Re: exporting zotxt or orgref links to HTML and ODF

Re: exporting zotxt or orgref links to HTML and ODF

[Matt Price]

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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
>

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Re: exporting zotxt or orgref links to HTML and ODF

[John Kitchin]

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

Re: exporting zotxt or orgref links to HTML and ODF

[Matt Price]

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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
>

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Re: exporting zotxt or orgref links to HTML and ODF

[John Kitchin]

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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 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?

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
>>
>
>

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Re: exporting zotxt or orgref links to HTML and ODF

[John Kitchin]

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

Re: exporting zotxt or orgref links to HTML and ODF

[Vikas Rawal]

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

John,

If your main objective is support for citations, why not go from Org to LaTeX, and then use Pandoc to convert from LaTeX to DocX? Is there an advantage in going through Markdown instead of LaTeX?

In my experiments in going Org->LaTeX->(via Pandoc)DocX, I find Bibtex citations to work well. But there are other limitations of Pandoc (for example, lack of support for various LaTeX environments for making tables).

Vikas 

Re: exporting zotxt or orgref links to HTML and ODF

[John Kitchin]

That could be an option. I was mostly looking at feasibility for org to
docx. There is no obvious advantage to go through markdown, I just had
some handy machinery in org-ref to export my cite links to the pandoc
format in that export. I have since figured out a simple way to insert
pandoc citations in org directly, and do an org -> docx in pandoc
directly.

It looks like there are limitations all around. My sense is pandoc is
just a temporary solution until there is (one day) a full org export to docx
solution. I am not that experienced with the ODT export, so i don't know
what the state of citation support in those are.

Luckily that is not something I need often, but a robust org to docx
export would be helpful to many!

Vikas Rawal writes:

>>
>> The conversion is not perfect, but it gets pretty far. Probably not far
>> enough to use for production except in the simplest cases.
>>
>>
>
> John,
>
> If your main objective is support for citations, why not go from Org to LaTeX, and then use Pandoc to convert from LaTeX to DocX? Is there an advantage in going through Markdown instead of LaTeX?
>
> In my experiments in going Org->LaTeX->(via Pandoc)DocX, I find Bibtex citations to work well. But there are other limitations of Pandoc (for example, lack of support for various LaTeX environments for making tables).
>
> Vikas

--
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

Re: exporting zotxt or orgref links to HTML and ODF

[Vikas Rawal]

For my use case, I find the native Org to Odt export has several limitations:

1. No support for bibtex
2. I end up using quite a bit of LaTeX-specific stuff for formatting tables and graphics. All of that gets messed up when I do Org to Odt export.

I agree, a robust org to odt/docx export would be very helpful.

Vikas


> On 29-Jan-2015, at 6:54 pm, John Kitchin <johnrkitchin@gmail.com> wrote:
> 
> That could be an option. I was mostly looking at feasibility for org to
> docx. There is no obvious advantage to go through markdown, I just had
> some handy machinery in org-ref to export my cite links to the pandoc
> format in that export. I have since figured out a simple way to insert
> pandoc citations in org directly, and do an org -> docx in pandoc
> directly.
> 
> It looks like there are limitations all around. My sense is pandoc is
> just a temporary solution until there is (one day) a full org export to docx
> solution. I am not that experienced with the ODT export, so i don't know
> what the state of citation support in those are.
> 
> Luckily that is not something I need often, but a robust org to docx
> export would be helpful to many!
> 
> Vikas Rawal writes:
> 
>>> 
>>> The conversion is not perfect, but it gets pretty far. Probably not far
>>> enough to use for production except in the simplest cases.
>>> 
>>> 
>> 
>> John,
>> 
>> If your main objective is support for citations, why not go from Org to LaTeX, and then use Pandoc to convert from LaTeX to DocX? Is there an advantage in going through Markdown instead of LaTeX?
>> 
>> In my experiments in going Org->LaTeX->(via Pandoc)DocX, I find Bibtex citations to work well. But there are other limitations of Pandoc (for example, lack of support for various LaTeX environments for making tables).
>> 
>> Vikas
> 
> --
> 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

Re: exporting zotxt or orgref links to HTML and ODF

[John Kitchin]

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

Re: exporting zotxt or orgref links to HTML and ODF

[Vikas Rawal]

> 
> With the latest version of org-ref, I can automate export from org
> through markdown to docx via pandoc like this:

Great job, once again!

Vikas

exporting zotxt or orgref links to HTML and ODF

[Matt Price]

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Hi eveyrone,

I've just looked back through my email archives and from what I can tell,
almost everyone who uses Org to write papers uses LaTex for the final
product.

I have never learned to use Latex, mostly because, as a humanist, almost
none of my colleagues can use LaTex files, and the same goes for journals I
interact with, which generally prefer Word submission(!).  Because of this,
I am still trying to figure out a way to use org-mode for scholarly
writing. At present, I write my first, very rough drafts in Org, then
export to ODT and add citations from Zotero (we don't really use Bibtex
either); after this step, I can't really go back to Org, which is of course
very frustrating.


I would prefer to write exclusively in Org, then export to ODT when I have
a high-quality draft that I want to share with colleagues; in some cases, I
would also like to export directly to HTML for posting on a blog or course
website. In fact, one use case that would really help me is a very simple
one: when writing course syllabi, I would really like to just get the full
references to course readings to show up in HTML exports.

My question: does anyone yet have a workflow that lets them export directly
to HTML or ODT?

I've just tried using zotxt again (
https://bitbucket.org/egh/zotxt-emacs/overview -- first time in a while);
it is remarkably easy to use in Org itself.  By default, though, the links
simply aren't handled in the HTML and ODT exports, and so the cites will be
completely absent.

Here is the text inserted by zotxt for a single citation:

----------------

[[zotero://select/items/0_TI27HJ5I][Suchman, Lucy. “Subject Objects.”
Feminist Theory 12, no. 2 (August 1, 2011): 119–45.
http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.]]
---------------

In HTML, I would like to replace this with something like this:

(<a href="#BibSuchman2011">Suchman 2011</a>)

and then have Org generate a bibligraphy somewhere, a bit like org-ref
seems to do, It would be nice if I could steal the styles from somehwere,
the way org-ref seems to do.

For ODT< it seems a little more complicated. Here is the rather lengthy
equivalent that Zotero itself produces for my default style (Chicago) in
Libreoffice:
---------------
<text:note text:id="ftn0"
text:note-class="footnote"><text:note-citation>1</text:note-citation><text:note-body><text:p
text:style-name="Footnote"><text:reference-mark-start
text:name="ZOTERO_ITEM CSL_CITATION
{&quot;citationID&quot;:&quot;5xzXuF2I&quot;,&quot;properties&quot;:{&quot;formattedCitation&quot;:&quot;{\\rtf
Lucy Suchman, \\uc0\\u8220{}Subject Objects,\\uc0\\u8221{} \\i Feminist
Theory\\i0{} 12, no. 2 (August 1, 2011): 119\\uc0\\u8211{}45,
http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.}&quot;,&quot;plainCitation&quot;:&quot;Lucy
Suchman, “Subject Objects,” Feminist Theory 12, no. 2 (August 1, 2011):
119–45,
http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.&quot;
},&quot;citationItems&quot;:[{&quot;id&quot;:149,&quot;uris&quot;:[&quot;
http://zotero.org/users/20/items/TI27HJ5I&quot;],&quot;uri&quot;:[&quot;
http://zotero.org/users/20/items/TI27HJ5I&quot;],&quot;itemData&quot;:{&quot;id&quot;:149,&quot;type&quot;:&quot;article-journal&quot;,&quot;title&quot;:&quot;Subject
objects&quot;,&quot;container-title&quot;:&quot;Feminist
Theory&quot;,&quot;page&quot;:&quot;119-145&quot;,&quot;volume&quot;:&quot;12&quot;,&quot;issue&quot;:&quot;2&quot;,&quot;URL&quot;:&quot;
http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml&quot
;,&quot;ISSN&quot;:&quot;14647001&quot;,&quot;author&quot;:[{&quot;family&quot;:&quot;Suchman&quot;,&quot;given&quot;:&quot;Lucy&quot;}],&quot;issued&quot;:{&quot;date-parts&quot;:[[&quot;2011&quot;,8,1]]}}}],&quot;schema&quot;:&quot;
https://github.com/citation-style-language/schema/raw/master/csl-citation.json&quot;}
RNDuhNYYpC1hN"/><text:span text:style-name="T3">Lucy Suchman, “Subject
Objects,” </text:span><text:span text:style-name="T4">Feminist
Theory</text:span><text:span text:style-name="T5"> 12, no. 2 (August 1,
2011): 119–45,
http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.</text:span><text:reference-mark-end
text:name="ZOTERO_ITEM CSL_CITATION
{&quot;citationID&quot;:&quot;5xzXuF2I&quot;,&quot;properties&quot;:{&quot;formattedCitation&quot;:&quot;{\\rtf
Lucy Suchman, \\uc0\\u8220{}Subject Objects,\\uc0\\u8221{} \\i Feminist
Theory\\i0{} 12, no. 2 (August 1, 2011): 119\\uc0\\u8211{}45,
http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.}&quot;,&quot;plainCitation&quot;:&quot;Lucy
Suchman, “Subject Objects,” Feminist Theory 12, no. 2 (August 1, 2011):
119–45,
http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.&quot;
},&quot;citationItems&quot;:[{&quot;id&quot;:149,&quot;uris&quot;:[&quot;
http://zotero.org/users/20/items/TI27HJ5I&quot;],&quot;uri&quot;:[&quot;
http://zotero.org/users/20/items/TI27HJ5I&quot;],&quot;itemData&quot;:{&quot;id&quot;:149,&quot;type&quot;:&quot;article-journal&quot;,&quot;title&quot;:&quot;Subject
objects&quot;,&quot;container-title&quot;:&quot;Feminist
Theory&quot;,&quot;page&quot;:&quot;119-145&quot;,&quot;volume&quot;:&quot;12&quot;,&quot;issue&quot;:&quot;2&quot;,&quot;URL&quot;:&quot;
http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml&quot
;,&quot;ISSN&quot;:&quot;14647001&quot;,&quot;author&quot;:[{&quot;family&quot;:&quot;Suchman&quot;,&quot;given&quot;:&quot;Lucy&quot;}],&quot;issued&quot;:{&quot;date-parts&quot;:[[&quot;2011&quot;,8,1]]}}}],&quot;schema&quot;:&quot;
https://github.com/citation-style-language/schema/raw/master/csl-citation.json&quot;}
RNDuhNYYpC1hN"/></text:p></text:note-body></text:note>
------------------------------

