From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: org-ref "no key found" Date: Mon, 15 Sep 2014 22:49:27 -0400 Message-ID: References: Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:58376) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1XTipp-0001E1-F4 for emacs-orgmode@gnu.org; Mon, 15 Sep 2014 22:49:46 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1XTipk-0004iH-6I for emacs-orgmode@gnu.org; Mon, 15 Sep 2014 22:49:41 -0400 Received: from smtp.andrew.cmu.edu ([128.2.157.38]:50835) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1XTipk-0004hx-1x for emacs-orgmode@gnu.org; Mon, 15 Sep 2014 22:49:36 -0400 In-Reply-To: (Julian M. Burgos's message of "Mon, 15 Sep 2014 11:17:03 +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 If you look in your messages do you see something like jit-lock errors? I do not recall exactly what the errors are but the ones I have seen that resemble what you describe have jit in them. I saw this recently in an ELPA version (maybe around Sept 1), and it went away when I updated the ELPA org version to the most recent one. "Julian M. Burgos" writes: > 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, > > 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: > > [[cite:Collie2000]] [[file:/home/julian/Documents/Refs/Collie2000.pdf][pdf]] > > And not as clickable links > 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 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