Missing country-code field in the affiliations schema

[fredguth]

Description

The affiliations schema does not have a country-code:string field.

affiliations:
  - id: string
    number: number
    name: string
    department: string
    group: string
    address: string
    city: string
    region: string
    country: string
    postal-code: string
    url: string

But this field is suposed to be used here.

Isn't it?

[mcanouil]

But this field is suposed to be used here.

Accessibility: For better accessibility, please ensure link text is descriptive and meaningful rather than using generic terms such as "here". This helps all users understand the link's destination. See Writing meaningful link text (WCAG).

Also note that what Quarto uses from Pandoc are in the Quarto CLI repository. Linking to Pandoc code has little meaning.
The affiliations.jats file in Quarto CLI in this case is the same and is at:

• quarto-cli/src/resources/formats/jats/pandoc/default-templates/affiliations.jats

  Line 35 in 15872fc

  <country$if(it.country-code)$ country="$it.country-code$"$endif$>$it.country$</country>$endif$

  
  "is supposed to be used": the template is more like "could be used". So, it's an optional field that is indeed missing in Quarto CLI in jats regards as it's not used anywhere else.

Thanks for the feature request and noticing this missing field!

[fredguth]

Ok, sorry for that. Part of the reason is not having English as first language.

[cderv]

Quarto uses a simplified version of JATS template, and so country-code is not supported.

This is the main template: https://github.com/quarto-dev/quarto-cli/blob/116be8898734b71bc9bf30d25f890e5516e4f278/src/resources/formats/jats/pandoc/template.xml

and affiliation is part of authors.xml template and only has the simplified version

quarto-cli/src/resources/formats/jats/pandoc/affiliation.xml

Lines 1 to 9 in 6f7568b

	$-- wrap affiliation if it has a known institution identifier
	$institution.xml()$
	$if(it.address)$<addr-line>${it.address}</addr-line>$endif$
	$if(it.city)$<city>$it.city$</city>$endif$
	$if(it.region)$<state>$it.region$</state>$endif$
	$if(it.country)$<country>$it.country$</country>$endif$
	$if(it.postal-code)$<postal-code>$it.postal-code$</postal-code>$endif$
	$if(it.url)$<ext-link ext-link-type="uri" xlink:href="$it.url$">$it.url$</ext-link>$endif$

So country-code is not used in jats format in Quarto CLI. It is not part of the normalization.

This would be a feature request: Is this a field you tried to use ?

[fredguth]

Yes, this is a field needed in the Scielo XML. Scielo is JATS based, but with lots of quirks. Some of them I wasn't able to fix with lua filters because of my own limitations with Lua and Pandoc internals. I run a python script to fix.

[cderv]

I think this means you need to provide your own JATS xml template and not really on quarto one. (template: custom.xml)

Then it may work to get all the meta you have. Unless the author normalization is the problem here.

[fredguth]

I have already implemented my own custom template, but I'm encountering an issue with the country-code field. Despite correctly populating this field in my frontmatter YAML, when I reference it.country-code in my template, it always renders empty. Here's my template code and YAML for reference:

<!-- From mytemplate.xml -->
<country$if(it.country-code)$ country="$it.country-code$"$endif$>$it.country$</country>  <!-- always returns empty despite being defined in YAML -->

# From my frontmatter
affiliations:
  - id: nevusp
    # Other fields...
    country: Brasil
    country-code: BR    # This value isn't being passed to the template
    url: https://usp.br

Is there a special syntax for accessing hyphenated field names in Quarto templates, or might this be a known limitation with the Scielo XML requirements?

[cderv]

This may be a limitation of our authors & affiliations normalization 🤔

We do normalize the YAML internally to offer flexibility in the templating. The top-level fields are a closed schema, and country-code is not one of the fields.

So it probably falls under arbitrary metadata: https://quarto.org/docs/journals/authors.html#arbitrary-metadata

Can you check inside it.metadata.country-code?

Maybe country-code is a new addition to the spec that we should have in the normalization? 🤔

[fredguth]

it.metadata.country-code works! 👍