Module:Autotaxobox
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Module:Autotaxobox (talk · · hist · links · doc · subpages · sandbox · testcases)
The purpose of this module is to provide support for automated taxobox templates (such as {{Automatic taxobox}} or {{Speciesbox}}), avoiding Mediawiki template expansion depth errors in the traversal of the taxonomic hierarchies encoded in taxonomy templates.
Currently, processing is arbitrarily limited to hierarchies containing at most 100 levels.
taxoboxColour
Given a taxon name, this function returns the correct colour of an automated taxobox for that taxon. It does so by searching up the taxonomic hierarchy for a 'real' taxon (i.e. not incertae sedis) that sets the taxobox colour, and then returning that colour. If no 'real' taxon is found, then if an incertae sedis taxon was found, the incertae sedis colour is returned, otherwise "transparent" is returned. (If the taxonomic hierarchy is too deep to process, the error colour is returned.)
Usage:
{{#invoke:Autotaxobox|taxoboxColour|taxon_name}}
Parameters:
- The unnamed parameter should be the name of a taxon for which "Template:Taxonomy/taxon_name" exists.
Examples:
- {{#invoke:Autotaxobox|taxoboxColour|Felis}} → rgb(235,235,210)
- {{#invoke:Autotaxobox|taxoboxColour|Acacia}} → rgb(180,250,180)
taxoboxList
Given a taxon name, this function returns the rows of taxa in an automated taxobox, based on the taxonomic hierarchy for the supplied taxon.
Usage:
{{#invoke:Autotaxobox|taxoboxList|taxon_name
|display_taxa = the number of taxa above taxon_name to force to be displayed
|authority = taxonomic authority for taxon_name
|parent_authority = taxonomic authority for taxon_name's parent
|gparent_authority = taxonomic authority for taxon_name's grandparent
|ggparent_authority = taxonomic authority for taxon_name's greatgrandparent
|ggparent_authority = taxonomic authority for taxon_name's greatgreatgrandparent
|bold_first = bold to embolden taxon_name in its row
}}
Parameters:
- The unnamed parameter should be the name of a taxon for which "Template:Taxonomy/taxon_name" exists. The others are explained above.
Examples:
{| class="wikitable"
{{#invoke:Autotaxobox|taxoboxList|Felis|authority=Linnaeus, 1758}}
|} →
| Kingdom: | Animalia |
| Phylum: | Chordata |
| Order: | Carnivora |
| Family: | Felidae |
| Subfamily: | Felinae |
| Genus: | Felis Linnaeus, 1758 |
taxonomyList
Given a taxon name, this function returns the rows of the taxonomy table displayed on the "Template:Taxonomy/taxon_name" page, based on the taxonomic hierarchy for the supplied taxon name.
When descending the taxonomic hierarchy, if a rank is found that is at either the same or a higher level than a rank already encountered (e.g. a family is found below a subfamily), the cell displaying the rank is given a reddish background; if it's the target taxon, the article is put into the tracking category Category:Taxonomy templates showing anomalous ranks. The numerical values defined in getRankTable() are used to determine the correct sequence of ranks.
Usage:
{{#invoke:Autotaxobox|taxonomyList|taxon_name}}
Parameters:
- The unnamed parameter should be the name of a taxon for which "Template:Taxonomy/taxon_name" exists.
Examples:
{| class="wikitable"
{{#invoke:Autotaxobox|taxonomyList|Felis}}
|} →
Bold ranks show taxa that will be shown in taxoboxes
because rank is principal or always_display=yes.
callTaxonomyKey
This function prepares for, and then calls, {{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 present, and then calling it.
Usage:
{{#invoke:Autotaxobox|callTaxonomyKey
|parent=
|rank=
|extinct=
|always_display=
|link_target=value of 'link' parameter in the taxonomy template
|link_text=value of unnamed parameter in the taxonomy template
|same_as=
}}
taxonInfo
Given the names of a taxon and the required item of information stored in the taxon's taxonomy template, this function returns the value of the item, following one "same as" link if available and the value would otherwise be the empty string. The function would normally be used externally via {{Taxon info}}.
Usage:
{{#invoke:Autotaxobox|taxonInfo|taxon_name|item_name}}
Parameters:
- The first unnamed parameter should be the name of a taxon for which "Template:Taxonomy/taxon_name" exists.
- The possible values of the second unnamed parameter are given at {{Taxon info/doc}}.
Examples:
- {{#invoke:Autotaxobox|taxonInfo|Felis|rank}} → genus
- {{#invoke:Autotaxobox|taxonInfo|Aves/skip|same_as}} → Template:Don't edit this line same as
- {{#invoke:Autotaxobox|taxonInfo|Aves/skip|parent}} → Chordata
taxonLink
Returns a wikilink to a taxon, if required including '†' before it and ' (?)' after it, and optionally italicized or bolded without a wikilink. It would normally be used via {{Taxon link}}. Some parameters can, under some circumstances, be omitted.
