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https://issues.apache.org/jira/browse/PDFBOX-3889?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16120162#comment-16120162
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Tilman Hausherr commented on PDFBOX-3889:
-----------------------------------------

If you want to use the owner password (despite that your file opens with the 
empty user password), then you need to pass it to loadNonSeq, e.g.
{code}
PDDocument.loadNonSeq(file, raf, password);
{code}
Do not call decrypt.

> javax.crypto.BadPaddingException: Given final block not properly padded
> -----------------------------------------------------------------------
>
>                 Key: PDFBOX-3889
>                 URL: https://issues.apache.org/jira/browse/PDFBOX-3889
>             Project: PDFBox
>          Issue Type: Bug
>          Components: Crypto
>    Affects Versions: 1.8.13
>         Environment: Java 1.8.  Pdfbox 1.8.13  Windows and Linux
>            Reporter: Lucille Wilson
>              Labels: security
>         Attachments: 14-03-1159.pdf
>
>   Original Estimate: 24h
>  Remaining Estimate: 24h
>
> Using the attached pdf, When running the pdf through 
> org.apache.pdfbox.pdmodel.encryption.SecurityHandler I get 
> BadPaddingException.
> The exception occurs when it is processing 
> nextObj = COSObject{3304,0} I see: nextCOSBase = 
> COSDictionary{(COSName{Length}:COSInt{3504}) (COSName{Subtype}:COSName{XML}) 
> (COSName{Type}:COSName{Metadata}) } 
> The problem is that SecurityHandler.proceedDecryption() runs  
> decryptObject(nextObj);
>  and then decrypt(base, objNum, genNum) and then decryptStream()
> However for this object decryptStream doesn't actually decrypt anything 
> because the type is xml.  
> So when decryptStream calls encryptData() encryptData() throws the bad packet 
> exception.
>  output.write(decryptCipher.doFinal()); throws the exception because the data 
> buffer is all zeros.  It has nothing in it.  I recommend that encryption be 
> skipped if the data buffer has all zeros.



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