Модуль:Infobox gene
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local p = { } -- local navbar = require('Module:Navbar')._navbar --local infobox = require('Module:Infobox3cols').infobox --local infoboxImage = require('Module:InfoboxImage').InfoboxImage --on a page {{#invoke:Sandbox/genewiki/alllua|getTemplateData|QID=Q14865053}} --in debug window --frame = mw.getCurrentFrame() --frame.args = {QID="Q14865053"} Q18031325 --print(p.getTemplateData(frame)) p.getTemplateData = function(frame) --make some guesses about whether the provided QID is a good one --could expand here if we had some kind of error handling framework --did we get it from the page local root_qid = mw.text.trim(frame.args['QID'] or "") --try to get it from the args local mm_qid = "" --pull all the entity objects that we will need local entity = {} local entity_protein = {} local entity_mouse = {} local entity_mouse_protein = {} local checkOrtholog = "" --flag used to see if mouse data avaliable local mouse_propertyID = "P684" local protein_propertyID = "P688" --get root gene entity if root_qid == "" then entity = mw.wikibase.getEntityObject() if entity then root_qid = entity.id else root_qid = "" end else --assuming we think its good make one call to retrieve and store its wikidata representation entity = mw.wikibase.getEntity(root_qid) end --need to figure out if it is protein or gene here local subclass = p.getValue(entity, "P279") or "" if string.find(subclass, 'protein') then --if protein switch entity to gene if entity.claims then claims = entity.claims["P702"] --encoded by end if claims then --go through each index and reassign entity entity = {} if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then for k, v in pairs(claims) do --this would be problematic if multiple genes for the protein local itemID = "Q" .. claims[#entity + 1].mainsnak.datavalue.value["numeric-id"] entity[#entity + 1] = mw.wikibase.getEntity(itemID) root_qid = itemID end end --will return nothing if no claims are found end entity = mw.wikibase.getEntity(root_qid) end --get the other related entities if entity then local claims = "" --get protein entity object if entity.claims then claims = entity.claims[protein_propertyID] end if claims then --go through each index and then make entity_protein indexed if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then for k, v in pairs(claims) do local protein_itemID = "Q" .. claims[#entity_protein + 1].mainsnak.datavalue.value["numeric-id"] entity_protein[#entity_protein + 1] = mw.wikibase.getEntity(protein_itemID) end end --will return nothing if no claims are found end --get mouse entity object if entity.claims then claims = entity.claims[mouse_propertyID] end if claims then if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then local mouse_itemID = "Q" .. claims[1].mainsnak.datavalue.value["numeric-id"] mm_qid = mouse_itemID entity_mouse = mw.wikibase.getEntity(mouse_itemID) checkOrtholog = 1 end --will return nothing if no claims are found else checkOrtholog = 0 end --get mouse protein entity object if entity_mouse and entity_mouse.claims then claims = entity_mouse.claims[protein_propertyID] end if claims then if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then for k, v in pairs(claims) do local protein_itemID = "Q" .. claims[#entity_mouse_protein + 1].mainsnak.datavalue.value["numeric-id"] entity_mouse_protein[#entity_mouse_protein + 1] = mw.wikibase.getEntity(protein_itemID) end end --will return nothing if no claims are found end end if entity then --only require the main gene entity --a list variables of all the data in the info box local name = p.getLabel(entity) local 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 = p.getValue(entity_protein, "P592") local IUPHAR_id = p.getValue(entity_protein, "P595") local ec_no = p.getValueProtein(entity_protein, "P591") 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","<br><br>","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, dis_ref = p.getDisease(entity, "P2293") local drug = p.getDrug(entity_protein, "P129") --define Global Color Scheme rowBGcolor = '#eee' titleBGcolor = '#ddd' sideTitleBGcolor = '#c3fdb8' p.createTable() p.renderUpperTitle(name) --p.renderCaption() p.renderImage(image) p.renderAvailableStructures(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs) --PDB