org-cite and export to ODT

org-cite and export to ODT

[Xianwen Chen (陈贤文)]

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I have been using org-ref and biblatex. They export well to PDF, through
LaTeX. I am able to export to ODT as well. However, I'm not able to have
the bibliography or the references in the produced ODT.

I searched online and found this tutorial:
https://kjambunathan.github.io/org-mode-ox-odt/Bibliography-and-Citations-in-ODT-export.html.
However, when following through the tutorial, I wasn't able to find
ox-jabref.

Thinking about the new org-cite, which is orgmode's native citation
solution, I'm wondering if it would be easier to use org-cite within
orgmode and export to ODT? A small example with configuration suggestion
will be highly appreciated!

Xianwen

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Re: org-cite and export to ODT

[John Kitchin]

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If you are trying to use org-ref for this see
https://www.youtube.com/watch?v=rRR-5NSpKyE and this example:
https://github.com/jkitchin/org-ref/blob/master/examples/basic-csl.org#opendocument.
You need to use a preprocessing hook (org-ref-csl-preprocess-buffer) with
org-ref to get the citations and bibliography .
John

-----------------------------------
Professor John Kitchin (he/him/his)
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu



On Thu, Dec 9, 2021 at 4:54 AM Xianwen Chen (陈贤文) <xianwen.chen@gmail.com>
wrote:

> I have been using org-ref and biblatex. They export well to PDF, through
> LaTeX. I am able to export to ODT as well. However, I'm not able to have
> the bibliography or the references in the produced ODT.
>
> I searched online and found this tutorial:
> https://kjambunathan.github.io/org-mode-ox-odt/Bibliography-and-Citations-in-ODT-export.html.
> However, when following through the tutorial, I wasn't able to find
> ox-jabref.
>
> Thinking about the new org-cite, which is orgmode's native citation
> solution, I'm wondering if it would be easier to use org-cite within
> orgmode and export to ODT? A small example with configuration suggestion
> will be highly appreciated!
>
> Xianwen
>

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Re: org-cite and export to ODT

[András Simonyi]

Dear All,

On Thu, 9 Dec 2021 at 10:54, Xianwen Chen (陈贤文) <xianwen.chen@gmail.com> wrote:

> Thinking about the new org-cite, which is orgmode's native citation solution, I'm wondering if it would be easier to use org-cite within orgmode and export to ODT? A small example with configuration suggestion will be highly appreciated!
>
> Xianwen

org-cite contains two citation export processors which are able to
export citations to ODT: oc-basic and oc-csl. A minimal example using
oc-csl could be along the following lines:

------------[ cut here ]------------
#+bibliography: /path/to/my.bib
#+cite_export: csl

[cite:@smith1998]

* References
#+print_bibliography:
------------[ cut here ]------------

details can be found in the Org manual
(https://orgmode.org/manual/Citation-handling.html#Citation-handling).

best wishes,
András

Re: org-cite and export to ODT

[Xianwen Chen (陈贤文)]

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Thank you all for the responses. I have to upgrade from orgmode 9.4.4 to
9.5 first, to try out org-cite.

I tried
https://github.com/jkitchin/org-ref/blob/master/examples/basic-csl.org#opendocument.
I added the following codes to my .emacs:

(let ((org-export-before-parsing-hook '(org-ref-cite-natmove ;; do this
first
org-ref-csl-preprocess-buffer
org-ref-refproc)))
  (org-open-file (org-odt-export-to-odt) 'system))

I tried to eval-region, after selecting these codes. I got the complain
that org-ref-cite-natmove's function definition is void.

Do I need to install or require something other than cite-ref?

