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Module:Autotaxobox

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Documentation for this module may be created at Module:Autotaxobox/doc 

--[[
This module provides support to the automated taxobox system – the templates
Automatic taxobox, Speciesbox, Subspeciesbox, Infraspeciesbox, etc.

In particular it provides a way of traversing the taxonomic hierarchy encoded
in taxonomy templates (templates with names of the form
"Template:Taxonomy/TAXON_NAME") without causing template expansion depth errors.
]]

local TaxonItalics = require('Module:TaxonItalics') -- use a function from Module:TaxonItalics to italicize a taxon name
local p = {}

--[[=========================================================================
Limit the maximum depth of a taxonomic hierarchy that can be traversed;
avoids excessive processing time and protects against incorrectly set up
hierarchies, e.g. loops.
=============================================================================]]
local MaxSearchLevels = 100

function p.getMaxSearchLevels()
	return MaxSearchLevels
end

--[[========================== taxoboxColour ================================
Determines the correct colour for a taxobox, by searching up the taxonomic
hierarchy from the supplied taxon for the first taxon (other than
'incertae sedis') that sets a taxobox colour. It is assumed that a valid
taxobox colour is defined using CSS rgb() syntax.
If no taxon that sets a taxobox colour is found, then 'transparent' is
returned unless the taxonomic hierarchy is too deep, when the error colour is
returned.
Usage: {{#invoke:Autotaxobox|taxoboxColour|TAXON}}
=============================================================================]]
function p.taxoboxColour(frame)
	local currTaxon = frame.args[1] or ''
	local i = 1 -- count levels processed
	local searching = currTaxon ~= '' -- still searching for a colour?
	local foundICTaxon = false -- record whether 'incertae sedis' found
	local colour = '' -- default is no colour
	while searching and i <= MaxSearchLevels do
		local plainCurrTaxon = p.stripExtra(currTaxon) -- remove trailing text after /
		if string.lower(plainCurrTaxon) == 'incertae sedis' then
			foundICTaxon = true
		else
			local possibleColour = frame:expandTemplate{ title = 'Template:Taxobox colour', args = { plainCurrTaxon } }
			if string.sub(possibleColour,1,3) == 'rgb' then
				colour = possibleColour
				searching = false
			end
		end
		if searching then
			local ok, parent = p.getTaxonInfoItem(frame, currTaxon, 'parent')
			if ok and parent ~= '' then
				currTaxon = parent
				i = i + 1
			else
				searching = false -- run off the top of the hierarchy or tried to use non-existent taxonomy template
			end
		end
	end
	if colour ~= '' then
		return colour
	elseif foundICTaxon then
		return frame:expandTemplate{ title = 'Template:Taxobox colour', args = { 'incertae sedis' } }
	elseif searching then
		-- hierarchy exceeds MaxSearchLevels levels
		return frame:expandTemplate{ title = 'Template:Taxobox/Error colour', args = { } }
	else
		return 'transparent'
	end
end

