Problem with Zotero's beta pdf reader and Zotfile's annotations export

Hi there

Recently I enrolled on Zotero's beta version to test the built in PDF reader. It seems quite nice and stable but I'm having an hard time exporting annotations using Zotfile. I've tried going back to a a 3rd party pdf reader and in that case I can export annotations.

So do I need to change any option or this is not compatible?

  • The new PDF reader can add annotations to notes natively. You don't need to use ZotFile for that, and ZotFile doesn't know anything about Zotero annotations.
  • So but how do you go about exporting annotation to let's say add it to your notetaking app?
  • edited September 16, 2021
    - You can copy and paste one or more annotations directly to the clipboard in the PDF view or the left-hand pane.

    - You can create a Zotero note from annotations in the right-hand Notes pane of the PDF reader or from the context menu in the items list.

    - You can drag individual annotations to notes in the Notes pane or a standalone note window.

    - You can copy notes into external editors.

    - You can use the new Add Note button in the word processor plugins to insert notes with annotations and active citations into documents and continue using the plugin to generate a bibliography.

    Additional export options for notes are coming soon.
  • I found that the "Extract Annotations" function is not working (right-click on item, Manage Attachments->Extract Annotations). However, if I open the PDF in Zotero there is a Notes(?) button [far-right of screen in the PDF menu bar] that will display "Item Notes" and "All Notes." In each of these options is a "+" (far-right of the title) and when pressed two options appear "Add Item Note" and "Add Item Note from Annotations." The latter will extract the annotations from the PDF (in my case those were made within the iPad app) into an Item Note. It is cludgy, but it does work. I wish the "Extract Annotations" would do this for me rather than all of these steps.
  • edited September 16, 2021
    @PatrickCLeech: That's one of the built-in options I listed above, meant for use while you're working in the PDF reader. As I said, you can also generate a note with all of the PDF's annotations right from the items list. These are built-in, one-click options, and I have no idea why you think they're kludgy — you can literally right-click on an item in the items list and choose "Add Note from Annotations".
  • @dstillman: I suspected that was one of the options you listed, but accessing the "Notes Pane" was not explained.
    Second, Zotero updated overnight, but I do not remember seeing the "Add Notes from Annotations" option in the context menu. I have tried it and it works beautifully!
  • OK, good to hear. (Both of these options have been available in the beta for months.)
  • I think I see why I missed it, the context menu option only appears when annotations are present (which makes sense); so when I first attempted I must have been on a file without annotations. Thanks!
  • Hi there. I'm running into the same issue. It seems to be a bug between the new reader and how Zotfile pulls annotations. It seems like the Zotero annotations are not saved to the actual PDF, so there is nothing to extract from Zotfiles perspective. The way I went around it was:

    1. Read and mark up in Zotero reader
    2. Once finished save the PDF file (file>save as) to desktop or somewhere
    3. Delete the PDF in Zotero
    4. Reimport the PDF from desktop into Zotero.
    5. Extra annotations.

  • @tlcallis To test if Zotero annotations are saved to the actual PDF file you have to open it with another PDF viewer and see if those annotations exist.
  • I have done that and they do not show up. The only way the annotations show is if you open the pdf in the built in reader where you made the annotations then they appear. But they will not generate an annotation export file from the library window since they do not exist. If you go to the file explorer where the pdf sits and open with an external reader the annotations are not there.
  • @ZebBe77 To export PDF file with annotations you have to open PDF tab and click "File -> Save As...", which will save a new PDF to a desired path. Currently you can't save annotations to the original PDF that is in Zotero data directory (although we are working on that).

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