Xianwen

On Thu, Dec 9, 2021 at 2:57 PM John Kitchin <jkitchin@andrew.cmu.edu> wrote:

> If you are trying to use org-ref for this see
> https://www.youtube.com/watch?v=rRR-5NSpKyE and this example:
> https://github.com/jkitchin/org-ref/blob/master/examples/basic-csl.org#opendocument.
> You need to use a preprocessing hook (org-ref-csl-preprocess-buffer) with
> org-ref to get the citations and bibliography .
> John
>
> -----------------------------------
> Professor John Kitchin (he/him/his)
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu
>
>
>
> On Thu, Dec 9, 2021 at 4:54 AM Xianwen Chen (陈贤文) <xianwen.chen@gmail.com>
> wrote:
>
>> I have been using org-ref and biblatex. They export well to PDF, through
>> LaTeX. I am able to export to ODT as well. However, I'm not able to have
>> the bibliography or the references in the produced ODT.
>>
>> I searched online and found this tutorial:
>> https://kjambunathan.github.io/org-mode-ox-odt/Bibliography-and-Citations-in-ODT-export.html.
>> However, when following through the tutorial, I wasn't able to find
>> ox-jabref.
>>
>> Thinking about the new org-cite, which is orgmode's native citation
>> solution, I'm wondering if it would be easier to use org-cite within
>> orgmode and export to ODT? A small example with configuration suggestion
>> will be highly appreciated!
>>
>> Xianwen
>>
>

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Re: org-cite and export to ODT

[John Kitchin]

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That code does not belong in your .emacs file. It should be in an
emacs-lisp block in your org-file like it is in the example. You should run
it from the org file.




John

-----------------------------------
Professor John Kitchin (he/him/his)
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu



On Wed, Dec 15, 2021 at 5:12 PM Xianwen Chen (陈贤文) <xianwen.chen@gmail.com>
wrote:

> Thank you all for the responses. I have to upgrade from orgmode 9.4.4 to
> 9.5 first, to try out org-cite.
>
> I tried
> https://github.com/jkitchin/org-ref/blob/master/examples/basic-csl.org#opendocument.
> I added the following codes to my .emacs:
>
> (let ((org-export-before-parsing-hook '(org-ref-cite-natmove ;; do this
> first
> org-ref-csl-preprocess-buffer
> org-ref-refproc)))
>   (org-open-file (org-odt-export-to-odt) 'system))
>
> I tried to eval-region, after selecting these codes. I got the complain
> that org-ref-cite-natmove's function definition is void.
>
> Do I need to install or require something other than cite-ref?
>
> Xianwen
>
> On Thu, Dec 9, 2021 at 2:57 PM John Kitchin <jkitchin@andrew.cmu.edu>
> wrote:
>
>> If you are trying to use org-ref for this see
>> https://www.youtube.com/watch?v=rRR-5NSpKyE and this example:
>> https://github.com/jkitchin/org-ref/blob/master/examples/basic-csl.org#opendocument.
>> You need to use a preprocessing hook (org-ref-csl-preprocess-buffer) with
>> org-ref to get the citations and bibliography .
>> John
>>
>> -----------------------------------
>> Professor John Kitchin (he/him/his)
>> Doherty Hall A207F
>> Department of Chemical Engineering
>> Carnegie Mellon University
>> Pittsburgh, PA 15213
>> 412-268-7803
>> @johnkitchin
>> http://kitchingroup.cheme.cmu.edu
>>
>>
>>
>> On Thu, Dec 9, 2021 at 4:54 AM Xianwen Chen (陈贤文) <xianwen.chen@gmail.com>
>> wrote:
>>
>>> I have been using org-ref and biblatex. They export well to PDF, through
>>> LaTeX. I am able to export to ODT as well. However, I'm not able to have
>>> the bibliography or the references in the produced ODT.
>>>
>>> I searched online and found this tutorial:
>>> https://kjambunathan.github.io/org-mode-ox-odt/Bibliography-and-Citations-in-ODT-export.html.
>>> However, when following through the tutorial, I wasn't able to find
>>> ox-jabref.
>>>
>>> Thinking about the new org-cite, which is orgmode's native citation
>>> solution, I'm wondering if it would be easier to use org-cite within
>>> orgmode and export to ODT? A small example with configuration suggestion
>>> will be highly appreciated!
>>>
>>> Xianwen
>>>
>>

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Re: org-cite and export to ODT

[Xianwen Chen (陈贤文)]

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Thank you John. I'm not sure why it does not work. Below is the minimal
example I created, using your example. I ran C-e o o to export to ODT. The
resulted ODT file didn't have the reference.

