Re: [O] org-ref exports nicely to html but not to odt
On Saturday, 5 Jan 2019 at 16:59, Uwe Brauer wrote: > Thanks, right now I am struggling to install the pandoc-citeproc > filter. On Debian, it's its own package so easy but I do know that, at least in the past, the version on Debian was quite significantly behind upstream. This may or may not matter to you, of course. -- Eric S Fraga via Emacs 27.0.50, Org release_9.1.14-1035-gfeb442
Re: [O] org-ref exports nicely to html but not to odt
>>> "Eric" == Eric S Fraga writes: > I use the following (attached) script to convert LaTeX files (usually > generated by org) to docx. It sometimes works well, or at least well > enough for my uses. Maybe you can adapt it to your needs. Thanks, right now I am struggling to install the pandoc-citeproc filter. smime.p7s Description: S/MIME cryptographic signature
Re: [O] org-ref exports nicely to html but not to odt
I use the following (attached) script to convert LaTeX files (usually
generated by org) to docx. It sometimes works well, or at least well
enough for my uses. Maybe you can adapt it to your needs.
--
Eric S Fraga via Emacs 27.0.50, Org release_9.1.14-1035-gfeb442
#!/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 " $CSL
pandoc --bibliography=/home/ucecesf/synced/share/texmf/bibtex/bib/bibliography.bib --csl=${CSL} --filter pandoc-citeproc ${BASE}.tex -o ${BASE}.docx
#pandoc --bibliography=/home/ucecesf/share/texmf/bibtex/bib/papers.bib --csl=/home/ucecesf/synced/share/citation.styles/elsevier-with-titles.csl --filter pandoc-citeproc ${BASE}.tex -o ${BASE}.docx
Re: [O] org-ref exports nicely to html but not to odt
> I have used pandoc a little a while ago. See > http://kitchingroup.cheme.cmu.edu/blog/2015/01/29/Export-org-mode-to-docx-with-citations-via-pandoc/ > If you search pandoc on my blog you may find some more. Thanks for pointing that out I did visit your blog. The resulting docx does not contain hyperref links to the references, as far as I can see. smime.p7s Description: S/MIME cryptographic signature
Re: [O] org-ref exports nicely to html but not to odt
>>> "Ken" == Ken Mankoff writes: > On 2019-01-04 at 22:37 +0100, Uwe Brauer wrote: >> I exported the org file in question to latex (I could also start >> directly with latex for that matter.) > Yes. >> Could I stick with bibtex? > Yes. No need to use biber + biblatex, you can stick with bibtex. > I only run that command because my massive 3000+ bib file contains > things that pandoc has trouble with (accents? Not sure). That command > extracts the bibtex entries used in the current document. > As I write this I realize this means you don't even need to compile > the PDF and/or run bibtex. If you have a TeX file and an appropriate > accompanying BiBTeX file, that should work. >> pandoc -f latex -t docx -o test.docx --bibliography /home/oub/texmf/bibtex/bib/bibgraf.bib test.tex >> >> /home/oub/texmf/bibtex/bib/bibgraf.bib is my main bibtex date base. >> >> But this did not work pandoc gets frozen. >> >> What do I miss. > I don't know. Try with a small bib file with 1 entry (and a TeX file > that only cites that one entry). Does that work? Then maybe your > bibgraf.bib has the same problem mine does (although I recall pandoc > issuing an error and crashing, not just freezing). I tried that and it did not work neither, I might need to write the pandoc list. smime.p7s Description: S/MIME cryptographic signature
Re: [O] org-ref exports nicely to html but not to odt
On 2019-01-04 at 22:37 +0100, Uwe Brauer wrote: > I exported the org file in question to latex (I could also start > directly with latex for that matter.) Yes. > Could I stick with bibtex? Yes. No need to use biber + biblatex, you can stick with bibtex. I only run that command because my massive 3000+ bib file contains things that pandoc has trouble with (accents? Not sure). That command extracts the bibtex entries used in the current document. As I write this I realize this means you don't even need to compile the PDF and/or run bibtex. If you have a TeX file and an appropriate accompanying BiBTeX file, that should work. > pandoc -f latex -t docx -o test.docx --bibliography > /home/oub/texmf/bibtex/bib/bibgraf.bib test.tex > > /home/oub/texmf/bibtex/bib/bibgraf.bib is my main bibtex date base. > > But this did not work pandoc gets frozen. > > What do I miss. I don't know. Try with a small bib file with 1 entry (and a TeX file that only cites that one entry). Does that work? Then maybe your bibgraf.bib has the same problem mine does (although I recall pandoc issuing an error and crashing, not just freezing). If this method works with a MWE, then the issue my be your full bib file. In this case you need to extract the entries used in this document (e.g. my method). Presumably this subset does not cause the pandoc issue. I also find extracting the entries useful for archiving a project. You can extract entries as I showed, or "bibexport .aux" (requires a compiled PDF), or http://korrekt.org/page/Note:How_to_Extract_Used_Entries_From_BibTeX_Files or other methods... -k.
