How to use normalized author metadata in Pandoc template (try #2)

[rcannood]

Description

This is related to #5778 where @rgaiacs wants to use by-author in a markdown pandoc template. @dragonstyle notes that the authors aren't normalized when rendering to markdown and asks whether there @rgaiacs has a use case.

I've got a use case! I'm trying to write an extension for converting qmd documents to the expected format for submitting a manuscript to JOSS. This fits well into my publishing workflow, as I will typically first publish qmd manuscripts to html or gfm, and want to convert it to the JOSS markdown format prior to submission to JOSS.

Here is an example of a JOSS formatted document:

---
title: 'Gala: A Python package for galactic dynamics'
tags:
  - Python
  - astronomy
  - dynamics
  - galactic dynamics
  - milky way
authors:
  - name: Adrian M. Price-Whelan
    orcid: 0000-0000-0000-0000
    equal-contrib: true
    affiliation: "1, 2" # (Multiple affiliations must be quoted)
  - name: Author Without ORCID
    equal-contrib: true # (This is how you can denote equal contributions between multiple authors)
    affiliation: 2
  - name: Author with no affiliation
    corresponding: true # (This is how to denote the corresponding author)
    affiliation: 3
affiliations:
 - name: Lyman Spitzer, Jr. Fellow, Princeton University, USA
   index: 1
 - name: Institution Name, Country
   index: 2
 - name: Independent Researcher, Country
   index: 3
---

# Summary

Foo

I was hoping to be able to write my template as:

---
$if(title)$title: $title$$endif$
$if(by-author)$
author:
$for(by-author)$
  - name: $by-author.name.literal$
    $if(by-author.orcid)$orcid: $by-author.orcid$$endif$
    $if(by-author.affiliations)$affiliation: $for(by-author.affiliations)$"$by-author.affiliations.ref$", $endfor$$endif$
$endfor$
$endif$
...
---

However, this doesn't seem to be working.

Is there already a way I can already forcibly turn on author normalization, or is there a different way for being able to access author metadata such as orcid and affiliation?

Thanks!

[cderv]

I believe this is quite specific because your output is markdown here.

We currently explicitly remove authors from metadata when output is markdown, and we do not normalize

quarto-cli/src/resources/filters/modules/authors.lua

Lines 921 to 929 in 7cfadb5

	local function processAuthorMeta(meta)
	-- prevents the front matter for markdown from containing
	-- all the rendered author information that we generate
	if _quarto.format.isMarkdownOutput() then
	meta[kAuthors] = nil
	return meta
	end
	-- prefer to render 'authors' if it is available

This was done in 108f74f

@dragonstyle it seems there is some use case where this can be useful as Journal like JOSS now expects a paper.md as submission
https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography

[dragonstyle]

Thanks for sharing this- it does indeed make sense. I'm going to open an enhancement request to explicitly enable normalization and I'll try to get to that soon!

[cscheid]

We currently explicitly remove authors from metadata when output is markdown, and we do not normalize

Sorry to drive by here. I just want to make a note that this is an instance where (I believe!) that we remove the authors from metadata in markdown output, because we tend to assume that markdown output is used as an "intermediate" file rather than a "full output". I've had a couple of other issues come up recently about how to resolve markdown output cleanly, and I wonder if we should spend some time figuring out what to do about that.

Specifically, I wonder if we should "bless" some specific markdown variant as the "clean output" (our users have already suggested gfm)

[cderv]

I'm going to open an enhancement request to explicitly enable normalization

For reference, issue created at #6139. Thanks Charles!

[rcannood]

Thanks for looking into this! I look forward to being able to create a format for JOSS using the proposed changes ☺️