Document Organizer MCP Server

Instructions

Implementation Reference

• src/index.ts:494-534 (handler)

  Core handler function that orchestrates PDF to Markdown conversion, selecting between marker or pymupdf4llm engines based on options, with input validation and comprehensive error handling.

  async function convertPdfToMarkdown(
    pdfPath: string,
    outputPath?: string,
    options: {
      engine?: "pymupdf4llm" | "marker";
      page_chunks?: boolean;
      write_images?: boolean;
      image_path?: string;
      table_strategy?: "fast" | "accurate";
      extract_content?: "text" | "figures" | "both";
      auto_clean?: boolean;
    } = {}
  ): Promise<ConversionResult> {
    const startTime = Date.now();
    
    try {
      // Validate PDF exists
      const validatedPdfPath = validatePath(pdfPath);
      await fs.access(validatedPdfPath);
      
      // Determine which engine to use
      const engine = options.engine || "marker";
      
      if (engine === "marker") {
        return await convertWithMarker(validatedPdfPath, outputPath, options);
      } else {
        return await convertWithPymupdf4llm(validatedPdfPath, outputPath, options);
      }
    } catch (error) {
      return {
        success: false,
        error: error instanceof Error ? error.message : String(error),
        page_count: 0,
        char_count: 0,
        images_extracted: 0,
        processing_time: Date.now() - startTime,
        memory_used: 0,
        warnings: []
      };
    }
  }

• src/index.ts:26-38 (schema)

  Zod schema defining the input parameters for the convert_pdf tool, including pdf_path, optional output_path, and detailed conversion options.

  const ConvertPdfArgsSchema = z.object({
    pdf_path: z.string().describe("Absolute path to the PDF file to convert"),
    output_path: z.string().optional().describe("Optional path to write markdown output. If not provided, returns content directly"),
    options: z.object({
      engine: z.enum(["pymupdf4llm", "marker"]).optional().default("marker").describe("PDF conversion engine (marker recommended for complex documents)"),
      page_chunks: z.boolean().optional().default(false).describe("Process as individual pages for memory efficiency (pymupdf4llm only)"),
      write_images: z.boolean().optional().default(false).describe("Extract embedded images to files"),
      image_path: z.string().optional().describe("Directory for extracted images (requires write_images: true)"),
      table_strategy: z.enum(["fast", "accurate"]).optional().default("accurate").describe("Table extraction strategy (pymupdf4llm only)"),
      extract_content: z.enum(["text", "figures", "both"]).optional().default("both").describe("Content to extract from PDF (pymupdf4llm only)"),
      auto_clean: z.boolean().optional().default(true).describe("Automatically clean marker formatting artifacts")
    }).optional().default({})
  });

• src/index.ts:1291-1295 (registration)

  Tool registration object defining the 'convert_pdf' tool's name, description, and input schema in the tools array.

    name: "convert_pdf",
    description: "Convert PDF files to Markdown format using marker (recommended) or pymupdf4llm. Marker provides superior quality for complex documents with tables and structured content, with automatic cleaning of formatting artifacts. Returns detailed conversion statistics including processing time and content metrics.",
    inputSchema: zodToJsonSchema(ConvertPdfArgsSchema) as ToolInput,
  },
  {

• src/index.ts:536-673 (helper)

  Helper function implementing PDF conversion specifically using the 'marker' engine, including subprocess execution, temporary directory management, automatic cleaning, and result processing.

  async function convertWithMarker(
    pdfPath: string,
    outputPath?: string,
    options: { auto_clean?: boolean } = {}
  ): Promise<ConversionResult> {
    const startTime = Date.now();
    
    try {
      // Check if marker is available
      const markerCheck = await checkMarker();
      if (!markerCheck.available) {
        throw new Error(`Marker not available: ${markerCheck.error}`);
      }
      
      // Create temporary output directory for marker
      const tempDir = await fs.mkdtemp(path.join(os.tmpdir(), 'marker-'));
      
