Mô đun:FishRef

require('strict')
local p = {}
local data = {}         
local templateArgs = {}  -- contains arguments passed to cite web
local target = {}        -- short cut to target table, e.g. fishbase, cof, etc
local function firstToUpper(str)
return (str:gsub("^%l", string.upper))
end
-- define citation template and custom parameters for various sources
--####################### Default functions ##########################
data.default = {}
-- currently being tested on Avibase, but Fossilworks, Tropicos, FNA and a few others are candidates
data.default.id = function (id, source)
	local title = id
	local url = source.customArgs'baseURL' .. (source.customArgs'searchStr' or "") .. id
	return title, url
end
data.default.error = function()
	return "Minimal requirement is two of id, url and title parameters"
end
data.default.search = function (search, source)
	local title = "Search for " .. search
	local url = source.customArgs'baseURL' .. source.customArgs'searchString' .. search .. source.customArgs'searchSuffix' 
	return title, url
end
-- handling for ID only (unused, original concept) 
p.genericIdCitation = function(frame, title, url)
if not templateArgs'id' then return "no id parameter detected" end

templateArgs'url'= target.CustomArgs'baseURL' .. target.CustomArgs'searchStr' .. templateArgs'id'

return p.citeWeb(frame, title, url)
end
--####################### FISH #####################################
--======================== Fishbase =============================**
data.fishbase = {
	citationArgs = {
	'editor1-last'="Froese",  'editor1-first'="Rainer", 'editor1-link'="Rainer Froese",
	'editor2-last'="Pauly",  'editor2-first'="Daniel",   
	--'last-author-amp' ="yes",
'website' = "Fishbase",
	--'publisher' = ""
	},
	customArgs = { exclude= "order, family,genus, species, subspecies, 1, 2, 3, 4",
	               baseURL = "http://www.fishbase.org/",
	               defaultTitle = "Search FishBase"
	},
}
data.fishbase.species = function(genus, species, subspecies)
		local title = genus .. " " .. species
		local url = data.fishbase.customArgs'baseURL' 
		            .. "summary/SpeciesSummary.php?genusname=" .. genus .. "&speciesname=" .. species
		if subspecies then 
			url = url .. "+" .. subspecies
			title = title .. " " .. subspecies
		end               
		title =  "" .. title  .. ""
		return title, url
end
data.fishbase.genus = function(genus)
		local title = "Species in genus " .. firstToUpper(genus) .. ""
		local url = data.fishbase.customArgs'baseURL' ..  "identification/SpeciesList.php?genus=" .. genus   
		return title, url
end
data.fishbase.order = function(order) 
		local title =  "Order " .. firstToUpper(order)
		local url = data.fishbase.customArgs'baseURL' ..  "Summary/OrdersSummary.php?order=" .. order
		return title, url
end
data.fishbase.family = function(family) 
		local title = "Family " .. firstToUpper(family)
		local url = data.fishbase.customArgs'baseURL' ..  "Summary/FamilySummary.php?family=" .. family
		return title, url
end
data.fishbase.error = function()   
	return "No recognised taxon options: order, family, genus, species, subspecies."
end
data.fishbase.custom = function()    
--TODO decide what to do with default date
local version = "April 2006 version"  -- Should we have a default (probably not)
if templateArgs'month' then version = templateArgs'month' end
if templateArgs'year' then version = templateArgs'year' .. " version" end
if templateArgs'month' then version = templateArgs'month' .. " " .. version end
templateArgs'version' = version
end
--================================ Catalog of Fishes ============================================**
data.cof = {
	citationArgs = {
		--baseURL = "http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?",
		'editor1-last'="Eschmeyer",  'editor1-first'="William N.", 'editor1-link'="William N. Eschmeyer",
		'editor2-last'="Fricke",  'editor2-first'="Ron",   
		'editor3-last'="van der Laan",  'editor3-first'="Richard", 
		'name-list-style' ="amp",
	    'website' = "Catalog of Fishes",
		'publisher' = "California Academy of Sciences"
	},
	customArgs = { exclude= "family,genus,species,genid,spid,id,list,1,2,3",
	               baseURL = "http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?",
	               defaultTitle = "CAS - Eschmeyer's Catalog of Fishes"
	}
}
data.cof.species = function(genus, species, subspecies)
		local taxon = genus .. " " .. species
	    local url = data.cof.customArgs'baseURL' ..  'tbl=species&genus=' .. genus .. '&species=' .. species
	    local title = "Species related to " .. "" .. firstToUpper(taxon) .. ""        -- .. "" species synonyms"
	    return title, url
end
data.cof.genus  = function(genus)
	    local url = data.cof.customArgs'baseURL' .. 'tbl=species&genus=' .. genus
	    local title = "Species in the genus " .. firstToUpper(genus) .. "" 
	    return title, url
end
-- note the family works with subfamilies using &family=SUBFAMILY
data.cof.family  = function(family)
	    local list = templateArgs'list' or "genus"
	    local url = data.cof.customArgs'baseURL' .. 'tbl=' .. list .. '&family=' .. family
local title = "Species"
if list == "genus" then  title = "Genera" end 
title = title .. ' in the family ' .. firstToUpper(family)  
return title, url
end
data.cof.genid = function(genid)
	    local searchStr =  "genid" .. '=' .. genid
local title =  searchStr
local url = data.cof.customArgs'baseURL' .. searchStr
return title, url
end
data.cof.spid = function(spid)
	    local searchStr =  "spid" .. '=' .. spid
local title =  searchStr
local url = data.cof.customArgs'baseURL' .. searchStr
return title, url
end
data.cof.error = function()
	return "Error. No recognised option set by template (need one of family, genus, species (also requires genus), spid, or genid"
end
--======================Fishes of the World 5===============================	
data.fotw5 = {
	citeTemplate = "Cite book",
	citationArgs = {
	    --'website' = "",
		first1 = "Joseph S.", last1 = "Nelson",
		first2="Terry C.", last2="Grande",
		first3="Mark V. H.", last3="Wilson", 
		--work = "Fishes of the World (work)",
		title = "Fishes of the World", edition="5th", year = 2016,
		publisher ="John Wiley and Sons", location="Hoboken",
		isbn = "978-1-118-34233-6", doi="10.1002/9781119174844" ,
	},
	customArgs = {exclude="gb-page,q,dq,1",
	              baseURL = "https://onlinelibrary.wiley.com/doi/book/10.1002/9781119174844", -- online library
	              defaultTitle = "Fishes of the World",
	              altTitle = "Fishes of the World",               -- wikilinked for when using chapter/section title
	              altURL = "https://sites.google.com/site/fotw5th/",  -- classification
	},
	GoogleBooks = { baseURL = "https://books.google.co.uk/books?id=",
		            id = "E-MLDAAAQBAJ",
		            defaultPage = "&pg=PP1"
	}
}
data.fotw5.default2 = function(targs)
local title = data.fotw5.citationArgs'work'
local url = data.fotw5.customArgs'baseURL'
local chapterParams =  { title      = title,
	                    'chapter-url'= data.fotw5.customArgs'googleBooks'
}
--return title, url, chapterParams
end
data.BentonVP4 = {
	citeTemplate = "Cite book",
	citationArgs = {
		first1 = "Michael J.", last1 = "Benton",
		title = "Vertebrate Palaeontology", edition="4th", year = 2014,
		publisher ="John Wiley & Sons", 
		isbn = "978-1-118-40764-6", 
	},
	customArgs = {exclude="gb-page,q,dq,1",
	              --baseURL = "",
	              defaultTitle = "Vertebrate Palaeontology",
	              altTitle = "Vertebrate Palaeontology"  -- wikilinked for when using chapter/section title
	},
	GoogleBooks = { baseURL = "https://books.google.co.uk/books?id=",
		            id = "qak-BAAAQBAJ",
		            defaultPage = "&pg=PP1",
	}
}
--====================TODO FishWisePro==================================================	
data.fishwisepro = {
	citationArgs = {
	    'website' = "FishWisePro",
	},
	customArgs = {exclude="family,genus,species,1",
	              baseURL = ""
	}
}
-- #################### AMPHIBIA and REPTILES ###############################
-- ================= Amphibian Species of the World (ASW6)
--Recommended citation: Frost, Darrel R. 2019. Amphibian Species of the World: an Online Reference. Version 6.0 (Date of access). Electronic Database accessible at http://research.amnh.org/herpetology/amphibia/index.html. American Museum of Natural History, New York, USA.
URL for family page: http://research.amnh.org/vz/herpetology/amphibia/Amphibia/Anura/Allophrynidae
baseURL      = http://research.amnh.org/vz/herpetology/amphibia/
suffix       = Amphibia/Anura/Allophrynidae
note: needs the whole hierarchy (except the superfamily which is optional)
Template for main taxonomic listing: access-date=27 September 2019
SEARCH http://research.amnh.org/vz/herpetology/amphibia/amphib/basic_search?basic_query=Atelopus&stree=&stree_id=
searchSuffix = amphib/basic_search?basic_query=Atelopus&stree=&stree_id=
SEARCH http://research.amnh.org/vz/herpetology/amphibia/content/search?taxon=Allophryn*&subtree=&subtree_id=&english_name=&author=&year=&country=
searchSuffix = /content/search?taxon=Allophryn*&subtree=&subtree_id=&english_name=&author=&year=&country=
minimul      = /content/search?taxon=Allophryn*&subtree

