From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: Problem with org-ref Date: Fri, 25 Dec 2015 09:07:40 -0500 Message-ID: References: <9B7FD49A-1A5F-42D3-9D9F-72BB151AF28C@gmail.com> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=001a11c3babe74a8b50527b97a4f Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:58760) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aCT1z-0003Z9-3G for emacs-orgmode@gnu.org; Fri, 25 Dec 2015 09:07:44 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aCT1x-0004Y7-AX for emacs-orgmode@gnu.org; Fri, 25 Dec 2015 09:07:43 -0500 Received: from mail-wm0-x22c.google.com ([2a00:1450:400c:c09::22c]:35280) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aCT1x-0004Xv-1B for emacs-orgmode@gnu.org; Fri, 25 Dec 2015 09:07:41 -0500 Received: by mail-wm0-x22c.google.com with SMTP id l126so205599892wml.0 for ; Fri, 25 Dec 2015 06:07:40 -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: Andreas Kiermeier Cc: "emacs-orgmode@gnu.org" --001a11c3babe74a8b50527b97a4f Content-Type: text/plain; charset=UTF-8 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 > 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 >> > > --001a11c3babe74a8b50527b97a4f Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
What about the value of=C2=A0org-ref-pdf-directory. This s= eems 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)
=C2=A0 file= -name-as-directory(nil)
=C2=A0 org-ref-open-bibtex-n= otes()
=C2=A0 doi-utils-insert-bibtex-entry-fr
=

John

------= -----------------------------
Professor John Kitchin=C2=A0
Doherty Ha= ll A207F
Department of Chemical Engineering
Carnegie Mellon Universit= y
Pittsburgh, PA 15213
412-268-7803

On Thu, Dec 24, 2015 at 10:16 PM, Andreas Ki= ermeier <andreas.kiermeier@gmail.com> wrote:
I've s= et the HOME environment variable to "C:/Users/andre_000/Documents"= ; and hence need the .. to get into the Dropbox folder.

Executing=C2=A0(find-file org-ref-bibliography-not= es) does find and open the correct notes file.

Using = an absolute path, as in:

(setq org-ref-bibliograp= hy-notes "C:/Users/andre_000/Dropbox/_biblio/org-ref/bibnotes.org"
=C2=A0 =C2=A0 =C2=A0 org-ref-defa= ult-bibliography '("C:/Users/andre_000/Dropbox/_biblio/refs.bib&qu= ot;))

results in the same error.
<= br>
After dropping a PDF file into the= .bib file I end up with the following additional entry (for example) in th= e 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
=C2=A0= :PROPERTIES:
=C2=A0 :Cust= om_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:<= /span>

Does the notes file need a specific set up in terms of hea= ders 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 <
>> a= ndreas.kiermeier@gmail.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
412-2= 68-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu


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