Re: Problem with org-ref

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

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Magic!
Thanks a lot, John.

On 26 December 2015 at 12:06, John Kitchin <jkitchin@andrew.cmu.edu> wrote:

> 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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