PDF Annotations do not include Markdown Links

alexanderjfink
edited March 21, 2022
I've just upgraded to Zotero 6 (was excited for this one!) and the PDF reader looks great at first glance. I'm so excited to have it. So a general thanks to the whole team for all your hard work on this.

I've been using ZotFile and understand why the annotations extraction feature was replaced by Zotero - I think this is great. However, though the extractions feature on the release blog shows a URI link that goes back to the specific page of the PDF linked to the note, I cannot reproduce this in my Zotero. When I copy/Quick Copy out of Zotero, or when Obsidian Cite pulls my annotations from Zotero, I get a citation without the link:

“Fixation is an inability to progress normally from one stage into another” (Apgar, 2020, p. 139)

I've tried looking around the forums for a solution and haven't found anything that seemed to work. I wondered if there was some carryover setting from my previous Zotero/ZotFile setup that was blocking it. I looked at your page on Note Templates and couldn't find anything related to a URI: https://www.zotero.org/support/note_templates

In my Advanced -> Config Editor, I looked at extensions.zotero.annotations.noteTemplates.* and here are my templates:

*.annotations.noteTemplates.highlight - <p>{{highlight quotes='true'}} {{citation}} {{comment}}</p>

*.annotations.noteTemplates.note - <p>{{citation}} {{comment}}</p>

*.annotations.noteTemplates.title - <h1>{{title}}<br />({{date}})</h1>

I also still see the zotfile.pdfExtraction configs as well. Could that be causing this problem? Or am I just totally misreading/doing something wrong?

  • karagawa
    I have the same problem and do not know how to fix it. The quick copy-paste of the note from Zotero 6 to Obsidian does not include any links. Any ideas?
  • karagawa
    btw, if you export your note/annotations using the "right-click" function, and open the file in obsidian, it DOES include links. Just the "copy-paste" function doesn't work as expected.
  • alexanderjfink
    edited March 20, 2022
    @karagawa thanks for responding. I'm not sure what you mean in your second comment here. What is the "right-click" function you mention? For example, when I choose "Add Note from Annotations" and then used Citations plug-in in Obsidian, I do not get the links as I would expect a replacement to Zotfile to do. I'm getting them neither with the "Add Note from Annotations" option or the Quick Copy option.
  • karagawa
    @alexanderjfink Hey, just "right-click" on your note in Zotero and there is a new function called "export note" and it allows you to include the Zotero link. You can open that exported .md file in OB and get what you want. I would like to have those link directly from "copy-paste" though
  • erazlogo
    edited March 20, 2022
    @alexanderjfink @karagawa you need to disable the Setup > Editor > "Auto convert HTML" in Obsidian. Then the links will show up but you won't be able to convert italics when pasting HTML. If you want to keep that function, just press Shift when you drag-and-drop.
  • alexanderjfink
    Thanks @erazlogo ! That did fix the direct note copy and paste. However, when I import all notes from Zotero using the Obsidian Citations plugin, it still pulls them all without the links, which is confusing (as it used to pull them with the links). I wonder whether that'll have to be a fix from the Obsidian Citations plugin side?
  • alexanderjfink
    OK, I've examined the BibTex export that Obsidian Citations uses ([Library].bib) file.. the annotations do not have the URL any longer, so it isn't a problem on the Obsidian side, but something to do with how things are getting exported via Zotero or Better BibTex. I will post if I figure it out. Thanks @erazlogo and @karagawa for your thoughts and help.
  • chuantang
    Thanks @alexanderjfink! Zotero 6 is amazing, but it kind of breaks down the traditional way we did for annotation export or so. I think I have the exact issue as you about Obsidian Citations and Better BibTex output format. I will post my solution if I find one. And please share yours when you figure it out. Many thanks!
  • dstillman
    All the information used to form the links in the built-in Markdown export is available in the source of the notes, and plugins can use it as they wish.
  • alexanderjfink
    Thanks @chuantang and @dstillman. I've posted this onto the Better BibTex discussions to see if it makes sense to address it there (https://github.com/retorquere/zotero-better-bibtex/discussions/2076). It's clear, as you say @dstillman, that Zotero is making the annotations available and they just aren't getting dumped into the Better BibTex export. So not sure still where the issue is, but it isn't an Obsidian Citations issue and doesn't appear to be anything with Zotero either. Thanks all for your thoughts on this.
  • fryang
    @alexanderjfink @chuantang

    Firstly, I tried to print out the "notes" generated by Better Bibtex with this postscript.

    if (Translator.BetterBibTeX) {
    Zotero.debug(item.notes)
    reference.add({name: 'test', value: item.notes[0]["note"], html: true})
    }

    Then, I exported one item with one note to a "Better bibtex" file.

    Afterward, I got this output in the bibtex file:

    ------------------------------------------------
    test = {\section{Annotations\\
    (3/22/2022, 5:09:25 PM)}

    \par
    ``TCP has been the dominant transport protocol for mobile internet since its origin. Its behaviors play an essential role in determining quality of service/experience (QoS and QoE) for mobile apps.'' (Li et al., 2015, p. 2731) This is a note}
    -------------------------------------------------

    and this output from Zotero Debug Console:

    --------------------------------------------------------------
    [ "0": { "key": "P84FUWMN" "version": 4687 "itemType": "note" "parentItem": "WZWK7RUK" "note": "

    Annotations
    (3/22/2022, 5:09:25 PM)

    \n

    “TCP has been the dominant transport protocol for mobile internet since its origin. Its behaviors play an essential role in determining quality of service/experience (QoS and QoE) for mobile apps.” (Li et al., 2015, p. 2731) This is a note

    \n
    " "tags": [] "relations": {} "dateAdded": "2022-03-22T09:09:25Z" "dateModified": "2022-03-22T09:09:34Z" "uri": "http://zotero.org/users/4752161/items/P84FUWMN" } ]
    ---------------------------------------------------------------------


    It seems like that Better Bibtex currently does not decode notes in the same way as "Export Note (Markdown)".

  • alexanderjfink
    Right - thanks @fryang. That seems to confirm it as a Better BibTex issue. And maybe I'll just need to use the Export Note feature in the mean time and copy-paste manually.
  • basil2000
    Is there an update on this issue by any chance? I noticed that your post, alexanderjfink, on GitHub remains unanswered.
    My current status: I updated Better BibTex and Zotero, but still have no backlinks included in the [Library].bib file.
  • emilianoeheyns
    edited February 7, 2023
    Can that be related to https://github.com/retorquere/zotero-better-bibtex/issues/2126? While the plugin part of BBT can of course access notes, at the time when we were discussing this on github, it looked to me like export translators weren't offered the annotation data.
  • fryang
    @basil2000 You can find this issue (https://github.com/retorquere/zotero-better-bibtex/issues/2094) where I managed to generate backlinks in the .bib file (thanks to the help from @emilianoeheyns).
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