Re: Problem with org-ref

[John Kitchin <jkitchin@andrew.cmu.edu>]

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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 • DOI: 10.1021/acscatal.5b00538 •
Publicati
on Date (Web): 11 May 2015
readers and citable by the Digital Object Identifier (DOI®). “Just
Accepted” 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 <jkitchin@andrew.cmu.edu>
> 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 match
>> 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 <marvinpas@gmail.com>
>> 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’t extract the doi ( no doi found in the file:///).
>>> I tried it pdf you used  in your video (Examples of Effective Data Sharing
>>> in Scientific Publishing), but I got the same error. Dragging the url to
>>> the bibtex file also doesn’t works for me.
>>>
>>> cheers,
>>> M
>>>
>>> PS by the way, your video was excellent :)
>>>
>>
>>
>

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