Org-ref incorrectly passing bibliography to helm-bibtex about org-ref

[jkitchin]

This has not changed any time recently. What does this command output in a typical org-file for you:

(org-ref-find-bibliography)

and what do you have the variable org-ref-default-bibliography set to in your init file?

[jkitchin]

I think I see the issue, BIBINPUTS is some environment variable you have set? and helm-bibtex does not search it. You should use (setq org-ref-default-bibliography '("file1" "file2")) in your init files to set a default set of these. It might be possible to use something like (getenv "BIBINPUTS") and split it as needed to get that list too.

[reconmaster]

I have org-ref-default-bibliography set to ("~/dropbox/bibliography/references.bib") as mentioned on the site. Evaluating (org-ref-find-bibliography)returns the same value. The only reason I mentioned BIBINPUTS is when using biblatex, I can do \addbibresource(references) and it will find the correct bib file. I only wondered if the issue is with BIBINPUTS is that the error message I get is the name of the correct file without the proper parent directory information. Maybe it has to do with the way org-ref passes the default bibliography to helm-bibtex? As I mentioned, none of my init file or the org paper has changed, I only upgraded org-ref to this new version supporting helm (which I like btw, just trying to figure out why this broke the C-c ] key).

[jkitchin]

Does that file actually exist? If not you should make it be an actual
bibtex file.

On Friday, April 17, 2015, Andrew Davis [email protected] wrote:

I have org-ref-default-bibliography set to
("~/dropbox/bibliography/references.bib") as mentioned on the site.
Evaluating (org-ref-find-bibliography)returns the same value. The only
reason I mentioned BIBINPUTS is when using biblatex, I can do
\addbibresource(references) and it will find the correcct bib file. I
only wondered if the issue is with BIBINPUTS is that the error message I
get is the name of the correct file without the proper parent directory
information. Maybe it has to do with the way org-ref passes the default
bibliography to helm-bibtex? As I mentioned, none of my init file or the
org paper has changed, I only upgraded org-ref to this new version
supporting helm (which I like btw, just trying to figure out why this broke
the C-c ] key).

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@johnkitchin
http://kitchingroup.cheme.cmu.edu

[reconmaster]

It's an actual file. helm-bibtex and org-ref can find it when I use the two work around methods mentioned in the original post. I also mentioned none of my setup has changed since I was using your org-ref that initially used reftex and worked. Can you use C-c ] without the bibliography:~/wherever/ref.bib in your file?

[jkitchin]

Weird. Yes, I routinely use org ref with no bibliography link.

The files get passed to helm bibtex here
https://github.com/jkitchin/org-ref/blob/master/org-ref.el#L3211

[jkitchin]

This sounds very strange. I have these variables set in my init file

(setq reftex-default-bibliography '("~/Dropbox/bibliography/references.bib"))

;; see [[org-ref]] for use of these variables
(setq org-ref-bibliography-notes "/Dropbox/bibliography/notes.org"
org-ref-default-bibliography '("/Dropbox/bibliography/references.bib")
org-ref-pdf-directory "~/Dropbox/bibliography/bibtex-pdfs/")

(setq helm-bibtex-bibliography "/Dropbox/bibliography/references.bib")
(setq helm-bibtex-library-path "/Dropbox/bibliography/bibtex-pdfs")

(setq helm-bibtex-pdf-open-function
(lambda (fpath)
(start-process "open" "open" "open" fpath)))

(setq helm-bibtex-notes-path "~/Dropbox/bibliography/helm-bibtex-notes")

I am pretty sure these are not all necessary, and that helm-bibtex-bibliography gets temporarily rebound in the org-ref-helm-insert-cite-link function. But, having it set in init.el enables helm-bibtex to work outside of org-ref.

org-ref should not be affected by BIBINPUTS at all.

[reconmaster]

Well it seems to be a problem when org-ref tries to pass its bibliography to helm-bibtex. If I modify the the org-ref-helm-insert-cite-link, C-c ] works as expected. Not familiar enough with elisp or org-ref to understand why the let function is necessary here. If there is a dependency on helm-bibtex, shouldn't correctly setting the helm bibliography be sufficient?

(defun org-ref-helm-insert-cite-link (arg)
  "org-ref function to use helm-bibtex to insert a citation link.
With one prefix arg, insert a ref link.
With two prefix args, insert a label link."
  (interactive "P")
  (cond
   ((equal arg nil)
     (;let ((helm-bibtex-bibliography (org-ref-find-bibliography)))
       helm-bibtex))
   ((equal arg '(4))
    (org-ref-helm-insert-ref-link))
   ((equal arg '(16))
    (org-ref-helm-insert-label-link))))

[jkitchin]

I don't understand why it won't for you though. You need the let statement to enable the use of the in document bibliography preferentially, but to fall back on the default if there is no document bibliography. It does that by temporarily redefining the variable. It is not enough to just set the helm bibliography variable for that. And, the variable should take a list of files, which is what it is set to in the let statement.

Can you send me the org file you are having trouble using C-c ] in?

[reconmaster]

Thanks for helping me find the problem. I had the following commented out at the end of my *.org file.

# \bibliography{ref}

Org-ref found this and was searching my local directory for the non-existent file. No changes need to be made in org-ref. This was my fault. Thanks John!
-A

[jkitchin]

no problem!

[TammoR]

This is a similar question. I also use ox-bibtex for html export and have

#+BIBLIOGRAPHY: ~/Dropbox/library/library plain limit:t option:-nokeywords option:--no-abstract

at the bottom of my document. Org-ref now tries to use this file and complains. If I change to
#+BIBLIOGRAPHY: /Users/tammruka/Dropbox/library/library**.bib**, org-ref works. But then ox-bibtex does not work anymore.

Any idea how I can get org-ref to use the bibliography file that I provide elsewhere and not get irritated by the

#+BIBLIOGRAPHY:

line?

[jkitchin]

The best path is probably for org-ref to not look at the #+BIBLIOGRAPHY line at all. It is not that helpful for exporting from org-ref I think, and is only a last resort anyway. I don't know if anyone relies on it though. Maybe I will try removing that and see if anyone complains...