Module:Taxonbar

require('Module:No globals')

local conf = require( 'Module:Taxonbar/conf' ) --configuration module local TaxonItalics = require('Module:TaxonItalics') --use a function from Module:TaxonItalics to italicize a taxon name

--========================================================================== --Local functions --==========================================================================

local function isNilOrEmpty( thing ) if thing == nil or thing == then return true end return nil end

local function getIdFromWikidata( item, property ) local id = nil if property == 'PWikispecies:$1' then local siteLinks = item.sitelinks if siteLinks then local speciesWiki = item.sitelinks.specieswiki if speciesWiki then id = speciesWiki.title end end return id elseif item.claims[property] == nil then return id end for _, statement in pairs( item.claims[property] ) do if statement.mainsnak.datavalue then id = statement.mainsnak.datavalue.value break end end return id end

local function getLink( property, val ) local link, returnVal = , {}

returnVal.isError = false

if mw.ustring.find( val, '//' ) then link = val else if type(property) == 'number' and property > 0 then local entityObject = mw.wikibase.getEntity('P'..property) local dataType

if entityObject then dataType = entityObject.datatype else returnVal.isError = true end

if dataType == 'external-id' then local formatterURL = nil if property == 3746 or property == 5397 then --use WOI & TSA's 2nd formatterURL for English version formatterURL = entityObject:getBestStatements('P1630')[2] end if formatterURL == nil then formatterURL = entityObject:getBestStatements('P1630')[1] end --default to [1] if formatterURL then if formatterURL.mainsnak.datavalue and formatterURL.mainsnak.datavalue.value then --nil check for ABA link = formatterURL.mainsnak.datavalue.value end end elseif dataType == 'url' then local subjectItem = entityObject:getBestStatements('P1629')[1] if subjectItem then local officialWebsite = mw.wikibase.getEntity(subjectItem.mainsnak.datavalue.value.id):getBestStatements('P856')[1] if officialWebsite then link = officialWebsite.mainsnak.datavalue.value end end elseif dataType == 'string' then local formatterURL = entityObject:getBestStatements('P1630')[1] if formatterURL then link = formatterURL.mainsnak.datavalue.value else local subjectItem = entityObject:getBestStatements('P1629')[1] if subjectItem then local officialWebsite = mw.wikibase.getEntity(subjectItem.mainsnak.datavalue.value.id):getBestStatements('P856')[1] if officialWebsite then link = officialWebsite.mainsnak.datavalue.value end end end else returnVal.isError = true end elseif type(property) == 'string' then link = property end

local valurl = val if mw.ustring.find( link, 'antweb.org' ) then valurl = mw.ustring.gsub(valurl, ' ', '%%20') end if type(property) == 'number' then --doublecheck language for Wildflowers of Israel ID if property == 3746 then link = mw.ustring.gsub(link, '/hebrew/', '/english/') end --format spaces in PfaF, e.g. for "Elaeagnus x ebbingei" if property == 4301 then valurl = mw.ustring.gsub(valurl, ' ', '+') end end valurl = mw.ustring.gsub(valurl,'%%','%%%%') link = mw.ustring.gsub(link, '$1', valurl) end

link = mw.ustring.gsub(link, '^[Hh][Tt][Tt][Pp]([Ss]?)://', 'http%1://') -- fix wikidata URL val = mw.ustring.match(val, '([^=/]*)/?$') -- get display name from end of URL if mw.ustring.find( link, '//' ) then returnVal.text = '['..link..' '..mw.text.encode(mw.uri.decode(val, 'PATH'),'%[%]')..']' elseif link == then returnVal.text = val else returnVal.text = ''..val..'' end return returnVal end

local function createRow( id, label, rawValue, link, withUid ) if link then local outStr = '*' .. label .. ' <span' if withUid then outStr = outStr..' class="uid"' end return outStr..'>' .. link .. '\n' else return '* ' .. mw.text.tag('span', {class='error'}, 'The identifier ' .. id .. ' ' .. rawValue .. ' is not valid.') .. '\n' end end

local function copyTable(inTable) if type(inTable) ~= 'table' then return inTable end local outTable = setmetatable({}, getmetatable(inTable)) for key, value in pairs (inTable) do outTable[copyTable(key)] = copyTable(value) end return outTable end

