Have intext citations that link to PDFs stored in Zotero

[laxnx]

Link to PDF from intext / inline citation instead of to bibliography

Sorry if this isn't really a Quarto thing. I'm in the process of writing my thesis, and I really like how Quarto has made me focus more on writing than formatting (cuz I made a template for my thesis), while usingg rbbt to link to Zotero and make my citations and bibliography.

I think that it'd be very helpful to share my manuscript alongside the PDF files, so that when someone is reading the manuscript, they can click on the intext citation and it'd take them to the PDF (or maybe even at a specific page or selection).

It's very difficult somehow to see this asked in the internet, but I found this: (Link to PDF from citation in Docs?), and it's pretty much the most similar to my desired feature.

I think this can be done by duplicating and storing all the reference PDFs in a folder, and have the Quarto intext citation reference that PDF. Then the exported manuscript and the PDF folder can be shared together to allow readers to also see the sources themselves. This would be really helpful when multiple people need to check each other's work, like my adviser reading my manuscript.

[mcanouil]

You can write a LUA filter.
Something like the example below will add a DOI link after the citation if the reference contains a DOI:

local references = {}

function get_references(doc)
  references = pandoc.utils.references(doc)
  return doc
end

function process_citations(elem)
  local cite_id = elem.citations[1].id
  
  -- Find the reference by ID
  local ref = nil
  for _, reference in ipairs(references) do
    if reference.id == cite_id then
      ref = reference
      break
    end
  end
  
  if ref and ref.DOI then
    local doi_text = pandoc.utils.stringify(ref.DOI)
    local doi_url = "https://doi.org/" .. doi_text
    local doi_link = pandoc.Link({pandoc.Str("DOI")}, doi_url)
    return {elem, pandoc.Str(" "), doi_link}
  end
  
  return elem
end

return {
  { Pandoc = get_references },
  { Cite = process_citations }
}

You would need this filter to come after Quarto's processing.

filters:
  - path: citation.lua
    at: post-quarto

[laxnx]

Thank you for your response. I'm rather inexperienced when it comes to making lua filters (I've already made a few little lua filters for my intended use case) and I think it might be difficult to implement the desired feature as a lua filter because I need a way to relate the citekey to a filepath to the reference pdf, not the DOI really. Also, I'm not sure how it would behave if I made a compound parenthetical citation like [@ref1; @ref2].

My initial idea was that I could add a link within the manuscript PDF that leads to the reference's PDF. But I think this is a PDF attachment and not exactly a link. Anyway, I think I can settle on the ff. workflow which already works on my end. It would also be nice if Quarto found a way to make this easier for everyone else.

1. Export Zotero collection of sources with the Better BibTeX setting, include files, and make sure to uncheck the "background export" so that files actually get exported. Using the BibTeX setting gives a weird filepath (see ff. example).

• BetterBibTeX: files/13698/Jo et al. - 2022 - Linking the state of environmental DNA to its appl.pdf
• BibTeX: Jo - 2023 - Utilizing the state of environmental DNA (eDNA) to.pdf:files/13446/Jo - 2023 - Utilizing the state of environmental DNA (eDNA) to.pdf:application/pdf

2. One can use the generated bib file to word search the citekey and get the appropriate filepath

3. The filepath is needed to put an inline LaTeX command at the citation.

I made a YAML parameter called pdfembeds, with options "T" or "F" to control whether pdf attachments appear or not. The following codeblock is the code I put in my before-title.tex template partial

\def\paramembeds{$params.pdfembeds$}
\def\classTembeds{T}
\def\classFembeds{F}

\if\paramembeds\classTembeds
\usepackage{attachfile2} 
\fi

\if\paramembeds\classFembeds
\usepackage{attachfile} %%loading this package somehow makes attachments not appear for some reason, which is what i want
\fi

4. Opening the exported manuscript in Adobe Acrobat allows viewing for these PDF attachments. Other PDF readers may block the opening of file attachments. The references are now embedded in the manuscript and I only need to share a single PDF file. Clicking on the pins opens the attached reference.