Zotero 7: Clicking links of EPUB and HTML annotation doesn't bring me to the highlight location

nhan000
edited August 30, 2023
In Zotero 6, dragging highlight into a Markdown-based note-taking apps will result in links such as:

“13.1 naming an ether” ([Klein, 2017, p. 558](zotero://select/library/items/R4XU76E9)) ([pdf](zotero://open-pdf/library/items/WCT6V3QH?page=578&annotation=YY3X9LPP))

And clicking the pdf link (zotero://open-pdf[…]) will bring me to the highlight location in Zotero. In Zotero 7, clicking this link for EPUB and HTML doesn't do anything. Is this feature not yet supported for EPUB and HTML files? If it's indeed hasn't been supported, If I make annotations now, will it work in the future when the feature is supported?

Also now that Zotero supports EPUB and HTML annotation, will the URI "zotero://open-pdf" change in the future (into something such as zotero://open-epub and zotero://open-html or Zotero will just use zotero://open-pdf for all 3 types of attachment?)

Another bug in Zotero 7 is that when clicking the highlight annotation for PDF, it takes me to the highlight location, but there's no flashing and color changing effect as in Zotero 6. It makes finding a highlight a bit harder if the page is annotated densely.
  • martynas_b
    So it doesn't work with EPUB and HTML files only, and with PDF files everything is perfectly fine?

    Yes, we're going to rename zotero://open-pdf to zotero://open, but still leave the former as an alias.
  • nhan000
    edited November 30, 2023
    Yep. Clicking the PDF link takes me to the highlight location in PDF, with the caveat that it doesn't flashing the highlighted selection as it did in Zotero 6 (also reported here https://forums.zotero.org/discussion/106833/zotero-7-beta-the-zotero-open-pdf-link-jump-loses-gradient-highlighting-style).

    For EPUB and HTML files, clicking the link doesn't do anything.

    Happened on
    - Windows 10, Zotero 7.0.0-beta.38+b79e0b3d7 (64-bit).
    - Windows 11, Zotero 7.0.0-beta.52+2f8e536f2 (64-bit) (partially fixed).

    Thanks for keeping the alias in the URI changes.

    Let me know if I should make another feature request, but I think it'd be nice to have the zotero://open protocol to work with all attachments, such as videos. If it's a file not supported by Zotero, when trigger by the protocol, Zotero will redirect it to the default app of the OS. This makes opening other types of attachments less cumbersome.
  • AbeJellinek
    Thanks - looking into this.
  • nhan000
    edited September 28, 2023
    It's still not yet fixed in the latest (7.0.0-beta.42+2db19ad4c) version.
  • drsb
    Can confirm the missing selection/highlighting of the annotation and in the left side bar for PDFs. (7.0.0-beta.42+2db19ad4c running on OpenSuse Leap 15.4.).
  • flowb
    It's still not yet fixed in the latest (7.0.0-beta.44+64a78412c (64-bit)) version. Very useful features, hoping to achieve the same functionality as Zotero6.


  • nhan000
    New update in this thread: https://forums.zotero.org/discussion/comment/448507/#Comment_448507
  • sojusnik
    See also those related threads:

    https://forums.zotero.org/discussion/110224/zotero-7-beta-highlights-and-underlines-are-copied-differently

    https://forums.zotero.org/discussion/110225/zotero-7-beta-linked-pdfs-are-always-opened-in-a-tab
  • zaisai
    Having the same problem. Linking to annotation / highlight only works for PDF.

    EPUB highlights / annotations don't link to the EPUB location - they just show up as:
    zotero://open-pdf/library/items/RAIXGZ5A?page=

    Using:
    Mac Sequoia 15.0.1, Zotero 7.0.10.

    Would love an update when this is fixed.
  • AbeJellinek
    @zaisai: The original issue reported in this thread was fixed before the official release of Zotero 7. This looks to be different.
    • What type of annotation are you trying to link to? Highlight, underline, note?
    • What text editor are you using?
    • What steps are you using to add the link to your document?
  • zaisai
    I'm reading EPUB documents in Zotero's native reader, creating highlights and notes, and then exporting them to Obsidian (so export to markdown files).

    I've got the following plugins installed to transfer my annotations:
    - Better BibTex installed for Zotero
    - Zotero Integrations installed for Obsidian

    I'm not sure how they work on the backend? But my template in Obsidian pulls the link in this format:
    zotero://open-pdf/library/items/{{annot.attachment.itemKey}}?page={{annot.page}}
  • AbeJellinek
    That template doesn’t look right for EPUBs (or items in group libraries - there’s just no reason you should have to construct these links manually at all, so I’m guessing there’s a better way). But you’re going to need to talk to the Obsidian plugin’s developer.
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