data.ASW6 ={
	citationArgs = {
		website  ="Amphibian Species of the World, an Online Reference.",
		version  = "Version 6.0",
		publisher = "American Museum of Natural History, New York",
		'last1'="Frost",  'first1'="Darrel R.", 'author1-link'="Darrel R. Frost",
	},
	customArgs = { exclude = "taxon,species,genus,family, superfamily,1,2,3",
	               baseURL = "http://research.amnh.org/herpetology/amphibia/",
	               defaultSuffix = "index.html",
	               defaultTitle = "ASW Home"  
	}
}
data.ASW6.species = function(genus, species, subspecies)
		-- search for genus+species  ()
	    local title = "Search for taxon: " .. "" .. genus .. " " .. species .. ""
	
		 	--local search = ""?action=names&taxon="" -- old version (pre ASW6)
		 	--local search =  "amphib/basic_search?basic_query="  -- basic search
	 	local search = "content/search?taxon="              -- guided search for taxon name
		 	
		local url = data.ASW6.customArgs'baseURL' .. search  -- .. genus .. '+AND+' .. species
		 	            .. '"' .. genus .. '+' .. species .. '"'
		return title, url
end
data.ASW6.genus = function(genus)
	return data.ASW6.taxon(genus)  -- use genus as alias of taxon
end
data.ASW6.taxon = function(taxon)		
	    local title = "Search for Taxon: " .. taxon
	    local url= data.ASW6.customArgs'baseURL' .. "content/search?taxon=" .. taxon
	    return title, url
end
data.ASW6.family = function(family) 
		local order = data.ASW6.checkOrder(family)
		local url= data.ASW6.customArgs'baseURL' .. "Amphibia/" .. order .. "/" .. firstToUpper(family)
		local title = firstToUpper(family) 
		return title, url
end
data.ASW6.checkOrder = function(family)
	local gymnophiona={ "Caeciliidae", "Chikilidae", "Dermophiidae", "Herpelidae", "Ichthyophiidae", "Indotyphlidae", "Rhinatrematidae", "Scolecomorphidae", "Siphonopidae", "Typhlonectidae" }
local caudata = { "Ambystomatidae", "Amphiumidae", "Cryptobranchidae", "Hynobiidae", "Plethodontidae", "Proteidae", "Rhyacotritonidae", "Salamandridae", "Sirenidae" }

for k,v in pairs(caudata) do
	if v == family then return "Caudata" end
end
for k,v in pairs(gymnophiona) do
	if v == family then return "Gymnophiona" end
end

return "Anura"
end   
--============================= AmphibiaWeb ===============================**
--   Citation: AmphibiaWeb. 2019.  University of California, Berkeley, CA, USA. Accessed 27 Sep 2019.
Code:     access-date=27 September 2019
--
data.amphibiaweb = {
	citationArgs = {
		website  = "AmphibiaWeb",
		publisher = "University of California, Berkeley",
		--'editor1-last'="",  'editor1-first'="", 'editor1-link'="",
	},
customArgs = { exclude = "taxon,species,genus,family,1,2,3",
	               baseURL = "https://amphibiaweb.org/",
	               defaultSuffix = "taxonomy/AW_FamilyPhylogeny.html",
	               defaultTitle = "AmphibiaWeb Family Taxonomy"
	}
}
data.amphibiaweb.species = function (genus, species, subspecies)
		local title = "" .. genus .. " " .. species .. ""
		 	--https://amphibiaweb.org/cgi/amphib_query?where-genus=Altiphrynoides&where-species=malcolmi
		local url = data.amphibiaweb.customArgs'baseURL' .. "cgi/amphib_query?rel-genus=equals&where-genus="
		 	                   .. genus .. "&rel-species=equals&where-species=" .. species
		return title, url
end
data.amphibiaweb.genus = function (genus)
		local title = "" .. genus ..  ""
		 	--https://amphibiaweb.org/cgi/amphib_query?where-genus=Altiphrynoides&where-species=malcolmi
		local url = data.amphibiaweb.customArgs'baseURL' .. "cgi/amphib_query?rel-genus=equals&where-genus=" 
		 	                .. genus .. "&include_synonymies=Yes&show_photos=Yes"
		return title, url
end	
data.amphibiaweb.family = function (family)		-- if family use standardised url
		 local url = data.amphibiaweb.customArgs'baseURL' .. "lists/" .. firstToUpper(templateArgs'family') .. ".shtml"
		 local title = templateArgs'family'
		 return title, url
end
	
--=========================== The Reptile Database
data.reptileDB = {
	-- http://reptile-database.reptarium.cz/species?genus=Epacrophis&species=boulengeri
	-- recommended citation: Uetz, P., Freed, P. & Hošek, J. (eds.) (2019) The Reptile Database, http://www.reptile-database.org, accessed insert date here
	citationArgs = {
		--website="reptile-database.org",
		website="The Reptile Database",
		'editor1-last'="Uetz",  'editor1-first'="P.", --'editor1-link'="Peter Uetz",
		'editor2-last'="Freed",  'editor2-first'="P.", 
		'editor3-last'="Hošek",  'editor3-first'="J.", 
		--year=2019
		
	},
	customArgs = { exclude = "taxon,species,genus,family,1,2,3",
	               baseURL = "http://reptile-database.reptarium.cz/"
	}
}
data.reptileDB.species = function(genus, species)
	    local title = "" .. genus .. " " .. species .. ""
	    --http://reptile-database.reptarium.cz/species?genus=Loxocemus&species=bicolor
		local url = data.reptileDB.customArgs'baseURL' .. "species?genus=" .. genus .. "&species=" .. species
		return  title, url
end
data.reptileDB.genus = function(genus)
	    local title = "" .. genus .. "" 
	    --http://reptile-database.reptarium.cz/advanced_search?genus=Malayopython&submit=Search
	    local url = data.reptileDB.customArgs'baseURL' .. "advanced_search?genus=" .. genus .. "&exact%5B0%5D=taxon&submit=search"
		return  title, url
end
data.reptileDB.family = function(family)
return data.reptileDB.taxon(family)
end
data.reptileDB.order = function(order)
return data.reptileDB.taxon(order)
end
data.reptileDB.taxon = function(taxon)
	    local title = taxon
		--http://reptile-database.reptarium.cz/advanced_search?taxon=Viperidae&exact%5B0%5D=taxon&submit=Search
		local url = data.reptileDB.customArgs'baseURL' .. "advanced_search?taxon=" .. taxon .. "&exact%5B0%5D=taxon&submit=search"
		return  title, url
end
	

--################################### BIRDS ########################################
--====================Handbook of the Birds of the World Alive (HBW Alive)==========**
data.HBWalive = {         
	citationArgs = {
		website="Handbook of the Birds of the World Alive", 
		publisher="Lynx Edicions"
	},
	customArgs = { exclude="order,family,genus,species,taxon,id,1",
	               baseURL = "https://www.hbw.com/",
	               defaultSuffix = "family/home",
	               defaultTitle = "Family | HBW Alive"
	               
