local p = { }

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

local wbr = '​' -- U+200B 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 return("VALUE_ERROR (" .. tostring(val) .. ")") end end --texts relevant to localization are tagged with -- localization required! or ";10n" --on a page 脚本错误:没有“Sandbox/genewiki/alllua”这个模块。 --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 = check_values(p.getLabel,{entity}) local entrez_gene = check_values(p.getValue, {entity, "P351", "n/a"} ) local entrez_gene_mm = check_values(p.getValue, {entity_mouse, "P351", "n/a"}) local image = check_values( p.getImage, {entity, "P18", " ", "250px"}) --need to set size local uniprotID_hs = check_values(p.getValueProtein, {entity_protein, "P352", "n/a"}) local uniprotID_mm = check_values(p.getValueProtein, {entity_mouse_protein, "P352", "n/a"}) local pdbIDs = check_values(p.getPDB, {entity_protein}) --makes a list with links to RCSB; wikitext (l10n) local gene_symbol = check_values(p.getValue, {entity, "P353"}) local aliases = check_values(p.getAliases, {entity, gene_symbol}) -- l10nmod: eliminate early local hgnc_id = check_values(p.getValue, {entity, "P354"}) local homologene_id = check_values(p.getValue, {entity, "P593"}) local omim_id = check_values(p.getValue, {entity, "P492"}) local mgi_id = check_values(p.getValue, {entity_mouse, "P671"}) local ChEMBL_id = check_values(p.getValue, {entity_protein, "P592"}) local IUPHAR_id = check_values(p.getValue, {entity_protein, "P595"}) local ec_no = check_values(p.getValueProtein, {entity_protein, "P591"}) local mol_funct = check_values(p.getGO, {entity_protein, "P680"}) local cell_comp = check_values(p.getGO, {entity_protein, "P681"}) local bio_process = check_values(p.getGO, {entity_protein, "P682"}) local expression_images = check_values(p.getImage, {entity,"P692","

","250px"}) local ensembl = check_values(p.getValue, {entity, "P594", "n/a"}) local ensembl_mm = check_values(p.getValue, {entity_mouse, "P594", "n/a"}) local refseq_mRNA = check_values(p.getRefseq_mRNA, {entity, "P639", "n/a"}) local refseq_mRNA_mm = check_values(p.getRefseq_mRNA, {entity_mouse, "P639", "n/a"}) local refseq_prot = check_values(p.getRefseq_protein, {entity_protein, "P637", "n/a"}) local refseq_prot_mm = check_values(p.getRefseq_protein, {entity_mouse_protein, "P637", "n/a"}) local gstart = check_values(p.getChromosomeLoc, {entity, "P644", "hg"}) local gend = check_values(p.getChromosomeLoc, {entity, "P645", "hg"}) local chr = check_values(p.trimChromosome, {entity}) local db = check_values(p.getAliasFromGenomeAssembly, {entity,"hg"}) local gstart_mm = check_values(p.getChromosomeLoc, {entity_mouse, "P644", "mm"}) local gend_mm = check_values(p.getChromosomeLoc, {entity_mouse, "P645", "mm"}) local db_mm = check_values(p.getAliasFromGenomeAssembly, {entity_mouse,"mm"}) local chr_mm = check_values( p.trimChromosome, {entity_mouse}) local disease, dis_ref = if p.getDisease(entity, "P2293") then disease, dis_ref = p.getDisease(entity, "P2293") else disease, dis_ref = {"VALUE_ERROR","VALUE_ERROR" } end if p.getDrug(entity_protein, "P129") then drug, drug_ref, drug_pqid, drug_pname = p.getDrug(entity_protein, "P129") else drug, drug_ref, drug_pqid, drug_pname = {"VALUE_ERROR","VALUE_ERROR" } end --local drug = check_values(p.getDrug, {entity_protein, "P129"})

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

p.createTable()

   	p.renderUpperTitle(name)
   	--p.renderCaption()
   	p.renderImage(image)
   	p.renderAvailableStructures(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs) --PDB info

p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene) if (disease ~= "" and dis_ref ~= "") then --removes section from those items without disease info p.renderDiseases(frame, disease, dis_ref, name, root_qid) end

if (drug ~= "" ) then --removes section from those items without drug info p.renderDrug(frame,drug, drug_ref, drug_pqid, drug_pname)

   	end

if (mol_funct ~= "" and cell_comp ~= "" and bio_process ~= "") then p.renderGeneOntology(mol_funct, cell_comp, bio_process, uniprotID_hs) end if expression_images ~= "" then p.renderRNAexpression(expression_images, entrez_gene) end p.renderOrthologs(frame, entrez_gene, entrez_gene_mm, ensembl, ensembl_mm, uniprotID_hs, uniprotID_mm, refseq_mRNA, refseq_mRNA_mm, refseq_prot, refseq_prot_mm, db, chr, gstart, gend, db_mm, chr_mm, gstart_mm, gend_mm) p.renderFooter(root_qid, mm_qid)

return tostring(root)

       --return table.concat(drug_pqid)
       

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')
       	-- l10n: zh Module:Infobox
           :css('width', '22em')
           :css('text-align', 'left')
           :css('font-size', 'small')
           :css('line-height', '1.5em')
   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)
               :done() --end th
           :done() --end tr

end

--This is a place holder for the image caption, which is stored in wikicommons comments unsure how to access p.renderCaption = function(entity) --caption end

--gets default image p.renderImage = function(image)

root :tag('tr')

       		:tag('td')
  					:attr('colspan', 4)
           		:css('text-align', 'center')
           		:wikitext(image)
        			:done() --end td
        		:done() --end tr
        		

end


p.renderAvailableStructures = function(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs)

   local title = '已知的结构' -- localization required!
   local pdb_link = "PDB" -- localization required!
   local searchTitle = "" 
   local listTitle = "PDBID列表" -- localization required!
   local PDBe_base = 'https://www.ebi.ac.uk/pdbe/searchResults.html?display=both&term='
   local RCSB_base = 'http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=UpAccessionIdQuery&accessionIdList='
   local url_uniprot = " " 
   
   
   if checkOrtholog == 1 and uniprotID_mm ~= 'n/a' then
   	searchTitle = 'Ortholog search: '
   	url_uniprot = uniprotID_mm..','..uniprotID_hs
   else
   	searchTitle = 'Human UniProt search: '
   	url_uniprot = uniprotID_hs
   end
   local PDBe_list = " " --create a list with " or " if there is more than one uniprot
   --get first uniprot in a list

if url_uniprot:match("([^,]+),") then--first check if there is a list if not just assume one value PDBe_list = string.gsub(url_uniprot, ",", "%%20or%%20") --add or's inststead of commas else PDBe_list = url_uniprot end

   local PDBe = "["..PDBe_base..PDBe_list.." PDBe] "
   local RCSB = "["..RCSB_base..url_uniprot.." RCSB] "
   
   if string.match(pdbIDs, '%w+') then --if there aren't any PDB_ID don't display this part of the infobox
   	--p.formatRow(title)---how to not close the tags is a mystery and I could condense code once I figure out
   	root

:tag('tr')

       		:tag('td')
  					:attr('colspan', 4)
           		:css('text-align', 'center')
           		:css('background-color', rowBGcolor)
           		:tag('table') 
           			:css('padding', '0')
           			:css('border', 'none')
           			:css('margin', '0')
           			:css('width', '100%')
           			:css('text-align', 'left')
           			:tag('tr')    --create title header
           				:tag('th')
           					:attr('colspan', '4')
           					:css('text-align', 'center')
           					:css('background-color',titleBGcolor)
           					:wikitext(title)
           					:done() --end th
           				:done() --end tr
           			
