From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: org-ref "no key found" Date: Sat, 13 Sep 2014 12:18:32 -0400 Message-ID: References: Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:43442) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1XSq24-0000E4-Mu for emacs-orgmode@gnu.org; Sat, 13 Sep 2014 12:18:44 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1XSq20-0000ty-LV for emacs-orgmode@gnu.org; Sat, 13 Sep 2014 12:18:40 -0400 Received: from mail-qg0-x230.google.com ([2607:f8b0:400d:c04::230]:38532) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1XSq20-0000to-Ej for emacs-orgmode@gnu.org; Sat, 13 Sep 2014 12:18:36 -0400 Received: by mail-qg0-f48.google.com with SMTP id q108so2161109qgd.7 for ; Sat, 13 Sep 2014 09:18:35 -0700 (PDT) In-Reply-To: (Julian M. Burgos's message of "Fri, 12 Sep 2014 12:08:13 +0100") 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: "Julian M. Burgos" Cc: emacs-orgmode@gnu.org No problem. Thanks for the tips to replicate this. It was pretty helpful in solving the problem (and thanks again to Nick who pointed me towards edebug-defun a while ago!) I think I have fixed this. The problem was org-ref was not finding a key that exists in a file. the way that is done all over org-ref is to insert the contents of the bibfile in temp buffer, and then use bibtex-search-entry on that buffer. It works like a charm usually, but not in the replicated steps you have below. once it works once, though, it seems to always work. Anyway, I think it is fixed now. there is a new version at https://github.com/jkitchin/jmax/blob/master/org/org-ref.org Thanks for reporting the bug! "Julian M. Burgos" writes: > Hi John, > > I am resending this... I think it did not went through the previous > time. > > I think I can replicate the org-ref bug now (if it is a bug). This is > the situation: > > a) If I open emacs, load a file that already has some link, and click on > the link (or place the cursor on it and press enter) I get the "no key > found" message and I cannot open the notes file (I get a "Wrong type > argument: stringp, nil"), although the link to the pdf file works. If I > open more than one file, links do not work in any of them. At this > point if I check the value of the "org-ref-default-bibliography" > variable, I get the correct path and filename of my .bib file. > > b) If I insert a new citation (using Ctrl-]) in any of the documents, > links work as they should in all documents (this is, I get the title and > I can open the notes file). >> > I should say that I am not using the org-ref-insert-bibliography-link > function, because I use biblatex and I prefer to insert the Latex > \printbibliography command. But if use it and insert the bibliography > link, the behaviour does not change. > > This is what I have in my .emacs file that is related to RefTex and > org-ref: > > -------------------------------------------------------------------------------------- > ;; Load RefTex > (add-hook 'LaTeX-mode-hook 'turn-on-reftex) ; with AUCTeX LaTeX mode > (autoload 'reftex-mode "reftex" "RefTeX Minor Mode" t) > (autoload 'turn-on-reftex "reftex" "RefTeX Minor Mode" nil) > (autoload 'reftex-citation "reftex-cite" "Make citation" nil) > (autoload 'reftex-index-phrase-mode "reftex-index" "Phrase mode" t) > (add-hook 'LaTeX-mode-hook 'turn-on-reftex) ; with AUCTeX LaTeX mode > (add-hook 'latex-mode-hook 'turn-on-reftex) ; with Emacs latex mode > > ;; Make RefTeX faster > (setq reftex-enable-partial-scans t) > (setq reftex-save-parse-info t) > (setq reftex-use-multiple-selection-buffers t) > (setq reftex-plug-into-AUCTeX t) > > (setq reftex-default-bibliography '("/home/julian/Documents/Refs/BibTex/references.bib")) > (setq reftex-sort-bibtex-matches "author") ; Sort entries found in BibTex database > (setq bibtex-dialect "biblatex") > > -------------------------------------------------------------------------------------- > (require 'org-ref) > > (setq org-ref-bibliography-notes "/home/julian/Documents/org files/notes.org" > org-ref-default-bibliography '("/home/julian/Documents/Refs/BibTex/references.bib") > org-ref-pdf-directory "/home/julian/Documents/Refs/") > (setq org-ref-default-citation-link "parencite") > -------------------------------------------------------------------------------------- > > Below I am sending you very simple .org and .bib files that (in my computer) > reproduce this behaviour. In this file I did use > org-ref-insert-bibliography-link. Let me know if I can give you any other information. > > All the best, > > Julian > > --Start trial.org file ---------------------------------------------------------------- > > * Trial > Some references > parencite:Brown2011a,Hobbs2006 > > bibliography:~/Documents/trial.bib > > --End trial.org file --------------------------------------------------------------------- > > > --Start trial.bib file ---------------------------------------------------------------- > > Article{Brown2011a, > Title = {Quantitative approaches in climate change ecology}, > Author = {Brown, C.J. and Schoeman, D.S. and Sydeman, W.J. and Brander, K. and Buckley, L.B. and Burrows, M. and Duarte, C.M. and Moore, P.J. and Pandolfi, J.M. and Poloczanska, E. and others}, > Journaltitle = {Global Change Biology}, > Year = {2011}, > > Crossref = {burnhm}, > File = {:Brown2011a.pdf:PDF}, > Publisher = {Wiley Online Library} > } > > @Article{Hobbs2006, > Title = {Alternatives to statistical hypothesis testing in ecology: a guide to self teaching}, > Author = {Hobbs, N.T. and Hilborn, R.}, > Journaltitle = {Ecological Applications}, > Year = {2006}, > Number = {1}, > Pages = {5--19}, > Volume = {16}, > > Crossref = {Quick2010}, > File = {:Hobbs2006.pdf:PDF}, > Publisher = {Eco Soc America} > } > > --End trial.bib file --------------------------------------------------------------------- > > > > >> Julian M. Burgos writes: >> >>> John, for some weird reason everything seems to be working now. Thanks >>> for your help... I will let you know if I break it again. >>> >>> John Kitchin writes: >>> >>>> that is odd. this means org-ref is not finding the key you clicked >>>> on. could you send me a small example that reproduces your problem (an >>>> org-file and the bib file)? >>>> >>>> "Julian M. Burgos" writes: >>>> >>>>> Hi John, >>>>> >>>>> No, they still do not work even after I click on the bibliography link >>>>> and get my .bib file opened. >>>>> >>>>> Julian >>>>> >>>>> John Kitchin writes: >>>>> >>>>>> "Julian M. Burgos" writes: >>>>>> >>>>>> If you click on the bibliography link to open the file, and then go back >>>>>> to your org-file, do the cite links work? >>>>>> >>>>>> I suspect the notes problem is related to the no key found problem. >>>>>> >>>>>>> Hello everyone, >>>>>>> >>>>>>> I am playing around with Joh Kitchin's excellent org-ref, and I am >>>>>>> having a few issues. In my .emacs file I have set up the values for the >>>>>>> org-ref-bibliography-notes, org-ref-default-bibliography, and >>>>>>> org-ref-pdf-directory. >>>>>>> >>>>>>> With this I can access my .bib database and use org-ref-insert-cite link >>>>>>> to add a citation link with no problems. But when I press enter on the >>>>>>> cite link, I get the following message: >>>>>>> >>>>>>> no key found >>>>>>> (No key found) (p)df (u)rl (n)otes (q) quit >>>>>>> >>>>>>> If I press "p" I get the pdf file, but if I press "n" I get the >>>>>>> following message: >>>>>>> >>>>>>> "Wrong type argument: stringp, nil". >>>>>>> >>>>>>> Any ideas how to solve this? >>>>>>> >>>>>>> Many thanks, >>>>>>> >>>>>>> Julian -- ----------------------------------- John Kitchin Professor Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 http://kitchingroup.cheme.cmu.edu