Re: exporting zotxt or orgref links to HTML and ODF

[John Kitchin <johnrkitchin@gmail.com>]

It turns out to be very easy to get pandoc citations into orgmode using
helm-bibtex. It is not even that difficult to make the pandoc citations
clickable to get similar features as in org-ref. They just don't have
the org-element support. Having tried this, I don't see any obvious
advantages over org-links (except that I still have to figure out how to
export org to org, with a translation of org-link to pandoc citation).

See this example:

http://kitchingroup.cheme.cmu.edu/blog/2015/01/29/Export-org-mode-to-docx-with-citations-via-pandoc/

The conversion is not perfect, but it gets pretty far. Probably not far
enough to use for production except in the simplest cases.


Matt Price writes:

> On Wed, Jan 28, 2015 at 8:48 PM, John Kitchin <johnrkitchin@gmail.com>
> wrote:
>
>> I can see how you could have a command insert links from a zotero
>> database. You just need some way to get a list of the keys for that. it
>> looks like zotxt could provide that. if not, it could be a few sqlite
>> commands to get it.
>>
> Lets say we have citations like: zotero:zotero-key or [@zotero-key]. These
>> are easy to get I think.
>>
>
>  I think zotxt already does this, though one would have to modify the link
> format for ocmpativility.  That part doesn't seem so hard, even for someone
> like me.
>
>>
>> I am still unclear on what you do after that. So far I only have used
>> bibtex as the backend database, and there are programs like bibtex and
>> pandox that create the bibliography from it. What is the end format you
>> want? and how would zotero be used to generate the bibliography?
>>
>> For my own use, the most important end formats are html and odt/docx.  Of
> course it would be nice if there was a more generic solution so other
> people could benefit.
> Erik has written a python script, pandoc-zotxt, which allows an interface
> with pandoc.  I'm not sure how it works - -I haven't started using pandoc
> in any serious way just yet.  (
> https://github.com/egh/zotxt/tree/master/pandoc-zotxt)
>
> It also looks easy to query the zotero database with a list of keys and
> retrieve a bibliography in html or plaintext formats.  That would, I guess
> be useful for HTML export.  For ODT I think the situation is somewhat more
> difficult, especially if one wants to retain "live" Zotero links in the
> final stage, working with Libreoffice.
>
> thanks again John,
> Matt
>
>
>
>> John
>>
>> -----------------------------------
>> John Kitchin
>> Professor
>> Doherty Hall A207F
>> Department of Chemical Engineering
>> Carnegie Mellon University
>> Pittsburgh, PA 15213
>> 412-268-7803
>> http://kitchingroup.cheme.cmu.edu
>>
>>
>> On Wed, Jan 28, 2015 at 8:34 PM, Matt Price <moptop99@gmail.com> wrote:
>>
>>> 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