I'm not sure what the best way to do this is; it may be that zotxt could be
extended to get zotero to do the heavy lifting here.

I know Erik H reads this list, so if you have any suggestions, Erik, I
would love to hear them.  But maybe other people also have suggestions
about modifying export filters - -that would also be really helpful for
me.  Thanks as always,

Matt

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Re: exporting zotxt or orgref links to HTML and ODF

[Matt Price]

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Hi will,

I haven't gotten very far with this yet, but adding a couple of lines to
the definition of org-add-link-type in org-zotxt.el (around line 150,
https://bitbucket.org/egh/zotxt-emacs/src/74702e2b2f2aa0427f099eb4fe69dce8709f67fc/org-zotxt.el?at=master)
at least allows for unformatted, plain-text reproduction of citations:

------------------
(org-add-link-type "zotero"
                   (lambda (rest)
                     (zotxt-select-key (substring rest 15)))
                   (lambda (path desc format)
                     (if (and (eq format 'latex)
                              (string-match "^@\\(.*\\)$" desc))
                         (format "\\cite{%s}" (match-string 1 desc))
                       nil)
                     (if ( eq format 'html)
                         (format "%s" desc)

                       nil)))
-------------------

A better option would be to somehow acquire the html that the Zotero
extension "zotxt" generates when zotxt.el requests the formatted citation
from it.  I'm not quite sure how to do this, but I htink the action happens
zotxt-choose-deferred, which starts on line 125 of zotxt.el (
https://bitbucket.org/egh/zotxt-emacs/src/74702e2b2f2aa0427f099eb4fe69dce8709f67fc/zotxt.el?at=master
):

---------------------

(defun zotxt-choose-deferred (&optional method search-string)  "Prompt
a user for a search string, then ask the user to select an item from
the citation.If METHOD is supplied, it should be one of
:title-creator-year, :fields, or :everything.If SEARCH-STRING is
supplied, it should be the search string."  (if (null method)
(let ((method-name              (zotxt-completing-read
"Zotero search method (nothing for title, creator, year): "
  zotxt-quicksearch-method-names              nil t nil nil "title,
creator, year")))        (setq method (cdr (assoc method-name
zotxt-quicksearch-method-names)))))  (if (null search-string)
(setq search-string            (read-string (format "Zotero
quicksearch (%s) query: " (cdr (assq method
zotxt-quicksearch-method-to-names))))))  (lexical-let ((d
(deferred:new)))    (request     (format "%s/search" zotxt-url-base)
  :params `(("q" . ,search-string)               ("method" . ,(cdr
(assq method zotxt-quicksearch-method-params)))
("format" . "bibliography"))     :parser 'json-read     :success
(function*               (lambda (&key data &allow-other-keys)
        (let* ((results (mapcar (lambda (e)
                (cons (cdr (assq 'text e))
                     (cdr (assq 'key e))))
            data))                        (count (length results))
                   (citation (if (= 0 count)
           nil                                    (if (= 1 count)
                                  (car (car results))
                    (zotxt-completing-read "Select item: " results))))
                       (key (cdr (assoc-string citation results))))
               (deferred:callback-post                     d (if (null
citation) nil                         `((:key ,key :citation
,citation))))))))    d))

-------------

My lisp isn't good enough to read this function properly, but apparently the
:citation property of the result item plist is set to the 'text'
object of each item.
If one could  also add the 'html' object which the zotxt Zotero plugin returns
(the nomenclature is a little misleading, I know), then that
information could be made available to emacs/org
for use on export.  See line 307-309 of the zotxt extension, here:
 https://bitbucket.org/egh/zotxt/src/a12d538ae9245b142fdb55550b2d241e43b82221/extension/bootstrap.js?at=master

Not sure if this helps much?  It's the best I have so far!  Thanks,
Matt



On Mon, Jan 26, 2015 at 12:49 PM, Monroe, Will <will.monroe@law.lsu.edu>
wrote:

>  Matt,
>
> I don't have much to contribute at this stage but as someone who uses org
> heavily for outlining and writing, zotero for citation management, and who
> is obliged to provide copies as Word documents (I'm an instructional
> designer at at law school), I appreciate the question.
>
> I also appreciate the point to zotxt!  Didn't know about that.
>
> I hope you get some good replies.
>
> Will
>
> -----------------------------
> Will Monroe, Ph.D.
> Head of Instructional Technology
> Paul M. Hebert Law Center
> 225.578.7838
> will.monroe@law.lsu.edu
>
> On 1/26/15 10:29 AM, Matt Price wrote:
>
>   Hi eveyrone,
>
>  I've just looked back through my email archives and from what I can tell,
> almost everyone who uses Org to write papers uses LaTex for the final
> product.
>
>  I have never learned to use Latex, mostly because, as a humanist, almost
> none of my colleagues can use LaTex files, and the same goes for journals I
> interact with, which generally prefer Word submission(!).  Because of this,
> I am still trying to figure out a way to use org-mode for scholarly
> writing. At present, I write my first, very rough drafts in Org, then
> export to ODT and add citations from Zotero (we don't really use Bibtex
> either); after this step, I can't really go back to Org, which is of course
> very frustrating.
>
>
>  I would prefer to write exclusively in Org, then export to ODT when I
> have a high-quality draft that I want to share with colleagues; in some
> cases, I would also like to export directly to HTML for posting on a blog
> or course website. In fact, one use case that would really help me is a
> very simple one: when writing course syllabi, I would really like to just
> get the full references to course readings to show up in HTML exports.
>
>  My question: does anyone yet have a workflow that lets them export
> directly to HTML or ODT?
>
>  I've just tried using zotxt again (
> https://bitbucket.org/egh/zotxt-emacs/overview -- first time in a while);
> it is remarkably easy to use in Org itself.  By default, though, the links
> simply aren't handled in the HTML and ODT exports, and so the cites will be
> completely absent.
>
>  Here is the text inserted by zotxt for a single citation:
>
> ----------------
>
> [[zotero://select/items/0_TI27HJ5I][Suchman, Lucy. “Subject Objects.”
> Feminist Theory 12, no. 2 (August 1, 2011): 119–45.
> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.]]
>
> ---------------
>
>  In HTML, I would like to replace this with something like this:
>
>  (<a href="#BibSuchman2011">Suchman 2011</a>)
>
>  and then have Org generate a bibligraphy somewhere, a bit like org-ref
> seems to do, It would be nice if I could steal the styles from somehwere,
> the way org-ref seems to do.
>
>  For ODT< it seems a little more complicated. Here is the rather lengthy
> equivalent that Zotero itself produces for my default style (Chicago) in
> Libreoffice:
> ---------------
> <text:note text:id="ftn0"
> text:note-class="footnote"><text:note-citation>1</text:note-citation><text:note-body><text:p
> text:style-name="Footnote"><text:reference-mark-start
> text:name="ZOTERO_ITEM CSL_CITATION
> {&quot;citationID&quot;:&quot;5xzXuF2I&quot;,&quot;properties&quot;:{&quot;formattedCitation&quot;:&quot;{\\rtf
> Lucy Suchman, \\uc0\\u8220{}Subject Objects,\\uc0\\u8221{} \\i Feminist
> Theory\\i0{} 12, no. 2 (August 1, 2011): 119\\uc0\\u8211{}45,
> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.}&quot;,&quot;plainCitation&quot;:&quot;Lucy
> Suchman, “Subject Objects,” Feminist Theory 12, no. 2 (August 1, 2011):
> 119–45,
> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.&quot;
> },&quot;citationItems&quot;:[{&quot;id&quot;:149,&quot;uris&quot;:[&quot;
> http://zotero.org/users/20/items/TI27HJ5I&quot;],&quot;uri&quot;:[&quot;
> http://zotero.org/users/20/items/TI27HJ5I&quot;],&quot;itemData&quot;:{&quot;id&quot;:149,&quot;type&quot;:&quot;article-journal&quot;,&quot;title&quot;:&quot;Subject
> objects&quot;,&quot;container-title&quot;:&quot;Feminist
> Theory&quot;,&quot;page&quot;:&quot;119-145&quot;,&quot;volume&quot;:&quot;12&quot;,&quot;issue&quot;:&quot;2&quot;,&quot;URL&quot;:&quot;
> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml&quot
> ;,&quot;ISSN&quot;:&quot;14647001&quot;,&quot;author&quot;:[{&quot;family&quot;:&quot;Suchman&quot;,&quot;given&quot;:&quot;Lucy&quot;}],&quot;issued&quot;:{&quot;date-parts&quot;:[[&quot;2011&quot;,8,1]]}}}],&quot;schema&quot;:&quot;
> https://github.com/citation-style-language/schema/raw/master/csl-citation.json&quot;}
> RNDuhNYYpC1hN"/><text:span text:style-name="T3">Lucy Suchman, “Subject
> Objects,” </text:span><text:span text:style-name="T4">Feminist
> Theory</text:span><text:span text:style-name="T5"> 12, no. 2 (August 1,
> 2011): 119–45,
> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.</text:span><text:reference-mark-end
> text:name="ZOTERO_ITEM CSL_CITATION
> {&quot;citationID&quot;:&quot;5xzXuF2I&quot;,&quot;properties&quot;:{&quot;formattedCitation&quot;:&quot;{\\rtf
> Lucy Suchman, \\uc0\\u8220{}Subject Objects,\\uc0\\u8221{} \\i Feminist
> Theory\\i0{} 12, no. 2 (August 1, 2011): 119\\uc0\\u8211{}45,
> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.}&quot;,&quot;plainCitation&quot;:&quot;Lucy
> Suchman, “Subject Objects,” Feminist Theory 12, no. 2 (August 1, 2011):
> 119–45,
> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.&quot;
> },&quot;citationItems&quot;:[{&quot;id&quot;:149,&quot;uris&quot;:[&quot;
> http://zotero.org/users/20/items/TI27HJ5I&quot;],&quot;uri&quot;:[&quot;
> http://zotero.org/users/20/items/TI27HJ5I&quot;],&quot;itemData&quot;:{&quot;id&quot;:149,&quot;type&quot;:&quot;article-journal&quot;,&quot;title&quot;:&quot;Subject
> objects&quot;,&quot;container-title&quot;:&quot;Feminist
> Theory&quot;,&quot;page&quot;:&quot;119-145&quot;,&quot;volume&quot;:&quot;12&quot;,&quot;issue&quot;:&quot;2&quot;,&quot;URL&quot;:&quot;
> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml&quot
> ;,&quot;ISSN&quot;:&quot;14647001&quot;,&quot;author&quot;:[{&quot;family&quot;:&quot;Suchman&quot;,&quot;given&quot;:&quot;Lucy&quot;}],&quot;issued&quot;:{&quot;date-parts&quot;:[[&quot;2011&quot;,8,1]]}}}],&quot;schema&quot;:&quot;
> https://github.com/citation-style-language/schema/raw/master/csl-citation.json&quot;}
> RNDuhNYYpC1hN"/></text:p></text:note-body></text:note>
> ------------------------------
>
>  I'm not sure what the best way to do this is; it may be that zotxt could
> be extended to get zotero to do the heavy lifting here.
>
>  I know Erik H reads this list, so if you have any suggestions, Erik, I
> would love to hear them.  But maybe other people also have suggestions
> about modifying export filters - -that would also be really helpful for
> me.  Thanks as always,
>
> Matt
>
>
>

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Re: exporting zotxt or orgref links to HTML and ODF

[Monroe, Will]

[-- Attachment #1: Type: text/html, Size: 29285 bytes --]

Re: exporting zotxt or orgref links to HTML and ODF

[Eric S Fraga]

On Monday, 26 Jan 2015 at 11:29, Matt Price wrote:

[...]

> My question: does anyone yet have a workflow that lets them export directly
> to HTML or ODT?

The following is for MS Word output, not ODT, but you can of course read
in Word files in Libreoffice and save as ODT if desired.

Although I do strive to only have to work in org (+ LaTeX), I do
sometimes have to generate Word files, especially for conference
publications.  In this case, I still use org but I generate the final
document using org -> LaTeX and then use pandoc to get me the doc file
using a shell script that looks like this:

--8<---------------cut here---------------start------------->8---
#!/bin/sh -f
BASE=$(basename $1 .tex)
CSL="/home/ucecesf/synced/share/citation.styles/acm-siggraph.csl"
if [ -f default.csl ]; then
    CSL="default.csl"
fi
echo "Converting " $BASE.tex " to " $BASE.docx " using bib style " $CSL
pandoc --bibliography=/home/ucecesf/share/texmf/bibtex/bib/papers.bib --csl=${CSL} --filter pandoc-citeproc ${BASE}.tex -o ${BASE}.docx
--8<---------------cut here---------------end--------------->8---

The key is pandoc with bib styles.  The scripts defaults to using an ACM
SIGGRAPH style but will use a "default" style if present in the current
directory.

Although you say your colleagues do not use BiBTeX, it does not stop you
from using it within org and then exporting the result...

With org exporting LaTeX fragments as images (hence my recent emails
about dvipng...), I get equations (on the printed page) and bibliography
without having to suffer using Word...

Good luck!

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.1, Org release_8.3beta-726-gd34b80.dirty

Re: exporting zotxt or orgref links to HTML and ODF

[Christian Moe]

Matt Price writes:

> My question: does anyone yet have a workflow that lets them export directly
> to HTML or ODT?

Hi, Matt,

Yes, now I have not just a workflow, but a code solution for
Org/Zotero/ODT export that has been tried and tested for a while. It now
supports multiple references in one citation, prefixes, suffixes,
locators, and year-only citations, and produces 'live' Zotero refmarks
in ODT, so you can do all the changes you want in LibreOffice
afterward. It also does some very limited but useful things for html
(DOI links and links that will work on Wordpress blogs with Katie
Seaborn's ZotPress extension).

It depends on Eric Hetzner's excellent zotero-plain and org-zotero
packages, and hence on the MozRepl extension on the Firefox side, though
you can use the ODT export functionality itself without those
dependencies.

I haven't yet announced it on the list, for three reasons. 1) Not very
polished. There's some messy code, a poor man's user interface, and no
editing support for multiple citations (but support for exporting
them!). 2) It's part of a more ambitious project I set myself for an
all-round citation system that I never got on with. 3) It uses this cool
idea I had for how to use citation links differently, but it imposes
certain syntax conventions on the user, and they may yet change in
backward-incompatible ways if I develop this further.

If this sounds interesting, I can post the code here 'as is' for you to
try out, but I'd better update the docs first, which could take a day or
two.

