Editing Module:Biota infobox/core

require('strict')

local p = {}
local templateArgs = {}
local info = {}

local paramData = require( 'Module:Biota infobox/data' ) -- contains the taxon ranks in order
local autotaxa = require("Module:Autotaxobox")
local parameters = require( 'Module:Biota infobox/param' ) 

--[[ ##################### CORE FUNCTIONS ###################################
       this core function emulates Template:Taxobox/core 
       it is followed by functions handling the different type of entry
]]
p.main = function(frame)
	-- this function emulates Template:Taxobox/core when called from taxobox feeder templates
	--  i.e. Taxobox, Automatic taxobox, Speciesbox, etc
	parameters.getArgs(frame) 
	templateArgs['image_upright'] = templateArgs['upright'] or 1   
    templateArgs['image2_upright'] = templateArgs['upright2']  or 1
    info.headerColor = templateArgs['colour']
	return p._core
    --TODO check it works
end
-- this is the core function, called either from main() or auto()
p.core = function(frame, args, localinfo) 
	templateArgs = args
	info = localinfo
	return p._core(frame) 
end

p._core = function(frame) 

	                                    -- TODO use mw.title.getCurrentTitle().basePageTitle
	info.name = templateArgs['name'] or tostring( mw.title.getCurrentTitle() ) --.rootPageTitle )

    if not info.headerColor then
    	info.headerColor = p.getTaxoboxColor(frame) -- so only transverse taxobox heirarchy once
    end
    
	--[[ create table (two versions)
	     1. use mwhtml library to build table in taxoboxTable
	     2. use wikitest to build table in wikitextTable
    ]]
	local taxoboxTable = mw.html.create('table'):addClass('infobox'):addClass('biota')
								                :addClass('biota-infobox')
	local wikitextTable = '\n{| class="infobox biota biota-infobox" '							                
								                
    info.subheader = ''
    if templateArgs['subheader'] and templateArgs['subheader'] ~= '' then
		info.subheader='<div style="font-weight:normal;font-size:smaller;">'..templateArgs['subheader']..'</div>'
    end
    
    --TODO do we need additional handling to check {{geological range}} templete 
    --        or handle oldest_fossil and youngest_fossil (these don't seem to be used now)
    -- Note: taxobox/core uses temporal_range
    local temporalRange = ''
    if templateArgs['temporal_range']  then
    	temporalRange = '<div><small>Temporal range: ' .. templateArgs['temporal_range'] .. '</small></div>' -- use <div> rather than <br/>
    end
    
    local rowHeader = taxoboxTable:tag('tr'):tag('th'):attr('colspan', '2'):addClass('section-header')
	                :cssText('background:' ..  info.headerColor .. ';')
					:wikitext(info.name .. info.subheader .. temporalRange)
    
    wikitextTable = wikitextTable .. '\n|-\n! colspan="2" class="section-header" style="background:' ..  info.headerColor .. ';" '
                      .. '|' .. info.name .. info.subheader .. temporalRange
    
    -- add images
    wikitextTable = wikitextTable ..  p.addImageSection(frame, taxoboxTable, 'image')
                                  .. p.addImageSection(frame, taxoboxTable, 'image2')
    
    --add conservation status 
	wikitextTable = wikitextTable .. p.addStatusSection(frame, taxoboxTable, 'status')
	                              .. p.addStatusSection(frame, taxoboxTable, 'status2')
	
	-- add taxonomy table (uses entered parameters or automatic taxonomy system)
	wikitextTable = wikitextTable .. p.addTaxonomySection(frame, taxoboxTable)
    
	-- add sections with binomial, trinomial, type species/genus (with authorities)
	wikitextTable = wikitextTable 
				..	p.addTaxonSection(frame, taxoboxTable, 'binomial', 'Binomial name')
				..	p.addTaxonSection(frame, taxoboxTable, 'trinomial', 'Trionomial name')
				..	p.addTaxonSection(frame, taxoboxTable, 'type_genus', 'Type genus')
					--TODO type_ichnogenus, type_oogenus
				..	p.addTaxonSection(frame, taxoboxTable, 'type_species', 'Type species')
					--TODO type_ichnospecies, type_oospecies
				..  p.addTaxonSection(frame, taxoboxTable, 'type_strain', 'Type strain')

