Module:Sandbox/Jts1882/Biota infobox/auto

 localp={}-- 
 localg={}-- these are variables with global scope in this sub-module
 g.info={}

 --[[ testing function to show automatic taxonomy within a table ]]
 functionp.showTaxonomyTable(frame)

 g.templateArgs={}
 g.info.auto=false

 g.taxonTable=p.loadTaxonomyTable(frame)

 localoutput='\n{| class="wikitable" \n|- style="vertical-align:top;" '
 --output = output .. '\n! Rank !! Taxon \n|-' -- oldversion starting new row 
 output=output..'\n! Rank !! Taxon'-- don't start a new row here

 g.htmlTable=mw.html.create('table')
 :addClass('infobox'):addClass('biota')
 :cssText("text-align: left; width: 200px; font-size: 100%")

 output=output..p.taxoboxList(frame)
 output=output..'\n|}'



 returntostring(g.htmlTable)..output
 --return '\n' ..p.showTaxonomyHierarchyRaw(frame, g.taxonTable) --output
 --return output
 end

 --[[ function to add rows for an automatic taxonomy to an taxobox-style infobox 
  -- called from parent to this submodule
  -- uses a modification of p.taxoboxList() form Module:Autotaxobox
  -- uses a function to emulate 
 ]]
 functionp.getTaxonomyTableRows(frame,htmlTable,templateArgs,info)
 g.htmlTable=htmlTable
 g.templateArgs=templateArgs
 g.info=info
 g.taxonTable=p.loadTaxonomyTable(frame)
 returnp.taxoboxList(frame)
 end
 --[[ testing function to output the heirarchy table from the automatic taxonomy as a wikitable
 ]]
 functionp.showTaxonomyHierarchyRaw(frame,taxonTable)
 localoutput='{| class="wikitable sortable" '
 fork,vinpairs(taxonTable[1])do
 output=output..'\n!'..k
 end
 fori=1,#taxonTable,1do
 output=output..'\n|-'
 fork,vinpairs(taxonTable[i])do
 output=output..'\n|'..v
 end
 end
 output=output..'\n|}'
 --return mw.dumpObject(taxonTable)
 returnoutput
 end
 --[[ function p.loadTaxonomyTable(frame) - loads a 2-D table of taxon information from automatic taxonomy system
  each row is the informaiton for a taxon 
  - this obtained useing Template:Taxonomy/TAXON with argument ['machine code'] = "all"
  - additionally adds blank taxon and authority columns
  row ={ parent, rank, link_target, link_text, always_display, extinct, same_as, refs, taxon, authority } 
 ]]

 functionp.loadTaxonomyTable(frame)

 localok,taxonInfo
 localtaxonTable={}
 locali=1

 -- load authorities from template parameters
 localauthorities={g.templateArgs['authority']or"",
 g.templateArgs['parent_authority']or"",
 g.templateArgs['grandparent_authority']or"",
 g.templateArgs['greatgrandparent_authority']or"",
 g.templateArgs['greatgreatgrandparent_authority']or"",
 g.templateArgs['greatgreatgreatgrandparent_authority']or"",
 g.templateArgs['greatgreatgreatgreatgrandparent_authority']or"",
 }
 -- get the name of the first taxon
 localtaxon=g.templateArgs['taxon']org.templateArgs['parent']or"Felis"
 --taxon= 'Felis' 
 --taxon= 'Worthenella' 
 --taxon= 'Fereuungulata'
 --local authority = 'authority'

 -- the following section is an alternative method for adding rows for species, subspecies, etc
 --[[START: insert rows for variety, subspecies, species and subgenus at base of automatic taxonomy]]
 ifg.templateArgs['species_name']then

 ifg.templateArgs['variety_name']then
 taxonTable[i]={taxon=g.templateArgs['variety_name'],
 rank='variety',
 authority=authorities[i]--g.templateArgs[authority],
 }
 i=i+1
 end
 ifg.templateArgs['subspecies_name']then
 taxonTable[i]={taxon=g.templateArgs['subspecies_name'],
 rank='subspecies',
 authority=authorities[i]-- g.templateArgs[authority],
 }
 i=i+1
 end
 -- TODO if subgenus

 taxonTable[i]={taxon=g.templateArgs['species_name'],
 rank='species',
 authority=authorities[i]-- g.templateArgs[authority],
 }
 i=i+1
 taxon=g.templateArgs['parent']
 end
 --[[END: insert rows for variety, subspecies species and subgenus at base of automatic taxonomy]]

