Module:Autotaxobox

--[[*************************************************************************
This module provides support to the automated taxobox system – the templates
Automatic taxobox, Speciesbox, Subspeciesbox, Infraspeciesbox, etc.

In particular it provides a way of traversing the taxonomic hierarchy encoded
in taxonomy templates (templates with names of the form
"Template:Taxonomy/TAXON_NAME") without causing template expansion depth
errors.
*****************************************************************************]]

require('strict')
local TaxonItalics = require('Module:TaxonItalics') -- use a function from Module:TaxonItalics to italicize a taxon name
local TableRow = '|-\n'
local TableEnd = '|}\n'
local p = {} -- functions made public
local l = {} -- internal functions, kept separate
local colour = '' -- colour for taxobox and taxonomy listings

--[[=========================================================================
Limit the maximum depth of a taxonomic hierarchy that can be traversed;
avoids excessive processing time and protects against incorrectly set up
hierarchies, e.g. loops.
The value can be obtained externally via
{{#invoke:Autotaxobox|getMaxSearchLevels}}
=============================================================================]]
local MaxSearchLevels = 100

function p.getMaxSearchLevels()
 return MaxSearchLevels
end

--[[========================== taxoboxColour ================================
Determines the correct colour for a taxobox, by searching up the taxonomic
hierarchy from the supplied taxon for the first taxon (other than
'incertae sedis') that sets a taxobox colour. It is assumed that a valid
taxobox colour is defined using CSS rgb() syntax.
If no taxon that sets a taxobox colour is found, then 'transparent'is
returned unless the taxonomic hierarchy is too deep, when the error colour is
returned.
Usage: {{#invoke:Autotaxobox|taxoboxColour|TAXON}}
=============================================================================]]
function p.taxoboxColour(frame)
 return p.getTaxoboxColour(frame, frame.args[1] or '')
end

function p.getTaxoboxColour(frame, currTaxon)
 -- note that colour is global to this function; default is empty string
 local i = 1 -- count levels processed
 local searching = currTaxon ~= '' -- still searching for a colour?
 local foundICTaxon = false -- record whether 'incertae sedis' found
 while searching and i <= MaxSearchLevels do
  local plainCurrTaxon, dummy = l.stripExtra(currTaxon) -- remove trailing text after /
  if string.lower(plainCurrTaxon) == 'incertae sedis' then
   foundICTaxon = true
  else
   local possibleColour = frame:expandTemplate{ title = 'Template:Taxobox colour', args = { plainCurrTaxon } }
   if string.sub(possibleColour,1,3) == 'rgb' then
    colour = possibleColour
    searching = false
   end
  end
  if searching then
   local ok, parent = p.getTaxonInfoItem(frame, currTaxon, 'parent')
   if ok and parent ~= '' then
    currTaxon = parent
    i = i + 1
   else
    searching = false -- run off the top of the hierarchy or tried to use non-existent taxonomy template
   end
  end
 end
 if colour == '' then
  if foundICTaxon then
   colour = frame:expandTemplate{ title = 'Template:Taxobox colour', args = { 'incertae sedis' } }
  elseif searching then
   -- hierarchy exceeds MaxSearchLevels levels
   colour = frame:expandTemplate{ title = 'Template:Taxobox/Error colour', args = { } }
  else
   colour = 'transparent'
  end
 end
 return colour
end

--[[= = = = = = = = = = = = =  topLevelTaxon  = = = = = = = = = = = = = = = = 
Defines the correct top level taxa, one of which should terminate every
taxonomic hierarchy encoded in taxonomy templates.
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function l.topLevelTaxon(taxon)
 return  taxon == 'Life' or taxon == 'Veterovata' or taxon == 'Ichnos'
end

--[[=========================== taxoboxList =================================
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
}}
=============================================================================]]
function p.taxoboxList(frame)
 local currTaxon = frame.args[1] or ''
 if currTaxon == '' then return '' end
 local displayN = (tonumber(frame.args['display_taxa']) or 1) + 1
 local authTable = {}
 authTable[1] = frame.args['authority'] or ''
 authTable[2] = frame.args['parent_authority'] or ''
 authTable[3] = frame.args['gparent_authority'] or ''
 authTable[4] = frame.args['ggparent_authority'] or ''
 authTable[5] = frame.args['gggparent_authority'] or ''
 local boldFirst = frame.args['bold_first'] or 'link' -- values 'link' or 'bold'
 local virus = frame.args['virus'] or 'no' -- values 'yes' or 'no'
 local offset = tonumber(frame.args['offset'] or 0)
 -- adjust the authority table if 'authority' refers to a rank lower than the target taxon
 if offset ~= 0 then
  for i = 1, 5 do
   local j = i + offset
   if j <= 5 then
    authTable[i] = authTable[j]
   else
    authTable[i] = ''
   end
  end
 end
 local taxonTable, taxonRankTable = l.makeTable(frame, currTaxon)
 local res = ''
 local topTaxonN = taxonTable.n
 -- display all taxa above possible greatgreatgrandparent, without authority
 for i = topTaxonN, 6, -1 do
  res = res .. l.showTaxon(frame, taxonTable[i], taxonRankTable[i], topTaxonN==i, '', displayN >= i, '', virus)
 end
 -- display all taxa above possible parent, with authority if given
 for i = math.min(topTaxonN, 5), 2, -1 do
  res = res .. l.showTaxon(frame, taxonTable[i], taxonRankTable[i], topTaxonN==i, authTable[i], displayN >= i, '', virus)
 end
 -- display target taxon, always displayed and emboldened
 res = res .. l.showTaxon(frame, taxonTable[1], taxonRankTable[1], topTaxonN==1, authTable[1], true, boldFirst, virus)
 return res
end

