Zotfile extension does not extract pdf annotations anymore

helencrump
Zotfile extension no longer extracts my pdf annotations. It just performs the action and returns a big red cross. I don't really know where to start to troubleshoot this. It is so annoying. Help appreciated.
  • adamsmith
    Have you tried this with PDFs that previously worked?
  • helencrump
    No, but now that I try it, PDFs that I extracted annotations previously still work. The only things that I might have changed in the meantime is OS to El Capitan and I changed my PDF default preference to Skim and not Preview. Does that help?
    Thanks for reply
  • adamsmith
    yup. Skim uses a non-standard format for annotations. ZotFile can't extract them.
  • helencrump
    Oh, gosh. That's a blow. I like Skim. What PDF reader do you recommend for best extracting annotations and is compatible with a Mac?
  • adamsmith
    I think Joscha himself just uses Preview. I don't use Mac.
  • helencrump
    OK - thanks for your help.
  • kithairon
    edited February 27, 2016
    All what adamsmith is saying is accurate. Skim in its default settings deliberately doesen't save notes into the pdf itself but into a second file (.skim) that lives in the same folder as the pdf – this is a feature.

    However, there is a possibility to force Skim to export its notes in standard readable format, i.e. that zotfile can then extract your notes into Zotero. While possible, it remains somewhat impracticable if you want to read in Skim and extract your notes more than once. Also, this only works for actual notes, ("Fixed note") and not for any highlights you mark in Skim.

    After you have made your notes and saved in Skim, choose File> Export and then the option "Embedded Notes". The resulting file is readable and Zotfile will extract the notes into Zotero.

    You can even set Zotfile to open the link in the Zotero note with Skim (instead of Preview) with help of Hidden Options in about:config by changing the
    zotfile.pdfExtraction.openPdfMac_skim to "true".

    I've settled to using Acrobat and Preview myself for annotations albeit I'm fond of Skim for some of its other features.
  • adamsmith
    (thanks for those details -- as I say, I don't use a Mac, so I'm only aware of the mere basics)
  • clousley
    I'm having this problem, too, but I am using Adobe Acrobat Pro, the same as I always have before. I have clicked Extract Annotations three times, and nothing appears. I check the source file, though, and the annotations exist.
  • adamsmith
    Make sure your zotfile is up to date. This was broken in 4.0.25
  • clousley
    Yes, just updated zotfile, and the problem has been fixed. Sorry for not finding the right thread before posting.
  • jec10
    Thanks, had the same problem with Zotfile pdf extractions, and updating Zotfile solved it.

    In regard to Mac PDF editors, I recommend Highlights for pdf reading (on the app store). Unlike Skim, it uses standard pdf comments and annotations that can be read by any app (and extracted with zotfile), but It also allows you to export annotations (including quotations that you have highlighted) as plain text, pdf, or markdown to import or cut and paste into other applications (Ulyssess, Scrivener, Onenote, Evernote, Mail, etc). When you highlight text in a pdf, Highlights shows the highlighted text in the comment side pane, making it easier to review your notes while reading.

    The latest version of Adobe Reader DC (free) also has improved its annotation features from previous versions. I find it better for reading and commenting on student papers or manuscripts from publishers, but still tend to do my research notes in Highlights.

    Preview is also a free option, but I find the comment options more limited than the other apps.
  • John_muccigrosso
    I'm a bit confused about how the PDF annotation extraction is supposed to work. Mostly I've been using it lately on copies of articles I've scanned myself and OCRed with tesseract.

    1. Changing the Skim pref to true doesn't seem to do anything different for me on my El Cap macbook with standalone Zotero 4. The PDF still opens in my default PDF reader when I double click or hit return on it. Extraction also looks the same as it does with the pref set to false.
    2. Extracting with poppler gives me different and better results from pdf.js (which is pretty awful on some of my scanned-article PDFs), but they don't match what is actually highlighted very well. In contrast Skim reads the comments _very_ well and with an applescript I can get them out easily. If I could figure out how to get the "actual" page numbers, I'd be pretty happy. I wouldn't miss the links into the PDF.
  • areinhartz
    I know this thread is a few years old but I am having this same issue with pdfs. I use a Mac and recently switched from Preview to Adobe for pdfs and while I can highlight the pdfs, the attempt to extract the annotations result in a big X. My zotfile is up-to-date. Any help greatly appreciated.
  • areinhartz
    And a quick update: I changed the default pdf viewer to Preview and the annotations extracted perfectly.
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