add extensions

_extensions/pandoc-ext/abstract-section/_extension.yaml

@@ -0,0 +1,6 @@
+name: abstract-section
+author: Albert Krewinkel
+version: 1.0.0
+contributes:
+  filters:
+    - abstract-section.lua

_extensions/pandoc-ext/abstract-section/abstract-section.lua

@@ -0,0 +1,59 @@
+--[[
+abstract-to-meta – move an "abstract" section into document metadata
+
+Copyright: © 2017–2021 Albert Krewinkel
+License:   MIT – see LICENSE file for details
+]]
+local abstract = {}
+
+--- Extract abstract from a list of blocks.
+function abstract_from_blocklist (blocks)
+  local body_blocks = {}
+  local looking_at_abstract = false
+
+  for _, block in ipairs(blocks) do
+    if block.t == 'Header' and block.level == 1 then
+      if block.identifier == 'abstract' then
+        looking_at_abstract = true
+      else
+        looking_at_abstract = false
+        body_blocks[#body_blocks + 1] = block
+      end
+    elseif looking_at_abstract then
+      if block.t == 'HorizontalRule' then
+        looking_at_abstract = false
+      else
+        abstract[#abstract + 1] = block
+      end
+    else
+      body_blocks[#body_blocks + 1] = block
+    end
+  end
+
+  return body_blocks
+end
+
+if PANDOC_VERSION >= {2,9,2} then
+  -- Check all block lists with pandoc 2.9.2 or later
+  return {{
+      Blocks = abstract_from_blocklist,
+      Meta = function (meta)
+        if not meta.abstract and #abstract > 0 then
+          meta.abstract = pandoc.MetaBlocks(abstract)
+        end
+        return meta
+      end
+  }}
+else
+  -- otherwise, just check the top-level block-list
+  return {{
+      Pandoc = function (doc)
+        local meta = doc.meta
+        local other_blocks = abstract_from_blocklist(doc.blocks)
+        if not meta.abstract and #abstract > 0 then
+          meta.abstract = pandoc.MetaBlocks(abstract)
+        end
+        return pandoc.Pandoc(other_blocks, meta)
+      end,
+  }}
+end

_extensions/pandoc-ext/author-info-blocks/_extension.yaml

@@ -0,0 +1,6 @@
+name: author-info-blocks
+author: Albert Krewinkel
+version: 1.0.0
+contributes:
+  filters:
+    - author-info-blocks.lua

