Module:Sandbox/genewiki/testdislua

local p = { }

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

--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	entity_genasscn = "" local mouse_propertyID = "P684" local protein_propertyID = "P688" local genasscn_propertyID = "P2293" --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 --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 genetic association object if entity.claims then claims = entity.claims[genasscn_propertyID] end if claims then if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then local genasscn_itemID = "Q" .. claims[1].mainsnak.datavalue.value["numeric-id"] --mm_qid = genasscn_itemID entity_genasscn = mw.wikibase.getEntity(genasscn_itemID) end end --get mouse protein entity object if entity_mouse and entity_mouse.claims then claims = entity_mouse.claims[protein_propertyID] end if claims then if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then for k, v in pairs(claims) do local protein_itemID = "Q" .. claims[#entity_mouse_protein + 1].mainsnak.datavalue.value["numeric-id"] entity_mouse_protein[#entity_mouse_protein + 1] = mw.wikibase.getEntity(protein_itemID) end end --will return nothing if no claims are found end end if entity then --only require the main gene entity --a list variables of all the data in the info box local name = p.getLabel(entity) local entrez_gene = p.getValue(entity, "P351") local entrez_gene_mm = p.getValue(entity_mouse, "P351", "n/a") local image = p.getImage(entity, "P18", " ", "250px") --need to set size local uniprotID_hs = p.getValueProtein(entity_protein, "P352", "n/a") local uniprotID_mm = p.getValueProtein(entity_mouse_protein, "P352", "n/a") local pdbIDs = p.getPDB(entity_protein) --makes a list with links to RCSB local aliases = p.getAliases(entity) local gene_symbol = p.getValue(entity, "P353") local hgnc_id = p.getValue(entity, "P354") local homologene_id = p.getValue(entity, "P593") local omim_id = p.getValue(entity, "P492") local mgi_id = p.getValue(entity_mouse, "P671") local ChEMBL_id = "" local ec_no = "" local mol_funct = p.getGO(entity_protein, "P680") local cell_comp = p.getGO(entity_protein, "P681") local bio_process = p.getGO(entity_protein, "P682") local expression_images = p.getImage(entity,"P692"," ","250px") local ensembl = p.getValue(entity, "P594", "n/a") local ensembl_mm = p.getValue(entity_mouse, "P594", "n/a") local refseq_mRNA = p.getRefseq_mRNA(entity, "P639", "n/a") local refseq_mRNA_mm = p.getRefseq_mRNA(entity_mouse, "P639", "n/a") local refseq_prot = p.getRefseq_protein(entity_protein, "P637", "n/a") local refseq_prot_mm = p.getRefseq_protein(entity_mouse_protein, "P637", "n/a") local gstart = p.getChromosomeLoc(entity, "P644", "hg") local gend = p.getChromosomeLoc(entity, "P645", "hg") local chr = p.trimChromosome(entity) local db = p.getAliasFromGenomeAssembly(entity,"hg") local gstart_mm = p.getChromosomeLoc(entity_mouse, "P644", "mm") local gend_mm = p.getChromosomeLoc(entity_mouse, "P645", "mm") local db_mm = p.getAliasFromGenomeAssembly(entity_mouse,"mm") local chr_mm = p.trimChromosome(entity_mouse) local disease = p.getValue(entity, "P2293") local disomim_id = p.getValue(entity_genasscn, "P492") --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, ec_no, entrez_gene) p.renderDiseases(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, disease, disomim_id) 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(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)

else return "root entity not set" end end

p.createTable = function(subbox)

if subbox == 'sub' then --doesn't work root :tag('table') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', 'auto') :css('min-width', '100%') :css('font-size', '100%') :css('clear', 'none') :css('float', 'none') :css('background-color', 'transparent') else root = mw.html.create('table') root :addClass('infobox') :css('width', '26.4em') :newline end

end

--Title above image p.renderUpperTitle = function(name) local title = name if not title then return "error: failed to get label"; end root :tag('tr') :tag('th') :attr('colspan', 4) :css('text-align', 'center') :css('font-size', '125%') :css('font-weight', 'bold') :wikitext(title) :newline end