	}
}
--############################## HBW ALIVE #########################################
-- family and species entries have mix of common name and taxon name so cannot be prempted; 
-- must use title + url (which uses default functions in this module)
data.HBWalive.order = function(order)
	local title = "Order " .. firstToUpper(order)
	--https://www.hbw.com/order/struthioniformes
	local url = target.customArgs'baseURL' .. "order/" .. order
	return title, url
end

--======================IOC World Bird List======================**
	        Gill, F & D Donsker (Eds). 2019. IOC World Bird List (v9.2). doi :  10.14344/IOC.ML.9.2.
	        Gill F, D Donsker & P Rasmussen  (Eds). 2020. IOC World Bird List (v10.2). doi :  10.14344/IOC.ML.10.1.
data.IOC = {         
	citationArgs = {
		website="IOC World Bird List", 
	--	version="Version 9.2",                               -- shouldn't default; should be hardcode so it doesn't change
		'editor1-last'="Gill",  'editor1-first'="F.",  'editor1-link'="Frank Gill (ornithologist)",
		'editor2-last'="Donsker",  'editor2-first'="D.",
		'editor3-last'="Rasmussen",  'editor3-first'="P.",  -- TODO only show from version 10.1 onwards
	--	doi = "10.14344/IOC.ML.9.2",                          -- this changes by version number and is not a useful part of the cictation
		publisher="International Ornithological Congress"
	},
	customArgs = { exclude="order,family,genus,species,taxon,id,1",
	               baseURL = "https://www.worldbirdnames.org/",
	               defaultSuffix = "",
	               defaultTitle = "IOC World Bird List: Welcome"
	               
	},
}
data.IOC.version = function()
	local version =  templateArgs'version' 
	local old = false
	if version then
		version = string.gsub( version, "Vversion ", "")
	local versionNumber = tonumber(version)
	if versionNumber  and ) with 
	local names = authors:gsub (',%s+', '|');       -- replace any comma
	                 --    :gsub ('%.?,?%s+and%s+', '|') -- replace 'separators' and) with 
	                 --    :gsub ('%.,%s+', '.|');       -- replace 'separators'  with 
	list = mw.text.split (names, '|');											-- split the string on the pipes into entries in list
		if #list == 0 then
			data.BOW.citationArgs'authors' = authors 					        	-- no 'names' of the proper form; return the original as a single |author= parameter
		else
			for i, name in ipairs (list) do											-- for each author in list 
		      	data.BOW.citationArgs'author'..i-1 = name 					    -- add |authorn= parameter names
				--	listi = table.concat ({'|author', (i == 1) and  or i, '=', name});	-- add |authorn= parameter names; create |author= instead of |author1=
			end
			data.BOW.citationArgs'author1' = data.BOW.citationArgs'author0' .. ', ' .. data.BOW.citationArgs'author1'
		end   

end
	 --if not url then url = data.BOW.customArgs'baseURL'  end
	 --if not title then title = "Title parameter required" end
	 
	 return title, url
end
-- basic handling for Taxonomy in Flux website
data.tif = {         
	citationArgs = {
		website="Taxonomy in Flux", 
		'editor1-last'="Boyd III",  'editor1-first'="John H.",    --'editor1-link'="",
	},
	customArgs = { exclude="order,family,genus,species,taxon,id,1",
	               baseURL = "http://jboyd.net/Taxo/",
	               defaultSuffix = "List.html",
	               defaultTitle = "Taxonomy in Flux"
	               
	},
}
-- ------------- Avibase
e.g. https://avibase.bsc-eoc.org/species.jsp?avibaseid=9144EF4017F2D8B1
data.avibase = {
		citationArgs = {
		website="Avibase", 
		'editor1-last'="Lepage",  'editor1-first'="Denis",    --'editor1-link'="",
	},
	customArgs = { exclude="order,family,genus,species,taxon,id,1",
	               baseURL = "https://avibase.bsc-eoc.org/",
	               searchStr = "species.jsp?avibaseid=",
	               defaultTitle = "Avibase - The World Bird Database"
	}
}
-- use default function
data.avibase.id = function (id)

local title = "Avibase id: " .. id
	local url = data.avibase.customArgs'baseURL' .. data.avibase.customArgs'searchStr' .. id
	return title, url
end
--
-- ============================= IUCN =============================================**
-- for species in taxon; for species assessments, us 
-- https://www.iucnredlist.org/search?query=Murexia&searchType=species 
-- https://www.iucnredlist.org/search?query=aonyx&searchType=species
data.iucn = {
	citationArgs = {
		website="IUCN Red List of Threatened Species", 
		--publisher="IUCN"
	},
	customArgs = { exclude="family,genus,species,taxon,id,1",
	               baseURL = "https://www.iucnredlist.org",
	               searchString = "/search?query=",
	               searchSuffix = "&searchType=species",
	               defaultSuffix = "",
	               defaultTitle="IUCN Red List of Threatened Species"
	}	
}
data.iucn.genus  = function(genus)  return data.iucn.taxon(genus, "TITLE_ITALICS") end
data.iucn.family = function(family) return data.iucn.taxon(family) end
data.iucn.order  = function(order)  return data.iucn.taxon(order) end
data.iucn.taxon  = function(taxon, titleItalics)
local title = firstToUpper(taxon)
if titleItalics then title = "" .. title .. "" end
local url = data.iucn.customArgs'baseURL' .. data.iucn.customArgs'searchString' .. taxon .. data.iucn.customArgs'searchSuffix'
return title, url
end   
-- ============================= ASM Mammal Diversity Database ====================**
data.asm = {
	citationArgs = {
		website="ASM Mammal Diversity Database", 
		publisher="American Society of Mammalogists"
	},
	customArgs = { exclude="family,genus,species,taxon,id,1,2,3",
	               baseURL = "https://www.mammaldiversity.org/",
	               defaultTitle="ASM Mammal Diversity Database"
	               
	}
}
data.asm.species = function(genus, species)
local title = "" .. genus .. " " .. species .. ""
		--https://mammaldiversity.org/species-account.php?genus=ursus&species=arctos
	local url = data.asm.customArgs'baseURL' .. "species-account.php?genus=" .. genus .. "&species=" .. species
	return title, url
end	    
data.asm.id = function(id)
	--local url = data.asm.customArgs'baseURL' .. "species-account/species-id=" .. templateArgs'id'
	--local title = "Species-id=" .. id
	
	-- new format https://www.mammaldiversity.org/explore.html#species-id=1006310
	local url = data.asm.customArgs'baseURL' .. "explore.html#species-id=" .. id -- templateArgs'id'
	local title = "Species-id=" .. id
	return title, url
end
data.asm.genus  = function(genus)  return data.asm.taxon(genus, "TITLE_ITALICS") end
data.asm.family = function(family) return data.asm.taxon(family) end
data.asm.order  = function(order)  return data.asm.taxon(order) end
data.asm.taxon  = function(taxon, titleItalics)
	--https://mammaldiversity.org/#ZmVsaWRhZSZnbG9iYWxfc2VhcmNoPXRydWUmbG9vc2U9dHJ1ZQ
	--                             Base64.encode(felidae&global_search=true&loose=true)
local title = firstToUpper(taxon)
if titleItalics then title = "" .. title .. "" end
local url = data.asm.customArgs'baseURL' 
.. '#' .. data.asm.Base64.encode(taxon.."&global_search=true&loose=false")
return title, url
end   
--############################## Base64 encode and decode (used for ASM#####################
local b='ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/'
-- encoding
data.asm.Base64 = {}
data.asm.Base64.encode = function(data)
return ((data:gsub('.', function(x) 
local r,b=,x:byte()
for i=8,1,-1 do r=r..(b%2^i-b%2^(i-1)>0 and '1' or '0') end
return r;
end)..'0000'):gsub('%d%d%d?%d?%d?%d?', function(x)
if (#x 0 and '1' or '0') end
return r;
end):gsub('%d%d%d?%d?%d?%d?%d?%d?', function(x)
if (#x ~= 8) then return  end
local c=0
for i=1,8 do c=c+(x:sub(i,i)=='1' and 2^(8-i) or 0) end
return string.char(c)
end))
end
--######################## Misc ##################################
-- 3 approaches to handling DB: 
1) use DB as website and use via to append WoRMS
2) use DB as website and use postscript to append WoRMS
3) use WoRMSa as website and designate DB as author (recommended by WoRMS) CURRENT
data.WoRMS = {
	citationArgs = {
	    author = "WoRMS",
	    website = "World Register of Marine Species",
	    --'via' = "World Register of Marine Species",
	    --postscript = ' from the World Register of Marine Species.'
	},
	customArgs = {exclude="id,db,1",
	              baseURL = "http://www.marinespecies.org/aphia.php?",
	              searchStr = "p=taxdetails&id=",
	              defaultTitle="World Register of Marine Species"
	}
}
data.WoRMS.id = function(id)
-- Two styles
1. http://www.marinespecies.org/aphia.php?p=taxdetails&id=14712
>  WoRMS (2018). Heterobranchia. Accessed at: http://marinespecies.org/aphia.php?p=taxdetails&id=14712 on 2018-11-28 
2. http://www.marinespecies.org/aphia.php?p=taxdetails&id=1057249
> MolluscaBase (2018). Ringipleura. Accessed through: World Register of Marine Species at: http://www.marinespecies.org/aphia.php?p=taxdetails&id=1057249 on 2018-11-28 

