Re: org-ref "no key found"

["Julian M. Burgos" <julian@hafro.is>]

Yes, you were right.  An update of org-mode fixed everything.  Thanks again!

John Kitchin writes:

> 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" <julian@hafro.is> 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" <julian@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" <julian@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" <julian@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: julian@hafro.is