zotero-bridge 1.0.1

package/dist/database.js

@@ -0,0 +1,1031 @@
+/**
+ * ZoteroBridge - Zotero SQLite Database Connection Module
+ *
+ * This module provides direct access to Zotero's SQLite database (zotero.sqlite)
+ * for reading and writing reference data.
+ *
+ * Uses sql.js for pure JavaScript SQLite support (no native compilation required)
+ *
+ * @author Combjellyshen
+ */
+import initSqlJs from 'sql.js';
+import { existsSync, readFileSync, writeFileSync } from 'fs';
+import { homedir } from 'os';
+import { join } from 'path';
+export class ZoteroDatabase {
+    db = null;
+    dbPath;
+    readonly;
+    SQL = null;
+    constructor(dbPath, readonly = false) {
+        this.dbPath = dbPath || this.findDefaultZoteroDB();
+        this.readonly = readonly;
+    }
+    /**
+     * Find the default Zotero database path based on OS
+     */
+    findDefaultZoteroDB() {
+        const home = homedir();
+        const possiblePaths = [];
+        // Windows paths
+        if (process.platform === 'win32') {
+            possiblePaths.push(join(home, 'Zotero', 'zotero.sqlite'), join(process.env.APPDATA || '', 'Zotero', 'Zotero', 'Profiles'));
+        }
+        // macOS paths
+        else if (process.platform === 'darwin') {
+            possiblePaths.push(join(home, 'Zotero', 'zotero.sqlite'), join(home, 'Library', 'Application Support', 'Zotero', 'Profiles'));
+        }
+        // Linux paths
+        else {
+            possiblePaths.push(join(home, 'Zotero', 'zotero.sqlite'), join(home, '.zotero', 'zotero'));
+        }
+        // Check each path
+        for (const p of possiblePaths) {
+            if (existsSync(p)) {
+                return p;
+            }
+        }
+        // Default fallback
+        return join(home, 'Zotero', 'zotero.sqlite');
+    }
+    /**
+     * Connect to the Zotero database
+     */
+    async connect() {
+        if (this.db) {
+            return;
+        }
+        if (!existsSync(this.dbPath)) {
+            throw new Error(`Zotero database not found at: ${this.dbPath}`);
+        }
+        // Initialize sql.js
+        this.SQL = await initSqlJs();
+        // Read the database file
+        const buffer = readFileSync(this.dbPath);
+        const db = new this.SQL.Database(buffer);
+        this.db = db;
+        // Enable foreign keys
+        db.run('PRAGMA foreign_keys = ON');
+    }
+    /**
+     * Save changes to the database file
+     */
+    save() {
+        if (!this.db || this.readonly) {
+            return;
+        }
+        const data = this.db.export();
+        const buffer = Buffer.from(data);
+        writeFileSync(this.dbPath, buffer);
+    }
+    /**
+     * Disconnect from the database
+     */
+    disconnect() {
+        if (this.db) {
+            if (!this.readonly) {
+                this.save();
+            }
+            this.db.close();
+            this.db = null;
+        }
+    }
+    /**
+     * Get the database instance
+     */
+    async getDB() {
+        if (!this.db) {
+            await this.connect();
+        }
+        return this.db;
+    }
+    /**
+     * Get database path
+     */
+    getPath() {
+        return this.dbPath;
+    }
+    /**
+     * Execute a query and return all results
+     */
+    queryAll(sql, params = []) {
+        if (!this.db) {
+            throw new Error('Database not connected');
+        }
+        const stmt = this.db.prepare(sql);
+        stmt.bind(params);
+        const results = [];
+        while (stmt.step()) {
+            const row = stmt.getAsObject();
+            results.push(row);
+        }
+        stmt.free();
+        return results;
+    }
+    /**
+     * Execute a query and return the first result
+     */
+    queryOne(sql, params = []) {
+        const results = this.queryAll(sql, params);
+        return results.length > 0 ? results[0] : null;
+    }
+    /**
+     * Execute a statement (INSERT, UPDATE, DELETE)
+     */
+    execute(sql, params = []) {
+        if (!this.db) {
+            throw new Error('Database not connected');
+        }
+        this.db.run(sql, params);
+        const changes = this.db.getRowsModified();
+        const lastId = this.queryOne('SELECT last_insert_rowid() as id');
+        return {
+            changes,
+            lastInsertRowid: lastId?.id || 0
+        };
+    }
+    // ============================================
+    // Collection (Directory) Operations
+    // ============================================
+    /**
+     * Get all collections
+     */
+    getCollections(libraryID = 1) {
+        return this.queryAll(`
+      SELECT collectionID, collectionName, parentCollectionID, key, libraryID
+      FROM collections
+      WHERE libraryID = ?
