YAML abstract with multi-line headers

[ns-rse]

Description

Hi,

I'm helping a colleague re-write their paper in a Quarto Scholarly Writing and they would like to include an abstract in the YAML Frontmatter. The intended journal they wish to publish in expects the abstract to have headings and sections.

Headings

A dummy example using headings...

---
title: "A simple example with multi-line abstract and headers"
author:
  - name: ns-rse
    orcid: 0000-0000-0000-0000
    corresponding: false
    roles: Collaborators
    affiliations:

keywords:
  - YAML
  - Markdown
abstract: |
## Introduction

This is the introduction

## Methods

This is the methods section.

## Results

We have results.

## Conclusion

And this is the conclusion.

plain-language-summary: |
    Some journals require abstracts with multiple sections. The above lays out such a structure in Markdown but fails to parse.
key-points:
  - Multi-line abstract fails to parse
  - Better discrimators between benign and malignant thyroid nodules are required in the UK
date: 2024-04-23
bibliography: references.bib
citation:
  container-title: "Silly example"
number-sections: true
---

## Rest of the document

blah, blah, blah

Error

On trying to render this the YAML fails to parse with...

ERROR: YAMLError: /home/neil/work/git/hub/mdp21oe/multicentre_thyroid/test.qmd:
can not read a block mapping entry; a multiline key may not be an implicit key at line 18, column 1:
    ## Methods
    ^

Stack trace:
can not read a block mapping entry; a multiline key may not be an implicit key at line 18, column 1:
    ## Methods
    ^
    at generateError (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:10471:12)
    at throwError (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:10474:11)
    at readBlockMapping (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:11098:24)
    at composeNode (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:11290:84)
    at readDocument (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:11404:5)
    at loadDocuments (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:11439:9)
    at load (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:11444:23)
    at parse2 (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:11454:12)
    at parseWithNiceErrors (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:19659:16)
    at readYamlFromMarkdown (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:19590:17)

Process quarto-preview-/home/neil/work/git/hub/mdp21oe/multicentre_thyroid/test.qmd exited abnormally with code 1

Bold

I've also tried ditching the Markdown Heading 2 (##) and tried using **bold** instead. Parsing gets further but fails further down.

Example

---
title: "A simple example with multi-line abstract and headers**
author:
  - name: ns-rse
    orcid: 0000-0000-0000-0000
    corresponding: false
    roles: Collaborators
    affiliations:

keywords:
  - YAML
  - Markdown
abstract: |
**Introduction**

This is the introduction

**Methods***

This is the methods section.

**Results**

We have results.

**Conclusion**

And this is the conclusion.

plain-language-summary: |
    Some journals require abstracts with multiple sections. The above lays out such a structure in Markdown but fails to parse.
key-points:
  - Multi-line abstract fails to parse
  - Better discrimators between benign and malignant thyroid nodules are required in the UK
date: 2024-04-23
bibliography: references.bib
citation:
  container-title: "Silly example"
number-sections: true
---

## Rest of the document

blah, blah, blah

Error

: YAMLError: /home/neil/work/git/hub/mdp21oe/multicentre_thyroid/test.qmd:
bad indentation of a mapping entry at line 38, column 21:
      container-title: "Silly example"
                        ^

Stack trace:
bad indentation of a mapping entry at line 38, column 21:
      container-title: "Silly example"
                        ^
    at generateError (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:10471:12)
    at throwError (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:10474:11)
    at readBlockMapping (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:11123:20)
    at composeNode (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:11290:84)
    at readDocument (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:11404:5)
    at loadDocuments (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:11439:9)
    at load (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:11444:23)
    at parse2 (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:11454:12)
    at parseWithNiceErrors (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:19659:16)
    at readYamlFromMarkdown (file:///home/neil/.local/quarto/quarto-1.4.502/bin/quarto.js:19590:17)

Process quarto-preview-/home/neil/work/git/hub/mdp21oe/multicentre_thyroid/test.qmd exited abnormally with code 1

I realise this is a YAML issue but I've been unable to find any suggestion of whether this is possible in YAML and whether we'll have to look at doing this by hand?

❱ quarto --version
1.4.553

[cscheid]

YAML abstract with multi-line with headers

Our templates don't support abstracts with headers. Unfortunately you'll have to design your own here, which is a relatively advanced topic. EDIT: I was wrong - see @mcanouil's answer here.

[mcanouil]

Is the main issue not the indentation? Multiline should be indented.
Also the example is missing closing quotes for title.

With a properly formatted it "works" (no errors).

[mcanouil]

Regarding templates: you can take a look at the various templates that already exist (mostly PDF/LaTeX): https://m.canouil.dev/quarto-extensions/extensions.html

Something that might be of interest: https://github.com/pandoc-ext/abstract-section

Additionally, you can get your headers unnumbered:

---
title: "A simple example with multi-line abstract and headers"
author:
  - name: ns-rse
    orcid: 0000-0000-0000-0000
    corresponding: false
    roles: Collaborators
    affiliations:
abstract: |
  ### Introduction {.unnumbered}

  This is the introduction

  ### Methods {.unnumbered}

  This is the methods section.

  ### Results {.unnumbered}

  We have results.

  ### Conclusion {.unnumbered}

  And this is the conclusion.
keywords:
  - YAML
  - Markdown
plain-language-summary: |
    Some journals require abstracts with multiple sections. The above lays out such a structure in Markdown but fails to parse.
key-points:
  - Multi-line abstract fails to parse
  - Better discrimators between benign and malignant thyroid nodules are required in the UK
date: 2024-04-23
citation:
  container-title: "Silly example"
number-sections: true
---

## Rest of the document

blah, blah, blah

[cscheid]

I could swear I had seen an example where headings inside \begin{abstract}\end{abstract} broke PDF rendering, but I'm clearly wrong!

[mcanouil]

I only tried PDF here, but the examples shared were all wrong😅

Edit: it works also for PDF

[ns-rse]

I'm an idiot ( 🤦 ) for forgetting to indent, thank you for the quick solution, really appreciate it. Renders to HTML ok too and excluding the numbering is an excellent additional tip, cheers.

Thank you @mcanouil for the solution and @cscheid for taking a look.