From mboxrd@z Thu Jan  1 00:00:00 1970
From: Andreas Kiermeier <andreas.kiermeier@gmail.com>
Subject: Re: Problem with org-ref
Date: Sat, 26 Dec 2015 10:33:08 +1030
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To: John Kitchin <jkitchin@andrew.cmu.edu>
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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 <jkitchin@andrew.cmu.edu> 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 <jkitchin@andrew.cmu.edu>
>> 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 <jkitchin@andrew.cmu.edu>
>>> 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
>>>
>>
>>
>

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<div dir=3D"ltr"><div class=3D"gmail_default" style=3D"font-family:arial,he=
lvetica,sans-serif;font-size:small">Thanks John.</div><div class=3D"gmail_d=
efault" style=3D"font-family:arial,helvetica,sans-serif;font-size:small"><b=
r></div><div class=3D"gmail_default" style=3D"font-family:arial,helvetica,s=
ans-serif;font-size:small">Yes, that was the case, because I had no intenti=
on of downloading the pdfs. So I had set</div><div class=3D"gmail_default" =
style=3D"font-family:arial,helvetica,sans-serif;font-size:small"><br></div>=
<div class=3D"gmail_default" style=3D"font-family:arial,helvetica,sans-seri=
f;font-size:small"><div class=3D"gmail_default">(setq doi-utils-download-pd=
f nil)</div><div><br></div><div>and left=C2=A0org-ref-pdf-directory nil. Se=
tting it to a valid directory gets rid of the error. Thanks.</div><div><br>=
</div><div>I would find it useful (given that I&#39;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&#39;ve stored it, or (b) not provi=
de a link (yet). Just a thought.</div><div><br></div><div>Thanks again for =
all your help.</div><div><br></div><div>Andreas</div><div><br></div></div><=
div class=3D"gmail_extra"><div class=3D"gmail_quote">On 26 December 2015 at=
 00:37, John Kitchin <span dir=3D"ltr">&lt;<a href=3D"mailto:jkitchin@andre=
w.cmu.edu" target=3D"_blank">jkitchin@andrew.cmu.edu</a>&gt;</span> wrote:<=
br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left=
:1px #ccc solid;padding-left:1ex"><div dir=3D"ltr">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.<div><br></div><div><div s=
tyle=3D"font-family:arial,helvetica,sans-serif;font-size:13px">Debugger ent=
ered--Lisp error: (wrong-type-argument stringp nil)</div><div style=3D"font=
-family:arial,helvetica,sans-serif;font-size:13px">=C2=A0 file-name-as-dire=
ctory(nil)</div><div style=3D"font-family:arial,helvetica,sans-serif;font-s=
ize:13px">=C2=A0 org-ref-open-bibtex-notes()</div><div style=3D"font-family=
:arial,helvetica,sans-serif;font-size:13px">=C2=A0 doi-utils-insert-bibtex-=
entry-fr</div></div></div><div class=3D"gmail_extra"><span class=3D""><br c=
lear=3D"all"><div><div><div dir=3D"ltr"><div><div dir=3D"ltr">John<br><br>-=
----------------------------------<br>Professor John Kitchin=C2=A0<br>Doher=
ty Hall A207F<br>Department of Chemical Engineering<br>Carnegie Mellon Univ=
ersity<br>Pittsburgh, PA 15213<br>412-268-7803</div><div dir=3D"ltr">@johnk=
itchin<br><a href=3D"http://kitchingroup.cheme.cmu.edu" target=3D"_blank">h=
ttp://kitchingroup.cheme.cmu.edu</a><br><br></div></div></div></div></div>
<br></span><div><div class=3D"h5"><div class=3D"gmail_quote">On Thu, Dec 24=
, 2015 at 10:16 PM, Andreas Kiermeier <span dir=3D"ltr">&lt;<a href=3D"mail=
to:andreas.kiermeier@gmail.com" target=3D"_blank">andreas.kiermeier@gmail.c=
om</a>&gt;</span> wrote:<br><blockquote class=3D"gmail_quote" style=3D"marg=
in:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir=3D"ltr"=
