Preserving citations between docx and markdown conversions

Preserving citations between docx and markdown conversions

[Alex]

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Hello! I am investigating using pandoc for my academic writing. I intend to 
do the majority of the writing in markdown but will have others reviewing 
and giving feedback through word (docx), and would like a way to 
re-integrate the edits back to markdown while keeping the text as close as 
possible. (md -> docx -> md)

In my markdown I have citations using the [@citekey] format:

Here is a reference to one of the entries in my bibliography [@Aigrain2021].

I would like a way to preserve citations when converting between docx and 
md.
I've tried the following approach but just get plain text (in the markdown) 
where the citation was.

Here is a reference to one of the entries in my bibliography (Aigrain
2021).

I am not sure whether the citations are being lost in the md to docx step 
or the docx to md step. (I am not familiar with the how word even stores 
citations)

Is what I want to do supported?
I have the files:
main.md
main.bib
nature-conservation.csl

The command I'm using to convert to docx (md -> docx):
pandoc --citeproc \
--bibliography main.bib \
--csl nature-conservation.csl \
-t docx+citations -o main.docx \
-f markdown+citations main.md

The command I'm using to convert back to markdown:
pandoc -s --citeproc \
--bibliography main.bib \
--csl nature-conservation.csl \
-t markdown+citations -o main.md \
-f docx+citations main.docx

Any ideas would be much appreciated. Thanks!

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[-- Attachment #2: nature-conservation.csl --]
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<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" version="1.0" default-locale="en-US">
  <!-- Pensoft Publishers, generated from "pensoft" metadata at https://github.com/citation-style-language/journals -->
  <info>
    <title>Nature Conservation</title>
    <id>http://www.zotero.org/styles/nature-conservation</id>
    <link href="http://www.zotero.org/styles/nature-conservation" rel="self"/>
    <link href="http://www.zotero.org/styles/pensoft-journals" rel="independent-parent"/>
    <link href="https://natureconservation.pensoft.net/about#CitationsandReferences" rel="documentation"/>
    <category citation-format="author-date"/>
    <category field="biology"/>
    <issn>1314-6947</issn>
    <eissn>1314-3301</eissn>
    <updated>2020-08-21T04:17:30+00:00</updated>
    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
  </info>
</style>

[-- Attachment #3: main.bib --]
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@article{Aigrain2021,
    title = {Beginner's Guide to next-Generation Sequencing},
    author = {Aigrain, Louise},
    date = {2021-12},
    journaltitle = {The Biochemist},
    volume = {43},
    number = {6},
    pages = {58--64},
    issn = {0954-982X},
    doi = {10.1042/bio_2021_135},
    url = {https://portlandpress.com/biochemist/article/43/6/58/229924/Beginner-s-guide-to-next-generation-sequencing},
    abstract = {Since the publication of the first draft of the human genome 20 years ago, several novel sequencing technologies have emerged. Whilst some drive the cost of DNA sequencing down, others address the difficult parts of the genome which remained inaccessible so far. But the next-generation sequencing (NGS) landscape is a fast-changing environment and one can easily get lost between second- and third- generation sequencers, or the pros and cons of short- versus long-read technologies. In this beginner's guide to NGS, we will review the main NGS technologies available in 2021. We will compare sample preparation protocols and sequencing methods, highlighting the requirements and advantages of each technology.},
}

[-- Attachment #4: main.md --]
[-- Type: text/markdown, Size: 192 bytes --]

---
title: Not Exactly a Title
subtitle: maybe
author: Yo mama
date: 14-02-2023
...

# Introduction

Here is a reference to one of the entries in my bibliography [@Aigrain2021].

# References

AW: Preserving citations between docx and markdown conversions

[denis.maier-NSENcxR/0n0]

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Pandoc will resolve citations when converting to docx. Your < -t docx+citations > seems to have no effect here.

However, there exists a filter that might be useful here: https://retorque.re/zotero-better-bibtex/exporting/pandoc/index.html#from-markdown-to-zotero-live-citations
This will enable you to convert markdown citations to Zotero fields. Obviously, this means you'll need to manage your references with Zotero.

Converting them back to Markdown citations should work out of the box since 2.18, see the changelog : https://pandoc.org/releases.html#pandoc-2.18-2022-04-04

Docx reader:

  *   Enable citations extension for docx reader (#7840<https://github.com/jgm/pandoc/issues/7840>). When enabled, Zotero, Mendeley, and EndNote citations embedded in a docx are parsed as native pandoc citations. (When disabled, the generated citation text and bibliography are passed through as regular text.) The bibliography generated by the plugin is suppressed. Instead, bibliographic data embedded in citation items is added to the references metadata field so that it can be used with --citeproc.
So, here you'll also see what the citations extension does for docx...

