fix(code): Fix live zotero gen with quarto 1.4

Quarto 1.4 does not like a bare 'zotero' metadata frontmatter key with
sub keys for the filter options. This commit updates the zotero-live
citations filter plugin by retorque and changes its configuration so
it takes settings either through the 'zotero' key or, if that one is
not found, through the 'zoterolive' key. Same options.

_quarto.yml

@@ -26,3 +26,10 @@ format:
     echo: false
     number-sections: true
     pdf-engine: tectonic
+
+bibliography: 02-data/intermediate/zotero-library.bib
+csl: /home/marty/documents/library/utilities/styles/APA-7.csl
+zoterolive:
+  library: wow-inequalities
+  client: zotero
+  csl-style: apa

scoping_review.qmd

@@ -1,6 +1,4 @@
 ---
-bibliography: 02-data/intermediate/zotero-library.bib
-csl: /home/marty/documents/library/utilities/styles/APA-7.csl
 papersize: A4
 linestretch: 1.5
 fontfamily: lmodern
@@ -14,11 +12,7 @@ lang: en
 title: Addressing Inequalities in the World of Work
 subtitle: Scoping Review on 'What Works'
 filters:
-    - src/pandoc-to-zotero-live.lua
+   - src/pandoc-to-zotero-live.lua
-zotero:
-    library: wow-inequalities
-    client: zotero
-    csl-style: apa
 ---
 
 ```{python}

src/pandoc-to-zotero-live.lua

@@ -1,8 +1,8 @@
 local pandoc = require("pandoc")
-print("zotero-live-citations caf41cc")
+print("zotero-live-citations cd1ef3f")
 local mt, latest = pandoc.mediabag.fetch("https://retorque.re/zotero-better-bibtex/exporting/zotero.lua.revision")
 latest = string.sub(latest, 1, 10)
-if "caf41cc" ~= latest then
+if "cd1ef3f" ~= latest then
 	print('new version "' .. latest .. '" available at https://retorque.re/zotero-better-bibtex/exporting')
 end
 
@@ -1946,6 +1946,21 @@ do
 			return copy
 		end
 
+		function module.dump(o)
+			if type(o) == "table" then
+				local s = "{ "
+				for k, v in pairs(o) do
+					if type(k) ~= "number" then
+						k = '"' .. k .. '"'
+					end
+					s = s .. "[" .. k .. "] = " .. module.dump(v) .. ","
+				end
+				return s .. "} "
+			else
+				return tostring(o)
+			end
+		end
+
 		function module.trim(s)
 			if s == nil then
 				return s
@@ -1973,42 +1988,6 @@ do
 
 		module.citekeys = {}
 
-		function module.authors(csl_or_item)
-			local authors = {}
-			local author
-
-			if csl_or_item.author ~= nil then
-				for _, author in ipairs(csl_or_item.author) do
-					if author.literal ~= nil then
-						table.insert(authors, author.literal)
-					elseif author.family ~= nil then
-						table.insert(authors, author.family)
-					end
-				end
-			elseif csl_or_item.creators ~= nil then
-				for _, author in ipairs(csl_or_item.creators) do
-					if author.name ~= nil then
-						table.insert(authors, author.name)
-					elseif author.lastName ~= nil then
-						table.insert(authors, author.lastName)
-					end
-				end
-			elseif csl_or_item.reporter ~= nil then
-				table.insert(authors, csl_or_item.reporter)
-			end
-
-			if utils.tablelength(authors) == 0 then
-				return nil
-			end
-
-			local last = table.remove(authors)
-			if utils.tablelength(authors) == 0 then
-				return last
-			end
-			authors = table.concat(authors, ", ")
-			return table.concat({ authors, last }, " and ")
-		end
-
 		local function load_items()
 			if state.fetched ~= nil then
 				return
@@ -2028,15 +2007,19 @@ do
 				return
 			end
 
-			citekeys = table.concat(citekeys, ",")
+			module.request.params.citekeys = citekeys
-			local url = module.url .. utils.urlencode(citekeys)
+			local url = module.url .. utils.urlencode(json.encode(module.request))
-			local mt, contents = pandoc.mediabag.fetch(url, ".")
+			local mt, body = pandoc.mediabag.fetch(url, ".")
-			local ok, fetched = pcall(json.decode, contents)
+			local ok, response = pcall(json.decode, body)
 			if not ok then
-				print("could not fetch Zotero items: " .. contents)
+				print("could not fetch Zotero items: " .. response .. "(" .. body .. ")")
 				return
 			end
-			state.fetched = fetched
+			if response.error ~= nil then
+				print("could not fetch Zotero items: " .. response.error.message)
+				return
+			end
+			state.fetched = response.result
 		end
 
 		function module.get(citekey)
@@ -2048,7 +2031,11 @@ do
 
 			if state.fetched.errors[citekey] ~= nil then
 				state.reported[citekey] = true
-				print("@" .. citekey .. ": " .. state.fetched.errors[citekey])
+				if state.fetched.errors[citekey] == 0 then
+					print("@" .. citekey .. ": not found")
+				else
+					print("@" .. citekey .. ": duplicates found")
+				end
 				return nil
 			end
 
@@ -2058,7 +2045,7 @@ do
 				return nil
 			end
 
-			return state.fetched.items[citekey], state.fetched.zotero[citekey]
+			return state.fetched.items[citekey]
 		end
 
 		return module
@@ -2103,12 +2090,13 @@ local zotero = require("zotero")
