generate JATS xml with "floating" figures and tables

[jhpoelen]

Hi!

I am using pandoc to create data reviews in various formats (pdf, docx, html, jats xml) for species interaction datasets indexed by Global Biotic Interactions (GloBI, https://globalbioticinteractions.org).

And, in collaboration with a publisher, I was asked to include the figures and tables in the "back" section, instead of the current inline. It seems that by default, pandoc generated JATS inlines figures and tables. For context see globalbioticinteractions/globalbioticinteractions#1014 and associated html version of the review report at https://depot.globalbioticinteractions.org/review/globalbioticinteractions/dopi

I've included the markdown source, output jats xml, and the command to connect them below

input:
index.md

output:
index.xml.txt

cat index.md\
 | pandoc --embed-resources --standalone --toc --citeproc -t jats -o -\
 > index.xml.txt

for context see also https://github.com/globalbioticinteractions/globinizer/blob/52c0dec75ba425b8bac941e32659d7568080e7fc/check-dataset.sh#L781C3-L781C68 .

Curious to hear your thoughts on how to generate JATS with "floating" figures and tables . . .

fyi @Daniel-Mietchen @teodorgeorgiev

[jgm]

@tarleb do you have thoughts on this?

[estedeahora]

if this change is advanced, could it be an optional behavior?

[teodorgeorgiev]

indeed float-group should be in article (after back, not in back)

[tarleb]

I'm having second thoughts about adding this to pandoc proper, so here's a custom Lua writer to produce the modified JATS. It's a tad more complicated than I expected, as JATS templates use partials, which made modifying the right part of the template more difficult.

Usage: pandoc --to=jats-float-group.lua .... Please let me know if it works as intended.

--- File: jats-float-group.lua
--- Author: Albert Krewinkel
--- License: MIT

local path     = require 'pandoc.path'
local system   = require 'pandoc.system'
local template = require 'pandoc.template'

local target_format = 'jats_publishing'

Extensions = pandoc.format.extensions(target_format)
Template = pandoc.template.default(target_format)

local function write_file(filepath, content)
  local fh = io.open(filepath, 'w')
  fh:write(content)
  fh:close()
end

function Writer (doc, opts)
  local format = {
    format = target_format,
    extensions = opts.extensions
  }

  -- Collect floats in a separate list, remove from main doc.
  local floats = pandoc.Blocks{}
  local move_to_floats = function (x)
    floats:insert(x)
    return {}
  end
  doc = doc:walk {
    Figure = move_to_floats,
    Table = move_to_floats,
  }

  -- Store floats in the metadata
  doc.meta['floats-group'] = floats

  -- modify the template on the fly, add `<floats-group>`
  if opts.template then
    local article = template.get 'article.jats_publishing'
    article = article:gsub(
      '</article>',
      '<floats-group>\n${floats-group}\n</floats-group>\n</article>'
    )
    local affiliations = template.get 'affiliations.jats'
    local deftemplate = template.default(target_format)

    system.with_temporary_directory('jats-template', function (tmpdir)
      local template_path = path.join{tmpdir, 'default.jats_publishing'}
      write_file(path.join{tmpdir, 'article.jats_publishing'}, article)
      write_file(path.join{tmpdir, 'affiliations.jats'}, affiliations)
      write_file(template_path, deftemplate)
      opts.template = template.compile(
        template.default(target_format),
        template_path)
    end)
  end

  return pandoc.write(doc, format, opts)
end

[denismaier]

if this change is advanced, could it be an optional behavior?

Yes, I also think it should be optional.

[tarleb]

I'm opting for a simple change that will simply add support for a floats-group variable to the template. The user then has the option to set the value manually in the metadata, or to use a filter.

E.g.

---
floats-group:
  - |
    ![figure](image.png)

  - |
    | table |
    |--
    | example |
---

The above Lua filter to set this value automatically becomes considerably simpler:

--- jats-floats-group.lua -- output JATS with figures, tables in separate tag
--- Author: Albert Krewinkel
--- License: MIT

local pandoc   = require 'pandoc'
local target_format = 'jats_publishing'

Extensions = pandoc.format.extensions(target_format)
Template = pandoc.template.default(target_format)

function Writer (doc, opts)
  local format = {
    format = target_format,
    extensions = opts.extensions
  }

  -- Collect floats in a separate list, remove from main doc.
  local floats = pandoc.Blocks{}
  local move_to_floats = function (x)
    floats:insert(x)
    return {}
  end
  doc = doc:walk {
    Figure = move_to_floats,
    Table = move_to_floats,
  }

  -- Store floats in the metadata
  doc.meta['floats-group'] = floats

  return pandoc.write(doc, format, opts)
end

Commit incoming.

[jhpoelen]

fyi @myrmoteras