Re: [O] org-ref exports nicely to html but not to odt
I have used pandoc a little a while ago. See http://kitchingroup.cheme.cmu.edu/blog/2015/01/29/Export-org-mode-to-docx-with-citations-via-pandoc/ If you search pandoc on my blog you may find some more. On Fri, Jan 4, 2019 at 5:28 PM Uwe Brauer wrote: > >>> "Ken" == Ken Mankoff writes: > >> On 2019-01-04 at 22:37 +0100, Uwe Brauer wrote: >>> I exported the org file in question to latex (I could also start >>> directly with latex for that matter.) > >> Yes. > >>> Could I stick with bibtex? > >> Yes. No need to use biber + biblatex, you can stick with bibtex. > >> I only run that command because my massive 3000+ bib file contains >> things that pandoc has trouble with (accents? Not sure). That command >> extracts the bibtex entries used in the current document. > >> As I write this I realize this means you don't even need to compile >> the PDF and/or run bibtex. If you have a TeX file and an appropriate >> accompanying BiBTeX file, that should work. > >>> pandoc -f latex -t docx -o test.docx --bibliography > /home/oub/texmf/bibtex/bib/bibgraf.bib test.tex >>> >>> /home/oub/texmf/bibtex/bib/bibgraf.bib is my main bibtex date base. >>> >>> But this did not work pandoc gets frozen. >>> >>> What do I miss. > >> I don't know. Try with a small bib file with 1 entry (and a TeX file >> that only cites that one entry). Does that work? Then maybe your >> bibgraf.bib has the same problem mine does (although I recall pandoc >> issuing an error and crashing, not just freezing). > > > I tried that and it did not work neither, I might need to write the > pandoc list. > -- John --- 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: [O] org-ref exports nicely to html but not to odt
>>> "Ken" == Ken Mankoff writes: > On 2019-01-04 at 18:08 +0100, Uwe Brauer wrote: >> When I export it to html, the bibliography comes out nice. When I >> export it to odt, the resulting odt files contains a lot of rubbish. >> >> A kludge is to export it to html and then open it with LO/OO and copy >> it in an empty odt file, but is there any other solution? > I find the best ODT comes from LaTeX -> pandoc -> ODT. I have the > following section at the bottom of my default Org template > workbook. That sounds very promising. But I am a bit confused. I exported the org file in question to latex (I could also start directly with latex for that matter.) Now I can run without a problem bibtex on that file and several times latex. But you propose to use biber which I have never used. So when I run in the command line biber test.tex --output_format bibtex INFO - This is Biber 2.4 INFO - Logfile is 'test.tex.blg' ERROR - Cannot find control file 'test.tex.bcf'! - did you pass the "backend=biber" option to BibLaTeX? INFO - ERRORS: 1 Could I stick with bibtex? Now suppse I can then I tried pandoc -f latex -t docx -o test.docx --bibliography /home/oub/texmf/bibtex/bib/bibgraf.bib test.tex /home/oub/texmf/bibtex/bib/bibgraf.bib is my main bibtex date base. But this did not work pandoc gets frozen. What do I miss. Thanks Uwe smime.p7s Description: S/MIME cryptographic signature
Re: [O] org-ref exports nicely to html but not to odt
On 2019-01-04 at 18:08 +0100, Uwe Brauer wrote:
> When I export it to html, the bibliography comes out nice. When I
> export it to odt, the resulting odt files contains a lot of rubbish.