><div style=3D"font-family:arial,helvetica,sans-serif;font-size:small">I&#3=
9;ve set the HOME environment variable to &quot;C:/Users/andre_000/Document=
s&quot; and hence need the .. to get into the Dropbox folder.<br></div><div=
 style=3D"font-family:arial,helvetica,sans-serif;font-size:small"><br></div=
><div style=3D"font-family:arial,helvetica,sans-serif;font-size:small">Exec=
uting=C2=A0<span style=3D"font-size:12.8px;font-family:arial,sans-serif">(f=
ind-file org-ref-bibliography-notes) does find and open the correct notes f=
ile.</span></div><div style=3D"font-family:arial,helvetica,sans-serif;font-=
size:small"><span style=3D"font-size:12.8px;font-family:arial,sans-serif"><=
br></span></div><div><span style=3D"font-size:12.8px">Using an absolute pat=
h, as in:</span></div><div><span style=3D"font-size:12.8px"><br></span></di=
v><div><div style=3D"font-size:12.8px">(setq org-ref-bibliography-notes &qu=
ot;C:/Users/andre_000/Dropbox/_biblio/org-ref/<a href=3D"http://bibnotes.or=
g" target=3D"_blank">bibnotes.org</a>&quot;</div><div style=3D"font-size:12=
.8px">=C2=A0 =C2=A0 =C2=A0 org-ref-default-bibliography &#39;(&quot;C:/User=
s/andre_000/Dropbox/_biblio/refs.bib&quot;))</div><div style=3D"font-size:1=
2.8px"><br></div><div style=3D"font-size:12.8px">results in the same error.=
</div><div style=3D"font-size:12.8px"><br></div><div style=3D"font-size:12.=
8px">After dropping a PDF file into the .bib file I end up with the followi=
ng additional entry (for example) in the <a href=3D"http://bibnotes.org" ta=
rget=3D"_blank">bibnotes.org</a> file. I thought I&#39;d include it just to=
 ensure that nothing gets chopped of - this entry correctly reflect the PDF=
.</div><div style=3D"font-size:12.8px"><br></div><div><div><span style=3D"f=
ont-size:12.8px">** TODO 2007 - Taenia Saginata in Europe</span></div><div>=
<span style=3D"font-size:12.8px">=C2=A0:PROPERTIES:</span></div><div><span =
style=3D"font-size:12.8px">=C2=A0 :Custom_ID: dorny_2007</span></div><div><=
span style=3D"font-size:12.8px">=C2=A0 :AUTHOR: Dorny \&amp; Praet</span></=
div><div><span style=3D"font-size:12.8px">=C2=A0 :JOURNAL: Veterinary Paras=
itology</span></div><div><span style=3D"font-size:12.8px">=C2=A0 :YEAR: 200=
7</span></div><div><span style=3D"font-size:12.8px">=C2=A0 :VOLUME: 149</sp=
an></div><div><span style=3D"font-size:12.8px">=C2=A0 :PAGES: 22-24</span><=
/div><div><span style=3D"font-size:12.8px">=C2=A0 :DOI: 10.1016/j.vetpar.20=
07.07.004</span></div><div><span style=3D"font-size:12.8px">=C2=A0 :URL: <a=
 href=3D"http://dx.doi.org/10.1016/j.vetpar.2007.07.004" target=3D"_blank">=
http://dx.doi.org/10.1016/j.vetpar.2007.07.004</a></span></div><div><span s=
tyle=3D"font-size:12.8px">=C2=A0:END:</span></div></div><div style=3D"font-=
size:12.8px"><br></div><div style=3D"font-size:12.8px">Does the notes file =
need a specific set up in terms of headers etc?</div></div><span><font colo=
r=3D"#888888"><div style=3D"font-family:arial,helvetica,sans-serif;font-siz=
e:small"><br></div></font></span></div><div class=3D"gmail_extra"><span><fo=
nt color=3D"#888888"><br clear=3D"all"><div><div><div dir=3D"ltr"><font siz=
e=3D"2" face=3D"arial, helvetica, sans-serif">-- <br>Dr Andreas Kiermeier |=
 Director<br>
Statistical Process Improvement Consulting and Training Pty Ltd<br>
Mbl: +61 (4)23 028 565 | Email: <a href=3D"mailto:andreas.kiermeier@gmail.c=
om" target=3D"_blank">andreas.kiermeier@gmail.com</a> <br>
Australia</font><br></div></div></div></font></span><div><div>
<br><div class=3D"gmail_quote">On 25 December 2015 at 13:17, John Kitchin <=
span dir=3D"ltr">&lt;<a href=3D"mailto:jkitchin@andrew.cmu.edu" target=3D"_=
