--[[*************************************************************************

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.

*****************************************************************************]]



require('strict')

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

local TableRow = '|-\n'

local TableEnd = '|}\n'

local p = {} -- functions made public

local l = {} -- internal functions, kept separate

local colour = '' -- colour for taxobox and taxonomy listings



--[[=========================================================================

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.

The value can be obtained externally via

{{#invoke:Autotaxobox|getMaxSearchLevels}}

=============================================================================]]

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)

	return p.getTaxoboxColour(frame, frame.args1 or '')

end



function p.getTaxoboxColour(frame, currTaxon)

	-- note that colour is global to this function; default is empty string

	local i = 1 -- count levels processed

	local searching = currTaxon ~= '' -- still searching for a colour?

	local foundICTaxon = false -- record whether 'incertae sedis' found

	while searching and i <= MaxSearchLevels do

		local plainCurrTaxon, dummy = l.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

		if foundICTaxon then

			colour = frame:expandTemplate{ title = 'Template:Taxobox colour', args = { 'incertae sedis' } }

		elseif searching then

			-- hierarchy exceeds MaxSearchLevels levels

			colour = frame:expandTemplate{ title = 'Template:Taxobox/Error colour', args = { } }

		else

			colour = 'transparent'

		end

	end

	return colour

end



--[[= = = = = = = = = = = = =  topLevelTaxon  = = = = = = = = = = = = = = = = 

Defines the correct top level taxa, one of which should terminate every

taxonomic hierarchy encoded in taxonomy templates.

= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]

function l.topLevelTaxon(taxon)

	return  taxon == 'Life' or taxon == 'Veterovata' or taxon == 'Ichnos'

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

|virus = 'yes' to apply virus taxa italicization standards

}}

=============================================================================]]

function p.taxoboxList(frame)

	local currTaxon = frame.args1 or ''

	if currTaxon == '' then return '' end

	local displayN = (tonumber(frame.args'display_taxa']) or 1) + 1

	local authTable = {}

	authTable1 = frame.args'authority' or ''

	authTable2 = frame.args'parent_authority' or ''

	authTable3 = frame.args'gparent_authority' or ''

	authTable4 = frame.args'ggparent_authority' or ''

	authTable5 = frame.args'gggparent_authority' or ''

	local boldFirst = frame.args'bold_first' or 'link' -- values 'link' or 'bold'

	local virus = frame.args'virus' or 'no' -- values 'yes' or 'no'

	local offset = tonumber(frame.args'offset' or 0)

	-- adjust the authority table if 'authority' refers to a rank lower than the target taxon

	if offset ~= 0 then

		for i = 1, 5 do

			local j = i + offset

			if j <= 5 then

				authTablei = authTablej

			else

				authTablei = ''

			end

		end

	end

	local taxonTable, taxonRankTable = l.makeTable(frame, currTaxon)

	local res = ''

	local topTaxonN = taxonTable.n

	-- display all taxa above possible greatgreatgrandparent, without authority

	for i = topTaxonN, 6, -1 do

		res = res .. l.showTaxon(frame, taxonTablei], taxonRankTablei], topTaxonN==i, '', displayN >= i, '', virus)

	end

	-- display all taxa above possible parent, with authority if given

	for i = math.min(topTaxonN, 5), 2, -1 do

		res = res .. l.showTaxon(frame, taxonTablei], taxonRankTablei], topTaxonN==i, authTablei], displayN >= i, '', virus)

	end

	-- display target taxon, always displayed and emboldened

	res = res .. l.showTaxon(frame, taxonTable1], taxonRankTable1], topTaxonN==1, authTable1], true, boldFirst, virus)

	return res

end



--[[= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =

Show one taxon row in a taxobox.

= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]

function l.showTaxon(frame, taxon, rank, isTopTaxon, auth, force, boldFirst, virus)

	-- it's an error if this is the top taxon and it's not a top level taxon (e.g. "Life")

	if isTopTaxon then

		if l.topLevelTaxon(taxon) then

			return '' -- don't display a top level taxon

		elseif (mw.title.new('Taxonomy/'..taxon, 'Template') or {}).exists then

			-- taxonomy template for this taxon has no parent specified

			return frame:expandTemplate{ title = 'Template:Create taxonomy', args = {taxon, msg='Taxonomy template does not specify a parent'} } .. '\n' .. TableRow

		else

			-- no taxonomy template for this taxon

			return frame:expandTemplate{ title = 'Template:Create taxonomy', args = {taxon, msg='Missing taxonomy template'} } .. '\n' .. TableRow

		end

	else

		-- if showing is not already forced, force if it's a principal rank or an authority is specified

		force = force or frame:expandTemplate{ title = 'Template:Principal rank', args = {rank} } == 'yes' or

		        auth ~= ''

		if not force then

			-- if showing is still not already forced, force if the taxonomy template has 'always_display' set

			local ok, alwaysDisplay = p.getTaxonInfoItem(frame, taxon, 'always_display')

			force = alwaysDisplay == 'yes' or  alwaysDisplay == 'true'

		end

		if force then

			local res = l.tableCell(frame:expandTemplate{ title = 'Template:Anglicise rank', args = {rank} } .. ':')

			local bold = 'no'

			if boldFirst == 'bold' then bold = 'yes' end

			if auth ~= '' then

				auth = '<br><small>' .. auth .. '</small>'

			end

			local res = res .. l.tableCell(l.getTaxonLink(frame, taxon, rank, bold, '', '', virus) .. auth) -- italic, abbreviated

			return res .. TableRow

		else

			return ''

		end

	end

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.args1 or ''

	if currTaxon == '' then

		return '{|class="infobox biota"\n' .. TableRow .. l.tableCell('') .. l.tableCell('ERROR: no taxon supplied') .. TableEnd

	end

	local taxonTable, taxonRankTable = l.makeTable(frame, currTaxon)

	local rankValTable = l.getRankTable()

	local lastRankVal = 1000000

	local orderOk = true

	-- check whether the taxonomy is for viruses; use already determined taxon colour if possible

	local virus = 'no'

	local taxoColour = colour

	if taxoColour == '' then

		if  taxonTabletaxonTable.n == 'Ichnos' or taxonTabletaxonTable.n == 'Veterovata' then

			taxoColour = frame:expandTemplate{ title = 'Template:Taxobox colour', args = { taxonTabletaxonTable.n } }

		else

			taxoColour = frame:expandTemplate{ title = 'Template:Taxobox colour', args = { taxonTabletaxonTable.n - 1 } }

		end

	end

	if taxoColour == frame:expandTemplate{ title = 'Template:Taxobox colour', args = { 'virus' } } then

		virus = 'yes'

	end

	-- add information message

	local res = '<p style="float:right">Bold ranks show taxa that will be shown in taxoboxes<br>because rank is principal or <code>always_display=yes</code>.</p>\n'



	-- start table

	res =  res .. '{| class="infobox biota" style="text-align: left; font-size:100%"\n' .. TableRow .. '! colspan=4 style="text-align: center; color:inherit; background-color: '

	            .. taxoColour .. '"|Ancestral taxa\n'

	-- deal first with the top level taxon; if there are no errors, it should be Life/Veterovata/Ichnos, which are 

	-- not displayed

	local taxon = taxonTabletaxonTable.n

	if not l.topLevelTaxon(taxon) then

		local msg = 'Taxonomy template missing'

		if mw.title.new('Taxonomy/'..taxon, 'Template').exists then

			msg = 'Parent taxon needed'

		end

		res = res .. TableRow .. l.tableCell('colspan=2', frame:expandTemplate{title = 'Template:Create taxonomy', args = {taxon, msg = msg}})

	end

	-- now output the rest of the table

	local currRankVal

	for i = taxonTable.n-1, 1, -1 do

		-- check ranks are in right order in the hierarchy

		taxon = taxonTablei

		local rank = taxonRankTablei

		currRankVal = l.lookupRankVal(rankValTable, rank)

		if currRankVal then

			orderOk = currRankVal < lastRankVal

			if orderOk then lastRankVal = currRankVal end

		else

			orderOk = true

		end

		-- see if the row will be displayed in a taxobox; bold the rank if so

		local boldRank = false

		local ok, alwaysDisplay = p.getTaxonInfoItem(frame, taxon, 'always_display')

		if ok and (alwaysDisplay == 'yes' or alwaysDisplay == 'true') then

			boldRank = true

		else

			boldRank = frame:expandTemplate{ title = 'Template:Principal rank', args = {rank} } == 'yes'