+      ORDER BY collectionName
+    `, [libraryID]);
+    }
+    /**
+     * Get collection by ID
+     */
+    getCollectionById(collectionID) {
+        return this.queryOne(`
+      SELECT collectionID, collectionName, parentCollectionID, key, libraryID
+      FROM collections
+      WHERE collectionID = ?
+    `, [collectionID]);
+    }
+    /**
+     * Get collection by name
+     */
+    getCollectionByName(name, libraryID = 1) {
+        return this.queryOne(`
+      SELECT collectionID, collectionName, parentCollectionID, key, libraryID
+      FROM collections
+      WHERE collectionName = ? AND libraryID = ?
+    `, [name, libraryID]);
+    }
+    /**
+     * Get subcollections of a collection
+     */
+    getSubcollections(parentCollectionID) {
+        return this.queryAll(`
+      SELECT collectionID, collectionName, parentCollectionID, key, libraryID
+      FROM collections
+      WHERE parentCollectionID = ?
+      ORDER BY collectionName
+    `, [parentCollectionID]);
+    }
+    /**
+     * Create a new collection
+     */
+    createCollection(name, parentCollectionID = null, libraryID = 1) {
+        const key = this.generateKey();
+        const result = this.execute(`
+      INSERT INTO collections (collectionName, parentCollectionID, libraryID, key, version)
+      VALUES (?, ?, ?, ?, 0)
+    `, [name, parentCollectionID, libraryID, key]);
+        if (!this.readonly) {
+            this.save();
+        }
+        return result.lastInsertRowid;
+    }
+    /**
+     * Rename a collection
+     */
+    renameCollection(collectionID, newName) {
+        const result = this.execute(`
+      UPDATE collections
+      SET collectionName = ?, version = version + 1
+      WHERE collectionID = ?
+    `, [newName, collectionID]);
+        if (!this.readonly && result.changes > 0) {
+            this.save();
+        }
+        return result.changes > 0;
+    }
+    /**
+     * Move a collection to a new parent
+     */
+    moveCollection(collectionID, newParentID) {
+        const result = this.execute(`
+      UPDATE collections
+      SET parentCollectionID = ?, version = version + 1
+      WHERE collectionID = ?
+    `, [newParentID, collectionID]);
+        if (!this.readonly && result.changes > 0) {
+            this.save();
+        }
+        return result.changes > 0;
+    }
+    /**
+     * Delete a collection
+     */
+    deleteCollection(collectionID) {
+        // First, remove all items from collection
+        this.execute('DELETE FROM collectionItems WHERE collectionID = ?', [collectionID]);
+        // Then delete the collection
+        const result = this.execute('DELETE FROM collections WHERE collectionID = ?', [collectionID]);
+        if (!this.readonly && result.changes > 0) {
+            this.save();
+        }
+        return result.changes > 0;
+    }
+    // ============================================
+    // Tag Operations
+    // ============================================
+    /**
+     * Get all tags with usage count
+     */
+    getTags() {
+        return this.queryAll(`
+      SELECT t.tagID, t.name, COUNT(it.itemID) as itemCount
+      FROM tags t
+      LEFT JOIN itemTags it ON t.tagID = it.tagID
+      GROUP BY t.tagID, t.name
+      ORDER BY t.name
+    `);
+    }
+    /**
+     * Get tag by name
+     */
+    getTagByName(name) {
+        return this.queryOne('SELECT tagID, name FROM tags WHERE name = ?', [name]);
+    }
+    /**
+     * Create a new tag
+     */
+    createTag(name, _type = 0) {
+        // Check if tag exists
+        const existing = this.getTagByName(name);
+        if (existing) {
+            return existing.tagID;
+        }
+        const result = this.execute('INSERT INTO tags (name) VALUES (?)', [name]);
+        if (!this.readonly) {
+            this.save();
+        }
+        return result.lastInsertRowid;
+    }
+    /**
+     * Add tag to item
+     */
+    addTagToItem(itemID, tagName, type = 0) {
+        // Get or create tag
+        const tagID = this.createTag(tagName, type);
+        // Check if already tagged
+        const existing = this.queryOne(`
+      SELECT 1 FROM itemTags WHERE itemID = ? AND tagID = ?
