zotero-bridge 1.0.1

package/dist/database.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -0,0 +1,12 @@
+#!/usr/bin/env node
+/**
+ * ZoteroBridge - MCP Server for Zotero SQLite Database
+ *
+ * A Model Context Protocol server that provides direct access to Zotero's
+ * SQLite database for collection management, tagging, PDF reading, and more.
+ *
+ * @author Combjellyshen
+ * @version 1.0.0
+ */
+export {};
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AAEA;;;;;;;;GAQG"}

package/dist/index.js

@@ -0,0 +1,504 @@
+#!/usr/bin/env node
+/**
+ * ZoteroBridge - MCP Server for Zotero SQLite Database
+ *
+ * A Model Context Protocol server that provides direct access to Zotero's
+ * SQLite database for collection management, tagging, PDF reading, and more.
+ *
+ * @author Combjellyshen
+ * @version 1.0.0
+ */
+import { Server } from '@modelcontextprotocol/sdk/server/index.js';
+import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
+import { CallToolRequestSchema, ListToolsRequestSchema, } from '@modelcontextprotocol/sdk/types.js';
+import { z } from 'zod';
+import { ZoteroDatabase } from './database.js';
+import { PDFProcessor } from './pdf.js';
+import { toolDefinitions, listCollectionsSchema, getCollectionSchema, createCollectionSchema, renameCollectionSchema, moveCollectionSchema, deleteCollectionSchema, getSubcollectionsSchema, listTagsSchema, addTagSchema, removeTagSchema, getItemTagsSchema, createTagSchema, searchItemsSchema, getItemDetailsSchema, addItemToCollectionSchema, removeItemFromCollectionSchema, getCollectionItemsSchema, getItemAbstractSchema, setItemAbstractSchema, getItemNotesSchema, addItemNoteSchema, extractPDFTextSchema, getPDFSummarySchema, getItemPDFsSchema, searchPDFSchema, generateAbstractFromPDFSchema, getDatabaseInfoSchema, rawQuerySchema, 
+// New schemas
+findByDOISchema, findByISBNSchema, findByIdentifierSchema, getItemAnnotationsSchema, getAttachmentAnnotationsSchema, getAnnotationsByTypeSchema, getAnnotationsByColorSchema, searchAnnotationsSchema, searchFulltextSchema, getFulltextContentSchema, searchFulltextWithContextSchema, getRelatedItemsSchema, findSimilarByTagsSchema, findSimilarByCreatorsSchema, findSimilarByCollectionSchema } from './tools.js';
+// Server configuration
+const SERVER_NAME = 'zotero-bridge';
+const SERVER_VERSION = '1.0.0';
+// Parse command line arguments
+function parseArgs() {
+    const args = process.argv.slice(2);
+    let dbPath;
+    let readonly = false;
+    for (let i = 0; i < args.length; i++) {
+        if (args[i] === '--db' || args[i] === '-d') {
+            dbPath = args[i + 1];
+            i++;
+        }
+        else if (args[i] === '--readonly' || args[i] === '-r') {
+            readonly = true;
+        }
+        else if (args[i] === '--help' || args[i] === '-h') {
+            console.log(`
+ZoteroBridge - MCP Server for Zotero SQLite Database
+
+Usage: zotero-bridge [options]
+
+Options:
+  -d, --db <path>     Path to zotero.sqlite database
+  -r, --readonly      Open database in read-only mode
+  -h, --help          Show this help message
+
+Example:
+  zotero-bridge --db ~/Zotero/zotero.sqlite
+  zotero-bridge --readonly
+      `);
+            process.exit(0);
+        }
+    }
+    return { dbPath, readonly };
+}
+// Initialize the server
+async function main() {
+    const { dbPath, readonly } = parseArgs();
+    // Initialize database
+    const db = new ZoteroDatabase(dbPath, readonly);
+    await db.connect(); // Connect to database
+    const pdf = new PDFProcessor(db);
+    // Create MCP server
+    const server = new Server({
+        name: SERVER_NAME,
+        version: SERVER_VERSION,
+    }, {
+        capabilities: {
+            tools: {},
+        },
+    });
+    // Handle tool listing
+    server.setRequestHandler(ListToolsRequestSchema, async () => {
+        return {
+            tools: toolDefinitions.map(tool => ({
+                name: tool.name,
+                description: tool.description,
+                inputSchema: {
+                    type: 'object',
+                    properties: Object.fromEntries(Object.entries(tool.inputSchema.shape || {}).map(([key, value]) => {
+                        const zodType = value;
+                        const schema = zodToJsonSchema(zodType);
+                        return [key, {
+                                ...schema,
+                                description: zodType.description || ''
+                            }];
+                    })),
+                    required: Object.entries(tool.inputSchema.shape || {})
+                        .filter(([_, value]) => !value.isOptional())
+                        .map(([key]) => key)
+                }
+            }))
+        };
+    });
+    // Handle tool calls
+    server.setRequestHandler(CallToolRequestSchema, async (request) => {
+        const { name, arguments: args } = request.params;
+        try {
+            let result;
+            switch (name) {
+                // ============================================