   					:tag('tr')
       					:tag('th')
       						:attr('rowspan', '2')
       						:css('background-color', sideTitleBGcolor)
       						:css('width', '43px')
        						:wikitext(pdb_link)
       						:done() --end th
           				:tag('td')
           					:attr('colspan', '2')
           					:css('background-color', rowBGcolor)
           					:wikitext(searchTitle)
           					:tag('span')
           						:attr('class', 'plainlinks')
           						:wikitext(PDBe)
           						:wikitext(RCSB)
           						:done() --end span
           					:done() --end td
           				:done() --end tr
          		
           			:tag('tr') --new row for collapsible list of PDB codes
           				:tag('td')
           					:tag('table')
           						:attr('class', 'collapsible collapsed')
           						:css('padding', '0')
           						:css('border', 'none')
           						:css('margin', '0')
           						:css('width', '100%')
           						:css('text-align', 'left')
           						:tag('tr')
           							:css('background-color',titleBGcolor)
           							:css('text-align', 'center')
           							:tag('th')
           								:attr('colspan', '2')
           								:wikitext(listTitle)
           								:done() --end th
           							:done() --end tr
           						:tag('tr')
           							:tag('td')
           								:attr('colspan', '2')
           								:css('background-color', rowBGcolor)
           								:tag('p')
           									:tag('span')
           										:attr('class', 'plainlinks')
           										:wikitext(pdbIDs)
           										:done() --end span
           									:done() --end p
           								:done() --end td
           							:done() --end tr
           						:done() --end table
           					:done() --end td
           				:done() --end tr
           			:done() --end table
           		:done() --end td
           	:done() --end tr
   else
   	return ""

end

end

p.renderIdentifiers = function(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene) local title = "识别号" -- localization required! local label_aliases = "别名" -- localization required! local symbol_url if gene_symbol == "" or gene_symbol == nil then symbol_url = "" else if hgnc_id == "" or hgnc_id == nil then symbol_url = gene_symbol

else symbol_url = ""..hgnc_id.." "..gene_symbol.."" end

   end

-- l10n: alias filter removed (pre-done) local label_ext_id = "外部ID" -- localization required!

omim_id = string.gsub(omim_id, "%s", "") local omim_list = mw.text.split(omim_id, ",") local omim = "" if (omim_id ~= nil and omim_id ~= "") then omim = "OMIM"..":" -- localization required! end for i, v in ipairs(omim_list) do if string.match(v, '%w+') then omim = omim..""..v.." "..v..", " end end omim = string.gsub(omim, ", $"," ") --remove comma from end

homologene_id = string.gsub(homologene_id, "%s", "") local homolo_list = mw.text.split(homologene_id, ",") local homolo ="" if (homologene_id ~= nil and homologene_id ~= "") then homolo = "HomoloGene"..":" end for i, v in ipairs(homolo_list) do if string.match(v, '%w+') then homolo = homolo..""..v.." "..v.." " end end homolo = string.gsub(homolo, ", $"," ") --remove comma from end


local genecards = "GeneCards"..":" genecards = genecards..""..gene_symbol.." "..gene_symbol.." "

mgi_id = string.gsub(mgi_id, "%s", "") local mgi_list = mw.text.split(mgi_id, ",") local mgi = "" if (mgi_id ~= nil and mgi_id ~= "") then mgi = "MGI"..":" -- localization required! end for i, v in ipairs(mgi_list) do if string.match(v, '%w+') then local mgi_number = string.sub(mgi_id, 5) mgi = mgi..""..mgi_id.." "..mgi_number.." " end end mgi = string.gsub(mgi, ", $"," ")--remove comma from end

local ChEMBL = "" if string.match(ChEMBL_id, '%w+') then ChEMBL = "ChEMBL"..":"..""..ChEMBL_id.." "..ChEMBL_id.." " end local IUPHAR = "" if string.match(IUPHAR_id, '%w+') then IUPHAR = "IUPHAR"..":"..""..IUPHAR_id.." "..IUPHAR_id.." " -- localization required! end local label_EC = "EC number" -- localization required! ec_no = string.gsub(ec_no, "%d%.%d+%.%d+%.%-,", "")--remove those with"-" in list ec_no = string.gsub(ec_no, "%d%.%d+%.%d+%.%-", "")--remove those with"-" not in list local link_ec_no = string.gsub(ec_no, "," ,"+") --create format for link

local EC = "" .. link_ec_no .. " " .. ec_no .. ""

root :tag('tr')

       	:tag('th')
       		:attr('colspan', '4')
       		:css('text-align', 'center')
       		:css('background-color', titleBGcolor)
        		:wikitext(title)
       		:done() --end th
       	:done() --end tr
       :tag('tr')
       	:tag('th')
       		:attr('scope', 'row')
       		:css('background-color', sideTitleBGcolor)
       		:tag('span')
           		:attr('class', 'plainlinks')
       			:wikitext(label_aliases)
       			:done() --end span
       		:done() --end th
  
       		:tag('td')
       			:attr('colspan','3')
       			:css('background', rowBGcolor)
       			:tag('span')
           		 	:attr('class', 'plainlinks')
       			 	:wikitext(symbol_url)
       				:done() --end span
       			:wikitext(';' .. aliases)
       			:done() --end td
       		:done() --end tr		
        	:done() --end tr
        	
       :tag('tr')
        	:tag('th')
       		:attr('scope', 'row')
       		:css('background-color', sideTitleBGcolor)
        		:wikitext(label_ext_id)
   			:done() --end th
       	:tag('td')
       		:attr('colspan', '3')
       		:css('background-color', rowBGcolor)
       		:tag('span')
           		:attr('class', 'plainlinks')
       			:wikitext(omim)
       			:wikitext(mgi)
       			:wikitext(homolo)
       			:wikitext(ChEMBL)
       			:wikitext(IUPHAR)
       			:wikitext(genecards)
       			:done() --end span
       		 :done() --end td
       	:done() --end tr

if ec_no ~= "" then root

     	:tag('tr')
       	:tag('th')
       		:attr('scope', 'row')
       		:css('background-color', sideTitleBGcolor)
        		:wikitext(label_EC)
       		:done() --end th
       	:tag('td')
       		:attr('colspan', '3')
       		:css('background-color', rowBGcolor)
       		:tag('span')
           		:attr('class', 'plainlinks')
       			:wikitext(EC)
       			:done() --end span

:done() --end td :done() --end tr

   end

end

p.renderDiseases = function(frame, disease, dis_ref, name, qid) local title = "相关疾病" -- localization required!

--check first to see if any of the diseases have references local ref_flag_all = false --check if any disease have references if not then don't render the headers local disease_name = --local disease_name = table.concat(disease, ", ") for index,value in ipairs(disease) do if (dis_ref[index] ~= nil and dis_ref[index] ~= ) then if disease_name == then disease_name = value else disease_name = disease_name..'、'.. wbr..value --l10n end ref_flag_all = true end end

   if ref_flag_all then
   	root

:tag('tr') :tag('td')

  					:attr('colspan', 4)
           		:css('text-align', 'center')
           		:css('background-color', rowBGcolor)

:tag('tr') --create title bar :tag('th') :attr('colspan', '3') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :done() --end th :done() --end tr :done() --end td :done() --end tr


local ref_url = "https://www.wikidata.org/wiki/"..qid.."#P2293" --direct page to property genetically associated disease local title = "与"..name.."相关的疾病;在维基数据上查看/编辑参考" local ref_link = disease_name..frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title = title, url = ref_url} })

root :tag('tr') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor) :tag('td') :css('background-color', rowBGcolor) :attr('scope', 'row') :attr('colspan', '3') :wikitext(ref_link) :done() --end td :done() --end tr

   end			
   

end


p.renderDrug = function(frame,drug, drug_ref, drug_pqid, drug_pname) local title = "为以下药物的标靶" --**lzlc**

   --check first to see if any of the drugs have references

local ref_flag_all = false --check if any drugs have references if not then don't render the headers drug_list_per_protein = {} -- a list of lists of drugs to put in reference string each protein will have a list --for i,v in ipairs(drug_pqid) do -- set all lists keys to empty so can append without key errors