local p = {}

--========================================================================== --Main --==========================================================================

function p.authorityControlTaxon( frame ) local resolveEntity = require( 'Module:ResolveEntityId' ) local parentArgs = copyTable(frame:getParent().args) local currentTitle = mw.title.getCurrentTitle() local currentEntityId = mw.wikibase.getEntityIdForCurrentPage()

local stringArgs = false local fromTitleCount, firstRow, rowCount = 1, 0, 0 local outString, errors = , local tFroms = {} --non-sequential table of unique froms local iFroms = 0 --integer size of tFroms, b/c Lua local categories = { , , , -- [3] placeholder for , -- [4] placeholder for , -- [5] placeholder for , -- [6] placeholder for , -- [7] placeholder for , -- [8] placeholder for , -- [9] placeholder for , --[10] placeholder for , --[11] placeholder for , --[12] placeholder for , --[13] placeholder for , --[14] placeholder for , --[15] placeholder for , --[16] placeholder for , --[17] placeholder for , --[18] placeholder for , --[19] placeholder for }

--Assess the page's relationship with Wikidata local currentItem = nil if currentTitle.namespace == 10 then --i.e. Module:Taxonbar/sandbox, Template:Taxonbar/doc, etc. if resolveEntity._id(parentArgs['from']) then currentItem = mw.wikibase.getEntity(parentArgs['from']) end if currentItem == nil then if resolveEntity._id(parentArgs['from1']) then currentItem = mw.wikibase.getEntity(parentArgs['from1']) end end elseif resolveEntity._id(currentEntityId) then currentItem = mw.wikibase.getEntity(currentEntityId) else --currentEntityId == nil/unresolvable categories[6] = end if currentItem then local acceptable = { ['Q16521'] = 'taxon', --strict ['Q310890'] = 'monotypic taxon', --strict ['Q2568288'] = 'ichnotaxon', --strict ['Q23038290'] = 'fossil taxon', --strict ['Q47487597'] = 'monotypic fossil taxon', --strict ['Q42621'] = 'hybrid', --lax ['Q235536'] = 'incertae sedis', --lax ['Q713623'] = 'clade', --lax ['Q848328'] = 'serotype', --lax ['Q857968'] = 'candidatus', --lax ['Q17487588'] = 'unavailable combination', --lax } categories[11] = --unset if acceptable found for _, instanceOfState in pairs ( currentItem:getBestStatements('P31') ) do --instance of local instanceOf = instanceOfState.mainsnak.datavalue.value.id if acceptable[instanceOf] then categories[11] = break end end end

--Cleanup args for k, v in pairs( frame:getParent().args ) do if type(k) == 'string' then --make args case insensitive local lowerk = mw.ustring.lower(k) if isNilOrEmpty( parentArgs[lowerk] ) then parentArgs[k] = nil parentArgs[lowerk] = v end --remap abc to abc1 if mw.ustring.find(lowerk,'%d$') == nil then --if no number at end of param if isNilOrEmpty( parentArgs[lowerk..'1'] ) then parentArgs[lowerk] = nil lowerk = lowerk..'1' parentArgs[lowerk] = v end end if v and v ~= then --remap 'for' to 'title' if mw.ustring.sub(lowerk,1,3) == 'for' then local forTitle = mw.ustring.gsub(lowerk,'^for','title',1) if isNilOrEmpty( parentArgs[forTitle] ) then parentArgs[lowerk] = nil lowerk = forTitle parentArgs[lowerk] = v end end --find highest from or title param if mw.ustring.sub(lowerk,1,4) == 'from' then local fromNumber = tonumber(mw.ustring.sub(lowerk,5,-1)) if fromNumber and fromNumber >= fromTitleCount then fromTitleCount = fromNumber end --look for duplicate froms while we're here if mw.ustring.find(v, '^Q%d') then if tFroms[v] then categories[8] = tFroms[v] = tFroms[v] + 1 else tFroms[v] = 1 iFroms = iFroms + 1 end if iFroms == 2 then categories[3] = end end elseif mw.ustring.sub(lowerk,1,5) == 'title' then local titleNumber = tonumber(mw.ustring.sub(lowerk,4,-1)) if titleNumber and titleNumber >= fromTitleCount then fromTitleCount = titleNumber end elseif mw.ustring.lower(v) ~= 'no' then stringArgs = true categories[5] = end end end end