	-- add sections showing subdivisions (i.e. child taxa)
	wikitextTable = wikitextTable 
                 .. p.addListSection(frame, taxoboxTable, 'subdivision', templateArgs['subdivision_ranks'] or 'Subdivisions')
                 ..	p.addListSection(frame, taxoboxTable, 'possible_subdivision', templateArgs['possible_subdivision_ranks'] or 'Possible subdivisions')
    
    -- diversity section (TODO consider how best to handle)
    wikitextTable = wikitextTable .. p.addTaxonSection(frame, taxoboxTable, 'diversity', 'Diversity') 

	-- show included groups (accepts 'included' or 'includes') [used for paraphyletic taxa]
	wikitextTable = wikitextTable .. p.addListSection(frame, taxoboxTable, 'includes', 'Groups included')
	--p.addListSection(frame, taxoboxTable, 'included', 'Groups included') -- use alias

    --add range map (should this be below binomial/trinomial?)
    wikitextTable = wikitextTable .. p.addImageSection(frame, taxoboxTable, 'range_map')

	-- show excluded groups (accepts 'excluded' or 'excludes') [used for paraphyletic taxa]
	local excludedHeaderText = '[[Cladistics|Cladistically]] included but traditionally excluded taxa'
	wikitextTable = wikitextTable .. p.addListSection(frame, taxoboxTable, 'excludes', excludedHeaderText)

    -- add addition binomials, trinomial and range maps
	wikitextTable = wikitextTable 
	         .. p.addTaxonSection(frame, taxoboxTable, 'binomial2', 'Binomial name (2)')
	         --p.addTaxonSection(frame, taxoboxTable, 'trinomial2', 'Trionomial name (2)')
             .. p.addImageSection(frame, taxoboxTable, 'range_map2')
             .. p.addTaxonSection(frame, taxoboxTable, 'binomial3', 'Binomial name (3)')
             --p.addTaxonSection(frame, taxoboxTable, 'trinomial3', 'Trionomial name (3)')
             .. p.addImageSection(frame, taxoboxTable, 'range_map3')
             .. p.addTaxonSection(frame, taxoboxTable, 'binomial4', 'Binomial name (4)')
             --p.addTaxonSection(frame, taxoboxTable, 'trinomial4', 'Trionomial name (4)')
             .. p.addImageSection(frame, taxoboxTable, 'range_map4')

	-- add synonyms section
	wikitextTable = wikitextTable .. p.addListSection(frame, taxoboxTable, 'synonyms', '[[Synonym (taxonomy)|Synonyms]]')

	-- add debug/tracking  info section
	if info.debug then
	    wikitextTable = wikitextTable ..p.addListSection(frame, taxoboxTable, 'debug', 'Debug/tracking info')
	end
	
	------------------add templateSyles and return taxobox table---------------------------
	
	local src = "Template:Biota infobox/styles.css" -- TemplateStyles file
    	
   	wikitextTable = 	wikitextTable .. '\n|}'

    local output =	wikitextTable            -- output the wikitext table
    --local output = tostring(taxoboxTable)    -- output the mw.html table
	
	return output .. p.templateStyle( frame, src ) .. info.parameterCategory 
	--return '<div style="float:right;">' .. output .. p.templateStyle( frame, src ) .. info.parameterCategory .. '</div>'
	
end  -- End the main function.	

