Modül:Gen bilgi kutusu

bullvar_katip · 28 Mayıs 2024

-- Bu modülün kaynak kodu sayfasından alınmıştır -- the module's source code is taken from local p = { } local navbar = require('Modül

olçub')._navbar local infobox = require('Modül:Üç sütunlu bilgi kutusu').infobox local infoboxImage = require('Modül:Bilgi kutusu resmi').InfoboxImage -- wrapped "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("DEĞER_HATASI (" .. tostring(val) .. ")") end end --texts relevant to localization are tagged with --**lclz** and/or *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, "P31") 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_qual "Q83310" 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 if checkOrtholog 1 then -- Don't have to go on if we already got it break end 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 qualifier id local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"] if qual_obj_id mouse_qual then --check if this is mouse or other mm_qid mouse_itemID entity_mouse mw.wikibase.getEntity(mouse_itemID) checkOrtholog 1 break 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 cytoband check_values(p.getValue, {entity, "P4196", "n/a"}) 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 chr_mm check_values( p.trimChromosome, {entity_mouse}) local db_mm check_values(p.getAliasFromGenomeAssembly, {entity_mouse,"mm"}) local cytoband_mm check_values(p.getValue, {entity_mouse, "P4196", "n/a"}) local disease, dis_ref if p.getDisease(entity, "P2293") then disease, dis_ref p.getDisease(entity, "P2293") else disease, dis_ref {"DEĞER_HATASI","DEĞER_HATASI" } 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 {"DEĞER_HATASI","DEĞER_HATASI" } 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) --uncomment here to add a section of the infobox about genetically related diseases, with references --if (disease ~ "" and dis_ref ~ "") then --removes section from those items without disease info -- p.renderDiseases(frame, disease, dis_ref, name, root_qid) --end --uncomment here to add a section of the infobox about drugs that target the protein product of this gene, with references --if (drug ~ "" ) then --removes section from those items without drug info -- p.renderDrug(frame,drug, drug_ref, drug_pqid, drug_pname) --end if (chr ~ "" and gstart ~ "" and gend ~ "") or (chr_mm ~ "" and gstart_mm ~ "" and gend_mm ~ "") then p.renderGeneLocation(frame, chr, gstart, gend, db, cytoband, ensembl, chr_mm, gstart_mm, gend_mm, db_mm, cytoband_mm, ensembl_mm, name) end if expression_images ~ "" then p.renderRNAexpression(expression_images, entrez_gene) end if (mol_funct ~ "" and cell_comp ~ "" and bio_process ~ "") then p.renderGeneOntology(mol_funct, cell_comp, bio_process, uniprotID_hs) 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 "Vikiveri'den bilgi alınırken bir hata oluştu" 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 "Hata: Etiket alımı başarısız"; 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 = 'Uygun yapılar' --**lclz** local pdb_link = "PDB" --**lclz** local searchTitle = "" local listTitle = "PDB kimlik kodlarının listesi" --**lclz** local PDBe_base = 'https://www.ebi.ac.uk/pdbe/searchResults.html?display=both&term=' local RCSB_base = 'http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=UpAccessionIdQuery&accessionIdList=' local url_uniprot = " " if checkOrtholog 1 and uniprotID_mm ~ 'n/a' then searchTitle 'Ortolog araması: ' url_uniprot uniprotID_mm..','..uniprotID_hs else searchTitle 'İnsan UniProt araması: ' 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 "Tanımlayıcılar" --**lclz** local label_aliases "Başka adlar" --**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 = "Dış kimlikler" --**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 = "Enzim Komisyon numarası" --**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 = ".. 