#+title: A basic example of org-ref for csl export
#+options: toc:nil
#+csl-style: apa-5th-edition.csl
#+csl-locale: en-US

* Bibliography

bibliography:~/data/library/bibliography/biblatex/biblatex.bib

cite:bayulken-et-al-2020-nbs-climate_change-pandemics

* build :noexport:

#+BEGIN_SRC emacs-lisp :results silent
(let ((org-export-before-parsing-hook '(org-ref-cite-natmove ;; do this
first
org-ref-csl-preprocess-buffer
org-ref-refproc)))
  (org-open-file (org-odt-export-to-odt) 'system))
#+END_SRC


On Wed, Dec 15, 2021 at 10:16 PM John Kitchin <jkitchin@andrew.cmu.edu>
wrote:

> That code does not belong in your .emacs file. It should be in an
> emacs-lisp block in your org-file like it is in the example. You should run
> it from the org file.
>
>
>
>
> John
>
> -----------------------------------
> Professor John Kitchin (he/him/his)
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu
>
>
>
> On Wed, Dec 15, 2021 at 5:12 PM Xianwen Chen (陈贤文) <xianwen.chen@gmail.com>
> wrote:
>
>> Thank you all for the responses. I have to upgrade from orgmode 9.4.4 to
>> 9.5 first, to try out org-cite.
>>
>> I tried
>> https://github.com/jkitchin/org-ref/blob/master/examples/basic-csl.org#opendocument.
>> I added the following codes to my .emacs:
>>
>> (let ((org-export-before-parsing-hook '(org-ref-cite-natmove ;; do this
>> first
>> org-ref-csl-preprocess-buffer
>> org-ref-refproc)))
>>   (org-open-file (org-odt-export-to-odt) 'system))
>>
>> I tried to eval-region, after selecting these codes. I got the complain
>> that org-ref-cite-natmove's function definition is void.
>>
>> Do I need to install or require something other than cite-ref?
>>
>> Xianwen
>>
>> On Thu, Dec 9, 2021 at 2:57 PM John Kitchin <jkitchin@andrew.cmu.edu>
>> wrote:
>>
>>> If you are trying to use org-ref for this see
>>> https://www.youtube.com/watch?v=rRR-5NSpKyE and this example:
>>> https://github.com/jkitchin/org-ref/blob/master/examples/basic-csl.org#opendocument.
>>> You need to use a preprocessing hook (org-ref-csl-preprocess-buffer) with
>>> org-ref to get the citations and bibliography .
>>> John
>>>
>>> -----------------------------------
>>> Professor John Kitchin (he/him/his)
>>> Doherty Hall A207F
>>> Department of Chemical Engineering
>>> Carnegie Mellon University
>>> Pittsburgh, PA 15213
>>> 412-268-7803
>>> @johnkitchin
>>> http://kitchingroup.cheme.cmu.edu
>>>
>>>
>>>
>>> On Thu, Dec 9, 2021 at 4:54 AM Xianwen Chen (陈贤文) <
>>> xianwen.chen@gmail.com> wrote:
>>>
>>>> I have been using org-ref and biblatex. They export well to PDF,
>>>> through LaTeX. I am able to export to ODT as well. However, I'm not able to
>>>> have the bibliography or the references in the produced ODT.
>>>>
>>>> I searched online and found this tutorial:
>>>> https://kjambunathan.github.io/org-mode-ox-odt/Bibliography-and-Citations-in-ODT-export.html.
>>>> However, when following through the tutorial, I wasn't able to find
>>>> ox-jabref.
>>>>
>>>> Thinking about the new org-cite, which is orgmode's native citation
>>>> solution, I'm wondering if it would be easier to use org-cite within
>>>> orgmode and export to ODT? A small example with configuration suggestion
>>>> will be highly appreciated!
>>>>
>>>> Xianwen
>>>>
>>>

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Re: org-cite and export to ODT

[John Kitchin]

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you are still not getting the directions. You don't export with C-c Ce oo
here. You run that src block by putting your cursor in it and typing C-c
C-c to run it.