--[[ ====================================================================================
     function to add conservation sections 
        uses template {{taxobox/species|{{{status_system|}}}|{{{status|}}}|{{{status_ref|}}}|extinct={{{extinct|}}} }} }}
 --]]
function p.addStatusSection(frame, taxoboxTable, status)

    -- must use table container to handle template output
    -- don't use header or content cells; the 'taxobox/species' template handles it
    -- just need to add background colour on the row
    local wikiText = ""
    if templateArgs[status] and templateArgs[status] ~= "" then
 
		local statusText = frame:expandTemplate{ title = 'taxobox/species', 
									          args = {templateArgs[status..'_system'] or '',
									    		      templateArgs[status] or '',
									    		      templateArgs[status..'_ref'] or '',
									    		      ['extinction_date'] = templateArgs['extinct'] or ''  
									    		      }
    	          	                        }
		local row = taxoboxTable:tag('tr')
		                                  --:cssText('background:' ..  p.getTaxoboxColor(frame) .. ';')
		local cell = row:tag('td'):attr('colspan', '2')
		           :wikitext('\n{|\n|- style="background:' ..  info.headerColor .. ';"')
		           :wikitext('\n'..tostring(statusText))
    	           :wikitext('\n|}')
        
       -- mw.addWarning ('taxobox/species returns:' .. '<pre>' .. statusText .. '</pre>')
        if status == "status2" then
        	wikiText = '\n|-' ..tostring(statusText) -- Horrible fudge to prevent header on second conservation status 
        	                                         --  mimicks taxobox in not having newline after \- so header doesn't show
        else
        	wikiText = '\n|-  colspan="2" style="background:' ..  info.headerColor .. ';" ' 
                      .. '\n' ..tostring(statusText)
        end
    end
    return wikiText 
end

--[[ ==============================================================================
     function to add sections for taxonomic information with authorities ('_authority' suffix)
        e.g. binomial, trinomial, type_species, type_genus; 
        diversity also handled here
--]]
function p.addTaxonSection(frame, taxoboxTable, target, headerText)
	
	local wikiText = ""
    -- return if we don't have value
	if not templateArgs[target]  or templateArgs[target] == '' then return "" end
	
	local bold = "" -- variable for bolding binomial and trinomial (type genus/species etc are not bolded)
	local showHeader = true
	
	local listHeader = (templateArgs[target..'_text'] or headerText) 

	-- custom processing section
	--if target == 'binomial' or target == 'binomial2' or target == 'binomial3' or target == 'binomial4' then
	if target == 'binomial' then
		headerText = '[[Binomial nomenclature|' .. listHeader .. ']]'
		bold ="'''"
	--elseif target == 'trinomial' or target == 'trinomial2' or target == 'trinomial3' or target == 'trinomial4' then
	elseif target == 'trinomial'  then
		local trinomenLink = "Trinomen" -- for zoological or default
		if info.auto ==  "infraspeciesbox" then trinomenLink = "Infraspecific name (botany)" end -- regnum contains plant/fung/Archaeplastida"
		headerText = '[['.. trinomenLink .. '|' .. headerText .. ']]'
		bold ="'''"
	elseif target == 'binomial2' or target == 'binomial3' or target == 'binomial4'
		   or target == 'trinomial2' or target == 'trinomial3' or target == 'trinomial4' then
		showHeader = false
		bold ="'''"
	elseif target == 'diversity'  then
	   headerText = '[[Biodiversity|' .. headerText .. ']]'
	else
	   --TODO is any handling needed for other option
	   headerText = '[[' .. headerText .. ']]'
	end
    
	if templateArgs[target..'_ref'] then
			headerText = headerText .. templateArgs[target..'_ref'] .. '\n'
	 end
	
	local contentString = ''   -- content for the content cell
	if target == 'diversity' and templateArgs['diversity'] ~= "" then
		if templateArgs[target..'_link'] and templateArgs[target..'_link'] ~= "" then 
		    contentString =  '\n[[' .. templateArgs[target..'_link'] .. '|' .. templateArgs[target] .. ']]\n' 
		else
			contentString =  '\n' .. templateArgs[target] .. '\n'
		end
	 else
	 	-- taxon name and authority (binomial, type species, etc)
		local authorityString = ''
		if templateArgs[target..'_authority'] then
			authorityString = '<br/><small>' .. templateArgs[target..'_authority'] .. '</small>' -- \n' 
		end 
		contentString =  bold .. templateArgs[target] .. bold .. authorityString .. '\n' 
		--contentString =  '\n' ..  bold .. templateArgs[target] .. bold .. authorityString .. '\n'  -- extra <p> inserted
    end 	 
	