+    `, [itemID, tagID]);
+        if (existing) {
+            return false;
+        }
+        this.execute('INSERT INTO itemTags (itemID, tagID) VALUES (?, ?)', [itemID, tagID]);
+        if (!this.readonly) {
+            this.save();
+        }
+        return true;
+    }
+    /**
+     * Remove tag from item
+     */
+    removeTagFromItem(itemID, tagName) {
+        const tag = this.getTagByName(tagName);
+        if (!tag) {
+            return false;
+        }
+        const result = this.execute('DELETE FROM itemTags WHERE itemID = ? AND tagID = ?', [itemID, tag.tagID]);
+        if (!this.readonly && result.changes > 0) {
+            this.save();
+        }
+        return result.changes > 0;
+    }
+    /**
+     * Get all tags for an item
+     * Note: type is in itemTags table, not tags table
+     */
+    getItemTags(itemID) {
+        return this.queryAll(`
+      SELECT t.tagID, t.name, it.type
+      FROM tags t
+      JOIN itemTags it ON t.tagID = it.tagID
+      WHERE it.itemID = ?
+      ORDER BY t.name
+    `, [itemID]);
+    }
+    // ============================================
+    // Item Operations
+    // ============================================
+    /**
+     * Get items in a collection
+     */
+    getCollectionItems(collectionID) {
+        return this.queryAll(`
+      SELECT i.itemID, i.key, i.itemTypeID, i.dateAdded, i.dateModified, i.libraryID
+      FROM items i
+      JOIN collectionItems ci ON i.itemID = ci.itemID
+      WHERE ci.collectionID = ?
+    `, [collectionID]);
+    }
+    /**
+     * Add item to collection
+     */
+    addItemToCollection(itemID, collectionID) {
+        // Check if already in collection
+        const existing = this.queryOne(`
+      SELECT 1 FROM collectionItems WHERE itemID = ? AND collectionID = ?
+    `, [itemID, collectionID]);
+        if (existing) {
+            return false;
+        }
+        this.execute('INSERT INTO collectionItems (itemID, collectionID) VALUES (?, ?)', [itemID, collectionID]);
+        if (!this.readonly) {
+            this.save();
+        }
+        return true;
+    }
+    /**
+     * Remove item from collection
+     */
+    removeItemFromCollection(itemID, collectionID) {
+        const result = this.execute('DELETE FROM collectionItems WHERE itemID = ? AND collectionID = ?', [itemID, collectionID]);
+        if (!this.readonly && result.changes > 0) {
+            this.save();
+        }
+        return result.changes > 0;
+    }
+    /**
+     * Get item by key
+     */
+    getItemByKey(key) {
+        return this.queryOne(`
+      SELECT itemID, key, itemTypeID, dateAdded, dateModified, libraryID
+      FROM items
+      WHERE key = ?
+    `, [key]);
+    }
+    /**
+     * Search items by title
+     */
+    searchItems(query, limit = 50, libraryID = 1) {
+        return this.queryAll(`
+      SELECT DISTINCT i.itemID, i.key, i.itemTypeID, i.dateAdded, i.dateModified,
+             iv.value as title
+      FROM items i
+      JOIN itemData id ON i.itemID = id.itemID
+      JOIN itemDataValues iv ON id.valueID = iv.valueID
+      JOIN fields f ON id.fieldID = f.fieldID
+      WHERE f.fieldName = 'title' 
+        AND iv.value LIKE ?
+        AND i.libraryID = ?
+      ORDER BY i.dateModified DESC
+      LIMIT ?
+    `, [`%${query}%`, libraryID, limit]);
+    }
+    /**
+     * Get item details with all fields
+     */
+    getItemDetails(itemID) {
+        // Get item basic info
+        const item = this.queryOne(`
+      SELECT itemID, key, itemTypeID, dateAdded, dateModified, libraryID
+      FROM items WHERE itemID = ?
+    `, [itemID]);
+        if (!item) {
+            return {};
+        }
+        // Get all item data fields
+        const fields = this.queryAll(`
+      SELECT f.fieldName, iv.value
+      FROM itemData id
+      JOIN fields f ON id.fieldID = f.fieldID
+      JOIN itemDataValues iv ON id.valueID = iv.valueID
+      WHERE id.itemID = ?