For org-ref, you have to use a preprocessing hook to replace the cite links
with the csl derived links before the export is done. That is what the src
block does. It temporarily defines org-export-before-parsing-hook to run
those three hook functions before making an odt file.

Alternatively you can do C-c C-e ro which will use the org-ref exporter
that at least runs the  org-ref csl preprocessor.

John

-----------------------------------
Professor John Kitchin (he/him/his)
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu



On Wed, Dec 15, 2021 at 6:58 PM Xianwen Chen (陈贤文) <xianwen.chen@gmail.com>
wrote:

> Thank you John. I'm not sure why it does not work. Below is the minimal
> example I created, using your example. I ran C-e o o to export to ODT. The
> resulted ODT file didn't have the reference.
>
> #+title: A basic example of org-ref for csl export
> #+options: toc:nil
> #+csl-style: apa-5th-edition.csl
> #+csl-locale: en-US
>
> * Bibliography
>
> bibliography:~/data/library/bibliography/biblatex/biblatex.bib
>
> cite:bayulken-et-al-2020-nbs-climate_change-pandemics
>
> * build :noexport:
>
> #+BEGIN_SRC emacs-lisp :results silent
> (let ((org-export-before-parsing-hook '(org-ref-cite-natmove ;; do this
> first
> org-ref-csl-preprocess-buffer
> org-ref-refproc)))
>   (org-open-file (org-odt-export-to-odt) 'system))
> #+END_SRC
>
>
> On Wed, Dec 15, 2021 at 10:16 PM John Kitchin <jkitchin@andrew.cmu.edu>
> wrote:
>
>> That code does not belong in your .emacs file. It should be in an
>> emacs-lisp block in your org-file like it is in the example. You should run
>> it from the org file.
>>
>>
>>
>>
>> John
>>
>> -----------------------------------
>> Professor John Kitchin (he/him/his)
>> Doherty Hall A207F
>> Department of Chemical Engineering
>> Carnegie Mellon University
>> Pittsburgh, PA 15213
>> 412-268-7803
>> @johnkitchin
>> http://kitchingroup.cheme.cmu.edu
>>
>>
>>
>> On Wed, Dec 15, 2021 at 5:12 PM Xianwen Chen (陈贤文) <
>> xianwen.chen@gmail.com> wrote:
>>
>>> Thank you all for the responses. I have to upgrade from orgmode 9.4.4 to
>>> 9.5 first, to try out org-cite.
>>>
>>> I tried
>>> https://github.com/jkitchin/org-ref/blob/master/examples/basic-csl.org#opendocument.
>>> I added the following codes to my .emacs:
>>>
>>> (let ((org-export-before-parsing-hook '(org-ref-cite-natmove ;; do this
>>> first
>>> org-ref-csl-preprocess-buffer
>>> org-ref-refproc)))
>>>   (org-open-file (org-odt-export-to-odt) 'system))
>>>
>>> I tried to eval-region, after selecting these codes. I got the complain
>>> that org-ref-cite-natmove's function definition is void.
>>>
>>> Do I need to install or require something other than cite-ref?
>>>
>>> Xianwen
>>>
>>> On Thu, Dec 9, 2021 at 2:57 PM John Kitchin <jkitchin@andrew.cmu.edu>
>>> wrote:
>>>
>>>> If you are trying to use org-ref for this see
>>>> https://www.youtube.com/watch?v=rRR-5NSpKyE and this example:
>>>> https://github.com/jkitchin/org-ref/blob/master/examples/basic-csl.org#opendocument.
>>>> You need to use a preprocessing hook (org-ref-csl-preprocess-buffer) with
>>>> org-ref to get the citations and bibliography .
>>>> John
>>>>
>>>> -----------------------------------
>>>> Professor John Kitchin (he/him/his)
>>>> Doherty Hall A207F
>>>> Department of Chemical Engineering
>>>> Carnegie Mellon University
>>>> Pittsburgh, PA 15213
>>>> 412-268-7803
>>>> @johnkitchin
>>>> http://kitchingroup.cheme.cmu.edu
>>>>
>>>>
>>>>
>>>> On Thu, Dec 9, 2021 at 4:54 AM Xianwen Chen (陈贤文) <
>>>> xianwen.chen@gmail.com> wrote:
>>>>
>>>>> I have been using org-ref and biblatex. They export well to PDF,
>>>>> through LaTeX. I am able to export to ODT as well. However, I'm not able to
>>>>> have the bibliography or the references in the produced ODT.
>>>>>
>>>>> I searched online and found this tutorial:
>>>>> https://kjambunathan.github.io/org-mode-ox-odt/Bibliography-and-Citations-in-ODT-export.html.
>>>>> However, when following through the tutorial, I wasn't able to find
>>>>> ox-jabref.
>>>>>
>>>>> Thinking about the new org-cite, which is orgmode's native citation
>>>>> solution, I'm wondering if it would be easier to use org-cite within
>>>>> orgmode and export to ODT? A small example with configuration suggestion
>>>>> will be highly appreciated!
>>>>>
>>>>> Xianwen
>>>>>
>>>>

