imported>I9606: have julias function working sort of, but can;t see where it tries to keep track of the coordinates.. don't think it does and don't think you can reverse the path the way it looks like she wants to.

2015-10-16T00:08:17Z

have julias function working sort of, but can;t see where it tries to keep track of the coordinates.. don't think it does and don't think you can reverse the path the way it looks like she wants to.

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--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".

Module:Sandbox/genewiki/experimental - Revision history

imported>I9606: have julias function working sort of, but can;t see where it tries to keep track of the coordinates.. don't think it does and don't think you can reverse the path the way it looks like she wants to.