--[[= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Show one taxon row in a taxobox.
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function l.showTaxon(frame, taxon, rank, isTopTaxon, auth, force, boldFirst, virus)
 -- it's an error if this is the top taxon and it's not a top level taxon (e.g. "Life")
 if isTopTaxon then
  if l.topLevelTaxon(taxon) then
   return '' -- don't display a top level taxon
  elseif (mw.title.new('Taxonomy/'..taxon, 'Template') or {}).exists then
   -- taxonomy template for this taxon has no parent specified
   return frame:expandTemplate{ title = 'Template:Create taxonomy', args = {taxon, msg='Taxonomy template does not specify a parent'} } .. '\n' .. TableRow
  else
   -- no taxonomy template for this taxon
   return frame:expandTemplate{ title = 'Template:Create taxonomy', args = {taxon, msg='Missing taxonomy template'} } .. '\n' .. TableRow
  end
 else
  -- if showing is not already forced, force if it's a principal rank or an authority is specified
  force = force or frame:expandTemplate{ title = 'Template:Principal rank', args = {rank} } == 'yes' or
          auth ~= ''
  if not force then
   -- if showing is still not already forced, force if the taxonomy template has 'always_display' set
   local ok, alwaysDisplay = p.getTaxonInfoItem(frame, taxon, 'always_display')
   force = alwaysDisplay == 'yes' or  alwaysDisplay == 'true'
  end
  if force then
   local res = l.tableCell(frame:expandTemplate{ title = 'Template:Anglicise rank', args = {rank} } .. ':')
   local bold = 'no'
   if boldFirst == 'bold' then bold = 'yes' end
   if auth ~= '' then
    auth = '<br><small>' .. auth .. '</small>'
   end
   local res = res .. l.tableCell(l.getTaxonLink(frame, taxon, rank, bold, '', '', virus) .. auth) -- italic, abbreviated
   return res .. TableRow
  else
   return ''
  end
 end
end

--[[========================== taxonomyList =================================
Returns the cells of the taxonomy table displayed on the right hand side of
"Template:Taxonomy...." pages.
Usage: {{#invoke:Autotaxobox|taxonomyList|TAXON}}
=============================================================================]]
function p.taxonomyList(frame)
 local currTaxon = frame.args[1] or ''
 if currTaxon == '' then
  return '{|class="infobox biota"\n' .. TableRow .. l.tableCell('') .. l.tableCell('ERROR: no taxon supplied') .. TableEnd
 end
 local taxonTable, taxonRankTable = l.makeTable(frame, currTaxon)
 local rankValTable = l.getRankTable()
 local lastRankVal = 1000000
 local orderOk = true
 -- check whether the taxonomy is for viruses; use already determined taxon colour if possible
 local virus = 'no'
 local taxoColour = colour
 if taxoColour == '' then
  if  taxonTable[taxonTable.n] == 'Ichnos' or taxonTable[taxonTable.n] == 'Veterovata' then
   taxoColour = frame:expandTemplate{ title = 'Template:Taxobox colour', args = { taxonTable[taxonTable.n] } }
  else
   taxoColour = frame:expandTemplate{ title = 'Template:Taxobox colour', args = { taxonTable[taxonTable.n - 1] } }
  end
 end
 if taxoColour == frame:expandTemplate{ title = 'Template:Taxobox colour', args = { 'virus' } } then
  virus = 'yes'
 end
 -- add information message
 local res = '<p style="float:right">Bold ranks show taxa that will be shown in taxoboxes<br>because rank is principal or <code>always_display=yes</code>.</p>\n'