      // Run marker conversion with correct syntax
      const result = await new Promise<{ success: boolean; content?: string; error?: string }>((resolve) => {
        const markerProcess = spawn('marker_single', [pdfPath, '--output_dir', tempDir], {
          stdio: ['pipe', 'pipe', 'pipe']
        });
  
        let stdout = '';
        let stderr = '';
  
        markerProcess.stdout.on('data', (data: Buffer) => {
          stdout += data.toString();
        });
  
        markerProcess.stderr.on('data', (data: Buffer) => {
          stderr += data.toString();
        });
  
        markerProcess.on('close', async (code: number | null) => {
          try {
            if (code === 0) {
              // Find the markdown file that marker created
              // Marker creates a directory with PDF basename, then puts .md file inside
              const pdfBaseName = path.basename(pdfPath, '.pdf');
              const markerDir = path.join(tempDir, pdfBaseName);
              const expectedOutput = path.join(markerDir, `${pdfBaseName}.md`);
              
              // Check if the expected structure exists
              let outputFile = expectedOutput;
              try {
                await fs.access(expectedOutput);
              } catch {
                // Look for marker directory and .md file inside it
                try {
                  const tempFiles = await fs.readdir(tempDir, { withFileTypes: true });
                  const markerDirEntry = tempFiles.find(entry => entry.isDirectory());
                  
                  if (markerDirEntry) {
                    const dirPath = path.join(tempDir, markerDirEntry.name);
                    const dirFiles = await fs.readdir(dirPath);
                    const mdFile = dirFiles.find(file => file.endsWith('.md'));
                    if (mdFile) {
                      outputFile = path.join(dirPath, mdFile);
                    } else {
                      resolve({ success: false, error: 'No markdown file found in marker directory' });
                      return;
                    }
                  } else {
                    resolve({ success: false, error: 'No marker output directory found' });
                    return;
                  }
                } catch {
                  resolve({ success: false, error: 'Failed to find marker output' });
                  return;
                }
              }
              
              // Read the converted content
              const content = await fs.readFile(outputFile, 'utf-8');
              resolve({ success: true, content });
            } else {
              resolve({ success: false, error: stderr || `Marker exited with code ${code}` });
            }
          } catch (readError) {
            resolve({ success: false, error: `Failed to read marker output: ${readError}` });
          } finally {
            // Clean up temp directory
            try {
              await fs.rm(tempDir, { recursive: true });
            } catch {}
          }
        });
  
        markerProcess.on('error', (error: Error) => {
          resolve({ success: false, error: error.message });
        });
      });
  
      if (!result.success || !result.content) {
        throw new Error(result.error || 'Marker conversion failed');
      }
      
      // Apply cleaning if enabled (default: true)
      let finalContent = result.content;
      if (options.auto_clean !== false) {
        finalContent = cleanMarkerOutput(result.content);
      }
      
      // Write to output file if specified
      if (outputPath) {
        await fs.writeFile(outputPath, finalContent, 'utf-8');
      }
      
      // Calculate statistics
      const charCount = finalContent.length;
      const pageCount = Math.max(1, Math.floor(charCount / 3000)); // Rough estimate
      
      return {
        success: true,
        markdown_content: finalContent,
        output_file: outputPath,
        page_count: pageCount,
        char_count: charCount,
        images_extracted: 0, // Marker doesn't extract images to separate files
        processing_time: Date.now() - startTime,
        memory_used: 0, // Would need process monitoring
        warnings: options.auto_clean !== false ? ['Content automatically cleaned (table-aware)'] : []
      };
      
    } catch (error) {
      return {
        success: false,
        error: error instanceof Error ? error.message : String(error),
        page_count: 0,
        char_count: 0,
        images_extracted: 0,
        processing_time: Date.now() - startTime,
        memory_used: 0,
        warnings: []
      };
    }
  }

• src/index.ts:675-827 (helper)

  Helper function implementing PDF conversion using pymupdf4llm via dynamically generated Python script execution, supporting advanced options like image extraction and page chunking.

  async function convertWithPymupdf4llm(
    pdfPath: string,
    outputPath?: string,
    options: {
      page_chunks?: boolean;
      write_images?: boolean;
      image_path?: string;
      table_strategy?: "fast" | "accurate";
      extract_content?: "text" | "figures" | "both";
    } = {}
  ): Promise<ConversionResult> {
    const startTime = Date.now();
    
    try {
      // Validate PDF exists
      const validatedPdfPath = validatePath(pdfPath);
      await fs.access(validatedPdfPath);
      