--end for index,value in ipairs(drug) do if (drug_ref[index] ~= nil and drug_ref[index] ~= ) then protein_qid = drug_pqid[index] if drug_list_per_protein[protein_qid] == or drug_list_per_protein[protein_qid] == nil then drug_list_per_protein[protein_qid] = value else -- localization required! (punct) drug_list_per_protein[protein_qid] = drug_list_per_protein[protein_qid]..'、'.. wbr ..value --each list of drugs keyed on protein qid end ref_flag_all = true end end

   if ref_flag_all then
   	root

:tag('tr') :tag('td')

  					:attr('colspan', 4)
           		:css('text-align', 'center')
           		:css('background-color', rowBGcolor)

:tag('tr') --create title bar :tag('th') :attr('colspan', '3') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :done() --end th :done() --end tr :done() --end td :done() --end tr

   	--loop to create reference links from drug lists
   	for k,v in pairs(drug_list_per_protein) do
       	local drug_name = v

local ref_url = "https://www.wikidata.org/wiki/"..k.."#P129" --direct page to property genetically associated disease

       	local title = "對"..drug_pname[k].."起作用的藥物;在維基數據上查看/編輯參考"

local ref_link = drug_name..frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title = title, url = ref_url} })

root :tag('tr')

  					:attr('colspan', 4)
           		:css('text-align', 'center')
           		:css('background-color', rowBGcolor)

:tag('td') :css('background-color', rowBGcolor) :attr('scope', 'row') :attr('colspan', '3') :wikitext(ref_link) :done() --end td :done() --end tr

       end
   end
   

end

p.renderGeneOntology = function(mol_funct, cell_comp, bio_process, uniprotID) local title = "基因本体" -- localization required! local mol_funct_title = "分子功能" -- localization required! local cell_comp_title = "细胞组分" -- localization required! local bio_process_title = "生物学过程" -- localization required! local amigo_link = "" .. " Amigo" local quickGO_link = "" .. " QuickGO"


root :tag('tr')

       	:tag('td')
  				:attr('colspan', 4)
           	:css('text-align', 'center')
           	:css('background-color', rowBGcolor)
           	:tag('table')
           		:attr('class', 'collapsible collapsed')
           		:css('padding', '0')
           		:css('border', 'none')
           		:css('margin', '0')
           		:css('width', '100%')
           		:css('text-align', 'left')
           		:tag('tr') --create title bar
       				:tag('th')
       					:attr('colspan', '4')
       					:css('text-align', 'center')
       					:css('background-color', titleBGcolor)
        					:wikitext(title)
       					:done() --end th
       				:done() --end tr
       			:tag('tr')
           			:tag('th')
           				:css('background-color', sideTitleBGcolor)
           				:wikitext(mol_funct_title)
           				:done() --end th
           			:tag('td')
           				:css('background-color', rowBGcolor)
           				:tag('span')
           					:attr('class', 'plainlinks')
           					:wikitext(mol_funct)
           					:done() --end span
           				:done() --end td
          				:done() --end tr
       			:tag('tr')
       				:tag('th')
           				:css('background-color', sideTitleBGcolor)
           				:wikitext(cell_comp_title)
           				:done() --end th
           			:tag('td')
           				:css('background-color', rowBGcolor)
           				:tag('span')
           					:attr('class', 'plainlinks')
           					:wikitext(cell_comp)
           					:done() --end span
           				:done() --end td
           			:done() --end tr
       			:tag('tr')
       				:tag('th')
           				:css('background-color', sideTitleBGcolor)
           				:wikitext(bio_process_title)
           				:done() --end th
           			:tag('td')
           				:css('background-color', rowBGcolor)
           				:tag('span')
           					:attr('class', 'plainlinks')
           					:wikitext(bio_process)
           					:done() --end span
           				:done() --end td
           			:done() --end tr
       			:tag('tr')
           			:tag('td')
           				:css('background-color', rowBGcolor)
           				:css('text-align', 'center')
           				:attr('colspan', '4')
           				:wikitext("Sources:")
           				:wikitext(amigo_link)
           				:wikitext(" / ")
           				:wikitext(quickGO_link)
           				:done() --end td
      					:done() --end tr

:done() --end table :done() --end td :done() --end tr end

p.renderRNAexpression = function(expression_images, entrez_gene) local title = "RNA表达模式" -- localization required! -- ^^^ zhnote: one-way NoteTA local biogps_link = ""..entrez_gene.."/ 更多参考(基因)表达数据" -- localization required! root :tag('tr')

       	:tag('th')
       		:attr('colspan', '4')
       		:css('text-align', 'center')
       		:css('background-color', titleBGcolor)
        		:wikitext(title)
       		:done() --end th
       	:done() --end tr
       :tag('tr')
       	:tag('td')
       		:attr('colspan', '4')
       		:css('text-align', 'center')
       		:css('background-color', rowBGcolor)
       		:wikitext(expression_images)
       		:done() --end td
       	:done() --end tr
       :tag('tr')
       	:tag('td')
       		:attr('colspan', '4')
       		:css('text-align', 'center')
       		:css('background-color', rowBGcolor)
       		:tag('span')
           		:attr('class', 'plainlinks')
       			:wikitext(biogps_link)
       			:done() --end span
       		:done() --end td
           :done() --end tr

end

p.renderOrthologs = function(frame, entrez_gene, entrez_gene_mm, ensembl, ensembl_mm, uniprot, uniprot_mm, refseq_mRNA, refseq_mRNA_mm, refseq_prot, refseq_prot_mm, db, chr, gstart, gend, db_mm, chr_mm,gstart_mm, gend_mm) local title = "直系同源" -- localization required! --to do make the list creation a function --create list for entrez ids

-- Special Cases for zh local category_chromosome_special = { ['X']=, ['Y']=, ['M']=, -- 不知道有没有用 } local category_chromosome = category_chromosome_special[chr] or if mw.title.getCurrentTitle().namespace ~= 0 then category_chromosome = "" end local entrezTitle = "Entrez" entrez_gene = string.gsub(entrez_gene, "%s", "") local entrez_link = "n/a" local entrez_collapse local entrez_default = "" local split_entrez = mw.text.split(entrez_gene, ",") local entrez_link_list = {} for k,v in ipairs(split_entrez) do if string.match(v, '%w+') and v ~= "n/a" then entrez_link_list[#entrez_link_list+1] = ""..entrez_gene.."&rn=1 "..entrez_gene.."" end end --if less than 5 don't create collapsible list if table.getn(entrez_link_list) < 5 then entrez_collapse = "none" if entrez_default == nil and table.getn(entrez_link_list) == 0 then entrez_link = "n/a" end else entrez_collapse = "collapsible collapsed" entrez_default = table.remove(entrez_link_list, 1) .. '
' .. table.remove(entrez_link_list, 1) .. '
' ..table.remove(entrez_link_list, 1) .. '
' .. table.remove(entrez_link_list, 1) .. '
' .. table.remove(entrez_link_list, 1) .. '
'--get first 5 elements in table and use for display end if entrez_link_list[#entrez_link_list] then entrez_link = table.concat(entrez_link_list, "
") end

--create list for mouse Entrez id entrez_gene_mm = string.gsub(entrez_gene_mm, "%s", "") local entrez_mm_link = "n/a" local entrez_mm_collapse local entrez_mm_default = "" local split_entrez_mm = mw.text.split(entrez_gene_mm, ",") local entrez_mm_link_list = {} for k,v in ipairs(split_entrez_mm) do if string.match(v, '%w+') and v ~= "n/a" then entrez_mm_link_list[#entrez_mm_link_list+1] = ""..v.."&rn=1 "..v.."" end end --if less than 5 don't create collapsible list if table.getn(entrez_mm_link_list) < 5 then entrez_mm_collapse = "none" if entrez_mm_default == nil and table.getn(entrez_mm_link_list) == 0 then entrez_mm_link = "n/a" end else entrez_mm_collapse = "collapsible collapsed" entrez_mm_default = table.remove(entrez_mm_link_list, 1) .. '
' .. table.remove(entrez_mm_link_list, 1) .. '
' ..table.remove(entrez_mm_link_list, 1) .. '
' .. table.remove(entrez_mm_link_list, 1) .. '
' .. table.remove(entrez_mm_link_list, 1) .. '
'--get first 5 elements in table and use for display end if entrez_mm_link_list[#entrez_mm_link_list] then entrez_mm_link = table.concat(entrez_mm_link_list, "
") end

