
+ * Delete an uploaded file record
+ *
+ * @param db - Database connection
+ * @param id - Uploaded file ID
+ * @returns boolean - true if a record was deleted
+ */
+export declare function deleteUploadedFile(db: Database.Database, id: string): boolean;
+//# sourceMappingURL=upload-operations.d.ts.map

package/dist/services/storage/database/upload-operations.d.ts.map

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package/dist/services/storage/database/upload-operations.js

@@ -0,0 +1,124 @@
+/**
+ * Upload operations for DatabaseService
+ *
+ * Handles all CRUD operations for uploaded_files table
+ * tracking Datalab cloud file uploads.
+ */
+import { runWithForeignKeyCheck } from './helpers.js';
+/**
+ * Insert an uploaded file record
+ *
+ * @param db - Database connection
+ * @param data - Uploaded file data
+ * @returns string - The uploaded file ID
+ */
+export function insertUploadedFile(db, data) {
+    const stmt = db.prepare(`
+    INSERT INTO uploaded_files (
+      id, local_path, file_name, file_hash, file_size, content_type,
+      datalab_file_id, datalab_reference, upload_status, error_message,
+      created_at, completed_at, provenance_id
+    ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+  `);
+    runWithForeignKeyCheck(stmt, [
+        data.id,
+        data.local_path,
+        data.file_name,
+        data.file_hash,
+        data.file_size,
+        data.content_type,
+        data.datalab_file_id,
+        data.datalab_reference,
+        data.upload_status,
+        data.error_message,
+        data.created_at,
+        data.completed_at,
+        data.provenance_id,
+    ], `inserting uploaded file: FK violation for provenance_id="${data.provenance_id}"`);
+    return data;
+}
+/**
+ * Get an uploaded file by ID
+ *
+ * @param db - Database connection
+ * @param id - Uploaded file ID
+ * @returns UploadedFile | null
+ */
+export function getUploadedFile(db, id) {
+    return (db.prepare('SELECT * FROM uploaded_files WHERE id = ?').get(id) ??
+        null);
+}
+/**
+ * Get an uploaded file by file hash (for deduplication)
+ *
+ * @param db - Database connection
+ * @param fileHash - SHA-256 hash of the file
+ * @returns UploadedFile | null - The first matching upload or null
+ */
+export function getUploadedFileByHash(db, fileHash) {
+    return (db
+        .prepare('SELECT * FROM uploaded_files WHERE file_hash = ? AND upload_status = ? ORDER BY created_at DESC LIMIT 1')
+        .get(fileHash, 'complete') ?? null);
+}
+/**
+ * List uploaded files with optional filtering
+ *
+ * @param db - Database connection
+ * @param options - Optional filter options (status, limit, offset)
+ * @returns UploadedFile[] - Array of uploaded files
+ */
+export function listUploadedFiles(db, options) {
+    let query = 'SELECT * FROM uploaded_files';
+    const params = [];
+    if (options?.status) {
+        query += ' WHERE upload_status = ?';
+        params.push(options.status);
+    }
+    query += ' ORDER BY created_at DESC';
+    if (options?.limit !== undefined) {
+        query += ' LIMIT ?';
+        params.push(options.limit);
+    }
+    if (options?.offset !== undefined) {
+        if (options?.limit === undefined) {
+            query += ' LIMIT 10000'; // bounded default
+        }
+        query += ' OFFSET ?';
+        params.push(options.offset);
+    }
+    return db.prepare(query).all(...params);
+}
+/**
+ * Update uploaded file status
+ *
+ * @param db - Database connection
+ * @param id - Uploaded file ID
+ * @param status - New upload status
+ * @param errorMessage - Optional error message (for 'failed' status)
+ */
+export function updateUploadedFileStatus(db, id, status, errorMessage) {
+    const completedAt = status === 'complete' ? new Date().toISOString() : null;
+    db.prepare('UPDATE uploaded_files SET upload_status = ?, error_message = ?, completed_at = COALESCE(?, completed_at) WHERE id = ?').run(status, errorMessage ?? null, completedAt, id);
+}
+/**
+ * Update uploaded file with Datalab file ID and reference after successful upload
+ *
+ * @param db - Database connection
+ * @param id - Uploaded file ID
+ * @param datalabFileId - Datalab cloud file ID
+ * @param datalabReference - Datalab reference string
+ */
+export function updateUploadedFileDatalabInfo(db, id, datalabFileId, datalabReference) {
+    db.prepare('UPDATE uploaded_files SET datalab_file_id = ?, datalab_reference = ? WHERE id = ?').run(datalabFileId, datalabReference, id);
+}
+/**
+ * Delete an uploaded file record
+ *
+ * @param db - Database connection
+ * @param id - Uploaded file ID
+ * @returns boolean - true if a record was deleted
+ */
+export function deleteUploadedFile(db, id) {
+    return db.prepare('DELETE FROM uploaded_files WHERE id = ?').run(id).changes > 0;
+}
+//# sourceMappingURL=upload-operations.js.map

