Re: org-cite and export to ODT
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
Re: org-cite and export to ODT
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 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) > 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 >> 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.c...@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 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.c...@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
Re: org-cite and export to ODT
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) 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 > 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.c...@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 >>> 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.c...@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 >
Re: org-cite and export to ODT
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 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) > 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 >> 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.c...@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 >>>
Re: org-cite and export to ODT
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) 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 > 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) >> 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 >>> >>
Re: org-cite and export to ODT
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 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) > 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 >> >
Re: org-cite and export to ODT
Dear All, On Thu, 9 Dec 2021 at 10:54, Xianwen Chen (陈贤文) 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
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) 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 >