blank">jkitchin@andrew.cmu.edu</a>&gt;</span> wrote:<br><blockquote class=
=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padd=
ing-left:1ex">That is an odd looking path. On Mac that would expand to some=
thing like<br>
<br>
/Users/Dropbox/_biblio/org-ref/<a href=3D"http://bibnotes.org" rel=3D"noref=
errer" target=3D"_blank">bibnotes.org</a><br>
<br>
and on linux<br>
<br>
/home/Dropbox/_biblio/org-ref/<a href=3D"http://bibnotes.org" rel=3D"norefe=
rrer" target=3D"_blank">bibnotes.org</a><br>
<br>
usually you should not have permission for that, and neither make sense<br>
to me.<br>
<br>
Does (file-exists-p org-ref-bibliography-notes) return true?<br>
<br>
or alternatively does (find-file org-ref-bibliography-notes) actually<br>
open a writable file?<br>
<br>
I would think this is what you want (unless you have some unusual setup<br>
and permissions):<br>
<br>
(setq org-ref-bibliography-notes &quot;~/Dropbox/_biblio/org-ref/<a href=3D=
"http://bibnotes.org" rel=3D"noreferrer" target=3D"_blank">bibnotes.org</a>=
&quot;<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0org-ref-default-bibliography &#39;(&quot;~/Dropb=
ox/_biblio/refs.bib&quot;))<br>
<br>
i.e. no .. in the path.<br>
<div><div><br>
Andreas Kiermeier writes:<br>
<br>
&gt; Hi John,<br>
&gt;<br>
&gt; I&#39;ve set it at follows (based on your setup) in my init.el file:<b=
r>
&gt;<br>
&gt; (setq org-ref-bibliography-notes &quot;~/../Dropbox/_biblio/org-ref/<a=
 href=3D"http://bibnotes.org" rel=3D"noreferrer" target=3D"_blank">bibnotes=
.org</a>&quot;<br>
&gt;=C2=A0 =C2=A0 =C2=A0 =C2=A0org-ref-default-bibliography &#39;(&quot;~/.=
./Dropbox/_biblio/refs.bib&quot;))<br>
&gt;<br>
&gt; So, non-nil.<br>
&gt;<br>
&gt; Andreas<br>
&gt;<br>
&gt; On 25 December 2015 at 00:45, John Kitchin &lt;<a href=3D"mailto:jkitc=
hin@andrew.cmu.edu" target=3D"_blank">jkitchin@andrew.cmu.edu</a>&gt; wrote=
:<br>
&gt;<br>
&gt;&gt;<br>
&gt;&gt; On Thu, Dec 24, 2015 at 1:04 AM, Andreas Kiermeier &lt;<br>
&gt;&gt; <a href=3D"mailto:andreas.kiermeier@gmail.com" target=3D"_blank">a=
ndreas.kiermeier@gmail.com</a>&gt; wrote:<br>
&gt;&gt;<br>
&gt;&gt;&gt; org-ref-open-bibtex-notes()<br>
&gt;&gt;<br>
&gt;&gt;<br>
&gt;&gt; That looks like a different error that occurs in=C2=A0 org-ref-ope=
n-bibtex-notes().<br>
&gt;&gt; Up to that point everything looks normal.<br>
&gt;&gt;<br>
&gt;&gt; What do you have your org-ref-bibliography-notes variable set to? =
The<br>
&gt;&gt; default value is nil which would cause that error.<br>
&gt;&gt;<br>
&gt;&gt;<br>
&gt;&gt;<br>
&gt;&gt; John<br>
&gt;&gt;<br>
&gt;&gt; -----------------------------------<br>
&gt;&gt; Professor John Kitchin<br>
&gt;&gt; Doherty Hall A207F<br>
&gt;&gt; Department of Chemical Engineering<br>
&gt;&gt; Carnegie Mellon University<br>
&gt;&gt; Pittsburgh, PA 15213<br>
&gt;&gt; <a href=3D"tel:412-268-7803" value=3D"+14122687803" target=3D"_bla=
nk">412-268-7803</a><br>
&gt;&gt; @johnkitchin<br>
&gt;&gt; <a href=3D"http://kitchingroup.cheme.cmu.edu" rel=3D"noreferrer" t=
arget=3D"_blank">http://kitchingroup.cheme.cmu.edu</a><br>
&gt;&gt;<br>
&gt;&gt;<br>
<br>
--<br>
Professor John Kitchin<br>
Doherty Hall A207F<br>
Department of Chemical Engineering<br>
Carnegie Mellon University<br>
Pittsburgh, PA 15213<br>
<a href=3D"tel:412-268-7803" value=3D"+14122687803" target=3D"_blank">412-2=
68-7803</a><br>
@johnkitchin<br>
<a href=3D"http://kitchingroup.cheme.cmu.edu" rel=3D"noreferrer" target=3D"=
_blank">http://kitchingroup.cheme.cmu.edu</a><br>
</div></div></blockquote></div><br></div></div></div>
</blockquote></div><br></div></div></div>
</blockquote></div><br></div></div>

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