scimax, Zotero references + pdfs

[rmosvold]

Hi! I have used Emacs for a long time, and am just starting to try out scimax, which I love so far! So thanks a lot for the wonderful work on this! There is just one thing I am not able to figure out, and I am not sure if it is a scimax thing or an org-ref thing — probably a little of both.

After having learned from a blog post by Wouter Spekkink, I found a nice setup where a bibtex file of my Zotero references was automatically kept up-to-date (BetterBibtex), and org-ref was able to find my Zotero pdfs and open them automatically. After having installed scimax, the reference handling works much better, except that the pdfs are no longer found. I realize that scimax has a much more complex initiation file system than I have previously used, so I wonder where and how would be the best way to configure this. And if others have written about a good workflow for references + pdf handling with scimax, I would love to know about that too!

[jkitchin]

probably you are seeing a change from org-ref 2 to org-ref 3. maybe something changed on finding Zotero pdfs. Now pdfs are found via bibtex-completion functions. Maybe you set bibtex-completion-pdf-open-function to the function that worked before, and it will work.

[rmosvold]

You are probably right! Before, I don't think I had set a bibtex-completion-pdf-open-function, but I had set bibtex-completion-pdf-field to "file". Could that be it? If so, where in the scimax config-files is the right place to change this?

[rmosvold]

I had also copied the functions from Spekkink's blog post:

;; The function below allows me to consult the pdf of the citation I currently have my cursor on.
(defun my/org-ref-open-pdf-at-point ()
"Open the pdf for bibtex key under point if it exists."
(interactive)
(let* ((results (org-ref-get-bibtex-key-and-file))
(key (car results))
(pdf-file (funcall org-ref-get-pdf-filename-function key)))
(if (file-exists-p pdf-file)
(find-file pdf-file)
(message "No PDF found for %s" key))))

(setq org-ref-completion-library 'org-ref-ivy-cite
org-export-latex-format-toc-function 'org-export-latex-no-toc
org-ref-get-pdf-filename-function
(lambda (key) (car (bibtex-completion-find-pdf key)))
;; See the function I defined above.
org-ref-open-pdf-function 'my/org-ref-open-pdf-at-point
;; For pdf export engines.
org-latex-pdf-process (list "latexmk -pdflatex='%latex -shell-escape -interaction nonstopmode' -pdf -bibtex -f -output-directory=%o %f")
;; I use orb to link org-ref, helm-bibtex and org-noter together (see below for more on org-noter and orb).
org-ref-notes-function 'orb-edit-notes)

[rmosvold]

I have explored this a bit further, but still haven't figured out about the Zotero pdfs. Setting the bibtex-completion-library-path and the bibtex-completion-bibliography as suggested on the org-ref github page provides a setting that works and where pdfs are found, so perhaps I just have to use this as a nice opportunity to find a new (and possibly better) way of organizing my work :-)

Lots of things that I love about scimax, and I'll continue to explore it, so thanks again for all the wonderful work that is being done!!!!

[jkitchin]

If you have bibtex-completion-pdf-field set to "file" I think bibtex completion will look in the field for opening a pdf, and then in the bibtex-completion-library-path. This should be fine if Zotero puts an actual path in that field.

If it doesn't do that, you need a function that takes the path that is there and converts it to the zotero path (see bibtex-completion-pdf-open-function)

If that doesn't work, I guess you might have to write your own function that takes a key, and then computes the pdf path and opens it.