 --[[ load the heirarchy of the automatic taxonomy 
  each row has the contents for a taxon returned by g.getTaxonInfo()
  which uses Template:Taxonomy/TAXON with argument machine code ="all"
  ]]
 whilei<100do

 ok,taxonTable[i]=g.getTaxonInfo(frame,taxon)

 --if ok and taxonTable[i]['parent'] ~= "" then
 ifokthen
 iftaxonTable[i]['same_as']andtaxonTable[i]['same_as']~=""then
 taxon=taxonTable[i]['same_as']
 localok,sameAsTable=g.getTaxonInfo(frame,taxon)
 ifokthen
 fork,vinpairs(taxonTable[i])do
 ifv==""then
 taxonTable[i][k]=sameAsTable[k]-- use same_as values if none set
 end
 end
 elsebreak;
 end
 else-- we have what data for the taxon directly
 -- TODO do something
 end

 -- add taxon to the table row
 iftaxonTable[i]['link_text']andtaxonTable[i]['link_text']~=""then
 taxonTable[i]['taxon']=taxonTable[i]['link_text']
 else
 taxonTable[i]['taxon']=taxonTable[i]['link_target']
 end
 -- authority from parent authroity sequence
 taxonTable[i]['authority']=(authorities[i]or"")

 iftaxonTable[i]['parent']==""then-- have we reached the top of the heirarchy?
 break
 else
 taxon=taxonTable[i]['parent']-- set the taxon for the next loop
 end
 elsebreak
 end
 i=i+1

 end

 --we have a complete table
 taxonTable.n=#taxonTable-1-- minus one as last one has parent=life and displays as Genus: Ursus

 returntaxonTable
 end

 --[[ loads a row of taxon information
  uses Template:Taxonomy/TAXON with argument ['machine code'] = "all"
  additionally adds blank taxon and authority columns
  row ={ parent, rank, link_target, link_text, always_display, extinct, same_as, refs, taxon, authority } 
 ]]
 functiong.getTaxonInfo(frame,taxon)

 localok,taxonInfo=pcall(frame.expandTemplate,frame,{title='Template:Taxonomy/'..taxon,
 args={['machine code']="all"}})
 ifokthen
 localsplit=mw.text.split(taxonInfo,"$",true)
 -- all: returns "parent$rank$link_target$unnamed parameter$always_display$extinct$same_as$refs"
 localtaxonRow={
 parent=split[1]or"",
 rank=split[2]or"",
 -- if link containing pipe, e.g. |link=Fereuungulata|Ferungulata =LINK_TARGET|LINK_TEXT
 link_target=split[3]or"",-- link_target = link or first part of link before pipe
 link_text=split[4]or"",-- then produces unnamed parameter 'link_text'
 always_display=split[5]or"",
 extinct=split[6]or"",
 same_as=split[7]or"",
 refs=split[8]or"",
 taxon="",-- create blank now to stop table reordering
 authority="",-- create blank now to stop table reordering
 }

 returnok,taxonRow
 end
 end

 --[[=========================== taxoboxList (old version) =================================

  -- Copied from Module:Autotaxobox on 19 December 2018
  -- modified to use full table of taxaonomy template parameters
  -- reason: to reduce template calls, especially in replacement for Template:Taxobox/showtaxon