_extensions/pandoc-ext/author-info-blocks/author-info-blocks.lua

@@ -0,0 +1,179 @@
+local List = require("pandoc.List")
+local utils = require("pandoc.utils")
+local stringify = utils.stringify
+local byAuthor
+local byAffiliation
+local Authors = {}
+local Affiliations = {}
+
+local authorHoriz
+
+local Corresponding = nil
+local function make_correspondance(name, email)
+	correspondance = List:new({
+		pandoc.Str("* Corresponding Author: "),
+		pandoc.Str(name),
+		pandoc.Str(" ("),
+		pandoc.Link(email, "mailto:" .. email),
+		pandoc.Str(")"),
+	})
+	Corresponding = List:new({ pandoc.Para(correspondance) })
+end
+
+local equalCont
+local function make_equal_contributor()
+	eq_statement = pandoc.Str("† These authors contributed equally to this work.")
+	equalCont = List:new({ pandoc.Para(eq_statement) })
+end
+
+local function create_author_list(byAuthor)
+	local authors = {}
+	for i, author in ipairs(byAuthor) do
+		local sups = {}
+
+		for j, aff in ipairs(author.affiliations) do
+			table.insert(sups, aff.number)
+		end
+		sups_str = table.concat(sups, ",")
+
+		local name = stringify(author.name.literal)
+
+		if author.attributes ~= nil then
+			if author.attributes["equal-contributor"] ~= nil and author.attributes["equal-contributor"] then
+				sups_str = sups_str .. ",†"
+				make_equal_contributor()
+			end
+			if author.attributes.corresponding ~= nil and author.attributes.corresponding then
+				local email = stringify(author.email)
+				sups_str = sups_str .. ",*"
+				make_correspondance(name, email)
+			end
+		end
+
+		local authorEntry = List:new({
+			pandoc.Str(name),
+			pandoc.Superscript(pandoc.Str(sups_str)),
+		})
+
+		if authorHoriz and i < #byAuthor then
+			authorEntry:extend({ pandoc.Str(", ") })
+		end
+
+		table.insert(authors, pandoc.Span(authorEntry))
+	end
+
+	if authorHoriz then
+		Authors = { pandoc.Para(authors) }
+	else
+		Authors = authors
+	end
+end
+
+local function create_affiliation_list(byAffiliation)
+	for i, aff in ipairs(byAffiliation) do
+		local full_aff = pandoc.List({})
+		if aff.name then
+			full_aff:insert(stringify(aff.name))
+		end
+
+		if aff.address then
+			full_aff:insert(stringify(aff.address))
+		end
+
+		if aff.city then
+			full_aff:insert(stringify(aff.city))
+		end
+
+		if aff["postal-code"] then
+			full_aff:insert(stringify(aff["postal-code"]))
+		end
+
+		if aff.region then
+			full_aff:insert(stringify(aff.region))
+		end
+
+		if aff.country then
+			full_aff:insert(stringify(aff.country))
+		end
+
+		local entry = table.concat(full_aff, ", ")
+		entry = aff.number .. ". " .. entry .. "."
+		table.insert(Affiliations, pandoc.Para(pandoc.Str(entry)))
+	end
+end
+
+local Abstract = nil
+local function create_abstract(ab)
+	Abstract = {}
+	table.insert(Abstract, pandoc.Header(1, "Abstract"))
+	table.insert(Abstract, pandoc.Para(ab))
+end
+
+local Keywords = nil
+local function create_keyword_list(kw)
+	Keywords = {}
+	-- quarto.log.output(kw)
+	local kws = pandoc.List({})
+	for i, keyword in ipairs(kw) do
+		kws:insert(stringify(keyword))
+	end
+	local kwentry = table.concat(kws, "; ")
+	kwentry = "Keywords: " .. kwentry .. "."
+	table.insert(Keywords, pandoc.Para(pandoc.Str(kwentry)))
+end
+
+local function remove_author_meta(meta)
+	meta.author = nil
+	meta.authors = nil
+	meta.affiliations = nil
+	meta["by-author"] = nil
+	meta["by-affiliation"] = nil
+	meta["abstract"] = nil
+	return meta
+end
+
+return {
+	{
+		Meta = function(meta)
+			byAuthor = meta["by-author"]
+			byAffiliation = meta["by-affiliation"]
+			if meta["author-horizontal"] ~= nil then
+				authorHoriz = meta["author-horizontal"]
+			else
+				authorHoriz = true
+			end
+			create_author_list(byAuthor)
+			create_affiliation_list(byAffiliation)
+			if meta["abstract"] ~= nil then
+				create_abstract(meta["abstract"])
+			end
+			if meta["keywords"] ~= nil then
+				create_keyword_list(meta["keywords"])
+			end
+			return meta
+		end,
+	},
+	{
+		Pandoc = function(doc)
+			local meta = doc.meta
+			local body = List:new({})
+			body:extend(Authors)
+			body:extend(Affiliations)
+			if equalCont ~= nil then
+				body:extend(equalCont)
+			end
+			if Corresponding ~= nil then
+				body:extend(Corresponding)
+			end
+			if Abstract then
+				body:extend(Abstract)
+			end
+			if Keywords then
+				body:extend(Keywords)
+			end
+			body:extend(doc.blocks)
+			meta = remove_author_meta(meta)
+			return pandoc.Pandoc(body, meta)
+		end,
+	},
+}

_extensions/pandoc-ext/scholarly-metadata/_extension.yaml

@@ -0,0 +1,6 @@
+name: scholarly-metadata
+author: Albert Krewinkel
+version: 1.0.0
+contributes:
+  filters:
+    - scholarly-metadata.lua