--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 :newline end

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

local title = 'Available structures' local pdb_link = "PDB" local searchTitle = "" local listTitle = "List of PDB id codes" local PDBe_base = 'http://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 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) :newline --p.createTable('sub') :tag('table') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'left') :newline

:tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color',titleBGcolor) :wikitext(title) :done :newline --p.rowLabel(pdb_link) :tag('tr') :tag('th') :attr('rowspan', '2') :css('background-color', sideTitleBGcolor) :css('width', '43px') :wikitext(pdb_link) :done :tag('td') :attr('colspan', '2') :css('background-color', rowBGcolor) :wikitext(searchTitle) :tag('span') :attr('class', 'plainlinks') :wikitext(PDBe) :wikitext(RCSB) :done :done :done --this may not be needed :newline --new row for collapsible list of PDB codes :tag('tr') :tag('td') :tag('table') :attr('class', 'collapsible collapsed') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'left') :newline :tag('tr') :css('background-color',titleBGcolor) :css('text-align', 'center') :newline :tag('th') :attr('colspan', '2') :wikitext(listTitle) :done :newline :done :tag('tr') :tag('td') :attr('colspan', '2') :css('background-color', rowBGcolor) :newline :tag('p') :tag('span') :attr('class', 'plainlinks') :wikitext(pdbIDs) :done :newline else return "" end

end

p.renderIdentifiers = function(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, ec_no, entrez_gene) local title = "Identifiers" local label_aliases = "Aliases" 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 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 aliases = string.gsub(aliases, "^,", "") --remove comma from start local label_ext_id = "External IDs" local omim = "" if string.match(omim_id, '%w+') then omim = "OMIM:".." "..""..omim_id.." " end local homolo ="" if string.match(homologene_id, '%w+') then homolo = "HomoloGene:".." "..""..homologene_id.." " end local genecards = "" if string.match(entrez_gene, '%w+') then genecards = "GeneCards:".." "..""..entrez_gene.." " end local mgi = "" if string.match(mgi_id, '%w+') then mgi = "MGI:".." "..""..mgi_id.." " end local ChEMBL = "" if string.match(ChEMBL_id, '%w+') then ChEMBL = "ChEMBL:".." "..""..ChEMBL_id.." " end root :tag('tr') :tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :newline

:tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(label_aliases) :done :newline :tag('td') :attr('colspan','3') :css('background', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(symbol_url) :done :wikitext(aliases) :done :newline

:tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(label_ext_id) :done :newline :tag('td') :attr('colspan', '3') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(omim) :wikitext(mgi) :wikitext(homolo) :wikitext(ChEMBL) :wikitext(genecards) :done :newline :done end

p.renderDiseases = function(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, disease, disomim_id) local title = "Disease" local entrezTitle = "Entrez" --check all values to see if exists so don't create nonsense links in infobox must have some alphanumberic character local entrez_link = "" if string.match(entrez_gene, '%w+') and entrez_gene ~= "n/a" then entrez_link = ""..entrez_gene.."" end local entrez_mm_link = entrez_gene_mm if string.match(entrez_gene_mm, '%w+') and entrez_gene_mm ~= "n/a" then entrez_mm_link = ""..entrez_gene_mm.."" end local shipType = "" if disease ~= "" then shipType = "genetic" end --local split_omim = mw.text.split(disomim_id,"%s*,%s*") local split_omim = mw.text.split(disomim_id,",") -- INCORRECT: entrez_gene = ".. "|" .. "OMIM entry" .."] " entrez_gene = ".." ".."OMIM entry".."] " disease = ""..disease.."" --entrez_gene = split_omim[1] -- result[0] will give "cat", result[1] will give "dog"

root :tag('tr') :tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :done :newline :tag('tr') :tag('th') :wikitext("Disease Name") :done :newline :tag('td') :wikitext("Relationship Type") :done :newline :tag('td') :wikitext("Data Source") :done :newline :done ---this section would be nice to do in a loop if the tag closures were figured out :tag('tr') :tag('th') :attr('scope', 'row') :wikitext(disease) :done :newline :tag('td') :tag('span') :wikitext(shipType) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(entrez_gene)--disomim_id[0])       		:done        		:newline	end