--create list of ensembl id local ensemblTitle = "Ensembl" ensembl = string.gsub(ensembl, "%s", "") local ensembl_link = "n/a" local ensembl_collapse local ensembl_default = "" local split_ensembl = mw.text.split(ensembl, ",") local ensembl_link_list = {} for k,v in ipairs(split_ensembl) do if string.match(v, '%w+') and v ~= "n/a" then ensembl_link_list[#ensembl_link_list+1] = ""..v..";db=core".." "..v.."" end end --if less than 5 don't create collapsible list if table.getn(ensembl_link_list) < 5 then ensembl_collapse = "none" if ensembl_default == nil and table.getn(ensembl_link_list) == 0 then ensembl_link = "n/a" end else ensembl_collapse = "collapsible collapsed" ensembl_default = table.remove(ensembl_link_list, 1) .. '
' .. table.remove(ensembl_link_list, 1) .. '
' ..table.remove(ensembl_link_list, 1) .. '
' .. table.remove(ensembl_link_list, 1) .. '
' .. table.remove(ensembl_link_list, 1) .. '
'--get first 5 elements in table and use for display end if ensembl_link_list[#ensembl_link_list] then ensembl_link = table.concat(ensembl_link_list, "
") end

--create list of mouse ensembl id local ensemblTitle = "Ensembl" ensembl_mm = string.gsub(ensembl_mm, "%s", "") local ensembl_mm_link = "n/a" local ensembl_mm_collapse local ensembl_mm_default = "" local split_ensembl_mm = mw.text.split(ensembl_mm, ",") local ensembl_mm_link_list = {} for k,v in ipairs(split_ensembl_mm) do if string.match(v, '%w+') and v ~= "n/a" then ensembl_mm_link_list[#ensembl_mm_link_list+1] = ""..v..";db=core".." "..v.."" end end --if less than 5 don't create collapsible list if table.getn(ensembl_mm_link_list) < 5 then ensembl_mm_collapse = "none" if ensembl_mm_default == nil and table.getn(ensembl_mm_link_list) == 0 then ensembl_mm_link = "n/a" end else ensembl_mm_collapse = "collapsible collapsed" ensembl_mm_default = table.remove(ensembl_mm_link_list, 1) .. '
' .. table.remove(ensembl_mm_link_list, 1) .. '
' ..table.remove(ensembl_mm_link_list, 1) .. '
' .. table.remove(ensembl_mm_link_list, 1) .. '
' .. table.remove(ensembl_mm_link_list, 1) .. '
'--get first 5 elements in table and use for display end if ensembl_mm_link_list[#ensembl_mm_link_list] then ensembl_mm_link = table.concat(ensembl_mm_link_list, "
") end


--create lists of uniprot ID local uniprotTitle = "UniProt" local uniprot_url = "http://www.uniprot.org/uniprot/"

local uniprot_link = "n/a" local uniprot_collapse local uniprot_default = "" --split string and loop through concatenate by
local split_uniprot = mw.text.split(uniprot, ",") local uniprot_link_list = {} local uniprot_first = {} --preferred values only display [O,P,Q] prefixed entries if they exist local uniprot_alternate = {} --[A-N,R-Z] entries local hash = {} --storage to look for duplicated values for k,v in ipairs(split_uniprot) do if not hash[v] then --only add if not found previously..some encodes uniprotID dup in different encodes local label = mw.text.trim(v) local concat_uniprot_link = uniprot_url .. label if string.match(v, '%w+') and v ~= "n/a" then if string.match(v, '^O') or string.match(v,'^P') or string.match(v, '^Q') then uniprot_first[#uniprot_first+1] = "[" .. concat_uniprot_link .. " " ..label .. "]" else uniprot_alternate[#uniprot_alternate+1] = "[" .. concat_uniprot_link .. " " ..label .. "]" end end hash[v] = true end end

   if table.getn(uniprot_first)>0 then --if there is something in the preferred values display else display anything else

uniprot_link_list = uniprot_first else uniprot_link_list = uniprot_alternate end

--if less than 5 don't create collapsible list if table.getn(uniprot_link_list) < 5 then uniprot_collapse = "none" if uniprot_default == nil and table.getn(uniprot_link_list) == 0 then uniprot_link = "n/a" end else uniprot_collapse = "collapsible collapsed" uniprot_default = table.remove(uniprot_link_list, 1) .. '
' .. table.remove(uniprot_link_list, 1) .. '
' ..table.remove(uniprot_link_list, 1) .. '
' .. table.remove(uniprot_link_list, 1) .. '
' .. table.remove(uniprot_link_list, 1) .. '
'--get first 5 elements in table and use for display end

if uniprot_link_list[#uniprot_link_list] then uniprot_link = table.concat(uniprot_link_list, "
") end

   --mouse uniprot lists

local uniprot_mm_link = "n/a" local uniprot_mm_collapse local uniprot_mm_default = "" --split string and loop through concatenate by
local split_uniprot_mm = mw.text.split(uniprot_mm, ",")

   local uniprot_mm_link_list = {}	
   local uniprot_mm_first = {} --preferred values only display [O,P,Q] prefixed entries if they exist
   local uniprot_mm_alternate = {} --[A-N,R-Z] entries
   local hash = {} --storage to look for duplicated values

for k,v in ipairs(split_uniprot_mm) do if not hash[v] then --only add if not found previously..some encodes uniprotID dup in different encodes local label = mw.text.trim(v) local concat_uniprot_link = uniprot_url .. label if string.match(v, '%w+') and v ~= "n/a" then if string.match(v, '^O') or string.match(v,'^P') or string.match(v, '^Q') then uniprot_mm_first[#uniprot_mm_first+1] = "[" .. concat_uniprot_link .. " " ..label .. "]" else uniprot_mm_alternate[#uniprot_mm_alternate+1] = "[" .. concat_uniprot_link .. " " ..label .. "]" end end hash[v] = true end end if table.getn(uniprot_mm_first)>0 then --if there is something in the preferred values display else display anything else uniprot_mm_link_list = uniprot_mm_first else uniprot_mm_link_list = uniprot_mm_alternate end

--if less than 5 don't create collapsible list if table.getn(uniprot_mm_link_list) < 5 then uniprot__mm_collapse = "none" if uniprot_mm_default == nil and table.getn(uniprot_mm_link_list) == 0 then uniprot_mm_link = "n/a" end else uniprot_mm_collapse = "collapsible collapsed" uniprot_mm_default = table.remove(uniprot_mm_link_list, 1) .. '
' .. table.remove(uniprot_mm_link_list, 1) .. '
' ..table.remove(uniprot_mm_link_list, 1) .. '
' .. table.remove(uniprot_mm_link_list, 1) .. '
' .. table.remove(uniprot_mm_link_list, 1) .. '
'--get first 5 elements in table and use for display end

if uniprot_mm_link_list[#uniprot_mm_link_list] then uniprot_mm_link = table.concat(uniprot_mm_link_list, "
") end


-- l10n: tentative:PBB old title local ncbi_link = "https://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=" local refseq_mRNATitle = "mRNA" .. wbr .. "序列"

