사용자:FriedC/연습장/2
local p = {}
local localSeparatorStr = "," -- **lclz** Correct it if your wiki has different setting, like zhwiki uses "、" for now local localNotApplicableStr = "n/a" -- **lclz** local root
--define Global Color Scheme local rowBGcolor = '#eee' local titleBGcolor = '#ddd' local sideTitleBGcolor = '#c3fdb8'
-- 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("VALUE_ERROR (" .. tostring(val) .. ")") end end
--texts relevant to localization are tagged with --**lclz** and/or *lclz* --on a page 스크립트 오류: "Sandbox/genewiki/alllua" 모듈이 없습니다. --in debug window --frame = mw.getCurrentFrame() --frame.args = {QID="Q14865053"} Q18031325 --print(p.getTemplateData(frame)) function p.getTemplateData(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.getEntity() 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, '단백질') then --if protein switch entity to gene **lclz** local claims 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 bgee_wikidata_id = 'Q54985720'
local expressed_in_tissues = check_values(p.getValue, {entity, "P5572", localNotApplicableStr, localSeparatorStr, bgee_wikidata_id}) --P5572: expressed in
local expressed_in_mouse_tissues = check_values(p.getValue, {entity_mouse, "P5572", localNotApplicableStr, localSeparatorStr, bgee_wikidata_id}) --P5572: expressed in
local entrez_gene = check_values(p.getValue, {entity, "P351", localNotApplicableStr} )
local entrez_gene_mm = check_values(p.getValue, {entity_mouse, "P351", localNotApplicableStr})
local image = check_values( p.getImage, {entity, "P18", " ", "250px"}) --need to set size
local uniprotID_hs = check_values(p.getValueProtein, {entity_protein, "P352", localNotApplicableStr})
local uniprotID_mm = check_values(p.getValueProtein, {entity_mouse_protein, "P352", localNotApplicableStr})
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", localNotApplicableStr})
local ensembl_mm = check_values(p.getValue, {entity_mouse, "P594", localNotApplicableStr})
local refseq_mRNA = check_values(p.getRefseq_mRNA, {entity, "P639", localNotApplicableStr})
local refseq_mRNA_mm = check_values(p.getRefseq_mRNA, {entity_mouse, "P639", localNotApplicableStr})
local refseq_prot = check_values(p.getRefseq_protein, {entity_protein, "P637", localNotApplicableStr})
local refseq_prot_mm = check_values(p.getRefseq_protein, {entity_mouse_protein, "P637", localNotApplicableStr})
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", localNotApplicableStr})
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", localNotApplicableStr})
local disease, dis_ref = p.getDisease(entity, "P2293")
local drug, drug_ref, drug_pqid, drug_pname = p.getDrug(entity_protein, "P129")
--local drug = check_values(p.getDrug, {entity_protein, "P129"})
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 ~= "" or expressed_in_tissues ~= localNotApplicableStr then p.renderRNAexpression(expression_images, entrez_gene, ensembl, expressed_in_tissues, ensembl_mm, expressed_in_mouse_tissues) 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 "정보 상자를 위한 위키데이터 항목을 검색하는 중 오류가 발생했습니다" end end
function p.createTable(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 function p.renderUpperTitle(name) local title = name if not title then return "error: failed to get label"; end
root :tag('tr') :tag('th') :attr('colspan', 4) :css('text-align', 'center') :css('font-size', '125%') :css('font-weight', 'bold') :wikitext(title) :done() --end th :done() --end tr end
--This is a place holder for the image caption, which is stored in wikicommons comments unsure how to access function p.renderCaption(entity) --caption end