+                // Collection Tools
+                // ============================================
+                case 'list_collections': {
+                    const params = listCollectionsSchema.parse(args);
+                    result = db.getCollections(params.libraryID);
+                    break;
+                }
+                case 'get_collection': {
+                    const params = getCollectionSchema.parse(args);
+                    if (params.collectionID) {
+                        result = db.getCollectionById(params.collectionID);
+                    }
+                    else if (params.name) {
+                        result = db.getCollectionByName(params.name, params.libraryID);
+                    }
+                    else {
+                        throw new Error('Either collectionID or name is required');
+                    }
+                    break;
+                }
+                case 'create_collection': {
+                    const params = createCollectionSchema.parse(args);
+                    const collectionID = db.createCollection(params.name, params.parentCollectionID || null, params.libraryID);
+                    result = { success: true, collectionID };
+                    break;
+                }
+                case 'rename_collection': {
+                    const params = renameCollectionSchema.parse(args);
+                    const success = db.renameCollection(params.collectionID, params.newName);
+                    result = { success };
+                    break;
+                }
+                case 'move_collection': {
+                    const params = moveCollectionSchema.parse(args);
+                    const success = db.moveCollection(params.collectionID, params.newParentID);
+                    result = { success };
+                    break;
+                }
+                case 'delete_collection': {
+                    const params = deleteCollectionSchema.parse(args);
+                    const success = db.deleteCollection(params.collectionID);
+                    result = { success };
+                    break;
+                }
+                case 'get_subcollections': {
+                    const params = getSubcollectionsSchema.parse(args);
+                    result = db.getSubcollections(params.parentCollectionID);
+                    break;
+                }
+                // ============================================
+                // Tag Tools
+                // ============================================
+                case 'list_tags': {
+                    listTagsSchema.parse(args);
+                    result = db.getTags();
+                    break;
+                }
+                case 'add_tag': {
+                    const params = addTagSchema.parse(args);
+                    const success = db.addTagToItem(params.itemID, params.tagName, params.type);
+                    result = { success };
+                    break;
+                }
+                case 'remove_tag': {
+                    const params = removeTagSchema.parse(args);
+                    const success = db.removeTagFromItem(params.itemID, params.tagName);
+                    result = { success };
+                    break;
+                }
+                case 'get_item_tags': {
+                    const params = getItemTagsSchema.parse(args);
+                    result = db.getItemTags(params.itemID);
+                    break;
+                }
+                case 'create_tag': {
+                    const params = createTagSchema.parse(args);
+                    const tagID = db.createTag(params.name, params.type);
+                    result = { success: true, tagID };
+                    break;
+                }
+                // ============================================
+                // Item Tools
+                // ============================================
+                case 'search_items': {
+                    const params = searchItemsSchema.parse(args);
+                    result = db.searchItems(params.query, params.limit, params.libraryID);
+                    break;
+                }
+                case 'get_item_details': {
+                    const params = getItemDetailsSchema.parse(args);
+                    if (params.itemID) {
+                        result = db.getItemDetails(params.itemID);
+                    }
+                    else if (params.itemKey) {
+                        const item = db.getItemByKey(params.itemKey);
+                        if (item) {
+                            result = db.getItemDetails(item.itemID);
+                        }
+                        else {
+                            result = null;
+                        }
+                    }
+                    else {
+                        throw new Error('Either itemID or itemKey is required');
+                    }
+                    break;
+                }
