From mboxrd@z Thu Jan 1 00:00:00 1970 From: "Julian M. Burgos" Subject: Re: org-ref "no key found" Date: Mon, 15 Sep 2014 11:17:03 +0100 Message-ID: References: Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:57277) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1XTUGB-0006Et-4U for emacs-orgmode@gnu.org; Mon, 15 Sep 2014 07:16:00 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1XTUG6-0000sk-BZ for emacs-orgmode@gnu.org; Mon, 15 Sep 2014 07:15:55 -0400 Received: from hafgarpur.hafro.is ([130.208.64.48]:39125) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1XTUG5-0000s9-R5 for emacs-orgmode@gnu.org; Mon, 15 Sep 2014 07:15:50 -0400 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: "Julian M. Burgos" Cc: emacs-orgmode@gnu.org, John Kitchin John, another issue...a really minor one, and I am not sure if it is org-ref related. When I open the notes file, the org faces are not applied evenly. In particular,=20 a) Text after #TITLE: or #AUTHOR appears as regular text. If I use M-x describe face, I get "default". If modify in any way the face changes to "org-document-info" as it should be. b) Within the heading of each reference, the "TODO" statement appears with the same face as the rest of the heading (org-level-2 face). c) Links to pdf files appear like this, with default face: =20 [[cite:Collie2000]] [[file:/home/julian/Documents/Refs/Collie2000.pdf][pd= f]] And not as clickable links=20 cite:Collie2000 pdf (underlined, in blue, with org-link face) Again, as soon as I change anything the org-link face is applied and I get a clickable link. Of all this, the pdf links are the real issue, as they are non-functional until I edit them. Strangely, :PROPERTIES: and :END: appear in their correct face. Also, if I "fix" the faces (editing the text or pressing enter so I get the right faces) and close the notes files, I get the same wriong faces when = I reopen the file. Does this makes sense? Do you know what could be the issue? Many thanks again, Julian Julian M. Burgos writes: > Excellent! Many thanks... now it works like a charm. > > John Kitchin writes: > >> No problem. Thanks for the tips to replicate this. It was pretty helpf= ul >> in solving the problem (and thanks again to Nick who pointed me toward= s >> edebug-defun a while ago!) >> >> I think I have fixed this. The problem was org-ref was not finding a k= ey >> 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.=20 >> >> 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 i= s >>> 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 ke= y >>> 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. I= f 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 bibliograph= y >>> 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 mod= e >>> (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 mod= e >>> (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/BibT= ex/references.bib")) >>> (setq reftex-sort-bibtex-matches "author") ; Sort entries found in = BibTex database=20 >>> (setq bibtex-dialect "biblatex") >>> >>> ---------------------------------------------------------------------= ----------------- >>> (require 'org-ref) >>> >>> (setq org-ref-bibliography-notes "/home/julian/Documents/org files/no= tes.org" >>> org-ref-default-bibliography '("/home/julian/Documents/Refs/Bib= Tex/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 co= mputer) >>> 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. =20 >>> >>> 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 =3D {Quantitative approaches in climate ch= ange ecology}, >>> Author =3D {Brown, C.J. and Schoeman, D.S. and Sy= deman, 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 =3D {Global Change Biology}, >>> Year =3D {2011}, >>> >>> Crossref =3D {burnhm}, >>> File =3D {:Brown2011a.pdf:PDF}, >>> Publisher =3D {Wiley Online Library} >>> } >>> >>> @Article{Hobbs2006, >>> Title =3D {Alternatives to statistical hypothesi= s testing in ecology: a guide to self teaching}, >>> Author =3D {Hobbs, N.T. and Hilborn, R.}, >>> Journaltitle =3D {Ecological Applications}, >>> Year =3D {2006}, >>> Number =3D {1}, >>> Pages =3D {5--19}, >>> Volume =3D {16}, >>> >>> Crossref =3D {Quick2010}, >>> File =3D {:Hobbs2006.pdf:PDF}, >>> Publisher =3D {Eco Soc America} >>> } >>> >>> --End trial.bib file ------------------------------------------------= --------------------- >>> >>> >>> >>> >>>> Julian M. Burgos writes: >>>> >>>>> John, for some weird reason everything seems to be working now. Th= anks >>>>> 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,=20 >>>>>>> >>>>>>> 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 probl= em. >>>>>>>> >>>>>>>>> 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 value= s 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 ente= r 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:=20 >>>>>>>>> >>>>>>>>> "Wrong type argument: stringp, nil". >>>>>>>>> >>>>>>>>> Any ideas how to solve this? >>>>>>>>> >>>>>>>>> Many thanks, >>>>>>>>> >>>>>>>>> Julian --=20 Julian Mariano Burgos, PhD Hafranns=C3=B3knastofnun/Marine Research Institute Sk=C3=BAlagata 4, 121 Reykjav=C3=ADk, Iceland S=C3=ADmi/Telephone : +354-5752037 Br=C3=A9fs=C3=ADmi/Telefax: +354-5752001 Netfang/Email: julian@hafro.is