Module:Biota infobox/core

require('Module:No globals')

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' )

-- 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 )

info.headerColor = p.getTaxoboxColor(frame) -- so only transverse taxobox heirarchy once

-- 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=' '..templateArgs['subheader']..' ' end --TODO do we need additional handling to check 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 = ' Temporal range: ' .. templateArgs['temporal_range'] .. ' ' -- use rather than 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', 'Bionomial 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 = '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', 'Bionomial name (2)') --p.addTaxonSection(frame, taxoboxTable, 'trinomial2', 'Trionomial name (2)') .. p.addImageSection(frame, taxoboxTable, 'range_map2') .. p.addTaxonSection(frame, taxoboxTable, 'binomial3', 'Bionomial name (3)') --p.addTaxonSection(frame, taxoboxTable, 'trinomial3', 'Trionomial name (3)') .. p.addImageSection(frame, taxoboxTable, 'range_map3') .. p.addTaxonSection(frame, taxoboxTable, 'binomial4', 'Bionomial 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', '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 p.templateStyle( frame, src ) .. output .. info.parameterCategory -- .. (info.parameterCategory or "") end -- End the main function.

-- ====================================================================================    function to add conservation sections         uses template  }} -- 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 status = frame:expandTemplate{ title = 'taxobox/species', args = {templateArgs[status..'_system'] or '', templateArgs[status] or '', templateArgs[status..'_ref'] or '', extinct=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(status)) :wikitext('\n|}') wikiText = '\n|- colspan="2" style="background:' ..  info.headerColor .. ';" ' .. '\n' ..tostring(status) 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 =  .. 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 =  .. 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 =  .. 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] .. '\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 = ' ' .. templateArgs[target..'_authority'] .. ' ' -- \n' end contentString = bold .. templateArgs[target] .. bold .. authorityString .. '\n' --contentString = '\n' .. bold .. templateArgs[target] .. bold .. authorityString .. '\n' -- extra 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

--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 = ' ' .. templateArgs[target .. '_caption'] .. ' '        	--imageCaptionString = ' ' .. templateArgs[target .. '_caption'] .. ' '        	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 = "Scientific classification" if templateArgs['virus_group'] then taxonomyHeader = "Virus classification" elseif templateArgs['ichnos'] then taxonomyHeader = "Trace fossil classification" elseif templateArgs['veterovata'] then taxonomyHeader = "Eggshell classification" else -- TODO add other options (DONE but not verified ichnos or veterovata) -- ! colspan=2 style="min-width:15em; text-align: center" | --        	--	    		-- 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 = ' ' .. ' '	end local status = "" if templateArgs['classification_status'] then status = ' (' .. templateArgs['classification_status'] .. ')' if templateArgs['classification_ref'] then status = status .. templateArgs['classification_ref'] end status = status .. ' '	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="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 -- ranks below genys using manual taxobox code local taxonRanks = { 'subgenus', 'species', 'hybrid', 'subspecies', 'population', 'variety', 'infraspecies_rank1' , 'infraspecies_rank2'} 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: --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 --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 = ' '..templateArgs[taxonRanks[k]..'_authority']..' ' end local taxonString = ''..taxonName..' '..authorityString

local row = taxonomyTable:tag('tr') row:tag('td'):wikitext(taxonRank..':') row:tag('td'):wikitext(taxonString) --:wikitext(' '..parent.args[taxonRanks[k]..'_authority']..' ') 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 --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