if not templateArgs'id' then return "no id parameter detected" end
local searchStr = "p=taxdetails&id=" .. templateArgs'id'

if templateArgs'db' then -- if database hosted by WoRMS
	templateArgs'author' = templateArgs'db'  -- this is recommended by WoRMS
	--templateArgs'website' = templateArgs'db'  -- alternative (and use |postscript)
	--templateArgs'publisher' = templateArgs'via'
--else -- WoRMS is primary source
	 templateArgs'via' = nil
	 templateArgs'postscript' = nil
end
--page WoRMS - World Register of Marine Species - Heterobranchia
local title = "WoRMS taxon details: AphiaID " .. id
local url = data.WoRMS.customArgs'baseURL' .. data.WoRMS.customArgs'searchStr' .. id
return title, url    
end
-- Catalgue of Life:
		Roskov Y., Ower G., Orrell T., Nicolson D., Bailly N., Kirk P.M., Bourgoin T., DeWalt R.E., Decock W., van Nieukerken E.J., Penev L. (eds.) (2020). 
		Species 2000 & ITIS Catalogue of Life, 2020-12-01. 
		Digital resource at www.catalogueoflife.org. Species 2000: Naturalis, Leiden, the Netherlands. ISSN 2405-8858.
		Species 2000 & ITIS Catalogue of Life, 2020-12-01. Digital resource at www.catalogueoflife.org. 
		Species 2000: Naturalis, Leiden, the Netherlands. ISSN 2405-8858.
data.col = {
	db       = "col",  -- need rethink this
	citationArgs = {
	    --author = "Catalogue of Life",
	    --'editor-last1' = "Roskov",   'editor-first1' = "Y.", 'editor-last2' = "Ower",     'editor-first2' = "G.", 	    'editor-last3' = "Orrell",   'editor-first3' = "T.", 'editor-last4' = "Nicolson", 'editor-first4' = "D.", 	    'editor-last5' = "Bailly",   'editor-first5' = "N.", 'editor-last6' = "Kirk",     'editor-first6' = "P.M.", 	    'editor-last7' = "Bourgoin", 'editor-first7' = "T.", 'editor-last8' = "DeWalt",   'editor-first8' = "R.E.", 	    'editor-last9' = "Decock",   'editor-first9' = "W.", 'editor-last10' = "van Nieukerken", 'editor-first10' = "E.J.", 	    'editor-last11' = "Penev", 'editor-first11' = "L.", 
	    --website   = "Catalogue of Life",
	    --website   = "Species 2000 & ITIS Catalogue of Life",
	    website   = "Species 2000 & ITIS Catalogue of Life",
	    publisher = "Species 2000: Naturalis, Leiden, the Netherlands",
	    --others    = "Species 2000 & ITIS"
	},
	customArgs = {exclude="id,db,1,2,3,4,5,legacy,option",
	              baseURL = "https://www.catalogueoflife.org/data/",
	              searchStr = "browse?taxonKey=",
	              defaultTitle="Catalogue of Life"
	}
}
data.col.id = function(id)   

-- Catalogue of Life
browse option:	https://www.catalogueoflife.org/data/browse?taxonKey=4JQ8
use id for taxoKey

taxon option    https://www.catalogueoflife.org/data/taxon/6HR5M

local title = "Catalogue of Life taxonKey " .. id
local url = data.col.customArgs'baseURL'


	if string.find( id,  "^0-9abcdef+$" ) then                                            -- if old-style id
		local year = "2019"        -- last old-style version available
	if templateArgs'version' and string.find( templateArgs'version', "^%d%d%d%d$"  ) then --if version specied
	year = templateArgs'version'
end
	if templateArgs'option' == "browse" then 
		    url = "http://www.catalogueoflife.org/annual-checklist/" .. year .. "/browse/tree/id/" .. id
		else -- default to option=taxon
		    url = "http://www.catalogueoflife.org/annual-checklist/" .. year .. "/details/species/id/" .. id
		end
else                                                                                  -- else use current version
	if templateArgs'option' == "browse" then 
		    url = url .. "browse?taxonKey=" .. id
		else -- default to option=taxon
		    url = url .. "taxon/" .. id
		end
end
	return title, url    
	
end
-- current links
				 https://www.catalogueoflife.org/data/search?q=" Chinchilla+chinchilla&type=EXACT
	legacy links with redirect
	    Species pages:    http://www.catalogueoflife.org/col/details/species/id/12dca9c49741815f82400bb7bff50553
	    Species searches: http://www.catalogueoflife.org/col/search/all/key/Dracula+antonii/
old-style links
		  http://www.catalogueoflife.org/col/details/species/id/7539827da517bd6273a4a3836578cb24
		      http://www.catalogueoflife.org/col/search/scientific/genus/Chinchilla/species/chinchilla/match/1/
		  http://www.catalogueoflife.org/col/browse/tree/id/003e480e646d0e7647ab67efc1218197
	year specific links
2019              http://www.catalogueoflife.org/annual-checklist/2019/details/species/id/7539827da517bd6273a4a3836578cb24
http://www.catalogueoflife.org/annual-checklist/2019/search/all/key/Chinchilla+chinchilla/fossil/1/match/1 
http://www.catalogueoflife.org/annual-checklist/2019/search/scientific/genus/Chinchilla/species/chinchilla/match/1/
?    http://www.catalogueoflife.org/annual-checklist/2016/browse/tree?6d600f4985f19b1207d41d847424edd0 
?    http://www.catalogueoflife.org/col/browse/tree/id/003e480e646d0e7647ab67efc1218197
browse            http://www.catalogueoflife.org/annual-checklist/2019/browse/tree/id/003e480e646d0e7647ab67efc1218197

data.col.default = function(mode)  -- this handles the old style template with positional parameters

	local para1 = templateArgs1 
	local para2 = templateArgs2 
	local para3 = templateArgs3  
	local para4 = templateArgs4  
	if para1 then para1 = mw.text.trim(para1) end
	if para2 then para2 = mw.text.trim(para2) end
	if para3 then para3 = mw.text.trim(para3) end
	if para4 then para4 = mw.text.trim(para4) end
	
	local title, url
	
	if para1 then
--local match = "7539827da517bd6273a4a3836578cb24" 
		local match = "^0-9abcdef+$" 
		if string.find( para1, match ) then
			url = "http://www.catalogueoflife.org/col/details/species/id/" .. para1  -- ""Old style id"
			--url ="https://www.catalogueoflife.org/data/search?q=" .. para1
			if para2 then
				title = para2
			else
				title = "Oldstyle id: " .. para1
			end
			
		else
			--https://www.catalogueoflife.org/data/search?q=" Chinchilla+chinchilla&type=EXACT
			
			if para1 ~= "" then
				url = "https://www.catalogueoflife.org/data/search?q=" .. para1 
				title = "" .. para1 
				if para2  then
					url = url .. "+" .. para2 
					title = title .. " " .. para2
				end
				url = url .. "&type=EXACT"
				title = title .. ""
			end
			
		end	
		if para3 then title = title .. " " .. para3 end   -- add authority
		if para4 == "nv" then templateArgs'trans-title' = "synonym" end   -- if nv add synonym. Note that this parameter is not used to add COinS metadata 
	else
		-- no parameter 1
	end
	