p.renderGeneOntology = function(mol_funct, cell_comp, bio_process, uniprotID) local title = "Gene ontology" local mol_funct_title = "Molecular function" local cell_comp_title = "Cellular component" local bio_process_title = "Biological process" local amigo_link = "[http://amigo.geneontology.org/" .. " Amigo]" local quickGO_link = "[http://www.ebi.ac.uk/QuickGO/" .. " QuickGO]"

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

p.renderRNAexpression = function(expression_images, entrez_gene) local title = "RNA expression pattern" local biogps_link = "More reference expression data" root :tag('tr') :tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :done :newline :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', rowBGcolor) :wikitext(expression_images) :done :newline :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(biogps_link) :done :newline end

p.renderOrthologs = function(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" local entrezTitle = "Entrez" --check all values to see if exists so don't create nonsense links in infobox must have some alphanumberic character local entrez_link = "" if string.match(entrez_gene, '%w+') and entrez_gene ~= "n/a" then entrez_link = ""..entrez_gene.."" end local entrez_mm_link = entrez_gene_mm if string.match(entrez_gene_mm, '%w+') and entrez_gene_mm ~= "n/a" then entrez_mm_link = ""..entrez_gene_mm.."" end local ensemblTitle = "Ensembl" local ensembl_link = ensembl --default to result so n/a defined if string.match(ensembl, '%w+') and ensembl ~= "n/a" then ensembl_link = ""..ensembl.."" end local ensembl_mm_link = ensembl_mm if string.match(ensembl_mm, '%w+') and ensembl_mm ~= "n/a" then ensembl_mm_link = ""..ensembl_mm.."" 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 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(uniprot, '%w+') and uniprot ~= "n/a" then uniprot_link_list[#uniprot_link_list+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"			end hash[v] = true end 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 = {} for k,v in ipairs(split_uniprot_mm) do 		local label = mw.text.trim(v) local concat_uniprot_link = uniprot_url .. label if string.match(uniprot_mm, '%w+') and uniprot_mm ~= "n/a" then uniprot_mm_link_list[#uniprot_mm_link_list+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"		end 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_link_mm_list, 1) .. ' ' .. table.remove(uniprot_link_mm_list, 1) .. ' ' ..table.remove(uniprot_link_mm_list, 1) .. ' ' .. table.remove(uniprot_link_mm_list, 1) .. ' ' .. table.remove(uniprot_link_mm_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 = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=" local refseq_mRNATitle = "RefSeq (mRNA)" --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 = {} 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 link_list[#link_list+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"		end 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 = {} for k,v in ipairs(split_refseq_mRNA_mm) do		if string.match(v, '%w+') and v ~= "n/a" then local label = mw.text.trim(v) local concat_ncbi_link = ncbi_link .. label if string.match(v, '%w+') and v ~= "n/a" then link_list_mm[#link_list_mm+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"			end end 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

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 = {} for k,v in ipairs(split_refseq_prot) do		if string.match(v, '%w+') and v ~= "n/a" then local label = mw.text.trim(v) local concat_ncbi_link = ncbi_link .. label if string.match(v, '%w+') and v ~= "n/a" then link_list_prot[#link_list_prot+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"			end end 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) --get first element 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_mm = {} for k,v in ipairs(split_refseq_prot_mm) do		if string.match(v, '%w+') and v ~= "n/a" then local label = mw.text.trim(v) local concat_ncbi_link = ncbi_link .. label if string.match(v, '%w+') and v ~= "n/a" then link_list_mm[#link_list_mm+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"			end end end --if less than 5 don't create collapsible list if table.getn(link_list_mm) < 6 then refseq_prot_mm_collapse = "none" if refseq_prot_mm_default == nil and table.getn(link_list_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_mm, 1) --get first element in table and use for display end if link_list_mm[#link_list_mm] then refseq_prot_mm_link = table.concat(link_list_mm, " ") end

