Error retriving bibtex from doi

[jsilve24]

First, off, thank you for putting this package together!

My config

(use-package org-bib
  :straight `(org-bib :type git :host github :repo "rougier/org-bib-mode")
  :config
  (setq org-bib-library-paths '("~/Dropbox/org")
	org-bib-default-library "~/Dropbox/org/references.org"
	org-bib-unsorted-header "Unsorted"))

What I run to get the error

(org-bib--get-crossref-info "https://doi.org/10.7554/eLife.21887")

The error:

bibtex-autokey-get-year: Year or date field ‘’ invalid

Any idea how to fix this?

[jsilve24]

Update, there doesn't seem to be any issue when I add a breakpoint to the function and step through it. If history is any lesson, I am going to guess this stems from a missing require statement.

[rougier]

Yes, you need to remove the "https://doi.org/" part when you query a DOI. Note that I've pushed a new branch (org-imenu) that hopefully will make things easier. I intend to merge it soon. If you want to test and give some feedback that would be wonderful.

[jsilve24]

Just tested the new branch. Not sure if it fixes the issues but I will note that I am now getting the following error on starting emacs.

Error (use-package): org-bib/:catch: Cannot open load file: No such file or directory, org-imenu Disable showing Disable logging

Also, would it be possible to add the unicode symbols on lines 341-343 of org-bib.el as defcustoms. They don't work with my current font (or some other issue) and I would prefer to replace them. I did this in my pull request: https://github.com/rougier/org-bib-mode/pull/7/files

(edit: I added them as defvars but that can be changed)

[rougier]

I removed the symbols and instead, you have a simple function to write the header. Currently it is:

(defun org-bib-headline-format (entry)
  (format "%s (%s)" (cdr (assq :title entry))
                    (cdr (assq :year entry))))

But you can rewirte it any way you like.

For the org-imenu, did you install it (https://github.com/rougier/org-imenu/)? You'll also need pdf-drop-mode (https://github.com/rougier/pdf-drop-mode/)

[jsilve24]

Thanks this helps. Still having some issues with importing from doi. Here is a doi: 10.1038/s41576-021-00434-9 running `org-bib-new-from-doi` gives bibtex-end-of-entry: Wrong type argument: stringp, nil Thanks!

[rougier]

You can test the doi with:

(pdf-drop-validate-doi "10.1038/s41576-021-00434-9")
(pdf-drop--bibtex-from-doi "10.1038/s41576-021-00434-9")

Did you drag and drop the pdf ?

[jsilve24]

(pdf-drop-validate-doi "10.1038/s41576-021-00434-9")

output: t

(pdf-drop--bibtex-from-doi "10.1038/s41576-021-00434-9")

output:

" @article{2021, title={Navigating the pitfalls of applying machine learning in genomics}, volume={23}, ISSN={1471-0064}, url={http://dx.doi.org/10.1038/s41576-021-00434-9}, DOI={10.1038/s41576-021-00434-9}, number={3}, journal={Nature Reviews Genetics}, publisher={Springer Science and Business Media LLC}, author={Whalen, Sean and Schreiber, Jacob and Noble, William S. and Pollard, Katherine S.}, year={2021}, month={Nov}, pages={169–181} }\n"

no I did not drag and drop the pdf, I just called org-bib-new-from-doi and then inserted

10.1038/s41576-021-00434-9

at the minibuffer prompt

[jsilve24]

Ahhh... just realized, it does work if I have org-bib-mode active but it doesn't work when bound to a global key binding...

[rougier]

Sorry for delay in my answer. org-bib-mode is kind of mandatory yes. Does that mean you would like to have an option to get the bibtex from a DOI from anywhere?

[jsilve24]

Yes (sorry for delay)

[rougier]

sorry for delay again, this will be a long thread. Now i'm a bit lost with the issue. Last point was to implement a bibtex-from-doi, right?