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 = "Genetik olarak ilişkili hastalıklar" --**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 "Genetik olarak "..name.." ile ilişkilendirilmiş hastalıkların Vikiveri'deki başvurularını gör/düzenle" 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 "İlaç tarafından hedeflenmiş" --**lclz** --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 "Fiziksel olarak "..drug_pname[k].." ile etkileşen ilaçların Vikiveri'deki başvurularını gör/düzenle" 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.renderGeneLocation function(frame, chr, gstart, gend, db, cytoband, ensembl, chr_mm, gstart_mm, gend_mm, db_mm, cytoband_mm, ensembl_mm, name) local titleHuman "Gen yerleşimi (İnsan)" --**lclz** local titleMouse "Gen yerleşimi (Fare)" --**lclz** local label_chr "Krom." --**lclz** local label_locus "Bant" --**lclz** local label_gstart "Başlangıç" --**lclz** local label_gend "Bitiş" --**lclz** local tooltip_arrowSign name.." için genom yerleşimi" --**lclz** local arrowSign_width 14 if chr ~ "" and gstart ~ "" and gend ~ "" then --Chromosome lengths are from GRCh38.p10 https://www.ncbi.nlm.nih.gov/grc/human/data?asm GRCh38.p10 --This table is used only for calculating "Where should red-rectangle put?" --Curretly, Aug 2017, it seems all gene data, which are stored in Wikidata, have start/end positions based on GRCh38. local chrLengthTable {} chrLengthTable["1"] 248956422 chrLengthTable["2"] 242193529 chrLengthTable["3"] 198295559 chrLengthTable["4"] 190214555 chrLengthTable["5"] 181538259 chrLengthTable["6"] 170805979 chrLengthTable["7"] 159345973 chrLengthTable["8"] 145138636 chrLengthTable["9"] 138394717 chrLengthTable["10"] 133797422 chrLengthTable["11"] 135086622 chrLengthTable["12"] 133275309 chrLengthTable["13"] 114364328 chrLengthTable["14"] 107043718 chrLengthTable["15"] 101991189 chrLengthTable["16"] 90338345 chrLengthTable["17"] 83257441 chrLengthTable["18"] 80373285 chrLengthTable["19"] 58617616 chrLengthTable["20"] 64444167 chrLengthTable["21"] 46709983 chrLengthTable["22"] 50818468 chrLengthTable["X"] 156040895 chrLengthTable["Y"] 57227415 chrLengthTable["MT"] 16569 local chrLength chrLengthTable[chr] --Different languages have different word order. local chrTextTable {}--**lclz** chrTextTable["1"] "1. Kromozom (insan)" chrTextTable["2"] "2. Kromozom (insan)" chrTextTable["3"] "3. Kromozom (insan)" chrTextTable["4"] "4. Kromozom (insan)" chrTextTable["5"] "5. Kromozom (insan)" chrTextTable["6"] "6. Kromozom (insan)" chrTextTable["7"] "7. Kromozom (insan)" chrTextTable["8"] "8. Kromozom (insan)" chrTextTable["9"] "9. Kromozom (insan)" chrTextTable["10"] "10. Kromozom (insan)" chrTextTable["11"] "11. Kromozom (insan)" chrTextTable["12"] "12. Kromozom (insan)" chrTextTable["13"] "13. Kromozom (insan)" chrTextTable["14"] "14. Kromozom (insan)" chrTextTable["15"] "15. Kromozom (insan)" chrTextTable["16"] "16. Kromozom (insan)" chrTextTable["17"] "17. Kromozom (insan)" chrTextTable["18"] "18. Kromozom (insan)" chrTextTable["19"] "19. Kromozom (insan)" chrTextTable["20"] "20. Kromozom (insan)" chrTextTable["21"] "21. Kromozom (insan)" chrTextTable["22"] "22. Kromozom (insan)" chrTextTable["X"] "X kromozomu (insan)" chrTextTable["Y"] "Y kromozomu (insan)" chrTextTable["MT"] "Mitokondriyal DNA (insan)" local chrText chrTextTable[chr] --about the calculation below, see https://en.wikipedia.org/wiki/User:Was_a_bee/Gene#3._Calculation_detail local markerWidth ((gend - gstart) * 294.133 )/ chrLength if markerWidth < 2 then markerWidth 2 else markerWidth math.ceil(markerWidth) end local markerLocation (147.0666 * (gstart + gend) / chrLength ) + 1.6 - (markerWidth / 2) local arrowSignLocation markerLocation + (markerWidth / 2) - (arrowSign_width / 2) markerLocation math.floor( markerLocation * 10 + 0.5 ) / 10 local source_link_chr "" local source_link_gstart "" local source_link_gend "" if( db "hg38" ) then source_link_chr = frame:extensionTag("ref", "GRCh38: Ensembl release 89: "..ensembl.." - Ensembl, May 2017", {name = "refGRCh38Ensembl"}) --**lclz** source_link_gstart = frame:extensionTag("ref", "", {name = "refGRCh38Ensembl"}) source_link_gend = frame:extensionTag("ref", "", {name = "refGRCh38Ensembl"}) elseif( db "hg37") then source_link_chr frame:extensionTag("ref", "GRCh37: Ensembl release 89: "..ensembl.." - Ensembl, May 2017", {name "refGRCh37Ensembl"}) --**lclz** source_link_gstart frame:extensionTag("ref", "", {name "refGRCh37Ensembl"}) source_link_gend frame:extensionTag("ref", "", {name "refGRCh37Ensembl"}) else