 -- start table
 res =  res .. '{| class="infobox biota" style="text-align: left; font-size:100%"\n' .. TableRow .. '! colspan=4 style="text-align: center; color:inherit; background-color: '
             .. taxoColour .. '"|Ancestral taxa\n'
 -- deal first with the top level taxon; if there are no errors, it should be Life/Veterovata/Ichnos, which are 
 -- not displayed
 local taxon = taxonTable[taxonTable.n]
 if not l.topLevelTaxon(taxon) then
  local msg = 'Taxonomy template missing'
  if mw.title.new('Taxonomy/'..taxon, 'Template').exists then
   msg = 'Parent taxon needed'
  end
  res = res .. TableRow .. l.tableCell('colspan=2', frame:expandTemplate{title = 'Template:Create taxonomy', args = {taxon, msg = msg}})
 end
 -- now output the rest of the table
 local currRankVal
 for i = taxonTable.n-1, 1, -1 do
  -- check ranks are in right order in the hierarchy
  taxon = taxonTable[i]
  local rank = taxonRankTable[i]
  currRankVal = l.lookupRankVal(rankValTable, rank)
  if currRankVal then
   orderOk = currRankVal < lastRankVal
   if orderOk then lastRankVal = currRankVal end
  else
   orderOk = true
  end
  -- see if the row will be displayed in a taxobox; bold the rank if so
  local boldRank = false
  local ok, alwaysDisplay = p.getTaxonInfoItem(frame, taxon, 'always_display')
  if ok and (alwaysDisplay == 'yes' or alwaysDisplay == 'true') then
   boldRank = true
  else
   boldRank = frame:expandTemplate{ title = 'Template:Principal rank', args = {rank} } == 'yes'
  end
  -- now return a row of the taxonomy table with anomalous ranks marked
  local errorStr = ''
  if not orderOk then errorStr = 'yes' end
  local link = l.getTaxonLink(frame, taxon, rank, '', '', '', virus) -- bold, italic, abbreviated
  res = res .. l.taxonomyListRow(frame, taxon, rank, link, boldRank, errorStr)
 end
 -- close table
 res = res .. TableEnd
 -- error-tracking for taxonomy templates
 -- if the last row has an anomalous rank, put the page in an error-tracking category
 local errCat1 = ''
 if not orderOk then
  errCat1 = '[[Category:Taxonomy templates showing anomalous ranks]]\n'
 end
 -- if the last row has a taxon name in the page name that does not match the link text,
 -- put the taxonomy template in a tracking category
 local dummy, linkText = p.getTaxonInfoItem(frame, taxon, 'link_text')
 local match = l.matchTaxonLink(taxon, linkText, currRankVal and currRankVal < rankValTable['genus'])
 local errCat2 = ''
 if not match then
  errCat2 = '[[Category:Taxonomy templates with name and link text not matching|' .. taxon .. ']]\n'
 end
 if errCat1..errCat2 ~= '' then
  res = res .. frame:expandTemplate{ title = 'Template other', args = { errCat1..errCat2} }
 end
 return res
end

--[[ = = = = = = = = = = = = = = taxonomyListRow  = = = = = = = = = = = = = = 
Returns a single row of the taxonomy table displayed on the right hand side
 of "Template:Taxonomy...." pages.
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function l.taxonomyListRow(frame, taxon, rank, link, boldRank, error)
 local res = ''
 if taxon == '' or rank == '' then return res end
 local baseTaxon, qualifier = l.stripExtra(taxon)
 -- if appropriate, make it clear that some taxa have been skipped via a ... row
 if qualifier == '/skip' then
  res = res .. TableRow .. l.tableCell('.....') .. l.tableCell('.....')
 end
 -- now generate a row of the table
 res = res .. TableRow
 local cellContent = ''
 local anglicizedRank = frame:expandTemplate{ title = 'Template:Anglicise rank', args = { rank } }
 if boldRank then
  cellContent = cellContent .. '<b>' .. anglicizedRank .. '</b>:'
 else
  cellContent = cellContent .. anglicizedRank .. ':'
 end
 if error == 'yes' then
  cellContent = '<span style="background-color:#FDD">' .. cellContent .. '</span>'
 end
 res = res .. l.tableCell(cellContent)
           .. l.tableCell('<span style="white-space:nowrap;">' .. link .. '</span>')
           .. l.tableCell('<span style="font-size:smaller;white-space:nowrap;">' .. qualifier  .. '</span>')
           .. l.tableCell('<span style="white-space:nowrap;">' .. frame:expandTemplate{ title = 'Template:Edit a taxon', args = { taxon } } .. '</span>')
 return res
end