--[[=========================== taxoboxList =================================
Returns the rows of taxa in an automated taxobox, based on the taxonomic
hierarchy for the supplied taxon.
Usage:
{{#invoke:Autotaxobox|taxoboxList|TAXON
|display_taxa = the number of taxa *above* TAXON to force to be displayed
|authority = taxonomic authority for TAXON
|parent_authority = taxonomic authority for TAXON's parent
|gparent_authority = taxonomic authority for TAXON's grandparent
|ggparent_authority = taxonomic authority for TAXON's greatgrandparent
|ggparent_authority = taxonomic authority for TAXON's greatgreatgrandparent
|bold_first = 'bold' to bold TAXON in its row
}}
=============================================================================]]
function p.taxoboxList(frame)
	local currTaxon = frame.args[1] or ''
	local displayN = (tonumber(frame.args['display_taxa']) or 1) + 1
	local auth = frame.args['authority'] or ''
	local parentAuth = frame.args['parent_authority'] or ''
	local gParentAuth = frame.args['gparent_authority'] or ''
	local ggParentAuth = frame.args['ggparent_authority'] or ''
	local gggParentAuth = frame.args['gggparent_authority'] or ''
	local boldFirst = frame.args['bold_first'] or 'link' -- values 'link' or 'bold'
	local taxonTable = p.makeTable(frame, currTaxon)
	local res = ''
	-- display all taxa above possible greatgreatgrandparent
	for i = taxonTable.n, 6, -1 do
		res = res .. frame:expandTemplate{ title = 'Template:Taxobox/showtaxon', args = { taxonTable[i], fc = tostring(displayN >= i) } }
	end
	-- display greatgreatgrandparent, if it exists
	if taxonTable.n >= 5 then
		res = res .. frame:expandTemplate{ title = 'Template:Taxobox/showtaxon', args = { taxonTable[5], authority = gggParentAuth, fc = tostring(displayN >= 5) } }
	end
	-- display greatgrandparent, if it exists; force the display if an infrataxon is below
	if taxonTable.n >= 4 then
		local force = tostring(displayN >= 4) or
		              frame.expandTemplate{ title = 'Template:Infrataxon()', args = { taxonTable[3] } } == 'true' or
		              frame.expandTemplate{ title = 'Template:Infrataxon()', args = { taxonTable[2] } } == 'true'
		res = res .. frame:expandTemplate{ title = 'Template:Taxobox/showtaxon', args = { taxonTable[4], authority = ggParentAuth, fc = tostring(force) } }
	end
	-- display grandparent, if it exists; force the display if an infrataxon is below
	if taxonTable.n >= 3 then
		local force = tostring(displayN >= 3) or
                      frame.expandTemplate{ title = 'Template:Infrataxon()', args = { taxonTable[2] } } == 'true'
        res = res .. frame:expandTemplate{ title = 'Template:Taxobox/showtaxon', args = { taxonTable[3], authority = gParentAuth, fc = tostring(force) } }
	end
	-- display parent, if it exists
	if taxonTable.n >= 2 then
		res = res .. frame:expandTemplate{ title = 'Template:Taxobox/showtaxon', args = { taxonTable[2], authority = parentAuth, fc = tostring(displayN >= 2) } }
	end
	-- display target taxon
	res = res .. frame:expandTemplate{ title = 'Template:Taxobox/showtaxon', args = { taxonTable[1], authority = auth, fc = 'true', format = boldFirst  } }
	return res
end

--[[========================== taxonomyList =================================
Returns the cells of the taxonomy table displayed on the right hand side of
"Template:Taxonomy...." pages.
Usage: {{#invoke:Autotaxobox|taxonomyList|TAXON}}
=============================================================================]]
function p.taxonomyList(frame)
	local currTaxon = frame.args[1] or ''
	if currTaxon == '' then return '| ||ERROR: no taxon supplied\n|-' end
	local taxonTable = p.makeTable(frame, currTaxon)
	local rankTable = p.getRankTable()
	local lastRankVal = 1000000
	local orderOk
	local res = ''
	for i = taxonTable.n, 1, -1 do
		-- check ranks are in right order in the hierarchy
		local ok, rank = p.getTaxonInfoItem(frame, taxonTable[i], 'rank')
		local currRankVal = rankTable[string.lower(rank)]
		if currRankVal then
			orderOk = currRankVal < lastRankVal
			if orderOk then lastRankVal = currRankVal end
		else
			orderOk = true
		end
		-- now return a row of the taxonomy table with anomalous ranks marked
		local errorStr = ''
		if not orderOk then errorStr = 'true' end
		res = res .. frame:expandTemplate{ title = 'Template:Taxonomy links', args = { taxonTable[i], error = errorStr } }
	end
	-- if the last row has an anomalous rank, put the page in the error-tracking category; category statements don't work
	-- inside tables, so need to close the current table first and then open a dummy one (close is in Template:Taxonomy key)
	if not orderOk then
		res = res .. '\n|}\n[[Category:Taxonomy templates showing anomalous ranks]]\n{|\n'
	end
	return res
end

