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A quick Google search returned this bug: "Bad file descriptor while saving a document w. imported PDFs".

It looks like you need to keep the PDFs to be merged open, until after you have saved and closed the combined PDF.

This is a ready to use code, merging four pdf files with itext.jar from http://central.maven.org/maven2/com/itextpdf/itextpdf/5.5.0/itextpdf-5.5.0.jar, more on http://tutorialspointexamples.com/

import com.itextpdf.text.Document;

import com.itextpdf.text.pdf.PdfContentByte;

import com.itextpdf.text.pdf.PdfImportedPage;

import com.itextpdf.text.pdf.PdfReader;

import com.itextpdf.text.pdf.PdfWriter;



/**

 * This class is used to merge two or more 

 * existing pdf file using iText jar.

 */

public class PDFMerger {



static void mergePdfFiles(List<InputStream> inputPdfList,

        OutputStream outputStream) throws Exception{

    //Create document and pdfReader objects.

    Document document = new Document();

    List<PdfReader> readers = 

            new ArrayList<PdfReader>();

    int totalPages = 0;



    //Create pdf Iterator object using inputPdfList.

    Iterator<InputStream> pdfIterator = 

            inputPdfList.iterator();



    // Create reader list for the input pdf files.

    while (pdfIterator.hasNext()) {

            InputStream pdf = pdfIterator.next();

            PdfReader pdfReader = new PdfReader(pdf);

            readers.add(pdfReader);

            totalPages = totalPages + pdfReader.getNumberOfPages();

    }



    // Create writer for the outputStream

    PdfWriter writer = PdfWriter.getInstance(document, outputStream);



    //Open document.

    document.open();



    //Contain the pdf data.

    PdfContentByte pageContentByte = writer.getDirectContent();



    PdfImportedPage pdfImportedPage;

    int currentPdfReaderPage = 1;

    Iterator<PdfReader> iteratorPDFReader = readers.iterator();



    // Iterate and process the reader list.

    while (iteratorPDFReader.hasNext()) {

            PdfReader pdfReader = iteratorPDFReader.next();

            //Create page and add content.

            while (currentPdfReaderPage <= pdfReader.getNumberOfPages()) {

                  document.newPage();

                  pdfImportedPage = writer.getImportedPage(

                          pdfReader,currentPdfReaderPage);

                  pageContentByte.addTemplate(pdfImportedPage, 0, 0);

                  currentPdfReaderPage++;

            }

            currentPdfReaderPage = 1;

    }



    //Close document and outputStream.

    outputStream.flush();

    document.close();

    outputStream.close();



    System.out.println("Pdf files merged successfully.");

}



public static void main(String args){

    try {

        //Prepare input pdf file list as list of input stream.

        List<InputStream> inputPdfList = new ArrayList<InputStream>();

        inputPdfList.add(new FileInputStream("..\pdf\pdf_1.pdf"));

        inputPdfList.add(new FileInputStream("..\pdf\pdf_2.pdf"));

        inputPdfList.add(new FileInputStream("..\pdf\pdf_3.pdf"));

        inputPdfList.add(new FileInputStream("..\pdf\pdf_4.pdf"));





        //Prepare output stream for merged pdf file.

        OutputStream outputStream = 

                new FileOutputStream("..\pdf\MergeFile_1234.pdf");



        //call method to merge pdf files.

        mergePdfFiles(inputPdfList, outputStream);     

    } catch (Exception e) {

        e.printStackTrace();

    }

    }

}

package article14;



import java.io.File;

import org.apache.pdfbox.pdmodel.PDDocument;

import org.apache.pdfbox.pdmodel.PDPage;

import org.apache.pdfbox.util.PDFMergerUtility;



public class Pdf

{

    public static void main(String args)

    {

        new Pdf().createNew();

        new Pdf().combine();

        }



    public void combine()

    {

        try

        {

        PDFMergerUtility mergePdf = new PDFMergerUtility();

        String folder ="pdf";

        File _folder = new File(folder);

        File filesInFolder;

        filesInFolder = _folder.listFiles();

        for (File string : filesInFolder)

        {

            mergePdf.addSource(string);    

        }

    mergePdf.setDestinationFileName("Combined.pdf");

    mergePdf.mergeDocuments();

        }

        catch(Exception e)

        {



        }  

    }



public void createNew()

{

    PDDocument document = null;

    try

    {

        String filename="test.pdf";

        document=new PDDocument();

        PDPage blankPage = new PDPage();

        document.addPage( blankPage );

        document.save( filename );

    }

    catch(Exception e)

    {



    }

}



}

Multiple pdf merged method using org.apache.pdfbox:

public void mergePDFFiles(List<File> files,

                          String mergedFileName) {

    try {

        PDFMergerUtility pdfmerger = new PDFMergerUtility();

        for (File file : files) {

            PDDocument document = PDDocument.load(file);

            pdfmerger.setDestinationFileName(mergedFileName);

            pdfmerger.addSource(file);

            pdfmerger.mergeDocuments(MemoryUsageSetting.setupTempFileOnly());

            document.close();

        }

    } catch (IOException e) {

        logger.error("Error to merge files. Error: " + e.getMessage());

    }

}

From main program, call mergePDFFiles method using list of files and target file name.

        String mergedFileName = "Merged.pdf";

        mergePDFFiles(files, mergedFileName);

After calling mergePDFFiles, load merged file

        File mergedFile = new File(mergedFileName);

If you want to combine two files where one overlays the other (example: document A is a template and document B has the text you want to put on the template), this works:

after creating "doc", you want to write your template (templateFile) on top of that -

   PDDocument watermarkDoc = PDDocument.load(getServletContext()

                .getRealPath(templateFile));

   Overlay overlay = new Overlay();



   overlay.overlay(watermarkDoc, doc);

Using iText (existing PDF in bytes)

    public static byte mergePDF(List<byte> pdfFilesAsByteArray) throws DocumentException, IOException {



    ByteArrayOutputStream outStream = new ByteArrayOutputStream();

    Document document = null;

    PdfCopy writer = null;



    for (byte pdfByteArray : pdfFilesAsByteArray) {



        try {

            PdfReader reader = new PdfReader(pdfByteArray);

            int numberOfPages = reader.getNumberOfPages();



            if (document == null) {

                document = new Document(reader.getPageSizeWithRotation(1));

                writer = new PdfCopy(document, outStream); // new

                document.open();

            }

            PdfImportedPage page;

            for (int i = 0; i < numberOfPages;) {

                ++i;

                page = writer.getImportedPage(reader, i);

                writer.addPage(page);

            }

        }



        catch (Exception e) {

            e.printStackTrace();

        }



    }



    document.close();

    outStream.close();

    return outStream.toByteArray();



}