Module:Sandbox/genewiki/experimental

Documentation for this module may be created at Module:Sandbox/genewiki/experimental/doc

--uncomment and add this to the debug console to run code.
--frame = mw.getCurrentFrame()
--frame.args = {"a", "b", from ="Q14865053"}
--print(p.hello(frame))

---require('Module:Wikidata')	

-- All Lua modules on Wikipedia must begin by defining a variable that will hold their
-- externally accessible functions. They can have any name and may also hold data.
p = {
	devmode	 = false
}



p.getQualifierID = function(frame)
	local propertyID = mw.text.trim(frame.args[1] or "") 
	local qualifierID = mw.text.trim(frame.args[2] or "")
	local input_parm = mw.text.trim(frame.args[3] or "")
	local itemID = mw.text.trim(frame.args[4] or "") --if direct link from wikidata item
	
	if input_parm == "FETCH_WIKIDATA" then
		local entity = ""
		if itemID ~= "" then
			entity = mw.wikibase.getEntityObject(itemID)
		else
			entity = mw.wikibase.getEntityObject()
		end
		if entity.claims[propertyID] ~= nil then
			local out = {}
			for k, v in pairs(entity.claims[propertyID]) do
				for k2, v2 in pairs(v.qualifiers[qualifierID]) do
					if v2.snaktype == 'value' then
							out[#out + 1] = "Q" .. v2.datavalue.value["numeric-id"]
					end
				end
			end
			return table.concat(out, ", ")
		else
			return ""
		end
	else
		return input_parm
	end
end

--- Try to replace this with one function that fails gracefully
--- Get the image URL associated the current article
---{{#invoke:Wikidata|getValueFromID|{{#invoke:Sandbox/genewiki/geneboxdev |getQIDFromID |{{#invoke:Wikidata|pageId}} |P688}}|P18|FETCH_WIKIDATA}}
--- breaks apart to be 
---{{#invoke:Wikidata|getValueFromID|
---	{{#invoke:Sandbox/genewiki/geneboxdev |getQIDFromID |
---		{{#invoke:Wikidata|pageId}} 
---	|P688}}
---|P18|FETCH_WIKIDATA}}
--- testing on ARF6 Q14865053 


p.testEntityId = function(wikidata_qid)
	--pcall pattern does not not work for this..
	--local entity = mw.wikibase.getEntity(wikidata_qid)
	--but it does for locally generated errors like this
	local entity = 2+"error"
	return entity
end

-- test entry point
-- local qid = mw.text.trim(frame.args['from'])
p.hello = function( frame ) 
	local qid = "1Q14865053"
	local out = ""
	--this is like a try statement
	local worked,value = pcall(p.testEntityId, qid) 
	if(worked)
		then out = value 
		else out = "error! "..value
	end
    return out    
end

--gets an image for a qif, doesn't die if no qid is given to it. 
--frame = mw.getCurrentFrame()
--frame.args = {QID="Q14865053"}
--print(p.getDefaultImage(frame))

p.getDefaultImage = function(frame)
	local wikidata_id = mw.text.trim(frame.args['QID'] or "")
	-- "nil" (a string, not the value nil), "number", "string", "boolean", "table", "function", "thread", and "userdata".
	if wikidata_id == nil 
		then return ""
	elseif string.len(wikidata_id) < 3  
		then return ""
	end
	
	local propertyID = "P18"
	local sep = mw.text.trim(" ")
	local imgsize = mw.text.trim("220px")
	local entity = mw.wikibase.getEntity(wikidata_id)
	local claims
	if entity and entity.claims then
		claims = entity.claims[propertyID]
	end
	if claims then
		if (claims[1] and claims[1].mainsnak.datatype == "commonsMedia") then
			local out = {}
			for k, v in pairs(claims) do
				local filename = v.mainsnak.datavalue.value
				out[#out + 1] = "[[File:" .. filename .. "|" .. imgsize .. "]]"
			end
				return table.concat(out, sep)
		else
			return ""
		end
	else
		return input_parm
	end
end

function p.ViewSomething(frame)
	local itemID ="Q14865053"
	local data = mw.wikibase.getEntityObject(itemID)
	if not data then
		return nil
	end

