Module:Biota infobox

require('Module:No globals') -- All Lua modules on Wikipedia must begin by defining a variable that will hold their -- externally accessible functions. They can have any name and may also hold data. local p = {} -- exposed variables local g = {} -- these are variables with global scope in this module

local info = {}         -- contains general purpose information (e.g. header background colour) info.debug = false -- ONLY SET THIS WHILE TESTING

--local paramData = require( 'Module:Sandbox/Jts1882/Biota Infobox/data' ) -- contains the taxon ranks in order --local autotaxa = require("Module:Sandbox/Jts1882/Biota Infobox/Autotaxobox") --local autotaxa = require("Module:Autotaxobox") local parameters = require( 'Module:Biota infobox/param' ) local core = require( 'Module:Biota infobox/core' )

-- ######################### PARAMETER HANDLING ############################

local templateArgs = {} -- contains preprocessed arguments from calling template --TODO use info.args instead of templateArgs?

-- ########################### MAIN AND OTHER ENTRY FUNCTIONS ##################################

-- main function callable in Wikipedia via the p.main = function(frame) --p.getArgs(frame) parameters.getArgs(frame, templateArgs, info) -- gets arguments, checks for value, aliases, and against valid parameter list

if info.auto then p.AutomaticTaxoboxOptions(frame) -- this emulates the automatic taxobox templates that feed the core else --genus|species|binomial name		           colour = p.getTaxoboxColor(frame) end

--return p._core(frame) return core.core(frame, templateArgs, info) end

-- this functions emulates Template:automatic taxobox and uses Template:Taxobox/core p.auto = function(frame) --info.auto = frame.args.auto or "automatictaxobox" p.getArgs(frame) -- gets arguments, checks for value, aliases, and against valid parameter list

if info.auto then p.AutomaticTaxoboxOptions(frame) -- this emulates the automatic taxobox templates that feed the core end -- additional parameters needed by Template:Taxobox/core templateArgs['edit link']="edit taxonomy" templateArgs['colour'] = p.getTaxoboxColor(frame) templateArgs['upright'] = templateArgs['image_upright'] or 1 templateArgs['upright2'] = templateArgs['image2_upright'] or 1 -- use Template:Taxobox/core return tostring(frame:expandTemplate{ title = 'taxobox/core', args = templateArgs   } ) end

--[[ ##################### CORE FUNCTIONS ###################################

this core function emulates Template:Taxobox/core it is followed by functions handling the different type of entry MOVED to subpage Module:Sandbox/Jts1882/Biota_Infobox/core ]]

-- ################## AUTOMATIC TAXOBOX SYSTEM HANDLING ################################

-- handle specific requirements of different options: auto, speciesbox etc function p.AutomaticTaxoboxOptions(frame) --TODO replace genus with first word (genus) to strip parenthetic term -- done in speciesbox? templateArgs['display_taxa'] = templateArgs['display_parents'] or 1  -- note change of parameter name local extinct = "" if templateArgs['extinct']  then --extinct = "†" extinct = frame:expandTemplate{ title = 'extinct' } -- use template to get tooltip -- speciesbox also checks the genus taxonomy template for extinct parameter end

-variables for SPECIESBOX, SUBSPECIESBOX and INFRASPECIESBOX- if info.auto == "hybridbox" then --templateArgs['parent'] = templateArgs['parent'] or templateArgs['genus'] or templateArgs['genus1'] local species1 = templateArgs['species'] or templateArgs['species1'] or templateArgs['father'] or templateArgs['father_species'] or "" local species2 = templateArgs['species2'] or templateArgs['mother'] or templateArgs['mother_species'] or templateArgs['species'] or "" local genus1  = templateArgs['genus'] or templateArgs['genus1']  or templateArgs['father_genus']    -- TODO use page local genus2  = templateArgs['genus2'] or templateArgs['mother_genus']   or templateArgs['genus'] local species3 = templateArgs['species3'] or "" local genus3  = templateArgs['genus3'] or templateArgs['genus'] or ""

