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

[John Kitchin]

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" <address@hidden> 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" <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

-- 
-----------------------------------
John Kitchin
Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu