Error opening tmp PDF from my Java application when run from JAR but not Eclipse

Question

I want to be able to open a PDF file when the user clicks on 'HELP' in my application. The PDF file is located with the JAR, extracted to a tmp directory and then selected to open by awt.Desktop.getDesktop () (to allow for windows and linux use).

When I run the app from Eclipse then it works fine, the PDF opens with no errors. When I export to JAR and run then I get an error stating the 'PDF document is damaged', if I navigate manually to the PDF document (on my ubuntu machine /tmp/546434564.pdf) then I get the same error when I try to open the file. I am confused what is going on. The file size of the 'damaged' PDF is the same as the working one, so I dont think it is a permission issue.

The code I am using is:

public Main() throws FontFormatException, IOException {

    //lets load the font
       Font font = Font.createFont(Font.TRUETYPE_FONT, this.getClass().getResourceAsStream("/Coalition_v2.ttf")).deriveFont(Font.PLAIN, 14); 
       System.out.println(font);

    //lets write the tmp file for help to the machine now
       try {
            java.io.InputStream iss = getClass().getResourceAsStream("/nullpdf.pdf"); //update the filename here when the help guide is written
            byte[] data = new byte[iss.available()];
            iss.read(data);
            iss.close();
            String tempFile = "file";
            File temp = File.createTempFile(tempFile, ".pdf");
            FileOutputStream fos = new FileOutputStream(temp);
            fos.write(data);
            fos.flush();
            fos.close();
        tmphelpfile = temp.getAbsolutePath();
        System.out.println(tmphelpfile);
        } catch (IOException ex) {
            ex.printStackTrace();
            System.out.println("TEMP FILE NOT CREATED - ERROR in tmp file writing");
        }

And then to call the pdf:

JMenu mnHelpGuide = new JMenu("Help Guide");
mnHelpGuide.addMouseListener(new MouseAdapter() {
    @Override
    public void mouseClicked(MouseEvent e) {
    //  Help();
        Desktop d = java.awt.Desktop.getDesktop ();  

        try {
            System.out.println(tmphelpfile);
            d.open (new java.io.File (String.valueOf(tmphelpfile)));
        } catch (IOException e1) {
            // TODO Auto-generated catch block
            System.out.println("Couldnt open your file - error on HELP Guide");
            e1.printStackTrace();
        } 
    }
    });

Answer 1

Thanks for the help guys. The problem was fixed by importing the ApachecommonsIO jar and then modifying the code to this:

 try {
                java.io.InputStream iss = getClass().getResourceAsStream("/nullpdf.pdf"); //update the filename here when the help guide is written
               // byte[] data = new byte[iss.available()];
                byte[] data = IOUtils.toByteArray(iss);
                iss.read(data);
                iss.close();
                String tempFile = "file";
                File temp = File.createTempFile(tempFile, ".pdf");
                FileOutputStream fos = new FileOutputStream(temp);
                fos.write(data);
                fos.flush();
                fos.close();
            tmphelpfile = temp.getAbsolutePath();
            System.out.println(tmphelpfile);
            } catch (IOException ex) {
                ex.printStackTrace();
                System.out.println("TEMP FILE NOT CREATED - ERROR in tmp file writing");
            }