Yours,
Christian


> I've just tried using zotxt again (
> https://bitbucket.org/egh/zotxt-emacs/overview[1] -- first time in a while);
> it is remarkably easy to use in Org itself.  By default, though, the links
> simply aren't handled in the HTML and ODT exports, and so the cites will be
> completely absent.
>
> Here is the text inserted by zotxt for a single citation:
>
> ----------------
>
> [[zotero://select/items/0_TI27HJ5I][Suchman, Lucy. “Subject Objects.”
> Feminist Theory 12, no. 2 (August 1, 2011): 119–45.
> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.[2]]]
> ---------------
>
> In HTML, I would like to replace this with something like this:
>
> (<a href="#BibSuchman2011">Suchman 2011</a>)
>
> and then have Org generate a bibligraphy somewhere, a bit like org-ref
> seems to do, It would be nice if I could steal the styles from somehwere,
> the way org-ref seems to do.
>
> For ODT< it seems a little more complicated. Here is the rather lengthy
> equivalent that Zotero itself produces for my default style (Chicago) in
> Libreoffice:
> ---------------
> <text:note text:id="ftn0"
> text:note-class="footnote"><text:note-citation>1</text:note-citation><text:note-body><text:p
> text:style-name="Footnote"><text:reference-mark-start
> text:name="ZOTERO_ITEM CSL_CITATION
> {&quot;citationID&quot;:&quot;5xzXuF2I&quot;,&quot;properties&quot;:{&quot;formattedCitation&quot;:&quot;{\\rtf
> Lucy Suchman, \\uc0\\u8220{}Subject Objects,\\uc0\\u8221{} \\i Feminist
> Theory\\i0{} 12, no. 2 (August 1, 2011): 119\\uc0\\u8211{}45,
> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.[3]}&quot;,&quot;plainCitation&quot;:&quot;Lucy
> Suchman, “Subject Objects,” Feminist Theory 12, no. 2 (August 1, 2011):
> 119–45,
> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.&quot;[4]
> },&quot;citationItems&quot;:[{&quot;id&quot;:149,&quot;uris&quot;:[&quot;
> http://zotero.org/users/20/items/TI27HJ5I&quot;[5]],&quot;uri&quot;:[&quot;
> http://zotero.org/users/20/items/TI27HJ5I&quot;[6]],&quot;itemData&quot;:{&quot;id&quot;:149,&quot;type&quot;:&quot;article-journal&quot;,&quot;title&quot;:&quot;Subject
> objects&quot;,&quot;container-title&quot;:&quot;Feminist
> Theory&quot;,&quot;page&quot;:&quot;119-145&quot;,&quot;volume&quot;:&quot;12&quot;,&quot;issue&quot;:&quot;2&quot;,&quot;URL&quot;:&quot;
> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml&quot[7]
> ;,&quot;ISSN&quot;:&quot;14647001&quot;,&quot;author&quot;:[{&quot;family&quot;:&quot;Suchman&quot;,&quot;given&quot;:&quot;Lucy&quot;}],&quot;issued&quot;:{&quot;date-parts&quot;:[[&quot;2011&quot;,8,1]]}}}],&quot;schema&quot;:&quot;
> https://github.com/citation-style-language/schema/raw/master/csl-citation.json&quot;[8]}
> RNDuhNYYpC1hN"/><text:span text:style-name="T3">Lucy Suchman, “Subject
> Objects,” </text:span><text:span text:style-name="T4">Feminist
> Theory</text:span><text:span text:style-name="T5"> 12, no. 2 (August 1,
> 2011): 119–45,
> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.[9]</text:span><text:reference-mark-end
> text:name="ZOTERO_ITEM CSL_CITATION
> {&quot;citationID&quot;:&quot;5xzXuF2I&quot;,&quot;properties&quot;:{&quot;formattedCitation&quot;:&quot;{\\rtf
> Lucy Suchman, \\uc0\\u8220{}Subject Objects,\\uc0\\u8221{} \\i Feminist
> Theory\\i0{} 12, no. 2 (August 1, 2011): 119\\uc0\\u8211{}45,
> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.[10]}&quot;,&quot;plainCitation&quot;:&quot;Lucy
> Suchman, “Subject Objects,” Feminist Theory 12, no. 2 (August 1, 2011):
> 119–45,
> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.&quot;[11]
> },&quot;citationItems&quot;:[{&quot;id&quot;:149,&quot;uris&quot;:[&quot;
> http://zotero.org/users/20/items/TI27HJ5I&quot;[12]],&quot;uri&quot;:[&quot;
> http://zotero.org/users/20/items/TI27HJ5I&quot;[13]],&quot;itemData&quot;:{&quot;id&quot;:149,&quot;type&quot;:&quot;article-journal&quot;,&quot;title&quot;:&quot;Subject
> objects&quot;,&quot;container-title&quot;:&quot;Feminist
> Theory&quot;,&quot;page&quot;:&quot;119-145&quot;,&quot;volume&quot;:&quot;12&quot;,&quot;issue&quot;:&quot;2&quot;,&quot;URL&quot;:&quot;
> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml&quot[14]
> ;,&quot;ISSN&quot;:&quot;14647001&quot;,&quot;author&quot;:[{&quot;family&quot;:&quot;Suchman&quot;,&quot;given&quot;:&quot;Lucy&quot;}],&quot;issued&quot;:{&quot;date-parts&quot;:[[&quot;2011&quot;,8,1]]}}}],&quot;schema&quot;:&quot;
> https://github.com/citation-style-language/schema/raw/master/csl-citation.json&quot;[15]}
> RNDuhNYYpC1hN"/></text:p></text:note-body></text:note>
> ------------------------------
>
> I'm not sure what the best way to do this is; it may be that zotxt could be
> extended to get zotero to do the heavy lifting here.
>
> I know Erik H reads this list, so if you have any suggestions, Erik, I
> would love to hear them.  But maybe other people also have suggestions
> about modifying export filters - -that would also be really helpful for
> me.  Thanks as always,
>
> Matt

Re: exporting zotxt or orgref links to HTML and ODF

[Rasmus]

Hi,

Christian Moe <mail@christianmoe.com> writes:

> I haven't yet announced it on the list, for three reasons. 1) Not very
> polished. There's some messy code, a poor man's user interface, and no
> editing support for multiple citations (but support for exporting
> them!). 2) It's part of a more ambitious project I set myself for an
> all-round citation system that I never got on with. 3) It uses this cool
> idea I had for how to use citation links differently, but it imposes
> certain syntax conventions on the user, and they may yet change in
> backward-incompatible ways if I develop this further.

I also have a very half-baked branch somewhere with preliminary code, but
mainly in terms of syntax/org-element (similar to pandoc).

IMO we /need/ to add proper citation support to Org, preferably with a
real syntax rather than these link-"solutions" and with good backend
support (bibtex & Zotero for starters, I guess).

#+begin_rant

The current state is a mess and not portable.  E.g. there's at least two
Zotero projects, there's John Kitchin's code, there's ox-bibtex.el (which
IMO is not suitable for complicated citation requirements), plus everyone
and their mother's have got custom citation links in their config via
custom org link types...

/Proper/ citation support (not links) is, IMO, the last thing that is
missing for good academic publishing support.

#+end_rant

—Rasmus


-- 
I hear there's rumors on the, uh, Internets. . .

Re: exporting zotxt or orgref links to HTML and ODF

[Matt Price]

[-- Attachment #1: Type: text/plain, Size: 1474 bytes --]

On Tue, Jan 27, 2015 at 8:30 AM, Rasmus <rasmus@gmx.us> wrote:

> Hi,
>
> Christian Moe <mail@christianmoe.com> writes:
>
> IMO we /need/ to add proper citation support to Org, preferably with a
> real syntax rather than these link-"solutions" and with good backend
> support (bibtex & Zotero for starters, I guess).
>
> #+begin_rant
>
> The current state is a mess and not portable.  E.g. there's at least two
> Zotero projects, there's John Kitchin's code, there's ox-bibtex.el (which
> IMO is not suitable for complicated citation requirements), plus everyone
> and their mother's have got custom citation links in their config via
> custom org link types...
>
> /Proper/ citation support (not links) is, IMO, the last thing that is
> missing for good academic publishing support.
>
> #+end_rant
>
> —Rasmus
>

(I know about zotxt -- is there another zotero project?)

I am certainly not the person to implement anything "properly!" But I do
agree -- if we had great citation support, with bibtex and Zotero
undrestood as portable backends, then (a) i would really be able to work in
org start to finish, and (b) I could start to recommend it to colleagues,
as I'm itching to do.

In the meantime, I think zotxt is the best starting point for me.  But I
would certainly be willing to test, debug, contribute minor patches, etc.
to anyone who wants to take the project on properly (it is almost certainly
beyond my limited skills).

[-- Attachment #2: Type: text/html, Size: 2203 bytes --]

Re: exporting zotxt or orgref links to HTML and ODF

[Rasmus]

Matt Price <moptop99@gmail.com> writes:

> On Tue, Jan 27, 2015 at 8:30 AM, Rasmus <rasmus@gmx.us> wrote:
>> #+begin_rant
>>
>> The current state is a mess and not portable.  E.g. there's at least two
>> Zotero projects, there's John Kitchin's code, there's ox-bibtex.el (which
>> IMO is not suitable for complicated citation requirements), plus everyone
>> and their mother's have got custom citation links in their config via
>> custom org link types...
>>
>> /Proper/ citation support (not links) is, IMO, the last thing that is
>> missing for good academic publishing support.
>>
>> #+end_rant
>
> (I know about zotxt -- is there another zotero project?)

This is the other one I had in mind:

      https://github.com/vspinu/zotelo

> (b) I could start to recommend it to colleagues, as I'm itching to do.

But the argument "it's easier/cleaner" seems to shatter when you get to
[[textcite:KEY]] compared to \textcite{KEY}...  Even worse when you have
to have notes, e.g. \textcite[pre][post]{KEY}.

—Rasmus

-- 
The right to be left alone is a human right

Re: exporting zotxt or orgref links to HTML and ODF

[John Kitchin]

I have not found the link syntax too constraining. Simple links like the
ones I use in org-ref are perfect for simple citation needs. It handles
all different kinds of citations (cite, citet, textcite,...) and
multiple citations. org-ref automates selection of keys and insertion
via reftex or helm. They are all we need for the kind of scientific
publication my group does. We have published six peer-reviewed
publications so far with just these simple links. I do concede that if
you use many "non-simple: features of biblatex, you are heading for
trouble with links. You can probably just use raw LaTeX then.