+    `, [itemID]);
+        // Get creators
+        const creators = this.queryAll(`
+      SELECT c.firstName, c.lastName, ct.creatorType, ic.orderIndex
+      FROM itemCreators ic
+      JOIN creators c ON ic.creatorID = c.creatorID
+      JOIN creatorTypes ct ON ic.creatorTypeID = ct.creatorTypeID
+      WHERE ic.itemID = ?
+      ORDER BY ic.orderIndex
+    `, [itemID]);
+        // Get tags
+        const tags = this.getItemTags(itemID);
+        // Get attachments
+        const attachments = this.queryAll(`
+      SELECT ia.itemID, ia.path, ia.contentType
+      FROM itemAttachments ia
+      WHERE ia.parentItemID = ?
+    `, [itemID]);
+        const result = {
+            ...item,
+            creators,
+            tags,
+            attachments
+        };
+        // Add field values
+        for (const field of fields) {
+            result[field.fieldName] = field.value;
+        }
+        return result;
+    }
+    // ============================================
+    // Item Abstract/Note Operations
+    // ============================================
+    /**
+     * Get item abstract
+     */
+    getItemAbstract(itemID) {
+        const result = this.queryOne(`
+      SELECT iv.value
+      FROM itemData id
+      JOIN fields f ON id.fieldID = f.fieldID
+      JOIN itemDataValues iv ON id.valueID = iv.valueID
+      WHERE id.itemID = ? AND f.fieldName = 'abstractNote'
+    `, [itemID]);
+        return result?.value || null;
+    }
+    /**
+     * Set item abstract
+     */
+    setItemAbstract(itemID, abstract) {
+        // Get abstractNote field ID
+        const field = this.queryOne("SELECT fieldID FROM fields WHERE fieldName = 'abstractNote'");
+        if (!field) {
+            return false;
+        }
+        // Get or create value
+        let valueRow = this.queryOne('SELECT valueID FROM itemDataValues WHERE value = ?', [abstract]);
+        if (!valueRow) {
+            const result = this.execute('INSERT INTO itemDataValues (value) VALUES (?)', [abstract]);
+            valueRow = { valueID: result.lastInsertRowid };
+        }
+        // Check if item already has abstract
+        const existing = this.queryOne(`
+      SELECT 1 FROM itemData WHERE itemID = ? AND fieldID = ?
+    `, [itemID, field.fieldID]);
+        if (existing) {
+            // Update
+            this.execute('UPDATE itemData SET valueID = ? WHERE itemID = ? AND fieldID = ?', [valueRow.valueID, itemID, field.fieldID]);
+        }
+        else {
+            // Insert
+            this.execute('INSERT INTO itemData (itemID, fieldID, valueID) VALUES (?, ?, ?)', [itemID, field.fieldID, valueRow.valueID]);
+        }
+        if (!this.readonly) {
+            this.save();
+        }
+        return true;
+    }
+    /**
+     * Get item notes
+     */
+    getItemNotes(itemID) {
+        return this.queryAll(`
+      SELECT in2.itemID, in2.note, in2.title
+      FROM itemNotes in2
+      WHERE in2.parentItemID = ?
+    `, [itemID]);
+    }
+    /**
+     * Add note to item
+     */
+    addItemNote(parentItemID, noteContent, title = '') {
+        // Get parent item's library ID
+        const parent = this.queryOne('SELECT libraryID FROM items WHERE itemID = ?', [parentItemID]);
+        if (!parent) {
+            throw new Error('Parent item not found');
+        }
+        // Get note item type ID
+        const noteType = this.queryOne("SELECT itemTypeID FROM itemTypes WHERE typeName = 'note'");
+        // Create item entry
+        const key = this.generateKey();
+        const now = new Date().toISOString().replace('T', ' ').replace('Z', '');
+        const itemResult = this.execute(`
+      INSERT INTO items (itemTypeID, dateAdded, dateModified, key, libraryID, version)
+      VALUES (?, ?, ?, ?, ?, 0)
+    `, [noteType.itemTypeID, now, now, key, parent.libraryID]);
+        const itemID = itemResult.lastInsertRowid;
+        // Create note entry
+        this.execute(`
+      INSERT INTO itemNotes (itemID, parentItemID, note, title)
+      VALUES (?, ?, ?, ?)
