From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: Problem with org-ref Date: Wed, 23 Dec 2015 20:33:53 -0500 Message-ID: References: <9B7FD49A-1A5F-42D3-9D9F-72BB151AF28C@gmail.com> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=001a1140d862f0318a05279ad42e Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:43303) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aBumz-0003dA-FV for emacs-orgmode@gnu.org; Wed, 23 Dec 2015 20:33:59 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aBumx-00021b-QL for emacs-orgmode@gnu.org; Wed, 23 Dec 2015 20:33:57 -0500 Received: from mail-wm0-x231.google.com ([2a00:1450:400c:c09::231]:38681) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aBumx-00021T-G9 for emacs-orgmode@gnu.org; Wed, 23 Dec 2015 20:33:55 -0500 Received: by mail-wm0-x231.google.com with SMTP id l126so169344242wml.1 for ; Wed, 23 Dec 2015 17:33:55 -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: marvin doyley , "emacs-orgmode@gnu.org" --001a1140d862f0318a05279ad42e Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable I tested part of this on Windows in a git bash shell: $ pdftotext -v pdftotext version 0.14.5 Copyright 2005-2010 The Poppler Developers - http://poppler.freedesktop.org Copyright 1996-2004 Glyph & Cog, LLC and then this works: $ pdftotext.exe kitchin-2015-examp.pdf - | grep DOI ACS Catal., Just Accepted Manuscript =E2=80=A2 DOI: 10.1021/acscatal.5b0053= 8 =E2=80=A2 Publicati on Date (Web): 11 May 2015 readers and citable by the Digital Object Identifier (DOI=C2=AE). =E2=80=9C= Just Accepted=E2=80=9D is an optional service offered sharing site which assigned the data set a DOI. 19 An alternative data repositor y could be an institutional data repository which also provides a DOI for citing. It remains t o be seen if stores that provide a citable DOI for the data set. The point is that this appro ach is very However, I see that in emacs, it appears another pdftotext is getting used, which does not work. ~/Desktop $ pdftotext -v pdftotext version 2.03 Copyright 1996-2003 Glyph & Cog, LLC that is the same version that runs in a cmd shell. The version that seems to work for me is at "C:\Program Files (x86)\Git\bin\pdftotext". I added a variable to set the location of this program, and then rely on the executable path. It was a little tricky to set this right, note the escaped quotes. #+BEGIN_SRC emacs-lisp (setq pdftotext-executable "\"C:/Program Files (x86)/Git/bin/pdftotext\"") #+END_SRC It turned out there was another issue with the uri in the drag-n-drop needing to be unescaped on windows because of the : in the path, which is also done now. I pushed these out. hopefully that makes some progress for you! or at least gives some hints on where to look for the problem. Merry Xmas! 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 Wed, Dec 23, 2015 at 6:56 PM, Andreas Kiermeier < andreas.kiermeier@gmail.com> wrote: > Hi John, > similar doi problem here. > My configuration is: > > - Windows 10 > - GNU Emacs 24.5.1 (i686-pc-mingw32) of 2015-04-11 on LEG570 > - Miktex (up-to-date) with pdftotext v0.32..0 > - org-ref v 0.5.0 (from melpa) > > Running pdftotext from the command line works and produces a text file > with doi info. > Let me know what I can do to help to test things. > Thanks. > Andreas > PS: Thank you for org-ref ... an awesome Xmas present! > > > On 24 December 2015 at 08:00, John Kitchin > wrote: > >> Thanks! Do you know if you have pdftotext working on your machine? The >> pdf drag-n-drop works by converting the pdf to text, and than matching a >> pattern to find a doi. If none is found, you get the message you noted. = The >> url dnd works similarly, but there are a bunch of recipes for what to ma= tch >> depending on the base of the url. >> >> I did that on a Mac, and I haven't tested it on a windows or Linux >> machine. >> >> 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 Wed, Dec 23, 2015 at 4:22 PM, marvin doyley >> wrote: >> >>> Hi John, >>> >>> I am playing with org-ref, the melpa version. >>> >>> Everything works fine except, one thing. When I drag a pdf to an empty >>> bibtex file it doesn=E2=80=99t extract the doi ( no doi found in the fi= le:///). >>> I tried it pdf you used in your video (Examples of Effective Data Shar= ing >>> in Scientific Publishing), but I got the same error. Dragging the url t= o >>> the bibtex file also doesn=E2=80=99t works for me. >>> >>> cheers, >>> M >>> >>> PS by the way, your video was excellent :) >>> >> >> > --001a1140d862f0318a05279ad42e Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
I tested part of this on Windows in a git bash shell:
<= div>
$ pdftotext -v
pdftotext version 0.14.5
Copyright 2005-2010 The Poppler Developers - http://poppler.freedesktop.org
Copyrigh= t 1996-2004 Glyph & Cog, LLC