	return title, url    
end
--======================  Fossilworks ===================================**
data.fossilworks = {
	citationArgs = {
		website="Fossilworks",
		--publisher="Paleobiology Database",
		--postscript = 'none',
		postscript = " from the Paleobiology Database.",
		--via="fossilworks.org"   -- an alternative format to using |website=
	},
	customArgs = { exclude = "id,collection,date,1",
	               baseURL = "http://www.fossilworks.org/cgi-bin/",
	               searchStr ="bridge.pl?a=taxonInfo&taxon_no=",
	               defaultTitle = "Fossilworks: Gateway to the Paleobiology Database"
	}
	--id = function(id) return p.genericIdCitation (frame, title, url)
}
data.fossilworks.id = function(id)
-- http://fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=83087	
if not templateArgs'id' then return "no id parameter detected" end
local searchStr = "bridge.pl?a=taxonInfo&taxon_no=" .. templateArgs'id'
templateArgs'url'= target.CustomArgs'baseURL' .. searchStr

local title = "PaleoDB taxon number: " .. id
local url = data.fossilworks.customArgs'baseURL' .. data.fossilworks.customArgs'searchStr' .. id
return title, url  
end
data.fossilworks.collection = function(collection)
	-- http://fossilworks.org/bridge.pl?a=collectionSearch&collection_no=20072
	local title = "PaleoDB collection number: " .. collection
	local url = data.fossilworks.customArgs'baseURL' .. "bridge.pl?a=collectionSearch&collection_no=" .. collection
	return title, url 
end
data.fossilworks.error = function()
	return "Requires id and title parameters"
end
--======================================= PLANTS =====================**
-- Plant authorities can end in a period. This is stripped by the citation templates. 
This function encloses titles ending in such authorities in double parentheses, i.e. ((title))   

local addAuthority = function(formattedTaxonName)
if templateArgs'authority' then
	local title = formattedTaxonName .. " " .. templateArgs'authority'
	return string.gsub( title, "(.*%.)$", "((%1))")  -- if authority ends in "." enclose ((title)) to prevent removal
end
return formattedTaxonName
end
-- Hassler, Michael (2004 - 2020): World Plants. Synonymic Checklist and Distribution of the World Flora. 
Version x.xx; last update xx.xx.xxxx. - www.worldplants.de. Last accessed dd/mm/yyyy.
https://www.worldplants.de/world-plants-complete-list/complete-plant-list#1599996425
Hassler, Michael (2004 - 2020): World Ferns. Synonymic Checklist and Distribution of Ferns and Lycophytes of the World. 
Version x.xx; last update xx.xx.xxxx. - www.worldplants.de/ferns/. Last accessed dd/mm/yyyy.
https://www.worldplants.de/world-ferns/ferns-and-lycophytes-list#1599997555
deeplinks:
		Genus:   Helosciadium
		Species:  Helosciadium longipedunculatum
		
		Genus:   Lycopodium
		Species:  Lycopodium clavatum
--
data.worldplants = {
	citationArgs = {
		last1 = "Hassler", first1 = "Michael",
		website="World Plants. Synonymic Checklist and Distribution of the World Flora.",
		--publisher=""
	},
	customArgs = { exclude = "id,authority,family,genus,species,1",
	               baseURL = "https://www.worldplants.de",
	               searchStr ="/world-plants-complete-list/complete-plant-list#",
	               defaultSuffix = "",
	               defaultTitle = "World Plants"
	}
}
data.worldplants.genus = function(genus)
	local title = addAuthority("" .. genus .. "")
	local genusString = genus 
	if templateArgs'authority' then genusString = genus .. "-" .. templateArgs'authority' end
	local url = data.worldplants.customArgs'baseURL' .. "?deeplink=" .. genusString
	return title, url  
end
data.worldplants.species = function(genus, species)
	local title = addAuthority("" .. genus .. " " .. species .. "")
	local url = data.worldplants.customArgs'baseURL' .. "?deeplink=" .. genus .. "-" .. species .. " " .. (templateArgs'authority' or "")
	return title, url  
end
-- experimental, don't leave live 
data.worldplants.taxon = function(taxon)
	local title =  taxon .. " " .. (templateArgs'authority' or "")
	local url = data.worldplants.customArgs'baseURL' .. "?deeplink=" .. taxon
	return title, url  
end
data.worldplants.family = function(family)
	local title = family .. " " .. (templateArgs'authority' or "")
	local url = data.worldplants.customArgs'baseURL' .. "?deeplink=" .. family
	return title, url  
end
--
data.worldferns = {
	citationArgs = {
		last1 = "Hassler", first1 = "Michael",
		website="World Ferns. Synonymic Checklist and Distribution of the World Flora.",
		--publisher=""
	},
	customArgs = { exclude = "id,authority,family,genus,species,1",
	               baseURL = "https://www.worldplants.de/",
	               searchStr ="world-ferns/ferns-and-lycophytes-list?name=",
	               defaultSuffix = "",
	               defaultTitle = "World Ferns"
	}
}
data.worldferns.genus = function(genus)
	local title = addAuthority("" .. genus .. "")
	local genusString = genus 
	if templateArgs'authority' then genusString = genus .. "-" .. templateArgs'authority' end
	local url = data.worldferns.customArgs'baseURL' .. data.worldferns.customArgs'searchStr' ..  genusString
	return title, url  
end
data.worldferns.species = function(genus, species)
	local title = addAuthority("" .. genus .. " " .. species .. "")
	local url = data.worldferns.customArgs'baseURL' .. data.worldferns.customArgs'searchStr' .. genus .. "-" .. species .. " " .. (templateArgs'authority' or "")
	return title, url  
end
--Plants of the World online
	   http://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:30003057-2  -- use id
	   http://powo.science.kew.org/?q=Selaginellaceae                        -- use search
	   http://powo.science.kew.org/?family=Selaginellaceae                   -- can also use family= gets same result as q=
	   http://powo.science.kew.org/?genus=Selago                             -- or genus
	   http://powo.science.kew.org/?genus=Selago&species=abietina            -- or genus + species
	   http://powo.science.kew.org/?genus=Selago&f=accepted_names            -- filter for accepted names
	   http://powo.science.kew.org/?genus=Selago&f=genus_f                   -- filter for genus (no species selected)
	   http://powo.science.kew.org/?genus=Selago&f=genus_f%2Caccepted_names  -- filter for genus and accepted names
	   http://powo.science.kew.org/?page.size=480&f=family_f%2Caccepted_names -- list of accepted families
	   -- all these searches get the search result (no apparent way to target the article when unique)
data.POWO = {
	citationArgs = {
		website="Plants of the World Online",
		publisher="Royal Botanic Gardens, Kew",
		--postscript = 'none',
	},
	customArgs = { exclude = "id,authority,family,genus,species,1",
	               baseURL = "http://powo.science.kew.org/taxon/",
	               searchStr ="urn:lsid:ipni.org:names:",
	               defaultSuffix = "",
	               defaultTitle = "Plants of the World Online"
	}
	--id = function(id) return p.genericIdCitation (frame, title, url)
}
-- http://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:30003057-2	
data.POWO.id = function(id)
	local id = data.POWO.getValidID()
	if not id then return data.POWO.error() end
local title = id                                                                          -- as default value
	local url = data.POWO.customArgs'baseURL' .. data.POWO.customArgs'searchStr' .. id
return title, url  
end
data.POWO.family = function(family)
	local title = addAuthority(family)
	local id = templateArgs'id'
	if not id then return data.POWO.error() end
	local url = data.POWO.customArgs'baseURL' .. data.POWO.customArgs'searchStr' .. id
return title, url  
end
data.POWO.genus = function(genus)
	local title = addAuthority("" .. genus .. "")
	local id = data.POWO.getValidID()
	if not id then return data.POWO.error() end
	local url = data.POWO.customArgs'baseURL' .. data.POWO.customArgs'searchStr' .. id
return title, url  
end
data.POWO.species = function(genus,species)
	local title = addAuthority("" .. genus .. " " .. species .. "")
	local id = data.POWO.getValidID()
	if not id then return data.POWO.error() end
	local url = data.POWO.customArgs'baseURL' .. data.POWO.customArgs'searchStr' ..id
return title, url  
end
data.POWO.getValidID = function()
	local id = templateArgs'id'
	if id then 
		return string.gsub( id, "urn:lsid:ipni.org:names:", "") -- don't want this twice
	end
	return nil
end
data.POWO.error = function()
	return 'Requires id and one of title, family, genus or species parameters'
end
--GRIN 
	Cite as: USDA, Agricultural Research Service, National Plant Germplasm System. 2021. Germplasm Resources Information Network (GRIN Taxonomy). National Germplasm Resources Laboratory, Beltsville, Maryland.
	URL: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomyfamily?type=tribe&id=1571. Accessed 27 October 2021. 
	Family record: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomyfamily?id=440
	   Genus list: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomygenuslist?id=440&type=family
	Subfamily record: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomyfamily?type=subfamily&id=1507
	   Genus list: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomygenuslist?id=3265&type=subfamily
	Tribe record: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomyfamily?type=tribe&id=1551 (Millettieae)
	   Genus list: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomygenuslist?id=1551&type=tribe
	Subtribe record: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomyfamily?type=subtribe&id=1507
	   Genus list: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomygenuslist?id=1507&type=subtribe
	Genus record: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomygenus?id=191 (Genus Adenodolichos Harms)
	  Species list: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomyspecieslist?id=191&type=genus
	Species record: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomydetail?id=489203 ( Adenodolichos paniculatus)
	
