iandol
commented
1 month ago Hi @bokamm, it would be easy to add the lua converter (it is a pandoc writer plugin), but pandoc does offer several native outputs already:
jats_archiving ([JATS](https://jats.nlm.nih.gov/) XML, Archiving and Interchange Tag Set)
jats_articleauthoring ([JATS](https://jats.nlm.nih.gov/) XML, Article Authoring Tag Set)
jats_publishing ([JATS](https://jats.nlm.nih.gov/) XML, Journal Publishing Tag Set)
jats (alias for jats_archiving)https://pandoc.org/MANUAL.html#option--to
The real problem is how to read the metadata. Scrivomatic uses my own filter to read academic metadata (author affiliations etc.) and I don't see how Pandoc will understand these, so we need to convert them to whatever JATs uses:
I don't yet understand if this is for read and/or write.
Here is how we can test:
1) make a simple document (save as jats.md):
---
title: A JATS Test
date: 2024-01-02
author:
- surname: Doe
given-names: Jane
orcid: XXXXXXXXXXXXX
affiliation: ioa
affiliation:
- id: ioa
organization: Inst. of Allopecia
country: Indonesia
article:
- doi: 10.234/23222.54
pmid: 3244343333
heading: testing
funding: Dept. of Thin Air
journal:
- publisher-id: JOHTEST
title: Journal of Hair
abstract: |
This is the abstract of the article. Blah blah blah.
tags: jats, pandoc, test
---
# Intro
Blah blah blah.
# Conclusion
Blah blah blah.2) Convert with pandoc -s -t jats -o jats.xml jats.md and look at the xml:
<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.2 20190208//EN"
"JATS-archivearticle1.dtd">
<article xmlns:mml="http://www.w3.org/1998/Math/MathML"
xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="1.2" article-type="other">
<front>
<journal-meta>
<journal-id></journal-id>
<journal-title-group>
</journal-title-group>
<issn></issn>
<publisher>
<publisher-name></publisher-name>
</publisher>
</journal-meta>
<article-meta>
<title-group>
<article-title>A JATS Test</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<contrib-id contrib-id-type="orcid">XXXXXXXXXXXXX</contrib-id>
<name>
<surname>Doe</surname>
<given-names>Jane</given-names>
</name>
<xref ref-type="aff" rid="aff-ioa"/>
</contrib>
<aff id="aff-ioa">
<institution-wrap>
<institution>Inst. of Allopecia</institution>
</institution-wrap>,
<country>Indonesia</country>
</aff>
</contrib-group>
<pub-date date-type="pub" publication-format="electronic" iso-8601-date="2024-01-02">
<day>2</day>
<month>1</month>
<year>2024</year>
</pub-date>
<permissions>
</permissions>
<abstract>
<p>This is the abstract of the article. Blah blah blah.</p>
</abstract>
<kwd-group kwd-group-type="author">
<kwd>jats, pandoc, test</kwd>
</kwd-group>
</article-meta>
</front>
<body>
<sec id="intro">
<title>Intro</title>
<p>Blah blah blah.</p>
</sec>
<sec id="conclusion">
<title>Conclusion</title>
<p>Blah blah blah.</p>
</sec>
</body>
<back>
</back>
</article>It seems Pandoc can read the YAML metadata we can store in Scrivener, and output to XML -- looks promising!
The journal output is wrong, not sure why...
I am totally ignorant of what JATS is supposed to look like. If you can get this to work manually (running the pandoc command directly) it will be easy for me to adapt to scrivomatic. The problem is that my metadata is not compatible with JATS so we may need some preprocessing to convert the metadata I use into the one JATS needs...
Do you need this for existing projects or you are starting a new one?
bokamm
This is a question about compiling directly to JATS XML (see Journal Publishing Tag Library). JATS XML includes various metadata for article publishing and can potentially be used for displaying an article in a dynamic format (giving access to references and supplementary material via tabs). PKP OJS can use this, for example: https://demo.publicknowledgeproject.org/ojs3/demo/index.php/immersion/article/view/918/463
It seems, pandoc could convert to JATS but I have not figured out how to do this. There was a lua converter but that has been archived (and uses an old JATS version): https://github.com/mfenner/pandoc-jats
Could the lua filter etc. be integrated into scrivomatic? I super appreciate scrivomatic but do not have the knowledge to update and integrate pandoc-jats for this. If it is too complicated or not possible, that is fine. If it is just a matter of copying and pasting the metadata block and lua files somewhere, I can try myself but would still appreciate guidance.
(If I can donate to scrivomatic somehow, I will sure do!)