From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: Problem with org-ref Date: Fri, 25 Dec 2015 20:36:33 -0500 Message-ID: References: <9B7FD49A-1A5F-42D3-9D9F-72BB151AF28C@gmail.com> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=047d7bae465c1f8a860527c31a0f Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:41444) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aCdmf-0003vd-6F for emacs-orgmode@gnu.org; Fri, 25 Dec 2015 20:36:38 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aCdmd-00018N-61 for emacs-orgmode@gnu.org; Fri, 25 Dec 2015 20:36:37 -0500 Received: from mail-wm0-x231.google.com ([2a00:1450:400c:c09::231]:34248) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aCdmc-00018A-RS for emacs-orgmode@gnu.org; Fri, 25 Dec 2015 20:36:35 -0500 Received: by mail-wm0-x231.google.com with SMTP id l126so211616635wml.1 for ; Fri, 25 Dec 2015 17:36:34 -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" --047d7bae465c1f8a860527c31a0f Content-Type: text/plain; charset=UTF-8 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 > 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 >>>> >>> >>> >> > --047d7bae465c1f8a860527c31a0f Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
That sounds ok. I pushed a change that sort of does what y= ou ask for. If the "calculated" pdf doesn't exist then you sh= ould get prompted for a pdf, and pressing enter for the default (no pdf) sh= ould not add a pdf link.=C2=A0

John

-----------------------------------
Professor John Kit= chin=C2=A0
Doherty Hall A207F
Department of Chemical Engineering
C= arnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu

=

On Fri, Dec 25, 2015 at 7:03 PM, Andreas Kie= rmeier <andreas.kiermeier@gmail.com> wrote:
Thanks John= .

Yes, that was the ca= se, because I had no intention of downloading the pdfs. So I had set
<= div class=3D"gmail_default" style=3D"font-family:arial,helvetica,sans-serif= ;font-size:small">
(setq doi-utils-download-pdf nil)

and left=C2=A0o= rg-ref-pdf-directory nil. Setting it to a valid directory gets rid of the e= rror. Thanks.

I would find it useful (given that I= 've disabled auto-download) if I was prompted for the location of the p= df. 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 <jkitchi= n@andrew.cmu.edu> wrote:
What about the value of=C2=A0org-ref-pdf-directory. This see= ms to be where your error is coming from. Your debugger info suggests it is= set to nil.

Debugger entered--Lisp error: (wrong-type-argumen= t stringp nil)
=C2=A0 file-name-as-directory(nil)
=C2=A0 org-ref-open-bibtex-= notes()
=C2=A0 doi-utils-insert-bibtex-entry-fr

John

-----------------------------------
Professor= John Kitchin=C2=A0
Doherty Hall A207F
Department of Chemical Enginee= ring
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803

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

Executing=C2=A0= (find-file or= g-ref-bibliography-notes) does find and open the correct notes file.=

<= /div>
Using an absolute path, as in:

(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"))
results in the same error.

Afte= r dropping a PDF file into the .bib file I end up with the following additi= onal entry (for example) in the bibnotes.org file. I thought I'd include it just to ensure t= hat 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
=C2=A0 :AUTHOR: Dorny \& Praet
= =C2=A0 :JOURNAL: Veterinary Parasitology
=C2=A0 :YEAR: 2007<= /div>
=C2=A0 :VOLUME: 149
=
=C2=A0 :PAGES: 22-24
=C2=A0 :DOI: 10.1016/j.vetpar.2007.07.004=
=C2=A0:END:

Does the notes file need a sp= ecific set up in terms of headers etc?
=

--
Dr Andreas Kiermeier | Directo= r
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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