Module:Sandbox/Jts1882/Biota infobox/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.
]]
local TaxonItalics = require('Module:TaxonItalics') -- use a function from Module:TaxonItalics to italicize a taxon name
local p = {}
--[[=========================================================================
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.
=============================================================================]]
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)
local currTaxon = frame.args[1] or ''
local i = 1 -- count levels processed
local searching = currTaxon ~= '' -- still searching for a colour?
local foundICTaxon = false -- record whether 'incertae sedis' found
local colour = '' -- default is no colour
while searching and i <= MaxSearchLevels do
local plainCurrTaxon = p.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
return colour
elseif foundICTaxon then
return frame:expandTemplate{ title = 'Template:Taxobox colour', args = { 'incertae sedis' } }
elseif searching then
-- hierarchy exceeds MaxSearchLevels levels
return frame:expandTemplate{ title = 'Template:Taxobox/Error colour', args = { } }
else
return 'transparent'
end
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
}}
=============================================================================]]
function p.taxoboxList(frame)
local currTaxon = frame.args[1] or ''
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 ''
local boldFirst = frame.args['bold_first'] or 'link' -- values 'link' or 'bold'
local taxonTable = p.makeTable(frame, currTaxon)
local res = ''
-- display all taxa above possible greatgreatgrandparent
for i = taxonTable.n, 6, -1 do
res = res .. frame:expandTemplate{ title = 'Template:Taxobox/showtaxon', args = { taxonTable[i], fc = tostring(displayN >= i) } }
end
-- display greatgreatgrandparent, if it exists
if taxonTable.n >= 5 then
res = res .. frame:expandTemplate{ title = 'Template:Taxobox/showtaxon', args = { taxonTable[5], authority = gggParentAuth, fc = tostring(displayN >= 5) } }
end
-- display greatgrandparent, if it exists; force the display if an infrataxon is below
if taxonTable.n >= 4 then
local force = tostring(displayN >= 4) or
frame.expandTemplate{ title = 'Template:Infrataxon()', args = { taxonTable[3] } } == 'true' or
frame.expandTemplate{ title = 'Template:Infrataxon()', args = { taxonTable[2] } } == 'true'
res = res .. frame:expandTemplate{ title = 'Template:Taxobox/showtaxon', args = { taxonTable[4], authority = ggParentAuth, fc = tostring(force) } }
end
-- display grandparent, if it exists; force the display if an infrataxon is below
if taxonTable.n >= 3 then
local force = tostring(displayN >= 3) or
frame.expandTemplate{ title = 'Template:Infrataxon()', args = { taxonTable[2] } } == 'true'
res = res .. frame:expandTemplate{ title = 'Template:Taxobox/showtaxon', args = { taxonTable[3], authority = gParentAuth, fc = tostring(force) } }
end
-- display parent, if it exists
if taxonTable.n >= 2 then
res = res .. frame:expandTemplate{ title = 'Template:Taxobox/showtaxon', args = { taxonTable[2], authority = parentAuth, fc = tostring(displayN >= 2) } }
end
-- display target taxon
res = res .. frame:expandTemplate{ title = 'Template:Taxobox/showtaxon', args = { taxonTable[1], authority = auth, fc = 'true', format = boldFirst } }
return res
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 '| ||ERROR: no taxon supplied\n|-' end
local taxonTable = p.makeTable(frame, currTaxon)
local rankTable = p.getRankTable()
local lastRankVal = 1000000
local orderOk
local res = ''
for i = taxonTable.n, 1, -1 do
-- check ranks are in right order in the hierarchy
local ok, rank = p.getTaxonInfoItem(frame, taxonTable[i], 'rank')
local currRankVal = rankTable[string.lower(rank)]
if currRankVal then
orderOk = currRankVal < lastRankVal
if orderOk then lastRankVal = currRankVal end
else
orderOk = true
end
-- now return a row of the taxonomy table with anomalous ranks marked
local errorStr = ''
if not orderOk then errorStr = 'true' end
res = res .. frame:expandTemplate{ title = 'Template:Taxonomy links', args = { taxonTable[i], error = errorStr } }
end
-- if the last row has an anomalous rank, put the page in the error-tracking category; category statements don't work
-- inside tables, so need to close the current table first and then open a dummy one (close is in Template:Taxonomy key)
if not orderOk then
res = res .. '\n|}\nCategory:Taxonomy templates showing anomalous ranks\n
| \n'
end 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 SAME_AS = 7 local PARENT = 1 local RANK = 2 local LINK_TARGET = 3 local LINK_TEXT = 4 local ALWAYS_DISPLAY = 5 local EXTINCT = 6 local REFS = 8 function p.callTaxonomyKey(frame) 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, '$', true) --'same as' taxon's taxonomy template must not have a 'same as' link if sameAsInfo[SAME_AS] == '' then if parent == '' then parent = sameAsInfo[PARENT] end if rank == '' then rank = sameAsInfo[RANK] end if extinct == '' then extinct = string.lower(sameAsInfo[EXTINCT]) end if alwaysDisplay == '' then alwaysDisplay = string.lower(sameAsInfo[ALWAYS_DISPLAY]) end if linkTarget == '' then linkTarget = sameAsInfo[LINK_TARGET] end if linkText == '' then linkText = sameAsInfo[LINK_TEXT] end if refs == '' and parent == sameAsInfo[PARENT] then refs = sameAsInfo[REFS] end else return 'Error: attempt to follow two "same as" links: end else return frame:expandTemplate{ title = 'Template:Taxonomy key/missing