--gets default image function p.renderImage(image) root :tag('tr') :tag('td') :attr('colspan', 4) :css('text-align', 'center') :wikitext(image) :done() --end td :done() --end tr end
function p.renderAvailableStructures(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs)
local title = '사용 가능한 구조' --**lclz** local pdb_link = "PDB" --**lclz** local searchTitle = "" local listTitle = "PDB ID 코드 목록" --**lclz** local PDBe_base = 'https://www.ebi.ac.uk/pdbe/searchResults.html?display=both&term=' local RCSB_base = 'https://www.rcsb.org/search?q=' ..'rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_name:UniProt%20AND%20' ..'rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_accession:' local url_uniprot = " "
if checkOrtholog == 1 and uniprotID_mm ~= 'n/a' then searchTitle = '동원체 검색: ' --**lclz** url_uniprot = uniprotID_mm..','..uniprotID_hs else searchTitle = '인간 유니프롯 검색: ' --**lclz** 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
function p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene) local title = "식별자" --**lclz** local label_aliases = "다른 이름" --**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 = ""..hgnc_id.." "..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 = "외부 ID" --**lclz**
omim_id = string.gsub(omim_id, "%s", "") local omim_list = mw.text.split(omim_id, localSeparatorStr) 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.." "..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, localSeparatorStr) local homolo ="" if (homologene_id ~= nil and homologene_id ~= "") then homolo = "HomoloGene"..": " end for i, v in ipairs(homolo_list) do if string.match(v, '%w+') then homolo = homolo..""..v.." "..v.." " end end homolo = string.gsub(homolo, ", $"," ") --remove comma from end
local genecards = "GeneCards"..": " genecards = genecards..""..gene_symbol.." "..gene_symbol.." "
mgi_id = string.gsub(mgi_id, "%s", "") local mgi_list = mw.text.split(mgi_id, localSeparatorStr) 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_id.." "..mgi_number.." " end end mgi = string.gsub(mgi, ", $"," ")--remove comma from end
local ChEMBL = "" if string.match(ChEMBL_id, '%w+') then ChEMBL = "ChEMBL"..": "..""..ChEMBL_id.." "..ChEMBL_id.." " end local IUPHAR = "" if string.match(IUPHAR_id, '%w+') then IUPHAR = "IUPHAR"..": "..""..IUPHAR_id.." "..IUPHAR_id.." " --**lclz** end -- *lclz* local label_EC = "EC 번호" --**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(mw.text.nowiki(aliases)) -- escape raw text so it cannot be wikitext markup :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
function p.renderDiseases(frame, disease, dis_ref, name, qid) local title = "유전관련질환" --**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 = name.."의 유전 관련 질병의 위키데이터 각주 보기/편집" --**lclz** local ref_link = disease_name..frame:extensionTag("ref",frame:expandTemplate{ title = '웹_인용', 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
function p.renderDrug(frame,drug, drug_ref, drug_pqid, drug_pname) local title = "유효 약제" --**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 local 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 local 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 = drug_pname[k].."의 물리적 상호작용을 하는 약제의 위키데이터 각주 보기/편집" --**lclz** local ref_link = drug_name..frame:extensionTag("ref",frame:expandTemplate{ title = '웹_인용', 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