[[textcite:KEY]] is not required unless KEY has some particular
characters like spaces or other link-breaking characters. textcite:KEY
works just fine for me.

I do agree that \textcite[pre][post]{KEY} is trickier and uglier to
solve. I have only found this approach

[[textcite:KEY][pre text::post text]]

to work particularly well, and you have to parse the description in the
export. I use :: as the divider, since it seems unlikely to be in either
element. It takes a little more thought to automate insertion of these,
but the link insertion machinery of org-mode will do it in org-ref.  If
you use descriptive links in org-mode, it collapses into just the
description, which I don't like but live with. The newest org-ref has a
minibuffer message feature that should show you a summary of the
citation when your cursor is idle on that link though.

I don't want to start a war over links vs dedicated element for
citations. I just want to point out that links work really well for a
large set of use cases, and other solutions are not likely to be as
simple to use. My thoughts are biased of course since I have invested a
lot of time and thought into org-ref, and I don't see the limitations you
suggest in our daily work.

If you send me some examples of what is not easy, maybe we can see if
org-ref can do it.

Rasmus writes:

> Matt Price <moptop99@gmail.com> writes:
>
>> On Tue, Jan 27, 2015 at 8:30 AM, Rasmus <rasmus@gmx.us> wrote:
>>> #+begin_rant
>>>
>>> The current state is a mess and not portable.  E.g. there's at least two
>>> Zotero projects, there's John Kitchin's code, there's ox-bibtex.el (which
>>> IMO is not suitable for complicated citation requirements), plus everyone
>>> and their mother's have got custom citation links in their config via
>>> custom org link types...
>>>
>>> /Proper/ citation support (not links) is, IMO, the last thing that is
>>> missing for good academic publishing support.
>>>
>>> #+end_rant
>>
>> (I know about zotxt -- is there another zotero project?)
>
> This is the other one I had in mind:
>
>       https://github.com/vspinu/zotelo
>
>> (b) I could start to recommend it to colleagues, as I'm itching to do.
>
> But the argument "it's easier/cleaner" seems to shatter when you get to
> [[textcite:KEY]] compared to \textcite{KEY}...  Even worse when you have
> to have notes, e.g. \textcite[pre][post]{KEY}.
>
> —Rasmus

--
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

Re: exporting zotxt or orgref links to HTML and ODF

[Christian Moe]

Matt Price writes:

> On Tue, Jan 27, 2015 at 8:30 AM, Rasmus <rasmus@gmx.us> wrote:
>
>> Hi,
>>
>> Christian Moe <mail@christianmoe.com> writes:

Actually, Rasmus wrote the following, not I.

>> IMO we /need/ to add proper citation support to Org, preferably with a
>> real syntax rather than these link-"solutions" and with good backend
>> support (bibtex & Zotero for starters, I guess).
>>
>> #+begin_rant
>>
>> The current state is a mess and not portable.  E.g. there's at least two
>> Zotero projects, there's John Kitchin's code, there's ox-bibtex.el (which
>> IMO is not suitable for complicated citation requirements), plus everyone
>> and their mother's have got custom citation links in their config via
>> custom org link types...
>>
>> /Proper/ citation support (not links) is, IMO, the last thing that is
>> missing for good academic publishing support.

But I don't necessarily disagree. I just figure I might try to prototype
the solutions I'd like to see toward the day someone steps up to the bat and
implements them in core with native syntax.

Yours,
Christian

Re: exporting zotxt or orgref links to HTML and ODF

[Richard Lawrence]

Rasmus <rasmus@gmx.us> writes:

> IMO we /need/ to add proper citation support to Org, preferably with a
> real syntax rather than these link-"solutions" and with good backend
> support (bibtex & Zotero for starters, I guess).
> ...
> /Proper/ citation support (not links) is, IMO, the last thing that is
> missing for good academic publishing support.

Although my home-baked solution presently works for me, I am inclined to
agree.

I've just had a glance at: http://pandoc.org/README.html#citations

It looks to me like Pandoc has a quite general solution, and it also
looks like Org could use Pandoc's citation syntax as-is.  I would
suggest borrowing this syntax as a starting point for building citation
support into Org.

#+BEGIN_QUOTE
Citations go inside square brackets and are separated by
semicolons. Each citation must have a key, composed of ‘@’ + the
citation identifier from the database, and may optionally have a prefix,
a locator, and a suffix. The citation key must begin with a letter or _,
and may contain alphanumerics, _, and internal punctuation characters
(:.#$%&-+?<>~/). Here are some examples:

Blah blah [see @doe99, pp. 33-35; also @smith04, ch. 1].

Blah blah [@doe99, pp. 33-35, 38-39 and *passim*].

Blah blah [@smith04; @doe99]. 

A minus sign (-) before the @ will suppress mention of the author in the
citation. This can be useful when the author is already mentioned in the
text:

Smith says blah [-@smith04].

You can also write an in-text citation, as follows:

@smith04 says blah.

@smith04 [p. 33] says blah.
#+END_QUOTE

Org does use single brackets and `@'-signs for other things (footnote
markers, priorities, statistics cookies, inactive timestamps, list
counters, inline export snippets -- I think that's it).  But these
should all be pretty easy to tell apart from citations using regular
expressions, so I wouldn't expect parsing this syntax to present any
difficulties.

Does anyone have citation needs that this syntax doesn't cover?

Using this syntax would also have the advantage that Pandoc can already
parse it, which would reduce friction for Org users who convert their
documents with Pandoc (and Pandoc users who need to deal with Org
inputs).  Since this seems like a significant contingent of Org users,
that's something to consider.

The bigger question is whether, in addition to a citation *syntax*, it
would be a lot of work to add support for the various citation database
formats, as well as the various output styles, and which ones to
support.

Best,
Richard

Re: exporting zotxt or orgref links to HTML and ODF

[Rasmus]

Hi,

Richard Lawrence <richard.lawrence@berkeley.edu> writes:

> Rasmus <rasmus@gmx.us> writes:
>
>> IMO we /need/ to add proper citation support to Org, preferably with a
>> real syntax rather than these link-"solutions" and with good backend
>> support (bibtex & Zotero for starters, I guess).
>> ...
>> /Proper/ citation support (not links) is, IMO, the last thing that is
>> missing for good academic publishing support.
>
> Although my home-baked solution presently works for me, I am inclined to
> agree.

It works for me as well, but it's still an ugly hack that I cannot advice
friends and colleagues to follow.

Still, I would much rather have quality-support like with entities.

> I've just had a glance at: http://pandoc.org/README.html#citations

Indeed.  Pandoc seems to most sensible.  I have a survey of
implementations in on my other computer (in a folder that is not synced
between my PCs).

> Org does use single brackets and `@'-signs for other things (footnote
> markers, priorities, statistics cookies, inactive timestamps, list
> counters, inline export snippets -- I think that's it).  But these
> should all be pretty easy to tell apart from citations using regular
> expressions, so I wouldn't expect parsing this syntax to present any
> difficulties.

Maybe something like:

@short-textcite-key, (@parentcite-key) and [@textcite-key :with options]
(@parencite-key :with options).

> Does anyone have citation needs that this syntax doesn't cover?

From my experience with social science publication, one needs to be able
to add options (e.g. cite-type, "citeyear", say) and pre and post notes.

> The bigger question is whether, in addition to a citation *syntax*, it
> would be a lot of work to add support for the various citation database
> formats, as well as the various output styles, and which ones to
> support.

I guess.  But it can be added gradually.

BTW: Org has an almost-agnostic format for storing citation data via
org-bibtex.el.  So perhaps it's easier to go from whatever to
org-bibtex-format and from there to ox-backend-format.  I think that's how
pandoc does it as well.
 
—Rasmus

-- 
May the Force be with you

Re: exporting zotxt or orgref links to HTML and ODF

[Richard Lawrence]

Rasmus <rasmus@gmx.us> writes:

> BTW: Org has an almost-agnostic format for storing citation data via
> org-bibtex.el.  So perhaps it's easier to go from whatever to
> org-bibtex-format and from there to ox-backend-format.  I think that's how
> pandoc does it as well.

Well, that would certainly suit me, as I already store my citation data
in org-bibtex format, and generate a .bib file as needed from it.  I
think Pandoc does something similar with YAML, either in-file or in a
separate bibliography file.  I do not know if the org-bibtex format will
play nicely with non-BibTeX citation databases, though; can anyone speak
to that?

Best,
Richard

Re: exporting zotxt or orgref links to HTML and ODF

[Christian Moe]

Richard Lawrence writes:

> It looks to me like Pandoc has a quite general solution, and it also
> looks like Org could use Pandoc's citation syntax as-is.  I would
> suggest borrowing this syntax as a starting point for building citation
> support into Org.