+    `, [itemID, parentItemID, noteContent, title]);
+        if (!this.readonly) {
+            this.save();
+        }
+        return itemID;
+    }
+    // ============================================
+    // Attachment Operations
+    // ============================================
+    /**
+     * Get attachment path
+     */
+    getAttachmentPath(itemID) {
+        const result = this.queryOne(`
+      SELECT path FROM itemAttachments WHERE itemID = ?
+    `, [itemID]);
+        if (!result?.path) {
+            return null;
+        }
+        // Handle different path formats
+        let path = result.path;
+        // Storage path format
+        if (path.startsWith('storage:')) {
+            const storagePath = this.getStoragePath();
+            const keyResult = this.queryOne('SELECT key FROM items WHERE itemID = ?', [itemID]);
+            path = join(storagePath, keyResult.key, path.replace('storage:', ''));
+        }
+        return path;
+    }
+    /**
+     * Get PDF attachments for an item
+     */
+    getPDFAttachments(parentItemID) {
+        return this.queryAll(`
+      SELECT ia.itemID, ia.path, ia.contentType
+      FROM itemAttachments ia
+      WHERE ia.parentItemID = ? AND ia.contentType = 'application/pdf'
+    `, [parentItemID]);
+    }
+    /**
+     * Get storage directory path
+     */
+    getStoragePath() {
+        // Storage is usually in the same directory as the database
+        return join(this.dbPath.replace('zotero.sqlite', ''), 'storage');
+    }
+    // ============================================
+    // Identifier Operations (DOI/ISBN)
+    // ============================================
+    /**
+     * Find item by DOI
+     */
+    findItemByDOI(doi) {
+        // Normalize DOI (remove common prefixes)
+        const normalizedDOI = doi.replace(/^https?:\/\/doi\.org\//i, '').replace(/^doi:/i, '').trim();
+        const result = this.queryOne(`
+      SELECT DISTINCT i.itemID, i.key, i.itemTypeID, i.dateAdded, i.dateModified,
+             iv.value as doi
+      FROM items i
+      JOIN itemData id ON i.itemID = id.itemID
+      JOIN itemDataValues iv ON id.valueID = iv.valueID
+      JOIN fields f ON id.fieldID = f.fieldID
+      WHERE f.fieldName = 'DOI' AND LOWER(iv.value) = LOWER(?)
+    `, [normalizedDOI]);
+        if (result) {
+            return this.getItemDetails(result.itemID);
+        }
+        return null;
+    }
+    /**
+     * Find item by ISBN
+     */
+    findItemByISBN(isbn) {
+        // Normalize ISBN (remove hyphens and spaces)
+        const normalizedISBN = isbn.replace(/[-\s]/g, '').trim();
+        const result = this.queryOne(`
+      SELECT DISTINCT i.itemID, i.key, i.itemTypeID, i.dateAdded, i.dateModified,
+             iv.value as isbn
+      FROM items i
+      JOIN itemData id ON i.itemID = id.itemID
+      JOIN itemDataValues iv ON id.valueID = iv.valueID
+      JOIN fields f ON id.fieldID = f.fieldID
+      WHERE f.fieldName = 'ISBN' AND REPLACE(REPLACE(iv.value, '-', ''), ' ', '') = ?
+    `, [normalizedISBN]);
+        if (result) {
+            return this.getItemDetails(result.itemID);
+        }
+        return null;
+    }
+    /**
+     * Find item by any identifier (DOI, ISBN, PMID, arXiv, etc.)
+     */
+    findItemByIdentifier(identifier, type) {
+        const fieldMap = {
+            'doi': 'DOI',
+            'isbn': 'ISBN',
+            'pmid': 'extra', // PMID is usually stored in extra field
+            'arxiv': 'extra',
+            'url': 'url'
+        };
+        if (type && fieldMap[type.toLowerCase()]) {
+            const fieldName = fieldMap[type.toLowerCase()];
+            if (type.toLowerCase() === 'doi') {
+                return this.findItemByDOI(identifier);
+            }
+            else if (type.toLowerCase() === 'isbn') {
+                return this.findItemByISBN(identifier);
+            }
+            const result = this.queryOne(`
+        SELECT DISTINCT i.itemID, i.key
+        FROM items i
+        JOIN itemData id ON i.itemID = id.itemID
+        JOIN itemDataValues iv ON id.valueID = iv.valueID
+        JOIN fields f ON id.fieldID = f.fieldID
+        WHERE f.fieldName = ? AND iv.value LIKE ?