	-- add table rows
	if templateArgs[target] and templateArgs[target] ~= '' then
		if showHeader then
			local rowHeader = taxoboxTable:tag('tr')
			rowHeader  :tag('th')
			           :attr('colspan', '2')
			           :addClass('section-header')
			           :cssText('background:' ..  info.headerColor .. ';')
			           :wikitext( headerText )                   
        	wikiText = wikiText .. '\n|- \n! colspan="2" class="section-header" style="background:' ..  info.headerColor .. ';" '
            		   .. '|' .. headerText

        end
		
		local rowList = taxoboxTable:tag('tr')
		rowList    :tag('td')
		           :attr('colspan', '2')
		           --:addClass('section-content')
		           :addClass('taxon-section')
		           --:cssText('text-align:center;') --font-weight:bold;')
		           :wikitext( contentString )
         wikiText = wikiText .. '\n|- \n| colspan="2" class="taxon-section" |' .. contentString
                             
	end	
    return wikiText
end

--[[ ====================================================================================
     function to produce sections for included taxa (subdivisions), synonyms, etc
      - each consists of two rows containing a header and the content
      - for paraphyletic groups it has include(d|s) and exclude(d|s) groups 
      - for general taxobox it has subdivision and possible subdivision (disabled here)
      - any can be modified for other purposes (e.g. sisters) by changing the header taxt with a -text parameter
  ]]
function p.addListSection(frame, taxoboxTable, target, headerText)
   
    if not templateArgs[target] or templateArgs[target] == "" then return "" end -- redundant for now
    
    local wikiText = ""
    local refString = ''
	if templateArgs[target..'_ref'] then
		   --add '_ref' option for 'synonym_ref' (the rest get it as a bonus) TODO check example
			refString = templateArgs[target..'_ref'] --.. '\n' 	
	 end
	local listHeader = (templateArgs[target..'_text'] or headerText) .. refString
	-- add table rows
	if templateArgs[target] and templateArgs[target] ~= ''then
		local rowHeader = taxoboxTable:tag('tr')
		rowHeader  :tag('th')
		           :attr('colspan', '2')
		           :addClass('section-header')
		           :cssText('background:' .. info.headerColor .. ';')
		           :wikitext(listHeader)
        wikiText = wikiText .. '\n|- \n! colspan="2" class="section-header" style="background:' ..  info.headerColor .. ';" '
               .. '|' .. listHeader

        
		local rowList = taxoboxTable:tag('tr')
		rowList    :tag('td')
		           :attr('colspan', '2')
		           :addClass('section-content')
		           :wikitext('\n' .. templateArgs[target] .. '\n' )	
        wikiText = wikiText .. '\n|- \n| colspan="2" class="section-content" '
               .. '|' .. '\n' .. templateArgs[target] .. '\n'


	 end	
	 return wikiText
end
-----------------------------------------------------------------------------------------------
--[[ ============================================================================
     function to add image sections
     - used for illustrative images at top and for range maps
--]]
function p.addImageSection(frame, taxoboxTable, target)
	 
	 local wikiText = ""
	 if templateArgs[target] and templateArgs[target] ~= '' then
	 	
        local imageWidth = ''
        local imageCaptionString = ''
        if templateArgs[target..'_caption'] then 
        	--imageCaptionString = '<br /><small><div style="text-align:center">' .. templateArgs[target .. '_caption'] .. '</div></small>' 
        	--imageCaptionString = '<br /><div>' .. templateArgs[target .. '_caption'] .. '</div>' 
        	imageCaptionString = templateArgs[target .. '_caption']
        end
        local imageAltString = ''
        if templateArgs[target..'_alt'] then
        	imageAltString = templateArgs[target..'_alt']
        elseif templateArgs[target..'_caption'] then
        	imageAltString = templateArgs[target..'_caption'] -- use caption for alt text if none provided
        end 
        local upright = templateArgs['image_upright'] or 1
        