--[[========================= callTaxonomyKey ===============================
Prepares for, and then calls, Template:Taxonomy key to display a taxonomy
template page. It does this by building up the information the template
requires, following one 'same as' link, if required.
Usage:
{{#invoke:Autotaxobox|callTaxonomyKey
|parent=
|rank=
|extinct=
|always_display=
|link_target=value of 'link' parameter in taxonomy template
|link_text=value of parameter 2 in taxonomy template
|same_as=
}}
=============================================================================]]
local PARENT = 1
local RANK = 2
local LINK_TARGET = 3
local LINK_TEXT = 4
local ALWAYS_DISPLAY = 5
local EXTINCT = 6
local SAME_AS = 7
local REFS = 8

function p.callTaxonomyKey(frame)
 local taxon = frame.args['taxon'] or ''
 local parent = frame.args['parent'] or ''
 local rank = frame.args['rank'] or ''
 local extinct = string.lower(frame.args['extinct']) or ''
 local alwaysDisplay = string.lower(frame.args['always_display']) or ''
 local linkTarget = frame.args['link_target'] or ''
 local linkText = frame.args['link_text'] or '' -- this is the "raw" link text, and can be ''
 local refs = frame.args['refs'] or ''
 local sameAsTaxon = frame.args['same_as'] or ''
 if sameAsTaxon ~= '' then
  -- try using the 'same as' taxon; it's an error if it doesn't exist
  local ok, sameAsInfoStr = pcall(frame.expandTemplate, frame, { title = 'Template:Taxonomy/' .. sameAsTaxon, args = {['machine code'] = 'all' } })
  if ok then
   local sameAsInfo = mw.text.split(sameAsInfoStr, '$', true)
   --'same as' taxon's taxonomy template must not have a 'same as' link
   if sameAsInfo[SAME_AS] == '' then
    if parent == '' then parent = sameAsInfo[PARENT] end
    if rank == '' then rank = sameAsInfo[RANK] end
    if extinct == '' then extinct = string.lower(sameAsInfo[EXTINCT]) end
    if alwaysDisplay == '' then alwaysDisplay = string.lower(sameAsInfo[ALWAYS_DISPLAY]) end
    if linkTarget == '' then linkTarget = sameAsInfo[LINK_TARGET] end
    if linkText == '' then linkText = sameAsInfo[LINK_TEXT] end
    if refs == '' and parent == sameAsInfo[PARENT] then refs = sameAsInfo[REFS] end
   else
    return '<span style="color:red; font-size:1.1em">Error: attempt to follow two "same as" links</span>: <code>same_as = ' .. sameAsTaxon .. '</code>, but [[Template:Taxonomy/' .. sameAsTaxon .. ']] also has a<code>same_as</code> parameter.'
   end
  else
   return frame:expandTemplate{ title = 'Template:Taxonomy key/missing template', args = {taxon=sameAsTaxon, msg='given as the value of <code>same as</code>'} }
  end
 end
 local link = linkTarget
 if linkText ~= '' and linkText ~= linkTarget then link = link .. "|" .. linkText end
 -- check consistency of extinct status; if this taxon is not extinct, parent must not be either
 local extinctError = 'no'
 if parent ~= '' and (extinct == '' or extinct == 'no' or extinct == 'false') then
  local ok, parentExtinct = p.getTaxonInfoItem(frame, parent, 'extinct')
  if ok and (parentExtinct == 'yes' or parentExtinct == 'true') then extinctError = 'yes' end
 end
 return frame:expandTemplate{ title = 'Template:Taxonomy key',
   args = {taxon=taxon, parent=parent, rank=rank, extinct=extinct, always_display=alwaysDisplay, link_target=linkTarget, link=link, refs=refs, same_as=sameAsTaxon, extinct_error = extinctError} }
end

--[[============================= showRefs ==================================
Shows the refs field in a taxonomy template, handing incertae sedis taxa and
using '–' for absent refs.
Usage: {{#invoke:Autotaxobox|showRefs|TAXON|REFS}}
=============================================================================]]
function p.showRefs(frame)
 local taxonName = frame.args[1] or ''
 local refs = frame.args[2] or ''
 return l.doShowRefs(taxonName, refs)
end

--[[= = = = = = = = = = = = = = doShowRefs  = = = = = = = = = = = = = = = = =
Show the refs field in a taxonomy template.
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function l.doShowRefs(taxonName, refs)
 if mw.text.split(taxonName, '/', true)[1] == 'Incertae sedis' then
  refs = 'not applicable (<i>incertae sedis</i>)'
 elseif refs == '' then
  refs = '–'
 end
 return refs
end

--[[============================ taxonInfo ==================================
Extracts and returns information from Template:Taxonomy/TAXON, following
one 'same as' link if required.
Usage: {{#invoke:Autotaxobox|taxonInfo|TAXON|ITEM}}
ITEM is one of: 'parent', 'rank', 'link target', 'link text', 'extinct',
'always display', 'refs', 'same as' or 'all'.
If ITEM is not specified, the default is 'all' – all values in a single string
separated by '$'.
=============================================================================]]
function p.taxonInfo(frame)
 local taxon = frame.args[1] or ''
 local item = frame.args[2] or ''
 if item == '' then item = 'all' end
 local ok, info = p.getTaxonInfoItem(frame, taxon, item)
 return info
end

