imported>Mensis Mirabilis: ←Created page with '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...'

2018-11-20T14:16:41Z

←Created page with '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...'

New page

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

Module:Sandbox/Mensis Mirabilis/gene - Revision history

imported>Mensis Mirabilis: ←Created page with '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...'