data.GRIN = {     
	citationArgs = {
		website="Germplasm Resources Information Network (GRIN)",
		publisher="Agricultural Research Service (ARS), United States Department of Agriculture (USDA)",
		--postscript = 'none',
	},
	customArgs = { exclude = "id,authority,family,genus,species,1",
	               baseURL = "https://npgsweb.ars-grin.gov/gringlobal",
	               searchStr ="/taxon/taxonomydetail?",                             -- for species record
	               defaultSuffix = "",
	               defaultTitle = "GRIN-Global"
	}
	--id = function(id) return p.genericIdCitation (frame, title, url)
}
data.GRIN.id = function(id)
local title = data.GRIN.customArgs'defaultTitle' .. ' ' .. id
local url = data.GRIN.customArgs'baseURL' .. data.GRIN.customArgs'searchStr' .. id
return title, url  
end
-- IPNI
--→ "Meconopsis Vig." International Plant Names Index (IPNI). Royal Botanic Gardens, Kew.
--- 	https://www.ipni.org/n/30149252-2
--- as authority=Vig.)) 
data.IPNI = {     
	citationArgs = {
		website="International Plant Names Index (IPNI)",
		publisher="Royal Botanic Gardens, Kew",
		--postscript = 'none',
	},
	customArgs = { exclude = "id,authority,family,genus,species,1",
	               baseURL = "https://www.ipni.org",
	               searchStr ="/n/",
	               defaultSuffix = "",
	               defaultTitle = "IPNI"
	}
	--id = function(id) return p.genericIdCitation (frame, title, url)
}
data.IPNI.id = function(id)
local title = id
local url = data.IPNI.customArgs'baseURL' .. data.IPNI.customArgs'searchStr' .. id
return title, url  
end
data.IPNI.species  = function(genus, species)  return data.IPNI.taxon(genus .. " " .. species, "TITLE_ITALICS") end
data.IPNI.genus  = function(genus)  return data.IPNI.taxon(genus, "TITLE_ITALICS") end
data.IPNI.taxon = function(taxon, italics)
	local title = taxon 
	if italics then title = "" .. title .. ""  end
	title = addAuthority(title)
--	if templateArgs'authority' then
		title = title .. " " .. templateArgs'authority'
		title = string.gsub( title, "(.*%.)$", "((%1))")  -- if authority ends in "." enclose ((title)) to prevent removal
	end 
	local url = data.IPNI.customArgs'baseURL' .. data.IPNI.customArgs'searchStr' .. templateArgs'id'
return title, url  
end
--World Flora Online 
	http://www.worldfloraonline.org/taxon/wfo-4000012284  -- id
data.WFO = {
	citationArgs = {
		website="World Flora Online",
		--publisher="Missouri Botanical Gardens",
		--postscript = 'none',
	},
	customArgs = { exclude = "id,family,genus,species,authority,1",
	               baseURL = "http://www.worldfloraonline.org",
	               searchStr ="/taxon/wfo-",                                       -- not strictly search string
	               defaultSuffix = "",
	               --defaultTitle = "World Flora Online"
	               defaultTitle = "An Online Flora of All Known Plants"
	}
}
data.WFO.id = function(id)
-- http://www.worldfloraonline.org/taxon/wfo-4000012284	

local title = id
local url = data.WFO.customArgs'baseURL' .. data.WFO.customArgs'searchStr' .. id
return title, url  
end
data.WFO.family = function(family)
	local title = addAuthority(family) 
	local url = data.WFO.customArgs'baseURL' .. data.WFO.customArgs'searchStr' .. templateArgs'id'
return title, url  
end
data.WFO.genus = function(genus)
	local title = addAuthority("" .. genus .. "") 
	local url = data.WFO.customArgs'baseURL' .. data.WFO.customArgs'searchStr' .. templateArgs'id'
return title, url  
end
data.WFO.species = function(genus,species)
	local title = addAuthority("" .. genus .. " " .. species .. "") 
	local url = data.WFO.customArgs'baseURL' .. data.WFO.customArgs'searchStr' .. templateArgs'id'
return title, url  
end
data.WFO.error = function()
	return "Requires id and title parameters"
end
data.Tropicos = {
	citationArgs = {
		website="Tropicos",
		--publisher="Missouri Botanical Gardens",
		--postscript = 'none',
	},
	customArgs = { exclude = "id,1",
	               baseURL = "http://legacy.tropicos.org/Name/",
	               searchStr ="",
	               defaultSuffix = "",
	               defaultTitle = "Tropicos"
	}
}
data.Tropicos.id = function(id)
-- hhttp://legacy.tropicos.org/Name/100444532	

local title = id
local url = data.Tropicos.customArgs'baseURL' .. data.Tropicos.customArgs'searchStr' .. id
return title, url  
end
data.Tropicos.error = function()
	return "Requires id and title parameters"
end
data.FNA = {
	citationArgs = {
		            website="Flora of North America",
		            --publisher="http://www.efloras.org",
		            --postscript = 'none',
	},
	customArgs = { exclude = "id,1",
	               baseURL = "http://www.efloras.org/florataxon.aspx",
	               searchStr ="?flora_id=1&taxon_id=",
	               defaultSuffix = "",
	               defaultTitle = "Flora of North America"
	}
	--id = function(id) return p.genericIdCitation (frame, title, url)
}
data.FNA.id = function(id)
-- http://www.efloras.org/florataxon.aspx?flora_id=1&taxon_id=125683

local title = id
local url = data.FNA.customArgs'baseURL' .. data.FNA.customArgs'searchStr' .. id
return title, url  
end
data.FNA.error = function()
	return "Requires id and title parameters"
end
-- ATRP: Australian Tropical Rainforest Plants 
data.ATRP = {
	citationArgs = {
		            website="Australian Tropical Rainforest Plants",
		            publisher="Commonwealth Scientific and Industrial Research Organisation (CSIRO)",
		            version = "Edition 8",
				    year = 2020,
		            --postscript = 'none',
		            last1= "Zich", first1="F. A.", 
		            last2= "Hyland",  first2= "B. P. M.", 'author2-link'="Bernard Hyland",
		            last3= "Whiffin", first3= "T.", 
		            last4= "Kerrigan",  first4= "R.A.",
		            --'display-authors'=3,
	},
	customArgs = { exclude = "genus, species,authority, id,1",
	               baseURL = "https://apps.lucidcentral.org/rainforest",
	               searchStr ="/text/entities/",
	               defaultSuffix = ".htm",
	               defaultTitle = "Australian Tropical Rainforest Plants"
	}
	--id = function(id) return p.genericIdCitation (frame, title, url)
}
data.ATRP.species = function(genus,species)
-- https://apps.lucidcentral.org/rainforest/text/entities/buckinghamia_celsissima.htm