--[[========================= callTaxonomyKey ===============================
Prepares for, and then calls, Template:Taxonomy key to display a taxonomy
template page. It does this by building up the information the template
requires, following one 'same as' link, if required.
Usage:
{{#invoke:Autotaxobox|callTaxonomyKey
|parent=
|rank=
|extinct=
|always_display=
|link_target=value of 'link' parameter in taxonomy template
|link_text=value of parameter 2 in taxonomy template
|same_as=
}}
=============================================================================]]
local SAME_AS = 7
local PARENT = 1
local RANK = 2
local LINK_TARGET = 3
local LINK_TEXT = 4
local ALWAYS_DISPLAY = 5
local EXTINCT = 6
local REFS = 8

function p.callTaxonomyKey(frame)
	local parent = frame.args['parent'] or ''
	local rank = frame.args['rank'] or ''
	local extinct = string.lower(frame.args['extinct']) or ''
	local alwaysDisplay = string.lower(frame.args['always_display']) or ''
	local linkTarget = frame.args['link_target'] or ''
	local linkText = frame.args['link_text'] or '' -- this is the "raw" link text, and can be ''
	local refs = frame.args['refs'] or ''
	local sameAsTaxon = frame.args['same_as'] or ''
	if sameAsTaxon ~= '' then
		-- try using the 'same as' taxon; it's an error if it doesn't exist
		local ok, sameAsInfoStr = pcall(frame.expandTemplate, frame, { title = 'Template:Taxonomy/' .. sameAsTaxon, args = {['machine code'] = 'all' } })
		if ok then
			local sameAsInfo = mw.text.split(sameAsInfoStr, '$', true)
			--'same as' taxon's taxonomy template must not have a 'same as' link
			if sameAsInfo[SAME_AS] == '' then
				if parent == '' then parent = sameAsInfo[PARENT] end
				if rank == '' then rank = sameAsInfo[RANK] end
				if extinct == '' then extinct = string.lower(sameAsInfo[EXTINCT]) end
				if alwaysDisplay == '' then alwaysDisplay = string.lower(sameAsInfo[ALWAYS_DISPLAY]) end
				if linkTarget == '' then linkTarget = sameAsInfo[LINK_TARGET] end
				if linkText == '' then linkText = sameAsInfo[LINK_TEXT] end
				if refs == '' and parent == sameAsInfo[PARENT] then refs = sameAsInfo[REFS] end
			else
				return '<span style="color:red; font-size:1.1em">Error: attempt to follow two "same as" links</span>: <code>same_as = ' .. sameAsTaxon .. '</code>, but [[Template:Taxonomy/' .. sameAsTaxon .. ']] also has a<code>same_as</code> parameter.'
			end
		else
			return frame:expandTemplate{ title = 'Template:Taxonomy key/missing template', args = {taxon=sameAsTaxon, msg='given as the value of <code>same as</code>'} }
		end
	end
	local link = linkTarget
	if linkText ~= '' and linkText ~= linkTarget then link = link .. "|" .. linkText end
	return frame:expandTemplate{ title = 'Template:Taxonomy key',
			args = {parent=parent, rank=rank, extinct=extinct, always_display=alwaysDisplay, link_target=linkTarget, link=link, refs=refs, same_as=sameAsTaxon} }
end

--[[============================ taxonInfo ==================================
Extracts and returns information from Template:Taxonomy/TAXON, following
one 'same as' link if required.
Usage: {{#invoke:Autotaxobox|taxonInfo|TAXON|ITEM}}
ITEM is one of: 'parent', 'rank', 'link target', 'link text', 'link', 'extinct',
'always display', 'refs', 'same as' or 'all'.
If ITEM is not specified, the default is 'all' – all values in a single string
separated by '$'.
=============================================================================]]
function p.taxonInfo(frame)
	local taxon = frame.args[1] or ''
	local item = frame.args[2] or ''
	if item == '' then item = 'all' end
	local ok, info = p.getTaxonInfoItem(frame, taxon, item)
	return info
end