Best,
Denis

Von: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org <pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> Im Auftrag von Alex
Gesendet: Dienstag, 7. November 2023 10:03
An: pandoc-discuss <pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
Betreff: Preserving citations between docx and markdown conversions

Sie erhalten nicht oft eine E-Mail von ac.ringeri-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org<mailto:ac.ringeri-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>. Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification>
Hello! I am investigating using pandoc for my academic writing. I intend to do the majority of the writing in markdown but will have others reviewing and giving feedback through word (docx), and would like a way to re-integrate the edits back to markdown while keeping the text as close as possible. (md -> docx -> md)

In my markdown I have citations using the [@citekey] format:

Here is a reference to one of the entries in my bibliography [@Aigrain2021].

I would like a way to preserve citations when converting between docx and md.
I've tried the following approach but just get plain text (in the markdown) where the citation was.

Here is a reference to one of the entries in my bibliography (Aigrain
2021).

I am not sure whether the citations are being lost in the md to docx step or the docx to md step. (I am not familiar with the how word even stores citations)

Is what I want to do supported?
I have the files:
main.md
main.bib
nature-conservation.csl

The command I'm using to convert to docx (md -> docx):
pandoc --citeproc \
--bibliography main.bib \
--csl nature-conservation.csl \
-t docx+citations -o main.docx \
-f markdown+citations main.md

The command I'm using to convert back to markdown:
pandoc -s --citeproc \
--bibliography main.bib \
--csl nature-conservation.csl \
-t markdown+citations -o main.md \
-f docx+citations main.docx

Any ideas would be much appreciated. Thanks!
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Re: Preserving citations between docx and markdown conversions

[Alex]

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Thanks for your help Denis,
I think I'm starting to get a grasp on how this is working. 

If I run my document through the zotero-better-bibtex filter, then the 
docx+citations reader. I get some markdown like this:

---
...
references:
- 
...
  citation-key: Aigrain2021
...
  id: 476
---

# Introduction

Here is a reference to one of the entries in my bibliography [@476].

# References {#references .unnumbered}

It seems the zotero/better-bibtex filter is using an internal id (476) 
instead of the original citation key. I presume this is required for the 
integration between Zotero and Word.
I might try and dig in to the docx to markdown conversion to:

   1. Switch the ids of the citations back to the original citation key 
   strings.
   2. Consider exporting the 'references' metadata as a separate .bib file 
   instead of in the header.
   
On Wednesday, November 8, 2023 at 2:33:30 AM UTC+11 denis...@unibe.ch wrote:

> Pandoc will resolve citations when converting to docx. Your « -t 
> docx+citations » seems to have no effect here.
>
>  
>
> However, there exists a filter that might be useful here: 
> https://retorque.re/zotero-better-bibtex/exporting/pandoc/index.html#from-markdown-to-zotero-live-citations
>
> This will enable you to convert markdown citations to Zotero fields. 
> Obviously, this means you’ll need to manage your references with Zotero.
>
> Converting them back to Markdown citations should work out of the box 
> since 2.18, see the changelog : 
> https://pandoc.org/releases.html#pandoc-2.18-2022-04-04 
>
> Docx reader:
>
>    - Enable citations extension for docx reader (#7840 
>    <https://github.com/jgm/pandoc/issues/7840>). When enabled, Zotero, 
>    Mendeley, and EndNote citations embedded in a docx are parsed as native 
>    pandoc citations. (When disabled, the generated citation text and 
>    bibliography are passed through as regular text.) The bibliography 
>    generated by the plugin is suppressed. Instead, bibliographic data embedded 
>    in citation items is added to the references metadata field so that it 
>    can be used with --citeproc.
>
> So, here you’ll also see what the citations extension does for docx…
>
>  
>
> Best,
>
> Denis
>
>  
>
> *Von:* pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org <pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> *Im 
> Auftrag von *Alex
> *Gesendet:* Dienstag, 7. November 2023 10:03
> *An:* pandoc-discuss <pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
> *Betreff:* Preserving citations between docx and markdown conversions
>
>  
>
> Sie erhalten nicht oft eine E-Mail von ac.ri...-Re5JQEeQqe9fmgfxC/sS/w@public.gmane.org Erfahren Sie, 
> warum dies wichtig ist <https://aka.ms/LearnAboutSenderIdentification>
>
> Hello! I am investigating using pandoc for my academic writing. I intend 
> to do the majority of the writing in markdown but will have others 
> reviewing and giving feedback through word (docx), and would like a way to 
> re-integrate the edits back to markdown while keeping the text as close as 
> possible. (md -> docx -> md)
>
>  
>
> In my markdown I have citations using the [@citekey] format:
>
>  
>
> Here is a reference to one of the entries in my bibliography 
> [@Aigrain2021].
>
>  
>
> I would like a way to preserve citations when converting between docx and 
> md.
>
> I've tried the following approach but just get plain text (in the 
> markdown) where the citation was.
>
>  
>
> Here is a reference to one of the entries in my bibliography (Aigrain
> 2021).
>
>  
>
> I am not sure whether the citations are being lost in the md to docx step 
> or the docx to md step. (I am not familiar with the how word even stores 
> citations)
>
>  
>
> Is what I want to do supported?
>
> I have the files:
>
> main.md
>
> main.bib
>
> nature-conservation.csl
>
>  
>
> The command I'm using to convert to docx (md -> docx):
>
> pandoc --citeproc \
> --bibliography main.bib \
> --csl nature-conservation.csl \
> -t docx+citations -o main.docx \
> -f markdown+citations main.md
>
>  
>
> The command I'm using to convert back to markdown:
>
> pandoc -s --citeproc \
> --bibliography main.bib \
> --csl nature-conservation.csl \
> -t markdown+citations -o main.md \
> -f docx+citations main.docx
>
>  
>
> Any ideas would be much appreciated. Thanks!
>
> -- 
> You received this message because you are subscribed to the Google Groups 
> "pandoc-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/pandoc-discuss/eead1157-56fa-4259-a223-a365c852e0cbn%40googlegroups.com 
> <https://groups.google.com/d/msgid/pandoc-discuss/eead1157-56fa-4259-a223-a365c852e0cbn%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>

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AW: Preserving citations between docx and markdown conversions

[denis.maier-NSENcxR/0n0]

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I guess it works like this: When you convert from md to docx (using the filter), Zotero BBT will use the citekey to create the fields in the docx file. Here, Zotero doesn’t use citation keys, but some internal id. (You can actually have a look by inspecting the field codes.) Then, when you go back to markdown, I think this is more an issue with how pandoc’s docx reader works.

Von: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org <pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> Im Auftrag von Alex
Gesendet: Mittwoch, 8. November 2023 22:32
An: pandoc-discuss <pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
Betreff: Re: Preserving citations between docx and markdown conversions

Sie erhalten nicht oft eine E-Mail von ac.ringeri-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org<mailto:ac.ringeri-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>. Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification>
Thanks for your help Denis,
I think I'm starting to get a grasp on how this is working.

If I run my document through the zotero-better-bibtex filter, then the docx+citations reader. I get some markdown like this:
---
...
references:
-
...
  citation-key: Aigrain2021
...
  id: 476
---

# Introduction

Here is a reference to one of the entries in my bibliography [@476].

# References {#references .unnumbered}

It seems the zotero/better-bibtex filter is using an internal id (476) instead of the original citation key. I presume this is required for the integration between Zotero and Word.
I might try and dig in to the docx to markdown conversion to:

  1.  Switch the ids of the citations back to the original citation key strings.
  2.  Consider exporting the 'references' metadata as a separate .bib file instead of in the header.
On Wednesday, November 8, 2023 at 2:33:30 AM UTC+11 denis...@unibe.ch<mailto:denis...-NSENcxR/0n0@public.gmane.org> wrote:
Pandoc will resolve citations when converting to docx. Your « -t docx+citations » seems to have no effect here.

However, there exists a filter that might be useful here: https://retorque.re/zotero-better-bibtex/exporting/pandoc/index.html#from-markdown-to-zotero-live-citations
This will enable you to convert markdown citations to Zotero fields. Obviously, this means you’ll need to manage your references with Zotero.