local subspecies1, subspecies2, subspecies3 = "", "", "" --if (templateArgs['subspecies1'] and templateArgs['subspecies2']) if templateArgs['subspecies1'] or templateArgs['subspecies2'] or (templateArgs['father_subspecies'] and templateArgs['mother_subspecies']) then subspecies1 = " " .. ((templateArgs['subspecies1'] or templateArgs['father_subspecies']) or "") subspecies2 = " " .. ((templateArgs['subspecies2'] or templateArgs['mother_subspecies']) or "") if templateArgs['subspecies3'] then subspecies3 = " " .. templateArgs['subspecies3'] species3 = species1 end end local link1   = templateArgs['link1'] or templateArgs['father_link'] or (genus1 .. " " .. species1 .. subspecies1) local link2   = templateArgs['link2'] or templateArgs['mother_link'] or (genus2 .. " " .. species2 .. subspecies2) local link3   = templateArgs['link3'] or (genus3 .. " " .. species3 .. subspecies3)

if not templateArgs['parent'] then templateArgs['parent'] = genus1 end --TODO disambiguate genus pages -- not needed unless using page name --genus1 = frame:expandTemplate{ title = 'Speciesbox/getGenus', args = {"", genus1 } } --	genus2 = frame:expandTemplate{ title = 'Speciesbox/getGenus', args = {"", genus2 } } if not templateArgs['genus2'] and not templateArgs['father_genus'] then genus1 = string.sub(genus1,1,1) .. "."  -- shorten generic names for intrageneric hybrids genus2 = string.sub(genus2,1,1) .. "."  			genus3 = string.sub(genus3,1,1) .. "."  		end -- shorten species name if subspecies of same species if subspecies1 ~= "" and not templateArgs['species2'] then species1 = string.sub(species1,1,1) .. "."  -- shorten specific epithet for intraspecific hybrids species2 = string.sub(species2,1,1) .. "."  			if subspecies3 ~= "" then species3 = string.sub(species3,1,1) .. "." end end

local maleSymbol, femaleSymbol = "", "" if templateArgs['father'] or templateArgs['father_genus'] or templateArgs['father_species'] or templateArgs['father_subspecies'] then maleSymbol = "♂" end if templateArgs['mother'] or templateArgs['mother_genus'] or templateArgs['mother_species'] or templateArgs['mother_subspecies'] then femaleSymbol = "♀" end templateArgs['hybrid'] = "" .. genus1 .. " " .. species1 .. subspecies1 .."" .. maleSymbol .. " × "  		                       .. "" .. genus2 .. " " .. species2 .. subspecies2 .. "" .. femaleSymbol

