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https://issues.apache.org/jira/browse/PDFBOX-4640?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16920962#comment-16920962
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Tilman Hausherr commented on PDFBOX-4640:
-----------------------------------------

{quote}The issue is when you flatten a document with other annotations (and 
their opacity is not 100%), so if we have a document with a PDF Form and other 
kind of annotations, and some of these opacity is less than 100%, PDFBox loses 
them. I think it is a bug.{quote}

That's what you wrote before. Sadly you didn't attach your other PDF, nor did 
you try with the command line utility. Your code is not self-working, some 
variables are not declared.

So I tried to reproduce your alleged bug with this code:
{code}
import java.io.File;
import org.apache.pdfbox.io.MemoryUsageSetting;
import org.apache.pdfbox.multipdf.PDFMergerUtility;
import org.apache.pdfbox.pdmodel.PDDocument;
import org.apache.pdfbox.pdmodel.PDPage;
import org.apache.pdfbox.pdmodel.interactive.form.PDAcroForm;

public class PDFBox4640
{
    public static void main(String[] args)
    {
        // create an empty document with 1 empty page (alternatively: load some 
document)
        PDDocument document = new PDDocument();
        document.addPage(new PDPage());

        File sourceFile = new File("highlighted pdf.pdf");

        PDFMergerUtility ut = new PDFMergerUtility();
        PDDocument sourceDocument = null;
        try
        {
            sourceDocument = PDDocument.load(sourceFile, 
MemoryUsageSetting.setupTempFileOnly());
            sourceDocument.getDocumentCatalog().setDocumentOutline(null);
            PDAcroForm acroForm = 
sourceDocument.getDocumentCatalog().getAcroForm();
            if (acroForm != null)
            {
                acroForm.flatten();
                acroForm.getFields().clear();
            }
            ut.appendDocument(document, sourceDocument);
            document.save("result.pdf");
        }

        catch (Exception ex)
        {

        }
    }
}
{code}
I have attached the result file. Your annotations are now on page 2 and all 
visible. Your document does not have any acroform.

> PDF Annotations missed when merging documents
> ---------------------------------------------
>
>                 Key: PDFBOX-4640
>                 URL: https://issues.apache.org/jira/browse/PDFBOX-4640
>             Project: PDFBox
>          Issue Type: Bug
>          Components: Utilities
>    Affects Versions: 2.0.16
>            Reporter: Daniel Martin Garcia
>            Priority: Major
>              Labels: merge
>         Attachments: highlighted pdf.pdf, result.pdf
>
>
> Hi,
> There is a bug when PDFBox merges documents with annotations, but the 
> annotation opacity is not 100%. If the opacity is less than 100%, the 
> annotation is lost.
>  
> I attach a document with an annotation which opacity is 60%, if you create a 
> test to merge this pdf with other PDF, the annotation won't be in the merged 
> pdf.



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