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Re: [O] org-ref "no key found"


From: Julian M. Burgos
Subject: Re: [O] org-ref "no key found"
Date: Mon, 15 Sep 2014 10:16:57 +0100
User-agent: mu4e 0.9.9.5; emacs 24.3.1

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" <address@hidden> 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" <address@hidden> 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" <address@hidden> 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: address@hidden



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