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Re: org-cite and export to ODT

[Xianwen Chen (陈贤文)]

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Thank you John. I tried to C-c C-e. I was reminded that
org-ref-cite-natmove's function definition is void.

I also don't have functions that start with org-ref-export. I suspect that
I didn't load a file or package.

Bruce and András, I upgraded org-mode on my system to 9.5. org-cite works
after I added

(require 'oc)

Your examples work. I also noticed that I didn't need the following line:

 #+cite_export: csl

Xianwen

On Thu, Dec 16, 2021 at 12:50 AM John Kitchin <jkitchin@andrew.cmu.edu>
wrote:

> you are still not getting the directions. You don't export with C-c Ce oo
> here. You run that src block by putting your cursor in it and typing C-c
> C-c to run it.
>
> For org-ref, you have to use a preprocessing hook to replace the cite
> links with the csl derived links before the export is done. That is what
> the src block does. It temporarily defines org-export-before-parsing-hook
> to run those three hook functions before making an odt file.
>
> Alternatively you can do C-c C-e ro which will use the org-ref exporter
> that at least runs the  org-ref csl preprocessor.
>
> John
>
> -----------------------------------
> Professor John Kitchin (he/him/his)
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu
>
>
>
> On Wed, Dec 15, 2021 at 6:58 PM Xianwen Chen (陈贤文) <xianwen.chen@gmail.com>
> wrote:
>
>> Thank you John. I'm not sure why it does not work. Below is the minimal
>> example I created, using your example. I ran C-e o o to export to ODT. The
>> resulted ODT file didn't have the reference.
>>
>> #+title: A basic example of org-ref for csl export
>> #+options: toc:nil
>> #+csl-style: apa-5th-edition.csl
>> #+csl-locale: en-US
>>
>> * Bibliography
>>
>> bibliography:~/data/library/bibliography/biblatex/biblatex.bib
>>
>> cite:bayulken-et-al-2020-nbs-climate_change-pandemics
>>
>> * build :noexport:
>>
>> #+BEGIN_SRC emacs-lisp :results silent
>> (let ((org-export-before-parsing-hook '(org-ref-cite-natmove ;; do this
>> first
>> org-ref-csl-preprocess-buffer
>> org-ref-refproc)))
>>   (org-open-file (org-odt-export-to-odt) 'system))
>> #+END_SRC
>>
>>
>> On Wed, Dec 15, 2021 at 10:16 PM John Kitchin <jkitchin@andrew.cmu.edu>
>> wrote:
>>
>>> That code does not belong in your .emacs file. It should be in an
>>> emacs-lisp block in your org-file like it is in the example. You should run
>>> it from the org file.
>>>
>>>
>>>
>>>
>>> John
>>>
>>> -----------------------------------
>>> Professor John Kitchin (he/him/his)
>>> Doherty Hall A207F
>>> Department of Chemical Engineering
>>> Carnegie Mellon University
>>> Pittsburgh, PA 15213
>>> 412-268-7803
>>> @johnkitchin
>>> http://kitchingroup.cheme.cmu.edu
>>>
>>>
>>>
>>> On Wed, Dec 15, 2021 at 5:12 PM Xianwen Chen (陈贤文) <
>>> xianwen.chen@gmail.com> wrote:
>>>
>>>> Thank you all for the responses. I have to upgrade from orgmode 9.4.4