if species3 ~= "" then templateArgs['hybrid'] = templateArgs['hybrid']  .. " × "  		                       .. "" .. genus3 .. " " .. species3  .. subspecies3 .. "" end --templateArgs['hybrid species'] = templateArgs['hybrid'] if subspecies1 ~= "" and not templateArgs['species2'] then templateArgs['species'] = ""    	                                .. genus1 .. " " .. templateArgs['species'] .. "" else templateArgs['species'] = nil end templateArgs['offset'] = 1 -- ======================= setup for SPECIESBOX ============================= elseif info.auto == "speciesbox" then -- gets genus and species from taxon, genus+species or page name                1. uses 'taxon' paramter ( given as binomial) if available                2. otherwise uses 'genus' and 'species' parameters                3. uses page name             the genus is used for the 'parent' taxon             	unless the parent is supplied (e.g. for subgenus)            	else use genus (from taxon or genus parameter or page name)            now using  and  {Speciesbox/getSpecies}}                code doing similar is commented out below           TODO use {{{{Speciesbox/name}}        -- local genus, species = "", "" genus = frame:expandTemplate{ title = 'Speciesbox/getGenus', args = {templateArgs['taxon'], templateArgs['genus']} } species = frame:expandTemplate{ title = 'Speciesbox/getSpecies', args = {templateArgs['taxon'], templateArgs['genus']} } if templateArgs['taxon'] then -- following line disableas using getGenus/getSpecies templates -- genus, species = string.match(templateArgs['taxon'], "(%S+)%s(%S+)") -- %S: All characters not in %s templateArgs['genus'] = genus templateArgs['species'] = species elseif templateArgs['genus'] and templateArgs['species'] then -- genus = Acanthocarpus (plant)	   	local genusParts =mw.text.split( templateArgs['genus'], " ", true )     -- string.match( s, '^%a*'', 1 )	    	if genusParts[1] ~= "" then 	    		--templateArgs['parent']=templateArgs['genus']  -- set parent (NO, parent should override)	    		genus = genusParts[1] 	    	end	    	now handled by getGenus/getSpecies templates -- templateArgs['taxon'] = genus .. ' ' .. templateArgs['species'] else -- TODO no valid taxon yet; use page name -- use first word of pagename - handled by 	   end if not templateArgs['parent'] or templateArgs['parent'] == "" then templateArgs['parent'] = templateArgs['genus']      -- set parent to genus if not supplied end --if not templateArgs['name'] or templateArgs['name'] == "" then -- if page name not set       	templateArgs['name'] = "" .. templateArgs['taxon'] .. ""        end --TODO use {{Speciesbox/name}} templateArgs['name'] = frame:expandTemplate{ title = 'Speciesbox/name' , args = { templateArgs['name'], templateArgs['taxon'], templateArgs['genus'], templateArgs['species'], mw.title.getCurrentTitle.baseText, templateArgs['italic_title' or 'yes'] } }

-- set binomial : the speciesbox template seems to use genus and species before taxon name -- "| binomial = {{Str letter/trim|{{{genus|{{{taxon| {{PAGENAME}} Acacia }}}}}}}} {{{species|{{remove first word|{{{taxon| {{PAGENAMEBASE}}  Acacia aemula }}}}}}}}" -- documentation suggest taxon, which is followed here templateArgs['binomial'] = "''" .. templateArgs['taxon'] .. "''"		templateArgs['binomial_authority'] = templateArgs['authority'] or nil

-- set species_name e.g. Panthera leo -> P. leo templateArgs['species_name'] = extinct .. "'" .. string.sub(templateArgs['genus'],1,1) .. '. ' .. templateArgs['species'] .. "'"       templateArgs['species']=templateArgs['species_name'] templateArgs['display_taxa']  = templateArgs['display_taxa'] -1 templateArgs['offset'] = 1 if templateArgs['subgenus'] and templateArgs['subgenus'] ~= "" then templateArgs['offset'] = templateArgs['offset'] + 1 templateArgs['subgenus_authority']             = templateArgs['parent_authority'] or "" end --templateArgs['species_authority']  = templateArgs['authority'] or "" -- don't show species_authority as duplicates binomial authority --shift authorities for speciesbox (two steps if subgenus set)	   if templateArgs['subgenus'] and templateArgs['subgenus'] ~= ""  then			templateArgs['subgenus_authority']              = templateArgs['parent_authority'] or ""			templateArgs['authority']                       = templateArgs['grandparent_authority'] or ""			templateArgs['parent_authority']                = templateArgs['greatgrandparent_authority'] or ""			templateArgs['grandparent_authority']           = templateArgs['greatgreatgrandparent_authority'] or ""			templateArgs['greatgrandparent_authority']      = templateArgs['greatgreatgreatgrandparent_authority'] or ""			templateArgs['greatgreatgrandparent_authority'] = templateArgs['greatgreatgreatgreatgrandparent_authority'] or ""		else                                                                			-- note: must set to "" if 'parent_authority's don't exist, otherwise the value of 'authority' is unchanged			templateArgs['authority']                       = templateArgs['parent_authority'] or ""  			templateArgs['parent_authority']                = templateArgs['grandparent_authority'] or ""			templateArgs['grandparent_authority']           = templateArgs['greatgrandparent_authority'] or ""			templateArgs['greatgrandparent_authority']      = templateArgs['greatgreatgrandparent_authority'] or ""			templateArgs['greatgreatgrandparent_authority'] = templateArgs['greatgreatgreatgrandparent_authority'] or ""			end templateArgs['taxon'] = nil -- For auto module -- ===================== set-up for SUBSPECIESBOX or INTRASPECIESBOX ================= elseif info.auto == "subspeciesbox" or info.auto == "infraspeciesbox" then -- From template description:	         "The genus name, species name and subspecies name" 	             [or "genus name, specific epithet and infraspecific epithet"]                  "                 must be supplied separately: the combined taxon parameter cannot be used.""              "The genus name is then the entry into the taxonomic hierarchy.""		    The trinomial name is set from these parameters and the parameter ignored.		   --NOTE no infraspeciebox is currently using trinomial parameter        -- -- Parameter checking. This could be here or moved to parameter checking function if templateArgs['genus'] and templateArgs['species'] and templateArgs['subspecies'] then -- valid parameters for subspecies (may have variety as well) elseif templateArgs['genus'] and templateArgs['species'] and templateArgs['variety'] then -- valid parameters for infraspecies (variety without subspecies) else -- insufficient parameters -- TODO add error message and return end local offset = 2 -- authority offset when subpecies OR variety --TODO strip genus of disambiguator (need to check this works) local genus =mw.text.split( templateArgs['genus'], " ", true ) if genus[1] ~= "" then templateArgs['genus'] = genus[1] end templateArgs['parent'] = templateArgs['genus'] -- genus must be supplied local fullName = templateArgs['genus'] .. ' ' .. templateArgs['species'] templateArgs['species_name'] = "'.. string.sub(templateArgs['genus'],1,1) .. '. ' .. templateArgs['species'] .. ""