 local config = {
 	client = "zotero",
 	scannable_cite = false,
-	csl_style = "apa7",
+	csl_style = "apa",
 	format = nil, -- more to document than anything else -- Lua does not store nils in tables
 	transferable = false,
+	sorted = true,
 }
 
--- -- -- bibliography marker generator -- -- --
+-- -- bibliography marker generator -- --
 function zotero_docpreferences_odt(csl_style)
 	return string.format(
 		'<data data-version="3" zotero-version="5.0.89">'
@@ -2180,12 +2168,23 @@ local function zotero_bibl_odt()
 	)
 end
 
--- -- -- citation market generators -- -- --
+-- -- -- citation marker generators -- -- --
+
+function clean_csl(item)
+	local cleaned = {}
+	for k, v in pairs(item) do
+		cleaned[k] = v
+	end
+	cleaned.custom = nil
+	return setmetatable(cleaned, getmetatable(item))
+end
+
 local function zotero_ref(cite)
 	local content = pandoc.utils.stringify(cite.content)
 	local csl = {
 		citationID = utils.next_id(8),
 		properties = {
+			unsorted = not config.sorted,
 			formattedCitation = content,
 			plainCitation = nil, -- otherwise we get a barrage of "you have edited this citation" popups
 			-- dontUpdate = false,
@@ -2198,24 +2197,27 @@ local function zotero_ref(cite)
 
 	notfound = false
 	for k, item in pairs(cite.citations) do
-		local itemData, zoteroData = zotero.get(item.id)
+		local itemData = zotero.get(item.id)
 		if itemData == nil then
 			notfound = true
 		else
 			local citation = {
-				id = zoteroData.itemID,
+				id = itemData.custom.itemID,
-				uris = { zoteroData.uri },
+				uris = { itemData.custom.uri },
 				-- uri = { zoteroData.uri },
-				itemData = itemData,
+				itemData = clean_csl(itemData),
 			}
 
 			if item.mode == "AuthorInText" then -- not formally supported in Zotero
 				if config.author_in_text then
-					local authors = zotero.authors(itemData)
+					local authors = itemData.custom.author
-					if authors == nil then
+					if authors == nil or authors == "" then
 						return cite
 					else
 						author_in_text = pandoc.utils.stringify(pandoc.Str(authors)) .. " "
+						author_in_text = '<w:r><w:t xml:space="preserve">'
+							.. utils.xmlescape(author_in_text)
+							.. "</w:t></w:r>"
 						citation["suppress-author"] = true
 					end
 				else
@@ -2258,7 +2260,7 @@ local function zotero_ref(cite)
 		field = field .. '</w:t></w:r><w:r><w:fldChar w:fldCharType="end"/></w:r>'
 
 		return pandoc.RawInline("openxml", field)
-	elseif config.format == "odt" then
+	else
 		if config.transferable then
 			local field = author_in_text
 				.. '<text:a xlink:type="simple" xlink:href="https://www.zotero.org/" text:style-name="Internet_20_link">'
@@ -2380,7 +2382,8 @@ end
 function Meta(meta)
 	-- create meta.zotero if it does not exist
 	if not meta.zotero then
-		meta.zotero = {}
+	    -- ADDED FOR QUARTO 1.4 COMPATIBILITY
+		meta.zotero = meta.zoterolive or {}
 	end
 
 	-- copy meta.zotero_<key>, which are likely command line params and take precedence, over to meta.zotero
@@ -2401,6 +2404,9 @@ function Meta(meta)
 
 	if meta.zotero["csl-style"] ~= nil then
 		config.csl_style = pandoc.utils.stringify(meta.zotero["csl-style"])
+		if config.csl_style == "apa7" then
+			config.csl_style = "apa"
+		end
 	end
 
 	config.transferable = test_boolean("transferable", meta.zotero["transferable"])
@@ -2421,26 +2427,31 @@ function Meta(meta)
 	config.client = meta.zotero.client
 
 	if config.client == "zotero" then
-		zotero.url = "http://127.0.0.1:23119/better-bibtex/export/item?pandocFilterData=true"
+		zotero.url = "http://127.0.0.1:23119/better-bibtex/json-rpc?"
 	elseif config.client == "jurism" then
-		zotero.url = "http://127.0.0.1:24119/better-bibtex/export/item?pandocFilterData=true"
+		zotero.url = "http://127.0.0.1:24119/better-bibtex/json-rpc?"
 	end
 
+	zotero.request = {
+		jsonrpc = "2.0",
+		method = "item.pandoc_filter",
+		params = {
+			style = config.csl_style or "apa",
+		},
+	}
 	if string.match(FORMAT, "odt") and config.scannable_cite then
 		-- scannable-cite takes precedence over csl-style
 		config.format = "scannable-cite"
-		zotero.url = zotero.url .. "&translator=jzon"
+		zotero.request.params.asCSL = false
 	elseif string.match(FORMAT, "odt") or string.match(FORMAT, "docx") then
 		config.format = FORMAT
-		zotero.url = zotero.url .. "&translator=json"
+		zotero.request.params.asCSL = true
 	end
 
 	if type(meta.zotero.library) ~= "nil" then
-		zotero.url = zotero.url .. "&library=" .. utils.urlencode(meta.zotero.library)
+		zotero.request.params.libraryID = meta.zotero.library
 	end
 
-	zotero.url = zotero.url .. "&citationKeys="
-
 	if config.format == "odt" and config.csl_style then
 		-- These will be added to the document metadata by pandoc automatically
 		meta.ZOTERO_PREF_1 = zotero_docpreferences_odt(config.csl_style)