--[[============================ taxonLink ==================================
Returns a wikilink to a taxon, if required including '†' before it and
' (?)' after it, and optionally italicized or bolded without a wikilink.
Usage:
{{#invoke:Autotaxobox|taxonLink
|taxon=           : having '/?' at the end triggers the output of ' (?)'
|extinct=         : 'yes' or 'true' trigger the output of '†'
|bold=            : 'yes' makes the core output bold and not wikilinked
|italic=          : 'yes' makes the core output italic
|link_target=     : target for the wikilink
link_text=        : text of the wikilink (may be same as link_target), without †, italics, etc.
}}
=============================================================================]]
function p.taxonLink(frame)
	local taxon = frame.args['taxon'] or ''
	local extinct = string.lower(frame.args['extinct'] or '')
	local bold = frame.args['bold'] or ''
	local italic = frame.args['italic'] or ''
	local linkTarget = frame.args['link_target'] or ''
	local linkText = frame.args['link_text'] or frame.args['plain_link_text'] or '' --temporarily allow alternative args
	-- if link text is missing, try to find a replacement
	if linkText == '' then
		if string.find(taxon, 'Incertae sedis', 1, true) then
			linkText = "''incertae sedis''"
			linkTarget = 'Incertae sedis'
		else
			linkText = p.stripExtra(taxon)
		end
	end
	if linkTarget == '' then linkTarget = linkText end
	if italic == 'yes' then linkText = TaxonItalics.italicizeTaxonName(linkText, false) end
	local link = ''
	if bold == 'yes' then link = '<b>' .. linkText .. '</b>'
	else
		if linkTarget == linkText then link = linkText
		else link = linkTarget .. '|' .. linkText
		end
		link = '[[' .. link .. ']]'
	end
	if (extinct == 'yes' or extinct == 'true') and not string.find(link, '†', 1, true) then
		link = '<span style="font-style:normal;font-weight:normal;">†</span>' .. link
	end
	if string.sub(taxon, -2) == '/?' and not string.find(link, '?', 1, true) then
		link = link .. '<span style="font-style:normal;font-weight:normal;"> (?)</span>'
	end
	return link
end

--[[========================== showRankTable ================================
Returns a wikitable showing the ranks and their values as set up by
getRankTable().
Usage: {{#invoke:Autotaxobox|showRankTable}}
=============================================================================]]

function p.showRankTable(frame)
	local rankTable = p.getRankTable()
	local res = '{| class="wikitable sortable"\n|+ Ranks checked in taxonomy templates\n! Rank !! Shown as !! Value\n'
	for k, v in pairs(rankTable) do
		local rankShown = frame:expandTemplate{ title = 'Template:Anglicise rank', args = { k } }
		res = res .. '|-\n|' .. k .. '||' .. rankShown .. '||' .. v .. '\n'
	end
	return res .. '|}\n'
end

--[[============================== find =====================================
Returns the taxon above the specified taxon with a given rank.
Usage: {{#invoke:Autotaxobox|find|TAXON|RANK}}
=============================================================================]]

function p.find(frame)
	local currTaxon = frame.args[1] or ''
	if currTaxon == '' then return '<span class="error">no taxon supplied</span>' end
	local rank = frame.args[2] or ''
	if rank == '' then return '<span class="error">no rank supplied</span>' end
	local inHierarchy = true -- still in the taxonomic hierarchy or off the top?
	local searching = true -- still searching
	while inHierarchy and searching do
		local ok, parent = p.getTaxonInfoItem(frame, currTaxon, 'parent')
			if ok and parent ~= '' then
			currTaxon = parent
			local ok, currRank = p.getTaxonInfoItem(frame, currTaxon, 'rank')
			if currRank == rank then
				searching = false
			end
		else
			inHierarchy = false
		end
	end
	if inHierarchy and not searching then return currTaxon
	else return '<span class="error">rank not found</span>'
	end
end