package/dist/services/storage/database/upload-operations.js.map

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package/dist/services/storage/database/user-operations.d.ts

@@ -0,0 +1,102 @@
+/**
+ * User and Audit Log Operations for DatabaseService
+ *
+ * Provides CRUD operations for users and audit_log tables.
+ * Users represent identity for multi-user collaboration.
+ * Audit log tracks user actions for compliance and accountability.
+ *
+ * CRITICAL: NEVER use console.log() - stdout is reserved for JSON-RPC protocol.
+ *
+ * @module database/user-operations
+ */
+import type Database from 'better-sqlite3';
+export interface User {
+    id: string;
+    external_id: string | null;
+    display_name: string;
+    email: string | null;
+    role: string;
+    created_at: string;
+    last_active_at: string | null;
+    metadata_json: string;
+}
+export interface AuditLogEntry {
+    id: number;
+    user_id: string | null;
+    session_id: string | null;
+    action: string;
+    entity_type: string | null;
+    entity_id: string | null;
+    details_json: string;
+    ip_address: string | null;
+    created_at: string;
+}
+export interface CreateUserParams {
+    display_name: string;
+    external_id?: string | null;
+    email?: string | null;
+    role?: string;
+    metadata_json?: string;
+}
+export interface InsertAuditLogParams {
+    user_id: string | null;
+    session_id: string | null;
+    action: string;
+    entity_type?: string | null;
+    entity_id?: string | null;
+    details_json?: string;
+    ip_address?: string | null;
+}
+export interface AuditLogQueryFilters {
+    user_id?: string;
+    action?: string;
+    entity_type?: string;
+    entity_id?: string;
+    date_from?: string;
+    date_to?: string;
+    limit?: number;
+    offset?: number;
+}
+export interface ListUsersOptions {
+    role?: string;
+    limit?: number;
+    offset?: number;
+}
+/**
+ * Create a new user.
+ * ID is auto-generated by SQLite (lower(hex(randomblob(16)))).
+ *
+ * @returns The created user record
+ * @throws Error if external_id already exists (UNIQUE constraint)
+ */
+export declare function createUser(db: Database.Database, params: CreateUserParams): User;
+/**
+ * Get a user by internal ID
+ */
+export declare function getUser(db: Database.Database, userId: string): User | null;
+/**
+ * Get a user by external ID
+ */
+export declare function getUserByExternalId(db: Database.Database, externalId: string): User | null;
+/**
+ * Update the last_active_at timestamp for a user
+ */
+export declare function updateUserActivity(db: Database.Database, userId: string): void;
+/**
+ * List users with optional filters
+ */
+export declare function listUsers(db: Database.Database, options?: ListUsersOptions): User[];
+/**
+ * Insert an entry into the audit log
+ */
+export declare function insertAuditLog(db: Database.Database, params: InsertAuditLogParams): number;
+/**
+ * Query audit log with filters
+ *
+ * @returns Array of matching audit log entries, ordered by created_at DESC
+ */
+export declare function queryAuditLog(db: Database.Database, filters: AuditLogQueryFilters): {
+    entries: AuditLogEntry[];
+    total: number;
+};
+//# sourceMappingURL=user-operations.d.ts.map

package/dist/services/storage/database/user-operations.d.ts.map

@@ -0,0 +1 @@
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