JATS: Decoding tag <table-wrap-foot> missing in <table-wrap>

[asisiuc]

Jats lacks <table-wrap-foot> tag content when converting to format JSON:

Steps to reproduce

This is captured in the jats as:

<table-wrap id="table1" position="float">
  <label>Table 1.</label>
  <caption></caption>
  <table></table>
  <table-wrap-foot>
    <fn>
      <p>
        <italic>Source:</italic>
        CEPAL (2016) and World Bank (2016).
      </p>
    </fn>
    <fn id="T1_FN1" fn-type="general">
      <p><italic>Notes</italic>: a/ 2005&#x2013;2010; b/ 2010; c/ Percentage of population; d/ Population ages
        25&#x2013;59; e/ Population ages 15&#x2013;64; f/ Percentage of households.
      </p>
    </fn>
  </table-wrap-foot>
</table-wrap>

After running

encoda convert -- convert ./../encoda/article.xml article.json --from jats

In the converted result <table-wrap-foot> tag is missing content.

[nokome]

Thanks for this @asisiuc .

For reference, the JATS standard says that <table-wrap-foot> is a "Container element to hold the footnotes, general notes, or other paragraphs at the end of a table."

The main question is which property of a Table node should these notes get added to. I see two options:

1. append it the existing caption property; downside is that this would be "lossy" in that it lumps <caption> and <table-wrap-foot> and so wouldn't allow the two to be displayed separately e.g. in HTML, upside is that it's the easiest to implement

2. use it for one of the existing properties of a table https://schema.stenci.la/table: content or description (of the two, I suggest description since that is an schema.org property, whereas content is a custom extension of the Stencila schema.

If we were to go ahead with using description, it should be fairly straightforward to implement in decodeTableWrap, along the lines of how we handle caption e.g.

  const descriptionElem = child(elem, 'caption')
  const description =
    descriptionElem !== null && Array.isArray(descriptionElem.elements)
      ? decodeElements(descriptionElem.elements, state)
      : undefined

...

  return [
    stencila.table({
      id: decodeInternalId(attr(elem, 'id')),
      label: textOrUndefined(child(elem, 'label')),
      caption,
      rows: [...headerRows, ...bodyRows],
      description
    }),
  ]

cc @FAtherden-eLife

[fred-atherden]

description sounds fine to me.

[asisiuc]

Thanks for your replay @FAtherden-eLife @nokome , it is a very good solution, so we analyzed and came to the conclusion that fn-type and id must also be included, because it is possible that it will be a kind of anchor in the future in the articles, so there is little different from logic to caption.

[nokome]

Thanks @asisiuc . I'm having a look at your PR now. Can you please "Allow edits from maintainers" so that I can make changes to your PR directly: https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/allowing-changes-to-a-pull-request-branch-created-from-a-fork

[asisiuc]

Thanks for the quick reply @nokome, but we have some issue with allowing to edit PR because of ISSUE, so in order to make this work, please add me as a contributor.

Thanks @asisiuc . I'm having a look at your PR now. Can you please "Allow edits from maintainers" so that I can make changes to your PR directly: https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/allowing-changes-to-a-pull-request-branch-created-from-a-fork

[nokome]

@asisiuc I have added you as a collaborator with write permissions to this repo. It will probably be easier if you create future PRs in this repo directly, rather than in your fork.

I am closing this PR, in favour of its duplicate #674.

[nokome]

Arrgh, sorry meant to close the PR, not this issue. Reopening.