--create list of links for refSeq mRNA local refseq_mRNA_link = "n/a" local refseq_mRNA_collapse local refseq_mRNA_default = "" --split string and loop through concatenate by
local split_refseq_mRNA = mw.text.split(refseq_mRNA, ",") local link_list_first = {} --hold those the have NM or NP values local link_list_alternate = {} --hold those that are XM or XP values local link_list = {} --if NM,NP display if not display XM, XP values for k,v in ipairs(split_refseq_mRNA) do local label = mw.text.trim(v) local concat_ncbi_link = ncbi_link .. label if string.match(v, '%w+') and v ~= "n/a" then if string.match(v, 'NM') or string.match(v, 'NP') then link_list_first[#link_list_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]" elseif string.match(v, 'XM') or string.match(v, 'XP') then link_list_alternate[#link_list_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]" end end

  end
  	if table.getn(link_list_first)>0 then

link_list = link_list_first else link_list = link_list_alternate end

--if less than 5 don't create collapsible list if table.getn(link_list) < 6 then refseq_mRNA_collapse = "none" if refseq_mRNA_default == nil and table.getn(link_list) == 0 then refseq_mRNA_link = "n/a" end else refseq_mRNA_collapse = "collapsible collapsed" refseq_mRNA_default = table.remove(link_list, 1) .. '
' .. table.remove(link_list, 1) .. '
' ..table.remove(link_list, 1) .. '
' .. table.remove(link_list, 1) .. '
' .. table.remove(link_list, 1) .. '
'--get first 5 elements in table and use for display end

if link_list[#link_list] then refseq_mRNA_link = table.concat(link_list, "
") end


--create list of links for refSeq mRNA for mouse local refseq_mRNA_mm_link = "n/a" local refseq_mRNA_mm_collapse local refseq_mRNA_mm_default = "" local split_refseq_mRNA_mm = mw.text.split(refseq_mRNA_mm, ",") local link_list_mm = {} --if NM,NP display if not display XM, XP values local link_list_first = {} --hold those the have NM or NP values local link_list_alternate = {} --hold those that are XM or XP values

for k,v in ipairs(split_refseq_mRNA_mm) do local label = mw.text.trim(v) local concat_ncbi_link = ncbi_link .. label if string.match(v, '%w+') and v ~= "n/a" then if string.match(v, 'NM') or string.match(v, 'NP') then link_list_first[#link_list_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]" elseif string.match(v, 'XM') or string.match(v, 'XP') then link_list_alternate[#link_list_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]" end end

   end

if table.getn(link_list_first)>0 then link_list_mm = link_list_first else link_list_mm = link_list_alternate end --if less than 5 don't create collapsible list if table.getn(link_list_mm) < 6 then refseq_mRNA_mm_collapse = "none" if refseq_mRNA_mm_default == nil and table.getn(link_list_mm) == 0 then refseq_mRNA_mm_link = "n/a" end else refseq_mRNA_mm_collapse = "collapsible collapsed" refseq_mRNA_mm_default = table.remove(link_list_mm, 1) .. '
' .. table.remove(link_list_mm, 1) .. '
' ..table.remove(link_list_mm, 1) .. '
' .. table.remove(link_list_mm, 1) .. '
' .. table.remove(link_list_mm, 1) .. '
'--get first 5 elements in table and use for display end

if link_list_mm[#link_list_mm] then refseq_mRNA_mm_link = table.concat(link_list_mm, "
") end


-- l10n: tentative; old box local refseq_protTitle = "蛋白序列" --create list of links for human refseq protein local refseq_prot_link = "n/a" local refseq_prot_collapse local refseq_prot_default = "" local split_refseq_prot = mw.text.split(refseq_prot, ",") local link_list_prot = {}

   local link_list_first = {} --hold those the have NM or NP values

local link_list_alternate = {} --hold those that are XM or XP values for k,v in ipairs(split_refseq_prot) do local label = mw.text.trim(v) local concat_ncbi_link = ncbi_link .. label if string.match(v, '%w+') and v ~= "n/a" then if string.match(v, 'NM') or string.match(v, 'NP') then link_list_first[#link_list_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]" elseif string.match(v, 'XM') or string.match(v, 'XP') then link_list_alternate[#link_list_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]" end end end if table.getn(link_list_first)>0 then link_list_prot = link_list_first else link_list_prot = link_list_alternate end --if less than 5 don't create collapsible list if table.getn(link_list_prot) < 6 then refseq_prot_collapse = "none" if refseq_prot_default == nil and table.getn(link_list_prot) == 0 then refseq_prot_link = "n/a" end else refseq_prot_collapse = "collapsible collapsed" refseq_prot_default = table.remove(link_list_prot, 1) .. '
' .. table.remove(link_list_prot, 1) .. '
' ..table.remove(link_list_prot, 1) .. '
' .. table.remove(link_list_prot, 1) .. '
' .. table.remove(link_list_prot, 1) .. '
'--get first 5 elements in table and use for display end


if link_list_prot[#link_list_prot] then refseq_prot_link = table.concat(link_list_prot, "
") end


--create list of links for mouse refseq protein local refseq_prot_mm_link = "n/a" local refseq_prot_mm_collapse local refseq_prot_mm_default = "" local split_refseq_prot_mm = mw.text.split(refseq_prot_mm, ",") local link_list_prot_mm = {} local link_list_first = {} --hold those the have NM or NP values local link_list_alternate = {} --hold those that are XM or XP values

for k,v in ipairs(split_refseq_prot_mm) do local label = mw.text.trim(v) local concat_ncbi_link = ncbi_link .. label if string.match(v, '%w+') and v ~= "n/a" then if string.match(v, 'NM') or string.match(v, 'NP') then link_list_first[#link_list_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]" elseif string.match(v, 'XM') or string.match(v, 'XP') then link_list_alternate[#link_list_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]" end end end if table.getn(link_list_first)>0 then link_list_prot_mm = link_list_first else link_list_prot_mm = link_list_alternate end --if less than 5 don't create collapsible list if table.getn(link_list_prot_mm) < 6 then refseq_prot_mm_collapse = "none" if refseq_prot_mm_default == nil and table.getn(link_list_prot_mm) == 0 then refseq_prot_mm_link = "n/a" end else refseq_prot_mm_collapse = "collapsible collapsed" refseq_prot_mm_default = table.remove(link_list_prot_mm, 1) .. '
' .. table.remove(link_list_prot_mm, 1) .. '
' ..table.remove(link_list_prot_mm, 1) .. '
' .. table.remove(link_list_prot_mm, 1) .. '
' .. table.remove(link_list_prot_mm, 1) .. '
'--get first 5 elements in table and use for display end if link_list_prot_mm[#link_list_prot_mm] then refseq_prot_mm_link = table.concat(link_list_prot_mm, "
") end

   -- l10n: tentative 

local locTitle = "基因位置" .. wbr .. "(UCSC)" local gstart_mb = p.locToMb(gstart, 2) local gend_mb = p.locToMb(gend, 2) local chr_loc_link = "" if (string.match(db, '%w+') and string.match(chr, '%w+') and string.match(gstart, '%w+') and string.match(gend, '%w+') )then chr_loc_link = ""..db.."&position=chr"..chr..":"..gstart.."-"..gend.." ".."Chr "..chr..": "..gstart_mb.." – "..gend_mb.." Mb" else chr_loc_link = "n/a" end local gstart_mm_mb = p.locToMb(gstart_mm, 2) local gend_mm_mb = p.locToMb(gend_mm, 2) local chr_loc_mm_link = "" if (string.match(db_mm, '%w+') and string.match(chr_mm, '%w+') and string.match(gstart_mm, '%w+') and string.match(gend_mm, '%w+') )then chr_loc_mm_link = ""..db_mm.."&position=chr"..chr_mm..":"..gstart_mm.."-"..gend_mm.." ".."Chr "..chr_mm..": "..gstart_mm_mb.." – "..gend_mm_mb.." Mb" else chr_loc_mm_link = "n/a" end

-- l10n local pubmedTitle = "PubMed" .. wbr .. "查找" local pubmed_link = entrez_gene if string.match(entrez_gene, '%w+') and entrez_gene ~= "n/a" then pubmed_link = frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title ="Human PubMed Reference:" , url = "https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene } } )--expandTemplate creates cite web template [ref_link..ect value] 请检查|url=值 (帮助).  end local pubmed_mm_link = entrez_gene_mm if string.match(entrez_gene_mm, '%w+') and entrez_gene_mm ~= "n/a" then pubmed_mm_link = frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title ="Mouse PubMed Reference:" , url ="https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene_mm } } )--expandTemplate creates cite web template [ref_link..ect value] 请检查|url=值 (帮助).  end

root :tag('tr')

       	:tag('th')
       		:attr('colspan', '4')
       		:css('text-align', 'center')
       		:css('background-color', titleBGcolor)
        		:wikitext(title)
       		:done() --end th
       	:done() --end tr
       :tag('tr')
       	:tag('th')
       		:attr('scope', 'row')
       		:css('background-color', sideTitleBGcolor)
       		:wikitext("物種") -- localization required!
       		:done() --end th
       	:tag('td')
       		:wikitext("人類") -- localization required!
       		:done() --end td
       	:tag('td')
       		:wikitext("小鼠") -- localization required!

