org-cite and pandoc

org-cite and pandoc

[Eric S Fraga]

Dear list,

I am needing to export a document, written in org using the new cite
syntax, to pandoc (native).  The export fails.  I realise that org-cite
is new and I don't expect the export to process any [cite:@key] lines
properly but it would be good to have the export at least generate a
pandoc file I can then work with.  Is this possible?

I recognise fully that ox-pandoc is in contrib so I don't expect
anything as such!  In the meantime, I'll simply remove all [cite:]
entries but I thought I'd raise this issue.

The error (with paths elided and lines truncated) I get is:

--8<---------------cut here---------------start------------->8---
Debugger entered--Lisp error: (wrong-type-argument stringp ("..."))
  split-string(("...") "\n")
  (cons (car it) (split-string val "\n"))
  (list (cons (car it) (split-string val "\n")))
  (progn (list (cons (car it) (split-string val "\n"))))
  (if val (progn (list (cons (car it) (split-string val "\n")))))
  (let ((val (plist-get info (cdr it)))) (if val (progn (list (cons (car it) (split-string val "\n"))))))
  (closure ((info :export-options nil :back-end ...
  mapcar((closure ((info :export-options nil :back-end #s(org-export-backend :name pandoc
  (apply 'append (mapcar #'(lambda (it) (ignore it) (let ((val (plist-get info ...)))
  (org-pandoc-put-options (apply 'append (mapcar #'(lambda (it) (ignore it) 
  org-pandoc-template(#("#+cite_export: natbi..." [...]))
  org-export-as(pandoc nil nil nil (:output-file "paper.tmpLAj6YU.org"))
  org-export-to-file(pandoc "paper.tmpLAj6YU.org" 
  org-pandoc-export(native nil nil nil nil nil 0)
  org-pandoc-export-to-native-and-open(nil nil nil nil)
  org-export-dispatch(nil)
  funcall-interactively(org-export-dispatch nil)
  command-execute(org-export-dispatch)
--8<---------------cut here---------------end--------------->8---


Thank you,
eric

-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-607-g185706
: Latest paper written in org: https://arxiv.org/abs/2106.05096

Re: org-cite and pandoc

[Bruce D'Arcus]

Yeah, ideally ox-pandoc would be updated to support org-cite.

I also, FYI, submitted an issue to pandoc awhile ago to update it's
org-cite support (it has support for an early draft).

https://github.com/jgm/pandoc/issues/7329

On Thu, Aug 5, 2021 at 10:07 AM Eric S Fraga <e.fraga@ucl.ac.uk> wrote:
>
> Dear list,
>
> I am needing to export a document, written in org using the new cite
> syntax, to pandoc (native).  The export fails.  I realise that org-cite
> is new and I don't expect the export to process any [cite:@key] lines
> properly but it would be good to have the export at least generate a
> pandoc file I can then work with.  Is this possible?
>
> I recognise fully that ox-pandoc is in contrib so I don't expect
> anything as such!  In the meantime, I'll simply remove all [cite:]
> entries but I thought I'd raise this issue.
>
> The error (with paths elided and lines truncated) I get is:
>
> --8<---------------cut here---------------start------------->8---
> Debugger entered--Lisp error: (wrong-type-argument stringp ("..."))
>   split-string(("...") "\n")
>   (cons (car it) (split-string val "\n"))
>   (list (cons (car it) (split-string val "\n")))
>   (progn (list (cons (car it) (split-string val "\n"))))
>   (if val (progn (list (cons (car it) (split-string val "\n")))))
>   (let ((val (plist-get info (cdr it)))) (if val (progn (list (cons (car it) (split-string val "\n"))))))
>   (closure ((info :export-options nil :back-end ...
>   mapcar((closure ((info :export-options nil :back-end #s(org-export-backend :name pandoc
>   (apply 'append (mapcar #'(lambda (it) (ignore it) (let ((val (plist-get info ...)))
>   (org-pandoc-put-options (apply 'append (mapcar #'(lambda (it) (ignore it)
>   org-pandoc-template(#("#+cite_export: natbi..." [...]))
>   org-export-as(pandoc nil nil nil (:output-file "paper.tmpLAj6YU.org"))
>   org-export-to-file(pandoc "paper.tmpLAj6YU.org"
>   org-pandoc-export(native nil nil nil nil nil 0)
>   org-pandoc-export-to-native-and-open(nil nil nil nil)
>   org-export-dispatch(nil)
>   funcall-interactively(org-export-dispatch nil)
>   command-execute(org-export-dispatch)
> --8<---------------cut here---------------end--------------->8---
>
>
> Thank you,
> eric
>
> --
> : Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-607-g185706
> : Latest paper written in org: https://arxiv.org/abs/2106.05096
>

Re: org-cite and pandoc

[Eric S Fraga]

On Thursday,  5 Aug 2021 at 10:13, Bruce D'Arcus wrote:
> Yeah, ideally ox-pandoc would be updated to support org-cite.

