Re: org-ref is not using default bibliography file

[Kai Chen <chk0105@mail.ustc.edu.cn>]

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Well I was wrong, after I expand my-dropbox-path to full path, the problem
is still there.

Here are the results, the upper one is with the bibliography link while the
one at the bottom is without. Only the format changes, one with a quoted |
but another with a leading :
Could this be the cause?

=== From notes.org ===
..... some text with citations
bibliography:/home/kai/Dropbox/bibliography/references.bib

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

#+RESULTS:
| /home/kai/Dropbox/bibliography/references.bib |

: /home/kai/Dropbox/bibliography/references.bib



On Sun, Dec 13, 2015 at 11:11 AM, Kai Chen <chk0105@mail.ustc.edu.cn> wrote:

> 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 <jkitchin@andrew.cmu.edu>
> 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
>



-- 
Regards

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

K.Chen

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