-- note: Mus musculus

       		:done() --end td
       	:done() --end tr
       :tag('tr')
       	:tag('th')
       		:attr('scope', 'row')
       		:css('background-color', sideTitleBGcolor)
       		:wikitext(entrezTitle)
       		:done() --end th
       	:tag('td')
       		:tag('table')
           		:attr('class', entrez_collapse)
           		:css('padding', '0')
           		:css('border', 'none')
           		:css('margin', '0')
           		:css('width', '100%')
           		:css('text-align', 'right')
           		:tag('tr')
           			:tag('th')
           				:attr('colspan', '1')
           				:tag('span')
           					:attr('class', 'plainlinks')
           					:wikitext(entrez_default)
           					:done() --end span
           				:done() --end th
           			:done() --end tr
           		:tag('tr')
           			:tag('td')
           				:attr('colspan', '1')
           				:tag('p')
           					:attr('class', 'plainlinks')
           					:wikitext(entrez_link)
           					:done() --end p
           				:done() --end td
           			:done() --end tr
           		:done() --end table
           	:done() --end td

:tag('td')

       		:tag('table')
           		:attr('class', entrez_mm_collapse)
           		:css('padding', '0')
           		:css('border', 'none')
           		:css('margin', '0')
           		:css('width', '100%')
           		:css('text-align', 'right')
           		:tag('tr')
           			:tag('th')
           				:attr('colspan', '1')
           				:tag('span')
           					:attr('class', 'plainlinks')
           					:wikitext(entrez_mm_default)
           					:done() --end span
           				:done() --end th
           			:done() --end tr
           		:tag('tr')
           			:tag('td')
           				:attr('colspan', '1')
           				:tag('p')
           					:attr('class', 'plainlinks')
           					:wikitext(entrez_mm_link)
           					:done() --end p
           				:done() --end td
           			:done() --end tr
           		:done() --end table
           	:done() --end td
           :done() --end tr
       :tag('tr')
       	:tag('th')
       		:attr('scope', 'row')
       		:css('background-color', sideTitleBGcolor)
       		:wikitext(ensemblTitle)
       		:done() --end th
       	:tag('td')
       		:tag('table')
           		:attr('class', ensembl_collapse)
           		:css('padding', '0')
           		:css('border', 'none')
           		:css('margin', '0')
           		:css('width', '100%')
           		:css('text-align', 'right')
           		:tag('tr')
           			:tag('th')
           				:attr('colspan', '1')
           				:tag('span')
           					:attr('class', 'plainlinks')
           					:wikitext(ensembl_default)
           					:done() --end span
           				:done() --end th
           			:done() --end tr
           		:tag('tr')
           			:tag('td')
           				:attr('colspan', '1')
           				:tag('p')
           					:attr('class', 'plainlinks')
           					:wikitext(ensembl_link)
           					:done() --end p
           				:done() --end td
           			:done() --end tr
           		:done() --end table
           	:done() --end td

:tag('td')

       		:tag('table')
           		:attr('class', ensembl_mm_collapse)
           		:css('padding', '0')
           		:css('border', 'none')
           		:css('margin', '0')
           		:css('width', '100%')
           		:css('text-align', 'right')
           		:tag('tr')
           			:tag('th')
           				:attr('colspan', '1')
           				:tag('span')
           					:attr('class', 'plainlinks')
           					:wikitext(ensembl_mm_default)
           					:done() --end span
           				:done() --end th
           			:done() --end tr
           		:tag('tr')
           			:tag('td')
           				:attr('colspan', '1')
           				:tag('p')
           					:attr('class', 'plainlinks')
           					:wikitext(ensembl_mm_link)
           					:done() --end p
           				:done() --end td
           			:done() --end tr
           		:done() --end table
           	:done() --end td
           :done() --end tr
       :tag('tr')
       	:tag('th')
       		:attr('scope', 'row')
       		:css('background-color', sideTitleBGcolor)
       		:wikitext(uniprotTitle)
       		:done() --end th
       	:tag('td')
       		:tag('table')
           		:attr('class', uniprot_collapse)
           		:css('padding', '0')
           		:css('border', 'none')
           		:css('margin', '0')
           		:css('width', '100%')
           		:css('text-align', 'right')
           		:tag('tr')
           			:tag('th')
           				:attr('colspan', '1')
           				:tag('span')
           					:attr('class', 'plainlinks')
           					:wikitext(uniprot_default)
           					:done() --end span
           				:done() --end th
           			:done() --end tr
           		:tag('tr')
           			:tag('td')
           				:attr('colspan', '1')
           				:tag('p')
           					:attr('class', 'plainlinks')
           					:wikitext(uniprot_link)
           					:done() --end p
           				:done() --end td
           			:done() --end tr
           		:done() --end table
           	:done() --end td
       	:tag('td')
       		:tag('table')
           		:attr('class', uniprot_mm_collapse)
           		:css('padding', '0')
           		:css('border', 'none')
           		:css('margin', '0')
           		:css('width', '100%')
           		:css('text-align', 'right')
           		:tag('tr')
           			:tag('th')
           				:attr('colspan', '1')
           				:tag('span')
           					:attr('class', 'plainlinks')
           					:wikitext(uniprot_mm_default)
           					:done() --end span
           				:done() --end th
           			:done() --end th
           		:tag('tr')
           			:tag('td')
           				:attr('colspan', '1')
           				:tag('p')
           					:attr('class', 'plainlinks')
           					:wikitext(uniprot_mm_link)
           					:done() --end p
           				:done() --end td
           			:done() --end tr
           		:done() --end table
       		:done() --end td
       	:done() --end tr
       :tag('tr')
       	:tag('th')
       		:attr('scope', 'row')
       		:css('background-color', sideTitleBGcolor)
       		:wikitext(refseq_mRNATitle)
       		:done() --end th
       	:tag('td') --RNASeq mRNA collapsible table 
       		:tag('table')
           		:attr('class', refseq_mRNA_collapse)
           		:css('padding', '0')
           		:css('border', 'none')
           		:css('margin', '0')
           		:css('width', '100%')
           		:css('text-align', 'right')
           		:tag('tr')
           			:tag('th')
           				:attr('colspan', '1')
           				:attr('class', 'plainlinks')
           				:wikitext(refseq_mRNA_default)
           				:done() --end th
           			:done() --end tr
           		:tag('tr')
           			:tag('td')
           				:attr('colspan', '1')
           				:tag('p')
           					:tag('span')
           						:attr('class', 'plainlinks')
           						:wikitext(refseq_mRNA_link)
           						:done() --end span
           					:done() --end p
           				:done() --end td
           			:done() --end tr
           		:done() --end table
           	:done() --end td	
       	:tag('td') --RNASeq mRNA collapsible table for mouse 
       		:tag('table')
           		:attr('class', refseq_mRNA_mm_collapse)
           		:css('padding', '0')
           		:css('border', 'none')
           		:css('margin', '0')
           		:css('width', '100%')
           		:css('text-align', 'right')
           		:tag('tr')
           			:tag('th')
           				:attr('colspan', '1')
           				:attr('class', 'plainlinks')
           				:wikitext(refseq_mRNA_mm_default)
           				:done() --end th
           			:done() --end tr
           		:tag('tr')
           			:tag('td')
           				:attr('colspan', '1')
           				:tag('p')
           					:tag('span')
           						:attr('class', 'plainlinks')
           						:wikitext(refseq_mRNA_mm_link)
           						:done() --end span
           					:done() --end p
           				:done() --end td
           			:done() --end tr
           		:done() --end table	
       		:done() --end td
       	:done() --end tr
       :tag('tr')
       	:tag('th')
       		:attr('scope', 'row')
       		:css('background-color', sideTitleBGcolor)
       		:wikitext(refseq_protTitle)
       		:done() --end th
       	:tag('td') --RNASeq protein collapsible table 
       		:tag('table')
           		:attr('class', refseq_prot_collapse)
           		:css('padding', '0')
           		:css('border', 'none')
           		:css('margin', '0')
           		:css('width', '100%')
           		:css('text-align', 'right')
           		:tag('tr')
           			:tag('th')
           				:attr('colspan', '1')
           				:attr('class', 'plainlinks')
           				:wikitext(refseq_prot_default)
           				:done() --end th
           			:done() --end tr
           		:tag('tr')
           			:tag('td')
           				:attr('colspan', '1')
           				:tag('p')
           					:tag('span')
           						:attr('class', 'plainlinks')
           						:wikitext(refseq_prot_link)
           						:done() --end span
           					:done() --end p
           				:done() --end td
           			:done() --end tr
           		:done() --end table
           	:done() --end td	

