From mboxrd@z Thu Jan 1 00:00:00 1970 From: Kai Chen Subject: org-ref is not using default bibliography file Date: Sun, 13 Dec 2015 00:43:46 +0800 Message-ID: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=001a11407fecc6a9330526b6246b Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:45304) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a7nGu-0003fK-MO for emacs-orgmode@gnu.org; Sat, 12 Dec 2015 11:43:50 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1a7nGt-0005kF-Bg for emacs-orgmode@gnu.org; Sat, 12 Dec 2015 11:43:48 -0500 Received: from mail-io0-x232.google.com ([2607:f8b0:4001:c06::232]:32798) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a7nGt-0005k9-4d for emacs-orgmode@gnu.org; Sat, 12 Dec 2015 11:43:47 -0500 Received: by iouu10 with SMTP id u10so158950754iou.0 for ; Sat, 12 Dec 2015 08:43:46 -0800 (PST) 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: emacs-orgmode@gnu.org --001a11407fecc6a9330526b6246b Content-Type: text/plain; charset=UTF-8 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 -- Regards Multi-Agent System Lab University of Science and Technology of China K.Chen --001a11407fecc6a9330526b6246b Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear list,

I just got to know org-ref, and I followed the github help page to manuall= y 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 w= hen 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 comman= d, but after I selected it and pressed enter, when the cursor is on the lin= k, 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, wh= ich 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 (setq org-ref-path (concat my-dropbox-path "= software/org-ref/"))

=C2=A0 (setq reftex-default-bibliography (= concat my-dropbox-path "bibliography/references.bib"))

=C2= =A0 ;; see org-ref for use of these variables
=C2=A0 (setq org-ref-bibli= ography-notes (concat my-dropbox-path "bibliography/notes.org")
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 org-ref-default-bibliography (concat my-dropbox-path "bibliography= /references.bib")
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 org-re= f-pdf-directory (concat my-dropbox-path "bibliography/bibtex-pdfs/&quo= t;))

=C2=A0 ;; *** helm-bibtex

=C2=A0 (setq helm-bibtex-bibli= ography (concat my-dropbox-path "bibliography/references.bib"))=C2=A0 (setq helm-bibtex-library-path (concat my-dropbox-path "bibli= ography/bibtex-pdfs"))

=C2=A0 ;; open pdf with system pdf viewe= r (works on mac)
=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= =C2=A0 (lambda (fpath)
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (start= -process "open" "*open*" "open" fpath))))
=
=C2=A0 ;; alternative
=C2=A0 ;; (setq helm-bibtex-pdf-open-function = 'org-open-file)

=C2=A0 (setq helm-bibtex-notes-path (concat my-d= ropbox-path "bibliography/helm-bibtex-notes"))

=C2=A0 (glo= bal-set-key [f10] 'org-ref-open-bibtex-notes)
=C2=A0 (global-set-key= [f11] 'org-ref-open-bibtex-pdf)
=C2=A0 (global-set-key [f12] 'o= rg-ref-open-in-browser)

=C2=A0 (add-to-list 'load-path org-ref-p= ath)

=C2=A0 ;; make sure you have dash, helm, helm-bibtex, ebib, s, = f, hydra and key-chord
=C2=A0 ;; in your load-path
=C2=A0 ;; auto-ins= tall dependencies
=C2=A0 (require 'org-ref)

=C2=A0 ;; optiona= l but very useful libraries in org-ref
=C2=A0 (require 'doi-utils)=C2=A0 (require 'jmax-bibtex)
=C2=A0 (require 'pubmed)
=C2= =A0 (require 'arxiv)
=C2=A0 (require 'sci-id)

#+END_SRC

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

K.Chen
--001a11407fecc6a9330526b6246b--