--Check for unknown parameters --create knowns list local acceptableArgs = { from = true, } --master list of l/c acceptable args for _, d in pairs( conf.databases ) do if d[1] ~= 'Wikidata' then --made obsolete by from acceptableArgs[mw.ustring.lower(d[1])] = true end end for _, a in pairs( conf.aliases ) do acceptableArgs[mw.ustring.lower(a[1])] = true end --create trimmed parents list local baseParentArgs = {} --condensed list of l/c parent args w/o trailing #s for k, v in pairs( parentArgs ) do if type(k) == 'string' then --ignore unnamed params, which have keys of type 'number' local lowerk = mw.ustring.lower(k) local base = mw.ustring.gsub(lowerk, '[%d]*$', ) baseParentArgs[base] = true end end --compare lists and spit out unknowns local unknownParams = {} for k, v in pairs( baseParentArgs ) do if acceptableArgs[k] == nil then categories[19] = unknownParams[#unknownParams + 1] = k end end --warn if unknown(s) present if #unknownParams > 0 then local plural = nil local itthem = nil if #unknownParams == 1 then plural = itthem = 'it' else plural = 's' itthem = 'them' end if frame:preprocess( '14776' ) == then

errors = errors..'

'..

'Warning: unknown parameter'..plural..' '..table.concat(unknownParams, ', ')..'.
'.. 'Please correct '..itthem..' or consider adding '..itthem..' to Wikidata.
'..

'This message is only shown in preview.

'

end end

--Append basionym to arg list, if not already provided if currentItem then local currentBasState = currentItem:getBestStatements('P566')[1] --basionym if currentBasState then local basionymId = currentBasState.mainsnak.datavalue.value.id if basionymId and resolveEntity._id(basionymId) and tFroms[basionymId] == nil then --check that basionym is a strict instance of taxon local basionymItem = mw.wikibase.getEntity(basionymId) if basionymItem then local acceptable = { ['Q16521'] = 'taxon', --strict ['Q310890'] = 'monotypic taxon', --strict ['Q2568288'] = 'ichnotaxon', --strict ['Q23038290'] = 'fossil taxon', --strict ['Q47487597'] = 'monotypic fossil taxon', --strict } for _, instanceOfState in pairs ( basionymItem:getBestStatements('P31') ) do --instance of local instanceOf = instanceOfState.mainsnak.datavalue.value.id if acceptable[instanceOf] then --housekeeping tFroms[basionymId] = 1 iFroms = iFroms + 1 fromTitleCount = fromTitleCount + 1 --append basionym & track parentArgs['from'..fromTitleCount] = basionymId categories[15] = break end end end end end end

--Append original combination to arg list, if not already provided if currentItem then local currentOCState = currentItem:getBestStatements('P1403')[1] --original combination if currentOCState then local orcoId = currentOCState.mainsnak.datavalue.value.id if orcoId and resolveEntity._id(orcoId) and tFroms[orcoId] == nil then --check that orco is a strict instance of taxon local orcoItem = mw.wikibase.getEntity(orcoId) if orcoItem then local acceptable = { ['Q16521'] = 'taxon', --strict ['Q310890'] = 'monotypic taxon', --strict ['Q2568288'] = 'ichnotaxon', --strict ['Q23038290'] = 'fossil taxon', --strict ['Q47487597'] = 'monotypic fossil taxon', --strict } for _, instanceOfState in pairs ( orcoItem:getBestStatements('P31') ) do --instance of local instanceOf = instanceOfState.mainsnak.datavalue.value.id if acceptable[instanceOf] then --housekeeping tFroms[orcoId] = 1 iFroms = iFroms + 1 fromTitleCount = fromTitleCount + 1 --append orco & track parentArgs['from'..fromTitleCount] = orcoId categories[16] = break end end end end end end

