[jira] [Created] (PDFBOX-4541) Incorrect? handling of direct/indirect objects

["Jonathan (JIRA)" <ji...@apache.org>]

Jonathan created PDFBOX-4541:
--------------------------------

             Summary: Incorrect? handling of direct/indirect objects
                 Key: PDFBOX-4541
                 URL: https://issues.apache.org/jira/browse/PDFBOX-4541
             Project: PDFBox
          Issue Type: Bug
          Components: Parsing, Writing
    Affects Versions: 2.0.14
            Reporter: Jonathan


We ran into some issues concerning blank pages in some of our resulting PDF documents. Investigation showed that some objects which were referenced were never actually written. We then noticed that these objects were never written because they missed the `isDirect` flag. We were able to mitigate this issue by adding
{code:java}
if (retval != null) {
    retval.setDirect(true);
}
return retval;
{code}
at the end of `BaseParser.parseDirObject()`.

While the pdfs were now displayed correctly, QPDFs check reported erroneous hint tables. The offsets there were calculated incorrectly because the objects were now written not only once, but, in fact, several times in places where they should have been merely referenced. We eventually resolved this issue by replacing the if-condiction
{code:java}
if (willEncrypt || incrementalUpdate || subValue instanceof COSDictionary || subValue == null)
{code}
in `COSWriter.visitFromArray(COSArray)` and `COSWriter.visitFromDictionay(COSDictionary)` with
{code:java}
if (willEncrypt || incrementalUpdate || subValue == null || !(subValue instanceof COSObject))
{code}



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