		end

		-- now return a row of the taxonomy table with anomalous ranks marked

		local errorStr = ''

		if not orderOk then errorStr = 'yes' end

		local link = l.getTaxonLink(frame, taxon, rank, '', '', '', virus) -- bold, italic, abbreviated

		res = res .. l.taxonomyListRow(frame, taxon, rank, link, boldRank, errorStr)

	end

	-- close table

	res = res .. TableEnd

	-- error-tracking for taxonomy templates

	-- if the last row has an anomalous rank, put the page in an error-tracking category

	local errCat1 = ''

	if not orderOk then

		errCat1 = '[[Category:Taxonomy templates showing anomalous ranks]]\n'

	end

	-- if the last row has a taxon name in the page name that does not match the link text,

	-- put the taxonomy template in a tracking category

	local dummy, linkText = p.getTaxonInfoItem(frame, taxon, 'link_text')

	local match = l.matchTaxonLink(taxon, linkText, currRankVal and currRankVal < rankValTable'genus'])

	local errCat2 = ''

	if not match then

		errCat2 = '[[Category:Taxonomy templates with name and link text not matching|' .. taxon .. ']]\n'

	end

	if errCat1..errCat2 ~= '' then

		res = res .. frame:expandTemplate{ title = 'Template other', args = { errCat1..errCat2} }

	end

	return res

end



--[[ = = = = = = = = = = = = = = taxonomyListRow  = = = = = = = = = = = = = = 

Returns a single row of the taxonomy table displayed on the right hand side

 of "Template:Taxonomy...." pages.

= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]

function l.taxonomyListRow(frame, taxon, rank, link, boldRank, error)

	local res = ''

	if taxon == '' or rank == '' then return res end

	local baseTaxon, qualifier = l.stripExtra(taxon)

	-- if appropriate, make it clear that some taxa have been skipped via a ... row

	if qualifier == '/skip' then

		res = res .. TableRow .. l.tableCell('.....') .. l.tableCell('.....')

	end

	-- now generate a row of the table

	res = res .. TableRow

	local cellContent = ''

	local anglicizedRank = frame:expandTemplate{ title = 'Template:Anglicise rank', args = { rank } }

	if boldRank then

		cellContent = cellContent .. '<b>' .. anglicizedRank .. '</b>:'

	else

		cellContent = cellContent .. anglicizedRank .. ':'

	end

	if error == 'yes' then

		cellContent = '<span style="background-color:#FDD">' .. cellContent .. '</span>'

	end

	res = res .. l.tableCell(cellContent)

	          .. l.tableCell('<span style="white-space:nowrap;">' .. link .. '</span>')

	          .. l.tableCell('<span style="font-size:smaller;white-space:nowrap;">' .. qualifier  .. '</span>')

	          .. l.tableCell('<span style="white-space:nowrap;">' .. frame:expandTemplate{ title = 'Template:Edit a taxon', args = { taxon } } .. '</span>')

	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 PARENT = 1

local RANK = 2

local LINK_TARGET = 3

local LINK_TEXT = 4

local ALWAYS_DISPLAY = 5

local EXTINCT = 6

local SAME_AS = 7

local REFS = 8



function p.callTaxonomyKey(frame)

	local taxon = frame.args'taxon' or ''

	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 sameAsInfoSAME_AS == '' then

				if parent == '' then parent = sameAsInfoPARENT end

				if rank == '' then rank = sameAsInfoRANK end

				if extinct == '' then extinct = string.lower(sameAsInfoEXTINCT]) end

				if alwaysDisplay == '' then alwaysDisplay = string.lower(sameAsInfoALWAYS_DISPLAY]) end

				if linkTarget == '' then linkTarget = sameAsInfoLINK_TARGET end

				if linkText == '' then linkText = sameAsInfoLINK_TEXT end

				if refs == '' and parent == sameAsInfoPARENT then refs = sameAsInfoREFS 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

	-- check consistency of extinct status; if this taxon is not extinct, parent must not be either

	local extinctError = 'no'

	if parent ~= '' and (extinct == '' or extinct == 'no' or extinct == 'false') then

		local ok, parentExtinct = p.getTaxonInfoItem(frame, parent, 'extinct')

		if ok and (parentExtinct == 'yes' or parentExtinct == 'true') then extinctError = 'yes' end

	end

	return frame:expandTemplate{ title = 'Template:Taxonomy key',

			args = {taxon=taxon, parent=parent, rank=rank, extinct=extinct, always_display=alwaysDisplay, link_target=linkTarget, link=link, refs=refs, same_as=sameAsTaxon, extinct_error = extinctError} }

end



--[[============================= showRefs ==================================

Shows the refs field in a taxonomy template, handing incertae sedis taxa and

using '–' for absent refs.