        local InfoboxImage = require( 'Module:InfoboxImage' ) --, parent.args[target]  )
        local params = { args = { 	image = templateArgs[target],
							        size = templateArgs[target..'_width'],
							        sizedefault = 'frameless',
							        alt = imageAltString,
							        upright = templateArgs[target..'_upright'] or upright 
							        }
					    }
					    
        local image = InfoboxImage.InfoboxImage(  params )
        
	    --local rowImage = taxoboxTable:tag('tr') 
	    local rowImage = mw.html.create('tr')
		rowImage:tag('td')
					 :attr('colspan', '2')
		             :addClass("image-section")
		             :wikitext(image)
		             --:wikitext(imageCaptionString)
		taxoboxTable:node(rowImage)
        wikiText= wikiText .. '\n|- \n|colspan="2" class="image-section" |' .. image 
	    
	    if imageCaptionString ~= "" then                  -- only insert row if caption string
		    local rowImageCaption = mw.html.create('tr')
			rowImageCaption:tag('td')
						 :attr('colspan', '2')
			             :addClass("image-section")
			             --:wikitext(image)
			             :wikitext(imageCaptionString)
	        taxoboxTable:node(rowImageCaption)
	        wikiText = wikiText ..  '\n|- \n|colspan="2" class="image-section" |' .. imageCaptionString
        end 
    end
    
    -- TODO handle upright
	return wikiText
end 

--[[ ============================ TAXONOMY SECTION =======================================
     adds a table showing the taxonomy
      - uses either manual parameters or the automatic taxonomy system
      - currently adds a table inside a cell (like paraphyletic group) rather than just adding rows (core taxobox system)
--]]    
 
function p.addTaxonomySection(frame, taxoboxTable)
    
    local wikiText = ""
	local taxonomyHeader = "[[Taxonomy_(biology)|Scientific classification]]"
	if templateArgs['virus_group']  then 
		taxonomyHeader = "[[Virus classification]]"
	elseif templateArgs['ichnos']  then 
		taxonomyHeader = "[[Trace fossil classification]]"
	elseif templateArgs['veterovata']  then 
		taxonomyHeader = "[[Veterovata|Eggshell classification]]"
	else
		-- TODO add other options (DONE but not verified ichnos or veterovata)
		-- ! colspan=2 style="min-width:15em; text-align: center{{#if:{{{colour|}}}|{{;}} background-color{{COLON}} {{{colour}}} }}" | 
		--   {{#if:{{{virus_group|{{{virus|}}}}}}|[[Virus classification]]
		--    	|{{#if:{{{ichnos|}}}|[[Trace fossil classification]]
	    --   	|{{#if:{{{veterovata|}}}|[[Veterovata|Eggshell classification]]
	    --   |[[Taxonomy (biology)|Scientific classification]]}} }} }} 
     	--	    {{#if:{{{edit link|}}}|{{edit taxonomy|{{{parent|}}} | {{{edit link}}} }}
		--   {{#if: {{{classification_status|}}} | <br>({{{classification_status}}}) | }} }}
		-- handle |classification_status=disputed (add ref)
	end
	
