Module:Taxonomy
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JSON template for adding a new taxon to Module:Taxonomy/data.json:
"Taxon Name": {
"parent": "The next taxon up from this one when going from lowest to highest",
"type": "Flora, Fauna, etc, remove this line if unchanged from parent taxon",
"page": "General Page's Title, remove this line if there is none",
"rank": "Clade"
},
(Remove the last comma if appending to the end of the document)
Genera and below should not be placed in the data, as they can change too easily.
main
Not finished yet
TaxoCheck
{{#invoke:Taxonomy|TaxoCheck|<name of taxon>}}
Basically just checks if a given taxon is in Module:Taxonomy/data.json. Returns "yes" if it is, "no" if it isn't, and "error" if you messed something up. This is intended to be used on species templates so that all taxa can be rounded up and migrated to the new system.
local p = {}
-- This module will allow taxonomy to be updated far more quickly, based only on a change to a single file. Work in progress.
local data = mw.loadJsonData('Module:Taxonomy/data.json')
function p.TaxoCheck(frame,other)
-- determines if a given taxon is in the new taxonomy system (will be used primarily to help find all taxa that need to be added)
local args = {}
local clade = ""
if other then
clade = other
else
args = frame.args
clade = args[1]
end
local taxocheckresult = "no"
if clade then
-- do the calculation
for k in pairs(data) do -- this is dumb. Who made it where this is how you retrieve data from a table in lua.
if k == clade then
taxocheckresult="yes"
break --this will make the taxocheck code slightly faster
end
end
--if data[clade] then taxoncheckresult = "yes" end
else
taxocheckresult = "error (Adding a new taxon? Make sure to add it to [[Module:Taxonomy/data.json]]!)"
end
return taxocheckresult
end
function p.getBiotaType(frame,other)
--Retrieves the biota type of the specified taxon
local taxon
if other then
taxon = other
else
taxon = frame.args[1]
end
local biotaType = ""
local timeoutCounter = 0
while biotaType == "" do
--iterate up the taxon's parentage until a type is defined
if data[taxon] then --In one part of the code this works, and in another it doesn't. may as well take the opportunity to troubleshoot now!
if data[taxon]["type"] then
biotaType = data[taxon]["type"]
else
if data[taxon]["parent"] then
taxon = data[taxon]["parent"]
else
biotaType = "error"
end
end
else
biotaType = "error"
end
timeoutCounter = timeoutCounter + 1
if timeoutCounter == 100 then
biotaType = "error"
break --failsafe if I screwed up my code, there's no circumstance where there will be a chain of 100 parent taxa before a type is defined
end
end
return biotaType
end
function p.jsongen(frame)
-- Generates taxonomy json based on an inputted category. This will be deprecated after migration is complete.
local errorStuff = ""
local category = frame.args[1]
local categoryContents = frame:callParserFunction{name = "#dpl:", args = {
namespace = "",
category = category,
mode = "userformat",
inlinetext = "@@",
format = ",%PAGE%,@@,",
}
}
if categoryContents == "" or categoryContents == "@@" then
errorstuff = errorStuff.."Category is empty"
end
if frame.args[2] then
errorStuff = errorStuff.."\n\nDPL category results: "..categoryContents
end
local pages = {}
for item in categoryContents:gmatch("[^@@]+") do
table.insert(pages,item)
end
local taxa = {}
local inconsistentTaxa = {} -- will figure out what to do with this later
local invalidPages = ""
for i, page in pairs (pages) do
-- Taxon table format: taxonname = {parent = taxonparent, rank = rank}
-- Getting taxa: Searching for the use of every taxon parameter and getting its content, in order
local currentPage = mw.title.new(page)
if currentPage then pageContent = currentPage:getContent()
local lasttaxon = "Eukaryota"
local currenttaxon = ""
local override = ""
local overrideRank = ""
indexStart, indexEnd, override = pageContent:find("|parent%s*=%s*(.-)%s*[}|]")
indexStart, indexEnd, overrideRank = pageContent:find("|Classification%s*=%s*(.-)%s*[}|]")
--if pageContent:find("|parent%s*=%s*(.-)%s*[}|]") then
-- indexStart, indexEnd, currenttaxon = pageContent:find("|parent%s*=%s*(.-)%s*[}|]")
-- if currenttaxon then
-- currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
-- if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then --[[taxa[currenttaxon] = {parent = lasttaxon, rank = "Kingdom"}]] end end
-- if currenttaxon ~= "" then lasttaxon = currenttaxon end
-- end
--end
if pageContent:find("|name%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|name%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = override, rank = overrideRank} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|domain%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|domain%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" and currenttaxon ~= "Eukaryota" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = "Life", rank = "Domain"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|superkingdom%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|superkingdom%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = lasttaxon, rank = "Superkingdom"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|kingdom%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|kingdom%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = lasttaxon, rank = "Kingdom"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|subkingdom%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|subkingdom%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = lasttaxon, rank = "Subkingdom"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|superphylum%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|superphylum%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = lasttaxon, rank = "Superphylum"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|phylum%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|phylum%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = lasttaxon, rank = "Phylum"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|subphylum%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|subphylum%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = lasttaxon, rank = "Subphylum"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|superclass%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|superclass%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = lasttaxon, rank = "Superclass"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|class%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|class%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = lasttaxon, rank = "Class"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|subclass%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|subclass%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = lasttaxon, rank = "Subclass"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|superorder%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|superorder%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = lasttaxon, rank = "Superorder"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|order%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|order%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = lasttaxon, rank = "Order"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|suborder%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|suborder%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = lasttaxon, rank = "Suborder"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|superfamily%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|superfamily%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = lasttaxon, rank = "Superfamily"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|family%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|family%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = lasttaxon, rank = "Family"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|subfamily%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|subfamily%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = lasttaxon, rank = "Subfamily"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
if pageContent:find("|tribe%s*=%s*(.-)%s*[}|]") then
indexStart, indexEnd, currenttaxon = pageContent:find("|tribe%s*=%s*(.-)%s*[}|]")
if currenttaxon then
currenttaxon = string.gsub(currenttaxon,"\n","") --removes linebreaks if there are any
if not taxa[currenttaxon] and currenttaxon ~= "" then if p.TaxoCheck(frame,currenttaxon) == "no" then taxa[currenttaxon] = {parent = lasttaxon, rank = "Tribe"} end end
if currenttaxon ~= "" then lasttaxon = currenttaxon end
end
end
else invalidPages = invalidPages..", "..page end
-- that was a lot! just goes to show how inefficient the old system was
end
if frame.args[2] then errorStuff = errorStuff.."\n\nPages that came up invalid: "..invalidPages end
local taxaJsonVersion = '<pre>{\n "Life": {\n "parent": "none",\n "type": "Undefined",\n "rank": "Clade"\n }' -- which is actually not a json object, but a string
for nameoftaxon,data in pairs (taxa) do
taxaJsonVersion = taxaJsonVersion..',\n "'..nameoftaxon..'": {\n "parent": "'..data["parent"]..'",\n "rank": "'..data["rank"]..'"\n }'
end
return taxaJsonVersion.."\n}</pre>".."\n\n"..errorStuff
end
function p.warnings(frame,taxinput)
-- Finds any warnings about an organism's taxa
local taxon
if taxinput then
taxon = taxinput
else
taxon = frame.args[1]
end
local finished = false
local warningString = ""
while finished == false do
if data[taxon] then
if data[taxon]["warn"] then
finished = true
warningString = data[taxon]["warn"]
else
if data[taxon]["parent"] then
taxon = data[taxon]["parent"]
else
finished = true
end
end
else
--error
finished = true
warningString = "Taxon data not found."
end
end
return warningString
end
function p.main(frame)
-- Gets the parent taxa of the inputted taxon
local currentaxon = frame.args[1]
local errorflag = false
local rankline = "'''Genus'''<br>'''Species'''"
local taxonline = ""
local errorline = ""
local smwline = ''
local taxa = {}
while currentaxon ~= "Life" do
if p.TaxoCheck(frame,currentaxon) == "no" then
errorflag = true
currentaxon = "Life"
else
local rank = "Clade"
local parent = "Life"
--for k in pairs(data) do -- this is dumb. Who made it where this is how you retrieve data from a table in lua.
--if k == clade then
--if k["parent"] then parent = k["parent"] else parent = "Life" errorflag = true end
--if k["rank"] then rank = k["rank"] else rank = "Clade" end
--end
--end
if data[currentaxon]["parent"] then parent = data[currentaxon]["parent"] end
if data[currentaxon]["rank"] then rank = data[currentaxon]["rank"] end
rankline = "'''"..rank.."'''<br>"..rankline
taxonline = "[["..currentaxon.."]][[Category:"..currentaxon.."]]<br>"..taxonline
if rank ~= "Clade" then smwline = smwline.."{{#set:"..rank.."="..currentaxon.."}}" end --backwards compatability
table.insert(taxa,currentaxon)
currentaxon = parent
end
end
taxonline = '<td style="border-top: solid 1px #999999; padding: 0.4em 1em 0.4em 0; text-align: left; vertical-align: top;" >'..taxonline
rankline = '<td style="border-top: solid 1px #999999; padding: 0.4em 1em 0.4em 0; vertical-align: right;" >'..rankline
if errorflag == true then errorline = "error (Adding a new taxon? Make sure to add it to [[Module:Taxonomy/data.json]]!){{#set:Maintenance=Migrated taxonomy error}}" end
smwline = smwline.."{{#set:|taxonomy="
local commadone = false
for i, taxon in pairs (taxa) do
if commadone == false then
smwline = smwline..taxon
commadone = true
else
smwline = smwline..", "..taxon
end
end
smwline = smwline..", {{#if:{{{genus|}}}|, {{{genus}}}}}|+sep=, }}"
local finaltext = smwline..errorline..rankline.."</td>"..taxonline
finaltext = frame:preprocess(finaltext)
return finaltext
end
return p