How to make the abstract from abstract-section extension appear in the bibtex citation block ?

[fradav]

Description

Hello

When using the standard metadata abstract entry in the frontmatter, it appears just fine in the bibtex citation.

---
title: "Summarizing Output for Reproducible Documents"
description: | 
  A summary of the best practices for summarizing output of reproducible scientific documents.
date: 5/4/2018
author:
  - name: Norah Jones 
    url: https://example.com/norahjones
    affiliation: Spacely Sprockets
    affiliation-url: https://example.com/spacelysprokets
abstract: |
  lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
citation: true
---

# Introduction

lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

# Methods

lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat n

Which renders correctly the citation as :

@online{jones2018,
  author = {Jones, Norah},
  title = {Summarizing {Output} for {Reproducible} {Documents}},
  date = {2018-05-04},
  langid = {en},
  abstract = {lorem ipsum dolor sit amet, consectetur adipiscing elit.
    Sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
    Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris
    nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in
    reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla
    pariatur. Excepteur sint occaecat cupidatat non proident, sunt in
    culpa qui officia deserunt mollit anim id est laborum.}
}

However, when using the abstract-section quarto extension, even if the abstract itself is rendered correctly in the core document, it doesn’t appear in the citation block anymore.

---
title: "Summarizing Output for Reproducible Documents"
description: | 
  A summary of the best practices for summarizing output of reproducible scientific documents.
date: 5/4/2018
author:
  - name: Norah Jones 
    url: https://example.com/norahjones
    affiliation: Spacely Sprockets
    affiliation-url: https://example.com/spacelysprokets
citation: true
filters:
  - abstract-section
---

# Abstract

lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

# Introduction

lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

# Methods

lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

It still appears as a valid abstract in the core document

But it has vanished from the citation block :

@online{jones2018,
  author = {Jones, Norah},
  title = {Summarizing {Output} for {Reproducible} {Documents}},
  date = {2018-05-04},
  langid = {en}
}

Note that it is correctly displayed by the meta with

{{< meta abstract >}}

[mcanouil]

This is an issue with the extension not Quarto CLI. Please see with the author(s) of the extension.

Note that your example is not reproducible as you don't provide the source of the extension.

[fradav]

Sorry, it’s the first extension abstract-section listed when you go the extension tab on the quarto website since a long time, so I (wrongly) assumed common knowledge 😀
I also assumed, that as long as the meta was correctly provided, the ext did its job and that something was possibly amiss in the quarto pipeline.
OK, I’ll go to the extension authors, then.

[mcanouil]

Extensions need to be installed thus the source needs to be known.
Note that there are more than 240 extensions, making the assumption future readers will know them all is unlikely to ever be verified, especially since extensions by different authors can have the same name.

https://m.canouil.dev/quarto-extensions/

[mcanouil]

@fradav You could try changing when the filter is applied when you call it: https://quarto.org/docs/prerelease/1.4/lua_changes.html#more-precise-targeting-of-ast-processing-phases

But be aware that you would need to specify the full relative path for the filter:

• Filter extensions can't be specified in combination with processing phases #11750
• filters and shortcodes do not respect Quarto's convention about leading / #12408

[fradav]

Thanks, I tried this

filters:
  - at: pre-ast
    path: _extensions/pandoc-ext/abstract-section/abstract-section.lua

It does exactly the same thing as described above, no change. However, forcing to the pre-render or post-render phase makes the {{< meta abstract >}} renders as ?meta:abstract, but I’m guessing it is expected.

[fradav]

I’m not sure I understand the issue: the lua filter precisely moves the abstract from the markdown section to the meta key "abstract" and it is properly handled in the rendering pipeline as this meta key. Is the citation feature hard-coding the metadata location in the yaml frontmatter in some manner?

[mcanouil]

The issue is that the metadata are read and used to generate the citation before it is modified by code cells or Lua filters, so there is no "abstract" at reading time.

[fradav]

Ok, now I understand, it is not exactly hardcoding, but it seems even worse from a workaround-finder perspective 😢

[mcanouil]

I don't think there is any as the generation happens in TypeScript.

[fradav]

May I ask you where exactly is it happening in the ts code ?
Update, don’t bother, I found it:
// The abstract

[fradav]

The way I see it is :

• this is to be declared as an issue/feature request for quarto
• this has to be documented somewhere that any of the implied metadata couldn’t be generated at "read time", so we don’t even bother to use extension/filters which tinker with them for the purpose of correct citation feature etc.

(not mutually exclusive)

What do you think?

[mcanouil]

this is to be declared as an issue/feature request for quarto

The team is aware. If there is something to be done and can be done, they will use this discussion as starting point. No need to do anything for now.

this has to be documented somewhere that any of the implied metadata couldn’t be generated at "read time", so we don’t even bother to use extension/filters which tinker with them for the purpose of correct citation feature etc.

Unlikely, it's not possible to list every thing that is not possible and in my opinion, it will only bring more confusion than clarification for most users.
Note that here Quarto does exactly what it is supposed to do in the way it was designed for this particular feature.
So this is not a bug. Now the extension/filter was initially for Pandoc and was made compatible with Quarto, so the focus was on Pandoc features, not the Quarto ones such as citations.