Module:Sandbox/Jts1882/Biota infobox explained

require('strict')-- 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 variableslocal g = -- these are variables with global scope in this module

local info = -- contains general purpose information (e.g. header background colour)info.debug = true -- 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:Sandbox/Jts1882/Biota infobox/param') local core = require('Module:Sandbox/Jts1882/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 ##################################

--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/corep.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) end

--

-- ################## AUTOMATIC TAXOBOX SYSTEM HANDLING ################################-------------------------------------------------------------------------------------------------- handle specific requirements of different options: auto, speciesbox etcfunction 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 -- 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'] local species2 = templateArgs['species2'] or templateArgs['mother'] or templateArgs['mother_species'] or templateArgs['species'] 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 -- genus2 = frame:expandTemplate 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 --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 templateArgs['name'] = frame:expandTemplate

-- set binomial : the speciesbox template seems to use genus and species before taxon name -- "| binomial = " -- 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 -- templateArgs['taxon'] = nil -- For auto module --

= set-up for SUBSPECIESBOX or INTRASPECIESBOX

elseif info.auto

"subspeciesbox" or info.auto

"infraspeciesbox" then -- -- 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 = infraspeciesbox: |species_authority = subspeciesbox: | species_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 -- ]] end -- end special handling for speciesbox, subspeciesbox, and automatic taxobox -- check taxonomy templates for automatic taxobox systtem --

end

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

P\n

Q\n

') --but include a wikitxt table in one cell -- :done

-- row:done --root=mw.html:allDone root:wikitext('ab') -- 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('cd') -- 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

Xx\n

Yx\n

\n') -- adds new table after

--frame:preprocess return tostring(root)

--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