+                case 'add_item_to_collection': {
+                    const params = addItemToCollectionSchema.parse(args);
+                    const success = db.addItemToCollection(params.itemID, params.collectionID);
+                    result = { success };
+                    break;
+                }
+                case 'remove_item_from_collection': {
+                    const params = removeItemFromCollectionSchema.parse(args);
+                    const success = db.removeItemFromCollection(params.itemID, params.collectionID);
+                    result = { success };
+                    break;
+                }
+                case 'get_collection_items': {
+                    const params = getCollectionItemsSchema.parse(args);
+                    result = db.getCollectionItems(params.collectionID);
+                    break;
+                }
+                // ============================================
+                // Abstract/Note Tools
+                // ============================================
+                case 'get_item_abstract': {
+                    const params = getItemAbstractSchema.parse(args);
+                    result = { abstract: db.getItemAbstract(params.itemID) };
+                    break;
+                }
+                case 'set_item_abstract': {
+                    const params = setItemAbstractSchema.parse(args);
+                    const success = db.setItemAbstract(params.itemID, params.abstract);
+                    result = { success };
+                    break;
+                }
+                case 'get_item_notes': {
+                    const params = getItemNotesSchema.parse(args);
+                    result = db.getItemNotes(params.itemID);
+                    break;
+                }
+                case 'add_item_note': {
+                    const params = addItemNoteSchema.parse(args);
+                    const noteID = db.addItemNote(params.itemID, params.content, params.title);
+                    result = { success: true, noteID };
+                    break;
+                }
+                // ============================================
+                // PDF Tools
+                // ============================================
+                case 'extract_pdf_text': {
+                    const params = extractPDFTextSchema.parse(args);
+                    result = await pdf.extractTextFromAttachment(params.attachmentItemID);
+                    break;
+                }
+                case 'get_pdf_summary': {
+                    const params = getPDFSummarySchema.parse(args);
+                    result = await pdf.getPDFSummary(params.attachmentItemID);
+                    break;
+                }
+                case 'get_item_pdfs': {
+                    const params = getItemPDFsSchema.parse(args);
+                    const attachments = db.getPDFAttachments(params.parentItemID);
+                    result = attachments.map(att => ({
+                        ...att,
+                        fullPath: db.getAttachmentPath(att.itemID)
+                    }));
+                    break;
+                }
+                case 'search_pdf': {
+                    const params = searchPDFSchema.parse(args);
+                    const content = await pdf.extractTextFromAttachment(params.attachmentItemID);
+                    if (content) {
+                        result = pdf.searchInPDF(content, params.query, params.caseSensitive);
+                    }
+                    else {
+                        result = [];
+                    }
+                    break;
+                }
+                case 'generate_abstract_from_pdf': {
+                    const params = generateAbstractFromPDFSchema.parse(args);
+                    const content = await pdf.extractTextFromAttachment(params.attachmentItemID);
+                    if (!content) {
+                        throw new Error('Could not extract PDF content');
+                    }
+                    const abstract = pdf.generateSimpleSummary(content, params.maxLength);
+                    if (params.saveToItem) {
+                        // Get parent item ID from attachment
+                        const attDetails = db.query('SELECT parentItemID FROM itemAttachments WHERE itemID = ?', [params.attachmentItemID])[0];
+                        if (attDetails?.parentItemID) {
+                            db.setItemAbstract(attDetails.parentItemID, abstract);
+                        }
+                    }
+                    result = { abstract, length: abstract.length };
+                    break;
+                }
+                // ============================================
+                // Utility Tools
+                // ============================================
+                case 'get_database_info': {
+                    getDatabaseInfoSchema.parse(args);
+                    result = {
+                        path: db.getPath(),
