From mboxrd@z Thu Jan 1 00:00:00 1970 From: Kai Chen Subject: Re: org-ref is not using default bibliography file Date: Sun, 13 Dec 2015 11:11:45 +0800 Message-ID: References: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=047d7b4144709fb7a90526beea9d Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:55809) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a7x4e-0007xg-9b for emacs-orgmode@gnu.org; Sat, 12 Dec 2015 22:11:49 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1a7x4c-0002yi-GD for emacs-orgmode@gnu.org; Sat, 12 Dec 2015 22:11:48 -0500 Received: from mail-ig0-x22f.google.com ([2607:f8b0:4001:c05::22f]:37564) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a7x4c-0002ye-9V for emacs-orgmode@gnu.org; Sat, 12 Dec 2015 22:11:46 -0500 Received: by igcto18 with SMTP id to18so62572399igc.0 for ; Sat, 12 Dec 2015 19:11:45 -0800 (PST) In-Reply-To: List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: John Kitchin Cc: emacs-orgmode@gnu.org --047d7b4144709fb7a90526beea9d Content-Type: text/plain; charset=UTF-8 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 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 --047d7b4144709fb7a90526beea9d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Thanks for your suggestion! The p= roblem 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) wil= l 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, i= t returns
~/Dropbox/bibliography/references.bib

It se= ems 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 man= ually
> install the package and set the default path similar to the configurat= ion
> provided in the follow link:
> https://github.com/jkitchin/org-ref
>
> And I installed all the dependency packages like helm-bibtex, hydra et= c.
>
> 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<= br> > entry. This can only work when I manually add a bibliography link at t= he
> 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
>=C2=A0 =C2=A0(setq org-ref-path (concat my-dropbox-path "software/= org-ref/"))
>
>=C2=A0 =C2=A0(setq reftex-default-bibliography (concat my-dropbox-path<= br> > "bibliography/references.bib"))
>
>=C2=A0 =C2=A0;; see org-ref for use of these variables
>=C2=A0 =C2=A0(setq org-ref-bibliography-notes (concat my-dropbox-path &= quot;bibliography/
> note= s.org")
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0org-ref-default-bibliography (concat = my-dropbox-path
> "bibliography/references.bib")
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0org-ref-pdf-directory (concat my-drop= box-path
> "bibliography/bibtex-pdfs/"))
>
>=C2=A0 =C2=A0;; *** helm-bibtex
>
>=C2=A0 =C2=A0(setq helm-bibtex-bibliography (concat my-dropbox-path
> "bibliography/references.bib"))
>=C2=A0 =C2=A0(setq helm-bibtex-library-path (concat my-dropbox-path
> "bibliography/bibtex-pdfs"))
>
>=C2=A0 =C2=A0;; open pdf with system pdf viewer (works on mac)
>=C2=A0 =C2=A0(when (eq system-type 'darwin)
>=C2=A0 =C2=A0 =C2=A0(setq helm-bibtex-pdf-open-function
>=C2=A0 =C2=A0 =C2=A0 =C2=A0(lambda (fpath)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(start-process "open" "= ;*open*" "open" fpath))))
>
>=C2=A0 =C2=A0;; alternative
>=C2=A0 =C2=A0;; (setq helm-bibtex-pdf-open-function 'org-open-file)=
>
>=C2=A0 =C2=A0(setq helm-bibtex-notes-path (concat my-dropbox-path
> "bibliography/helm-bibtex-notes"))
>
>=C2=A0 =C2=A0(global-set-key [f10] 'org-ref-open-bibtex-notes)
>=C2=A0 =C2=A0(global-set-key [f11] 'org-ref-open-bibtex-pdf)
>=C2=A0 =C2=A0(global-set-key [f12] 'org-ref-open-in-browser)
>
>=C2=A0 =C2=A0(add-to-list 'load-path org-ref-path)
>
>=C2=A0 =C2=A0;; make sure you have dash, helm, helm-bibtex, ebib, s, f,= hydra and
> key-chord
>=C2=A0 =C2=A0;; in your load-path
>=C2=A0 =C2=A0;; auto-install dependencies
>=C2=A0 =C2=A0(require 'org-ref)
>
>=C2=A0 =C2=A0;; optional but very useful libraries in org-ref
>=C2=A0 =C2=A0(require 'doi-utils)
>=C2=A0 =C2=A0(require 'jmax-bibtex)
>=C2=A0 =C2=A0(require 'pubmed)
>=C2=A0 =C2=A0(require 'arxiv)
>=C2=A0 =C2=A0(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
--047d7b4144709fb7a90526beea9d--