Usage: {{#invoke:Autotaxobox|showRefs|TAXON|REFS}}

=============================================================================]]

function p.showRefs(frame)

	local taxonName = frame.args1 or ''

	local refs = frame.args2 or ''

	return l.doShowRefs(taxonName, refs)

end



--[[= = = = = = = = = = = = = = doShowRefs  = = = = = = = = = = = = = = = = =

Show the refs field in a taxonomy template.

= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]

function l.doShowRefs(taxonName, refs)

	if mw.text.split(taxonName, '/', true)[1 == 'Incertae sedis' then

		refs = 'not applicable (<i>incertae sedis</i>)'

	elseif refs == '' then

		refs = '–'

	end

	return refs

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', '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.args1 or ''

	local item = frame.args2 or ''

	if item == '' then item = 'all' end

	local ok, info = p.getTaxonInfoItem(frame, taxon, item)

	return info

end



--[[= = = = = = = = = = = getTaxonInfoItem  = = = = = = = = = = = = = = = = =

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)

	local ok, info

	-- item == 'dagger' is a special case

	if item == 'dagger' then

		ok, info = p.getTaxonInfoItem(frame, taxon, 'extinct')

		if ok then

			if info == 'yes' or info == 'true' then

				info = '&dagger;'

			else

				info = ''

			end

		end

	-- item ~= 'dagger'

	else

		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

	end

	if ok then

		-- if item is 'link_text', trim info and check whether '(?)' needs to be added

		if item == 'link_text' then

			-- there is a newline at the end of linkText when taxonomy template has "|link = LINK_TARGET|LINK_TEXT"

			info = mw.text.trim(info)

			if string.sub(taxon, -2) == '/?' and not string.find(info, '?', 1, true) then

				info = info .. '<span style="font-style:normal;font-weight:normal;">&nbsp;(?)</span>'

			end

		end

	else

		info = '[[Template:Taxonomy/' .. taxon .. ']]' --error indicator in code before conversion to Lua

	end

	return ok, 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 abbreviated = frame.args'abbreviated' 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

	return l.makeLink(taxon, extinct, bold, italic, abbreviated, linkTarget, linkText)

end



--[[= = = = = = = = = = = = = = getTaxonLink  = = = = = = = = = = = = = = = =

Internal function to drive l.makeLink().

= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]

function l.getTaxonLink(frame, taxon, rank, bold, italic, abbreviated, virus)

	local ok, extinct = p.getTaxonInfoItem(frame, taxon, 'extinct')

	if italic == '' then

		italic = frame:expandTemplate{ title = 'Template:Is italic taxon', args = { rank, virus = virus } }

	end

	local ok, linkTarget = p.getTaxonInfoItem(frame, taxon, 'link_target')

	local ok, linkText = p.getTaxonInfoItem(frame, taxon, 'link_text')

	return l.makeLink(taxon, extinct, bold, italic, abbreviated, linkTarget, linkText)

end



--[[= = = = = = = = = = = = = = makeLink  = = = = = = = = = = = = = = = = = =

Actually make the link.

= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]

function l.makeLink(taxon, extinct, bold, italic, abbreviated, linkTarget, linkText)

	local dummy

	-- 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, dummy = l.stripExtra(taxon)

		end

	end

	if linkTarget == '' then linkTarget = linkText end

	if italic == 'yes' then linkText = TaxonItalics.italicizeTaxonName(linkText, false, abbreviated=='yes') 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;">&nbsp;(?)</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 = l.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 .. TableRow .. l.tableCell(k) .. l.tableCell(rankShown) .. l.tableCell(v)

	end

	return res .. TableEnd

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.args1 or ''

	if currTaxon == '' then return '<span class="error">no taxon supplied</span>' end

	local rank = frame.args2 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.args1 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.args1 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.args1 or ''

	if currTaxon == '' then return 'ERROR: no taxon supplied' end

	return l.doListAll(l.makeTable(frame, currTaxon))

end



function l.doListAll(taxonTable, taxonRankTable)

	local lst = taxonTable1 .. '-' .. tostring(taxonRankTable1])

	for i = 2, taxonTable.n, 1 do

		lst = lst .. ', ' .. taxonTablei .. '-' .. taxonRankTablei

	end

	return lst

end



--[[=========================== removeQualifier ================================

External utility function to remove a qualifier (any part after a "/") from a 

taxon name.

