#1159 "Find unlinked files" crashes

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When using the "find unlinked files" tool, it only works for a small amount of files (pdf-files in my case). If it is for example 15-300 files (I tried different amounts of files), after hitting "Apply", the "Importing into Database" freezes after importing several files.


  • Oliver Kopp

    Oliver Kopp - 2013-05-27

    Is it really dependent on the amount of files? Here, it worked with hundreds of files. Maybe the PDF content importer causes problems. In any case, can you send me a ZIP with the files causing troubles? My email username @ users.sf.net works.

  • Oliver Kopp

    Oliver Kopp - 2013-05-27
    • assigned_to: Oliver Kopp
  • Hannes Schniepp

    Hannes Schniepp - 2015-02-17

    I have the same issue here. However, I found out that it is not the number of files that is the problem in my case. There are rather particular files (I would say about 5-10% of all my PDFs) that cause a problem. It is very reproducible; I am happy to provide sample PDFs.

    When the problem happens, JabRef becomes unresponsive, but at zero CPU load. JabRef then has to be killed, because the modal Search window cannot be closed (hitting the close button does nothing).

    The command line reports some kind of exception (see below).
    Any help in this matter would be greatly, greatly appreciated!


    Warning: empty BibTeX key: N/A: "N/A" (2006) (grouping may not work for this entry)
    Could not get key binding for "Open folder"
    Exception in thread "Thread-7" java.lang.IllegalArgumentException: Comparison method violates its general contract!
    at java.util.TimSort.mergeHi(TimSort.java:868)
    at java.util.TimSort.mergeAt(TimSort.java:485)
    at java.util.TimSort.mergeCollapse(TimSort.java:408)
    at java.util.TimSort.sort(TimSort.java:214)
    at java.util.TimSort.sort(TimSort.java:173)
    at java.util.Arrays.sort(Arrays.java:659)
    at java.util.Collections.sort(Collections.java:217)
    at org.apache.pdfbox.util.PDFTextStripper.writePage(PDFTextStripper.java:565)
    at org.apache.pdfbox.util.PDFTextStripper.processPage(PDFTextStripper.java:457)
    at org.apache.pdfbox.util.PDFTextStripper.processPages(PDFTextStripper.java:381)
    at org.apache.pdfbox.util.PDFTextStripper.writeText(PDFTextStripper.java:340)
    at net.sf.jabref.imports.PdfContentImporter.importEntries(PdfContentImporter.java:238)
    at net.sf.jabref.imports.EntryFromPDFCreator.createBibtexEntry(EntryFromPDFCreator.java:74)
    at net.sf.jabref.imports.EntryFromFileCreator.createEntry(EntryFromFileCreator.java:84)
    at net.sf.jabref.imports.EntryFromFileCreatorManager.addEntrysFromFiles(EntryFromFileCreatorManager.java:125)
    at net.sf.jabref.FindUnlinkedFilesDialog$8.run(FindUnlinkedFilesDialog.java:545)
    at java.lang.Thread.run(Thread.java:745)

  • Hannes Schniepp

    Hannes Schniepp - 2015-02-17

    I am attaching a PDF that triggers the problem.

    • Oliver Kopp

      Oliver Kopp - 2016-03-11

      Thank you. With the current MASTER branch (2016-03-11, dc5b332), there is no exception displayed. Possibly, because meanwhile the used libraries have been updated.

  • Oliver Kopp

    Oliver Kopp - 2016-03-11
    • status: open --> closed
  • Ashfaque Shafique

    I would like to open this ticket again. I downloaded the 64 bit version just yesterday and this is happening to me as well. It seems like a few specific PDFs cause this problem and the only way is to kill the job.


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