From mboxrd@z Thu Jan 1 00:00:00 1970 From: Andreas Kiermeier Subject: Re: Problem with org-ref Date: Sat, 26 Dec 2015 10:33:08 +1030 Message-ID: References: <9B7FD49A-1A5F-42D3-9D9F-72BB151AF28C@gmail.com> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=001a113a6f605bc1750527c1ce55 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:55653) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aCcKs-0000WX-FQ for emacs-orgmode@gnu.org; Fri, 25 Dec 2015 19:03:52 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aCcKq-0005nT-HT for emacs-orgmode@gnu.org; Fri, 25 Dec 2015 19:03:50 -0500 Received: from mail-qg0-x234.google.com ([2607:f8b0:400d:c04::234]:33567) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aCcKq-0005nN-BN for emacs-orgmode@gnu.org; Fri, 25 Dec 2015 19:03:48 -0500 Received: by mail-qg0-x234.google.com with SMTP id k90so192997076qge.0 for ; Fri, 25 Dec 2015 16:03:48 -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" --001a113a6f605bc1750527c1ce55 Content-Type: text/plain; charset=UTF-8 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 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 >> 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 >>> >> >> > --001a113a6f605bc1750527c1ce55 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Thanks John.
Yes, that was the case, because I had no intenti= on of downloading the pdfs. So I had set

=
(setq doi-utils-download-pd= f nil)

and left=C2=A0org-ref-pdf-directory nil. Se= tting it to a valid directory gets rid of the error. Thanks.

=
I would find it useful (given that I've disabled auto-downlo= ad) 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 provi= de a link (yet). Just a thought.

Thanks again for = all your help.

Andreas

<= div class=3D"gmail_extra">
On 26 December 2015 at= 00:37, John Kitchin <jkitchin@andrew.cmu.edu> wrote:<= br>
What about the value of= =C2=A0org-ref-pdf-directory. This seems to be where your error is coming fr= om. Your debugger info suggests it is set to nil.

Debugger ent= ered--Lisp error: (wrong-type-argument stringp nil)
=C2=A0 file-name-as-dire= ctory(nil)
=C2=A0 org-ref-open-bibtex-notes()
=C2=A0 doi-utils-insert-bibtex-= entry-fr

John

-= ----------------------------------
Professor John Kitchin=C2=A0
Doher= ty Hall A207F
Department of Chemical Engineering
Carnegie Mellon Univ= ersity
Pittsburgh, PA 15213
412-268-7803

On Thu, Dec 24= , 2015 at 10:16 PM, Andreas Kiermeier <andreas.kiermeier@gmail.c= om> wrote:
I= 9;ve set the HOME environment variable to "C:/Users/andre_000/Document= s" and hence need the .. to get into the Dropbox folder.

Exec= uting=C2=A0(f= ind-file org-ref-bibliography-notes) does find and open the correct notes f= ile.
<= br>
Using an absolute pat= h, as in:

(setq org-ref-bibliography-notes &qu= ot;C:/Users/andre_000/Dropbox/_biblio/org-ref/bibnotes.org"
=C2=A0 =C2=A0 =C2=A0 org-ref-default-bibliography '("C:/User= s/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 followi= ng 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
= =C2=A0:PROPERTIES:
=C2=A0 :Custom_ID: dorny_2007
<= span style=3D"font-size:12.8px">=C2=A0 :AUTHOR: Dorny \& Praet
=C2=A0 :JOURNAL: Veterinary Paras= itology
=C2=A0 :YEAR: 200= 7
=C2=A0 :VOLUME: 149
=C2=A0 :PAGES: 22-24<= /div>
=C2=A0 :DOI: 10.1016/j.vetpar.20= 07.07.004
=C2=A0 :URL: = http://dx.doi.org/10.1016/j.vetpar.2007.07.004
=C2=A0: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 <= 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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