Dear all, I am using doom emacs and recently the biblio module was added there. It is using citar instead of helm-bibtex and now I can not figure out how to associate pdfs with bibtex entries. Usually I use doi-insert-bibtex to add new references. Then I download the pdf and associate it with the bibtex entry (unfortunately, I don’t remember the command, it is no longer available since the new biblio module no longer uses helm-bibtex I think. Then I imported the bibtex entries into org roam using a special capture template (this still works). Now the pdf field in my org files is empty for new bibtex entries and I have no idea how to restore the pdf → bibtex entry mapping (tbh I have no clue how it worked before, I was just very happy it did). Any ideas on how to restore this functionality? Thanks a lot!
Take a look at your older BibTeX entries you created with doi-insert-bibtex and doi-utils-get-bibtex-entry-pdf (I assume you used the latter to download PDFs). Do they contain the BibTeX field file? It should hold the path to your PDF associated with the BibTeX entry. If yes, then you have at least two options that readily come into my mind:
- install back the
doi-utilslibrary, which is a part of Org-ref not Helm-bibtex. So basically install Org-ref. You don’t need to use Org-ref citations or whatever but you need thedoi-utilslibrary. You should now be able to proceed with your usual workflow. - download a PDF manually. Open your BibTeX file and find the BibTeX entry in question. Add the
filefield and set it to the path of the downloaded PDF. You may want to put the PDF in the same directory you used to keep your PDFs earlier, e.g. check the older entries and note the paths stored in thefilefield, but that’s up to you:
@article{someEntry,
author = ...,
date = ...,
doi = ...,
file = {/path/to/your/file.pdf},
journaltitle = ...,
pages = ...,
If no, well, you used a different mechanism. Helm-bibtex indeed supports different mechanisms, you should figure which one.
Then I imported the bibtex entries into org roam using a special capture template (this still works).
Yes. This is the only part Org-roam-bibtex is responsible for.
Now the pdf field in my org files is empty for new bibtex entries
Yes. Because Org-roam-bibtex cannot retrieve this information because it is likely absent from new entries.
Thank you both for getting back to me so quickly! This is probably more a doom config specific question so thanks for still taking your time and giving me hints!
@mshevchuk: my bibtex entries do not contain a file field and never did, I still wonder how/where the mapping was stored before… I tried installing back the doi-utils library by including org-ref in my packages.el, this brought back all the functions I used earlier (doi-utils-get-bibtex-entry-pdf and especially org-ref-bibtex-assoc-pdf-with-entry), so thanks for the hint! Now I am only looking for a way to create another embark-action in citar to bind those two functions, but I read something about this in the documentation. The doi-utils-get-bibtex-entry-pdf does set the file field now, I still have no idea how this mapping was created before but probably something similar to the citar KEY.FILEENDING just implicit without the corresponding bibtex entry… Sometimes it is hard to keep track of which modules/functions and how they are used in doom.
@bruce: The README is very concise (in a good way!) and does include a section about file associations which I read, I was just struggling with “how to download/move/rename pdfs automatically so citar does find them” but thanks to @mshevchuk I consider this solved.
Thanks again! Should I mark this question as solved somehow?
No, it is not. The respective Doom modules do little tweaking in this specific case apart from just loading the packages. It’s more about interplay between different packages, so your question is of general interest.
You are right. So by looking at the source code of org-ref-bibtex-assoc-pdf-with-entry, what this function does is it lets you select a downloaded file in the prompt, reads the BibTeX entry at point to get the citation key, renames the selected file to CITEKEY.ext, and copies/moves it to the location specified in bibtex-completion-library-path. Then whenever you want to open the file with Org-ref or Helm-bibtex, the function bibtex-completion-find-pdf-in-library just looks for the file CITEKEY.ext in that location.
So with respect to ORB and Org-roam template expansion, if you want to keep your old workflow you again have two options:
- Keep using
org-ref-bibtex-assoc-pdf-with-entry - If you want to uninstall Org-ref, you’ll need to manually rename new PDFs and move them to
bibtex-completion-library-path.
ORB actually uses bibtex-completion-find-pdf under the hood, so if you have a file CITEKEY.ext in bibtex-completion-library-path it will eagerly pick it up during a template expansion no matter how this file ended up in that location.
You are right, and the interplay of different packages is sometimes hard to grasp (at least for me).