Converting them back to Markdown citations should work out of the box since 2.18, see the changelog : https://pandoc.org/releases.html#pandoc-2.18-2022-04-04

Docx reader:

  *   Enable citations extension for docx reader (#7840<https://github.com/jgm/pandoc/issues/7840>). When enabled, Zotero, Mendeley, and EndNote citations embedded in a docx are parsed as native pandoc citations. (When disabled, the generated citation text and bibliography are passed through as regular text.) The bibliography generated by the plugin is suppressed. Instead, bibliographic data embedded in citation items is added to the references metadata field so that it can be used with --citeproc.
So, here you’ll also see what the citations extension does for docx…

Best,
Denis

Von: pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org <pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> Im Auftrag von Alex
Gesendet: Dienstag, 7. November 2023 10:03
An: pandoc-discuss <pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
Betreff: Preserving citations between docx and markdown conversions

Sie erhalten nicht oft eine E-Mail von ac.ri...-Re5JQEeQqe9fmgfxC/sS/w@public.gmane.org Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification>
Hello! I am investigating using pandoc for my academic writing. I intend to do the majority of the writing in markdown but will have others reviewing and giving feedback through word (docx), and would like a way to re-integrate the edits back to markdown while keeping the text as close as possible. (md -> docx -> md)

In my markdown I have citations using the [@citekey] format:

Here is a reference to one of the entries in my bibliography [@Aigrain2021].

I would like a way to preserve citations when converting between docx and md.
I've tried the following approach but just get plain text (in the markdown) where the citation was.

Here is a reference to one of the entries in my bibliography (Aigrain
2021).

I am not sure whether the citations are being lost in the md to docx step or the docx to md step. (I am not familiar with the how word even stores citations)

Is what I want to do supported?
I have the files:
main.md
main.bib
nature-conservation.csl

The command I'm using to convert to docx (md -> docx):
pandoc --citeproc \
--bibliography main.bib \
--csl nature-conservation.csl \
-t docx+citations -o main.docx \
-f markdown+citations main.md

The command I'm using to convert back to markdown:
pandoc -s --citeproc \
--bibliography main.bib \
--csl nature-conservation.csl \
-t markdown+citations -o main.md \
-f docx+citations main.docx

Any ideas would be much appreciated. Thanks!
--
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Re: Preserving citations between docx and markdown conversions

[Paul M.]

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Might it be simpler to leave the citekeys unprocessed during the initial
conversion to Word?

I think the citekyes format is simple enough to be self explanatory, and
the markup is no more disruptive to reading then a standard author date
citation style. You can tell your collaborators that these will be replaced
by appropriately formatted citations at the final edit stage.

On Tue, Nov 7, 2023 at 10:18 AM Alex <ac.ringeri-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:

> Hello! I am investigating using pandoc for my academic writing. I intend
> to do the majority of the writing in markdown but will have others
> reviewing and giving feedback through word (docx), and would like a way to
> re-integrate the edits back to markdown while keeping the text as close as
> possible. (md -> docx -> md)
>
> In my markdown I have citations using the [@citekey] format:
>
> Here is a reference to one of the entries in my bibliography
> [@Aigrain2021].
>
> I would like a way to preserve citations when converting between docx and
> md.
> I've tried the following approach but just get plain text (in the
> markdown) where the citation was.
>
> Here is a reference to one of the entries in my bibliography (Aigrain
> 2021).
>
> I am not sure whether the citations are being lost in the md to docx step
> or the docx to md step. (I am not familiar with the how word even stores
> citations)
>
> Is what I want to do supported?
> I have the files:
> main.md
> main.bib
> nature-conservation.csl
>
> The command I'm using to convert to docx (md -> docx):
> pandoc --citeproc \
> --bibliography main.bib \
> --csl nature-conservation.csl \
> -t docx+citations -o main.docx \
> -f markdown+citations main.md
>
> The command I'm using to convert back to markdown:
> pandoc -s --citeproc \
> --bibliography main.bib \
> --csl nature-conservation.csl \
> -t markdown+citations -o main.md \
> -f docx+citations main.docx
>
> Any ideas would be much appreciated. Thanks!
>
> --
> You received this message because you are subscribed to the Google Groups
> "pandoc-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/pandoc-discuss/eead1157-56fa-4259-a223-a365c852e0cbn%40googlegroups.com
> <https://groups.google.com/d/msgid/pandoc-discuss/eead1157-56fa-4259-a223-a365c852e0cbn%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>

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AW: Preserving citations between docx and markdown conversions

[denis.maier-NSENcxR/0n0]

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Probably a good suggestion.

Von: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org <pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> Im Auftrag von Paul M.
Gesendet: Dienstag, 7. November 2023 16:43
An: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
Betreff: Re: Preserving citations between docx and markdown conversions

Sie erhalten nicht oft eine E-Mail von pmmagic-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org<mailto:pmmagic@gmail.com>. Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification>
Might it be simpler to leave the citekeys unprocessed during the initial conversion to Word?