---	local f = frame.args[1] and frame or frame:getParent()

	local i = 1
	while true do
---		local index = f.args[i]
---		if not index then
			if type(data) == "table" then
				return mw.text.jsonEncode(data, mw.text.JSON_PRESERVE_KEYS + mw.text.JSON_PRETTY)
			else
				return tostring(data)
			end
---		end
		
		data = data[index] or data[tonumber(index)]
		if not data then
			return
		end
		
		i = i + 1
	end
end

p.getChromosomeLocJulia = function(frame)
	local propertyID = mw.text.trim(frame.args[1] or "") 
	local qualifierID = mw.text.trim(frame.args[2] or "")
	local input_parm = mw.text.trim(frame.args[3] or "")
	local qualifierIds = p.getQualifierID(frame)
	local newest_build = ""
	local preferred_value = "not set"
	if qualifierIds then
		local list_itemID = mw.text.split(qualifierIds,",")
		for index,value in ipairs(list_itemID) do
  			local entity = mw.wikibase.getEntityObject(value)
			local alias = ""
			if entity['aliases'] ~= nil then
        		local test = entity['aliases']['en']
				for key, value in ipairs(test) do
					if string.match(value['value'], '^hg') then
						alias = value['value']
					end
				end
				local build_no = alias:gsub("hg", "")
				if newest_build < build_no or newest_build == "" then
					newest_build = build_no
					preferred_value = "path here"
				end
			end
		end
		return preferred_value
	else
		return "nnn"
	end
	return "mmm"
end

---getChromosomeLoc 
---input propertyID ie(Genomic start) P644
---      qualifierID (ie GenLoc Assembly) P659
---      input_parm (ie FETCH_WIKIDATA)  
---      {{#invoke:Sandbox/genewiki/geneboxdev|getChromosomeLoc|P644|P659|FETCH_WIKIDATA}}
---output preferred chromosome location start value in this case it would be 49893092

--for debug window -- Q14865053
--frame = mw.getCurrentFrame()
--frame.args = {"P644","P659","FETCH_WIKIDATA","Q14865053"}
--print(p.getChromosomeLoc(frame))

p.getChromosomeLoc = function(frame)
	-- will contain the numeric value for the requested coordinate
	local output = ""
	local sep = " "
	-- can only be P644 (genomic start) or P645 (genomic end) for this to work
	-- should probably try to catch that.  Might also increase legibility to use specific variable names when possible
	local propertyID = mw.text.trim(frame.args[1] or "") 
	-- this can really only be P659 right now.  I'm not sure of the value of including it as a parameter as other values will likely break this function
	local qualifierID = mw.text.trim(frame.args[2] or "")
	-- Why do we include this here?  What should happen if FETCH_WIKIDATA is not included? 
	local input_parm = mw.text.trim(frame.args[3] or "")
	-- this can needs to be fed to the function either by a call to {{#invoke:Wikidata|pageId}} or by setting it directly (e.g. if the function was applied on a page other than the targeted gene)
	--alert if this id is not a valid thing in wikidata, a Lua error will occur that says
	--The ID entered is unknown to the system. Please use a valid entity ID.
	local itemID = mw.text.trim(frame.args[4] or "")
	-- will track the different builds pulled from the qualifiers
	local newest_build = "0"
	-- starts the process
	local entity = mw.wikibase.getEntityObject(itemID)
	local claims
	--gets a table of claims on the (genomic start or end) property Q19847637
	if entity and entity.claims then
		claims = entity.claims[propertyID]
	end
	--will return nothing if no claims are found
	if claims then
		--checking to be sure claims is populated, not sure it its needed
		if (claims[1] ) then
			--useful for debugging
			--local out = {}
			--pulls the genome location from the claim
			for k, v in pairs(claims) do
				local location = v.mainsnak.datavalue.value
				--debugging
				--out[#out + 1] = k.." location:" .. location.. " || " 
				--gets the qualifiers linked to the current claim
				local quals = v.qualifiers.P659 
				--if there are any
				if quals then
					for qk, qv in pairs(quals) do
						local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]
						--get to the entity targeted by the qualifier property.  Genome builds are Items in wikidata
						local qual_obj = mw.wikibase.getEntityObject(qual_obj_id)
						local alias = ""
						--this uses the aliases to pull out version numbers
						--seems like there ought to be a better way to do this, but likely would need to change the data added by the bot
						if qual_obj["aliases"] ~= nil then
							local test = qual_obj["aliases"]["en"]
							for key, value in ipairs(test) do
								if string.match(value['value'], '^hg') then
									alias = value['value']
									local build_no = alias:gsub("hg","")
									--report only the most location associated with the most recent build
									--if there is more than one location per build, just give one back as that is not our problem right now.
									if build_no > newest_build then
										output = location
										newest_build = build_no
									end
								end
							end
						end
					end
				--in case there are no qualifiers, but there is a location, might as well return it
				else output = location 
				end
			end
				return output
		else
			return ""
		end
	else
		return ""
		--debug
		--"no claims for "..itemID.." prop "..propertyID
	end
end


-- All modules end by returning the variable containing its functions to Wikipedia.
return p

-- We can now use this module by calling {{#invoke: HelloWorld | hello }}.
-- The #invoke command begins with the module's name, in this case "HelloWorld",
-- then takes the name of one of its functions as an argument, in this case "hello".