Indeed but even exporting without error would be good, assuming of
course that the error I reported is actually due to org-cite.  It might
not be; I've never exported to pandoc before!  This is for a journal
that expects submissions in pandoc (never had this before) which (in
some ways) is nice as at least it's not Word...
-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-607-g185706
: Latest paper written in org: https://arxiv.org/abs/2106.05096

Re: org-cite and pandoc

[András Simonyi]

Perhaps a useful workaround would be to first "export to Org" (with
org-org-export-as-org)?
AFAICS this replaces the Org cites with their export
processor-rendered counterparts, e.g.,
with suitable Natbib cite commands when the
#+cite_export: natbib
line is used.

best regards,
András

On Thu, 5 Aug 2021 at 16:41, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> Indeed but even exporting without error would be good, assuming of
> course that the error I reported is actually due to org-cite.  It might
> not be; I've never exported to pandoc before!  This is for a journal
> that expects submissions in pandoc (never had this before) which (in
> some ways) is nice as at least it's not Word...
> --
> : Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-607-g185706
> : Latest paper written in org: https://arxiv.org/abs/2106.05096
>

Re: org-cite and pandoc

[Eric S Fraga]

On Thursday,  5 Aug 2021 at 17:00, András Simonyi wrote:
> Perhaps a useful workaround would be to first "export to Org" (with
> org-org-export-as-org)?

Excellent suggestion!  Thank you.

Doing so clearly indicates that my problem is *not* with org-cite but
with ox-pandoc.  Strange.

I had mentioned that ox-pandoc was in org-contrib; it is not.  It is in
MELPA.

Okay, I will need to investigate further.  There must be something in my
configuration that is affecting ox-pandoc as others seem to be using it
just fine.

Thanks again,
eric

-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-607-g185706
: Latest paper written in org: https://arxiv.org/abs/2106.05096

Re: org-cite and pandoc

[Eric S Fraga]

After some investigation...

It seems that the presence of the #+bibliography: line is what causes
ox-pandoc to fail.  Removing this line is sufficient for me to get the
export working.

Thanks again,
eric

-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-607-g185706
: Latest paper written in org: https://arxiv.org/abs/2106.05096

Re: org-cite and pandoc

[Eric S Fraga]

By the way, ox-md also fails if there is a #+bibliography
line.  Removing it allows for the export.  Very strange.

-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-607-g185706
: Latest paper written in org: https://arxiv.org/abs/2106.05096

Re: org-cite and pandoc

[Nicolas Goaziou]

Hello,

Eric S Fraga <e.fraga@ucl.ac.uk> writes:

> By the way, ox-md also fails if there is a #+bibliography
> line.  Removing it allows for the export.  Very strange.

Would you have an ECM? I cannot reproduce it.

Regards,
-- 
Nicolas Goaziou

Re: org-cite and pandoc

[Eric S Fraga]

On Saturday,  7 Aug 2021 at 22:09, Nicolas Goaziou wrote:
> Would you have an ECM? I cannot reproduce it.

Unfortunately, I cannot reproduce it with emacs -Q [1].  Has to be
something in my configuration but I have no idea what.  No time at
present to bisect etc. but I will in due course hopefully.

Sorry for the noise.

thank you,
eric

Footnotes:
[1] the one real disadvantage of using Emacs as my window manager,
     i.e. exwm, is the hassle involved in actually running Emacs with
     -Q. :-(

-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-617-g926dba
: Latest paper written in org: https://arxiv.org/abs/2106.05096

Re: org-cite and pandoc

[Bruce D'Arcus]

On Thu, Aug 5, 2021 at 10:41 AM Eric S Fraga <e.fraga@ucl.ac.uk> wrote:
> This is for a journal that expects submissions in pandoc (never had this before) which (in
> some ways) is nice as at least it's not Word...

Never heard of that before either; very cool!

Bruce

Re: org-cite and pandoc

[Eric S Fraga]

On Thursday,  5 Aug 2021 at 11:29, Bruce D'Arcus wrote:
> Never heard of that before either; very cool!

See my update... <blush> markdown, not pandoc.  Although pandoc's native
format is quite useful, just not readable. ;-)

-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-607-g185706
: Latest paper written in org: https://arxiv.org/abs/2106.05096

Re: org-cite and pandoc

[Eric S Fraga]

On Thursday,  5 Aug 2021 at 15:41, Eric S Fraga wrote:
> that expects submissions in pandoc (never had this before) which (in

Ignore this, by the way; I meant to type markdown, not pandoc.

-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-607-g185706
: Latest paper written in org: https://arxiv.org/abs/2106.05096