I think the citekyes format is simple enough to be self explanatory, and the markup is no more disruptive to reading then a standard author date citation style. You can tell your collaborators that these will be replaced by appropriately formatted citations at the final edit stage.

On Tue, Nov 7, 2023 at 10:18 AM Alex <ac.ringeri-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org<mailto:ac.ringeri-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>> wrote:
Hello! I am investigating using pandoc for my academic writing. I intend to do the majority of the writing in markdown but will have others reviewing and giving feedback through word (docx), and would like a way to re-integrate the edits back to markdown while keeping the text as close as possible. (md -> docx -> md)

In my markdown I have citations using the [@citekey] format:

Here is a reference to one of the entries in my bibliography [@Aigrain2021].

I would like a way to preserve citations when converting between docx and md.
I've tried the following approach but just get plain text (in the markdown) where the citation was.

Here is a reference to one of the entries in my bibliography (Aigrain
2021).

I am not sure whether the citations are being lost in the md to docx step or the docx to md step. (I am not familiar with the how word even stores citations)

Is what I want to do supported?
I have the files:
main.md
main.bib
nature-conservation.csl

The command I'm using to convert to docx (md -> docx):
pandoc --citeproc \
--bibliography main.bib \
--csl nature-conservation.csl \
-t docx+citations -o main.docx \
-f markdown+citations main.md

The command I'm using to convert back to markdown:
pandoc -s --citeproc \
--bibliography main.bib \
--csl nature-conservation.csl \
-t markdown+citations -o main.md \
-f docx+citations main.docx

Any ideas would be much appreciated. Thanks!
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AW: Preserving citations between docx and markdown conversions

[denis.maier-NSENcxR/0n0]

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However, while you can just omit `--citeproc` when targeting docx, once you go back you’ll end up with citations like `\[@doe\]`, i.e. brackets will be escaped in the markdown. It’s obviously easy enough to take care of that with search-replace, but it’s not a fully automatic solution.

Von: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org <pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> Im Auftrag von denis.maier-NSENcxR/0n0@public.gmane.org
Gesendet: Freitag, 10. November 2023 22:12
An: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
Betreff: AW: Preserving citations between docx and markdown conversions

Probably a good suggestion.

Von: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org<mailto:pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> <pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org<mailto:pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>> Im Auftrag von Paul M.
Gesendet: Dienstag, 7. November 2023 16:43
An: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org<mailto:pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
Betreff: Re: Preserving citations between docx and markdown conversions

Sie erhalten nicht oft eine E-Mail von pmmagic-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org<mailto:pmmagic@gmail.com>. Erfahren Sie, warum dies wichtig ist<https://aka.ms/LearnAboutSenderIdentification>
Might it be simpler to leave the citekeys unprocessed during the initial conversion to Word?

I think the citekyes format is simple enough to be self explanatory, and the markup is no more disruptive to reading then a standard author date citation style. You can tell your collaborators that these will be replaced by appropriately formatted citations at the final edit stage.

On Tue, Nov 7, 2023 at 10:18 AM Alex <ac.ringeri-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org<mailto:ac.ringeri-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>> wrote:
Hello! I am investigating using pandoc for my academic writing. I intend to do the majority of the writing in markdown but will have others reviewing and giving feedback through word (docx), and would like a way to re-integrate the edits back to markdown while keeping the text as close as possible. (md -> docx -> md)

In my markdown I have citations using the [@citekey] format:

Here is a reference to one of the entries in my bibliography [@Aigrain2021].

I would like a way to preserve citations when converting between docx and md.
I've tried the following approach but just get plain text (in the markdown) where the citation was.

Here is a reference to one of the entries in my bibliography (Aigrain
2021).

