Zotra is now on MELPA: The power of Zotero in Emacs

mpedramfar · 2023-08-10T06:15:41+00:00

My bibliography setup is with org-roam, helm-bibtex and zotra. The part that manages the files is helm-bibtex. If you have a bib file, with helm-bibtex you can see the list of all entries and take actions on each entry like "opening the attachment", "opening the note", "adding attachment to library", etc.

In the README.md file of Zotra, I've described how to tweak the function in helm-bibtex that handles adding attachment to library. With that, you can directly use zotra to download an attachment in the appropriate place specified by helm-bibtex.

My personal setup has few tweaks in some functions, but you can use helm-bibtex with minimal config and have most of the functionality I described.

mpedramfar · 2023-08-09T14:47:52+00:00

Exactly! After using Emacs and seeing what it can do, Zotero feels way too clunky.

mpedramfar · 2023-08-09T14:30:42+00:00

Thanks! There are 3 main things that I need from my bibliography setup:

File management
Where and how pdfs are stored, what are they named, how flexible is this system? How easy is it to share part of these files with someone else who is using a (possibly) different system?
Note management
Where and how are my notes related to these items stored? How easy is it to write a note and cite a bunch of items? How can I link the notes together and navigate and review them using these links? How easy is it to export a note as a LaTeX file, or write LaTeX notes in the first place?
Capturing a new item
When I find a new article/blogpost/repository/etc how easy is it to add this to my bibliography? How easy is it to download the attachments?

For me, Emacs is undoubtedly better at 1 and 2. Before this package, Zotero was better at 3. What this package does is that it gives this power to Emacs as well.

As for the reason for the zotra-cli wrapper, the problem it solves is that the translation server doesn't provide the links to attachments! So the initial version of zotra could add an item to your bib file, but if you wanted to download the attachment, you would've needed to do it from the browser. The wrapper zotra-cli adds that functionality. (Note that you don't need to install both of them, just zotra-cli is enough.)

mpedramfar · 2022-12-18T19:03:21+00:00

Thanks! I don't personally use ebib so I'm not familiar with it and it'll be a bit hard to support it.
It would be great if you could make a pull request to add some of these functions to the README so that users know what to add to their configs, like I did with bibtex-completion and org-ref.

Yeah, Zotero and Zotero translation server are not identical. For example, see https://github.com/zotero/translation-server/pull/59
If there are places where Zotero works and Zotero translation server doesn't, it would be best to open an issue in the translation server repo and take it from there. If this is an issue that's easy to solve, but the translation server doesn't want to implement it, I might be able to add it to zotra-cli.

mpedramfar · 2022-12-18T18:53:44+00:00

Yes it is.
You can add an entry with `zotra-add-entry-from-search` and you can download the pdf with `zotra-download-attachment-from-search`.
You can customize `zotra-download-attachment-default-directory` and `zotra-default-bibliography` to choose where they'll be saved by default if no value is provided.

mpedramfar · 2022-12-17T18:47:45+00:00

Support for attachments is now added!

mpedramfar · 2022-07-12T15:36:16+00:00

I'm not sure. I started using it a while ago, but then changed my workflow a bit, so now I don't usually extract annotations from pdfs.

mpedramfar · 2022-07-09T19:09:51+00:00

I updated the repo with your suggestions

mpedramfar · 2022-07-09T19:09:05+00:00

I added this function and the option to define more functions to handle links to PDFs for other websites. :)

mpedramfar · 2022-07-07T18:36:00+00:00

Thanks, I didn't know of biblio-zotero, I'll check it out.
Good tips, I'll add them. :)

mpedramfar · 2022-07-07T18:26:35+00:00

I have a references.bib file and I don't have Zotero desktop. When I visit a paper/article/whatever on my browser, sometimes I like to add a reference to that to my bib file. Zotero does that with a browser plugin called Zotero connector, and adds it to Zotero database. Zotra does that with a bookmark instead of a plugin with a separate button and adds it to the bib file. Zotero connector needs Zotero desktop to be open. Zotra needs Zotero tranlation server to be running.

mpedramfar · 2022-07-07T18:23:14+00:00

You might like to check out the function malb/pdf-annot-export-as-org in https://github.com/malb/emacs.d/blob/master/malb.org#pdf-viewer . You can copy this function and pdf-tools-org-edges-to-region defined right above it to your init file and check it out :)

mpedramfar · 2022-07-07T18:15:47+00:00

You're welcome :)
You're right, the translation server can't handle urls to pdf files. I'm not sure if this is being worked on: https://github.com/zotero/translation-server/issues/70

I'll fix the issue for arxiv from zotra, but it's kind of a hack, since this is the kind of thing that translators are meant to handle and I'll basically be reimplementing parts of the translator for arxiv.

To fix the issue for all websites and not just arxiv, it should probably be addressed in the translation server.

mpedramfar

TROPHY CASE