From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: org-ref: citation types (insert full citation); bib style; bib scope Date: Fri, 06 Jan 2017 16:10:00 +0000 Message-ID: References: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=94eb2c06d6b0903b6f05456f403e Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:50112) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cPX5r-0000xY-Dw for emacs-orgmode@gnu.org; Fri, 06 Jan 2017 11:10:17 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cPX5o-0004PO-2c for emacs-orgmode@gnu.org; Fri, 06 Jan 2017 11:10:15 -0500 Received: from mail-wm0-f54.google.com ([74.125.82.54]:36346) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1cPX5n-0004Os-Nc for emacs-orgmode@gnu.org; Fri, 06 Jan 2017 11:10:12 -0500 Received: by mail-wm0-f54.google.com with SMTP id c85so30681371wmi.1 for ; Fri, 06 Jan 2017 08:10:11 -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" To: Matt Price Cc: Org Mode --94eb2c06d6b0903b6f05456f403e Content-Type: text/plain; charset=UTF-8 That is possible. I am out now, but this afternoon I will send another note on how to do it. On Fri, Jan 6, 2017 at 11:05 AM Matt Price wrote: > On Fri, Jan 6, 2017 at 10:26 AM, John Kitchin > wrote: > > > > > Matt Price writes: > > > > > > > After several years, I'm finally trying to move to bibtex from zotero, > > > > partly because org-zotxt has stopped working for me (both link insertion > > > > and html export seem at least temporarily broken). > > > > > > > > The UI for org-ref is pretty fantastic, and I love it. I'm having trouble > > > > getting the behaviour I want fro mthe actual links, though. My needs may > > > > be somewhat atypical but I'm hoping someone else has figured these > > > > questions out already. > > > > > > > > * citation types > > > > The org-ref manual talks about different citation types, but the external > > > > link it suggests is not loading: > > > > http://ctan.unixbrain.com/macros/latex/contrib/natbib/natnotes.pdf > > > > > > try: http://tug.ctan.org/macros/latex/contrib/natbib/natnotes.pdf > > > ok, thx. > > > > > > > > > > > > > Does anyone know what the other options are? In particular, for the > syllabi > > > > I'm currently creating I'd like to just insert the org-formatted citation > > > > information itself -- is this possible? > > > > > > Can you give an example? > > > > > I htink I'm looking for something impossible. org-zotxt allowed me to use > a link type "citation", which just inserted the full citation in org syntax: > > Hayles, K. (1999). /How we became posthuman: virtual bodies in > cybernetics, literature, and informatics/. Chicago, Ill.: University of > Chicago Press. [[ > http://search.library.utoronto.ca/details?7949488&uuid=5aaa42cf-ffd2-41e3-ac6b-60e649f9f289 > ]] > > rather than generating a link. If I had an option to do this in my > syllabi, it would greatly simplify my work flow. > > > > > > I'd like to be able to point my > > > > students directly to my github repo, and it will ultimately be more > > > > convenient to have the links already present in the source code, since > > > > github doesn't reoslve org-ref > > > > What I mean is, that I'd like to stop building course websites and instead > just point students to github repos where my docs live in an org format. > This means I reallywant the citatiion information, and not citation links. > E.g.: > > > > https://github.com/titaniumbones/New113/blob/master/New113Syllabus.org#2017-01-26-thu-state-surveillance > > > > > > > > > > > > > * bib style > > > > When I right-click on a link and select "copy the formatted citation", I > > > > don't get the URL field, which my students need. I assume that's because > > > > I'm not using the right bibliographic style. How do I set the citation > > > > format? Would I use the bibliographystyle link, or a header argument > > > > somewhere? > > > > > > Support for this is kind of rudimentary, because it is really difficult > > > to get properly formatted strings for all references. > > > > > > When you click on a cite link and select copy formatted entry what > > > happens is the bibfile is opened to that entry and then the result of > > > org-ref-bib-citation is copied. It is pretty simple, and limited. At the > > > moment, I think helm-bibtex does the actual formatting if you load it, > > > and it does not appear to be customizable. See > bibtex-completion-apa-format-reference > > > > > > I will work on this a little bit and see if some improvements can be > > > made. > > > thanks you John! > > > > > > > > > > > > Also, is it possible to set this option to use org formatting instead of > > > > html formatting? > > > > > > You could use a function like this on a link to get something more > > > customizable. > > > > > > (defun better-formatted-citation () > > > (interactive) > > > (kill-new (org-ref-get-bibtex-entry-citation (car > (org-ref-get-bibtex-key-and-file))))) > > > > > > see the variable org-ref-bibliography-entry-format, you can set this to > > > be whatever format you want. > > > > ah, looks pretty simple, I should be able to do this. > > > > > > > > > * Bibliography scope > > > > I guess I don't really know how to build a bibliographic file to go with > a > > > > particular project. At present I am using my full Zotero library > exported > > > > to bibtex as a default. Is there a way to just build the bibliography > from > > > > the set of sources cited in the paper? > > > > > > M-x org-ref-extract-bibtex-entries should put a new heading in the buffer > > > with the relevant bibtex entries. > > > > excellent, thank you! > > > > > > > > > > Thanks everyone, and of course especially John for this amazing tool. > > > > > > > > Matt > > > > > > > > > -- > > > 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 > > > --94eb2c06d6b0903b6f05456f403e Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
That is possible. I am out now, but this afternoon I will send another= note on how to do it.=C2=A0


On Fri, Jan 6, 2017 at 11:05 AM Matt Price <moptop99@gmail.com> wrote:
On Fri, Jan 6, 2017 at 10:2= 6 AM, John Kitchin <jkitchin@andrew.cmu.= edu> wrote:



Matt Price writes:





> After several year= s, I'm finally trying to move to bibtex from zotero,


> partly because org-zotxt has stopped working for me (both= link insertion


> and html export seem at= least temporarily broken).