 Returns the rows of taxa in an automated taxobox, based on the taxonomic
 hierarchy for the supplied taxon.
 Usage:
 {{#invoke:Autotaxobox|taxoboxList|TAXON
 |display_taxa = the number of taxa *above* TAXON to force to be displayed
 |authority = taxonomic authority for TAXON
 |parent_authority = taxonomic authority for TAXON's parent
 |gparent_authority = taxonomic authority for TAXON's grandparent
 |ggparent_authority = taxonomic authority for TAXON's greatgrandparent
 |ggparent_authority = taxonomic authority for TAXON's greatgreatgrandparent
 |bold_first = 'bold' to bold TAXON in its row
 |virus = 'yes' to apply virus taxa italicization standards
 }}
 =============================================================================]]
 functionp.taxoboxList(frame)
 --local currTaxon = frame.args[1] or ''
 localdisplayN=(tonumber(g.templateArgs['display_taxa'])or1)+1
 --local displayN = (tonumber(frame.args['display_taxa']) or 1) + 1
 --local auth = frame.args['authority'] or ''
 --local parentAuth = frame.args['parent_authority'] or ''
 --local gParentAuth = frame.args['gparent_authority'] or ''
 --local ggParentAuth = frame.args['ggparent_authority'] or ''
 --local gggParentAuth = frame.args['gggparent_authority'] or ''
 localboldFirst=frame.args['bold_first']or'link'-- values 'link' or 'bold'
 localvirus=frame.args['virus']or'no'-- values 'yes' or 'no'

 -- local taxonTable = l.makeTable(frame, currTaxon) 
 localtaxonTable=g.taxonTable-- modifications using full table
 --taxonTable.n = #taxonTable
 --displayN = 10 -- force display
 --[[]
 	taxonTable[1]['authority'] = frame.args['authority'] or 'authority'
 	taxonTable[2]['authority'] = frame.args['parent_authority'] or 'parent auth'
 	taxonTable[3]['authority'] = frame.args['gparent_authority'] or 'gp auth' 
 	taxonTable[4]['authority'] = frame.args['ggparent_authority'] or 'ggp auth' 
 	taxonTable[5]['authority'] = frame.args['gggparent_authority'] or 'gggp auth' ]]
 localtest=g.templateArgs['authority']or'authority'
 --[[ TODO check that taxonTable[i] exists
 	taxonTable[1]['authority'] = g.templateArgs['authority'] or ''
 	taxonTable[2]['authority'] = g.templateArgs['parent_authority'] or ''
 	taxonTable[3]['authority'] = g.templateArgs['grandparent_authority'] or '' 
 	taxonTable[4]['authority'] = g.templateArgs['greatgrandparent_authority'] or '' 
 	taxonTable[5]['authority'] = g.templateArgs['greatgreatgrandparent_authority'] or '' ]]

 -- determine when to force: when i<displayN and when infrataxons in i=2 and i=3 (why?)
 fori=1,displayN,1do-- use 'always_display' to flag a force
 taxonTable[i]['always_display']="yes"
 end
 --[[check for lower infrataxons for i=4 and i=3 TODO verify this works
  if g.isInfraTaxon(taxonTable[3]['rank']) then -- if i=3 an infrataxon 
  	 taxonTable[4]['always_display'] = "yes" -- then always display i=4
  end
  if g.isInfraTaxon(taxonTable[2]['rank']) then -- if i=2 an infrataxon 
  	 taxonTable[4]['always_display'] = "yes" -- then always display i=3 and i=4
  	 taxonTable[3]['always_display'] = "yes" 
  end]]


 localres=''

 -- generic display to replace >6, 5,4,3,2,1 sections
 fori=taxonTable.n,1,-1do
 ifi==1thenboldFirst="bold"end
 res=res..g.showTaxonRow(frame,i,boldFirst,virus)
 --res = res .. g.showTaxonRow(frame, i, taxonTable[i]['taxon'], taxonTable[i]['authority'], taxonTable[i]['always_display'], boldFirst, virus)

 end
 returnres
 end
 --[[ function to check if an infrarank (not major rank) that should be displayed
  - emulates template Template:Infrataxon(), which uses Template:Principal rank
 ]]
 functiong.isPrincipalRank(rank)
 -- Remove "ichno" and "oo" and then check for a major taxon ("oordo" becomes "rdo"):
 rank=string.gsub(rank,"ichno","")
 rank=string.gsub(rank,"oo","")

