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https://issues.apache.org/jira/browse/PDFBOX-1016?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13052555#comment-13052555
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Timo Boehme commented on PDFBOX-1016:
-------------------------------------

If you applied the patch from this Fix (with XrefTrailerResolver.java etc.) you 
should get the correct order where 2 overwrites 1. In XrefTrailerResolver first 
the list of XREFs ist build (in setStartxref()), which means in this case [2; 
1] and this list is reversed [1; 2] and with the reversed list the table is 
build (first entries from 1 are applied, than entries from 2, possibly 
overwriting entries from 1).
Only in case startxref was not set or points to a wrong byte offset the 
algorithm falls back to current trunk behavior using xrefs in order they appear 
in document (here [2; 1]). In this case you should have got a warning in log.
Could you please check that startxref is set and no warning messages are 
generated?
 

> Specification conform xref/trailer parsing + Fix
> ------------------------------------------------
>
>                 Key: PDFBOX-1016
>                 URL: https://issues.apache.org/jira/browse/PDFBOX-1016
>             Project: PDFBox
>          Issue Type: Bug
>          Components: Parsing
>    Affects Versions: 1.6.0
>            Reporter: Timo Boehme
>         Attachments: COSDocument.diff, PDFParser.diff, 
> PDFXrefStreamParser.diff, XrefTrailerResolver.java, XrefTrailerResolver.java
>
>   Original Estimate: 10m
>  Remaining Estimate: 10m
>
> PDFBOX currently reads xref table/trailer and XRef objects without using 
> startxref or 'Prev' information which results in applying not active data 
> resulting in using wrong objects or resulting in parsing exceptions because 
> old trailer settings do not apply anymore. This happens especially with 
> updated PDF documents where changes are simply appended  and old objects/xref 
> entries remain but are not referenced. My last patch (PDFBOX-1014) tried to 
> solve this for a specific case but it was based on assumptions which do not 
> hold in every case.
> The specification compliant way is to read the last startxref which points to 
> the last xref object which itself may reference further xref objects using 
> 'Prev' attribute.
> I have written a fix which works the standard way and can fall back to the 
> old behavior in case startxref is wrong or missing. The fix tries to be as 
> unobtrusive as possible. A new class (o.a.p.pdfparser.XrefTrailerResolver) is 
> filled with all xref table/trailer and XRef object data. After document is 
> parsed (and last startxref is read) this class creates xref table and trailer 
> using startxref and 'Prev' information. Beside this new class there are small 
> changes to PDFParser and COSDocument.
> This bugfix/improvement should bring PDFBOX a good step closer to be PDF 
> specification conform - especially as long as the new specification conform 
> parser project is not finished.
> This bugfix supersedes the fix from PDFBOX-1014.

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