--[[= = = = = = = = = = = getTaxonInfoItem  = = = = = = = = = = = = = = = = =
Utility function to extract an item of information from a 
taxonomy template, following one 'same as' link if required.
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function p.getTaxonInfoItem(frame, taxon, item)
 local ok, info
 -- item == 'dagger' is a special case
 if item == 'dagger' then
  ok, info = p.getTaxonInfoItem(frame, taxon, 'extinct')
  if ok then
   if info == 'yes' or info == 'true' then
    info = '&dagger;'
   else
    info = ''
   end
  end
 -- item ~= 'dagger'
 else
  ok, info = pcall(frame.expandTemplate, frame, { title = 'Template:Taxonomy/' .. taxon, args = {['machine code'] = item } })
  if ok then
   if info == '' then
    -- try 'same as'
    local sameAsTaxon = frame:expandTemplate{ title = 'Template:Taxonomy/' .. taxon, args = {['machine code'] = 'same as' } }
    if sameAsTaxon ~= '' then
     ok, info = pcall(frame.expandTemplate, frame, { title = 'Template:Taxonomy/' .. sameAsTaxon, args = {['machine code'] = item } })
    end
   end
  end
 end
 if ok then
  -- if item is 'link_text', trim info and check whether '(?)' needs to be added
  if item == 'link_text' then
   -- there is a newline at the end of linkText when taxonomy template has "|link = LINK_TARGET|LINK_TEXT"
   info = mw.text.trim(info)
   if string.sub(taxon, -2) == '/?' and not string.find(info, '?', 1, true) then
    info = info .. '<span style="font-style:normal;font-weight:normal;">&nbsp;(?)</span>'
   end
  end
 else
  info = '[[Template:Taxonomy/' .. taxon .. ']]' --error indicator in code before conversion to Lua
 end
 return ok, info
end

--[[============================ taxonLink ==================================
Returns a wikilink to a taxon, if required including '†' before it and
' (?)' after it, and optionally italicized or bolded without a wikilink.
Usage:
{{#invoke:Autotaxobox|taxonLink
|taxon=           : having '/?' at the end triggers the output of ' (?)'
|extinct=         : 'yes' or 'true' trigger the output of '†'
|bold=            : 'yes' makes the core output bold and not wikilinked
|italic=          : 'yes' makes the core output italic
|link_target=     : target for the wikilink
|link_text=        : text of the wikilink (may be same as link_target), without †, italics, etc.
}}
=============================================================================]]
function p.taxonLink(frame)
 local taxon = frame.args['taxon'] or ''
 local extinct = string.lower(frame.args['extinct'] or '')
 local bold = frame.args['bold'] or ''
 local italic = frame.args['italic'] or ''
 local abbreviated = frame.args['abbreviated'] or ''
 local linkTarget = frame.args['link_target'] or ''
 local linkText = frame.args['link_text'] or frame.args['plain_link_text'] or '' --temporarily allow alternative args
 return l.makeLink(taxon, extinct, bold, italic, abbreviated, linkTarget, linkText)
end

--[[= = = = = = = = = = = = = = getTaxonLink  = = = = = = = = = = = = = = = =
Internal function to drive l.makeLink().
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function l.getTaxonLink(frame, taxon, rank, bold, italic, abbreviated, virus)
 local ok, extinct = p.getTaxonInfoItem(frame, taxon, 'extinct')
 if italic == '' then
  italic = frame:expandTemplate{ title = 'Template:Is italic taxon', args = { rank, virus = virus } }
 end
 local ok, linkTarget = p.getTaxonInfoItem(frame, taxon, 'link_target')
 local ok, linkText = p.getTaxonInfoItem(frame, taxon, 'link_text')
 return l.makeLink(taxon, extinct, bold, italic, abbreviated, linkTarget, linkText)
end

--[[= = = = = = = = = = = = = = makeLink  = = = = = = = = = = = = = = = = = =
Actually make the link.
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function l.makeLink(taxon, extinct, bold, italic, abbreviated, linkTarget, linkText)
 local dummy
 -- if link text is missing, try to find a replacement
 if linkText == '' then
  if string.find(taxon, 'Incertae sedis', 1, true) then
   linkText = "''incertae sedis''"
   linkTarget = 'Incertae sedis'
  else
   linkText, dummy = l.stripExtra(taxon)
  end
 end
 if linkTarget == '' then linkTarget = linkText end
 if italic == 'yes' then linkText = TaxonItalics.italicizeTaxonName(linkText, false, abbreviated=='yes') end
 local link = ''
 if bold == 'yes' then link = '<b>' .. linkText .. '</b>'
 else
  if linkTarget == linkText then link = linkText
  else link = linkTarget .. '|' .. linkText
  end
  link = '[[' .. link .. ']]'
 end
 if (extinct == 'yes' or extinct == 'true') and not string.find(link, '†', 1, true) then
  link = '<span style="font-style:normal;font-weight:normal;">†</span>' .. link
 end
 if string.sub(taxon, -2) == '/?' and not string.find(link, '?', 1, true) then
  link = link .. '<span style="font-style:normal;font-weight:normal;">&nbsp;(?)</span>'
 end
 return link
end