local title = addAuthority("" .. genus .. " " .. species .. "") --"" .. genus .. " " .. species .. ""
local url = data.ATRP.customArgs'baseURL' .. data.ATRP.customArgs'searchStr' .. genus .. "_" .. species .. data.ATRP.customArgs'defaultSuffix'
return title, url  
end
data.ATRP.error = function()
	return "Requires genus and species parameters"
end
-- ============================= Mosses (Goffinet's site) =================================================-- for species in taxon; for species assessments, us 
-- https://bryology.uconn.edu/classification/#Hypnanae
-- https://bryology.uconn.edu/classification/#Bryales
data.goffinet = {
	citationArgs = {
		first1="B.", last1="Goffinet", 
		first2="W.R.", last2="Buck",
		website="Classification of extant moss genera"
		--publisher="xxx"
	},
	customArgs = { exclude="family,genus,species,taxon,id,1",
	               baseURL = "https://bryology.uconn.edu/classification/",
	               searchString = "#",
	               searchSuffix = "",
	               defaultSuffix = "",
	               defaultTitle="Classification of the Bryophyta"
	}	
}
data.goffinet.genus  = function(genus)  return data.goffinet.taxon(genus, "GENUS") end
data.goffinet.family = function(family) return data.goffinet.taxon(family, "FAMILY") end
data.goffinet.order  = function(order)  return data.goffinet.taxon(order, "ORDER") end
data.goffinet.taxon  = function(taxon, rank)
local title = firstToUpper(taxon)
if rank == "GENUS" then title = "" .. title .. "" end
if not (rank == "GENUS" or rank == "FAMILY") then  -- upper case anchors for orders and above
	if taxon ~= "Bryanae" and taxon ~= "Hypnanae" and taxon ~= "Bryales" and taxon ~= "Bryidae" then -- check for exceptions (inconsistencies at website)
		taxon = taxon:upper()
	end
end
local url = data.goffinet.customArgs'baseURL' .. data.goffinet.customArgs'searchString' .. taxon .. data.goffinet.customArgs'searchSuffix'
return title, url
end 
-- AlgaeBase
taxonomy browser url (Volvox) = https://www.algaebase.org/browse/taxonomy/?id=6898
genus article url (Volvox) =  https://www.algaebase.org/search/genus/detail/?genus_id=43497 (different id)
genus article url (Torodinium)= https://www.algaebase.org/search/genus/detail/?genus_id=44698
Please cite this record as:   M.D. Guiry in Guiry, M.D. & Guiry, G.M. 2020. AlgaeBase. 
World-wide electronic publication, National University of Ireland, Galway. 
http://www.algaebase.org; searched on 10 May 2020.              
data.AlgaeBase = {
	citationArgs = {
		           website="AlgaeBase",
	               'editor1-last'="Guiry", 'editor1-first'="M.D.",
	               'editor2-last'="Guiry", 'editor2-first'="G.M.",
		           publisher="National University of Ireland, Galway",
	},
	customArgs = { exclude = "id,1,genus_id,species_id,spid,genid",
	               baseURL = "https://www.algaebase.org/",
	               searchStr ="browse/taxonomy/?id=",
	               defaultSuffix = "",
	               defaultTitle = "AlgaeBase"
	}
}
data.AlgaeBase.id = function(id)
-- https://www.algaebase.org/browse/taxonomy/?id=6898 (id for taxonomy page)

local title = id
local url = data.AlgaeBase.customArgs'baseURL' .. data.AlgaeBase.customArgs'searchStr' .. id
return title, url  
end
data.AlgaeBase.genid = function(genid)
-- https://www.algaebase.org/search/genus/detail/?genus_id=43497 (different id for genus page)

local title = genid
local url = data.AlgaeBase.customArgs'baseURL' .. "search/genus/detail/?genus_id=" .. genid
return title, url  
end
data.AlgaeBase.spid = function(spid)
-- https://www.algaebase.org/search/species/detail/?species_id=52713 (id for species page)

local title = spid
local url = data.AlgaeBase.customArgs'baseURL' .. "search/species/detail/?species_id=" .. spid
return title, url  
end
data.AlgaeBase.error = function()
	return "Requires id and title parameters"
end
--############################## General Functions ########################################
local function getArgs (frame, args)
	local parents = mw.getCurrentFrame():getParent()
		
	for k,v in pairs(parents.args) do
		--check content
		if v and v ~= "" then
			argsk=v --parents.argsk
		end
	end
	for k,v in pairs(frame.args) do
		--check content
		if v and v ~= "" then
			argsk=v 
		end
	end
end
local function initialise(frame, sourceDB)
	
	target=sourceDB
	templateArgs = sourceDB.citationArgs -- get custom arguments for target (fishbase, cof etc

	getArgs(frame, templateArgs) -- get template arguments from parent frame and frane
	
	
	local url = (target.customArgs'baseURL' or "") .. (target.customArgs'defaultSuffix' or "")
	local title = target.customArgs'defaultTitle' or ""
	return title, url
end 
-- moved up top for scope
local function firstToUpper2(str)
return (str:gsub("^%l", string.upper))
end
-- clear template arguments that won't be recognised by 
local function clearCustomArgs()
	
	local excludeTable = { 'genus', 'species', 'subspecies', 'family', 'order', 'taxon', 
		                   'id', 'search' , 'citation', 1, 2, 3, 4 }                          -- add defaults ?
	
	if target.customArgs'exclude' then
		local customTable = mw.text.split (target.customArgs'exclude' , "%s*,%s*");	
		for k,v in pairs(customTable) do
	    	table.insert (excludeTable, v )
		end
	end	
		for k,v in pairs(excludeTable) do
	    	if tonumber (v) then
	    		v = tonumber (v)  --convert positional parameters (numbers as string) to a number
			end
			templateArgsv=nil --clear content
		end
end
-- function handling the cite web template
p.citeWeb = function(frame, title, url)

-- set url and title if not provided (template parameters override above)
if not templateArgs'url' and url then
		templateArgs'url'= url
end
if not templateArgs'title' and title then
	    	templateArgs'title' = title
	end
clearCustomArgs()--blank template parameters not for cite web
	
	local citeTemplate = 'cite web'          -- use Template:Cite web unless specified
	--if target.citeTemplate then citeTemplate = target.citeTemplate end
	return frame:expandTemplate{ title = citeTemplate, args = templateArgs  }
end
-- p.CiteBook
-- for reasons of consisitency within BioRef/FishRef the title parameter is the section-title of 
p.citeBook = function(frame, title, url, chapterParams) -- very much a msw3 function


--if (1==1) then return templateArgs'title'  end

-- set url and title if not provided (template parameters override above)
if not templateArgs'url' and url then
		templateArgs'url'= url
		if target.GoogleBooks then
			templateArgs'url' = target.GoogleBooks'baseURL' .. target.GoogleBooks'id'
		                   	.. (target.GoogleBooks'defaultPage' or "&pg=PP1")
			
		end
end
if not templateArgs'title' and title then
	--    	templateArgs'title' = title 
	end
	if templateArgs'title' ~= title or templateArgs'taxon-title' then -- do we have a section title provided
		templateArgs'section' = templateArgs'title'  -- chapter/section title passed as title parameter
		templateArgs'title'   = title -- the work is the book title given in the source data
		if target.GoogleBooks then
			
			templateArgs'section-url' = target.GoogleBooks'baseURL' .. target.GoogleBooks'id'
			local pageSuffix = target.GoogleBooks'defaultPage' or ""
			if templateArgs'page' or templateArgs'gb-page' then
				pageSuffix = "&pg=PT" .. (templateArgs'gb-page' or templateArgs'page' )
			end
			local searchStr = ""
		    -- quoted search 
		    if templateArgs'q' then searchStr = "&q=" .. mw.text.encode( templateArgs'q' ) end
		    -- search #if:|&q=}}
		    if templateArgs'dq' then searchStr = "&dq=" .. mw.text.encode( templateArgs'dq' ) end
		    
		    
		    templateArgs'section-url' = templateArgs'section-url' .. pageSuffix ..  searchStr
templateArgs'url' = nil   -- no need for second link to google books
		end
	    -- if the chapter/section is linked, we can link the main book chapter differently 
	    if target.customArgs'altTitle' then -- if we are using a chapter/section, we can wikilink the book title 
	    	templateArgs'title' = target.customArgs'altTitle'  -- alternative to allow wikilink
	    elseif target.customArgs'altURL' then
	    	templateArgs'url' = target.customArgs'altURL'
	    end
	end -- end if using supplied title for chapter/section
clearCustomArgs()--blank template parameters not for cite web
	
