Re: Problem with org-ref

[Andreas Kiermeier <andreas.kiermeier@gmail.com>]

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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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