--[[=============================== nth =====================================
External utility function primarily intended for use in checking and debugging.
Returns the nth level above a taxon in a taxonomic hierarchy, where the taxon
itself is counted as the first level.
Usage: {{#invoke:Autotaxobox|nth|TAXON|n=N}}
=============================================================================]]
function p.nth(frame)
	local currTaxon = frame.args[1] or ''
	if currTaxon == '' then return 'ERROR: no taxon supplied' end
	local n = tonumber(frame.args['n'] or 1)
	if n > MaxSearchLevels then
		return 'Exceeded maximum number of levels allowed (' .. MaxSearchLevels .. ')'
	end
	local i = 1
	local inHierarchy = true -- still in the taxonomic hierarchy or off the top?
	while i < n and inHierarchy do
		local ok, parent = p.getTaxonInfoItem(frame, currTaxon, 'parent')
			if ok and parent ~= '' then
			currTaxon = parent
			i = i + 1
		else
			inHierarchy = false
		end
	end
	if inHierarchy then return currTaxon
	else return 'Level ' .. n .. ' is past the top of the taxonomic hierarchy'
	end
end

--[[============================= nLevels ===================================
External utility function primarily intended for use in checking and debugging.
Returns number of levels in a taxonomic hierarchy, starting from
the supplied taxon as level 1.
Usage: {{#invoke:Autotaxobox|nLevels|TAXON}}
=============================================================================]]
function p.nLevels(frame)
	local currTaxon = frame.args[1] or ''
	if currTaxon == '' then return 'ERROR: no taxon supplied' end
	local i = 1
	local inHierarchy = true -- still in the taxonomic hierarchy or off the top?
	while inHierarchy and i < MaxSearchLevels  do
		local ok, parent = p.getTaxonInfoItem(frame, currTaxon, 'parent')
		if ok and parent ~= '' then
			currTaxon = parent
			i = i + 1
		else
			inHierarchy = false
		end
	end
	if inHierarchy then return MaxSearchLevels .. '+'
	else return i
	end
end

--[[============================= listAll ===================================
External utility function primarily intended for use in checking and debugging.
Returns a comma separated list of a taxonomic hierarchy, starting from
the supplied taxon.
Usage: {{#invoke:Autotaxobox|listAll|TAXON}}
=============================================================================]]
function p.listAll(frame)
	local currTaxon = frame.args[1] or ''
	if currTaxon == '' then return 'ERROR: no taxon supplied' end
	return p.listTaxa(p.makeTable(frame, currTaxon))
end

--[[=========================================================================
Internal functions
=============================================================================]]

--[[= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Internal utility function to strip off any extra parts of a taxon name, i.e.
anything after a '/'. Thus "Felidae/?" would be reduced to "Felidae".
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function p.stripExtra(taxonName)
	local i = string.find(taxonName,'/')
	if i then
		return string.sub(taxonName,1,i-1)
	else
		return taxonName
	end
end

--[[= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Internal utility function to convert a taxon table to a comma-separated list.
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function p.listTaxa(taxonTable)
	local lst = taxonTable[1]
	for i = 2, taxonTable.n, 1 do
		lst = lst .. ', ' .. taxonTable[i]
	end
	return lst
end

--[[= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Internal utility function to extract an item of information from a 
taxonomy template, following one 'same as' link if required.
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function p.getTaxonInfoItem(frame, taxon, item)
	-- item == 'link' is a special case
	if item == 'link' then
		return p.getTaxonInfoLink(frame, taxon)
	end
	-- item ~= 'link'
	local ok, info = pcall(frame.expandTemplate, frame, { title = 'Template:Taxonomy/' .. taxon, args = {['machine code'] = item } })
	if ok then
		if info == '' then
			-- try 'same as'
			local sameAsTaxon = frame:expandTemplate{ title = 'Template:Taxonomy/' .. taxon, args = {['machine code'] = 'same as' } }
			if sameAsTaxon ~= '' then
				ok, info = pcall(frame.expandTemplate, frame, { title = 'Template:Taxonomy/' .. sameAsTaxon, args = {['machine code'] = item } })
			end
		end
	end
	if ok then
		-- if item is 'link_text' check whether '(?)' needs to be added
		if item == 'link_text' and string.sub(taxon, -2) == '/?' and not string.find(info, '?', 1, true) then
			info = info .. '<span style="font-style:normal;font-weight:normal;"> (?)</span>'
		end
	else
		info = '[[Template:Taxonomy/' .. taxon .. ']]' --error indicator in code before conversion to Lua
	end
	return ok, info
end

