Re: Problem with org-ref

[John Kitchin <jkitchin@andrew.cmu.edu>]

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That sounds ok. I pushed a change that sort of does what you ask for. If
the "calculated" pdf doesn't exist then you should get prompted for a pdf,
and pressing enter for the default (no pdf) should not add a pdf link.

John

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


On Fri, Dec 25, 2015 at 7:03 PM, Andreas Kiermeier <
andreas.kiermeier@gmail.com> wrote:

> Thanks John.
>
> Yes, that was the case, because I had no intention of downloading the
> pdfs. So I had set
>
> (setq doi-utils-download-pdf nil)
>
> and left org-ref-pdf-directory nil. Setting it to a valid directory gets
> rid of the error. Thanks.
>
> I would find it useful (given that I've disabled auto-download) if I was
> prompted for the location of the pdf. That way I could either (a) provide a
> link to the pdf wherever I've stored it, or (b) not provide a link (yet).
> Just a thought.
>
> Thanks again for all your help.
>
> Andreas
>
> On 26 December 2015 at 00:37, John Kitchin <jkitchin@andrew.cmu.edu>
> wrote:
>
>> What about the value of org-ref-pdf-directory. This seems to be where
>> your error is coming from. Your debugger info suggests it is set to nil.
>>
>> Debugger entered--Lisp error: (wrong-type-argument stringp nil)
>>   file-name-as-directory(nil)
>>   org-ref-open-bibtex-notes()
>>   doi-utils-insert-bibtex-entry-fr
>>
>> John
>>
>> -----------------------------------
>> Professor John Kitchin
>> Doherty Hall A207F
>> Department of Chemical Engineering
>> Carnegie Mellon University
>> Pittsburgh, PA 15213
>> 412-268-7803
>> @johnkitchin
>> http://kitchingroup.cheme.cmu.edu
>>
>>
>> On Thu, Dec 24, 2015 at 10:16 PM, Andreas Kiermeier <
>> andreas.kiermeier@gmail.com> wrote:
>>
>>> I've set the HOME environment variable to "C:/Users/andre_000/Documents"
>>> and hence need the .. to get into the Dropbox folder.
>>>
>>> Executing (find-file org-ref-bibliography-notes) does find and open the
>>> correct notes file.
>>>
>>> Using an absolute path, as in:
>>>
>>> (setq org-ref-bibliography-notes
>>> "C:/Users/andre_000/Dropbox/_biblio/org-ref/bibnotes.org"
>>>       org-ref-default-bibliography
>>> '("C:/Users/andre_000/Dropbox/_biblio/refs.bib"))
>>>
>>> results in the same error.
>>>
>>> After dropping a PDF file into the .bib file I end up with the following
>>> additional entry (for example) in the bibnotes.org file. I thought I'd
>>> include it just to ensure that nothing gets chopped of - this entry
>>> correctly reflect the PDF.
>>>
>>> ** TODO 2007 - Taenia Saginata in Europe
>>>  :PROPERTIES:
>>>   :Custom_ID: dorny_2007
>>>   :AUTHOR: Dorny \& Praet
>>>   :JOURNAL: Veterinary Parasitology
>>>   :YEAR: 2007
>>>   :VOLUME: 149
>>>   :PAGES: 22-24
>>>   :DOI: 10.1016/j.vetpar.2007.07.004
>>>   :URL: http://dx.doi.org/10.1016/j.vetpar.2007.07.004
>>>  :END:
>>>
>>> Does the notes file need a specific set up in terms of headers etc?
>>>
>>>
>>> --
>>> Dr Andreas Kiermeier | Director
>>> Statistical Process Improvement Consulting and Training Pty Ltd
>>> Mbl: +61 (4)23 028 565 | Email: andreas.kiermeier@gmail.com
>>> Australia
>>>
>>> On 25 December 2015 at 13:17, John Kitchin <jkitchin@andrew.cmu.edu>
>>> wrote:
>>>
>>>> That is an odd looking path. On Mac that would expand to something like
>>>>
>>>> /Users/Dropbox/_biblio/org-ref/bibnotes.org
>>>>
>>>> and on linux
>>>>
>>>> /home/Dropbox/_biblio/org-ref/bibnotes.org
>>>>
>>>> usually you should not have permission for that, and neither make sense
>>>> to me.
>>>>
>>>> Does (file-exists-p org-ref-bibliography-notes) return true?
>>>>
>>>> or alternatively does (find-file org-ref-bibliography-notes) actually
>>>> open a writable file?
>>>>
>>>> I would think this is what you want (unless you have some unusual setup
>>>> and permissions):
>>>>
>>>> (setq org-ref-bibliography-notes "~/Dropbox/_biblio/org-ref/
>>>> bibnotes.org"
>>>>        org-ref-default-bibliography '("~/Dropbox/_biblio/refs.bib"))
>>>>
>>>> i.e. no .. in the path.
>>>>
>>>> Andreas Kiermeier writes:
>>>>
>>>> > Hi John,
>>>> >
>>>> > I've set it at follows (based on your setup) in my init.el file:
>>>> >
>>>> > (setq org-ref-bibliography-notes "~/../Dropbox/_biblio/org-ref/
>>>> bibnotes.org"
>>>> >       org-ref-default-bibliography '("~/../Dropbox/_biblio/refs.bib"))
>>>> >
>>>> > So, non-nil.
>>>> >
>>>> > Andreas
>>>> >
>>>> > On 25 December 2015 at 00:45, John Kitchin <jkitchin@andrew.cmu.edu>
>>>> wrote:
>>>> >
>>>> >>
>>>> >> On Thu, Dec 24, 2015 at 1:04 AM, Andreas Kiermeier <
>>>> >> andreas.kiermeier@gmail.com> wrote:
>>>> >>
>>>> >>> org-ref-open-bibtex-notes()
>>>> >>
>>>> >>
>>>> >> That looks like a different error that occurs in
>>>> org-ref-open-bibtex-notes().
>>>> >> Up to that point everything looks normal.
>>>> >>
>>>> >> What do you have your org-ref-bibliography-notes variable set to? The
>>>> >> default value is nil which would cause that error.
>>>> >>
>>>> >>
>>>> >>
>>>> >> John
>>>> >>
>>>> >> -----------------------------------
>>>> >> Professor John Kitchin
>>>> >> Doherty Hall A207F
>>>> >> Department of Chemical Engineering
>>>> >> Carnegie Mellon University
>>>> >> Pittsburgh, PA 15213
>>>> >> 412-268-7803
>>>> >> @johnkitchin
>>>> >> http://kitchingroup.cheme.cmu.edu
>>>> >>
>>>> >>
>>>>
>>>> --
>>>> Professor John Kitchin
>>>> Doherty Hall A207F
>>>> Department of Chemical Engineering
>>>> Carnegie Mellon University
>>>> Pittsburgh, PA 15213
>>>> 412-268-7803
>>>> @johnkitchin
>>>> http://kitchingroup.cheme.cmu.edu
>>>>
>>>
>>>
>>
>

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