info p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene) if (disease ~= "" and dis_ref ~= "") then --removes section from those items without disease info p.renderDiseases(disease, dis_ref) end if (drug ~= "" ) then --removes section from those items without drug info p.renderDrug(drug) end if (mol_funct ~= "" and cell_comp ~= "" and bio_process ~= "") then p.renderGeneOntology(mol_funct, cell_comp, bio_process, uniprotID_hs) end if expression_images ~= "" then p.renderRNAexpression(expression_images, entrez_gene) end p.renderOrthologs(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 "An Error has occurred retrieving Wikidata item for infobox" end end p.createTable = function(subbox) if subbox == 'sub' then --doesn't work root :tag('table') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', 'auto') :css('min-width', '100%') :css('font-size', '100%') :css('clear', 'none') :css('float', 'none') :css('background-color', 'transparent') else root = mw.html.create('table') root :addClass('infobox') :css('width', '26.4em') :newline() end end --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 = 'Доступные структуры' local pdb_link = "[[Protein_Data_Bank|PDB]]" local searchTitle = "" local listTitle = "Список идентификаторов PDB" local PDBe_base = 'www.ebi.ac.uk/pdbe/searchResults.html?display=both&term=' local RCSB_base = 'www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=UpAccessionIdQuery&accessionIdList=' local url_uniprot = " " if checkOrtholog == 1 and uniprotID_mm ~= 'n/a' then searchTitle = 'Поиск ортологов: ' 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('tr') --create title header :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, IUPHAR_id, ec_no, entrez_gene) local title = "Идентификаторы" local label_aliases = "[[Международная организация по изучению генома человека|Символы]]" 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 = "[www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id="..hgnc_id.." "..gene_symbol.."]" end end 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 = "Внешние IDs" 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 = "[[Mendelian_Inheritance_in_Man|OMIM:]]".." " end for i, v in ipairs(omim_list) do if string.match(v, '%w+') then omim = omim.."[omim.org/entry/"..v.." "..v.."], " end end omim = string.gsub(omim, ", $"," ") --remove comma from end homologene_id = string.gsub(homologene_id, "%s", "") local homolo_list = mw.text.split(homologene_id, ",") local homolo ="" if (homologene_id ~= nil and homologene_id ~= "") then homolo = "[[HomoloGene|HomoloGene:]]".." " end for i, v in ipairs(homolo_list) do if string.match(v, '%w+') then homolo = homolo.."[www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=homologene&dopt=HomoloGene&list_uids="..v.." "..v.."] " end end homolo = string.gsub(homolo, ", $"," ") --remove comma from end entrez_gene = string.gsub(entrez_gene, "%s", "") local entrez_list = mw.text.split(entrez_gene, ",") local genecards = "" if (entrez_list ~= nil and entrez_list ~= "") then genecards = "[[GeneCards|GeneCards:]]".." " end for i, v in ipairs(entrez_list) do if string.match(v, '%w+') then genecards = genecards.."[www.genecards.org/cgi-bin/carddisp.pl?id_type=entrezgene&id="..v.." "..v.."] " end end genecards = string.gsub(genecards, ", $"," ") --remove comma from end 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 = "[[Mouse_Genome_Informatics|MGI:]]".." " 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.."[www.informatics.jax.org/marker/"..mgi_id.." "..mgi_number.."] " end end mgi = string.gsub(mgi, ", $"," ")--remove comma from end local ChEMBL = "" if string.match(ChEMBL_id, '%w+') then ChEMBL = "[[ChEMBL|ChEMBL:]]".." ".."[www.ebi.ac.uk/chembldb/index.php/target/inspect/CHEMBL"..ChEMBL_id.." "..ChEMBL_id.."] " end local IUPHAR = "" if string.match(IUPHAR_id, '%w+') then IUPHAR = "[[International_Union_of_Basic_and_Clinical_Pharmacology|IUPHAR:]]".." ".."