	local citeTemplate = 'cite book'          -- use Template:Cite web unless specified
	--if target.citeTemplate then citeTemplate = target.citeTemplate end
	return frame:expandTemplate{ title = citeTemplate, args = templateArgs  }
end
-- common function for genus and species
local function getGenusSpecies()
	--TODO standardise genus species handling
	local genus, species, subspecies
	if (templateArgs'genus'  or templateArgs2 ) then 
	    genus = templateArgs'genus' or templateArgs2
genus = firstToUpper(mw.text.trim(genus))
	end
	if (templateArgs'species'  or templateArgs3 ) then 
	    species = templateArgs'species' or templateArgs3
	    species = 	mw.text.trim(species)
	end
	if (templateArgs'subspecies'  or templateArgs4 ) then 
	    subspecies = templateArgs'subspecies' or templateArgs4
	    subspecies = 	mw.text.trim(subspecies)
	end
	
	return genus, species, subspecies
end
--#################### MSW3   -- uses cite book
p.MSW3 = function(frame) 
	local msw = require('Module:FishRef/MSW')
	initialise(frame, msw.MSW3)
	return msw.MSW3.main(frame,templateArgs)
end
p.MSW3merged = function(frame) 
	local data = require('Module:FishRef/MSW')
	return p._main(frame, data.MSW3)
end
p.MSW3_standalone = function(frame) 
	
	local data = require('Module:FishRef/MSW')
	initialise(frame, data.MSW3)
local url = target.CustomArgs'baseURL' 


if templateArgs'title' and templateArgs'id' then
	templateArgs'chapter-url'= url .. target.CustomArgs'searchStr'  ..  templateArgs'id'
	templateArgs'chapter' = templateArgs'title'

	templateArgs'title' = target.CustomArgs'bookTitle'
	if templateArgs'page' then
		templateArgs'url' = target.CustomArgs'googleBooksURL' .. templateArgs'page' 
		else
	        --return "Page number for google books required"
	end
elseif templateArgs'order' then
	templateArgs'chapter' =  "Order " .. templateArgs'order'
	local chapter = target.chapterstemplateArgs'order'
	for k,v in pairs(chapter) do   -- add chapter specific parameters
		templateArgsk = v 
	end
	templateArgs'chapter-url'= url .. target.CustomArgs'searchStr'  ..  templateArgs'id'
	templateArgs'url'= target.CustomArgs'googleBooksURL'  ..  templateArgs'page'
	if templateArgs'pages' and templateArgs'page' then templateArgs'page' = nil end
else -- default output
	templateArgs'url'= target.CustomArgs'googleBooksURL'  .. "1" -- default to book
	templateArgs'url'= url 
end
-- using cite book
	clearCustomArgs()--blank template parameters not for cite web
	return frame:expandTemplate{ title = 'cite book', args = templateArgs  }
end
--########################### Functions for access (using invoke) ##############################################
--================ Fishbase, Catalog of Fishes (cof) ============**
p.fishbase    = function(frame) return p._main(frame, data.fishbase) end
p.cof         = function(frame) return p._main(frame, data.cof) end 
p.fotw5       = function(frame) return p._main(frame, data.fotw5) end 
--=================== ASW6, AmphibiaWeb, ReptileDB
p.reptileDB   = function(frame) return p._main(frame, data.reptileDB) end
p.ASW6        = function(frame) return p._main(frame, data.ASW6) end
p.amphibiaweb = function(frame) return p._main(frame, data.amphibiaweb) end
--=========== Birds
p.HBWa        = function(frame) return p._main(frame, data.HBWalive) end
p.HBWalive    = function(frame) return p._main(frame, data.HBWalive)  end
p.IOC         = function(frame) return p._main(frame, data.IOC) end
--======= Mammals
p.asm         = function(frame) return p._main(frame, data.asm) end
-- MSW3 has custom handling (see above)
--=========== Other
p.fossilworks = function(frame) return p._main(frame, data.fossilworks) end
p.worms       = function(frame) return p._main(frame, data.WoRMS) end
p.WoRMS       = function(frame) return p._main(frame, data.WoRMS) end
p.col         = function(frame) return p._main(frame, data.col) end 
--fallback = function() return "hello" end
--#########################################################
p.main = function(frame) 
	local source = mw.text.trim(frame.args1)
	
	if source == "MSW3" then return p.MSW3(frame) end
	
	if source == "ref" or source == "reference" then source = "Reference" end   -- aliases
	if source == "Reference" then return p.Reference(frame) end

if source == "HBWa" then source = "HBWalive" end   -- aliases
if source == "powo" then source = "POWO" end   -- aliases
	--return psource'test'
	if source == "fishbase" 
		or source == "cof" 
		or source == "fotw5" or source == "Fotw5" 
		or source == "reptileDB" 
		or source == "amphibiaweb" 
		or source == "ASW6" 
		or source == "asm" 
		or source == "HBWalive" or source == "HBWa" 
		or source == "fossilworks" 
		or source == "WoRMS" or source == "worms" 
		or source == "POWO" or source == "powo" 
		or source == "WFO" 
		or source == "AlgaeBase"
		-- and so on
	    then return p._main(frame,datasource)
	else
		-- 
		-- is there a point in the default if it needs the named object/table?
		return p._main(frame,datasource)
	end
end
p._main = function(frame, source) 
--TODO in modular version source will be provided in frame arguments 
--local source = mw.getCurrentFrame():getParent().args1
local chapterParams = {} -- used for cite book (only MSW3 at moment)

if not source then return "Error: unrecognised source." end

local title, url = initialise(frame, source)

--taxon related parameters
local genus, species, subspecies

if source.db ~= "col" then                             -- col legacy uses positional parameters differently
	genus, species, subspecies = getGenusSpecies()             
end

local family = templateArgs'family'
local order = templateArgs'order'
local taxon = templateArgs'taxon'
	
	local id = templateArgs'id'                                       --id related parameters
	local spid = templateArgs'spid' or templateArgs'species_id'
	local genid = templateArgs'genid' or templateArgs'genus_id'
	local citation = templateArgs'citation' 
local collection = templateArgs'collection' or templateArgs'collection_no' 
	local search = templateArgs'search'
local mode, value

-- the functions
if genus and species and source.species then
	title, url = source.species(genus,species,subspecies)
else -- functions with just their own name as parameter
	
	if genus then mode = "genus"; value = genus 
	elseif family then mode = "family"; value = family
	elseif order then mode = "order"; value = order
	elseif taxon then mode = "taxon"; value = taxon
	elseif id then mode = "id"; value = id
	elseif spid then mode = "spid"; value = spid
	elseif genid then mode = "genid"; value = genid	
elseif search then mode = "search"; value = search	
elseif citation then mode = "citation"; value = citation	
elseif collection then mode = "collection"; value = collection	
	else
		-- no suitable parameter (use default page)
		if source.default then
			title, url, chapterParams = source.default(title, url)
		end
	end
end
if mode then
	if sourcemode then
		title, url, chapterParams = sourcemode(value)  
	elseif data.defaultmode then
		title, url, chapterParams = data.defaultmode(value, source)
	else
		if source.error then return source.error() end             -- custom error message
	    return "Error: parameter not supported for this source" .. " (" .. mode .. ")"
	end
else 
	-- if no mode then use the default title and url set by initialize()
end
if source.citeTemplate == "Cite book" then
	return p.citeBook(frame, title, url, chapterParams)
end
	return p.citeWeb(frame, title, url)
	
end  -- End the function.
p.Reference = function(frame)
	
	local refs = require('Module:FishRef/refs')
	getArgs(frame, templateArgs)
	
	if templateArgs2 then
		local reference = mw.text.trim(templateArgs2)
		if reference ~= "" and refsreference then 
			if templateArgs'pages' then 
				refsreference = refsreference:gsub("}}", "|pages="..templateArgs'pages'.."}}")
				refsreference = refsreference:gsub("|pages=^|{}%%*(|^|{}}%%*|pages=)", "%1")
			end
			if templateArgs'expand' and templateArgs'expand'=='no' or templateArgs'raw'  then
				return refsreference
			else
				return frame:preprocess(refsreference)
			end
		else
			return 'Reference not found: "'	.. templateArgs2 .. '"'
		end
	end
	return "Reference parameter missing."
end -- End the function.
-- All modules end by returning the variable containing its functions to Wikipedia.
return p