+      `, [fieldName, `%${identifier}%`]);
+            if (result) {
+                return this.getItemDetails(result.itemID);
+            }
+        }
+        // Try all identifier types
+        const doi = this.findItemByDOI(identifier);
+        if (doi)
+            return doi;
+        const isbn = this.findItemByISBN(identifier);
+        if (isbn)
+            return isbn;
+        return null;
+    }
+    // ============================================
+    // Annotation Operations
+    // ============================================
+    /**
+     * Get all annotations for an item's attachments
+     */
+    getItemAnnotations(parentItemID) {
+        return this.queryAll(`
+      SELECT 
+        ia.itemID as annotationID,
+        ia.parentItemID as attachmentID,
+        ia.type as annotationType,
+        ia.text as annotationText,
+        ia.comment as annotationComment,
+        ia.color as annotationColor,
+        ia.pageLabel,
+        ia.sortIndex,
+        ia.position,
+        i.dateAdded,
+        i.dateModified,
+        i.key
+      FROM itemAnnotations ia
+      JOIN items i ON ia.itemID = i.itemID
+      JOIN itemAttachments att ON ia.parentItemID = att.itemID
+      WHERE att.parentItemID = ?
+      ORDER BY ia.sortIndex
+    `, [parentItemID]);
+    }
+    /**
+     * Get annotations from a specific attachment
+     */
+    getAttachmentAnnotations(attachmentID) {
+        return this.queryAll(`
+      SELECT 
+        ia.itemID as annotationID,
+        ia.parentItemID as attachmentID,
+        ia.type as annotationType,
+        ia.text as annotationText,
+        ia.comment as annotationComment,
+        ia.color as annotationColor,
+        ia.pageLabel,
+        ia.sortIndex,
+        ia.position,
+        i.dateAdded,
+        i.dateModified,
+        i.key
+      FROM itemAnnotations ia
+      JOIN items i ON ia.itemID = i.itemID
+      WHERE ia.parentItemID = ?
+      ORDER BY ia.sortIndex
+    `, [attachmentID]);
+    }
+    /**
+     * Get annotations filtered by type
+     */
+    getAnnotationsByType(parentItemID, types) {
+        const placeholders = types.map(() => '?').join(',');
+        return this.queryAll(`
+      SELECT 
+        ia.itemID as annotationID,
+        ia.parentItemID as attachmentID,
+        ia.type as annotationType,
+        ia.text as annotationText,
+        ia.comment as annotationComment,
+        ia.color as annotationColor,
+        ia.pageLabel,
+        ia.sortIndex,
+        ia.position,
+        i.dateAdded,
+        i.dateModified
+      FROM itemAnnotations ia
+      JOIN items i ON ia.itemID = i.itemID
+      JOIN itemAttachments att ON ia.parentItemID = att.itemID
+      WHERE att.parentItemID = ? AND ia.type IN (${placeholders})
+      ORDER BY ia.sortIndex
+    `, [parentItemID, ...types]);
+    }
+    /**
+     * Get annotations filtered by color
+     */
+    getAnnotationsByColor(parentItemID, colors) {
+        const placeholders = colors.map(() => '?').join(',');
+        return this.queryAll(`
+      SELECT 
+        ia.itemID as annotationID,
+        ia.parentItemID as attachmentID,
+        ia.type as annotationType,
+        ia.text as annotationText,
+        ia.comment as annotationComment,
+        ia.color as annotationColor,
+        ia.pageLabel,
+        ia.sortIndex,
+        ia.position,
+        i.dateAdded,
+        i.dateModified
+      FROM itemAnnotations ia
+      JOIN items i ON ia.itemID = i.itemID
+      JOIN itemAttachments att ON ia.parentItemID = att.itemID
+      WHERE att.parentItemID = ? AND ia.color IN (${placeholders})
+      ORDER BY ia.sortIndex
+    `, [parentItemID, ...colors]);
+    }
+    /**
+     * Search annotations by text content
+     */
+    searchAnnotations(query, parentItemID) {
+        const baseQuery = `
+      SELECT 
+        ia.itemID as annotationID,
+        ia.parentItemID as attachmentID,
+        ia.type as annotationType,
+        ia.text as annotationText,
+        ia.comment as annotationComment,
+        ia.color as annotationColor,
+        ia.pageLabel,
+        att.parentItemID as itemID,
+        i.dateAdded,
+        i.dateModified
+      FROM itemAnnotations ia
+      JOIN items i ON ia.itemID = i.itemID
+      JOIN itemAttachments att ON ia.parentItemID = att.itemID
+      WHERE (ia.text LIKE ? OR ia.comment LIKE ?)
