Re: org-ref "no key found"

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

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