source_link "" source_link_gstart "" source_link_gend "" end local wikitext_for_ideogram_image "" --wikitext used for showing gene location if chr "MT" then -- wikitext for mitochondrial DNA --wikitext_for_ideogram_image = wikitext_for_ideogram_image.."" else -- wikitext for autosome and sex chromosome wikitext_for_ideogram_image = wikitext_for_ideogram_image.."" end root :tag('tr') :tag('td') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor) :tag('table') :attr('class', 'collapsible expand') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'left') :tag('tr') :tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(titleHuman) :done --end th :done --end tr :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', rowBGcolor) :wikitext("") :done --end td :done --end tr :tag('tr') :tag('th') :attr('scope', 'row') :attr('width', '15%') :css('background-color', sideTitleBGcolor) :wikitext(label_chr) :done --end th :tag('td') :attr('colspan', '3') :attr('width', '85%') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(""..chrText..""..source_link_chr) :done --end span :done --end td :done --end tr :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', rowBGcolor) :wikitext(wikitext_for_ideogram_image) :done --end td :done --end tr :tag('tr') :tag('th') :attr('scope', 'row') :attr('rowspan', '2') :attr('width', '15%') :css('background-color', sideTitleBGcolor) :wikitext(label_locus) :done --end th :tag('td') :attr('rowspan', '2') :attr('width', '35%') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(cytoband) :done --end span :done --end td :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(label_gstart) :done --end th :tag('td') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(p.separateWithComma(gstart).." bç"..source_link_gstart) :done --end span :done --end td :done --end tr :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(label_gend) :done --end th :tag('td') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(p.separateWithComma(gend).." bç"..source_link_gend) :done --end span :done --end td :done --end tr :done --end table :done --end td :done --end tr end if chr_mm ~= "" and gstart_mm ~= "" and gend_mm ~= "" then --Chromosome lengths are from GRCm38.p5 https://www.ncbi.nlm.nih.gov/grc/mouse/data?asm=GRCm38.p5 local chrLengthTable_mm = {} chrLengthTable_mm["1"] = 195471971 chrLengthTable_mm["2"] = 182113224 chrLengthTable_mm["3"] = 160039680 chrLengthTable_mm["4"] = 156508116 chrLengthTable_mm["5"] = 151834684 chrLengthTable_mm["6"] = 149736546 chrLengthTable_mm["7"] = 145441459 chrLengthTable_mm["8"] = 129401213 chrLengthTable_mm["9"] = 124595110 chrLengthTable_mm["10"] = 130694993 chrLengthTable_mm["11"] = 122082543 chrLengthTable_mm["12"] = 120129022 chrLengthTable_mm["13"] = 120421639 chrLengthTable_mm["14"] = 124902244 chrLengthTable_mm["15"] = 104043685 chrLengthTable_mm["16"] = 98207768 chrLengthTable_mm["17"] = 94987271 chrLengthTable_mm["18"] = 90702639 chrLengthTable_mm["19"] = 61431566 chrLengthTable_mm["X"] = 171031299 chrLengthTable_mm["Y"] = 91744698 chrLengthTable_mm["MT"] = 16299 local chrLength_mm = chrLengthTable_mm[chr_mm] --Different languages have different word order. local chrTextTable_mm = {}--**lclz** chrTextTable_mm["1"] = "1. Kromozom (fare)" chrTextTable_mm["2"] = "2. Kromozom (fare)" chrTextTable_mm["3"] = "3. Kromozom (fare)" chrTextTable_mm["4"] = "4. Kromozom (fare)" chrTextTable_mm["5"] = "5. Kromozom (fare)" chrTextTable_mm["6"] = "6. Kromozom (fare)" chrTextTable_mm["7"] = "7. Kromozom (fare)" chrTextTable_mm["8"] = "8. Kromozom (fare)" chrTextTable_mm["9"] = "9. Kromozom (fare)" chrTextTable_mm["10"] = "10. Kromozom (fare)" chrTextTable_mm["11"] = "11. Kromozom (fare)" chrTextTable_mm["12"] = "12. Kromozom (fare)" chrTextTable_mm["13"] = "13. Kromozom (fare)" chrTextTable_mm["14"] = "14. Kromozom (fare)" chrTextTable_mm["15"] = "15. Kromozom (fare)" chrTextTable_mm["16"] = "16. Kromozom (fare)" chrTextTable_mm["17"] = "17. Kromozom (fare)" chrTextTable_mm["18"] = "18. Kromozom (fare)" chrTextTable_mm["19"] = "19. Kromozom (fare)" chrTextTable_mm["X"] = "X kromozomu (fare)" chrTextTable_mm["Y"] = "Y kromozomu (fare)" chrTextTable_mm["MT"] = "Mitokondriyal DNA (fare)" local