	-- add symbol and link to taxonomy editor
	local editLink = ''
	if info.auto then
		local tooltip = templateArgs['edit link'] or "Edit this classification"
		local style = 'font-size:smaller; float:right; padding-right:0.4em; margin-left:-3em;'
		local link = 'Template:Taxonomy/' .. templateArgs['parent']
		if info.db == "wikidata" then
			local message = 'Select%20preview%20to%20see%20Wikidata%20hierarchy'
			local url='https://en.wikipedia.org/w/index.php?action=edit&section=new&preloadtitle=' .. message 
			      .. '&title=Template:Biota_infobox/Wikidata/preview&preload=User:Jts1882/Taxonomy/preload2&preloadparams%5b%5d='
			link =  url .. string.gsub( templateArgs['parent'], " ", "_")
		end
		editLink  = '<span class="plainlinks" style="'.. style ..'">'
			.. '[[File:OOjs UI icon edit-ltr.svg|15px|link=' .. link .. '|' .. tooltip  .. ']]</span>'
			--.. '[[File:Red Pencil Icon.png|link=' .. link .. '|' .. tooltip  .. ']]</span>'
			
	end
	local status = ""
	if templateArgs['classification_status'] then 
		status = '<div style="font-weight:normal;" >(' .. templateArgs['classification_status'] .. ')'
	    if templateArgs['classification_ref'] then status = status .. templateArgs['classification_ref'] end
		status = status .. '</div>'
	end
	
	local rowTaxonomyHeader = taxoboxTable:tag('tr')
	rowTaxonomyHeader:tag('th')
	           :attr('colspan', '2')
	           :addClass('section-header')
	           :cssText('background:' ..  info.headerColor .. ';')
	           :wikitext(taxonomyHeader)
	           :wikitext(editLink)
	           :wikitext(status)
    
    wikiText = wikiText .. '\n|- \n! colspan="2" class="section-header" style="min-width:15em;text-align:center;background:' ..  info.headerColor .. ';" '
               .. '|' .. taxonomyHeader .. editLink .. status
    
    --[[ get taxonomy list, either using automatic taxobox system or manual system     
         manual: get ranks and taxa from template parameter
         auto (default): get ranks and taxa from taxonomy template parameters
         module: get ranks and taxa from dataa submodules
         wikidata: get ranks and taxa from wikidata
    ]]
    -- shows ranks of genus or above for all auto modes
	if info.db == "module" then 
	    local wdModule = require( 'Module:Biota infobox/Wikidata' ) 
	    wikiText = wikiText .. wdModule.addModuleTaxonomy(frame, taxoboxTable,  templateArgs)   -- use module copy of template data
	elseif info.db == "wikidata" then 
	    --wikiText = wikiText ..'\n|-|\n|' .. p.addWikidataTaxonomy(frame, taxoboxTable)   -- use wikidata
        local wdModule = require( 'Module:Biota infobox/Wikidata' ) 

        wikiText = wikiText .. wdModule.addWikidataTaxonomy(frame, taxoboxTable,  templateArgs)   -- use wikidata
		
		-- TODO need to handle colour 
        -- the default is class="section-header" colspan="2" style="background:rgb(250,240,230);"
        -- wikiText = wikiText:gsub('style="background:rgb%(250,240,230%);"', 'style="background:red;"')
        -- gsub must be applied to wikitextTable
        -- use more generally to avoid traversing the hierarchy twice)
	elseif info.auto then 
		--[[ get automatic taxonomy hierarchy (three different variants)
		      1) direct call to taxoboxList() - preferred if issues with setting frame arguments can be resolved (used in live version)
		      2) experimental version of taxoboxList()
		      3) [ET] using Template:Taxobox/taxonomy
		]]
	    wikiText = wikiText ..'\n|-|\n|' .. p.addAutomaticTaxonomy(frame, taxoboxTable)   -- use #invoke of module
	end
	if info.auto then
		-- use manual taxobox for subgeneric ranks:  subgenus,species, subspecies, variety (also for informal group)
    -- ranks below genys using manual taxobox code 
	    local taxonRanks = { 'subgenus', 'species', 'hybrid',  'subspecies', 'population', 'variety' , 'infraspecies_rank1' , 'infraspecies_rank2', 'informal'} 
		