--Append monotypic genus/species to arg list of monotypic species/genus, if not already provided if currentItem then for _, instanceOfState in pairs ( currentItem:getBestStatements('P31') ) do --instance of local taxonRank = nil local parentItem = nil local parentTaxon = nil local parentTaxonRank = nil local parentMonoGenus = nil --holy grail/tbd local instanceOf = instanceOfState.mainsnak.datavalue.value.id if instanceOf and (instanceOf == 'Q310890' or instanceOf == 'Q47487597') then --monotypic/fossil taxon local taxonRankState = currentItem:getBestStatements('P105')[1] --taxon rank if taxonRankState then taxonRank = taxonRankState.mainsnak.datavalue.value.id end

if taxonRank and taxonRank == 'Q7432' then --species --is monotypic species; add genus local parentTaxonState = currentItem:getBestStatements('P171')[1] --parent taxon if parentTaxonState then parentTaxon = parentTaxonState.mainsnak.datavalue.value.id end --confirm parent taxon rank == genus & monotypic if parentTaxon and resolveEntity._id(parentTaxon) then parentItem = mw.wikibase.getEntity(parentTaxon) if parentItem then local parentTaxonRankState = parentItem:getBestStatements('P105')[1] --taxon rank if parentTaxonRankState then parentTaxonRank = parentTaxonRankState.mainsnak.datavalue.value.id end if parentTaxonRank and parentTaxonRank == 'Q34740' then --parent == genus for _, parentInstanceOfState in pairs ( parentItem:getBestStatements('P31') ) do --instance of local parentInstanceOf = parentInstanceOfState.mainsnak.datavalue.value.id if parentInstanceOf and (parentInstanceOf == 'Q310890' or parentInstanceOf == 'Q47487597') then --monotypic/fossil taxon parentMonoGenus = parentTaxon --confirmed break end end if parentMonoGenus and tFroms[parentMonoGenus] == nil then --housekeeping tFroms[parentMonoGenus] = 1 iFroms = iFroms + 1 fromTitleCount = fromTitleCount + 1 --append monotypic genus & track parentArgs['from'..fromTitleCount] = parentMonoGenus categories[17] = break end end end end if parentMonoGenus == nil or tFroms[parentMonoGenus] == nil then categories[18] = break end elseif taxonRank and taxonRank == 'Q34740' then --genus --is monotypic genus; add species --... end

end end end --if currentItem

--Setup navbox local navboxParams = { name = 'Taxonbar', bodyclass = 'hlist', listclass = , groupstyle = 'text-align: left;', }

for f = 1, fromTitleCount, 1 do local elements, title = {}, nil --cleanup parameters if parentArgs['from'..f] == then parentArgs['from'..f] = nil end if parentArgs['title'..f] == then parentArgs['title'..f] = nil end --remap aliases for _, a in pairs( conf.aliases ) do local alias, name = mw.ustring.lower(a[1]), mw.ustring.lower(a[2]) if parentArgs[alias..f] and parentArgs[name..f] == nil then parentArgs[name..f] = parentArgs[alias..f] parentArgs[alias..f] = nil end end --Fetch Wikidata item local from = resolveEntity._id(parentArgs['from'..f]) local item = mw.wikibase.getEntity(from) local label = nil if type(item) == 'table' then local statements = item:getBestStatements('P225')[1] --taxon name if statements then local datavalue = statements.mainsnak.datavalue if datavalue then label = datavalue.value end end label = label or item:getLabel() else if parentArgs['from'..f] then categories[1] = categories[4] = errors = errors .. mw.text.tag('strong', {class='error'}, 'Error: "' .. parentArgs['from'..f] .. '" is not a valid Wikidata entity ID.
') end end if label and label ~= then title = mw.title.new(label) end if title == nil and parentArgs['title'..f] then title = mw.title.new(parentArgs['title'..f]) end if title == nil and f == 1 then title = currentTitle end

