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

[John Kitchin]

does that mean it is working now?

Kai Chen writes:

> 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
>>
>>

--
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