Re: [O] org-ref is not using default bibliography file

[Kai Chen]

Thanks for your suggestion! The problem lies in a variable I set which points to the directory of my Dropbox folder, to ensure emacs portable on different OS.

When I have the bibliography link in the org file, the (org-ref-find-bibliography) will return the absolute path to the .bib file, which in my case is
/home/kai/Dropbox/bibliography/references.bib
But if I do not have the link, it returns

~/Dropbox/bibliography/references.bib

It seems some modules are resolving the '~' while some others are not.

Cheers,

Kai

On Sun, Dec 13, 2015 at 2:15 AM, John Kitchin <address@hidden> wrote:

That sounds odd.

What is the output of this src block in your file?

#+BEGIN_SRC emacs-lisp
(org-ref-find-bibliography)
#+END_SRC

Kai Chen writes:

> Dear list,
>
> I just got to know org-ref, and I followed the github help page to manually
> install the package and set the default path similar to the configuration
> provided in the follow link:
> https://github.com/jkitchin/org-ref
>
> And I installed all the dependency packages like helm-bibtex, hydra etc.
>
> But when I am citing (using "C-c ]") an existing entry which is in the
> default references.bib file, I can see the entry after I stroke the
> command, but after I selected it and pressed enter, when the cursor is on
> the link, the mini-buffer says:
> !!! No entry found !!!
> But previously the org-ref-helm-insert-cite-link properly showed that
> entry. This can only work when I manually add a bibliography link at the
> bottom of the file, which means org-ref is not using the default
> bibliography file.
>
> So what should I check to fix this issue?
>
> Thanks for your help!
>
> The following is my configuration of org-ref:
>
> #+BEGIN_SRC emacs-lisp
>   (setq org-ref-path (concat my-dropbox-path "software/org-ref/"))
>
>   (setq reftex-default-bibliography (concat my-dropbox-path
> "bibliography/references.bib"))
>
>   ;; see org-ref for use of these variables
>   (setq org-ref-bibliography-notes (concat my-dropbox-path "bibliography/
> notes.org")
>         org-ref-default-bibliography (concat my-dropbox-path
> "bibliography/references.bib")
>         org-ref-pdf-directory (concat my-dropbox-path
> "bibliography/bibtex-pdfs/"))
>
>   ;; *** helm-bibtex
>
>   (setq helm-bibtex-bibliography (concat my-dropbox-path
> "bibliography/references.bib"))
>   (setq helm-bibtex-library-path (concat my-dropbox-path
> "bibliography/bibtex-pdfs"))
>
>   ;; open pdf with system pdf viewer (works on mac)
>   (when (eq system-type 'darwin)
>     (setq helm-bibtex-pdf-open-function
>       (lambda (fpath)
>         (start-process "open" "*open*" "open" fpath))))
>
>   ;; alternative
>   ;; (setq helm-bibtex-pdf-open-function 'org-open-file)
>
>   (setq helm-bibtex-notes-path (concat my-dropbox-path
> "bibliography/helm-bibtex-notes"))
>
>   (global-set-key [f10] 'org-ref-open-bibtex-notes)
>   (global-set-key [f11] 'org-ref-open-bibtex-pdf)
>   (global-set-key [f12] 'org-ref-open-in-browser)
>
>   (add-to-list 'load-path org-ref-path)
>
>   ;; make sure you have dash, helm, helm-bibtex, ebib, s, f, hydra and
> key-chord
>   ;; in your load-path
>   ;; auto-install dependencies
>   (require 'org-ref)
>
>   ;; optional but very useful libraries in org-ref
>   (require 'doi-utils)
>   (require 'jmax-bibtex)
>   (require 'pubmed)
>   (require 'arxiv)
>   (require 'sci-id)
>
> #+END_SRC

--

Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu

--

Regards

Multi-Agent System Lab
University of Science and Technology of China

K.Chen