Pandoc Full Support For JATSXML Specification?

[aerithnetzer]

Hello,

This may be a simple question, we are currently building a product that will aid in the discovery of data and code affiliated with academic articles. I am unsure if Pandoc currently supports the full JATSXML code specification. It seems in the documentation that some elements are not writable. Does there happen to be any work/documentation on this? I am happy to help with a PR if needed.

Thanks!

[jgm]

First it would help to know whether you are talking about reading JATS or writing it. I assume you're talking about reading JATS? The pandoc AST is strictly less expressive than JATSXML, so inevitably some distinctions will be lost when reading JATS with pandoc.

[aerithnetzer]

I may be misunderstanding the JATS specification, so forgive me if I am. Yes, the code element link you refer to is the correct tag I am referring to. But, according to the documentation says that the code element may be contained in the supplementary-material tag, which itself may be contained in the article-meta tag. To me, this means that the code element you refer to can in fact be part of the metadata. For our library's use case (attempting to create articles that are interlinked with the code and data used in the article), code that is meant to supplement the article, say, for reproducibility, it does make sense to use it as metadata. Given this, is there a way to represent this in markdown YAML?

Hopefully this makes more sense/context.

[jgm]

That helps. Can you give a short snippet of the sort of XML you're hoping to generate?

[aerithnetzer]

Hello! Sorry for delayed reply, out of town. Hope you had a good weekend.

      
<!-- ...XML header info-->
<article-meta>      
      <supplementary-material>
        <!-- Other supplementary materials-->
        <code>
          <!-- Link to github url where repo can be used to aid in study reproducibility, etc. -->
          <ext-link ext-link-type="uri" xlink:href="github.com/aerithnetzer/somegithubrepo"></ext-link>
        </code>
    </supplementary-material>
</article-meta>
<!-- Rest of the document... -->

This is what I am hoping to generate.

[jgm]

As far as I can tell, supplementary-material is only allowed in article-meta, not journal-meta, so I will add it to the default template only for -t jats_articleauthoring.

Once it is added, you'll be able to get what you want with pandoc -t jats_articleauthoring -s using:

---
title: My Title
supplementary-material: |
  ```{=jats}               
  <code>
    <ext-link ext-link-type="uri" xlink:href="github.com/aerithnetzer/somegithubrepo"></ext-link>
  </code>
  ```
...

[aerithnetzer]

Awesome, thanks a ton