It's been years since I looked at Pandoc, and I think they've added some
functionality since then. Prefix, locator, suffix, and multiple
references in one human-readable citation: Great! And /much/ nicer to
look at than latex \cite commands with their frankly bizarre placement
of locators etc.

> Blah blah [see @doe99, pp. 33-35; also @smith04, ch. 1].

In my current homebrewn solution for Zotero, I have tried to do
something similarly readable using Org link syntax (sorry, Rasmus!) with
the database entry ID as link target, and parsing the description part
for prefix/author-date/locator/suffix, but with a slightly different
syntax than Pandoc uses. In my solution the above would be:

Blah blah [[zotero:0_A43F89;0_E25CB3][(see: Doe 1999: p.33-35; also:
Smith 2004: ch. 1)]].

> A minus sign (-) before the @ will suppress mention of the author in the
> citation. This can be useful when the author is already mentioned in the
> text:
>
> Smith says blah [-@smith04].

In my current Zotero solution:

Smith says blah [[zotero:0_E25CB3][(2004)]].

> Does anyone have citation needs that this syntax doesn't cover?

It's great, as long as your database uses mnemonic citekeys like
doe99. Zotero doesn't, but uses keys that are meaningless to humans,
like 0_A43F89.  Unfortunately [see @0_A43F89, p. 5] wouldn't look nearly
as nice as [see @doe99, p.5], and it wouldn't help you remember what you
referenced.

I think the typical workflow combining Zotero with Pandoc is to export a
BibTex file from Zotero and reference the BibTex citekeys from
there. I could live with that much of the time.

But that workflow doesn't help with something I often want to do, which
is to export to ODT and have 'live' Zotero citations that I can continue
to work with in LibreOffice.

> Using this syntax would also have the advantage that Pandoc can already
> parse it, which would reduce friction for Org users who convert their
> documents with Pandoc (and Pandoc users who need to deal with Org
> inputs).  Since this seems like a significant contingent of Org users,
> that's something to consider.

That's a good point. OTOH, don't Org users convert their documents with
Pandoc mostly because cross-backend citation support is lacking? 

> The bigger question is whether, in addition to a citation *syntax*, it
> would be a lot of work to add support for the various citation database
> formats, as well as the various output styles, and which ones to
> support.

Possibly more work if it's worth if we adopt Pandoc syntax,
since Pandoc-citeproc seems to handle nearly everything that is based on
plain text.

To truly support citations natively, we'd essentially have to implement
something like citeproc in elisp. Not that I haven't been thinking about
that...

Yours,
Christian

Re: exporting zotxt or orgref links to HTML and ODF

[Rasmus]

[-- Attachment #1: Type: text/plain, Size: 2006 bytes --]

Hi,

Christian Moe <mail@christianmoe.com> writes:

>> Blah blah [see @doe99, pp. 33-35; also @smith04, ch. 1].
>
> In my current homebrewn solution for Zotero, I have tried to do
> something similarly readable using Org link syntax (sorry, Rasmus!) with
> the database entry ID as link target, and parsing the description part
> for prefix/author-date/locator/suffix, but with a slightly different
> syntax than Pandoc uses. In my solution the above would be:
>
> Blah blah [[zotero:0_A43F89;0_E25CB3][(see: Doe 1999: p.33-35; also:
> Smith 2004: ch. 1)]].

The problem is that your information can become out of sync if you are not
careful, e.g.:

> [[zotero:0_A43F89;0_E25CB3][(see: Doe 1999: p.33-35; also: Smith 2004: ch. 1)]]
> [[zotero:0_A43F89;0_E25CB3][(see: Forbar 1999: p.33-35)]]

IMO nice displays should be solved with overlays(?) like org-entities,
tex-fold-mode etc.

>> Does anyone have citation needs that this syntax doesn't cover?
>
> It's great, as long as your database uses mnemonic citekeys like
> doe99. Zotero doesn't, but uses keys that are meaningless to humans,
> like 0_A43F89.  Unfortunately [see @0_A43F89, p. 5] wouldn't look nearly
> as nice as [see @doe99, p.5], and it wouldn't help you remember what you
> referenced.

Selection is solved by Reftex or Zotero or whatever.  Still, bad keys are
an issue!  One idea would be to allow file-specific pointers to citations
or allow easy insertion of entries in org-bibtex format.


> But that workflow doesn't help with something I often want to do, which
> is to export to ODT and have 'live' Zotero citations that I can continue
> to work with in LibreOffice.

Are they like bib(la)tex citations?  Like with click and dynamic
bibliography and the like.

> Possibly more work if it's worth if we adopt Pandoc syntax,
> since Pandoc-citeproc seems to handle nearly everything that is based on
> plain text.

bibtex.el and org-bibtex.el seems rather competent.  Of course, styles is
an issue.

Here's my notes on this topic:


[-- Attachment #2: notes-on-citation.org --]
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[-- Attachment #3: Type: text/plain, Size: 18 bytes --]


-- 
Bang bang

Re: exporting zotxt or orgref links to HTML and ODF

[John Kitchin]

Christian Moe writes:

> Richard Lawrence writes:
>
>> It looks to me like Pandoc has a quite general solution, and it also
>> looks like Org could use Pandoc's citation syntax as-is.  I would
>> suggest borrowing this syntax as a starting point for building citation
>> support into Org.
>
> It's been years since I looked at Pandoc, and I think they've added some
> functionality since then. Prefix, locator, suffix, and multiple
> references in one human-readable citation: Great! And /much/ nicer to
> look at than latex \cite commands with their frankly bizarre placement
> of locators etc.
>
>> Blah blah [see @doe99, pp. 33-35; also @smith04, ch. 1].
>
> In my current homebrewn solution for Zotero, I have tried to do
> something similarly readable using Org link syntax (sorry, Rasmus!) with
> the database entry ID as link target, and parsing the description part
> for prefix/author-date/locator/suffix, but with a slightly different
> syntax than Pandoc uses. In my solution the above would be:
>
> Blah blah [[zotero:0_A43F89;0_E25CB3][(see: Doe 1999: p.33-35; also:
> Smith 2004: ch. 1)]].
>
>> A minus sign (-) before the @ will suppress mention of the author in the
>> citation. This can be useful when the author is already mentioned in the
>> text:
>>
>> Smith says blah [-@smith04].
>
> In my current Zotero solution:
>
> Smith says blah [[zotero:0_E25CB3][(2004)]].
>
>> Does anyone have citation needs that this syntax doesn't cover?
>
> It's great, as long as your database uses mnemonic citekeys like
> doe99. Zotero doesn't, but uses keys that are meaningless to humans,
> like 0_A43F89.  Unfortunately [see @0_A43F89, p. 5] wouldn't look nearly
> as nice as [see @doe99, p.5], and it wouldn't help you remember what you
> referenced.

This doesn't have to be case. Even bibtex keys are not mnemonic enough
in my opinion (maybe it is fairer to put the limitation on what I can
remember though ;) I recently implemented a neat idea in org-ref that
will show you the full citation in the minibuffer when your cursor is
idle over a cite link. See https://www.youtube.com/watch?v=8cEb6F9AEu0
to see it in action. I played around with many variations of tool tips,
etc... and settled on the minibuffer as the lightest weight, least
disruptive flow.

On the other hand, if the concern about mnemonic is remembering what to
type in, then you should consider using a completion tool. org-ref has
completion by key (which I do not use because I do not remember keys),
but also key selection through either reftex or helm-bibtex. It is
surprisingly easy to make a helm selection buffer. All you need is a way
to get the possible candidates from zotero, e.g. by parsing the entries
to get a list of (description . zotero-key) for each entry. description
is what you see in helm to narrow, and zotero-key is what is sent to an
action function that takes care of formatting and inserting the keys.

>
> I think the typical workflow combining Zotero with Pandoc is to export a
> BibTex file from Zotero and reference the BibTex citekeys from
> there. I could live with that much of the time.
>
> But that workflow doesn't help with something I often want to do, which
> is to export to ODT and have 'live' Zotero citations that I can continue
> to work with in LibreOffice.

I don't do this often, but if you know what the zotero citation format
in odt is, I think you could get org to export it for that backend.

>
>> Using this syntax would also have the advantage that Pandoc can already
>> parse it, which would reduce friction for Org users who convert their
>> documents with Pandoc (and Pandoc users who need to deal with Org
>> inputs).  Since this seems like a significant contingent of Org users,
>> that's something to consider.
>
> That's a good point. OTOH, don't Org users convert their documents with
> Pandoc mostly because cross-backend citation support is lacking?
>
>> The bigger question is whether, in addition to a citation *syntax*, it
>> would be a lot of work to add support for the various citation database
>> formats, as well as the various output styles, and which ones to
>> support.
>
> Possibly more work if it's worth if we adopt Pandoc syntax,
> since Pandoc-citeproc seems to handle nearly everything that is based on
> plain text.
>
> To truly support citations natively, we'd essentially have to implement
> something like citeproc in elisp. Not that I haven't been thinking about
> that...
>
> Yours,
> Christian

--
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

Re: exporting zotxt or orgref links to HTML and ODF

[Matt Price]

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I am very eager to see this work of yours, Christian.  I also would very
much like to find a way to have a single, well-supported citation framework
in org -- I certainly think John's work looks incredible, and zotxt is very
powerful, but it would be fantastic if one could just choose a
bibliographic backend and export seamlessly to any supported format.  It
would be a big step forward.  I guess I don't quite see, yet, what has to
happen for the work of various contributors to be consolidated; clearly
Erik, You, and John have worked in overlapping and distinct directions, but
I would be veyr enthusiastic about helping a unified approach emerge,
espeically one that supported Zotero.