      // Build Python conversion script for pymupdf4llm
      const pythonScript = `
  import pymupdf4llm
  import json
  import sys
  import os
  import gc
  import psutil
  
  def get_memory_usage():
      process = psutil.Process(os.getpid())
      return process.memory_info().rss / 1024 / 1024  # MB
  
  # Get initial memory
  initial_memory = get_memory_usage()
  
  try:
      # Set up conversion options
      kwargs = {}
      ${options.page_chunks ? "kwargs['page_chunks'] = True" : ""}
      ${options.write_images ? "kwargs['write_images'] = True" : ""}
      ${options.image_path ? `kwargs['image_path'] = "${options.image_path}"` : ""}
      
      # Convert PDF to markdown
      pdf_path = "${validatedPdfPath.replace(/\\/g, '\\\\\\\\')}"
      md_content = pymupdf4llm.to_markdown(pdf_path, **kwargs)
      
      # Get memory usage after conversion
      peak_memory = get_memory_usage()
      
      # Calculate statistics
      char_count = len(md_content)
      page_count = 0  # pymupdf4llm doesn't directly expose page count
      images_extracted = 0  # Would need to count files in image_path if provided
      
      # Estimate page count from content (rough heuristic)
      if isinstance(md_content, list):
          page_count = len(md_content)
          md_content = "\\n\\n---\\n\\n".join(md_content)
      else:
          # Estimate based on typical PDF page length
          page_count = max(1, char_count // 3000)
      
      # Count extracted images if image_path was provided
      ${options.write_images && options.image_path ? `
      if os.path.exists("${options.image_path}"):
          images_extracted = len([f for f in os.listdir("${options.image_path}") if f.lower().endswith(('.png', '.jpg', '.jpeg', '.gif'))])
      ` : ""}
      
      result = {
          "success": True,
          "markdown_content": md_content,
          "page_count": page_count,
          "char_count": char_count,
          "images_extracted": images_extracted,
          "memory_used": peak_memory - initial_memory,
          "warnings": []
      }
      
      # Write to file if output_path provided
      ${outputPath ? `
      output_path = "${validatePath(outputPath).replace(/\\/g, '\\\\\\\\')}"
      with open(output_path, 'w', encoding='utf-8') as f:
          f.write(md_content)
      result["output_file"] = output_path
      ` : ""}
      
      print(json.dumps(result))
      
  except Exception as e:
      result = {
          "success": False,
          "error": str(e),
          "page_count": 0,
          "char_count": 0,
          "images_extracted": 0,
          "memory_used": get_memory_usage() - initial_memory,
          "warnings": []
      }
      print(json.dumps(result))
      sys.exit(1)
  `;
  
      // Execute conversion
      const result = await new Promise<ConversionResult>((resolve, reject) => {
        const pythonProcess = spawn('python3', ['-c', pythonScript], {
          stdio: ['pipe', 'pipe', 'pipe']
        });
  
        let stdout = '';
        let stderr = '';
  
        pythonProcess.stdout.on('data', (data: Buffer) => {
          stdout += data.toString();
        });
  
        pythonProcess.stderr.on('data', (data: Buffer) => {
          stderr += data.toString();
        });
  
        pythonProcess.on('close', (code: number | null) => {
          try {
            const result = JSON.parse(stdout.trim()) as ConversionResult;
            result.processing_time = Date.now() - startTime;
            
            if (stderr.trim()) {
              result.warnings.push(stderr.trim());
            }
            
            resolve(result);
          } catch (parseError) {
            reject(new Error(`Failed to parse conversion result: ${parseError}, stdout: ${stdout}, stderr: ${stderr}`));
          }
        });
  
        pythonProcess.on('error', (error: Error) => {
          reject(error);
        });
      });
  
      return result;
  
    } catch (error) {
      return {
        success: false,
        error: error instanceof Error ? error.message : String(error),
        page_count: 0,
        char_count: 0,
        images_extracted: 0,
        processing_time: Date.now() - startTime,
        memory_used: 0,
        warnings: []
      };
    }
  }