Re: exporting zotxt or orgref links to HTML and ODF

[John Kitchin <johnrkitchin@gmail.com>]

There is a separation between the citation bits in an org-file (whether
they are org-links, or the pandoc format, etc...) and the formatted
bibliography. org-ref is really focused on providing functionality to
insert the citation keys (using reftex, or helm-bibtex right now, but
there are many other options that could do this like ebib, perhaps
zotxt, ido-completion, etc...), and references and labels. Then, once
the citations are in, org-ref provides functionality to see what is
cited, open the reference, pdf, search in scientific search engines,
other utilities, etc... I can imagine there being backend (bibtex,
ox-bibtex, zotero, ...) specific functions to do these things (usually
you have to get some information from the entry to act, like get a doi
to open a url, etc...).

The formatting of the bibliography is almost always done by a dedicated
program, e.g. bibtex, biblatex, or now in some cases pandoc. org-ref
just provides functionality to export org and transform the links into
the format required for those programs. If it were possible to figure
out how to insert zotero links in a docx, then zotero would take over to
make the bibliography in the docx. Ditto for mendeley, Endnote, Papers,
... The only exceptions to this are html where org-ref enables a crude
and limited export of the bibliography for blog posts. I am not
interested in having org-ref do much more than this, because the
dedicated tools do such a good job in my opinion, it isn't worth
duplicating the effort.


Matt Price writes:

> John,
>
> this does look very powerful.  Do you see a path forward that would help
> add zotero support to org-ref, probably using Erik's zotxt library?  Does
> that seem like a worthwhile goal for you?
>
> Matt
>
>
> On Wed, Jan 28, 2015 at 6:01 PM, John Kitchin <johnrkitchin@gmail.com>
> wrote:
>
>> With the latest version of org-ref, I can automate export from org
>> through markdown to docx via pandoc like this:
>>
>> #+BEGIN_SRC emacs-lisp
>> (defun ox-export-to-docx-and-open ()
>>  "Export the current org file as a docx via markdown."
>>  (interactive)
>> (let* ((bibfile (expand-file-name (car (org-ref-find-bibliography))))
>>        ;; this is probably a full path
>>        (current-file (buffer-file-name))
>>        (basename (file-name-sans-extension current-file))
>>        (md-file (concat basename ".md"))
>>        (docx-file (concat basename ".docx")))
>>
>>   (when (file-exists-p docx-file) (delete-file docx-file))
>>   (org-export-to-file 'md md-file)
>>   (shell-command (format
>>                   "pandoc -s -S --bibliography=%s %s -o %s"
>>                   bibfile md-file docx-file))
>>   (org-open-file docx-file '(16))))
>> #+END_SRC
>>
>>
>> this works because i defined a markdown format function that converts
>> the cite link to pandoc format on export. I could avoid the markdown
>> translation if I could do an org to org export that would do that. With
>> a little work we could define file tags like:
>>
>> #+PANDOC_CSL: some-csl-file
>>
>> that would also get passed to the pandoc command to determine the style
>> of the citation and bibliography.
>>
>>
>>
>>
>> Matt Price writes:
>>
>> > i think I may have seen it these on the list at one point, but it's very
>> > helpful to be reminded.
>> >
>> > I do think that the default fonts, etc., are a bit of an acquired taste
>> for
>> > humanists; and I've gotten used to using custom styles in html & odt for
>> > size & placing of images; but even without following the instructions
>> > carefully, export seems to work, which is pretyt amazing!
>> >
>> > Vikas recommends involving pandoc manually, as Erik H. has also suggested
>> > to me; I would like to aovid doing that if possible, but if it has to be
>> > done i guess I can find some way of automating it.
>> >
>> > There are clearly a lot of options in this space; I am still interested
>> in
>> > using Zotero if I can, so will continue working with zotxt, but hopefully
>> > in a way that gets me closer to other people's usage patterns.
>> >
>> > thanks,
>> > Matt
>> >
>> >
>> > On Wed, Jan 28, 2015 at 3:31 PM, Vicente Vera <vicentemvp@gmail.com>
>> wrote:
>> >
>> >> Hello. Interesting thread!
>> >> Matt, have you read Vikas guide to writing papers with Org?
>> >> https://github.com/vikasrawal/orgpaper
>> >> From my point of view, using LaTeX through Org isn't difficult at all.
>> >> You'll need to tweak a few things (packages, figures, etc.), but it's
>> >> definitely easier for a beginner that starting a LaTeX document from
>> >> scratch.
>> >> Here's another article about writing LaTeX (social science) papers:
>> >> https://github.com/kjhealy/workflow-paper
>> >>
>>
>> --
>> 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