-- if subspecies is set (could be with or without variety) local separator = " "                              -- subspecies separator (default zoological) if templateArgs['subspecies'] then                 -- might not be if variety if info.auto == "infraspeciesbox"  then separator = "  subsp.  "   end templateArgs['subspecies_name']= extinct .. "'" .. string.sub(templateArgs['genus'],1,1) .. '. ' .. string.sub(templateArgs['species'],1,1) .. '.' .. separator .. templateArgs['subspecies'] .. "'" 			fullName = templateArgs['genus'] .. ' ' .. templateArgs['species'] .. separator .. templateArgs['subspecies'] templateArgs['trinomial'] = "''" .. fullName .. "''"           --templateArgs['subspecies_authority'] = templateArgs['authority']  -- replicates authoity in trinomial (unwanted?) end if templateArgs['variety'] or templateArgs['varietas'] then -- should now be aliased local vSeparator = "  var.  " --alias done? templateArgs['variety']= templateArgs['variety'] or templateArgs['varietas'] -- will use variety as parameter TODO alias this templateArgs['variety_name'] = extinct .. "'" .. string.sub(templateArgs['genus'],1,1) .. '. ' .. string.sub(templateArgs['species'],1,1) .. '.' .. vSeparator .. templateArgs['variety'] .. "'" 			templateArgs['trinomial'] = "''" .. templateArgs['genus'] .. ' ' .. templateArgs['species'] .. vSeparator .. templateArgs['variety'] .. "''"           --templateArgs['variety_authority'] = templateArgs['authority'] -- replicates authority in trinomial if templateArgs['subspecies'] then 	-- subspecies needs to linked instead of bold local redirectName = templateArgs['genus'] .. ' ' .. templateArgs['species'] .. " subsp. " .. templateArgs['subspecies'] local shortName = "''" .. string.sub(templateArgs['genus'],1,1) .. '. ' .. string.sub(templateArgs['species'],1,1) .. '.' .. separator .. templateArgs['subspecies'] .. "''" 				templateArgs['subspecies_name'] = "' .. shortName .. "" offset = offset + 1 -- offset when susbpecies AND variety templateArgs['subspecies_authority'] = templateArgs['parent_authority'] end end --TODO what else do subspeciesbix and infraspeciesbox cover?)