if title then if isNilOrEmpty( parentArgs['wikidata'..f] ) and (title.namespace == 0) then if parentArgs['from'..f] then parentArgs['wikidata'..f] = parentArgs['from'..f] elseif item then parentArgs['wikidata'..f] = item.id end end if title.namespace == 0 or stringArgs then --only in mainspace or if manual overrides exist local sourceCount = 0 for _, params in pairs( conf.databases ) do params[1] = mw.ustring.lower(params[1]) local propId = params[3] --Wikidata fallback if requested if (item and item.claims) and (type(propId) == 'string' or (type(propId) == 'number' and propId > 0)) then local wikidataId = getIdFromWikidata( item, 'P' .. propId ) local v = parentArgs[params[1]..f] if wikidataId then if isNilOrEmpty(v) then parentArgs[params[1]..f] = wikidataId else if v and v ~= 'no' and v ~= wikidataId then categories[9] = elseif v and v == wikidataId then categories[10] = end end end end local val = parentArgs[params[1]..f] if val and val ~= and mw.ustring.lower(val) ~= 'no' then if type(propId) == 'number' then if propId < 0 then propId = -propId end --allow link if propId > 0 then --link table.insert( elements, createRow( params[1], params[2]..':', val, getLink( propId, val ).text, true ) ) else --propId == 0; no link table.insert( elements, createRow( params[1], params[2]..':', val, val, true ) ) end else table.insert( elements, createRow( params[1], params[2]..':', val, getLink( propId, val ).text, true ) ) end if params[1] ~= 'wikidata' and params[1] ~= 'wikispecies' then sourceCount = sourceCount + 1 end end end

if sourceCount >= 30 then categories[14] = elseif sourceCount >= 25 then categories[13] = --endash elseif sourceCount >= 20 then categories[12] = --endash end

--Generate navbox title if sourceCount > 0 then --TODO: don't count Wikispecies towards 'taxon ID count' rowCount = rowCount + 1 if firstRow == 0 then firstRow = f end --set title from wikidata if it doesn't exist if isNilOrEmpty( parentArgs['title'..f] ) then parentArgs['noTitle'..f] = true parentArgs['title'..f] = title.text end --if it exists now, set row heading to title if not isNilOrEmpty( parentArgs['title'..f] ) then navboxParams['group'..f] = TaxonItalics.italicizeTaxonName(parentArgs['title'..f], false) else navboxParams['group'..f] = end navboxParams['list'..f] = table.concat( elements ) elseif currentEntityId then categories[7] = end

--Categorize if not isNilOrEmpty( parentArgs['from'..f] ) then --blank "missing from" if 'from' exists categories[1] = --blank "desynced" if 'from' matches current page if parentArgs['from'..f] == currentEntityId then categories[2] = end end --cannot be "desynced" if no 'from' params if categories[1] ~= then categories[2] = end end end end --for f = 1, fromTitleCount, 1

if rowCount > 0 then local Navbox = require('Module:Navbox') if rowCount > 1 then --remove duplicates and move page title to top local rowIDs = {} for f = 1,fromTitleCount,1 do if not isNilOrEmpty( parentArgs['title'..f] ) then if rowIDs[parentArgs['wikidata'..f]] then --remove duplicate navboxParams['group'..f] = nil navboxParams['list'..f] = nil else rowIDs[parentArgs['wikidata'..f]] = true if f > firstRow and (parentArgs['title'..f] == currentTitle.text or parentArgs['wikidata'..f] == currentEntityId) then --move item linked to page to top if navboxParams['group'..f] and navboxParams['group'..f] ~= and navboxParams['list'..f] and navboxParams['list'..f] ~= then local tempGroup, tempList = navboxParams['group'..f], navboxParams['list'..f] navboxParams['group'..f], navboxParams['list'..f] = navboxParams['group'..firstRow], navboxParams['list'..firstRow] navboxParams['group'..firstRow], navboxParams['list'..firstRow] = tempGroup, tempList end end end end end --adjust navbox for number of rows navboxParams['title'] = 'Taxon identifiers' if rowCount > 2 then navboxParams['navbar'] = 'plain' else navboxParams['state'] = 'off' navboxParams['navbar'] = 'off' end elseif parentArgs['noTitle'..firstRow] then navboxParams['group'..firstRow] = 'Taxon identifiers' else navboxParams['group'..firstRow] = 'Taxon identifiers
' .. navboxParams['group'..firstRow] end

--return navbox outString = Navbox._navbox(navboxParams) end --if rowCount > 0

--Add categories if string.sub(currentTitle.subpageText,1,9) == 'testcases' then parentArgs['demo'] = true end if not isNilOrEmpty( parentArgs['demo'] ) then outString = outString .. mw.text.nowiki(table.concat(categories)) .. '
' elseif currentTitle.namespace == 0 then outString = outString .. table.concat(categories) end

return outString .. errors end

return p