template', args = {taxon=sameAsTaxon, msg='given as the value of end end local link = linkTarget if linkText ~= '' and linkText ~= linkTarget then link = link .. "|" .. linkText end return frame:expandTemplate{ title = 'Template:Taxonomy key', args = {parent=parent, rank=rank, extinct=extinct, always_display=alwaysDisplay, link_target=linkTarget, link=link, refs=refs, same_as=sameAsTaxon} } end --[[============================ taxonInfo ================================== Extracts and returns information from Template:Taxonomy/TAXON, following one 'same as' link if required. Usage: {{#invoke:Autotaxobox|taxonInfo|TAXON|ITEM}} ITEM is one of: 'parent', 'rank', 'link target', 'link text', 'link', 'extinct', 'always display', 'refs', 'same as' or 'all'. If ITEM is not specified, the default is 'all' – all values in a single string separated by '$'. =============================================================================]] 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 --[[============================ 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 linkTarget = frame.args['link_target'] or '' local linkText = frame.args['link_text'] or frame.args['plain_link_text'] or '' --temporarily allow alternative args -- 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 = p.stripExtra(taxon) end end if linkTarget == '' then linkTarget = linkText end if italic == 'yes' then linkText = TaxonItalics.italicizeTaxonName(linkText, false) end local link = '' if bold == 'yes' then link = '' .. linkText .. '' 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 = '†' .. link end if string.sub(taxon, -2) == '/?' and not string.find(link, '?', 1, true) then link = link .. ' (?)' 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 = p.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 .. ' | ||
| \n|' .. k .. ' | ' .. rankShown .. ' | ' .. v .. '\n'
end return res .. ' |
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 'no taxon supplied' end
local rank = frame.args[2] or ''
if rank == '' then return 'no rank supplied' 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 'rank not found'
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 p.listTaxa(p.makeTable(frame, currTaxon))
end
--[[=========================================================================
Internal functions
=============================================================================]]
--[[= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Internal utility function to strip off any extra parts of a taxon name, i.e.
anything after a '/'. Thus "Felidae/?" would be reduced to "Felidae".
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function p.stripExtra(taxonName)
local i = string.find(taxonName,'/')
if i then
return string.sub(taxonName,1,i-1)
else
return taxonName
end
end
--[[= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Internal utility function to convert a taxon table to a comma-separated list.
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function p.listTaxa(taxonTable)
local lst = taxonTable[1]
for i = 2, taxonTable.n, 1 do
lst = lst .. ', ' .. taxonTable[i]
end
return lst
end
--[[= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Internal 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)
-- item == 'link' is a special case
if item == 'link' then
return p.getTaxonInfoLink(frame, taxon)
end
local ok, info
-- item == 'dagger' is another special case
if item == 'dagger' then
ok, info = p.getTaxonInfoItem(frame, taxon, 'extinct')
if ok then
if info == 'yes' or info == 'true' then
info = '†'
else
info = ''
end
end
-- item ~= 'link' or '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' check whether '(?)' needs to be added
if item == 'link_text' and string.sub(taxon, -2) == '/?' and not string.find(info, '?', 1, true) then
info = info .. ' (?)'
end
else
info = 'Template:Taxonomy/' .. taxon .. '' --error indicator in code before conversion to Lua
end
return ok, info
end
function p.getTaxonInfoLink(frame, taxon)
local ok, linkText, linkTarget
local link = ''
ok, linkText = p.getTaxonInfoItem(frame, taxon, 'link_text')
if ok then
ok, linkTarget = p.getTaxonInfoItem(frame, taxon, 'link_target')
if ok then
if linkText == linkTarget then link = linkText
else link = linkTarget .. '|' .. linkText
end
end
end
return ok, link
end
--[[= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
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.
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =]]
function p.makeTable(frame, currTaxon)
local i = 1
local inHierarchy = true -- still in the taxonomic hierarchy or off the top?
local taxonTable = {}
taxonTable[1] = currTaxon;
while i < MaxSearchLevels and inHierarchy do
local ok, parent = p.getTaxonInfoItem(frame, currTaxon, 'parent')
if ok and parent ~= '' then
currTaxon = parent
i = i + 1
taxonTable[i] = currTaxon
else
inHierarchy = false -- run off the top of the hierarchy or tried to use non-existent taxonomy template
end
end
taxonTable.n = i
return taxonTable
end
--[[= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
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 p.getRankTable()
return {
classis = 1400,
cohort = 1100,
divisio = 1500,
domain = 1700,
familia = 800,
forma = 100,
genus = 600,
grandordo = 1005,
['grandordo-mb'] = 1002,
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,
supertribus = 703,
tribus = 700,
varietas = 200,
zoodivisio = 1300,
zoosectio = 900,
zoosubdivisio = 1298,
zoosubsectio = 898,
}
end
return p