function p.renderGeneLocation(frame, chr, gstart, gend, db, cytoband, ensembl, chr_mm, gstart_mm, gend_mm, db_mm, cytoband_mm, ensembl_mm, name) local titleHuman = "유전자 위치 (인간)" --**lclz** local titleMouse = "유전자 위치 (쥐)" --**lclz** local label_chr = "염색체" --**lclz** local label_locus = "자리" --**lclz** local label_gstart = "시작" --**lclz** local label_gend = "끝" --**lclz** local tooltip_arrowSign = name.."의 유전자 위치" --**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** linked articles chrTextTable["1"] = "염색체 1 (인간)" chrTextTable["2"] = "염색체 2 (인간)" chrTextTable["3"] = "염색체 3 (인간)" chrTextTable["4"] = "염색체 4 (인간)" chrTextTable["5"] = "염색체 5 (인간)" chrTextTable["6"] = "염색체 6 (인간)" chrTextTable["7"] = "염색체 7 (인간)" chrTextTable["8"] = "염색체 8 (인간)" chrTextTable["9"] = "염색체 9 (인간)" chrTextTable["10"] = "염색체 10 (인간)" chrTextTable["11"] = "염색체 11 (인간)" chrTextTable["12"] = "염색체 12 (인간)" chrTextTable["13"] = "염색체 13 (인간)" chrTextTable["14"] = "염색체 14 (인간)" chrTextTable["15"] = "염색체 15 (인간)" chrTextTable["16"] = "염색체 16 (인간)" chrTextTable["17"] = "염색체 17 (인간)" chrTextTable["18"] = "염색체 18 (인간)" chrTextTable["19"] = "염색체 19 (인간)" chrTextTable["20"] = "염색체 20 (인간)" chrTextTable["21"] = "염색체 21 (인간)" chrTextTable["22"] = "염색체 22 (인간)" chrTextTable["X"] = "X 염색체 (인간)" chrTextTable["Y"] = "Y 염색체 (인간)" chrTextTable["MT"] = "미토콘드리아 DNA (인간)" 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, source_link_gstart, source_link_gend if( db == "hg38" ) then source_link_chr = frame:extensionTag("ref", ""..ensembl.." GRCh38: Ensembl release 89: "..ensembl.." - 앙상블, 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", ""..ensembl.." GRCh37: Ensembl release 89: "..ensembl.." - 앙상블, May 2017", {name = "refGRCh37Ensembl"}) --**lclz** source_link_gstart = frame:extensionTag("ref", "", {name = "refGRCh37Ensembl"}) source_link_gend = frame:extensionTag("ref", "", {name = "refGRCh37Ensembl"}) else source_link_chr = "" 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.."
--wikitext_for_ideogram_image = wikitext_for_ideogram_image.."
"
"
else -- wikitext for autosome and sex chromosome
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."
wikitext_for_ideogram_image = wikitext_for_ideogram_image..""..chrText..""
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 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(titleHuman) :done() --end th :done() --end tr :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', rowBGcolor) :wikitext(""..chrText.."") :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).." bp"..source_link_gstart) -- **lclz** Change it if it is inappropriate :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).." bp"..source_link_gend) -- **lclz** Change it if it is inappropriate :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** Articles not yet created chrTextTable_mm["1"] = "염색체 1 (쥐)" chrTextTable_mm["2"] = "염색체 2 (쥐)" chrTextTable_mm["3"] = "염색체 3 (쥐)" chrTextTable_mm["4"] = "염색체 4 (쥐)" chrTextTable_mm["5"] = "염색체 5 (쥐)" chrTextTable_mm["6"] = "염색체 6 (쥐)" chrTextTable_mm["7"] = "염색체 7 (쥐)" chrTextTable_mm["8"] = "염색체 8 (쥐)" chrTextTable_mm["9"] = "염색체 9 (쥐)" chrTextTable_mm["10"] = "염색체 10 (쥐)" chrTextTable_mm["11"] = "염색체 11 (쥐)" chrTextTable_mm["12"] = "염색체 12 (쥐)" chrTextTable_mm["13"] = "염색체 13 (쥐)" chrTextTable_mm["14"] = "염색체 14 (쥐)" chrTextTable_mm["15"] = "염색체 15 (쥐)" chrTextTable_mm["16"] = "염색체 16 (쥐)" chrTextTable_mm["17"] = "염색체 17 (쥐)" chrTextTable_mm["18"] = "염색체 18 (쥐)" chrTextTable_mm["19"] = "염색체 19 (쥐)" chrTextTable_mm["X"] = "X 염색체 (쥐)" chrTextTable_mm["Y"] = "Y 염색체 (쥐)" chrTextTable_mm["MT"] = "미토콘드리아 DNA (쥐)" 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", ""..ensembl_mm.." GRCm38: Ensembl release 89: "..ensembl_mm.." - 앙상블, 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.."
--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.."
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm..""..chrText_mm..""