:tag('td') --RNASeq protein collapsible table for mouse

       		:tag('table')
           		:attr('class', refseq_prot_mm_collapse)
           		:css('padding', '0')
           		:css('border', 'none')
           		:css('margin', '0')
           		:css('width', '100%')
           		:css('text-align', 'right')
           		:tag('tr')
           			:tag('th')
           				:attr('colspan', '1')
           				:attr('class', 'plainlinks')
           				:wikitext(refseq_prot_mm_default)
           				:done() --end th
           			:done() --end tr
           		:tag('tr')
           			:tag('td')
           				:attr('colspan', '1')
           				:tag('p')
           					:tag('span')
           						:attr('class', 'plainlinks')
           						:wikitext(refseq_prot_mm_link)
           						:done() --end span
           					:done() --end p
           				:done() --end td
           			:done() --end tr
           		:done() --end table
           	:done() --end td
   		:done() --end tr
       :tag('tr')
       	:tag('th')
       		:attr('scope', 'row')
       		:css('background-color', sideTitleBGcolor)
       		:wikitext(locTitle)
       		:done() --end th
       	:tag('td')
       		:tag('span')
           		:attr('class', 'plainlinks')
       			:wikitext(chr_loc_link)
       			:done() --end span
       		:done() --end td
       	:tag('td')
       		:tag('span')
           		:attr('class', 'plainlinks')
       			:wikitext(chr_loc_mm_link)
       			:done() --end span
       		:done() --end td
       	:done() --end tr
       :tag('tr')
       	:tag('th')
       		:attr('scope', 'row')
       		:css('background-color', sideTitleBGcolor)
       		:wikitext(pubmedTitle)
       		:done() --end th
       	:tag('td')
       		:tag('span')
           		:attr('class', 'plainlinks')
       			:wikitext(pubmed_link)
       			:done() --end span
       		:done() --end td
       	:tag('td')
       		:tag('span')
           		:attr('class', 'plainlinks')
       			:wikitext(pubmed_mm_link)
       			:done() --end span
       		:wikitext(category_chromosome)
       		:done() --end td
   		:done() --end tr

end

p.formatRow = function(title) root :tag('tr')

       	:tag('td')
  				:attr('colspan', '4')
           	:css('text-align', 'center')
           	:css('background-color', rowBGcolor)
           	:tag('table') 
           		:css('padding', '0')
           		:css('border', 'none')
           		:css('margin', '0')
           		:css('width', '100%')
           		:css('text-align', 'left')
           		:tag('tr')    --create title header
           			:css('background-color',titleBGcolor)
           			:css('text-align', 'center')
           			:tag('th')
           				:attr('colspan',"2")
           				:wikitext(title)
           				:done() --end th
           			:done() --end tr
           		:done() --end table
           	:done() --end td
           :done() --end tr

end

p.renderFooter = function(Qid, Qid_mm)

local text = "維基數據" -- localization required!
local hs_link = "檢視/編輯 人類" -- localization required!
local mm_link = ""
local link_no_hs
local link_no_mm

if Qid_mm == "" then
	link_no_mm = 0
	link_no_hs = 4
else 
	link_no_mm = 2
	link_no_hs = 2
	mm_link = "檢視/編輯 小鼠" -- localization required!
end

root
	:tag('tr')
		:tag('td')
			:attr('colspan', '4')
			:css('text-align', 'center')
			:css('font-size','x-small')
			:css('background-color', rowBGcolor)
			:wikitext(text)
			:done() --end td
		:tag('table')
         	:css('padding', '0')
         	:css('border', 'none')
         	:css('margin', '0')
         	:css('width', '100%')
         	:css('text-align', 'center')
			:tag('tr')
				:tag('td')
					:attr('colspan', link_no_hs)
					:css('background-color', rowBGcolor)
					:css('text-align', 'center')

:css('font-size','x-small') :wikitext(hs_link) :done() --end td :tag('td')

					:attr('colspan', link_no_mm)
					:css('background-color', rowBGcolor)
					:css('text-align', 'center')

:css('font-size','x-small') :wikitext(mm_link) :done() --end td :done() --end tr :done() --end table :done() --end tr root:done() --end root table end

--this code isn't used was hoping could do some generalization of rows p.rowLabel=function(label) root :tag('tr')

       :tag('th')
       	:attr('rowspan', '2')
       	:css('background-color', sideTitleBGcolor)
       	:css('width', '43px')
        	:wikitext(label)
       	--:done()

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


--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.getValueProtein = function(protein_entities, propertyID, return_val) if return_val == nil then return_val = "" end local sep = ","

   local overall_results = {} --should return empty if nothing assigned

for key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a whole local claims local entity = val --each protein in encodes if entity and entity.claims then claims = entity.claims[propertyID] end if claims then local results -- 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 results = table.concat(out, sep) else results = entity:formatPropertyValues(propertyID).value end overall_results[#overall_results+1] = results --individual propertyID value stored in this index end end

local str_overall_results = table.concat(overall_results, sep) --weirdness happens when add a sep = " " otherwise each value represented one time if string.match(str_overall_results, '%w+') then return str_overall_results else return return_val end end


--general function to get value given an entity and property p.getQid = function(entity) local Qid if entity and entity.id then Qid = entity.id return Qid else return "" end end

--get random value that is preferred ranked p.getRefseq_mRNA = function(entity, propertyID, return_val) if return_val == nil then return_val = "" end local input_rank = "RANK_PREFERRED" ---this is mostly like won't do anything because ranking isn't maintained in wikidata local claims

if 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 sitelink = mw.wikibase.sitelink("Q" .. v.mainsnak.datavalue.value["numeric-id"]) local label = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"]) if label == nil then label = "Q" .. v.mainsnak.datavalue.value["numeric-id"] end

if sitelink then out[#out + 1] = "" .. label .. "" else out[#out + 1] = "[[:d:Q" .. v.mainsnak.datavalue.value["numeric-id"] .. "|" .. label .. "]]" end end return table.concat(out, ",") else local results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value