[www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId="..IUPHAR_id.." "..IUPHAR_id.."] " end local label_EC = "[[Enzyme_Commission_number|EC number]]" 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 = "[www.genome.jp/dbget-bin/www_bget?enzyme+" .. link_ec_no .. " " .. ec_no .. "]" root :tag('tr') :tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :newline() :tag('tr') :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('tr') :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(IUPHAR) :wikitext(genecards) :done() :newline() :done() if ec_no ~= "" then root :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(label_EC) :done() :newline() :tag('td') :attr('colspan', '3') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(EC) :done() :newline() :done() end end p.renderDiseases = function(disease, dis_ref) local title = "Связанные наследственные заболевания" local disease_title = "Название болезнии" local source_title = "'''Ссылки'''" --check first to see if any of the diseases have references local ref_flag = {} --check each disease for a reference local ref_flag_all = "" --check if any disease have references if not then don't render the headers for index,value in ipairs(disease) do if (dis_ref[index] ~= nil and dis_ref[index] ~= '') then ref_flag[index] = "true" ref_flag_all = "true" end end if ref_flag_all == "true" then root :tag('tr') :tag('td') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor) :newline() :tag('tr') --create title bar :tag('th') :attr('colspan', '3') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :done() :newline() :tag('tr') :tag('th') :css('background-color', sideTitleBGcolor) :attr('colspan', '2') :wikitext(disease_title) :done() :newline() :tag('td') :css('background-color', sideTitleBGcolor) :attr('colspan', '2') :wikitext(source_title) :done() :newline() :done() end for index,value in ipairs(disease) do local i = 0 local ref_collapse = "" local ref_default = "" local ref_link = "" local ref_link_list = "" if ref_flag[index] == "true" then if (dis_ref[index] ~= nil or dis_ref[index] ~= '') then ref_link_list = mw.text.split(dis_ref[index], ",") end --if less than 4 don't create collapsible list if table.getn(ref_link_list) < 5 then ref_collapse = "none" else ref_collapse = "collapsible collapsed" for i =1, 5 do --get at most 4 elements to display ref_default = ref_default..table.remove(ref_link_list, 1) .. ' ' end local br_count = 0 for i =1, table.getn(ref_link_list) do --get at most 4 elements to display ref_link = ref_link..table.remove(ref_link_list, 1) .. ' ' if br_count < 5 then br_count = br_count + 1 else br_count = 0 ref_link = ref_link ..'<br>' end end end if ref_link_list[#ref_link_list] then ref_link = table.concat(ref_link_list, " ") end root :tag('tr') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor) :newline() :tag('th') :css('background-color', rowBGcolor) :attr('scope', 'row') :attr('colspan', '2') :wikitext(value) :done() :newline() :tag('td') :tag('span') :attr('colspan', '2') :tag('table') :attr('class', ref_collapse) :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'right') :tag('tr') :newline() :tag('th') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(ref_default) :done() :done() :newline() :done() :tag('tr') :tag('td') :attr('colspan', '1') :newline() :tag('p') :attr('class', 'plainlinks') :wikitext(ref_link) :newline() :done() :done() :done() :done() :newline() end end end --p.renderDrug = function(drug, drug_ref) p.renderDrug = function(drug) local title = "Targeted by Drug" local drug_title = "Drug Name" local source_title = "'''References'''" --check first to see if any of the drugs have references --local ref_flag = {} --check each drug for a reference local ref_flag_all = "" --check if any drugs have references if not then don't render the headers for k,v in pairs(drug) do ref_flag_all = "true" end if ref_flag_all == "true" then root :tag('tr') :tag('td') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor) :newline() :tag('tr') --create title bar :tag('th') :attr('colspan', '3') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :done() :newline() :tag('tr') :tag('th') :css('background-color', sideTitleBGcolor) :attr('colspan', '2') :wikitext(drug_title) :done() :newline() :tag('td') :css('background-color', sideTitleBGcolor) :attr('colspan', '2') :wikitext(source_title) :done() :newline() :done() end for key,value in pairs(drug) do local i = 0 local ref_collapse = "" local ref_default = "" local ref_link = "" local ref_link_list = {} local ref_split = mw.text.split(value, ",") local hash = {} --storage to look for duplicated values in case for k,v in ipairs(ref_split) do if not hash[v] then --only add if not found previously ref_link_list[#ref_link_list+1] = v hash[v] = true end end --if less than 4 don't create collapsible list if table.getn(ref_link_list) < 5 then ref_collapse = "none" else ref_collapse = "collapsible collapsed" for i =1, 5 do --get at most 4 elements to display ref_default = ref_default..table.remove(ref_link_list, 1) .. ' ' end local br_count = 0 for i =1, table.getn(ref_link_list) do --get at most 4 elements to display ref_link = ref_link..table.remove(ref_link_list, 1) .. ' ' if br_count < 5 then br_count = br_count + 1 else br_count = 0 ref_link = ref_link ..'<br>' end end end if ref_link_list[#ref_link_list] then ref_link = table.concat(ref_link_list, " ") end root :tag('tr') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor) :newline() :tag('th') :css('background-color', rowBGcolor) :attr('scope', 'row') :attr('colspan', '2') --:wikitext(value) :wikitext(key) :done() :newline() :tag('td') :tag('span') :attr('colspan', '2') :tag('table') :attr('class', ref_collapse) :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'right') :tag('tr') :newline() :tag('th') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(ref_default) :done() :done() :newline() :done() :tag('tr') :tag('td') :attr('colspan', '1') :newline() :tag('p') :attr('class', 'plainlinks') :wikitext(ref_link) :newline() :done() :done() :done() :done() :newline() end end p.renderGeneOntology = function(mol_funct, cell_comp, bio_process, uniprotID) local title = "[[Генная онтология|Генная онтология]]" local mol_funct_title = "Функции" local cell_comp_title = "Компонент клетки" local bio_process_title = "Биологический процесс" local amigo_link = "[amigo.geneontology.org/" .. " Amigo]" local quickGO_link = "[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("Источники:") :wikitext(amigo_link) :wikitext(" / ") :wikitext(quickGO_link) :done() :done() end p.renderRNAexpression = function(expression_images, entrez_gene) local title = "Профиль экспрессии РНК" local biogps_link = "[biogps.org/gene/"..entrez_gene.."/ Больше информации]" 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 = "Ортологи" --to do make the list creation a function --create list for entrez ids local category_chromosome = '' if chr == "X" or chr == "Y" then category_chromosome = '[[Категория:Гены '..chr..'-хромосомы]]' else category_chromosome = '[[Категория:Гены '..chr..'-й хромосомы]]' end local entrezTitle = "[[Entrez|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] = "[www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=default&list_uids="..entrez_gene.."&rn=1 "..entrez_gene.."]" end end --if less than 5 don't create collapsible list if table.getn(entrez_link_list) < 5 then entrez_collapse = "none" if entrez_default == nil and table.getn(entrez_link_list) == 0 then entrez_link = "n/a" end else entrez_collapse = "collapsible collapsed" entrez_default = table.remove(entrez_link_list, 1) .. '<br>' .. table.remove(entrez_link_list, 1) .. '<br>' ..table.remove(entrez_link_list, 1) .. '<br>' .. table.remove(entrez_link_list, 1) .. '<br>' .. table.remove(entrez_link_list, 1) .. '<br>'--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, "<br>") 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] = "[www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=default&list_uids="..v.."&rn=1 "..v.."]" end end --if less than 5 don't create collapsible list if table.getn(entrez_mm_link_list) < 5 then entrez_mm_collapse = "none" if entrez_mm_default == nil and table.getn(entrez_mm_link_list) == 0 then entrez_mm_link = "n/a" end else entrez_mm_collapse = "collapsible collapsed" entrez_mm_default = table.remove(entrez_mm_link_list, 1) .. '<br>' .. table.remove(entrez_mm_link_list, 1) .. '<br>' ..table.remove(entrez_mm_link_list, 1) .. '<br>' .. table.remove(entrez_mm_link_list, 1) .. '<br>' .. table.remove(entrez_mm_link_list, 1) .. '<br>'--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, "<br>") end --create list of ensembl id local ensemblTitle = "[[Ensembl|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] = "[www.ensembl.org/Homo_sapiens/geneview?gene="..v..";db=core".." "..v.."]" end