function p.getTaxonInfoLink(frame, taxon)
	local ok, linkText, linkTarget
	local link = ''
	ok, linkText = p.getTaxonInfoItem(frame, taxon, 'link_text')
	if ok then
		ok, linkTarget = p.getTaxonInfoItem(frame, taxon, 'link_target')
		if ok then
			if linkText == linkTarget then link = linkText
			else link = linkTarget .. '|' .. linkText
			end
		end
	end
	return ok, link
end

--[[= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Internal utility function to return a table (array) constructed from a
taxonomic hierarchy stored in "Template:Taxonomy/..." templates.
TABLE.n holds the total number of taxa; TABLE[1]..TABLE[TABLE.n] the taxon
names.
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function p.makeTable(frame, currTaxon)
	local i = 1
	local inHierarchy = true -- still in the taxonomic hierarchy or off the top?
	local taxonTable = {}
	taxonTable[1] = currTaxon;
	while i < MaxSearchLevels and inHierarchy do
		local ok, parent = p.getTaxonInfoItem(frame, currTaxon, 'parent')
		if ok and parent ~= '' then
			currTaxon = parent
			i = i + 1
			taxonTable[i] = currTaxon
		else
			inHierarchy = false -- run off the top of the hierarchy or tried to use non-existent taxonomy template
		end
	end
	taxonTable.n = i
	return taxonTable
end

--[[= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Internal utility function to set up a table of numerical values corresponding
to 'Linnaean' ranks, with upper ranks having higher values. In a valid
taxonomic hierarchy, a lower rank should never have a higher value than a
higher rank. The actual numerical values are arbitrary so long as they are
ordered.
The ranks should correspond to those in Template:Anglicise ranks.
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function p.getRankTable()
	return {
		classis = 1400,
		cohort = 1100,
		divisio = 1500,
		domain = 1700,
		familia = 800,
		forma = 100,
		genus = 600,
		grandordo = 1005,
		['grandordo-mb'] = 1002,
		infraclassis = 1397,
		infralegio = 1197,
		infraordo = 997,
		infraphylum = 1497,
		infraregnum = 1597,
		infratribus = 697,
		legio = 1200,
		magnordo = 1006,
		microphylum = 1495,
		micrordo = 995,
		mirordo = 1004,
		['mirordo-mb'] = 1001,
		nanophylum = 1494,
		nanordo = 994,
		ordo = 1000,
		parafamilia = 800,
		parvordo = 996,
		phylum = 1500,
		regnum = 1600,
		sectio = 500,
		--series = 400, used too inconsistently to check
		species = 300,
		subclassis = 1398,
		subcohort = 1098,
		subdivisio = 1498,
		subfamilia = 798,
		subgenus = 598,
		sublegio = 1198,
		subordo = 998,
		subphylum = 1498,
		subregnum = 1598,
		subsectio = 498,
		subspecies = 298,
		subtribus = 698,
		superclassis = 1403,
		supercohort = 1103,
		superdivisio = 1503,
		superdomain = 1703,
		superfamilia = 803,
		superlegio = 1203,
		superordo = 1003,
		superphylum = 1503,
		superregnum = 1603,
		supertribus = 703,
		tribus = 700,
		varietas = 200,
		zoodivisio = 1300,
		zoosectio = 900,
		zoosubdivisio = 1298,
		zoosubsectio = 898,
	}
end

return p
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