Keeping Notes (Or Open PDFs via Zotero)

June 30, 2021

Following a recommendation from a colleague, I have been trying Obsidian to keep notes, link them, etc.

I installed its citation plugin to write literature notes and the like from the bibliography I keep in Zotero.

Pretty cool, I have to say. Personally, I like Obsidian keeps the content in plain text files (markdown), so you are not irreversibly bound to a product.

For the extra mile, I also installed Zotfile to extract into Zotero the notes I add to the PDFs, and Mdnotes to convert those notes to markdown, so I can copy them into the notes in Obsidian.

Definitely do not handle confidential stuff this way, too many plugins involved. But for my purposes, I do not worry.

Anyway, the missing bit is that the markdown notes will include links that look like zotero://open-pdf/library/items/ID?page=p, so from the notes you can open directly on your PDF viewer the page where the note is. But those links may not work out of the box, at least not in Fedora.

In order to fix this, first we need a .desktop file for Zotero, specifying the MimeType x-scheme-handler/zotero, which tells that zotero:// URLs are to be open with Zotero.

cd ~/.local/share/applications
cat zotero.desktop

[Desktop Entry]
Comment=
Terminal=false
Name=Zotero
Exec=/home/aalvarez/Tools/Zotero_linux-x86_64/zotero -url %u
Type=Application
Icon=/home/aalvarez/Tools/Zotero_linux-x86_64/chrome/icons/default/default256.png
MimeType=x-scheme-handler/zotero;

Note the annoyingly undocumented -url parameter.

Last, we need to register the MimeType

xdg-mime default zotero.desktop x-scheme-handler/zotero

And, with that, we can open the zotero URLs as folllows:

xdg-open "zotero://open-pdf/library/items/ZQRC5HT9?page=5"

Still doesn’t work from Obsidian?

May need to refresh mimeinfo.cache

cd $HOME/.local/share/applications
update-desktop-database .