+                        storagePath: db.getStoragePath(),
+                        readonly,
+                        collectionsCount: db.getCollections().length,
+                        tagsCount: db.getTags().length
+                    };
+                    break;
+                }
+                case 'raw_query': {
+                    const params = rawQuerySchema.parse(args);
+                    // Security check - only allow SELECT queries
+                    if (!params.sql.trim().toUpperCase().startsWith('SELECT')) {
+                        throw new Error('Only SELECT queries are allowed');
+                    }
+                    result = db.query(params.sql, params.params);
+                    break;
+                }
+                // ============================================
+                // Identifier Tools (DOI/ISBN)
+                // ============================================
+                case 'find_by_doi': {
+                    const params = findByDOISchema.parse(args);
+                    result = db.findItemByDOI(params.doi);
+                    break;
+                }
+                case 'find_by_isbn': {
+                    const params = findByISBNSchema.parse(args);
+                    result = db.findItemByISBN(params.isbn);
+                    break;
+                }
+                case 'find_by_identifier': {
+                    const params = findByIdentifierSchema.parse(args);
+                    result = db.findItemByIdentifier(params.identifier, params.type);
+                    break;
+                }
+                // ============================================
+                // Annotation Tools
+                // ============================================
+                case 'get_item_annotations': {
+                    const params = getItemAnnotationsSchema.parse(args);
+                    result = db.getItemAnnotations(params.itemID);
+                    break;
+                }
+                case 'get_attachment_annotations': {
+                    const params = getAttachmentAnnotationsSchema.parse(args);
+                    result = db.getAttachmentAnnotations(params.attachmentID);
+                    break;
+                }
+                case 'get_annotations_by_type': {
+                    const params = getAnnotationsByTypeSchema.parse(args);
+                    result = db.getAnnotationsByType(params.itemID, params.types);
+                    break;
+                }
+                case 'get_annotations_by_color': {
+                    const params = getAnnotationsByColorSchema.parse(args);
+                    result = db.getAnnotationsByColor(params.itemID, params.colors);
+                    break;
+                }
+                case 'search_annotations': {
+                    const params = searchAnnotationsSchema.parse(args);
+                    result = db.searchAnnotations(params.query, params.itemID);
+                    break;
+                }
+                // ============================================
+                // Fulltext Search Tools
+                // ============================================
+                case 'search_fulltext': {
+                    const params = searchFulltextSchema.parse(args);
+                    result = db.searchFulltext(params.query, params.libraryID);
+                    break;
+                }
+                case 'get_fulltext_content': {
+                    const params = getFulltextContentSchema.parse(args);
+                    result = { content: db.getFulltextContent(params.attachmentID) };
+                    break;
+                }
+                case 'search_fulltext_with_context': {
+                    const params = searchFulltextWithContextSchema.parse(args);
+                    result = db.searchFulltextWithContext(params.query, params.contextLength, params.libraryID);
+                    break;
+                }
+                // ============================================
+                // Related/Similar Items Tools
+                // ============================================
+                case 'get_related_items': {
+                    const params = getRelatedItemsSchema.parse(args);
+                    result = db.getRelatedItems(params.itemID);
+                    break;
+                }
+                case 'find_similar_by_tags': {
+                    const params = findSimilarByTagsSchema.parse(args);
+                    result = db.findSimilarByTags(params.itemID, params.minSharedTags);
+                    break;
+                }
+                case 'find_similar_by_creators': {
+                    const params = findSimilarByCreatorsSchema.parse(args);
+                    result = db.findSimilarByCreators(params.itemID);
+                    break;
+                }
+                case 'find_similar_by_collection': {
+                    const params = findSimilarByCollectionSchema.parse(args);
