imported>Julialturner: added footer

2016-05-25T06:34:14Z

added footer

New page

local p = { }

local navbar = require('Module:Navbar')._navbar
local infobox = require('Module:Infobox3cols').infobox
local infoboxImage = require('Module:InfoboxImage').InfoboxImage

--on a page {{#invoke:Sandbox/genewiki/alllua|getTemplateData|QID=Q14865053}}
--in debug window
--frame = mw.getCurrentFrame()
--frame.args = {QID="Q14865053"} Q18031325
--print(p.getTemplateData(frame))
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"
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, "P279") 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
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
local mouse_itemID = "Q" .. claims[1].mainsnak.datavalue.value["numeric-id"]
mm_qid = mouse_itemID
entity_mouse = mw.wikibase.getEntity(mouse_itemID)
checkOrtholog = 1
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 name = p.getLabel(entity)
local disease, dis_ref = p.getDisease(entity, "P2293")

--define Global Color Scheme
rowBGcolor = '#eee'
titleBGcolor = '#ddd'
sideTitleBGcolor = '#c3fdb8'

p.createTable()
p.renderUpperTitle(name)
if (disease ~= "" and dis_ref ~= "") then --removes section from those items without disease info
p.renderDiseases(disease, dis_ref, root_qid)
end
p.renderFooter()

return tostring(root)

else return "An Error has occurred retrieving Wikidata item for infobox"
end
end

p.createTable = function(subbox)

if subbox == 'sub' then --doesn't work
root
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', 'auto')
:css('min-width', '100%')
:css('font-size', '100%')
:css('clear', 'none')
:css('float', 'none')
:css('background-color', 'transparent')

else
root = mw.html.create('table')
root
:addClass('infobox')
:css('width', '26.4em')
:newline()
end

end

-- look into entity object
p.getLabel = function(entity)
local data = entity

local f = {'labels','en','value'}

local i = 1
while true do
local index = f[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

--Title above image
p.renderUpperTitle = function(name)
local title = name
if not title then return "error: failed to get label"; end

root
:tag('tr')
:tag('th')
:attr('colspan', 4)
:css('text-align', 'center')
:css('font-size', '125%')
:css('font-weight', 'bold')
:wikitext(title)
:newline()
end

p.renderDiseases = function(disease, dis_ref, Qid)
local title = "Genetically Related Diseases"
local disease_title = "Disease Name"
local source_title = "'''References'''"

local ref_flag = {} --check each disease for a reference
local ref_flag_all = "true" --not used in this code

if ref_flag_all == "true" then --header section
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:newline()

:tag('tr') --create title bar
:tag('th')
:attr('colspan', '3')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:done()
:newline()
:tag('tr')
:tag('th')
:css('background-color', sideTitleBGcolor)
:attr('colspan', '2')
:wikitext(disease_title)
:done()
:newline()
:tag('td')
:css('background-color', sideTitleBGcolor)
:attr('colspan', '2')
:wikitext(source_title)
:done()
:newline()
:done()
end
for index,value in ipairs(disease) do --loop through each disease
local i = 0
local ref_collapse = ""
local ref_default = ""
local ref_link = ""
local ref_link_list = {}
--check to see if the reference exists if not provide link to wikidata item to add reference
if (dis_ref[index] == nil or dis_ref[index] == '') then
table.insert(ref_link_list, "[[:d:"..Qid.."#P2293|click to add reference]]")
else
ref_link_list = mw.text.split(dis_ref[index], ",")
end

--if less than 4 don't create collapsible list
if table.getn(ref_link_list) < 5 then
ref_collapse = "none"
else
ref_collapse = "collapsible collapsed"
for i =1, 5 do --get at most 4 elements to display
ref_default = ref_default..table.remove(ref_link_list, 1) .. ' '
end
local br_count = 0
for i =1, table.getn(ref_link_list) do --get at most 4 elements to display
ref_link = ref_link..table.remove(ref_link_list, 1) .. ' '

if br_count < 5 then
br_count = br_count + 1
else
br_count = 0
ref_link = ref_link ..'<br>'
end
end
end

if ref_link_list[#ref_link_list] then
ref_link = table.concat(ref_link_list, " ")
end
root
:tag('tr')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:newline()

:tag('th')
:css('background-color', rowBGcolor)
:attr('scope', 'row')
:attr('colspan', '2')
:wikitext(value)
:done()
:newline()
:tag('td')
:tag('span')
:attr('colspan', '2')

:tag('table')
:attr('class', ref_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:newline()
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(ref_default)
:done()
:done()
:newline()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:newline()
:tag('p')
:attr('class', 'plainlinks')
:wikitext(ref_link)
:newline()
:done()
:done()
:done()
:done()
:newline()
end

end

local function getReference(qID, index, entity, property_id, ref_index)
local f = {"claims",property_id,index,"references",ref_index,"snaks","P854",1,"datavalue","value"}
local id = qID
--if id and (#id == 0) then
-- id = nil
--end
local data = entity
if not data then
return nil
end

local i = 1
while true do
local index = f[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

--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.getDisease= function(entity, propertyID)
local claims
if return_val == nil then return_val = "" end
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 = {}
local datasource = {}
--{{#invoke:Wikidata |ViewSomething |id=Q18023174 |claims|P2293|1|references|1|snaks|P854|1|datavalue|value}}
--maybe there is a more direct way to find this than looping through the json object

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

local id = "Q" .. v.mainsnak.datavalue.value["numeric-id"]
local linkTarget = mw.wikibase.sitelink(id)
local refLink = ""
local i
for i=1,100 do --limits to 100 references displayed
local ref = ""
ref = getReference("", k, entity, "P2293", i)
if (ref ~= nil and ref ~= '') then
refLink = refLink..",["..ref.."]"
--else
-- refLink = "[[:d:"..Qid.."#P2293|click to add reference]]" --link to disease association section to add reference
end
end
--if refLink = "" then --skip if there isn't a reference found
datasource[#out + 1] = refLink
if linkTarget then
out[#out + 1] = "[["..datav.."|"..datav.."]]"
else
out[#out + 1] = "[[:d:" .. id .. "|" .. datav .. "]]"
end
--end
end
return out, datasource
else
-- just return best values
--return entity:formatPropertyValues(propertyID).value
return return_val, return_val
end
else
return return_val
end
return return_val
end

p.renderFooter = function()
local text = "[[Module:Sandbox/genewiki/generefbox|Module:Sandbox/genewiki/generefbox]]"

root
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('font-size','small')
:css('background-color', rowBGcolor)
:wikitext('The alternate rendering for the references can be found at line 252 in this source module ')
:wikitext(text)
:done()
:newline()
:done()

end

return p

Module:Sandbox/genewiki/generefbox - Revision history

imported>Julialturner: added footer