chrText_mm = chrTextTable_mm[chr_mm] --about the calculation below, see https://en.wikipedia.org/wiki/User:Was_a_bee/Gene#3._Calculation_detail local markerWidth_mm = ((gend_mm - gstart_mm) * 294.133 )/ chrLength_mm if markerWidth_mm < 2 then markerWidth_mm = 2 else markerWidth_mm = math.ceil(markerWidth_mm) end local markerLocation_mm = (147.0666 * (gstart_mm + gend_mm) / chrLength_mm ) + 1.6 - (markerWidth_mm / 2) local arrowSignLocation_mm = markerLocation_mm + (markerWidth_mm / 2) - (arrowSign_width / 2) markerLocation_mm = math.floor( markerLocation_mm * 10 + 0.5 ) / 10 local source_link_chr_mm = "" local source_link_gstart_mm = "" local source_link_gend_mm = "" if( db_mm "mm10" or db_mm "mm0") then --"mm0" happens because of function "getAliasFromGenomeAssembly" is not prepared for mouse data. --But as of now, Aug. 2017, it seems that all data which is stored in Wikidata are based on GRCm38/mm10. --So treating mouse genomic data as GRCm38/mm10 if not specified. source_link_chr_mm = frame:extensionTag("ref", "GRCm38: Ensembl release 89: "..ensembl_mm.." - Ensembl, May 2017", {name = "refGRCm38Ensembl"}) --**lclz** source_link_gstart_mm = frame:extensionTag("ref", "", {name = "refGRCm38Ensembl"}) source_link_gend_mm = frame:extensionTag("ref", "", {name = "refGRCm38Ensembl"}) else source_link_chr_mm = "" source_link_gstart_mm = "" source_link_gend_mm = "" end local wikitext_for_ideogram_image_mm = "" --wikitext used for showing gene location if chr_mm == "MT" then -- wikitext for mitochondrial DNA --wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."" else -- wikitext for autosome and sex chromosome wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."" end 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') :tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(titleMouse) :done --end th :done --end tr :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', rowBGcolor) :wikitext("") :done --end td :done --end tr :tag('tr') :tag('th') :attr('scope', 'row') :attr('width', '15%') :css('background-color', sideTitleBGcolor) :wikitext(label_chr) :done --end th :tag('td') :attr('colspan', '3') :attr('width', '85%') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(chrText_mm..source_link_chr_mm) :done --end span :done --end td :done --end tr :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', rowBGcolor) :wikitext(wikitext_for_ideogram_image_mm) :done --end td :done --end tr :tag('tr') :tag('th') :attr('scope', 'row') :attr('rowspan', '2') :attr('width', '15%') :css('background-color', sideTitleBGcolor) :wikitext(label_locus) :done --end th :tag('td') :attr('rowspan', '2') :attr('width', '35%') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(cytoband_mm) :done --end span :done --end td :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(label_gstart) :done --end th :tag('td') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(p.separateWithComma(gstart_mm).." bç"..source_link_gstart_mm) :done --end span :done --end td :done --end tr :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(label_gend) :done --end th :tag('td') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(p.separateWithComma(gend_mm).." bç"..source_link_gend_mm) :done --end span :done --end td :done --end tr :done --end table :done --end td :done --end tr end end p.renderRNAexpression = function(expression_images, entrez_gene) local title = "RNA ekspresyonu deseni" --**lclz** local biogps_link = "Daha çok ekspresyon verisi başvurusu" --**lclz** root :tag('tr') :tag('td') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor) :tag('table') :attr('class', 'collapsible expand') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'left') :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 :done --end table :done --end td :done --end tr end p.renderGeneOntology = function(mol_funct, cell_comp, bio_process, uniprotID) local title = "Gen ontolojisi" --**lclz** local mol_funct_title = "Moleküler işlevi" --**lclz** local cell_comp_title = "Hücresel bileşeni" --**lclz** local bio_process_title = "Biyolojik süreci" --**lclz** local amigo_link = ".. " Amigo" local quickGO_link = ".. " QuickGO" root :tag('tr') :tag('td') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor) :tag('table') :attr('class', 'collapsible collapsed') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'left') :tag('tr') --create title bar :tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :done --end th :done --end tr :tag('tr') :tag('th') :css('background-color', sideTitleBGcolor) :wikitext(mol_funct_title) :done --end th :tag('td') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(mol_funct) :done --end span :done --end td :done --end tr :tag('tr') :tag('th') :css('background-color', sideTitleBGcolor) :wikitext(cell_comp_title) :done --end th :tag('td') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(cell_comp) :done --end span :done --end td :done --end tr :tag('tr') :tag('th') :css('background-color', sideTitleBGcolor) :wikitext(bio_process_title) :done --end th :tag('td') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(bio_process) :done --end span :done --end td :done --end tr :tag('tr') :tag('td') :css('background-color', rowBGcolor) :css('text-align', 'center') :attr('colspan', '4') :wikitext("Kaynaklar:") :wikitext(amigo_link) :wikitext(" / ") :wikitext(quickGO_link) :done --end td :done --end tr :done --end table :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 = "Ortologlar" --**lclz** --to do make the list creation a function --create list for entrez ids local category_chromosome = 'Kategori:İnsan kromozom '..chr..' üzerindeki genler'-- *lclz*: Category name if chr "MT" then category_chromosome 'Kategori:İnsan mitokondri genleri'-- *lclz*: Category name for mtDNA genes end 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 "https://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 "Yerleşim (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 local chr_ucsc if chr "MT" then chr_ucsc = "M" --UCSC uses "M" (not "MT") in URL for mitochondrial DNA else chr_ucsc = chr end chr_loc_link = "".."Krom. "..chr_ucsc..": "..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 local chr_mm_ucsc if chr_mm == "MT" then chr_mm_ucsc = "M" --UCSC uses "M" (not "MT") in URL for mitochondrial DNA else chr_mm_ucsc = chr_mm end chr_loc_mm_link = "".."Krom. "..chr_mm_ucsc..": "..gstart_mm_mb.." – "..gend_mm_mb.." Mb" else chr_loc_mm_link = "n/a" end local pubmedTitle = "PubMed araması" -- *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 ="İnsan PubMed Başvurusu:" , url = "https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene, website = "National Center for Biotechnology Information, U.S. National Library of Medicine" } } )--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 ="Fare PubMed Başvurusu:" , url ="https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene_mm, website = "National Center for Biotechnology Information, U.S. National Library of Medicine" } } )--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("Türler") --**lclz** :done --end th :tag('td') :wikitext("İnsan") --**lclz** :done --end td :tag('td') :wikitext("Fare") --**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 = "Vikiveri" --**lclz** local hs_link = "İnsan'ı Gör/Düzenle" --**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 = "Fare'yi Gör/Düzenle" --**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 :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','tr','value'} local i = 1 while true do local index = f 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] = "[[:d:Q" .. v.mainsnak.datavalue.value["numeric-id"] .. "|" .. label .. "]]" end end return table.concat(out, ", ") else local results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value --loop through results until get a NP or NM or just return whatever is in first element --[[local results_split = mw.text.split(results, ",") local preffered_results = " " if results_split[1] then preferred_result = mw.text.trim(results_split[1]) --return first element if desired prefix not found and remove whitespace end local id --refseq id in question for i, id in ipairs(results_split) do local trim_id = mw.text.trim(id) if string.match( trim_id, '^NM_%d+') then preferred_result = trim_id --overwrite each time found only need one to display end end if preferred_result then return preferred_result --return a id starting