local locTitle = "Location (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 = "".."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_link = "n/a" end local pubmedTitle = "PubMed search" local pubmed_link = entrez_gene if string.match(entrez_gene, '%w+') and entrez_gene ~= "n/a" then pubmed_link = "" 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 = "" end root :tag('tr') :tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :done :newline :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext("Species") :done :newline :tag('td') :wikitext("Human") :done :newline :tag('td') :wikitext("Mouse") :done :newline :done ---this section would be nice to do in a loop if the tag closures were figured out :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(entrezTitle) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(entrez_link) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(entrez_mm_link) :done :newline :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(ensemblTitle) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(ensembl_link) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(ensembl_mm_link) :done :newline :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(uniprotTitle) :done :newline :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') :newline :tag('th') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(uniprot_default) :done :done :newline :done :tag('tr') :tag('td') :attr('colspan', '1') :newline :tag('p') :attr('class', 'plainlinks') :wikitext(uniprot_link) :newline :done :done :done :done :newline :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') :newline :tag('th') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(uniprot_mm_default) :done :done :newline :done :tag('tr') :tag('td') :attr('colspan', '1') :newline :tag('p') :attr('class', 'plainlinks') :wikitext(uniprot_mm_link) :newline :done :done :done :done :newline :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(refseq_mRNATitle) :done :newline :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') :newline :tag('th') :attr('colspan', '1') :attr('class', 'plainlinks') :wikitext(refseq_mRNA_default) :done :newline :done :tag('tr') :tag('td') :attr('colspan', '1') :newline :tag('p') :tag('span') :attr('class', 'plainlinks') :wikitext(refseq_mRNA_link) :done :newline :done :done :done :done :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') :newline :tag('th') :attr('colspan', '1') :attr('class', 'plainlinks') :wikitext(refseq_mRNA_mm_default) :done :newline :done :tag('tr') :tag('td') :attr('colspan', '1') :newline :tag('p') :tag('span') :attr('class', 'plainlinks') :wikitext(refseq_mRNA_mm_link) :done :newline :done :done :done :done :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(refseq_protTitle) :done :newline :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') :newline :tag('th') :attr('colspan', '1') :attr('class', 'plainlinks') :wikitext(refseq_prot_default) :done :newline :done :tag('tr') :tag('td') :attr('colspan', '1') :newline :tag('p') :tag('span') :attr('class', 'plainlinks') :wikitext(refseq_prot_link) :done :newline :done :done :done :done :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') :newline :tag('th') :attr('colspan', '1') :attr('class', 'plainlinks') :wikitext(refseq_prot_mm_default) :done :done :tag('tr') :tag('td') :attr('colspan', '1') :newline :tag('p') :tag('span') :attr('class', 'plainlinks') :wikitext(refseq_prot_mm_link) :done :newline :done :done :done :done :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(locTitle) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(chr_loc_link) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(chr_loc_mm_link) :done :newline :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(pubmedTitle) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(pubmed_link) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(pubmed_mm_link) :done :newline end

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

p.renderFooter = function(Qid, Qid_mm) local text = "Wikidata" local hs_link = "View/Edit Human" 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" 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 :newline :tag('table') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'center')

:tag('td') :attr('colspan', link_no_hs) :css('background-color', rowBGcolor) :css('text-align', 'center') :css('font-size','x-small') :wikitext(hs_link) :done :tag('td') :attr('colspan', link_no_mm) :css('background-color', rowBGcolor) :css('text-align', 'center') :css('font-size','x-small') :wikitext(mm_link) :done :newline :done

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] = "" .. 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

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, ", ") 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 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

p.trimChromosome = function(entity) local string_to_trim = p.getValue(entity, "P1057") local out = '' if string.find(string_to_trim, 'chromosome.') then out = string_to_trim:gsub("chromosome ", "") end if string.find(string_to_trim, 'mouse.chromosome.') then out = string_to_trim:gsub("mouse chromosome ", "") 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

return p