end --if less than 5 don't create collapsible list if table.getn(ensembl_link_list) < 5 then ensembl_collapse = "none" if ensembl_default == nil and table.getn(ensembl_link_list) == 0 then ensembl_link = "n/a" end else ensembl_collapse = "collapsible collapsed" ensembl_default = table.remove(ensembl_link_list, 1) .. '<br>' .. table.remove(ensembl_link_list, 1) .. '<br>' ..table.remove(ensembl_link_list, 1) .. '<br>' .. table.remove(ensembl_link_list, 1) .. '<br>' .. table.remove(ensembl_link_list, 1) .. '<br>'--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, "<br>") end --create list of mouse ensembl id local ensemblTitle = "[[Ensembl|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] = "[www.ensembl.org/Homo_sapiens/geneview?gene="..v..";db=core".." "..v.."]" end end --if less than 5 don't create collapsible list if table.getn(ensembl_mm_link_list) < 5 then ensembl_mm_collapse = "none" if ensembl_mm_default == nil and table.getn(ensembl_mm_link_list) == 0 then ensembl_mm_link = "n/a" end else ensembl_mm_collapse = "collapsible collapsed" ensembl_mm_default = table.remove(ensembl_mm_link_list, 1) .. '<br>' .. table.remove(ensembl_mm_link_list, 1) .. '<br>' ..table.remove(ensembl_mm_link_list, 1) .. '<br>' .. table.remove(ensembl_mm_link_list, 1) .. '<br>' .. table.remove(ensembl_mm_link_list, 1) .. '<br>'--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, "<br>") end --create lists of uniprot ID local uniprotTitle = "[[UniProt|UniProt]]" local uniprot_url = "www.uniprot.org/uniprot/" local uniprot_link = "n/a" local uniprot_collapse local uniprot_default = "" --split string and loop through concatenate by <br> 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) .. '<br>' .. table.remove(uniprot_link_list, 1) .. '<br>' ..table.remove(uniprot_link_list, 1) .. '<br>' .. table.remove(uniprot_link_list, 1) .. '<br>' .. table.remove(uniprot_link_list, 1) .. '<br>'--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, "<br>") 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 <br> 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) .. '<br>' .. table.remove(uniprot_mm_link_list, 1) .. '<br>' ..table.remove(uniprot_mm_link_list, 1) .. '<br>' .. table.remove(uniprot_mm_link_list, 1) .. '<br>' .. table.remove(uniprot_mm_link_list, 1) .. '<br>'--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, "<br>") end local ncbi_link = "www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=" local refseq_mRNATitle = "RefSeq (мРНК)" --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 <br> 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) .. '<br>' .. table.remove(link_list, 1) .. '<br>' ..table.remove(link_list, 1) .. '<br>' .. table.remove(link_list, 1) .. '<br>' .. table.remove(link_list, 1) .. '<br>'--get first 5 elements in table and use for display end if link_list[#link_list] then refseq_mRNA_link = table.concat(link_list, "<br>") 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) .. '<br>' .. table.remove(link_list_mm, 1) .. '<br>' ..table.remove(link_list_mm, 1) .. '<br>' .. table.remove(link_list_mm, 1) .. '<br>' .. table.remove(link_list_mm, 1) .. '<br>'--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, "<br>") end local refseq_protTitle = "RefSeq (белок)" --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) .. '<br>' .. table.remove(link_list_prot, 1) .. '<br>' ..table.remove(link_list_prot, 1) .. '<br>' .. table.remove(link_list_prot, 1) .. '<br>' .. table.remove(link_list_prot, 1) .. '<br>'--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, "<br>") 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) .. '<br>' .. table.remove(link_list_prot_mm, 1) .. '<br>' ..table.remove(link_list_prot_mm, 1) .. '<br>' .. table.remove(link_list_prot_mm, 1) .. '<br>' .. table.remove(link_list_prot_mm, 1) .. '<br>'--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, "<br>") end local locTitle = "Локус (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 = "[genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db="..db.."&position=chr"..chr..":"..gstart.."