		wikiText = wikiText .. p.addManualTaxonomy(frame, taxoboxTable, taxonRanks)
	else
		wikiText = wikiText .. p.addManualTaxonomy(frame, taxoboxTable, paramData.taxonRanks) -- just add rows manually
    end
    return wikiText
end
-------------------------------------------------AUTOMATIC TAXONOMY (using invoke of module function) -----------
function p.addAutomaticTaxonomy(frame, taxoboxTable) -- use invoke of module function
	--emulate template: {{taxobox/taxonomy}}
	--which uses {{#invoke:Autotaxobox|taxoboxList
	--local autotaxa = require("Module:Autotaxobox") -- also needed for colours so global now

    local bold_first = 'bold'
    if templateArgs['species'] or templateArgs['hybrid'] then 	bold_first = 'link'    end
    if templateArgs['link_parent'] then 	bold_first = 'link'    end

    local args = {	templateArgs['parent'],  -- or tostring( mw.title.getCurrentTitle() ), 
					display_taxa	    = templateArgs['display_taxa'] or 1,
					offset              = templateArgs['offset'] or 0,
					authority           = templateArgs['authority'],
			        parent_authority    = templateArgs['parent_authority'],
			        gparent_authority   = templateArgs['grandparent_authority'],
			        ggparent_authority  = templateArgs['greatgrandparent_authority'],
			        gggparent_authority = templateArgs['greatgreatgrandparent_authority'],
			        virus=templateArgs['virus'],
			        bold_first          = bold_first
	          }
	          
    frame.args = args
   -- templateArgs['debug'] =  mw.dumpObject(frame) 

	local autoTaxonomy = autotaxa.taxoboxList(frame)
	
    if (1==1) then return autoTaxonomy end
    
    local row = taxoboxTable:tag('tr')  --  incompatible with the templates called
                        :wikitext('\n|rank ||taxon name ')  
                        :wikitext('\n'.. autoTaxonomy )  -- autoTaxonomy ends with a new row (|-)at end
                        :wikitext('\n|x ||y ')                 -- so add blank cells to complete extra row
                                                               --   this and affects spacing in taxonomy rows
                        --:wikitext('\n')                      -- spacing fine, newline for table wikitext
                        
                    
    --[[ note:  the output of {{taxobox/showtaxon}} [used by invoke:Autotaxobox|taxoboxList] ends with a newline token
                this and affects spacing in taxonomy rows
                leaving the empty row results in spurious paragraphs above the table
      ]]
	return 
end

----------------------------------------MANUAL TAXONOMY--------------------------------

function p.addManualTaxonomy(frame,taxoboxTable, taxonRanks)
	
	--local parent = mw.getCurrentFrame():getParent()
	--local taxonRanks = data.taxonRanks
	
	-- following {{Paraphyletic group, a table is add to the cell in the classification row
	--local taxonomyTable = mw.html.create('table'):addClass('taxonomy')
	
	-- an alternative is to dispense with the extra table and just add the rows (like taxobox/core), 
	--    which would need colspan=2 on other rows (DONE)
	local taxonomyTable = 	taxoboxTable  
	local wikiText = ""
	
	for k,v in pairs(taxonRanks) do
		
		if templateArgs[v] then
		    local taxonName = templateArgs[v]
		    
		    local taxonRank = frame:expandTemplate{ title = "anglicise rank", args = {taxonRanks[k]} }
		    if v == 'infraspecies_rank1' and templateArgs['infraspecies_rank1_name'] then
		        taxonRank = templateArgs['infraspecies_rank1_name']
		    elseif  v == 'infraspecies_rank2' and templateArgs['infraspecies_rank2_name']then
		        taxonRank = templateArgs['infraspecies_rank2_name']
		    elseif  v == 'population' and templateArgs['population_rank_name']then
		        taxonRank = templateArgs['population_rank_name']
		    end
		    