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(""..chrText_mm.."") :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).." bp"..source_link_gstart_mm) -- **lclz** Change it if it is inappropriate :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).." bp"..source_link_gend_mm) -- **lclz** Change it if it is inappropriate :done() --end span :done() --end td :done() --end tr :done() --end table :done() --end td :done() --end tr end end
--Get the render elements collapse option, collapsed anatomic entities (defaut text), --and anatomic entity list for the gene expression list rendering. function p.renderExpressionList(expressed_in_tissues, default_text) --create list of expressed in anatomic entities if default_text == nil then default_text = "" end local anatomic_entity_labels = localNotApplicableStr local collapse = "none" local split_values = mw.text.split(expressed_in_tissues, localSeparatorStr) local anatomic_entity_list = {} local anatomic_entities = {} local results for k,v in ipairs(split_values) do if string.match(v, '%w+') and v ~= localNotApplicableStr then
anatomic_entity_list[#anatomic_entity_list+1] = "
"
anatomic_entities[#anatomic_entities+1] = v
end
end
--if less than 11 don't create collapsible list
if table.getn(anatomic_entity_list) < 11 then
if table.getn(anatomic_entity_list) == 0 then
anatomic_entity_labels = localNotApplicableStr
default_text = ""
end
else
collapse = "collapsible collapsed"
default_text = default_text .. '
' .. table.remove(anatomic_entities, 1) .. '
' .. table.remove(anatomic_entities, 1) .. '
' ..table.remove(anatomic_entities, 1) .. '
' .. table.remove(anatomic_entities, 1) .. '
' .. table.remove(anatomic_entities, 1) .. '
'--get first 5 elements in table and use for display
end
if anatomic_entity_list[#anatomic_entity_list] then
anatomic_entity_labels = table.concat(anatomic_entity_list, "
")
end
results = {collapse, default_text, anatomic_entity_labels}
return results
end
function p.renderRNAexpression(expression_images, entrez_gene,
ensembl, bgee_expression, ensembl_mouse, bgee_expression_mouse)
local bgee_gene_page = "https://bgee.org/gene/"
local title = "RNA 발현 패턴" --**lclz**
local biogps_link = ""
local biogps_title = "BioGPS"
biogps_title = "" .. biogps_title .. ""
-- If no expression image exist in BioGPS, the N/A is displayed
if expression_images ~= "" then
biogps_link = ""..entrez_gene.."/ 추가 참조 발현 데이터" --**lclz**
else
expression_images = localNotApplicableStr
end
local ensembl_id = string.match(ensembl,"%a+%d+") or ""
local ensembl_id_mouse = string.match(ensembl_mouse,"%a+%d+") or ""
local bgee_title = "Bgee"
bgee_title = "" .. bgee_title .. ""
local bgee_default = "["..bgee_gene_page..ensembl_id.." 최상위 발현]"
bgee_expression = p.renderExpressionList(bgee_expression, bgee_default)
local bgee_collapse = bgee_expression[1]
bgee_default = bgee_expression[2]
local bgee_tissues = bgee_expression[3]
local bgee_default_mm = "["..bgee_gene_page..ensembl_id_mouse.." 최상위 발현]"
bgee_expression_mouse = p.renderExpressionList(bgee_expression_mouse, bgee_default_mm)
local bgee_collapse_mm = bgee_expression_mouse[1]
bgee_default_mm = bgee_expression_mouse[2]
local bgee_tissues_mm = bgee_expression_mouse[3]
local bgee_more_link = ""
if bgee_tissues ~= localNotApplicableStr then
bgee_more_link = "["..bgee_gene_page..ensembl_id.." More reference expression data]"
end
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('table')
:attr('class', 'collapsible')
: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('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(bgee_title)
:done() --end th
:tag('td')
:tag('table')
:attr('class', 'none')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:tag('th')
:wikitext("인간")
:done() --end th
:tag('th')
:wikitext("쥐(동원체)")
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:tag('table')
:attr('class', bgee_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'center')
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:css('margin', '-3px')
:wikitext(bgee_default)
:done() --end span
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('div')
:css('margin', '-12px 0px -10px 0px')
:attr('class', 'plainlinks')
:tag('ul')
:css('line-height', '15%')
:css('margin', '9px')
:wikitext(bgee_tissues)