 ifrank=="regnum"orrank=="phylum"orrank=="divisio"orrank=="classis"orrank=="ordo"orrank=="rdo"
 orrank=="familia"orrank=="genus"orrank=="species"orrank=="subspecies"orrank=="variety"then
 returntrue
 else
 returnfalse-- rank is an infrarank
 end
 --return not g.isInfraTaxon(rank)
 end
 functiong.isInfraTaxon(rank)
 --Remove "ichno" and "oo" and then check for a major taxon ("oordo" becomes "rdo"):
 rank=string.gsub(rank,"ichno","")
 rank=string.gsub(rank,"oo","")

 ifrank=="regnum"orrank=="phylum"orrank=="divisio"orrank=="classis"orrank=="ordo"orrank=="rdo"
 orrank=="familia"orrank=="genus"orrank=="species"orrank=="subspecies"orrank=="variety"then
 returnfalse
 else
 returntrue-- rank is an infrarank
 end
 end
 --[[ function g.showTaxonRow () - show a row of the taxonomy table
  - emulates Template:Taxobox/showtaxon
  - uses Template:Taxon link and Template:anglicise rank
 ]]
 functiong.showTaxonRow(frame,i,boldFirst,virus)

 --[[ return frame:expandTemplate{ title = 'Template:Taxobox/showtaxon', 
  args = { g.taxonTable[i]['taxon'], 
  authority=g.taxonTable[i]['authority'], 
  fc = g.taxonTable[i]['always_display'], 
  format = boldFirst, 
  virus = virus } }
 ]]
 -- do we want to display the taxon?
 ifg.taxonTable[i]['always_display']=="yes"-- the flag for whether to force display a taxon
 org.taxonTable[i]['always_display']=="true"
 org.isPrincipalRank(g.taxonTable[i]['rank'])then-- or major ranks
 -- continue
 else--if g.isInfraTaxon(g.taxonTable[i]['rank']) then -- or a major rank (=not a minor rank)
 return""
 end


 --{{Taxon link|{{{1|Ursa}}}|bold={{#ifeq:{{{format|link}}}|bold|yes|no}}|virus={{{virus|no}}}}}
 localbold="no"
 ifboldFirst=="bold"thenbold="yes"end
 --taxon name
 localtaxonName=g.taxonTable[i]['taxon']-- plain name
 localrank=g.taxonTable[i]['rank']
 ifrank=="species"orrank=="subspecies"orrank=="variety"then
 -- no processing of name necessary (already set to species_name, subspecies_name, etc)
 else
 taxonName=frame:expandTemplate{title="Taxon link",
 args={taxonName,bold=bold,virus=virus}}
 end
 --rank
 localtaxonRank=g.taxonTable[i]['rank']
 taxonRank=frame:expandTemplate{title="anglicise rank",args={g.taxonTable[i]['rank']}}

 ifg.taxonTable[i]['rank']=="virus_group"then
 taxonName=frame:expandTemplate{title="Virus group",args={g.taxonTable[i]['taxon']}}
 --	taxonRank = "Group" -- handled by anglicise rank template
 end

 localauthorityString=''
 ifg.taxonTable[i]['authority']andg.taxonTable[i]['authority']~=""then
 authorityString='<br /><small>'..g.taxonTable[i]['authority']..'</small>'
 end

 --[[ now output the html 
 	 the autotaxobox templates had already started a new row and ended with new row
 	 this was the stumbling block for the nodal approach uing the Lua html library (mw.html) 
 	 which required the embedded table
 	]]
 -- new method append row to the table structure using mw:html library
 localrow=g.htmlTable:tag('tr')
 localcell=row:tag('td'):wikitext(taxonRank..":"..i)
 cell=row:tag('td'):wikitext(taxonName..authorityString)

 -- old method: return wikitext for table row
 localrowWiki='\n|-\n|'..taxonRank..':'..i..'||'..taxonName..authorityString
 --return row .. '\n|-' -- return with new row started

 returnrowWiki-- so don't start the new row 
 end

 returnp