		    if taxonRanks[k] == "virus_group" then
		    	taxonName = frame:expandTemplate{ title = "Virus group", args = {templateArgs[v]} }
		    --	taxonRank = "Group" -- handled by anglicise rank template
		    end
		    local authorityString = ''
		    if templateArgs[taxonRanks[k]..'_authority'] then
		    	authorityString = '<br /><small>'..templateArgs[taxonRanks[k]..'_authority']..'</small>'
		    end
		    local taxonString = '<span class="'.. taxonRanks[k] ..'">'..taxonName..'</span>'..authorityString

		    local row = taxonomyTable:tag('tr')
	     	row:tag('td'):wikitext(taxonRank..':')
		    row:tag('td'):wikitext(taxonString)
		    --:wikitext('<br /><small>'..parent.args[taxonRanks[k]..'_authority']..'</small>')
            
            wikiText = wikiText  .. '\n|- \n|' .. taxonRank..': \n|' .. taxonString
		end 
	end -- end for loop
	
	--return tostring(taxonomyTable)
	return wikiText
	
end

--[[ ########################### UTILITY FUNCTIONS ###############################################

-----------------------------------------TAXOBOX COLOUR--------------------------------------
   -- gets colour for headers using manual or automatic taxobox schemes
]]	
function p.getTaxoboxColor(frame)
	
	local colorAs = templateArgs['color_as'] or nil
	
	if  info.auto and not templateArgs['virus_group'] then 
	   --[[(1) if color_as|colour_as|color as|colour as set, use template {{Taxobox colour|color_as}}
	   	   (2) else use the auto taxonnomy tree to find colour: {{#invoke:Autotaxobox|taxoboxColour| }}
	    {{#invoke:Autotaxobox|taxoboxColour|{{{parent|{{{genus|{{first word|{{{taxon|{{PAGENAME}} }}
	--]]
		--[[if (templateArgs['color_as'] and templateArgs['color_as'] ~= "") or
		   (templateArgs['colour_as'] and templateArgs['colour_as'] ~= "") or
		   (templateArgs['color as'] and templateArgs['color as'] ~= "") or
		   (templateArgs['colour as'] and templateArgs['colour as'] ~= "") then
		    
		   local colorAs = ""
		   if templateArgs['color_as'] then colorAs = templateArgs['color_as']  end
		   if templateArgs['colour_as']  then colorAs =  templateArgs['colour_as'] end
		   if templateArgs['color as'] then colorAs =  templateArgs['color as'] end
		   if templateArgs['colour as']  then colorAs =  templateArgs['colour as']  end]]
		if colorAs then -- templateArgs['color_as'] and templateArgs['color_as'] ~= ""   then
			
		    return frame:expandTemplate{ title = 'Taxobox colour', args = {colorAs} }
		    
		else
			-- us #invoke:Autotaxobox|taxoboxColour|{{{parent}}} [parent should be set]
			
			frame.args[1] = templateArgs['parent']
			
	        return autotaxa.taxoboxColour(frame)
			--return	"palegreen"
		end
	else -- use manual taxobox colours
		--{{Taxobox colour|{{{regnum|{{{virus_group|{{{unranked_phylum|{{{phylum|''[[Incertae sedis]]''}}}}}}}}}}}}}}
		if not colorAs then  --templateArgs['color_as']    then
     
			local group =''
			if templateArgs['regnum'] then
				group = templateArgs['regnum']
			elseif templateArgs['virus_group'] then
				group = templateArgs['virus_group']
			elseif templateArgs['unranked_phylum'] then
				group = templateArgs['unranked_phylum']
			elseif templateArgs['phylum'] then
				group = templateArgs['phylum']
			else
				group = "''[[Incertae sedis]]''"          -- TODO check if this is what was desired
			end
            colorAs = group
        end
	    return frame:expandTemplate{ title = 'Taxobox colour', args = {colorAs} }
	end
end
-------------------------------------------------------------------
function p.templateStyle( frame, src )
   return frame:extensionTag( 'templatestyles', '', { src = src } );
   
end	
function p.firstToUpper(str)
    return (str:gsub("^%l", string.upper))
end

function p.test(frame)
	return info.auto	
end

return p