with NP or NM else return return_val --return first element because desired prefix not found and remove whitespaces end --]] return results 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 "https://www.rcsb.org/structure/" 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. -- inceleme -- 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. -- inceleme local test = entity['aliases']['tr'] 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" --genomic assembly 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 --as of Aug. 2017, P659-genomic assembly is stored only in human genomic data. GRCh38 (newer) or GRCh37(older). --Mouse genomic data doesn't have P659-genomic assembly data. But mouse has only one version. GRCm38/mm10. 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,"") --For example, prefix is "hg" (this is set when the function was called), --alias is "hg38" (which is data stored in Wikidata). Then "build_no" becomes "38". --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 = --"mitochondrion" and "chromosome MT" is used for mitochondrial DNA. --See d:Special:WhatLinksHere/Q18694495 if string.find(string_to_trim, 'chromosome MT') or string.find(string_to_trim, 'mitochondri') then --match both 'mitochondrio'/'mitochondrial' out = "MT" elseif string.find(string_to_trim, 'Kromozom') 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 return out end p.locToMb function(num, idp) num tonumber(num) if num nil then return "" else local mb = num/1000000 local mult = 10^(idp or 0) return math.floor(mb * mult + 0.5) / mult end end p.isempty = function(s) return s nil or s end p.getGO = function(protein_entities, propertyID) --propertyID ie molecular, cellular, function local overall_results = {} local results = "" --string to return for key, val in pairs(protein_entities) do local claims local entity = val if entity.claims then claims = entity.claims[propertyID] -- ie molecular, cellular, function end local propertyID_child = "P686" -- Gene Ontology ID if claims then if (claims[1] and claims[1].mainsnak.snaktype "value" and claims[1].mainsnak.datavalue.type "wikibase-entityid") then --local out = {} for k, v in pairs(claims) do local itemID_child = "Q" .. v.mainsnak.datavalue.value["numeric-id"] --get Qid of property item so can get the GOid local entity = mw.wikibase.getEntityObject(itemID_child) local claims local result_GOID = if entity and entity.claims then claims = entity.claims[propertyID_child] end if claims then result_GOID = entity:formatPropertyValues(propertyID_child, mw.wikibase.entity.claimRanks).value else result_GOID = nil --no GO ID end local sitelink = "http://amigo.geneontology.org/amigo/term/" local label = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"]) if label == nil then label = "Q" .. v.mainsnak.datavalue.value["numeric-id"] end local wiki_link = "" if sitelink and result_GOID ~= nil then wiki_link = " [" .. sitelink .. result_GOID .. " " .. label .."]" else wiki_link = " [[:d:Q" .. v.mainsnak.datavalue.value["numeric-id"] .. "|" .. label .. "]]" end overall_results[#overall_results+1] = wiki_link end else results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value end end --overall_results[#overall_results+1] = results --each protein GO terms stored in this index, so table contains all the GO terms with duplicates end local hash = {} --temp check local res = {} --no dups for _,v in ipairs(overall_results) do if (not hash[v]) then res[#res+1] = v hash[v] = true end end return table.concat(res, "") end local function getReference(qID, entity, property_id, ref_index) local f = {"claims",property_id, ref_index, "references"} local id = qID --if id and (#id 0) then -- id nil --end local data entity if not data then return nil end local i 1 while true do local index f 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 p.separateWithComma= function(bp) --Separate number with comma. For example when this function gets "12345678", returns "12,345,678" local commaSeparated = bp while true do commaSeparated, k = string.gsub(commaSeparated, "^(-?%d+)(%d%d%d)", '%1,%2') if (k==0) then break end end return commaSeparated end return p

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