Thanks everyone,
Matt

On Tue, Jan 27, 2015 at 3:01 PM, Christian Moe <mail@christianmoe.com>
wrote:

>
> Richard Lawrence writes:
>
> > It looks to me like Pandoc has a quite general solution, and it also
> > looks like Org could use Pandoc's citation syntax as-is.  I would
> > suggest borrowing this syntax as a starting point for building citation
> > support into Org.
>
> It's been years since I looked at Pandoc, and I think they've added some
> functionality since then. Prefix, locator, suffix, and multiple
> references in one human-readable citation: Great! And /much/ nicer to
> look at than latex \cite commands with their frankly bizarre placement
> of locators etc.
>
> > Blah blah [see @doe99, pp. 33-35; also @smith04, ch. 1].
>
> In my current homebrewn solution for Zotero, I have tried to do
> something similarly readable using Org link syntax (sorry, Rasmus!) with
> the database entry ID as link target, and parsing the description part
> for prefix/author-date/locator/suffix, but with a slightly different
> syntax than Pandoc uses. In my solution the above would be:
>
> Blah blah [[zotero:0_A43F89;0_E25CB3][(see: Doe 1999: p.33-35; also:
> Smith 2004: ch. 1)]].
>
> > A minus sign (-) before the @ will suppress mention of the author in the
> > citation. This can be useful when the author is already mentioned in the
> > text:
> >
> > Smith says blah [-@smith04].
>
> In my current Zotero solution:
>
> Smith says blah [[zotero:0_E25CB3][(2004)]].
>
> > Does anyone have citation needs that this syntax doesn't cover?
>
> It's great, as long as your database uses mnemonic citekeys like
> doe99. Zotero doesn't, but uses keys that are meaningless to humans,
> like 0_A43F89.  Unfortunately [see @0_A43F89, p. 5] wouldn't look nearly
> as nice as [see @doe99, p.5], and it wouldn't help you remember what you
> referenced.
>
> I think the typical workflow combining Zotero with Pandoc is to export a
> BibTex file from Zotero and reference the BibTex citekeys from
> there. I could live with that much of the time.
>
> But that workflow doesn't help with something I often want to do, which
> is to export to ODT and have 'live' Zotero citations that I can continue
> to work with in LibreOffice.
>
> > Using this syntax would also have the advantage that Pandoc can already
> > parse it, which would reduce friction for Org users who convert their
> > documents with Pandoc (and Pandoc users who need to deal with Org
> > inputs).  Since this seems like a significant contingent of Org users,
> > that's something to consider.
>
> That's a good point. OTOH, don't Org users convert their documents with
> Pandoc mostly because cross-backend citation support is lacking?
>
> > The bigger question is whether, in addition to a citation *syntax*, it
> > would be a lot of work to add support for the various citation database
> > formats, as well as the various output styles, and which ones to
> > support.
>
> Possibly more work if it's worth if we adopt Pandoc syntax,
> since Pandoc-citeproc seems to handle nearly everything that is based on
> plain text.
>
> To truly support citations natively, we'd essentially have to implement
> something like citeproc in elisp. Not that I haven't been thinking about
> that...
>
> Yours,
> Christian
>
>
>
>
>
>
>

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Re: exporting zotxt or orgref links to HTML and ODF

[Erik Hetzner]

On Tue, 27 Jan 2015 at 09:24:00 PST,
Richard Lawrence <richard.lawrence@berkeley.edu> wrote:
> 
> 
> Although my home-baked solution presently works for me, I am inclined to
> agree.
> 
> I've just had a glance at: http://pandoc.org/README.html#citations
> 
> It looks to me like Pandoc has a quite general solution, and it also
> looks like Org could use Pandoc's citation syntax as-is.  I would
> suggest borrowing this syntax as a starting point for building citation
> support into Org.

Hi all,

I agree completely. For what it’s worth, using pandoc citations now
will work right now if you output to markdown and then parse in
pandoc. e.g.

  [see @doe:2006article, p. 10]

will work.

I wrote a parser for pandoc citations (that assumes you start with a
citation string, that is, it doesn’t work unless you have extracted
the citation string from the document):

  https://bitbucket.org/egh/zot4rst/src/master/xciterst/parser.py

but it doesn’t seem that org-element.el uses a grammar, so I’m not
sure how much that would help. There is also, of course, the pandoc
parser.

best, Erik
--
Sent from my free software system <http://fsf.org/>.

Re: exporting zotxt or orgref links to HTML and ODF

[Erik Hetzner]

On Tue, 27 Jan 2015 at 22:37:20 PST,
Erik Hetzner <egh@e6h.org> wrote:
>
> […]
> 
> I wrote a parser for pandoc citations (that assumes you start with a
> citation string, that is, it doesn’t work unless you have extracted
> the citation string from the document):
> 
>   https://bitbucket.org/egh/zot4rst/src/master/xciterst/parser.py
> 
> but it doesn’t seem that org-element.el uses a grammar, so I’m not
> sure how much that would help. There is also, of course, the pandoc
> parser.

I have started porting this parser to elisp. So far it can’t parse
much, but it shouldn’t be too hard to finish.

  https://gitlab.com/egh/org-pdcite

This includes parser combinator functionality for elisp.

best, Erik
--
Sent from my free software system <http://fsf.org/>.

Re: exporting zotxt or orgref links to HTML and ODF

[Vikas Rawal]

> 
> My question: does anyone yet have a workflow that lets them export directly to HTML or ODT?  


In my experience, exporting from Org to LateX, and then using pandoc to convert to odt works better than converting directly from Org to odt. This is particularly the case if you are using citations. Of course, I use Bibtex but you may want to see Zotero support in Pandoc.

Vikas

Re: exporting zotxt or orgref links to HTML and ODF

[Matt Price]

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For me, the main issue with this route is that I don't understand LaTex at
all, and it seems like there's a bit of a steep learning curve to get to a
working set up.  Maybe someone can recommend a good guide for starting out
in LaTex?  It does seem like somehting one should learn, I suppose.


On Tue, Jan 27, 2015 at 7:01 AM, Vikas Rawal <
vikaslists@agrarianresearch.org> wrote:

> >
> > My question: does anyone yet have a workflow that lets them export
> directly to HTML or ODT?
>
>
> In my experience, exporting from Org to LateX, and then using pandoc to
> convert to odt works better than converting directly from Org to odt. This
> is particularly the case if you are using citations. Of course, I use
> Bibtex but you may want to see Zotero support in Pandoc.
>
> Vikas

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Re: exporting zotxt or orgref links to HTML and ODF

[Eric S Fraga]

On Tuesday, 27 Jan 2015 at 08:12, Matt Price wrote:
> For me, the main issue with this route is that I don't understand LaTex at
> all, and it seems like there's a bit of a steep learning curve to get to a
> working set up.  Maybe someone can recommend a good guide for starting out
> in LaTex?  It does seem like somehting one should learn, I suppose.

There are many tutorials on the web.  A simple "latex tutorial" web
search brings back many links.  I can send you a couple of PDF documents
off-list, if you wish, of documents I have used in the past.

The original text by Leslie Lamport is also a very good starting point.

I do wonder, however, how much you need to know if you are using
org.  In fact, you can probably learn a lot by looking at the LaTeX that
org produces...  and many of us are happy to help with the odd org-LaTeX
issues that can arise!


-- 
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.1, Org release_8.3beta-726-gd34b80.dirty

Re: exporting zotxt or orgref links to HTML and ODF

[Albert Krewinkel]

Vikas Rawal <vikaslists@agrarianresearch.org> writes:

>> My question: does anyone yet have a workflow that lets them export directly to HTML or ODT?  
>
> In my experience, exporting from Org to LateX, and then using pandoc to
> convert to odt works better than converting directly from Org to odt.

Being one of the authors of pandocs org-mode reader, I'm very interested
in learning the issues you experienced when converting directly to odt.
Could you give some feedback on that?

Thanks in advance,

Albert

-- 
Albert Krewinkel
GPG: 8eed e3e2 e8c5 6f18 81fe  e836 388d c0b2 1f63 1124

Re: exporting zotxt or orgref links to HTML and ODF

[Christian Moe]

Well, color me embarrassed. I never even noticed the switch to
zotxt. And I never tried with Standalone either. Just tinkered happily
away with Eric's excellent old solution and Firefox. Maybe I should check
out both before posting an obsolute solution with unnecessary
dependencies...