--[[========================== showRankTable ================================
Returns a wikitable showing the ranks and their values as set up by
getRankTable().
Usage: {{#invoke:Autotaxobox|showRankTable}}
=============================================================================]]
function p.showRankTable(frame)
 local rankTable = l.getRankTable()
 local res = '{| class="wikitable sortable"\n|+ Ranks checked in taxonomy templates\n! Rank !! Shown as !! Value\n'
 for k, v in pairs(rankTable) do
  local rankShown = frame:expandTemplate{ title = 'Template:Anglicise rank', args = { k } }
  res = res .. TableRow .. l.tableCell(k) .. l.tableCell(rankShown) .. l.tableCell(v)
 end
 return res .. TableEnd
end

--[[============================== find =====================================
Returns the taxon above the specified taxon with a given rank.
Usage: {{#invoke:Autotaxobox|find|TAXON|RANK}}
=============================================================================]]
function p.find(frame)
 local currTaxon = frame.args[1] or ''
 if currTaxon == '' then return '<span class="error">no taxon supplied</span>' end
 local rank = frame.args[2] or ''
 if rank == '' then return '<span class="error">no rank supplied</span>' end
 local inHierarchy = true -- still in the taxonomic hierarchy or off the top?
 local searching = true -- still searching
 while inHierarchy and searching do
  local ok, parent = p.getTaxonInfoItem(frame, currTaxon, 'parent')
   if ok and parent ~= '' then
   currTaxon = parent
   local ok, currRank = p.getTaxonInfoItem(frame, currTaxon, 'rank')
   if currRank == rank then
    searching = false
   end
  else
   inHierarchy = false
  end
 end
 if inHierarchy and not searching then return currTaxon
 else return '<span class="error">rank not found</span>'
 end
end

--[[=============================== nth =====================================
External utility function primarily intended for use in checking and debugging.
Returns the nth level above a taxon in a taxonomic hierarchy, where the taxon
itself is counted as the first level.
Usage: {{#invoke:Autotaxobox|nth|TAXON|n=N}}
=============================================================================]]
function p.nth(frame)
 local currTaxon = frame.args[1] or ''
 if currTaxon == '' then return 'ERROR: no taxon supplied' end
 local n = tonumber(frame.args['n'] or 1)
 if n > MaxSearchLevels then
  return 'Exceeded maximum number of levels allowed (' .. MaxSearchLevels .. ')'
 end
 local i = 1
 local inHierarchy = true -- still in the taxonomic hierarchy or off the top?
 while i < n and inHierarchy do
  local ok, parent = p.getTaxonInfoItem(frame, currTaxon, 'parent')
   if ok and parent ~= '' then
   currTaxon = parent
   i = i + 1
  else
   inHierarchy = false
  end
 end
 if inHierarchy then return currTaxon
 else return 'Level ' .. n .. ' is past the top of the taxonomic hierarchy'
 end
end

--[[============================= nLevels ===================================
External utility function primarily intended for use in checking and debugging.
Returns number of levels in a taxonomic hierarchy, starting from
the supplied taxon as level 1.
Usage: {{#invoke:Autotaxobox|nLevels|TAXON}}
=============================================================================]]
function p.nLevels(frame)
 local currTaxon = frame.args[1] or ''
 if currTaxon == '' then return 'ERROR: no taxon supplied' end
 local i = 1
 local inHierarchy = true -- still in the taxonomic hierarchy or off the top?
 while inHierarchy and i < MaxSearchLevels  do
  local ok, parent = p.getTaxonInfoItem(frame, currTaxon, 'parent')
  if ok and parent ~= '' then
   currTaxon = parent
   i = i + 1
  else
   inHierarchy = false
  end
 end
 if inHierarchy then return MaxSearchLevels .. '+'
 else return i
 end
end

--[[============================= listAll ===================================
External utility function primarily intended for use in checking and debugging.
Returns a comma separated list of a taxonomic hierarchy, starting from
the supplied taxon.
Usage: {{#invoke:Autotaxobox|listAll|TAXON}}
=============================================================================]]
function p.listAll(frame)
 local currTaxon = frame.args[1] or ''
 if currTaxon == '' then return 'ERROR: no taxon supplied' end
 return l.doListAll(l.makeTable(frame, currTaxon))
end

function l.doListAll(taxonTable, taxonRankTable)
 local lst = taxonTable[1] .. '-' .. tostring(taxonRankTable[1])
 for i = 2, taxonTable.n, 1 do
  lst = lst .. ', ' .. taxonTable[i] .. '-' .. taxonRankTable[i]
 end
 return lst
end