+    `;
+        if (parentItemID) {
+            return this.queryAll(baseQuery + ' AND att.parentItemID = ? ORDER BY ia.sortIndex', [`%${query}%`, `%${query}%`, parentItemID]);
+        }
+        return this.queryAll(baseQuery + ' ORDER BY i.dateModified DESC', [`%${query}%`, `%${query}%`]);
+    }
+    // ============================================
+    // Fulltext Search Operations
+    // ============================================
+    /**
+     * Search in Zotero's fulltext index
+     * fulltextWords: wordID, word
+     * fulltextItemWords: wordID, itemID
+     */
+    searchFulltext(query, libraryID = 1) {
+        // Zotero stores fulltext words in fulltextWords table
+        // and word-item associations in fulltextItemWords
+        return this.queryAll(`
+      SELECT DISTINCT 
+        i.itemID,
+        i.key,
+        att.parentItemID,
+        fi.indexedChars,
+        fi.totalChars,
+        fi.indexedPages,
+        fi.totalPages
+      FROM fulltextItems fi
+      JOIN itemAttachments att ON fi.itemID = att.itemID
+      JOIN items i ON att.itemID = i.itemID
+      JOIN items parent ON att.parentItemID = parent.itemID
+      WHERE parent.libraryID = ?
+        AND fi.itemID IN (
+          SELECT fiw.itemID 
+          FROM fulltextItemWords fiw
+          JOIN fulltextWords fw ON fiw.wordID = fw.wordID
+          WHERE fw.word LIKE ?
+        )
+      ORDER BY parent.dateModified DESC
+    `, [libraryID, `%${query.toLowerCase()}%`]);
+    }
+    /**
+     * Get fulltext content for an attachment
+     * Note: fulltextContent table may not exist in all Zotero versions
+     */
+    getFulltextContent(attachmentID) {
+        // Try fulltextContent table first (Zotero 7+)
+        try {
+            const content = this.queryOne(`
+        SELECT content FROM fulltextContent WHERE itemID = ?
+      `, [attachmentID]);
+            if (content?.content) {
+                return content.content;
+            }
+        }
+        catch {
+            // Table doesn't exist, continue to fallback
+        }
+        // Fallback: try to reconstruct from fulltextWords and fulltextItemWords
+        try {
+            const words = this.queryAll(`
+        SELECT fw.word 
+        FROM fulltextItemWords fiw
+        JOIN fulltextWords fw ON fiw.wordID = fw.wordID
+        WHERE fiw.itemID = ?
+        ORDER BY fw.word
+      `, [attachmentID]);
+            if (words.length > 0) {
+                return words.map(w => w.word).join(' ');
+            }
+        }
+        catch {
+            // Tables don't exist or query failed
+        }
+        return null;
+    }
+    /**
+     * Get fulltext index status for an item
+     */
+    getFulltextStatus(attachmentID) {
+        return this.queryOne(`
+      SELECT 
+        itemID,
+        indexedChars,
+        totalChars,
+        indexedPages,
+        totalPages,
+        synced
+      FROM fulltextItems
+      WHERE itemID = ?
+    `, [attachmentID]);
+    }
+    /**
+     * Advanced fulltext search with context
+     */
+    searchFulltextWithContext(query, contextLength = 100, libraryID = 1) {
+        const results = this.searchFulltext(query, libraryID);
+        return results.map(result => {
+            const content = this.getFulltextContent(result.itemID);
+            let context = '';
+            if (content) {
+                const lowerContent = content.toLowerCase();
+                const lowerQuery = query.toLowerCase();
+                const index = lowerContent.indexOf(lowerQuery);
+                if (index !== -1) {
+                    const start = Math.max(0, index - contextLength);
+                    const end = Math.min(content.length, index + query.length + contextLength);
+                    context = (start > 0 ? '...' : '') +
+                        content.substring(start, end) +
+                        (end < content.length ? '...' : '');
+                }
+            }
+            // Get parent item details
+            const parentDetails = result.parentItemID ? this.getItemDetails(result.parentItemID) : null;
+            return {
+                ...result,
+                context,
+                parentItem: parentDetails ? {
+                    itemID: parentDetails.itemID,
+                    key: parentDetails.key,
+                    title: parentDetails.title,
+                    creators: parentDetails.creators
+                } : null
+            };
+        });
+    }
+    // ============================================
+    // Related Items / Similar Items
+    // ============================================
+    /**
+     * Get related items (manually linked)
+     */
+    getRelatedItems(itemID) {
+        // Zotero stores relations in itemRelations table
+        const relations = this.queryAll(`
+      SELECT 
+        ir.predicateID,
+        ir.object as relatedURI
+      FROM itemRelations ir
+      WHERE ir.itemID = ?