+                    result = db.findSimilarByCollection(params.itemID);
+                    break;
+                }
+                default:
+                    throw new Error(`Unknown tool: ${name}`);
+            }
+            return {
+                content: [
+                    {
+                        type: 'text',
+                        text: JSON.stringify(result, null, 2)
+                    }
+                ]
+            };
+        }
+        catch (error) {
+            const errorMessage = error instanceof Error ? error.message : String(error);
+            return {
+                content: [
+                    {
+                        type: 'text',
+                        text: JSON.stringify({ error: errorMessage })
+                    }
+                ],
+                isError: true
+            };
+        }
+    });
+    // Start the server
+    const transport = new StdioServerTransport();
+    await server.connect(transport);
+    // Handle shutdown
+    process.on('SIGINT', () => {
+        db.disconnect();
+        process.exit(0);
+    });
+    process.on('SIGTERM', () => {
+        db.disconnect();
+        process.exit(0);
+    });
+    console.error(`ZoteroBridge MCP Server v${SERVER_VERSION} started`);
+    console.error(`Database: ${db.getPath()}`);
+}
+// Helper function to convert Zod type to JSON Schema
+function zodToJsonSchema(zodType) {
+    // Unwrap optional, default, and nullable types
+    if (zodType instanceof z.ZodOptional) {
+        return zodToJsonSchema(zodType._def.innerType);
+    }
+    if (zodType instanceof z.ZodDefault) {
+        return zodToJsonSchema(zodType._def.innerType);
+    }
+    if (zodType instanceof z.ZodNullable) {
+        return zodToJsonSchema(zodType._def.innerType);
+    }
+    // Handle basic types
+    if (zodType instanceof z.ZodString) {
+        return { type: 'string' };
+    }
+    if (zodType instanceof z.ZodNumber) {
+        return { type: 'number' };
+    }
+    if (zodType instanceof z.ZodBoolean) {
+        return { type: 'boolean' };
+    }
+    // Handle array types - MUST include items
+    if (zodType instanceof z.ZodArray) {
+        const elementType = zodType._def.type;
+        const itemSchema = zodToJsonSchema(elementType);
+        // If items schema is empty (from ZodAny), use a more explicit schema
+        if (Object.keys(itemSchema).length === 0) {
+            return {
+                type: 'array',
+                items: { type: 'string' } // Default to string for any type to ensure valid JSON Schema
+            };
+        }
+        return {
+            type: 'array',
+            items: itemSchema
+        };
+    }
+    // Handle object types
+    if (zodType instanceof z.ZodObject) {
+        return { type: 'object' };
+    }
+    // Handle ZodAny - return empty object (accepts any value)
+    if (zodType instanceof z.ZodAny) {
+        return {};
+    }
+    // Default to string
+    return { type: 'string' };
+}
+main().catch((error) => {
+    console.error('Fatal error:', error);
+    process.exit(1);
+});
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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package/dist/pdf.d.ts

@@ -0,0 +1,57 @@
+/**
+ * ZoteroBridge - PDF Processing Module
+ *
+ * Handles PDF text extraction and content analysis
+ *
+ * @author Combjellyshen
+ */
+import { ZoteroDatabase } from './database.js';
+export interface PDFContent {
+    text: string;
+    numPages: number;
+    info: Record<string, any>;
+    metadata: Record<string, any> | null;
+}
+export interface PDFSummary {
+    itemID: number;
+    title: string;
+    numPages: number;
+    wordCount: number;
+    preview: string;
+    path: string;
+}
+export declare class PDFProcessor {
+    private db;
+    constructor(db: ZoteroDatabase);
+    /**
+     * Extract text from a PDF file
+     */
+    extractText(pdfPath: string): Promise<PDFContent>;
+    /**
+     * Extract text from a PDF attachment by item ID
+     */
+    extractTextFromAttachment(attachmentItemID: number): Promise<PDFContent | null>;
+    /**
+     * Extract text from all PDF attachments of a parent item
+     */
+    extractTextFromItem(parentItemID: number): Promise<Map<number, PDFContent>>;
+    /**
+     * Get a summary of a PDF attachment
+     */
+    getPDFSummary(attachmentItemID: number): Promise<PDFSummary | null>;
+    /**
+     * Generate an abstract/summary from PDF content
+     * This is a simple extraction - for AI-generated summaries,
+     * use the extracted text with an LLM
+     */
+    generateSimpleSummary(content: PDFContent, maxLength?: number): string;
+    /**
+     * Search for text within PDF content
+     */
+    searchInPDF(content: PDFContent, query: string, caseSensitive?: boolean): string[];
+    /**
+     * Get PDF info/metadata
+     */
+    getPDFInfo(pdfPath: string): Promise<Record<string, any>>;
+}
+//# sourceMappingURL=pdf.d.ts.map

package/dist/pdf.d.ts.map

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