_extensions/pandoc-ext/scholarly-metadata/scholarly-metadata.lua

@@ -0,0 +1,197 @@
+--[[
+ScholarlyMeta – normalize author/affiliation meta variables
+
+Copyright (c) 2017-2021 Albert Krewinkel, Robert Winkler
+
+Permission to use, copy, modify, and/or distribute this software for any purpose
+with or without fee is hereby granted, provided that the above copyright notice
+and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
+REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
+INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
+TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
+THIS SOFTWARE.
+]]
+local List = require("pandoc.List")
+
+--- Returns the type of a metadata value.
+--
+-- @param v a metadata value
+-- @treturn string one of `Blocks`, `Inlines`, `List`, `Map`, `string`, `boolean`
+local function metatype(v)
+	if PANDOC_VERSION <= "2.16.2" then
+		local metatag = type(v) == "table" and v.t and v.t:gsub("^Meta", "")
+		return metatag and metatag ~= "Map" and metatag or type(v)
+	end
+	return pandoc.utils.type(v)
+end
+
+local type = pandoc.utils.type or metatype
+
+-- Split a string at commas.
+local function comma_separated_values(str)
+	local acc = List:new({})
+	for substr in str:gmatch("([^,]*)") do
+		acc[#acc + 1] = substr:gsub("^%s*", ""):gsub("%s*$", "") -- trim
+	end
+	return acc
+end
+
+--- Ensure the return value is a list.
+local function ensure_list(val)
+	if type(val) == "List" then
+		return val
+	elseif type(val) == "Inlines" then
+		-- check if this is really a comma-separated list
+		local csv = comma_separated_values(pandoc.utils.stringify(val))
+		if #csv >= 2 then
+			return csv
+		end
+		return List:new({ val })
+	elseif type(val) == "table" and #val > 0 then
+		return List:new(val)
+	else
+		-- Anything else, use as a singleton (or empty list if val == nil).
+		return List:new({ val })
+	end
+end
+
+--- Returns a function which checks whether an object has the given ID.
+local function has_id(id)
+	return function(x)
+		return x.id == id
+	end
+end
+
+--- Copy all key-value pairs of the first table into the second iff there is no
+-- such key yet in the second table.
+-- @returns the second argument
+function add_missing_entries(a, b)
+	for k, v in pairs(a) do
+		b[k] = b[k] or v
+	end
+	return b
+end
+
+--- Create an object with a name. The name is either taken directly from the
+-- `name` field, or from the *only* field name (i.e., key) if the object is a
+-- dictionary with just one entry. If neither exists, the name is left unset
+-- (`nil`).
+function to_named_object(obj)
+	local named = {}
+	if type(obj) == "Inlines" then
+		-- Treat inlines as the name
+		named.name = obj
+		named.id = pandoc.utils.stringify(obj)
+	elseif type(obj) ~= "table" then
+		-- if the object isn't a table, just use its value as a name.
+		named.name = pandoc.MetaInlines({ pandoc.Str(tostring(obj)) })
+		named.id = tostring(obj)
+	elseif obj.name ~= nil then
+		-- object has name attribute → just create a copy of the object
+		add_missing_entries(obj, named)
+		named.id = pandoc.utils.stringify(named.id or named.name)
+	elseif next(obj) and next(obj, next(obj)) == nil then
+		-- Single-entry table. The entry's key is taken as the name, the value
+		-- contains the attributes.
+		key, attribs = next(obj)
+		if type(attribs) == "string" or type(attribs) == "Inlines" then
+			named.name = attribs
+		else
+			add_missing_entries(attribs, named)
+			named.name = named.name or pandoc.MetaInlines({ pandoc.Str(tostring(key)) })
+		end
+		named.id = named.id and pandoc.utils.stringify(named.id) or key
+	else
+		-- this is not a named object adhering to the usual conventions.
+		error("not a named object: " .. tostring(obj))
+	end
+	return named
+end
+
+--- Resolve affiliations placeholders to full named objects
+local function resolve_affiliations(affiliations, known_affiliations)
+	local unresolved_affiliations
+	if affiliations == nil then
+		unresolved_affiliations = {}
+	elseif type(affiliations) == "string" or type(affiliations) == "number" then
+		unresolved_affiliations = { affiliations }
+	else
+		unresolved_affiliations = affiliations
+	end
+
+	local result = List:new({})
+	for i, inst in ipairs(unresolved_affiliations) do
+		result[i] = known_affiliations[tonumber(inst)]
+			or known_affiliations:find_if(has_id(pandoc.utils.stringify(inst)))
+			or to_named_object(inst)
+	end
+	return result
+end
+
+--- Insert a named object into a list; if an object of the same name exists
+-- already, add all properties only present in the new object to the existing
+-- item.
+function merge_on_id(list, namedObj)
+	local elem, idx = list:find_if(has_id(namedObj.id))
+	local res = elem and add_missing_entries(namedObj, elem) or namedObj
+	local obj_idx = idx or (#list + 1)
+	-- return res, obj_idx
+	list[obj_idx] = res
+	return res, #list
+end
+
+--- Flatten a list of lists.
+local function flatten(lists)
+	local result = List:new({})
+	for _, lst in ipairs(lists) do
+		result:extend(lst)
+	end
+	return result
+end
+
+--- Canonicalize authors and affiliations
+local function canonicalize(raw_author, raw_affiliations)
+	local affiliations = ensure_list(raw_affiliations):map(to_named_object)
+	local authors = ensure_list(raw_author):map(to_named_object)
+
+	for _, author in ipairs(authors) do
+		author.affiliations = resolve_affiliations(ensure_list(author.affiliations), affiliations)
+	end
+
+	-- Merge affiliations defined in author objects with those defined in the
+	-- top-level list.
+	local author_insts = flatten(authors:map(function(x)
+		return x.affiliations
+	end))
+	for _, inst in ipairs(author_insts) do
+		merge_on_id(affiliations, inst)
+	end
+
+	-- Add list indices to affiliations for numbering and reference purposes
+	for idx, inst in ipairs(affiliations) do
+		inst.index = pandoc.MetaInlines({ pandoc.Str(tostring(idx)) })
+	end
+
+	-- replace affiliations with their indices
+	local to_index = function(inst)
+		return tostring(select(2, affiliations:find_if(has_id(inst.id))))
+	end
+	for _, author in ipairs(authors) do
+		author.affiliations = pandoc.MetaList(author.affiliations:map(to_index))
+	end
+
+	return authors, affiliations
+end
+
+return {
+	{
+		Meta = function(meta)
+			meta.author, meta.affiliations = canonicalize(meta.author, meta.affiliations)
+			return meta
+		end,
+	},
+}