--[[=========================== removeQualifier ================================
External utility function to remove a qualifier (any part after a "/") from a 
taxon name.
Usage: {{#invoke:Autotaxobox|removeQualifier|TAXON}}
=============================================================================]]
function p.removeQualifier(frame)
 local baseName, qualifier = l.stripExtra(frame.args[1])
 return baseName
end

--[[=========================================================================
Internal functions
=============================================================================]]

--[[= = = = = = = = = = = = stripExtra  = = = = = = = = = = = = = = = = = = =
Internal utility function to strip off any extra parts of a taxon name, i.e.
anything after a '/'. Thus 'Felidae/?' would be split into 'Felidae' and '?'.
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function l.stripExtra(taxonName)
 local i = mw.ustring.find(taxonName, '/', 1, true)
 if i then
  return mw.ustring.sub(taxonName, 1, i-1), mw.ustring.sub(taxonName, i, -1)
 else
  return taxonName, ''
 end
end

--[[= = = = = = = = = = = = splitTaxonName  = = = = = = = = = = = = = = = = =
Internal utility function to split a taxon name into its parts and return
them. Possible formats include:
* taxon
* taxon (disambig)
* taxon (Subgenus)
* taxon/qualifier
* combinations, e.g. taxon (disambig)/qualifier
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function l.splitTaxonName(taxon)
 -- get any qualifier present
 local qualifier = ''
 local i = mw.ustring.find(taxon, '/', 1, true)
 if i then
  qualifier = mw.ustring.sub(taxon, i+1, -1)
  taxon = mw.ustring.sub(taxon, 1, i-1)
 end
 -- get any disambiguator or subgenus
 local disambig = ''
 local subgenus = ''
 i = mw.ustring.find(taxon, ' (', 1, true)
 if i then
  local parenTerm = mw.ustring.sub(taxon, i+2, -2)
  taxon = mw.ustring.sub(taxon, 1, i-1)
  local char1 = mw.ustring.sub(parenTerm, 1, 1)
  if char1 == mw.ustring.lower(char1) then
   disambig = parenTerm
  else
   subgenus = parenTerm
  end
 end
 return taxon, disambig, subgenus, qualifier
end

--[[= = = = = = = = = = = = matchTaxonLink  = = = = = = = = = = = = = = = = =
Function to determine whether the taxon name derived from the name of the 
taxonomy template (passed in the parameter taxon) matches the link text
(passed in the parameter linkText).
The taxon name may have any of the formats:
* baseTaxon/qualifier
* baseTaxon (disambig)
* baseTaxon (Subgenus) [distinguished by the capital letter]
* a qualifier may be present after the previous two formats.

Examples of matches (baseTaxon ~ linkText):
* Pinus ~ Pinus
* Pinus sect. Trifoliae ~ Pinus sect. Trifoliae
* Pinus sect. Trifoliae ~ ''Pinus'' sect. ''Trifoliae'' [italic markers ignored]
* Pinus sect. Trifoliae ~ P. sect. Trifoliae [abbreviated genus name matches]
* Bombus (Pyrobombus) ~ Bombus (Pyrobombus)
* Bombus (Pyrobombus) ~ B. (Pyrobombus)
* Bombus (Pyrobombus) ~ Pyrobombus [link text may just be the subgenus]
* Heteractinida ~ "Heteractinida" [double-quotes are ignored in link text]
* "Heteractinida" ~ Heteractinida [double-quotes are ignored in base taxon name]
* Incertae sedis ~ anything [link text is ignored for matching in this case]
* Cetotheriidae with qualifier=? ~ Cetotheriidae (?)
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function l.matchTaxonLink(taxon, linkText, rankBelowGenus)
 local dummy
 linkText, dummy = mw.ustring.gsub(linkText, "''", '') -- remove any italic wikitext in the link text
 linkText, dummy = mw.ustring.gsub(linkText, '<.->', '') -- strip all tags used to format the link text
 linkText, dummy = mw.ustring.gsub(linkText, '"', '') -- remove any occurrences of " in the link text
 local baseTaxon, disambig, subgenus, qualifier = l.splitTaxonName(taxon) -- split up the taxon name
 baseTaxon, dummy = mw.ustring.gsub(linkText, '"', '') -- remove any occurrences of " in the base taxon name
 local match = linkText == baseTaxon or
               linkText == subgenus or
               linkText == baseTaxon .. ' (' .. subgenus .. ')' or
               linkText ==  mw.ustring.sub(baseTaxon, 1, 1) .. '. (' .. subgenus .. ')' or
               baseTaxon == 'Incertae sedis' or
               rankBelowGenus and linkText == mw.ustring.gsub(baseTaxon, '([A-Z]).- (.*)', '%1. %2') or 
               mw.ustring.find(qualifier, '?', 1, true) and mw.ustring.find(linkText, baseTaxon, 1, true) == 1
 return match
end

