Re: [O] Problem with org-ref

[John Kitchin]

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 <address@hidden> 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: address@hidden
Australia

On 25 December 2015 at 13:17, John Kitchin <address@hidden> 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 <address@hidden> wrote:
>
>>
>> On Thu, Dec 24, 2015 at 1:04 AM, Andreas Kiermeier <
>> address@hidden> 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