Re: org-ref is not using default bibliography file

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

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Thanks for pointing out!!!

This did the trick for me (using backquote `):

(setq reftex-default-bibliography `(,(concat my-dropbox-path
"bibliography/references.bib")))

Thanks again for your prompt help!

Cheers,
Kai

On Sun, Dec 13, 2015 at 11:59 AM, John Kitchin <jkitchin@andrew.cmu.edu>
wrote:

> That probably means some variable should be a list and it isn't, it is
> just a string.
>
>
> On Saturday, December 12, 2015, Kai Chen <chk0105@mail.ustc.edu.cn> wrote:
>
>> 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
>>
>
>
> --
> John
>
> -----------------------------------
> 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

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