I decided to stick to option 1., since automating this process was my goal in the beginning.
Unfortunately, I now face another Problem: my old notes are no longer recognized (all entries are still displayed as having notes indicated by the icon to the left) and whenever I want to open the notes of a bibtex entry (citar-open-notes), orb (I assume) is prompting for capture template selection, even if I created that note file previously (with the new system), any ideas what could be going wrong here? Thanks!
Edit: I also noticed the created note org files no longer contain a ROAM_REFS entry in the property drawer, which is likely the cause of this issue I assume.
Edit2: while going through the called functions, I noticed that orb-edit-note (which is called because I set (setq citar-open-note-function 'orb-citar-edit-note) first tries to call org-roam-find-ref which I only found as org-roam-ref-find, but the org-roam-node-find function should be able to fetch the correct node.
Currently, ORB does not provide support for note indicator in Citar. This will be added later. Normally, you shouldn’t see a note indicator. Maybe Citar is actually not configured to use ORB?
Edit: I also noticed the created note org files no longer contain a
ROAM_REFSentry in the property drawer, which is likely the cause of this issue I assume.
This is an indication that either Citar is not calling ORB or that you do not have org-roam-bibtex-mode running.
while going through the called functions, I noticed that
orb-edit-note(which is called because I set(setq citar-open-note-function 'orb-citar-edit-note)first tries to callorg-roam-find-refwhich I only found asorg-roam-ref-find, but theorg-roam-node-findfunction should be able to fetch the correct node.
orb-edit-note does not call org-roam-ref-find anymore. It’s just an outdated docstring, I’ll fix it now.
any ideas what could be going wrong here?
Not sure what’s wrong. Do you have org-roam-bibtex-mode turned on? Or maybe it is some loading issues? Try restarting Emacs or reinstalling the packages… Also, you do not need to set citar-open-note-function, just activate org-roam-bibtex-mode.
Maybe Citar is actually not configured to use ORB?
How would I make sure that citar is configured to use orb? I have (setq citar-open-note-function 'orb-citar-edit-note) in my config but nothing else (to my knowledge) connects citar and orb.
This is an indication that either Citar is not calling ORB or that you do not have
org-roam-bibtex-moderunning.
I did not have it running :), forgot to comment it back in since it caused issues with an earlier configuration state.
With that fixed, it is now working (mostly), thanks a lot! The only issue left is: when I am in an org roam file and try to open the notes of a reference I am still prompted with the node creation template selection dialog, even if org-roam-bibtex-mode is running, it does work in regular org files and everywhere else… So I consider this fixed, good enough for me 
Edit: org-roam-db-sync did the trick for the last part…
We’ve discussed a bit possibly adding a related command:
Not following this closely, but the citar note function will add the ROAM_REFS property if org-roam is present. Not sure what’s going on, but orb isn’t required for this.
That’s about it.
That unfortunately is very vague a description for me. And an almost impossible one since Org-roam files are just regular Org files. What exactly do you do? Are these the Org-cite [cite:@citekey] references, which you are opening with embark-act or something else?
Sorry, let’s try this: I am editing an arbitrary org roam file and calling citar-open, select a reference and then SPC-; n to open its notes. Then I am prompted for a node creation template every time I do this. This works (I am not prompted for a node creation template but taken to the correct org roam file) in any other buffer and after updating the roam database. I don’t know why those two things influence each other, if you need more information from my side, please let me know.
Can you try M-x citar-open-notes? It should be basically the same in effect just omitting the SPC-; n step.
This is also strange. Do you have org-roam-db-auto-sync-mode enabled?
I do have org-roam-db-auto-sync-mode enabled, and without going through the embark act part the result is still the same (I like having a single point of entry for all library related stuff, thats why I use it this way).
FWIW, we recently expanded citar-open to include notes as well. I don’t think I’ve yet updated the doom biblio module to include that though. But I’ll likely do that soon-ish.
It seems Doom’s biblio module is pinned to a fairly old Citar commit. Skimming through commit headlines I didn’t find anything that could relate to your issue, but who knows. Try (unpin! citar) in your packages.el.
Actually, I just went to bump the biblio module, and realized henrik already bumped tools yesterday.
I upgraded doom emacs but the problem persists. But this is good enough for me 
Well, I won’t insist on fixing it then 
. It’s just itching me I can’t reproduce any of your issues 
.