-"..gend.." ".."Chr "..chr..": "..gstart_mb.." – "..gend_mb.." Mb]" else chr_loc_link = "n/a" end local gstart_mm_mb = p.locToMb(gstart_mm, 2) local gend_mm_mb = p.locToMb(gend_mm, 2) local chr_loc_mm_link = "" if (string.match(db_mm, '%w+') and string.match(chr_mm, '%w+') and string.match(gstart_mm, '%w+') and string.match(gend_mm, '%w+') )then chr_loc_mm_link = "[genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db="..db_mm.."&position=chr"..chr_mm..":"..gstart_mm.."-"..gend_mm.." ".."Chr "..chr_mm..": "..gstart_mm_mb.." – "..gend_mm_mb.." Mb]" else chr_loc_mm_link = "n/a" end local pubmedTitle = "Поиск [[PubMed|PubMed]]" local pubmed_link = entrez_gene if string.match(entrez_gene, '%w+') and entrez_gene ~= "n/a" then pubmed_link = "[www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene.."]" 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 = "[www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene_mm.."]" 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("Виды") :done() :newline() :tag('td') :wikitext("'''Человек'''") :done() :newline() :tag('td') :wikitext("'''Мышь'''") :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('table') :attr('class', entrez_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(entrez_default) :done() :done() :newline() :done() :tag('tr') :tag('td') :attr('colspan', '1') :newline() :tag('p') :attr('class', 'plainlinks') :wikitext(entrez_link) :newline() :done() :done() :done() :done() :newline() :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') :newline() :tag('th') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(entrez_mm_default) :done() :done() :newline() :done() :tag('tr') :tag('td') :attr('colspan', '1') :newline() :tag('p') :attr('class', 'plainlinks') :wikitext(entrez_mm_link) :newline() :done() :done() :done() :done() :newline() :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(ensemblTitle) :done() :newline() :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') :newline() :tag('th') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(ensembl_default) :done() :done() :newline() :done() :tag('tr') :tag('td') :attr('colspan', '1') :newline() :tag('p') :attr('class', 'plainlinks') :wikitext(ensembl_link) :newline() :done() :done() :done() :done() :newline() :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') :newline() :tag('th') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(ensembl_mm_default) :done() :done() :newline() :done() :tag('tr') :tag('td') :attr('colspan', '1') :newline() :tag('p') :attr('class', 'plainlinks') :wikitext(ensembl_mm_link) :newline() :done() :done() :done() :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() :wikitext(category_chromosome) 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|Викиданные]]" local hs_link = "[[d:"..Qid.."|Просмотр/Править (Человек)]]" 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 = "[[d:"..Qid_mm.."|Просмотр/Править (Мышь)]]" 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('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() :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','ru','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] = "[[" .. sitelink .. "|" .. 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 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] = "[[File:" .. filename .. "|" .. imgsize .. "]]" end return table.concat(out, sep) else return "" end else return "" end end p.getPDB = function(protein_entities) local pdb_propertyID = "P638" local overall_results = {} for key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a whole local claims local entity = val if entity and entity.claims then claims = entity.claims[pdb_propertyID] end local sitelink = "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] = "[[:d:Q" .. v.mainsnak.datavalue.value .. "|" .. 