--[[= = = = = = = = = = = = = makeTable = = = = = = = = = = = = = = = = = = =
Internal utility function to return a table (array) constructed from a
taxonomic hierarchy stored in "Template:Taxonomy/..." templates.
TABLE.n holds the total number of taxa; TABLE[1]..TABLE[TABLE.n] the taxon
names.
The last taxon in the table will either (a) have a taxonomy template but with
no parent given (e.g. 'Life') or (b) not have a taxonomy template.
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function l.makeTable(frame, currTaxon)
 local taxonTable = {}
 local taxonRankTable = {}
 local ok, rank, parent
 local i = 1
 local topReached = false -- reached the top of the taxonomic hierarchy?
 repeat
  taxonTable[i] = currTaxon
  ok, rank = p.getTaxonInfoItem(frame, currTaxon, 'rank')
  if ok then taxonRankTable[i] = string.lower(rank) else taxonRankTable[i] = '' end
  ok, parent = p.getTaxonInfoItem(frame, currTaxon, 'parent')
  if ok and parent ~= '' then
   currTaxon = parent
   i = i + 1
  else
   topReached = true -- reached the top of the hierarchy or tried to use a non-existent taxonomy template
  end
 until topReached or i > MaxSearchLevels
 taxonTable.n = math.min(i, MaxSearchLevels)
 return taxonTable, taxonRankTable
end

--[[= = = = = = = = = = = = getRankTable  = = = = = = = = = = = = = = = = = =
Internal utility function to set up a table of numerical values corresponding
to 'Linnaean' ranks, with upper ranks having higher values. In a valid
taxonomic hierarchy, a lower rank should never have a higher value than a
higher rank. The actual numerical values are arbitrary so long as they are
ordered.
The ranks should correspond to those in Template:Anglicise ranks.
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function l.getRankTable()
 return {
  classis = 1400,
  cohort = 1100,
  divisio = 1500,
  domain = 1700,
  epifamilia =  802,
  familia = 800,
  forma = 100,
  genus = 600,
  grandordo = 1005,
  ['grandordo-mb'] = 1002,
  hyperfamilia = 805;
  infraclassis = 1397,
  infralegio = 1197,
  infraordo = 997,
  infraphylum = 1497,
  infraregnum = 1597,
  infratribus = 697,
  legio = 1200,
  magnordo = 1006,
  microphylum = 1495,
  micrordo = 995,
  mirordo = 1004,
  ['mirordo-mb'] = 1001,
  nanophylum = 1494,
  nanordo = 994,
  ordo = 1000,
  parafamilia = 800,
  parvclassis = 1396; -- same as subterclassis
  parvordo = 996,
  phylum = 1500,
  regnum = 1600,
  sectio = 500,
  --series = 400, used too inconsistently to check
  species = 300,
  subclassis = 1398,
  subcohort = 1098,
  subdivisio = 1498,
  subfamilia = 798,
  subgenus = 598,
  sublegio = 1198,
  subordo = 998,
  subphylum = 1498,
  subregnum = 1598,
  subsectio = 498,
  subspecies = 298,
  subterclassis = 1396; -- same as parvclassis
  subtribus = 698,
  superclassis = 1403,
  supercohort = 1103,
  superdivisio = 1503,
  superdomain = 1703,
  superfamilia = 803,
  superlegio = 1203,
  superordo = 1003,
  superphylum = 1503,
  superregnum = 1603,
  supersectio = 503,
  supertribus = 703,
  tribus = 700,
  varietas = 200,
  zoodivisio = 1300,
  zoosectio = 900,
  zoosubdivisio = 1298,
  zoosubsectio = 898,
 }
end

--[[= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Function to look up the arbitrary numerical value of a rank in a rank value
table. "Ichno" and "oo" ranks are not stored separately, so if present the
prefix is removed.
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function l.lookupRankVal(rankValTable, rank)
 local rankVal = rankValTable[rank]
 if not rankVal then
  -- may be an "ichno" or "oo" rank; try removing "ichno-" or "oo-"
  local baseRank = mw.ustring.gsub(mw.ustring.gsub(rank, '^ichno', ''), '^oo', '')
  if baseRank == 'rdo' then baseRank = 'ordo' end
  -- if an "ichno" or "oo" rank, lower rank value slightly so it is ok below the base rank
  rankVal = rankValTable[baseRank]
  if rankVal then
   rankVal = rankVal - 0.1
  end
 end
 return rankVal
end

--[[= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function l.tableCell(arg1, arg2)
 local text, style
 if arg2 then
  style = arg1
  text = arg2
 else
  style = ''
  text = arg1
 end
 local res = '|'
 if style ~= '' then
  res = res .. style .. '|'
 end
 return res .. text .. '\n'
end

return p