Module:Sandbox/genewiki/alllua

local p = { }

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

-- wrapaped "protected call", return "value error" with error info on error local function check_values(f,args) --local u= table.upack(args) local exist, val = pcall(f, unpack(args)) if exist and val ~= nil then return(val) else -- Leaking some debugging info won't hurt.... return("VALUE_ERROR (" .. tostring(val) .. ")")		end end --texts relevant to localization are tagged with --**lclz** --on a page --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" --actually ortholog property additional orthologs can exist local protein_propertyID = "P688"

--get root gene entity if root_qid == "" then entity = mw.wikibase.getEntityObject if entity then root_qid = entity.id else root_qid = "" end else --assuming we think its good make one call to retrieve and store its wikidata representation entity = mw.wikibase.getEntity(root_qid) end --need to figure out if it is protein or gene here local subclass = p.getValue(entity, "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 local qualifierID = "P703" --found in taxon local mouse_tax = "Mus musculus" 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 mouse_itemID = "Q" .. v.mainsnak.datavalue.value["numeric-id"] local quals if v.qualifiers then quals = v.qualifiers.P703 end if quals then for qk, qv in pairs(quals) do							--get the taxon name in qualifier local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"] mw.wikibase.label(qual_obj_id) local qual_obj = mw.wikibase.label(qual_obj_id) if string.match(qual_obj, mouse_tax) then --check if this is mouse or other mm_qid = mouse_itemID entity_mouse = mw.wikibase.getEntity(mouse_itemID) checkOrtholog = 1 end end end end end --will return nothing if no claims are found else checkOrtholog = 0 end --get mouse protein entity object if entity_mouse and entity_mouse.claims then claims = entity_mouse.claims[protein_propertyID] end if claims then if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then for k, v in pairs(claims) do local protein_itemID = "Q" .. claims[#entity_mouse_protein + 1].mainsnak.datavalue.value["numeric-id"] entity_mouse_protein[#entity_mouse_protein + 1] = mw.wikibase.getEntity(protein_itemID) end end --will return nothing if no claims are found end end if entity then --only require the main gene entity --a list variables of all the data in the info box local 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 local aliases = check_values(p.getAliases, {entity}) local gene_symbol = check_values(p.getValue, {entity, "P353"}) 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 -- *lclz*: Some projects, like zhwiki (again), use inline styles on -- infobox modules in addition to the class. Be sure to check them out. :addClass('infobox') :css('width', '26.4em') 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 = 'Available structures' --**lclz** local pdb_link = "PDB" --**lclz** local searchTitle = "" local listTitle = "List of PDB id codes" --**lclz** local PDBe_base = 'https://www.ebi.ac.uk/pdbe/searchResults.html?display=both&amp;term=' local RCSB_base = 'http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=UpAccessionIdQuery&amp;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 = "Identifiers" --**lclz** local label_aliases = "Aliases" --**lclz** 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 = ""..gene_symbol.."" end end

-- *lclz*: see getAliases. You can, say, use another punctuation for your language. aliases = string.gsub(aliases, ', '..gene_symbol..'$', '') --get rid of gene name if last in alias list aliases = string.gsub(aliases, gene_symbol..', ', '') --get rid of gene name if first in aliases list aliases = string.gsub(aliases, ', '..gene_symbol..',', ',') --get rid of gene name if in aliases list aliases = string.gsub(aliases, ", ,", ",") --remove comma from middle aliases = string.gsub(aliases, ", $", "") --remove comma from end local label_ext_id = "External IDs" --**lclz** 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:".." " --**lclz** end for i, v in ipairs(omim_list) do		if string.match(v, '%w+') then omim = omim..""..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.." " end end homolo = string.gsub(homolo, ", $"," ")	--remove comma from end

local genecards = "GeneCards:".." " genecards = genecards..""..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:".." " --**lclz** 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_number.." " end end mgi = string.gsub(mgi, ", $"," ")--remove comma from end

local ChEMBL = "" if string.match(ChEMBL_id, '%w+') then ChEMBL = "ChEMBL:".." "..""..ChEMBL_id.." " end local IUPHAR = "" if string.match(IUPHAR_id, '%w+') then IUPHAR = "IUPHAR:".." "..""..IUPHAR_id.." " --**lclz** end -- *lclz* local label_EC = "EC number" --**lclz** 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 = "[http://www.genome.jp/dbget-bin/www_bget?enzyme+" .. 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 = "Genetically Related Diseases" --**lclz**

