Zotero with integration of pdf.js - already available in Beta

Zotero is integrating pdf.js - already available in Beta version

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Pasting part of my reply from New Native Annotations in Zotero (Currently on Beta) · Discussion #77 · argenos/zotero-mdnotes · GitHub :

I took a little time to set up a profile to test with the beta over the weekend, and the beta simply has too many limitations currently. I’ll add my summarized comments from discord and other issues below. As you say, this will likely be addressed later, and I remain to be convinced that the annotation lock-in is worth it.

The main limitations I found:

  • Limited amount of colours (5 max, predefined)
  • It only does highlights (no underlines, which are essential to me, others might use other PDF viewers that support other types of annotations too).
  • The extracted annotations when saved as a note don’t have the zotero:// link to the page. They have added something similar that works within Zotero, but that makes it useless right now if you want to export/copy-paste that note somewhere else.

The advantages:

Other things missing that Zotfile offers (Most likely some of those gaps can be covered by mdnotes possibly during export):

  • Grouping annotations by colour
  • Custom formatting for the note title, highlights and annotations (particularly relevant if you want to make distinctions between the latter two)
  • Wildcards
    • Using the colour and colour category wildcards to format the note’s contents
    • Formatting the date as you see fit

I understand the appeal for some to have everything under a single app (Zotero), but the viewing/annotating experience is still very limited and any PDF viewer can do a lot more. I assume this will get better with time, but for now I’m not convinced.

Please note that if you use the beta the mdnotes workflow is limited to the way Zotero processes your annotations. The annotations are not saved on your PDF, they live in Zotero’s DB, so you won’t be able to extract them with Zotfile (or view them somewhere else). The workaround for now (strike-through is mine):

in desktop in the right hand side if you click “new note” it gives option to select “from annotations” and then it basically enables the entire zotfile/mdnotes workflow. The note is made from the annotations and i can convert to markdown successfully.

The note created from your annotations by Zotero do not contain zotero:// links to your PDF (these were obtained by Zotfile in the stable/previous workflow). If you rely on this, or on custom formatting for differentiating between highlights and notes, I recommend holding off until I update mdnotes.


Another workaround is to

  1. highlight normally
  2. save the pdf as a new file (I usually do this to ~/Downloads so I don’t mix them up)
  3. reimport to the existing entry
  4. extract the annotations from the newly imported file
  5. delete the original pdf
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This discussion may be relevant


9 days ago

Hyperlink the page number with a zotero://open-pdf URL, you mean? The extraction itself certainly isn’t going to do that. Those URLs were always primarily just a hack in ZotFile to let extracted annotations open the PDF page, and Zotero now supports that natively.

But the note contains all the information necessary to get back to the annotation position, and someone could create a plugin (or update an existing plugin such as zotero-mdnotes) to export notes with that data converted into zotero:// hyperlinks for use outside of Zotero. It’s not impossible we could have a built-in export option for notes that did that if there was sufficient demand.

I’m aware! It is indeed possible for the mdnotes plugin to eventually re-create the Zotero links (see the GitHub discussion linked above)

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one problem I had with previous set up was that opening didn’t worked for me using SumatraPDF and Adobe Reader (couldn’t go to the page and only opened the file) but Zotero native reader opens it reliably. I am still not decided on which way to go. Is there a good and free pdf reader that not having this issue? I couldn’t find much on this matter online, maybe it is just me but I have this issue on two different laptops and operating systems. And I find Adobe Reader setting very annoying and inconvenient.

Personally, I use Okular, which works on Linux and Windows as far as I’m aware. I’ve also heard Xodo recommended a lot in the server.

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thank you, this is much better and works very smoothly. highlighting on multiple layers is enjoyable in this app.
but still can’t open zotero links to the page. it just opens the document. I wonder if it is OS’s fault or on zotero. obivously it is not because pdf reader. i can’t find anything on this issue