Re: Problem with org-ref

[Andreas Kiermeier <andreas.kiermeier@gmail.com>]

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Hi John,

thanks for the quick feedback and fix. Yes, the version that comes with
GitHub (on Windows) works when set this way, though I had to specify
slightly differently (i.e quotes & backslashes):

(setq pdftotext-executable
"C:/Users/andre_000/AppData/Local/GitHub/PortableGit_c7e0cbde92ba565cb218a521411d0e854079a28c/mingw32/bin/pdftotext.exe")

But now the following error occurs, after inserting the new bibtex entry
and creating a new note (in the notes file):

org-ref-open-bibtex-notes: Wrong type argument: stringp, nil

Turning debugging on yields the following:

Debugger entered--Lisp error: (wrong-type-argument stringp nil)
  file-name-as-directory(nil)
  org-ref-open-bibtex-notes()
  doi-utils-insert-bibtex-entry-from-doi("10.1016/j.vetpar.2010.10.058")
  doi-utils-add-bibtex-entry-from-doi("10.1016/j.vetpar.2010.10.058"
"c:/Users/andre_000/Dropbox/_biblio/refs.bib")

org-ref-pdf-dnd-protocol("file:C%3A/Users/andre_000/Dropbox/Consulting/Projects/RedMeat/MLA_Beef_Measles-C_bovis/literature/VetPara_McFadden_2011.pdf"
private)
  byte-code(" \306 \211 \203%

Looks like something is still not quite right with the ":" in the pathname.

​Cheers,

Andreas​

On 24 December 2015 at 12:03, John Kitchin <jkitchin@andrew.cmu.edu> wrote:

> 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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