>


> The UI for org-ref is pretty fantastic, and I love= it. I'm having trouble


> getting the= behaviour I want fro mthe actual links, though.=C2=A0 My needs may


> be somewhat atypical but I'm hoping someon= e else has figured these


> questions out = already.


>

> * citation types


> The org-ref manu= al talks about different citation types, but the external


> link it suggests is not loading:
=

> h= ttp://ctan.unixbrain.com/macros/latex/contrib/natbib/natnotes.pdf





try: http://tug.ctan.org/macro= s/latex/contrib/natbib/natnotes.pdf

=
<= div class=3D"gmail_msg">ok, thx.
=






>


> Does anyone know what the other options are? In par= ticular, for the syllabi


> I'm curren= tly creating I'd like to just insert the org-formatted citation


> information itself -- is this possible?





Can you giv= e an example?




I htink I'm looking for somethi= ng impossible.=C2=A0 org-zotxt allowed me to use a link type "citation= ", which just inserted the full citation in org syntax:

Hayles, K. (1999). /How we became posthuma= n: virtual bodies in cybernetics, literature, and informatics/. Chicago, Il= l.: University of Chicago Press. [[http://search.library.utoronto.ca/details?= 7949488&uuid=3D5aaa42cf-ffd2-41e3-ac6b-60e649f9f289]]

rather tha= n generating a link.=C2=A0 If I had an option to do this in my syllabi, it = would greatly simplify my work flow.
=C2=A0


> I'= ;d like to be able to point my


> students= directly to my github repo, and it will ultimately be more


> convenient to have the links already present in the so= urce code, since


> github doesn't reo= slve org-ref



=
What I mean is, that I'd = like to stop building course websites and instead just point students to gi= thub repos where my docs live in an org format.=C2=A0 This means I reallywa= nt the citatiion information, and not citation links.=C2=A0 E.g.:

https://github.com/titaniumbones/New113/blob/master/New113Syllabus.o= rg#2017-01-26-thu-state-surveillance


<= div class=3D"gmail_msg">




>

=
> * bib style


> When I right-click= on a link and select "copy the formatted citation", I


> don't get the URL field, which my students = need. I assume that's because


> I'= ;m not using the right bibliographic style. How do I set the citation


> format?=C2=A0 Would I use the bibliographyst= yle link, or a header argument


> somewher= e?





Su= pport for this is kind of rudimentary, because it is really difficult


to get properly formatted strings for all referen= ces.





When yo= u click on a cite link and select copy formatted entry what


happens is the bibfile is opened to that entry and then the= result of


org-ref-bib-citation is copied. I= t is pretty simple, and limited. At the


mome= nt, I think helm-bibtex does the actual formatting if you load it,


and it does not appear to be customizable. See bibte= x-completion-apa-format-reference





I will work on this a little bit and see if some imp= rovements can be


made.

thanks = you John!





>


>= ; Also, is it possible to set this option to use org formatting instead of<= br class=3D"gmail_msg">

> html formatting?





You could use a function li= ke this on a link to get something more


cust= omizable.





(d= efun better-formatted-citation ()


=C2=A0 (in= teractive)


=C2=A0 (kill-new (org-ref-get-bib= tex-entry-citation (car (org-ref-get-bibtex-key-and-file)))))





see the variable org-ref-= bibliography-entry-format, you can set this to

<= br>be whatever format you want.



<= /div>
ah, looks pretty simple, I should be able to do this.
<= span class=3D"m_9023299483925980295gmail- gmail_msg">

>


> * Bibliography scope

> I guess I don't really know how to build a bibliographic file= to go with a


> particular project.=C2=A0= At present I am using my full Zotero library exported


> to bibtex as a default. Is there a way to just build the bi= bliography from


> the set of sources cite= d in the paper?




=
M-x org-ref-extract-bibtex-entries should put a new heading in t= he buffer


with the relevant bibtex entries.<= br class=3D"gmail_msg">


excellent, thank you!
=C2=A0

=
>


> Thanks everyone, and of course= especially John for this amazing tool.


>=


> Matt







<= span class=3D"m_9023299483925980295gmail-HOEnZb gmail_msg">--


Professor Joh= n Kitchin


Doherty Hall A207F


Department of Chemical Engineering
<= br>
Carnegie Mellon University


Pittsburgh= , PA 15213


412-268-7803

@johnkitchin


<= a href=3D"http://kitchingroup.cheme.cmu.edu" rel=3D"noreferrer" class=3D"gm= ail_msg" target=3D"_blank">http://kitchingroup.cheme.cmu.edu


<= /blockquote>
--94eb2c06d6b0903b6f05456f403e--