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" <jul...@hafro.is> 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" <jul...@hafro.is> 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" <jul...@hafro.is> 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 -- Julian Mariano Burgos, PhD Hafrannsóknastofnun/Marine Research Institute Skúlagata 4, 121 Reykjavík, Iceland Sími/Telephone : +354-5752037 Bréfsími/Telefax: +354-5752001 Netfang/Email: jul...@hafro.is