+    `, [itemID]);
+        // Extract item keys from URIs and get their details
+        const relatedItems = [];
+        for (const rel of relations) {
+            // URI format: http://zotero.org/users/xxx/items/ITEMKEY
+            const match = rel.relatedURI.match(/\/items\/([A-Z0-9]+)$/);
+            if (match) {
+                const relatedItem = this.getItemByKey(match[1]);
+                if (relatedItem) {
+                    relatedItems.push(this.getItemDetails(relatedItem.itemID));
+                }
+            }
+        }
+        return relatedItems;
+    }
+    /**
+     * Find similar items by shared tags
+     */
+    findSimilarByTags(itemID, minSharedTags = 2) {
+        return this.queryAll(`
+      SELECT 
+        i.itemID,
+        i.key,
+        COUNT(it2.tagID) as sharedTagCount,
+        GROUP_CONCAT(t.name, ', ') as sharedTags
+      FROM items i
+      JOIN itemTags it2 ON i.itemID = it2.itemID
+      JOIN tags t ON it2.tagID = t.tagID
+      WHERE it2.tagID IN (
+        SELECT tagID FROM itemTags WHERE itemID = ?
+      )
+      AND i.itemID != ?
+      GROUP BY i.itemID
+      HAVING COUNT(it2.tagID) >= ?
+      ORDER BY sharedTagCount DESC
+      LIMIT 20
+    `, [itemID, itemID, minSharedTags]);
+    }
+    /**
+     * Find similar items by shared creators
+     */
+    findSimilarByCreators(itemID) {
+        return this.queryAll(`
+      SELECT DISTINCT
+        i.itemID,
+        i.key,
+        COUNT(ic2.creatorID) as sharedCreatorCount
+      FROM items i
+      JOIN itemCreators ic2 ON i.itemID = ic2.itemID
+      WHERE ic2.creatorID IN (
+        SELECT creatorID FROM itemCreators WHERE itemID = ?
+      )
+      AND i.itemID != ?
+      GROUP BY i.itemID
+      ORDER BY sharedCreatorCount DESC
+      LIMIT 20
+    `, [itemID, itemID]);
+    }
+    /**
+     * Find similar items by shared collection
+     */
+    findSimilarByCollection(itemID) {
+        return this.queryAll(`
+      SELECT DISTINCT
+        i.itemID,
+        i.key,
+        c.collectionName
+      FROM items i
+      JOIN collectionItems ci2 ON i.itemID = ci2.itemID
+      JOIN collections c ON ci2.collectionID = c.collectionID
+      WHERE ci2.collectionID IN (
+        SELECT collectionID FROM collectionItems WHERE itemID = ?
+      )
+      AND i.itemID != ?
+      LIMIT 50
+    `, [itemID, itemID]);
+    }
+    // ============================================
+    // Utility Methods
+    // ============================================
+    /**
+     * Generate a unique Zotero key
+     *
+     * Zotero uses a specific character set that excludes ambiguous characters:
+     * - No '0' (zero) - confused with 'O'
+     * - No '1' (one) - confused with 'I' or 'L'
+     * - No 'I' - confused with '1' or 'L'
+     * - No 'L' - confused with '1' or 'I'
+     * - No 'O' - confused with '0'
+     *
+     * Valid characters: 23456789ABCDEFGHJKMNPQRSTUVWXYZ
+     */
+    generateKey() {
+        const chars = '23456789ABCDEFGHJKMNPQRSTUVWXYZ';
+        let key = '';
+        for (let i = 0; i < 8; i++) {
+            key += chars.charAt(Math.floor(Math.random() * chars.length));
+        }
+        return key;
+    }
+    /**
+     * Execute a raw SQL query
+     */
+    query(sql, params = []) {
+        return this.queryAll(sql, params);
+    }
+    /**
+     * Execute a raw SQL statement
+     */
+    run(sql, params = []) {
+        return this.execute(sql, params);
+    }
+}
+//# sourceMappingURL=database.js.map