--trinomial_authority = {{{authority|{{{trinomial authority|{{{trinomial_authority|}}} }}} }}}           infraspeciesbox: |species_authority = {{{parent_authority|{{{parent authority|{{{binomial authority|{{{binomial_authority|}}}}}}}}}}}}            subspeciesbox: | species_authority = {{{parent authority|{{{binomial authority|{{{binomial_authority|}}}}}}}}}              note: subspeciesbox doesn't recognise patent_authority with underscore          monthly reports on subspeciesbox and infraspeciesbox              no uses of parent_authority, binomial_authority or trinomial authority              no uses of grandparent, greatgrandparent etc authorites templateArgs['trinomial_authority'] = templateArgs['authority'] or nil

if not templateArgs['name'] or templateArgs['name'] == "" then -- if page name not set templateArgs['name'] = templateArgs['trinomial'] end -- these are used by manual taxobox to complete the taxonomy table templateArgs['species'] = templateArgs['species_name'] templateArgs['subspecies'] = templateArgs['subspecies_name'] templateArgs['variety'] =templateArgs['variety_name'] --QUESTION what happens to parent taxa when subspecies and variety? -- set species and subgenus authorities if templateArgs['subgenus'] then offset = offset + 1 if offset == 4 then    -- when subgenus, species, subspecies and variety templateArgs['subgenus_authority'] = templateArgs['subgenus_authority'] or templateArgs['greatgrandparent_authority'] or "" templateArgs['species_authority']  = templateArgs['grandparent_authority'] or "" elseif offset == 3 then -- when subgenus, species, (subspecies OR variety) templateArgs['subgenus_authority'] = 	templateArgs['subgenus_authority'] or templateArgs['grandparent_authority'] or "" templateArgs['species_authority']  = templateArgs['parent_authority'] or "" end else -- only need to set species authority or subspecues (if also variety) if offset == 3 then   -- species, subspecies and variety templateArgs['species_authority']  = templateArgs['grandparent_authority'] or "" templateArgs['subspecies_authority']  = templateArgs['parent_authority'] or "" elseif offset == 2 then -- species, (subspecies or variety) templateArgs['species_authority']  = templateArgs['parent_authority'] or "" end end templateArgs['display_taxa']  = (templateArgs['display_taxa'] or 1) -2 templateArgs['offset'] = offset

-- need to set subgenus_authority, species_authority, subspecies_authority and variety_authority --shift authorities for subspeciesbox (two steps or three if subgenus set)	   if templateArgs['subgenus'] and templateArgs['subgenus'] ~= ""  then			templateArgs['subgenus_authority']              = templateArgs['grandparent_authority'] or ""			templateArgs['authority']                       = templateArgs['greatgrandparent_authority'] or ""			templateArgs['parent_authority']                = templateArgs['greatgreatgrandparent_authority'] or ""			templateArgs['grandparent_authority']           = templateArgs['greatgreatgreatgrandparent_authority'] or ""			templateArgs['greatgrandparent_authority']      = templateArgs['greatgreatgreatgreatgrandparent_authority'] or ""			templateArgs['greatgreatgrandparent_authority'] = templateArgs['greatgreatgreatgreatgreatgrandparent_authority'] or ""		else			templateArgs['authority']                       = templateArgs['grandparent_authority'] or ""			templateArgs['parent_authority']                = templateArgs['greatgrandparent_authority'] or ""			templateArgs['grandparent_authority']           = templateArgs['greatgreatgrandparent_authority'] or ""			templateArgs['greatgrandparent_authority']      = templateArgs['greatgreatgreatgrandparent_authority'] or ""			templateArgs['greatgreatgrandparent_authority'] = templateArgs['greatgreatgreatgreatgrandparent_authority']	 or ""		end -- ========================= setup for AUTOMATIC TAXOBOX ================================ -- CHECK authomatic taxobox pagename overrides taxon (e.g. Tortrix? destructus) for header --        it does but no italics in header for Tortrix? destructus