>>>> to 9.5 first, to try out org-cite.
>>>>
>>>> I tried
>>>> https://github.com/jkitchin/org-ref/blob/master/examples/basic-csl.org#opendocument.
>>>> I added the following codes to my .emacs:
>>>>
>>>> (let ((org-export-before-parsing-hook '(org-ref-cite-natmove ;; do this
>>>> first
>>>> org-ref-csl-preprocess-buffer
>>>> org-ref-refproc)))
>>>>   (org-open-file (org-odt-export-to-odt) 'system))
>>>>
>>>> I tried to eval-region, after selecting these codes. I got the complain
>>>> that org-ref-cite-natmove's function definition is void.
>>>>
>>>> Do I need to install or require something other than cite-ref?
>>>>
>>>> Xianwen
>>>>
>>>> On Thu, Dec 9, 2021 at 2:57 PM John Kitchin <jkitchin@andrew.cmu.edu>
>>>> wrote:
>>>>
>>>>> If you are trying to use org-ref for this see
>>>>> https://www.youtube.com/watch?v=rRR-5NSpKyE and this example:
>>>>> https://github.com/jkitchin/org-ref/blob/master/examples/basic-csl.org#opendocument.
>>>>> You need to use a preprocessing hook (org-ref-csl-preprocess-buffer) with
>>>>> org-ref to get the citations and bibliography .
>>>>> John
>>>>>
>>>>> -----------------------------------
>>>>> Professor John Kitchin (he/him/his)
>>>>> Doherty Hall A207F
>>>>> Department of Chemical Engineering
>>>>> Carnegie Mellon University
>>>>> Pittsburgh, PA 15213
>>>>> 412-268-7803
>>>>> @johnkitchin
>>>>> http://kitchingroup.cheme.cmu.edu
>>>>>
>>>>>
>>>>>
>>>>> On Thu, Dec 9, 2021 at 4:54 AM Xianwen Chen (陈贤文) <
>>>>> xianwen.chen@gmail.com> wrote:
>>>>>
>>>>>> I have been using org-ref and biblatex. They export well to PDF,
>>>>>> through LaTeX. I am able to export to ODT as well. However, I'm not able to
>>>>>> have the bibliography or the references in the produced ODT.
>>>>>>
>>>>>> I searched online and found this tutorial:
>>>>>> https://kjambunathan.github.io/org-mode-ox-odt/Bibliography-and-Citations-in-ODT-export.html.
>>>>>> However, when following through the tutorial, I wasn't able to find
>>>>>> ox-jabref.
>>>>>>
>>>>>> Thinking about the new org-cite, which is orgmode's native citation
>>>>>> solution, I'm wondering if it would be easier to use org-cite within
>>>>>> orgmode and export to ODT? A small example with configuration suggestion
>>>>>> will be highly appreciated!
>>>>>>
>>>>>> Xianwen
>>>>>>
>>>>>

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Re: org-cite and export to ODT

[Eric S Fraga]

On Wednesday, 15 Dec 2021 at 23:57, Xianwen Chen (陈贤文) wrote:
> Thank you John. I'm not sure why it does not work. Below is the
> minimal example I created, using your example. I ran C-e o o to export
> to ODT. The resulted ODT file didn't have the reference.

I don't use org-ref but, just in case this helps, the new cite engine
needs a line asking to generate the actual bibliography, i.e.

#+printbibliography:

at the point in your document where you want it to apear.

-- 
: Eric S Fraga, with org release_9.5.1-254-g14ed65 in Emacs 29.0.50
: Latest paper written in org: https://arxiv.org/abs/2106.05096