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 11:29:57 +0800 Message-ID: References: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=001a11407fecb23f180526bf2b51 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:59007) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a7xMG-0002Gd-1p for emacs-orgmode@gnu.org; Sat, 12 Dec 2015 22:30:01 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1a7xMD-0006QX-VU for emacs-orgmode@gnu.org; Sat, 12 Dec 2015 22:30:00 -0500 Received: from mail-io0-x22f.google.com ([2607:f8b0:4001:c06::22f]:33229) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a7xMD-0006QT-OW for emacs-orgmode@gnu.org; Sat, 12 Dec 2015 22:29:57 -0500 Received: by iouu10 with SMTP id u10so166298748iou.0 for ; Sat, 12 Dec 2015 19:29:57 -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 --001a11407fecb23f180526bf2b51 Content-Type: text/plain; charset=UTF-8 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 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 > 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 --001a11407fecb23f180526bf2b51 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Well I was wrong, after I expand my-dropbox-path= to full path, the problem is still there.

Here are the result= s, 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?

<= div>=3D=3D=3D From notes.org =3D=3D=3D
=
..... some text with citations
bibliography:/home/= kai/Dropbox/bibliography/references.bib

#+BEGIN_SRC emacs-lisp
(o= rg-ref-find-bibliography)
#+END_SRC

#+RESULTS:
| /home/kai/Dro= pbox/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 D= ropbox folder, to ensure emacs portable on different OS.

When = I have the bibliography link in the org file, the (org-ref-find-bibliograph= y) 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 l= ink, 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:<= br>
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 Syst= em Lab
University of Science and Technology of China

K.Che= n



--
Regards

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

K.Chen
--001a11407fecb23f180526bf2b51--