Will report back in a little while.

Yours,
Christian

Matt Price writes:

> Christian,
>
> I would love to see this.  I am using Erik's rewritten
> zotero-plain/org-zotero (zotxt-emacs); it works fine with
> zotero-standalone, so MozRepl not required, I don't think.  I'm not sure if
> the link syntax is still the same as in the original versions.
>
> So yes, please do send the code if you are willing.  If you have hints
> about the more ambitious citation system, I and I'm sure others would love
> to see them.
>
> thanks,
> Matt
>
>
> On Tue, Jan 27, 2015 at 4:18 AM, Christian Moe <mail@christianmoe.com>
> wrote:
>
>>
>> Matt Price writes:
>>
>> > My question: does anyone yet have a workflow that lets them export
>> directly
>> > to HTML or ODT?
>>
>> Hi, Matt,
>>
>> Yes, now I have not just a workflow, but a code solution for
>> Org/Zotero/ODT export that has been tried and tested for a while. It now
>> supports multiple references in one citation, prefixes, suffixes,
>> locators, and year-only citations, and produces 'live' Zotero refmarks
>> in ODT, so you can do all the changes you want in LibreOffice
>> afterward. It also does some very limited but useful things for html
>> (DOI links and links that will work on Wordpress blogs with Katie
>> Seaborn's ZotPress extension).
>>
>> It depends on Eric Hetzner's excellent zotero-plain and org-zotero
>> packages, and hence on the MozRepl extension on the Firefox side, though
>> you can use the ODT export functionality itself without those
>> dependencies.
>>
>> I haven't yet announced it on the list, for three reasons. 1) Not very
>> polished. There's some messy code, a poor man's user interface, and no
>> editing support for multiple citations (but support for exporting
>> them!). 2) It's part of a more ambitious project I set myself for an
>> all-round citation system that I never got on with. 3) It uses this cool
>> idea I had for how to use citation links differently, but it imposes
>> certain syntax conventions on the user, and they may yet change in
>> backward-incompatible ways if I develop this further.
>>
>> If this sounds interesting, I can post the code here 'as is' for you to
>> try out, but I'd better update the docs first, which could take a day or
>> two.
>>
>> Yours,
>> Christian
>>
>>
>> > I've just tried using zotxt again (
>> > https://bitbucket.org/egh/zotxt-emacs/overview -- first time in a
>> while);
>> > it is remarkably easy to use in Org itself.  By default, though, the
>> links
>> > simply aren't handled in the HTML and ODT exports, and so the cites will
>> be
>> > completely absent.
>> >
>> > Here is the text inserted by zotxt for a single citation:
>> >
>> > ----------------
>> >
>> > [[zotero://select/items/0_TI27HJ5I][Suchman, Lucy. “Subject Objects.”
>> > Feminist Theory 12, no. 2 (August 1, 2011): 119–45.
>> >
>> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.
>> ]]
>> > ---------------
>> >
>> > In HTML, I would like to replace this with something like this:
>> >
>> > (<a href="#BibSuchman2011">Suchman 2011</a>)
>> >
>> > and then have Org generate a bibligraphy somewhere, a bit like org-ref
>> > seems to do, It would be nice if I could steal the styles from somehwere,
>> > the way org-ref seems to do.
>> >
>> > For ODT< it seems a little more complicated. Here is the rather lengthy
>> > equivalent that Zotero itself produces for my default style (Chicago) in
>> > Libreoffice:
>> > ---------------
>> > <text:note text:id="ftn0"
>> >
>> text:note-class="footnote"><text:note-citation>1</text:note-citation><text:note-body><text:p
>> > text:style-name="Footnote"><text:reference-mark-start
>> > text:name="ZOTERO_ITEM CSL_CITATION
>> >
>> {&quot;citationID&quot;:&quot;5xzXuF2I&quot;,&quot;properties&quot;:{&quot;formattedCitation&quot;:&quot;{\\rtf
>> > Lucy Suchman, \\uc0\\u8220{}Subject Objects,\\uc0\\u8221{} \\i Feminist
>> > Theory\\i0{} 12, no. 2 (August 1, 2011): 119\\uc0\\u8211{}45,
>> >
>> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.}&quot
>> ;,&quot;plainCitation&quot;:&quot;Lucy
>> > Suchman, “Subject Objects,” Feminist Theory 12, no. 2 (August 1, 2011):
>> > 119–45,
>> >
>> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.&quot
>> ;
>> > },&quot;citationItems&quot;:[{&quot;id&quot;:149,&quot;uris&quot;:[&quot;
>> > http://zotero.org/users/20/items/TI27HJ5I&quot;],&quot;uri&quot;:[&quot;
>> > http://zotero.org/users/20/items/TI27HJ5I&quot;
>> ],&quot;itemData&quot;:{&quot;id&quot;:149,&quot;type&quot;:&quot;article-journal&quot;,&quot;title&quot;:&quot;Subject
>> > objects&quot;,&quot;container-title&quot;:&quot;Feminist
>> >
>> Theory&quot;,&quot;page&quot;:&quot;119-145&quot;,&quot;volume&quot;:&quot;12&quot;,&quot;issue&quot;:&quot;2&quot;,&quot;URL&quot;:&quot;
>> >
>> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml&quot
>> >
>> ;,&quot;ISSN&quot;:&quot;14647001&quot;,&quot;author&quot;:[{&quot;family&quot;:&quot;Suchman&quot;,&quot;given&quot;:&quot;Lucy&quot;}],&quot;issued&quot;:{&quot;date-parts&quot;:[[&quot;2011&quot;,8,1]]}}}],&quot;schema&quot;:&quot;
>> >
>> https://github.com/citation-style-language/schema/raw/master/csl-citation.json&quot
>> ;}
>> > RNDuhNYYpC1hN"/><text:span text:style-name="T3">Lucy Suchman, “Subject
>> > Objects,” </text:span><text:span text:style-name="T4">Feminist
>> > Theory</text:span><text:span text:style-name="T5"> 12, no. 2 (August 1,
>> > 2011): 119–45,
>> > http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml
>> .</text:span><text:reference-mark-end
>> > text:name="ZOTERO_ITEM CSL_CITATION
>> >
>> {&quot;citationID&quot;:&quot;5xzXuF2I&quot;,&quot;properties&quot;:{&quot;formattedCitation&quot;:&quot;{\\rtf
>> > Lucy Suchman, \\uc0\\u8220{}Subject Objects,\\uc0\\u8221{} \\i Feminist
>> > Theory\\i0{} 12, no. 2 (August 1, 2011): 119\\uc0\\u8211{}45,
>> >
>> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.}&quot
>> ;,&quot;plainCitation&quot;:&quot;Lucy
>> > Suchman, “Subject Objects,” Feminist Theory 12, no. 2 (August 1, 2011):
>> > 119–45,
>> >
>> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml.&quot
>> ;
>> > },&quot;citationItems&quot;:[{&quot;id&quot;:149,&quot;uris&quot;:[&quot;
>> > http://zotero.org/users/20/items/TI27HJ5I&quot;],&quot;uri&quot;:[&quot;
>> > http://zotero.org/users/20/items/TI27HJ5I&quot;
>> ],&quot;itemData&quot;:{&quot;id&quot;:149,&quot;type&quot;:&quot;article-journal&quot;,&quot;title&quot;:&quot;Subject
>> > objects&quot;,&quot;container-title&quot;:&quot;Feminist
>> >
>> Theory&quot;,&quot;page&quot;:&quot;119-145&quot;,&quot;volume&quot;:&quot;12&quot;,&quot;issue&quot;:&quot;2&quot;,&quot;URL&quot;:&quot;
>> >
>> http://resolver.scholarsportal.info/resolve/14647001/v12i0002/119_so.xml&quot
>> >
>> ;,&quot;ISSN&quot;:&quot;14647001&quot;,&quot;author&quot;:[{&quot;family&quot;:&quot;Suchman&quot;,&quot;given&quot;:&quot;Lucy&quot;}],&quot;issued&quot;:{&quot;date-parts&quot;:[[&quot;2011&quot;,8,1]]}}}],&quot;schema&quot;:&quot;
>> >
>> https://github.com/citation-style-language/schema/raw/master/csl-citation.json&quot
>> ;}
>> > RNDuhNYYpC1hN"/></text:p></text:note-body></text:note>
>> > ------------------------------
>> >
>> > I'm not sure what the best way to do this is; it may be that zotxt could
>> be
>> > extended to get zotero to do the heavy lifting here.
>> >
>> > I know Erik H reads this list, so if you have any suggestions, Erik, I
>> > would love to hear them.  But maybe other people also have suggestions
>> > about modifying export filters - -that would also be really helpful for
>> > me.  Thanks as always,
>> >
>> > Matt
>>
>>