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Re: [O] org-ref: citation types (insert full citation); bib style; bib s

From: John Kitchin
Subject: Re: [O] org-ref: citation types (insert full citation); bib style; bib scope
Date: Fri, 06 Jan 2017 15:42:39 -0500
User-agent: mu4e 0.9.19; emacs

New org-ref update ;)

I overhauled the formatted citation support in org-ref today.

Now, you can do the following things:

1. from the C-c ] interface (helm-bibtex, helm-cite or ivy-cite) you can
mark some entries and choose an action that inserts formatted strings.
The default backend for this is text, but you can change that to
org, and add new backends to the variable
org-ref-formatted-citation-formats. The backend is defined in the variable

It is better than it was (we used to use org-ref-reftex-format-citation
which had limited fields and character codes). Now the templates use
s-format and the bibtex-completion code, so you can access any bibtex
field that is there. This is not a real substitute for a citation
processor, e.g. if your template has ${volume}(${issue}), and those
fields do not exist, they will just be empty, e.g. 5(). I don't have
plans to address this limitation at this point. 

2. If you click on a citation link, you can select an action to copy the
formatted entry for that key.

3. On a bibtex entry, you can use the org-ref-bibtex-hydra/body to copy
a formatted string of the entry.

>> > 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
> ]]

You would want to have these settings with a new org-ref:
(setq org-ref-formatted-citation-backend "org")

(setf (cdr (assoc "book" (cdr (assoc "org"
 "${author} ${year}. /${title}/, ${address}:${publisher}. [[${url}]]")

Then you can insert the citation and get this (there is no address for
the publisher in my entry). With helm bibtex as the backend, you would
type C-c ], select an entry, and press f8 (or tab and select the insert
formatted action). In the ivy backend, you type M-o f. Both of them
support multiple selections.

Dominik, C. 2014. /The org mode 8 reference manual - organize your life with 
gnu emacs/, :Samurai Media Limited. [[http://amazon.com/o/ASIN/9881327709/]]

There is not a way to control the casing of the title here, it is
sentence cased by the bibtex-completion library. I also don't have plans
to address that.

> 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

Does this mean you have an entry with the url in it? Say you have it as
a misc entry.

  Title =        {Atomic Simulation Environment},
  Howpublished = {https://wiki.fysik.dtu.dk/ase/},
  note =         {The Atomic Simulation Environment is a set of Python libraries
                  for running molecular simulations and analyzing the results.}

That entry type isn't defined in the formats (there should be a default
entry, but it isn't formatted the way you want), but you could add it like this:

(push '("misc" . "${author} ${year}. /${title}/, [[${howpublished}]]")(cdr 
(assoc "org"

then insert a citation from the entry that looks like this:

 . /Atomic Simulation Environment/, [[https://wiki.fysik.dtu.dk/ase/]]

>> >
>> > * 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?

You don't use the bibliographystyle, it is mostly only for building PDF
from LaTeX.

There is some more advanced code in the citeproc directory of org-ref,
but it is early in development (and has been for a year or more ;), and
it has a really limited set of styles. It is still a long time before it
is production ready.

This code has been tested about 1/2 a day now. Try it out and let me
know if you have any troubles.

>> 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

Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213

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