From mboxrd@z Thu Jan 1 00:00:00 1970 From: Andreas Kiermeier Subject: Re: Problem with org-ref Date: Fri, 25 Dec 2015 13:46:14 +1030 Message-ID: References: <9B7FD49A-1A5F-42D3-9D9F-72BB151AF28C@gmail.com> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=001a11c124b020e03f0527b06387 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:48733) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aCIsC-0001nt-OR for emacs-orgmode@gnu.org; Thu, 24 Dec 2015 22:16:58 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aCIsB-0001x8-1l for emacs-orgmode@gnu.org; Thu, 24 Dec 2015 22:16:56 -0500 Received: from mail-qg0-x22d.google.com ([2607:f8b0:400d:c04::22d]:34635) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aCIsA-0001x4-Sg for emacs-orgmode@gnu.org; Thu, 24 Dec 2015 22:16:54 -0500 Received: by mail-qg0-x22d.google.com with SMTP id 6so28356763qgy.1 for ; Thu, 24 Dec 2015 19:16:54 -0800 (PST) In-Reply-To: List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: John Kitchin Cc: "emacs-orgmode@gnu.org" --001a11c124b020e03f0527b06387 Content-Type: text/plain; charset=UTF-8 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 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 > 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 > --001a11c124b020e03f0527b06387 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
I've set the HOME environment varia= ble to "C:/Users/andre_000/Documents" and hence need the .. to ge= t into the Dropbox folder.

Executing=C2=A0(find-file org-ref-bibliography-notes) does find and open the co= rrect notes file.

Using an absolute path, as in:

<= /span>
(setq org-ref-bibliography-notes "C:/Users/andre= _000/Dropbox/_biblio/org-ref/bibnotes.org"
=C2= =A0 =C2=A0 =C2=A0 org-ref-default-bibliography '("C:/Users/andre_0= 00/Dropbox/_biblio/refs.bib"))

Afte= r dropping a PDF file into the .bib file I end up with the following additi= onal entry (for example) in the bibnotes.or= g file. I thought I'd include it just to ensure that nothing gets c= hopped of - this entry correctly reflect the PDF.

** TODO 2007 - Taenia Saginata in Europe
=C2=A0:PROPERTIES:
=C2=A0 :Custom_ID: dorny_2007
=C2=A0 :AUTHOR:= Dorny \& Praet
=C2=A0 :JOURNAL: Veterinary Parasitology
= =C2=A0 :YEAR: 2007
=C2=A0 :VOLUME: 149
=C2=A0 :PAGES: 22-24
=C2=A0 :DOI: 10.1016/j.= vetpar.2007.07.004
=C2=A0:END:

Does th= e 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 <= span dir=3D"ltr"><jkitchin@andrew.cmu.edu> wrote:
That is an odd looking path. On Mac that would expand to some= thing 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= "
=C2=A0 =C2=A0 =C2=A0 =C2=A0org-ref-default-bibliography '("~/Dropb= ox/_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"
>=C2=A0 =C2=A0 =C2=A0 =C2=A0org-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@g= mail.com> wrote:
>>
>>> org-ref-open-bibtex-notes()
>>
>>
>> That looks like a different error that occurs in=C2=A0 org-ref-ope= n-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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