Annotations added in an external app do not carry zotero links even after import

agapeko

In my ideal workflow, I would like to do my reading and annotations in a more powerful pdf reader that suits my personal needs, such as sioyek, import these annotations into Zotero with links, and then make clickable notes using obsidian or other similar apps.

It can be enormously helpful if Zotero adds this little feature.

Sorry for my clumsy English, and thanks for reading this presumptuous supplication of mine.
  • agapeko
    My bad. It turns out that only imported sticky notes don't have link with them, imported highlights work perfectly.

    But I still wonder why sticky notes and notes created by selecting area with no comment can't have copyable links.
  • dstillman
    I'm not totally sure what you're referring to. Can you provide Steps to Reproduce?
  • agapeko
    edited November 12, 2022
    Thanks for replying.


    Steps to reproduce:

    1. I made some sticky notes to a pdf file in adobe acrobat.

    2. Open the said pdf with zotero pdf viewer.

    3. Select File > import annotations

    4. Ctrl+C any of those sticky notes, copy and paste them into notepad and obsidian.

    5. I found no zotero links copied.


    Conclusion:

    Most likely this doesn't constitute an error. But what I found out is that whether imported from an external pdf reader or not, with regard to annotations, Zotero doesn't offer links to sticky notes, and similarly doesn't give links to "select area" notes if you haven't written comments on them.

    It would be quite nice if zotero could support links to annotation in these situations as it does with highlights.
  • dstillman
    So first, as you say, that wouldn't have anything to do with their being external annotations.

    But then this should certainly work. What's the actual output that you're getting? You should be get something like this for a note annotation in plain-text mode:
    ([Smith, 2018, p. 87](zotero://select/library/items/IMYBKDS2)) This is my note.
    Though that's actually a bug — there should be a PDF link as well, which already is included for highlight and image annotations.

    Note that, for Obsidian in its default mode, you would have to enable Zotero links for "Rich Text/HTML" from the Export pane of the preferences. You should get the Markdown links by default when pasting into a plain-text editor. But it sounds like you're seeing those links for highlights, so I'm a bit confused what you're seeing here.
  • hrald
    edited August 27, 2023
    I just came across this exact same bug (was looking for it being filed somewhere already, before creating a new GitHub issue – and thus came across this thread).

    The zotero links to the annotation (rather than just the item) only work for annotations of the types 'highlighted text' and 'highlighted area'.
    None of the others, i.e. sticky notes, underlines, text annotation, freehand annotation, carry zotero links to the annotation, when copying.
    I used a clipboard viewer to verify this, so it is not an issue involving the application that is receiving the pasted note.
    (This is Zotero 7, downloaded and installed yesterday.)

    @dstillman : I suppose this should be pretty easy to fix, as the annotation types that do not work share quite some code with those working already?

    Would also appreciate a hint towards any plugin or other solution for getting this working.

  • dstillman
    @hrald: The OP didn't respond to my last question, and I don't know what you're reporting here. We always need Steps to Reproduce.
  • hrald
    @dstillman: I was referring to your previous post "You should be get something like this for a note annotation in plain-text mode:
    '([Smith, 2018, p. 87](zotero://select/library/items/IMYBKDS2)) This is my note. ' Though that's actually a bug — there should be a PDF link as well, which already is included for highlight and image annotations."

    How to reproduce:
    1. Add a new annotation of any type other than text highlight or area highlight (i.e. a sticky note, underline, text annotation or freehand annotation) to a PDF using the Zotero (7) reader.

    2. In the left side-bar with list of annotation, select the annotation you just created.

    3. Copy the annotation (⌘+C on Mac)

    4. Paste into a plain-text application (or view the clipboard contents using a clipboard viewer)

    You will see something like "(Seo et al., 2023, p. 1) this is inside a sticky note" with the citation being a hyperlink that highlights the PDF in the library – but it does not take you to the location of the annotation inside the document.

    For an area highlight, following the same steps, I get: "(pdf) 
(Seo et al., 2023, p. 1) using this instead of sticky note as a workaround?" where the "(pdf)" is a hyperlink that takes me directly to the location of the annotation inside the document.

    I expected, that any type of annotation, when copied, should come with such a deep link to the location in the pdf.
  • dstillman
    OK, that was a confusing description — we're talking about plain-text output, so all you need to do is share the actual output for both cases — but yes, the lack of a "(pdf)" link for some annotation types hasn't yet been fixed and now applies to new annotation types as well.
  • hrald
    Just want to add another case, where there is lack of "(pdf)" link: iOS/iPad app.

    Does not seem too relevant at first, but would allow for nice workflows using iPad and Mac in parallel and leveraging either the shared clipboard and/or Universal Control.

    Would also be curious to hear if more options f.e. directly including the image when copying area highlights are in discussion.
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