--elseif info.auto == "automatictaxobox" then elseif info.auto == "virus" or info.auto == "virusbox" then templateArgs['virus'] = "yes" templateArgs['color_as'] = "Virus" if not templateArgs['parent'] then if templateArgs['taxon'] then templateArgs['parent'] = templateArgs['taxon'] elseif templateArgs['species'] then templateArgs['parent'] = templateArgs['species'] templateArgs['species'] = nil else templateArgs['parent'] = tostring( mw.title.getCurrentTitle) or "" end else templateArgs['link_parent'] = "yes"           -- if parent given, we want to link it			end else

-- "the automated taxobox first looks for the taxonomy template that matches the supplied |taxon= parameter " --      "(or, if none is supplied, the article's title, ignoring any parenthetical expressions). " if not templateArgs['taxon'] or templateArgs['taxon'] == "" then --templateArgs['taxon'] = templateArgs['name'] or tostring( mw.title.getCurrentTitle) templateArgs['taxon'] = tostring( mw.title.getCurrentTitle) or "" --TODO strip name of parenthetical terms off page title if templateArgs['taxon'] ~= "" then --TODO error message and exit end end if templateArgs['parent'] then templateArgs['link_parent'] = "yes"             -- if parent given, we want to link it    	else templateArgs['parent'] = templateArgs['taxon']  -- otherwise set parent end --TODO set name if parameter no supplies -- {{PAGENAME}} 		   {{Automatic taxobox/floating intro|taxon={{{taxon|{{PAGENAME}}}}} }} end	-- end special handling for speciesbox, subspeciesbox, and automatic taxobox -- check taxonomy templates for automatic taxobox systtem --{{#ifexist:Template:Taxonomy/{{{taxon| {{PAGENAME}} Acacia }}} --      |  	--       |{{Automatic taxobox/floating intro|taxon={{{taxon|{{PAGENAME}}}}} }} -->}}

end

--- function p.templateStyle( frame, src ) return frame:extensionTag( 'templatestyles', '', { src = src } ); end

- function p.testTables(frame) if 1==1 then return end -- disable local root = mw.html.create('table'):addClass('wikitable')

local row = root:tag('tr')               -- add row using lua library local cell = row:tag('td') cell:wikitext('row A:') cell = row:tag('td'):wikitext('content A')

row = root:tag('tr')                     -- add row using lua library cell = row:tag('td'):wikitext('row B:') cell = row:tag('td') :wikitext('\n{|\n|-\n|P\n|Q\n|}') --but include a wikitxt table in one cell -- :done

-- row:done --root=mw.html:allDone root:wikitext(' a  b  ') -- add row to root using html root:wikitext('\n|-\n|X\n|Y\n')             -- add row to root using wikitext (FAILS) root:wikitext('\r|-\r|I\r|J\r')             -- FAIL output |- |X |Y root:wikitext(frame:preprocess('\n|-\n|U\n|V\n')) -- FAIL output |- |U |V root:wikitext(' \n|M\n|N\n ')

row=root:tag('tr'):node(' c d ')    -- adds row successfully row=root:tag('tr'):node('\n|Xc\n|Xd\n')   -- fails to adds row row = root:tag('tr')                      -- add another row using lua library cell = row:tag('td'):wikitext('row C:') cell = row:tag('td'):wikitext('content C')

root:node('\n{|\n|-\n|Xx\n|Yx\n|}\n')   -- adds new table after

--frame:preprocess return 	 tostring(root)

-- CONCLUSION: cannot mix wikitext freely in the node structure          A complete wikitext table can be included in a cell (e.g. used for automatic taxonomy now)           An alternative is to use wikitext for the whole taxobox table end

-- --- TEST AUTO TAXONOMY FUNCTIONS - function p.test(frame) local a = require("Module:Sandbox/Jts1882/Biota Infobox/auto")

--local taxonTable = a.loadTaxonomyTable(frame) now done in showTaxonomyTable return a.showTaxonomyTable(frame) end

-- All modules end by returning the variable containing its functions to Wikipedia. return p