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 {{#invoke:Wikidata|pageId}} 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, 'хромосома') then out = string.match(string_to_trim, "%d+")--extract number from string if out == nil then out = string.match(string_to_trim, "X") or string.match(string_to_trim, "Y") end end if string.find(string_to_trim, 'митохондр') then out = "M" end return out end p.locToMb = function(num, idp) num = tonumber(num) if num == nil then return "" else local mb = num/1000000 local mult = 10^(idp or 0) return math.floor(mb * mult + 0.5) / mult end end p.isempty = function(s) return s == nil or s == '' end p.getGO = function(protein_entities, propertyID) --propertyID ie molecular, cellular, function local overall_results = {} local results = "" --string to return for key, val in pairs(protein_entities) do local claims local entity = val if entity.claims then claims = entity.claims[propertyID] -- ie molecular, cellular, function end local propertyID_child = "P686" -- Gene Ontology ID if claims then if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then --local out = {} for k, v in pairs(claims) do local itemID_child = "Q" .. v.mainsnak.datavalue.value["numeric-id"] --get Qid of property item so can get the GOid local entity = mw.wikibase.getEntityObject(itemID_child) local claims local result_GOID = '' if entity and entity.claims then claims = entity.claims[propertyID_child] end if claims then result_GOID = entity:formatPropertyValues(propertyID_child, mw.wikibase.entity.claimRanks).value else result_GOID = nil --no GO ID end local sitelink = "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 = "<big>•</big> [" .. sitelink .. result_GOID .. " " .. label .."]<br>" else wiki_link = "<big>•</big> [[:d:Q" .. v.mainsnak.datavalue.value["numeric-id"] .. "|" .. label .. "]]<br>" 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, index, entity, property_id, ref_index) local f = {"claims",property_id,index,"references",ref_index,"snaks","P854",1,"datavalue","value"} local id = qID --if id and (#id == 0) then -- id = nil --end local data = entity if not data then return nil end local i = 1 while true do local index = f[i] if not index then if type(data) == "table" then return mw.text.jsonEncode(data, mw.text.JSON_PRESERVE_KEYS + mw.text.JSON_PRETTY) else return tostring(data) end end data = data[index] or data[tonumber(index)] if not data then return "" end i = i + 1 end end p.getDisease= function(entity, propertyID) local claims if return_val == nil then return_val = "" end if entity and entity.claims then claims = entity.claims[propertyID] end if claims then -- if wiki-linked value output as link if possible if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then local out = {} local datasource = {} --{{#invoke:Wikidata |ViewSomething |id=Q18023174 |claims|P2293|1|references|1|snaks|P854|1|datavalue|value}} --maybe there is a more direct way to find this than looping through the json object for k, v in pairs(claims) do local datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"]) if datav == nil then datav = " " end local id = "Q" .. v.mainsnak.datavalue.value["numeric-id"] local linkTarget = mw.wikibase.sitelink(id) local refLink = "" local i for i=1,100 do --limits to 100 references displayed local ref = "" ref = getReference("", k, entity, "P2293", i) if (ref ~= nil and ref ~= '') then refLink = refLink..",["..ref.."]" end end --if refLink = "" then --skip if there isn't a reference found datasource[#out + 1] = refLink if linkTarget then out[#out + 1] = "[["..datav.."|"..datav.."]]" else out[#out + 1] = "[[:d:" .. id .. "|" .. datav .. "]]" end --end end return out, datasource else -- just return best values --return entity:formatPropertyValues(propertyID).value return return_val, return_val end else return return_val end return return_val end p.getDrug= function(protein_entities, propertyID) local out = {} local datasource = {} for key, val in pairs(protein_entities) do local claims local entity = val 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 i for i=1,100 do --limits to 100 references displayed local ref = "" ref = getReference(protein_id, k, entity, "P129", i) if (ref ~= nil and ref ~= '') then refLink = refLink..",["..ref.."]" end end local wikiLink = "[["..datav.."|"..datav.."]]" local wikidataLink = "[[:d:" .. id .. "|" .. datav .. "]]" if (refLink ~= nil and refLink ~= '') then if linkTarget then if out[wikiLink] then out[wikiLink] = out[wikiLink]..","..refLink else out[wikiLink] = refLink end else if out[wikidataLink] then out[wikidataLink] = out[wikidataLink]..","..refLink else out[wikidataLink] = refLink end end--end if linkTarget end -- end if refLink end --end k,v claims loop end --end claims[1] end --if claims end -- end protein_entities loop return out end return p