New Beta PDF viewer reader, possible bug or work-around help please?

Hello. I've been a longtime Zotero user.

And I'm so thankful for its development.

I couldn't have done my research without it.

However, I've recently installed the new beta - because I heard it had a really sweet PDF viewer - and I wanted to check it out. So far, the annotations work great. I'm really happy that Zotero correctly identifies the page number, whereas other PDF applications like Adobe, or Sumatra, struggle with that. This is amazing in Zotero I am so happy I could cry. :)

So for example, you can see from one of my screenshots that I did an annotation on page 61 of the PDF. Even though internally, the PDF, indicates a page number of 78 of 207. In terms of the textbook, it is indeed page 61 that the annotation is found on. So Zotero did great work, identifying that!

However, the problem really lies here: now that I've finished reading the textbook, let's say, and I would like to extract my annotations for study. And for further research. But it seems that no matter what I do, the new beta simply does not export correct annotation pages, it resorts back to the "incorrect" internal page numbering, not the logical one that I would assume.

Imagine studying a textbook with a ton of annotations. This could be a headache of wrong citations.

Is there any workaround for this please, how to get correct page numbers on extract since it's already correct upon creating the annotation?

And on that note, I couldn't find any way to extract my annotations in the new beta without first saving them in the PDF, and thus removing them from the Zotero ecosystem. Is this correct behavior? If so, no problem just curious. If not, what did I miss?

Because when you do store annotations in the PDF file, you get a warning that says basically the functionality will be limited. And so after I select that option then I am able to extract annotations. And that is when I received the incorrect page number, which would be very difficult with hundreds of annotations and page references for a research paper.

Is there anything you could tell me how we can get this workaround in Zotero? Correctly export the correct page number? Clearly, it saves it correctly in the PDF viewer when you create the annotation that's very easily repeatable. :)

However, I just can't find a way to export them correctly. It keeps taking the incorrect number of the PDF, not the actual page number. I was optimistic about the new beta. And so I'm hoping that there is a solution or workaround. Thank you again for all the hard work in making this program the powerhouse that it is.

If this solution requires a bounty or more funding for bug squashing, I'd be happy to contribute more to the project. Thank you so much. I hope I spoke clearly.

I hope my detailed information helped in some way too. I tried my best.


Screenshot #1: Zotero new PDF viewer handles correct pages numbers flawlessly when saving annotations. This is huge!!! :) Page 61 is correct, not page 78.

Screenshot #2: Zotero exports annotations incorrectly, instead choosing page 78, which is the internal page number, not the correct page 61 as it did upon saving annotation in PDF viewer.

Screenshot #3: Zotero cannot save annotations unless you store all annotations in a PDF and export / lose functionality in Zotero.
  • For the new beta you no longer need Zotfile extension to extract annotations. Just right-click on an item and use "Add Note from Annotations". That will solve all your mentioned problems.
  • Hi,
    Thank you for trying to help me.

    But sorry, I don't see this option anywhere. How can I select it please?


    I have just downloaded and installed the newest beta from Zotero.

    Thank you.
  • edited December 9, 2021
    Shoot, I feel stupid. I just realized I wasn't clicking on the top level item. I now see the option. Wow. This is great. So this will be how Zotero functions moving forward, yes?

    May I ask one more thing. Let's say I finish adding the note with all annotations for an entire book. Can I export this entire note of annotations into a LibreOffice document or PDF or something? Or do I just have to select all and copy paste manually?

    Also, the font choice for the note of annotations doesn't quite look right to my eyes. Can that be changed, or only size?

    Thank you so much. I could cry this new Zotero PDF viewer is a dream. So happy.
  • Yes, currently only parent item has it.

    And for the "Add to Note" you must open a note on the right-hand pane to activate the option.
  • Let's say I finish adding the note with all annotations for an entire book. Can I export this entire note of annotations into a LibreOffice document or PDF or something?
    Yes, there's a new Add Note button in the word processor plugin (mentioned in the preview announcement).
    Also, the font choice for the note of annotations doesn't quite look right to my eyes. Can that be changed, or only size?
    Could you say more, or upload a screenshot somewhere and provide a link? It should be the same font as the rest of Zotero.
  • I don't see the new Add Note button, do I have to enable it separately? I have the Zotero toolbar in Writer visible, but no Add Note appears.

  • The updated plugin should've been installed automatically, but if that didn't happen for you, you can reinstall it manually from the Cite pane of the Zotero preferences.
  • edited December 11, 2021
    I see. I will check that thank you.

    One last thing about my original post.

    It seems that, even though I can create a note from annotations correctly now, all the 'selected area' annotations appear as images but can't be copy/pasted into Joplin or outside of Zotero. It's just a blank placeholder. Yes, it shows the image but it doesn't copy anything, no path, nothing.

    How is Zotero "saving" the selected area annotations, as jpgs? I don't understand. It feels locked in to Zotero.

    Are these selected area annotations just fake snapshots where they are literally just "mirroring" the PDF screenshot and not actually a JPG or PNG? It seems like that when I look at the markdown code after copying this annotation into Joplin.
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