>
> A kludge is to export it to html and then open it with LO/OO and copy
> it in an empty odt file, but is there any other solution?
I find the best ODT comes from LaTeX -> pandoc -> ODT. I have the following
section at the bottom of my default Org template workbook.
-k.
* DOCX :noexport:
Exporting to DOCX by using pandoc to convert the LaTeX export to DOCX seems to
work much better than using Org directly. This means you need to export to
LaTeX, properly compile the latex (to get the references correct), then run the
BibTeX code block below 1x (and re-run each time you update any references),
then run the Pandoc code block to convert the TeX file to DOCX.
** BibTeX :noexport:
#+BEGIN_SRC sh :results verbatim :var fn=(file-name-sans-extension
(buffer-name))
biber ${fn} --output_format bibtex
#+END_SRC
#+RESULTS:
** Pandoc
#+BEGIN_SRC sh :results verbatim :var fn=(file-name-sans-extension
(buffer-name))
pandoc -f latex -t docx -o ${fn}.docx --bibliography ./${fn}_biber.bib ${fn}.tex
#+END_SRC
#+RESULTS:
Re: [O] org-ref exports nicely to html but not to odt
It is identical to the html output, it just that odt doesn't render the html tags. You can just customize that variable to get rid of the html markers, and then it will look better. I don't know how to get bold/italics in odt though. John --- 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 On Fri, Jan 4, 2019 at 3:43 PM Uwe Brauer wrote: > >>> "John" == John Kitchin writes: > >> Export to backends other than LaTeX have pretty limited support. >> I assume by a lot of rubbish you mean there is a lot of html markers > in >> the bibliography. > > Right. > >> You can customize how these are formatted to some extent in the >> variable: org-ref-bibliography-entry-format > >> This is not a citation preprocessor though, so it will not do things >> like numbered references, or handle markup in the bibtex entries. > > I would be happy if the odt output were similar or identical to the > html output. > > >> You might check out https://github.com/andras-simonyi/citeproc-org, > it >> might have more capability along those lines. > > Thanks > >
Re: [O] org-ref exports nicely to html but not to odt
>>> "John" == John Kitchin writes: > Export to backends other than LaTeX have pretty limited support. > I assume by a lot of rubbish you mean there is a lot of html markers in > the bibliography. Right. > You can customize how these are formatted to some extent in the > variable: org-ref-bibliography-entry-format > This is not a citation preprocessor though, so it will not do things > like numbered references, or handle markup in the bibtex entries. I would be happy if the odt output were similar or identical to the html output. > You might check out https://github.com/andras-simonyi/citeproc-org, it > might have more capability along those lines. Thanks smime.p7s Description: S/MIME cryptographic signature
Re: [O] org-ref exports nicely to html but not to odt
Export to backends other than LaTeX have pretty limited support. I assume by a lot of rubbish you mean there is a lot of html markers in the bibliography. You can customize how these are formatted to some extent in the variable: org-ref-bibliography-entry-format This is not a citation preprocessor though, so it will not do things like numbered references, or handle markup in the bibtex entries. You might check out https://github.com/andras-simonyi/citeproc-org, it might have more capability along those lines. Uwe Brauer writes: > Hi > > Please look at the following example > > #+begin_example > * Bibliography > > citep:tao08:_global > > bibliographystyle:plain > bibliography:test.bib > > #+end_example > > When I export it to html, the bibliography comes out nice. > When I export it to odt, the resulting odt files contains a lot of > rubbish. > > A kludge is to export it to html and then open it with LO/OO and copy > it in an empty odt file, but is there any other solution? > > regards > > Uwe Brauer -- 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
