From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: org-ref is not using default bibliography file Date: Sat, 12 Dec 2015 22:59:26 -0500 Message-ID: References: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=047d7bae465c29e2db0526bf95d6 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:34496) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a7xoo-0007Dv-3c for emacs-orgmode@gnu.org; Sat, 12 Dec 2015 22:59:31 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1a7xol-00040f-Uz for emacs-orgmode@gnu.org; Sat, 12 Dec 2015 22:59:30 -0500 Received: from mail-wm0-x234.google.com ([2a00:1450:400c:c09::234]:38675) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a7xol-00040b-Lr for emacs-orgmode@gnu.org; Sat, 12 Dec 2015 22:59:27 -0500 Received: by wmpp66 with SMTP id p66so20602025wmp.1 for ; Sat, 12 Dec 2015 19:59:26 -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: Kai Chen Cc: "emacs-orgmode@gnu.org" --047d7bae465c29e2db0526bf95d6 Content-Type: text/plain; charset=UTF-8 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 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 > 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 > -- 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 --047d7bae465c29e2db0526bf95d6 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable That probably means some variable should be a list and it isn't, it is = just a string.=C2=A0

On Saturday, December 12, 2015, Ka= i Chen <chk0105@mail.ustc.ed= u.cn> wrote:
Well I was wrong, after I expand my-dropbox-path to full path, the pr= oblem is still there.

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

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

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

#+RESULTS:
| /home/kai/Dropbo= x/bibliography/references.bib |

: /home/kai/Dropbox/bibliography/ref= erences.bib



On Sun, Dec 13, 2015 at 11:11 AM, Kai Chen <chk0105@mail.ustc.edu.cn>= wrote:
<= div>
Thanks for your suggestion! The problem lies in a variable I set w= hich 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/referenc= es.bib
But if I do not have the link, it returns
~/Dropbox/bibl= iography/references.bib

It seems some modules are resolving th= e '~' while some others are not.

Cheers,
Kai<= br>

<= /div>

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
U= niversity of Science and Technology of China

K.Chen



--
<= div>
Regards

Multi-Agent System Lab
University of Scien= ce and Technology of China

K.Chen


--
John
=
-----------------------------------
Professor John Kitchin=C2=A0
= Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon= University
Pittsburgh, PA 15213
412-268-7803

--047d7bae465c29e2db0526bf95d6--