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 22:36:20 -0500 Message-ID: References: Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:60181) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a7xSU-0004Dn-ES for emacs-orgmode@gnu.org; Sat, 12 Dec 2015 22:36:27 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1a7xSR-0007lN-86 for emacs-orgmode@gnu.org; Sat, 12 Dec 2015 22:36:26 -0500 Received: from mail-qk0-x22e.google.com ([2607:f8b0:400d:c09::22e]:32859) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a7xSR-0007lH-2O for emacs-orgmode@gnu.org; Sat, 12 Dec 2015 22:36:23 -0500 Received: by qkck189 with SMTP id k189so57956630qkc.0 for ; Sat, 12 Dec 2015 19:36:22 -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 does that mean it is working now? Kai Chen writes: > 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 >> >> -- 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