Usage: {{#invoke:Autotaxobox|removeQualifier|TAXON}}

=============================================================================]]

function p.removeQualifier(frame)

	local baseName, qualifier = l.stripExtra(frame.args1])

	return baseName

end



--[[=========================================================================

Internal functions

=============================================================================]]



--[[= = = = = = = = = = = = stripExtra  = = = = = = = = = = = = = = = = = = =

Internal utility function to strip off any extra parts of a taxon name, i.e.

anything after a '/'. Thus 'Felidae/?' would be split into 'Felidae' and '?'.

= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]

function l.stripExtra(taxonName)

	local i = mw.ustring.find(taxonName, '/', 1, true)

	if i then

		return mw.ustring.sub(taxonName, 1, i-1), mw.ustring.sub(taxonName, i, -1)

	else

		return taxonName, ''

	end

end



--[[= = = = = = = = = = = = splitTaxonName  = = = = = = = = = = = = = = = = =

Internal utility function to split a taxon name into its parts and return

them. Possible formats include:

* taxon

* taxon (disambig)

* taxon (Subgenus)

* taxon/qualifier

* combinations, e.g. taxon (disambig)/qualifier

= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]

function l.splitTaxonName(taxon)

	-- get any qualifier present

	local qualifier = ''

	local i = mw.ustring.find(taxon, '/', 1, true)

	if i then

		qualifier = mw.ustring.sub(taxon, i+1, -1)

		taxon = mw.ustring.sub(taxon, 1, i-1)

	end

	-- get any disambiguator or subgenus

	local disambig = ''

	local subgenus = ''

	i = mw.ustring.find(taxon, ' (', 1, true)

	if i then

		local parenTerm = mw.ustring.sub(taxon, i+2, -2)

		taxon = mw.ustring.sub(taxon, 1, i-1)

		local char1 = mw.ustring.sub(parenTerm, 1, 1)

		if char1 == mw.ustring.lower(char1) then

			disambig = parenTerm

		else

			subgenus = parenTerm

		end

	end

	return taxon, disambig, subgenus, qualifier

end



--[[= = = = = = = = = = = = matchTaxonLink  = = = = = = = = = = = = = = = = =

Function to determine whether the taxon name derived from the name of the 

taxonomy template (passed in the parameter taxon) matches the link text

(passed in the parameter linkText).

The taxon name may have any of the formats:

* baseTaxon/qualifier

* baseTaxon (disambig)

* baseTaxon (Subgenus) [distinguished by the capital letter]

* a qualifier may be present after the previous two formats.



Examples of matches (baseTaxon ~ linkText):

* Pinus ~ Pinus

* Pinus sect. Trifoliae ~ Pinus sect. Trifoliae

* Pinus sect. Trifoliae ~ ''Pinus'' sect. ''Trifoliae'' [italic markers ignored]

* Pinus sect. Trifoliae ~ P. sect. Trifoliae [abbreviated genus name matches]

* Bombus (Pyrobombus) ~ Bombus (Pyrobombus)

* Bombus (Pyrobombus) ~ B. (Pyrobombus)

* Bombus (Pyrobombus) ~ Pyrobombus [link text may just be the subgenus]

* Heteractinida ~ "Heteractinida" [double-quotes are ignored in link text]

* "Heteractinida" ~ Heteractinida [double-quotes are ignored in base taxon name]

* Incertae sedis ~ anything [link text is ignored for matching in this case]

* Cetotheriidae with qualifier=? ~ Cetotheriidae (?)

= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]

function l.matchTaxonLink(taxon, linkText, rankBelowGenus)

	local dummy

	linkText, dummy = mw.ustring.gsub(linkText, "''", '') -- remove any italic wikitext in the link text

	linkText, dummy = mw.ustring.gsub(linkText, '<.->', '') -- strip all tags used to format the link text

	linkText, dummy = mw.ustring.gsub(linkText, '"', '') -- remove any occurrences of " in the link text

	local baseTaxon, disambig, subgenus, qualifier = l.splitTaxonName(taxon) -- split up the taxon name

	baseTaxon, dummy = mw.ustring.gsub(linkText, '"', '') -- remove any occurrences of " in the base taxon name

	local match = linkText == baseTaxon or

	              linkText == subgenus or

	              linkText == baseTaxon .. ' (' .. subgenus .. ')' or

	              linkText ==  mw.ustring.sub(baseTaxon, 1, 1) .. '. (' .. subgenus .. ')' or

	              baseTaxon == 'Incertae sedis' or

	              rankBelowGenus and linkText == mw.ustring.gsub(baseTaxon, '([A-Z]).- (.*)', '%1. %2') or 

	              mw.ustring.find(qualifier, '?', 1, true) and mw.ustring.find(linkText, baseTaxon, 1, true) == 1

	return match

end



--[[= = = = = = = = = = = = = makeTable = = = = = = = = = = = = = = = = = = =

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.

The last taxon in the table will either (a) have a taxonomy template but with

no parent given (e.g. 'Life') or (b) not have a taxonomy template.

= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]

function l.makeTable(frame, currTaxon)

	local taxonTable = {}

	local taxonRankTable = {}

	local ok, rank, parent

	local i = 1

	local topReached = false -- reached the top of the taxonomic hierarchy?

	repeat

		taxonTablei = currTaxon

		ok, rank = p.getTaxonInfoItem(frame, currTaxon, 'rank')

		if ok then taxonRankTablei = string.lower(rank) else taxonRankTablei = '' end

		ok, parent = p.getTaxonInfoItem(frame, currTaxon, 'parent')

		if ok and parent ~= '' then

			currTaxon = parent

			i = i + 1

		else

			topReached = true -- reached the top of the hierarchy or tried to use a non-existent taxonomy template

		end

	until topReached or i > MaxSearchLevels

	taxonTable.n = math.min(i, MaxSearchLevels)

	return taxonTable, taxonRankTable

end



--[[= = = = = = = = = = = = getRankTable  = = = = = = = = = = = = = = = = = =

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 l.getRankTable()

	return {

		classis = 1400,

		cohort = 1100,

		divisio = 1500,

		domain = 1700,

		epifamilia =  802,

		familia = 800,

		forma = 100,

		genus = 600,

		grandordo = 1005,

		'grandordo-mb' = 1002,

		hyperfamilia = 805;

		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,

		parvclassis = 1396; -- same as subterclassis

		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,

		subterclassis = 1396; -- same as parvclassis

		subtribus = 698,

		superclassis = 1403,

		supercohort = 1103,

		superdivisio = 1503,

		superdomain = 1703,

		superfamilia = 803,

		superlegio = 1203,

		superordo = 1003,

		superphylum = 1503,

		superregnum = 1603,

		supersectio = 503,

		supertribus = 703,

		tribus = 700,

		varietas = 200,

		zoodivisio = 1300,

		zoosectio = 900,

		zoosubdivisio = 1298,

		zoosubsectio = 898,

	}

end



--[[= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =

Function to look up the arbitrary numerical value of a rank in a rank value

table. "Ichno" and "oo" ranks are not stored separately, so if present the

prefix is removed.

= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]

function l.lookupRankVal(rankValTable, rank)

	local rankVal = rankValTablerank

	if not rankVal then

		-- may be an "ichno" or "oo" rank; try removing "ichno-" or "oo-"

		local baseRank = mw.ustring.gsub(mw.ustring.gsub(rank, '^ichno', ''), '^oo', '')

		if baseRank == 'rdo' then baseRank = 'ordo' end

		-- if an "ichno" or "oo" rank, lower rank value slightly so it is ok below the base rank

		rankVal = rankValTablebaseRank

		if rankVal then

			rankVal = rankVal - 0.1

		end

	end

	return rankVal

end



--[[= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =

= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]

function l.tableCell(arg1, arg2)

	local text, style

	if arg2 then

		style = arg1

		text = arg2

	else

		style = ''

		text = arg1

	end

	local res = '|'

	if style ~= '' then

		res = res .. style .. '|'

	end

	return res .. text .. '\n'

end



return p