--loop through results until get a NP or NM or just return whatever is in first element --[[local results_split = mw.text.split(results, ",")

local preffered_results = " " if results_split[1] then preferred_result = mw.text.trim(results_split[1]) --return first element if desired prefix not found and remove whitespace end local id --refseq id in question for i, id in ipairs(results_split) do local trim_id = mw.text.trim(id)

 				if string.match( trim_id, '^NM_%d+') then 
 					preferred_result = trim_id --overwrite each time found only need one to display
 				end

end if preferred_result then return preferred_result --return a id starting with NP or NM else return return_val --return first element because desired prefix not found and remove whitespaces end --]] return results:gsub(",", ",") -- l10n: I don't know how this happened but whatever end else return return_val end end

p.getRefseq_protein = function(protein_entities, propertyID, return_val) local sep = "," local overall_results = {} --should return empty if nothing assigned

for key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a whole

local claims local entity = val --each protein in encodes if entity.claims then claims = entity.claims["P637"] end if claims then local results -- 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 results = table.concat(out, sep) else results = entity:formatPropertyValues("P637", mw.wikibase.entity.claimRanks).value results = results:gsub(",", ",") -- l10n: I don't know how this happened but whatever end overall_results[#overall_results+1] = results --a list is in each index end

end --why are there duplicate results here local str_overall_results = table.concat(overall_results, sep) return str_overall_results

end --[[ local results_split = mw.text.split(str_overall_results, sep) --split complete list so can loop through..probably a more direct way to do this --loop through results until get a NP or NM or just return whatever is in first element


local preffered_result = results_split[1] or ""

for i, id in ipairs(results_split) do local trim_id = mw.text.trim(id) --check of id starts with NP or NM if string.match( trim_id, '^NP_%d+') then preferred_result = trim_id --overwrite each time found only need one to display end end --check if something in preffered_result if not get first element in result_split if p.isempty(preffered_result) then return return_val else return preferred_result --return a id starting with NP or NM end

end --]]

--gets an image p.getImage = function(entity, propertyID, sep, imgsize)

	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] = "" .. imgsize .. "" 
			end   
				return table.concat(out, sep)   
		else   
			return ""   
		end   

else

		return ""   
	end   

end

p.getPDB = function(protein_entities) local pdb_propertyID = "P638" local overall_results = {} for key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a whole local claims local entity = val if entity and entity.claims then claims = entity.claims[pdb_propertyID] end local sitelink = "http://www.rcsb.org/pdb/explore/explore.do?pdbId=" if claims then local results if (claims[1] and claims[1].mainsnak.snaktype == "value") then


local out = {} for k, v in pairs(claims) do local label = mw.wikibase.label(v.mainsnak.datavalue.value) if label == nil then label = v.mainsnak.datavalue.value end

if sitelink then out[#out + 1] = "[" .. sitelink .. label .. " " ..label .. "]" else out[#out + 1] = "" .. label .. "" end end results = table.concat(out, "、" .. wbr) -- l10n: punct else results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value end overall_results[#overall_results+1] = results --individual propertyID values stored in this index end end return table.concat(overall_results, ",%%s") end


function p.getAliases(entity, gene_symbol) local aliasSet = {} if entity['aliases'] ~= nil then for _, lang in ipairs({'en', 'zh'}) do -- l10n: zh testing! local aliases = entity['aliases'][lang] if aliases then for _, alias in ipairs(aliases) do aliasSet[alias['value']] = true end end end end

local keys = {} for k, v in pairs(aliasSet) do if k ~= gene_symbol then table.insert(keys, k) -- "if v" omitted end end table.sort(keys) return table.concat(keys, '、' .. wbr) end


--get a geneome start P644 or end P645 p.getChromosomeLoc = function(entity, propertyID, prefix) -- 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 = "P659" --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 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 if v.qualifiers then quals = v.qualifiers.P659 end --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'], prefix) then alias = value['value'] local build_no = alias:gsub(prefix,"") --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

p.getAliasFromGenomeAssembly = function(entity, prefix) -- will contain the numeric value for the requested coordinate local output = "" local sep = " " local propertyID = "P644" --genomic start used local qualifierID = "P659"

local newest_build = "0" local claims if 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 quals if v.qualifiers then quals = v.qualifiers.P659 end --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'], prefix) then alias = value['value'] local build_no = alias:gsub(prefix,"") --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 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 prefix..newest_build else return "" end else return "" end end

p.trimChromosome = function(entity) local string_to_trim = p.getValue(entity, "P1057") local out = -- localization required! if string.find(string_to_trim, '染色体') or string.find(string_to_trim, '染色体') 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 if string.find(string_to_trim, '线粒体') or string.find(string_to_trim, '线粒体') then out = "M" end return out end

p.locToMb = function(num, idp)

 num = tonumber(num)
 if num == nil then 
 	return ""
 else
 	local mb = num/1000000
 	local mult = 10^(idp or 0)
 	return math.floor(mb * mult + 0.5) / mult
 end

end

p.isempty = function(s)

 	return s == nil or s == 

end


p.getGO = function(protein_entities, propertyID) --propertyID ie molecular, cellular, function

local overall_results = {} local results = "" --string to return

for key, val in pairs(protein_entities) do

local claims local entity = val if entity.claims then claims = entity.claims[propertyID] -- ie molecular, cellular, function end local propertyID_child = "P686" -- Gene Ontology ID

if claims then

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 itemID_child = "Q" .. v.mainsnak.datavalue.value["numeric-id"] --get Qid of property item so can get the GOid local entity = mw.wikibase.getEntityObject(itemID_child) local claims local result_GOID = if entity and entity.claims then claims = entity.claims[propertyID_child] end if claims then result_GOID = entity:formatPropertyValues(propertyID_child, mw.wikibase.entity.claimRanks).value else result_GOID = nil --no GO ID end local sitelink = "http://amigo.geneontology.org/amigo/term/" local label = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"]) if label == nil then label = "Q" .. v.mainsnak.datavalue.value["numeric-id"] end local wiki_link = "" if sitelink and result_GOID ~= nil then wiki_link = " [" .. sitelink .. result_GOID .. " " .. label .."]
" else wiki_link = " [[:d:Q" .. v.mainsnak.datavalue.value["numeric-id"] .. "|" .. label .. "]]
" end overall_results[#overall_results+1] = wiki_link end

else results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value end

end --overall_results[#overall_results+1] = results --each protein GO terms stored in this index, so table contains all the GO terms with duplicates end

local hash = {} --temp check local res = {} --no dups

for _,v in ipairs(overall_results) do

  		if (not hash[v]) then
      		res[#res+1] = v 
      		hash[v] = true
  		end

end return table.concat(res, "") end

local function getReference(qID, entity, property_id, ref_index) local f = {"claims",property_id, ref_index, "references"} 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

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 = {} --https://omim.org/entry/131244 --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 ref = "" ref = getReference("", entity, "P2293", k) if (ref ~= nil and ref ~= ) then --refLink = refLink..","..ref refLink = ref end

               --if refLink = "" then --skip if there isn't a reference found

if linkTarget then out[#out + 1] = ""..datav.."" else out[#out + 1] = "" .. datav .. "" end datasource[#out] = refLink --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.getDrug= function(protein_entities, propertyID)

   local out = {}

local datasource = {} local pname = {} local pqid = {}


for key, val in pairs(protein_entities) do local claims local entity = val local name = check_values(p.getLabel,{entity}) if entity.claims then claims = entity.claims[propertyID] -- ie physically interacts with end local protein_id if entity then protein_id = entity.id else protein_id = "" 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 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 ref = getReference(protein_id, entity, "P129",k) --just check if anything returned if (ref ~= nil and ref ~= ) then refLink = ref end if linkTarget then out[#out + 1] = ""..datav.."" else out[#out + 1] = "" .. datav .. "" end pname[protein_id] = name pqid[#out] = protein_id datasource[#out] = refLink end --end k,v claims loop end --end claims[1] end --if claims

   end -- end protein_entities loop

return out, datasource, pqid, pname end

return p