and then th= is works:
$ pdftotext.exe kitchin-2015-examp.pdf - | grep DO= I
ACS Catal., Just Accepted Manuscript =E2=80=A2 DOI: 10.1021/acs= catal.5b00538 =E2=80=A2 Publicati
on Date (Web): 11 May 2015
readers and citable by the Digital Object Identifier (DOI=C2=AE). =E2= =80=9CJust Accepted=E2=80=9D is
an optional service offered
=
sharing site which assigned the data set a DOI. 19 An alternative data= repositor
y could be an
institutional data repository = which also provides a DOI for citing. It remains t
o be seen if
stores that provide a citable DOI for the data set. The point is t= hat this appro
ach is very

However= , I see that in emacs, it appears another pdftotext is getting used, which = does not work.
~/Desktop $ pdftotext -v
pdftotext = version 2.03
Copyright 1996-2003 Glyph & Cog, LLC
=

that is the same version that runs in a cmd shell.

The version that seems to work for me is at=C2=A0"= ;C:\Program Files (x86)\Git\bin\pdftotext".

I= added a variable to set the location of this program, and then rely on the= executable path. It was a little tricky to set this right, note the escape= d quotes.

#+BEGIN_SRC emacs-lisp
(s= etq pdftotext-executable "\"C:/Program Files (x86)/Git/bin/pdftot= ext\"")
#+END_SRC


It turned out there was another issue with the uri in the drag-n-d= rop needing to be unescaped on windows because of the : in the path, which = is also done now.=C2=A0

I pushed these out. hopefu= lly that makes some progress for you! or at least gives some hints on where= to look for the problem.

Merry Xmas!
<= div class=3D"gmail_extra">
John

-------------------= ----------------
Professor John Kitchin=C2=A0
Doherty Hall A207F
D= epartment of Chemical Engineering
Carnegie Mellon University
Pittsbur= gh, PA 15213
412-268-7803

On Wed, Dec 23, 2015 at 6:56 PM, Andreas Kie= rmeier <andreas.kiermeier@gmail.com> wrote:
Hi John,
similar doi problem here.
My = configuration is:
  • Windows 10
  • GNU Emacs 24.5.1 (i686-pc-min= gw32) of 2015-04-11 on LEG570
  • Miktex (up-to-date) with pdftotext v0.32..0
  • org-ref= v 0.5.0 (from melpa)
Running pdftotext from the command line works and produces a te= xt file with doi info.
Let me know what I can do to help to test things.
Thanks.
Andreas
PS: = Thank you for org-ref ... an awesome Xmas present!


On 24 December= 2015 at 08:00, John Kitchin <jkitchin@andrew.cmu.edu>= wrote:
Thanks! Do you k= now if you have pdftotext working on your machine? The pdf drag-n-drop work= s by converting the pdf to text, and than matching a pattern to find a doi.= If none is found, you get the message you noted. The url dnd works similar= ly, but there are a bunch of recipes for what to match depending on the bas= e of the url.

I did that on a Mac, and I haven't tes= ted it on a windows or Linux machine.=C2=A0

J= ohn

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

On Wed, Dec 23, 2015 at 4:22 PM, marvin doyl= ey <marvinpas@gmail.com> wrote:
Hi John,

I am playing wi= th org-ref, =C2=A0the melpa version.

Everything works fine except, o= ne thing.=C2=A0 When I drag a pdf to an empty bibtex file it doesn=E2=80=99= t extract the doi ( no doi found in the=C2=A0file:///). I tried it p= df you used =C2=A0in your video (Examples of Effective Data Sharing in Scie= ntific Publishing), but I got the same error. Dragging the url to the bibte= x file also doesn=E2=80=99t works for me.

cheers,
M

PS by the way, your video was excellent :)



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