Re: org-ref is not using default bibliography file

[John Kitchin <jkitchin@andrew.cmu.edu>]

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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
> <javascript:_e(%7B%7D,'cvml','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
>> <javascript:_e(%7B%7D,'cvml','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

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