Editing Module:Sandbox/Mensis Mirabilis/gene

local p = { }

local function check_values(f,args)
	    --local u= table.upack(args)
		local exist, val = pcall(f, unpack(args))
		if exist and val ~= nil then
			return(val)
		else
			-- Leaking some debugging info won't hurt....
			return("'''VALUE_ERROR''' (" .. tostring(val) .. ")")
		end
end

p.getTemplateData = function(frame)

	--make some guesses about whether the provided QID is a good one
	--could expand here if we had some kind of error handling framework
	--did we get it from the page
	local root_qid = mw.text.trim(frame.args['QID']  or "") --try to get it from the args
	local mm_qid = ""
	--pull all the entity objects that we will need
	local	entity = {} 
	local	entity_protein = {}
	local	entity_mouse = {}
	local	entity_mouse_protein = {}
	local	checkOrtholog = "" --flag used to see if mouse data avaliable
	
	local mouse_propertyID = "P684" --actually ortholog property additional orthologs can exist
	local protein_propertyID = "P688" 

	--get root gene entity
	if root_qid == "" then
		entity = mw.wikibase.getEntityObject()
		if entity then root_qid = entity.id else root_qid = "" end
			
	else
		--assuming we think its good make one call to retrieve and store its wikidata representation
		entity = mw.wikibase.getEntity(root_qid)
	end
	
  	--need to figure out if it is protein or gene here
	local subclass = p.getValue(entity, "P31") or ""
	if string.find(subclass, 'protein') then --if protein switch entity to gene
		if entity.claims then
	 		claims = entity.claims["P702"] --encoded by
	 	end
		if claims then
			--go through each index and reassign entity
			entity = {}
			if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
				for k, v in pairs(claims) do --this would be problematic if multiple genes for the protein
					local itemID = "Q" .. claims[#entity + 1].mainsnak.datavalue.value["numeric-id"]
					entity[#entity + 1] = mw.wikibase.getEntity(itemID)
					root_qid = itemID
				end
				
			end --will return nothing if no claims are found
		end
		 entity = mw.wikibase.getEntity(root_qid) 	
	 end
	
	
	--get the other related entities
	if entity then
		local claims = ""
	 	--get protein entity object
	 	if entity.claims then
	 		claims = entity.claims[protein_propertyID]
	 	end
		if claims then
			--go through each index and then make entity_protein indexed
			if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
				for k, v in pairs(claims) do
					local protein_itemID = "Q" .. claims[#entity_protein + 1].mainsnak.datavalue.value["numeric-id"]
					entity_protein[#entity_protein + 1] = mw.wikibase.getEntity(protein_itemID)
				end
				
			end --will return nothing if no claims are found
		end
	
	 	--get mouse entity object
	 	if entity.claims then
			claims = entity.claims[mouse_propertyID]
		end
		local qualifierID = "P703" --found in taxon
		local mouse_qual = "Q83310"
		if claims then
			if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
				for k, v in pairs(claims) do
					if checkOrtholog == 1 then -- Don't have to go on if we already got it
						break
					end

				  	local mouse_itemID = "Q" .. v.mainsnak.datavalue.value["numeric-id"]
					local quals 
					if v.qualifiers then
						quals = v.qualifiers.P703
					end
					if quals then
						for qk, qv in pairs(quals) do
							--get the taxon qualifier id
							local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]
							if qual_obj_id == mouse_qual then --check if this is mouse or other
								mm_qid = mouse_itemID 
								entity_mouse = mw.wikibase.getEntity(mouse_itemID)
								checkOrtholog = 1
								break
							end
						end
					end
				end
			end --will return nothing if no claims are found
		else
			checkOrtholog = 0
		end
	
	 	--get mouse protein entity object
	 	if entity_mouse and entity_mouse.claims then
			claims = entity_mouse.claims[protein_propertyID]
		end
	 	if claims then
	 		if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
				for k, v in pairs(claims) do
					local protein_itemID = "Q" .. claims[#entity_mouse_protein + 1].mainsnak.datavalue.value["numeric-id"]
					entity_mouse_protein[#entity_mouse_protein + 1] = mw.wikibase.getEntity(protein_itemID)
				end
			end --will return nothing if no claims are found
	 	end	
	
	end
	
	
	if entity then --only require the main gene entity
		--a list variables of all the data in the info box
		local chr = check_values(p.trimChromosome, {entity})
		--local drug = check_values(p.getDrug, {entity_protein, "P129"})
		
		--define Global Color Scheme
		rowBGcolor = '#eee'
		titleBGcolor = '#ddd'
		sideTitleBGcolor = '#c3fdb8'


		return tostring(root)
        --return table.concat(drug_pqid)
        
	else return "An Error has occurred retrieving Wikidata item for infobox"
	end	
end

--general function to get value given an entity and property
p.getValue = function(entity, propertyID, return_val)

	local claims
	if return_val == nil then return_val = "" end
    local sep = " " --could ad as input parameter if need be
	if entity and entity.claims then
		claims = entity.claims[propertyID]
	end
	if claims then
		-- if wiki-linked value output as link if possible
		if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
			local out = {}
			for k, v in pairs(claims) do
				local datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])
				if datav == nil then datav = " " end 
				out[#out + 1] = datav			
			end
			return table.concat(out, sep)
		else
		-- just return best values
			return entity:formatPropertyValues(propertyID).value
		end
	else
		return return_val
	end
end

p.trimChromosome = function(entity)
	local string_to_trim = p.getValue(entity, "P1057")
	local out = ''
	
	--"mitochondrion" and "chromosome MT" is used for mitochondrial DNA.
	--See [[d:Special:WhatLinksHere/Q18694495]]
	if string.find(string_to_trim, 'chromosome MT') or string.find(string_to_trim, 'mitochondri') then --match both 'mitochondrio'/'mitochondrial'
		out = "MT"
	elseif string.find(string_to_trim, 'chromosome') then
		out = string.match(string_to_trim, "%d+")--extract number from string
		if out == nil then
			out = string.match(string_to_trim, "X") or string.match(string_to_trim, "Y")
		end
	end
	return out	
end

local chr = check_values(p.trimChromosome, {entity})
local category_chromosome = '[[Category:Genes on human chromosome '..chr..']]'

function p._main(args)

	return chr
end

return p