Usage:
{{#invoke:Autotaxobox|taxonLink(having '/?' at the end triggers the output of ' (?)')
|taxon=
|extinct=
|bold=
|italic=
|link_target=target for the wikilink
|plain_link_text= text of the wikilink
}}
Examples:
- {{#invoke:Autotaxobox|taxonLink|taxon=Felis|italic=yes}} → Felis
- {{#invoke:Autotaxobox|taxonLink|taxon=Incertae sedis/Animalia}} → incertae sedis
- {{#invoke:Autotaxobox|taxonLink|link_target=Pterosaur|plain_link_text=Pterosauromorpha|extinct=yes}} → †Pterosauromorpha
- {{#invoke:Autotaxobox|taxonLink|taxon=Dinosauria/?|link_target=Dinosaur|plain_link_text=Dinosauria|extinct=yes}} → †Dinosauria (?)
showRankTable
Returns a sortable wikitable containing the ranks and corresponding numerical values defined in getRankTable() and used in checking the consistency of a taxonomic hierarchy. If a taxon has a value in the rank table, it should always be lower than one higher in the taxonomic hierarchy.
Usage:
{{#invoke:Autotaxobox|showRankTable}}
Utilities
These functions are intended to be used only in analysing taxonomic hierarchies, e.g. in testing and debugging, and not for direct use in templates used in the automated taxobox system.
nth
Given a taxon name, this function returns the nth taxon above it in the taxonomic hierarchy.
Usage:
{{#invoke:Autotaxobox|nth|taxon_name|n=integer}}
Parameters:
- The unnamed parameter should be the name of a taxon for which "Template:Taxonomy/taxon_name" exists.
- n is the level whose taxon is to be found
Examples:
- {{#invoke:Autotaxobox|nth|Felis|n=1}} → Felis
- {{#invoke:Autotaxobox|nth|Felis|n=15}} → Eutheria
nLevels
Given a taxon name, this function returns the number of levels at and above it in the taxonomic hierarchy.
Usage:
{{#invoke:Autotaxobox|nLevels|taxon_name}}
Parameters:
- The unnamed parameter should be the name of a taxon for which "Template:Taxonomy/taxon_name" exists.
Examples:
- {{#invoke:Autotaxobox|nLevels|Felis}} → 53
- {{#invoke:Autotaxobox|nLevels|Pteranodon}} → 1
listAll
Given a taxon name, this function returns a comma-separated list of all the levels at and above it in the taxonomic hierarchy.
Usage:
{{#invoke:Autotaxobox|listAll|taxon_name}}
Parameters:
- The unnamed parameter should be the name of a taxon for which "Template:Taxonomy/taxon_name" exists.
Examples:
- {{#invoke:Autotaxobox|listAll|Plantae}} → Plantae-regnum, Archaeplastida-unranked, Diaphoretickes-unranked, Eukaryota-domain, Life-
- {{#invoke:Autotaxobox|listAll|Felis}} → Felis-genus, Felinae-subfamilia, Felidae-familia, Feliformia-subordo, Carnivora-ordo, Carnivoraformes-clade, Carnivoramorpha-clade, Pan-Carnivora-clade, Ferae-clade, Ferungulata-clade, Scrotifera-clade, Laurasiatheria-superordo, Boreoeutheria-magnordo, Placentalia-infraclassis, Eutheria-clade, Theria-subclassis, Tribosphenida-cladus, Zatheria-cladus, Prototribosphenida-clade, Cladotheria-cladus, Trechnotheria-cladus, Theriiformes-clade, Theriimorpha-clade, Mammalia/skip-, Amniota-clade, Reptiliomorpha-clade, Tetrapoda-superclassis, Stegocephalia-clade, Elpistostegalia-clade, Eotetrapodiformes-clade, Tetrapodomorpha-clade, Rhipidistia-clade, Sarcopterygii-cladus, Euteleostomi-clade, Teleostomi-clade, Eugnathostomata-clade, Gnathostomata-infraphylum, Vertebrata-subphylum, Olfactores-clade, Chordata-phylum, Deuterostomia-superphylum, Nephrozoa-clade, Bilateria-clade, ParaHoxozoa-cladus, Eumetazoa-subregnum, Animalia-regnum, Filozoa-unranked, Holozoa-unranked, Opisthokonta-unranked, Obazoa-unranked, Unikonta-unranked, Eukaryota-domain, Life-
--[[*************************************************************************
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; 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;">' .. 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 = '†'
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;"> (?)</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;"> (?)</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