I am not sure whether the citations are being lost in the md to docx step or the docx to md step. (I am not familiar with the how word even stores citations)

Is what I want to do supported?
I have the files:
main.md
main.bib
nature-conservation.csl

The command I'm using to convert to docx (md -> docx):
pandoc --citeproc \
--bibliography main.bib \
--csl nature-conservation.csl \
-t docx+citations -o main.docx \
-f markdown+citations main.md

The command I'm using to convert back to markdown:
pandoc -s --citeproc \
--bibliography main.bib \
--csl nature-conservation.csl \
-t markdown+citations -o main.md \
-f docx+citations main.docx

Any ideas would be much appreciated. Thanks!
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Re: Preserving citations between docx and markdown conversions

[Alex]

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Thanks for the additional suggestions. I ended up writing a rough filter 
that works for my simple example: 
https://github.com/aringeri/pandoc-citation-linking/blob/main/app/Main.hs

   - The export from markdown to docx requires the better bibtex filter: 
   https://github.com/retorquere/zotero-better-bibtex/blob/master/pandoc/pandoc-zotero-live-citemarkers.lua
   - Once the docx file is created, open it up in word and hit the 'refresh 
   zotero' button, then my filter above should be able to recover the original 
   citation keys.
   
I'm not too sure this is the idiomatic way of doing it in pandoc. I'm sure 
I will develop on this as I figure out my workflow. It's good to know that 
pandoc is very customizable.
On Saturday, November 11, 2023 at 8:15:55 AM UTC+11 denis...@unibe.ch wrote:

> However, while you can just omit `--citeproc` when targeting docx, once 
> you go back you’ll end up with citations like `\[@doe\]`, i.e. brackets 
> will be escaped in the markdown. It’s obviously easy enough to take care of 
> that with search-replace, but it’s not a fully automatic solution.
>
>  
>
> *Von:* pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org <pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> *Im 
> Auftrag von *denis...-NSENcxR/0n0@public.gmane.org
> *Gesendet:* Freitag, 10. November 2023 22:12
> *An:* pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
> *Betreff:* AW: Preserving citations between docx and markdown conversions
>
>  
>
> Probably a good suggestion.
>
>  
>
> *Von:* pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org <pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> *Im 
> Auftrag von *Paul M.
> *Gesendet:* Dienstag, 7. November 2023 16:43
> *An:* pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
> *Betreff:* Re: Preserving citations between docx and markdown conversions
>
>  
>
> Sie erhalten nicht oft eine E-Mail von pmm...-Re5JQEeQqe9fmgfxC/sS/w@public.gmane.org Erfahren Sie, 
> warum dies wichtig ist <https://aka.ms/LearnAboutSenderIdentification>
>
> Might it be simpler to leave the citekeys unprocessed during the initial 
> conversion to Word? 
>
>  
>
> I think the citekyes format is simple enough to be self explanatory, and 
> the markup is no more disruptive to reading then a standard author date 
> citation style. You can tell your collaborators that these will be replaced 
> by appropriately formatted citations at the final edit stage.  
>
>  
>
> On Tue, Nov 7, 2023 at 10:18 AM Alex <ac.ri...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
>
> Hello! I am investigating using pandoc for my academic writing. I intend 
> to do the majority of the writing in markdown but will have others 
> reviewing and giving feedback through word (docx), and would like a way to 
> re-integrate the edits back to markdown while keeping the text as close as 
> possible. (md -> docx -> md)
>
>  
>
> In my markdown I have citations using the [@citekey] format:
>
>  
>
> Here is a reference to one of the entries in my bibliography 
> [@Aigrain2021].
>
>  
>
> I would like a way to preserve citations when converting between docx and 
> md.
>
> I've tried the following approach but just get plain text (in the 
> markdown) where the citation was.
>
>  
>
> Here is a reference to one of the entries in my bibliography (Aigrain
> 2021).
>
>  
>
> I am not sure whether the citations are being lost in the md to docx step 
> or the docx to md step. (I am not familiar with the how word even stores 
> citations)
>
>  
>
> Is what I want to do supported?
>
> I have the files:
>
> main.md
>
> main.bib
>
> nature-conservation.csl
>
>  
>
> The command I'm using to convert to docx (md -> docx):
>
> pandoc --citeproc \
> --bibliography main.bib \
> --csl nature-conservation.csl \
> -t docx+citations -o main.docx \
> -f markdown+citations main.md
>
>  
>
> The command I'm using to convert back to markdown:
>
> pandoc -s --citeproc \
> --bibliography main.bib \
> --csl nature-conservation.csl \
> -t markdown+citations -o main.md \
> -f docx+citations main.docx
>
>  
>
> Any ideas would be much appreciated. Thanks!
>
> -- 
> You received this message because you are subscribed to the Google Groups 
> "pandoc-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/pandoc-discuss/eead1157-56fa-4259-a223-a365c852e0cbn%40googlegroups.com 
> <https://groups.google.com/d/msgid/pandoc-discuss/eead1157-56fa-4259-a223-a365c852e0cbn%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>
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> .
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> .
>

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