--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..", "..value -- *lclz*: punctuation 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 = "Diseases that are genetically associated with "..name.." view/edit references on wikidata" 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 = "Targeted by Drug" --**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 -- *lclz*: comma drug_list_per_protein[protein_qid] = drug_list_per_protein[protein_qid]..', '..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 = "Drugs that physically interact with "..drug_pname[k].." view/edit references on wikidata" 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 = "Gene ontology" --**lclz** local mol_funct_title = "Molecular function" --**lclz** local cell_comp_title = "Cellular component" --**lclz** local bio_process_title = "Biological process" --**lclz** local amigo_link = "[http://amigo.geneontology.org/" .. " Amigo]" local quickGO_link = "[https://www.ebi.ac.uk/QuickGO/" .. " 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 expression pattern" --**lclz** local biogps_link = "More reference expression data" --**lclz** 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 = "Orthologs" --**lclz** --to do make the list creation a function --create list for entrez ids -- *lclz*: Category name local category_chromosome = '' 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.."" 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.."" 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.."" 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.."" 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 local ncbi_link = "https://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=" local refseq_mRNATitle = "RefSeq (mRNA)" -- *lclz*: sometimes --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 -- *lclz*: sometimes local refseq_protTitle = "RefSeq (protein)" --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

local locTitle = "Location (UCSC)" -- *lclz* 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 = "".."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 = "".."Chr "..chr_mm..": "..gstart_mm_mb.." – "..gend_mm_mb.." Mb" else chr_loc_mm_link = "n/a" end

local pubmedTitle = "PubMed search" -- *lclz* 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 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 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("Species") --**lclz** :done --end th       	:tag('td') :wikitext("Human") --**lclz** :done --end td       	:tag('td') :wikitext("Mouse") --**lclz** :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 = "Wikidata" --**lclz** local hs_link = "View/Edit Human" --**lclz** 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 = "View/Edit Mouse" --**lclz** 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 --Julia :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('font-size','x-small') :css('background-color', rowBGcolor) :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 -- *lclz*: Sometimes Wikibase returns punctuations other than "," depending on --        your site's language. Consider adding a gsub here. 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] = "" .. 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 end else return return_val end end

-- *lclz*: same as getRefseq_mRNA 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 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] = "" 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, ", ") -- *lclz*: punctuation (CJK comma, etc.) 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) a = '' if entity['aliases'] ~= nil then -- *lclz*: You will need a different language here. --        If you are aiming for an "en" fallback, consider a set data structure. -- zhwp went a bit further here: they moved this call after "gene_symbol", -- so that this function can perform the deduplication here instead of -- in renderIdentifiers. That way they skip messing with commas and spaces. local test = entity['aliases']['en'] if test then for key, value in ipairs(test) do a = a .. ', ' .. value['value'] end return a		else return "" end else return "" end 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

-- *lclz*: Your language's wikidata may have different nouns for chromosome and --        mitochodria. p.trimChromosome = function(entity) local string_to_trim = p.getValue(entity, "P1057") local out = '' if string.find(string_to_trim, 'chromosome') then out = string.match(string_to_trim, "%d+")--extract number from string if out == nil then out = string.match(string_to_trim, "X") or string.match(string_to_trim, "Y") end end if string.find(string_to_trim, 'mitochondrial') 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 = " • " .. 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 = {} --			--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