:done() --end ul
:done() --end div
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:tag('td')
:tag('table')
:attr('class', bgee_collapse_mm)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'center')
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:css('margin', '-3px')
:wikitext(bgee_default_mm)
:done() --end span
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('div')
:css('margin', '-12px 0px -10px 0px')
:attr('class', 'plainlinks')
:tag('ul')
:css('line-height', '15%')
:css('margin', '9px')
:wikitext(bgee_tissues_mm)
:done() --end ul
:done() --end div
:done() --end td
:done() --end tr
:done() --end table
: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(bgee_more_link)
:done() --end span
: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(biogps_title)
:done() --end th
:tag('td')
:tag('table')
:attr('class', bgee_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
: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
:done() --end table
:done() --end td
:done() --end tr
end
function p.renderGeneOntology(mol_funct, cell_comp, bio_process, uniprotID)
local title = "유전자 온톨로지" --**lclz**
local mol_funct_title = "분자 함수" --**lclz**
local cell_comp_title = "세포 성분" --**lclz**
local bio_process_title = "생물학적 과정" --**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('td')
:css('background-color', sideTitleBGcolor)
:css('font-weight', 'bold')
:wikitext(mol_funct_title)
:done() --end td
:tag('td')
:css('background-color', rowBGcolor)
:tag('div')
:attr('class', 'plainlinks')
:wikitext(mol_funct)
:wikitext( '\n' ) -- newline before ending div tag, to ensure next section formats properly
:done() --end div
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:css('background-color', sideTitleBGcolor)
:css('font-weight', 'bold')
:wikitext(cell_comp_title)
:done() --end td
:tag('td')
:css('background-color', rowBGcolor)
:tag('div')
:attr('class', 'plainlinks')
:wikitext(cell_comp)
:wikitext( '\n' ) -- newline before ending div tag, to ensure next section formats properly
:done() --end div
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:css('background-color', sideTitleBGcolor)
:css('font-weight', 'bold')
:wikitext(bio_process_title)
:done() --end td
:tag('td')
:css('background-color', rowBGcolor)
:tag('div')
:attr('class', 'plainlinks')
:wikitext(bio_process)
:wikitext( '\n' ) -- newline before ending div tag, to ensure next section formats properly
:done() --end div
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:css('background-color', rowBGcolor)
:css('text-align', 'center')
:attr('colspan', '4')
:wikitext("출처:") -- **lclz**
:wikitext(amigo_link)
:wikitext(" / ")
:wikitext(quickGO_link)
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
end
function p.renderOrthologs(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 = "동원체" --**lclz**
--to do make the list creation a function
--create list for entrez ids
local category_chromosome = -- *lclz*: Category name
if chr == "MT" then
category_chromosome = -- *lclz*: Category name for mtDNA genes
end
if mw.title.getCurrentTitle().namespace ~= 0 then
category_chromosome = ""
end
local entrezTitle = "앙트레"
entrez_gene = string.gsub(entrez_gene, "%s", "")
local entrez_link = localNotApplicableStr
local entrez_collapse
local entrez_default = ""
local split_entrez = mw.text.split(entrez_gene, localSeparatorStr)
local entrez_link_list = {}
for k,v in ipairs(split_entrez) do
if string.match(v, '%w+') and v ~= localNotApplicableStr then
entrez_link_list[#entrez_link_list+1] = ""..entrez_gene.."&rn=1 "..entrez_gene..""
end
end
--if less than 5 don't create collapsible list
if table.getn(entrez_link_list) < 5 then
entrez_collapse = "none"
if entrez_default == nil and table.getn(entrez_link_list) == 0 then entrez_link = localNotApplicableStr 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 = localNotApplicableStr
local entrez_mm_collapse
local entrez_mm_default = ""
local split_entrez_mm = mw.text.split(entrez_gene_mm, localSeparatorStr)
local entrez_mm_link_list = {}
for k,v in ipairs(split_entrez_mm) do
if string.match(v, '%w+') and v ~= localNotApplicableStr then
entrez_mm_link_list[#entrez_mm_link_list+1] = ""..v.."&rn=1 "..v..""
end
end
--if less than 5 don't create collapsible list
if table.getn(entrez_mm_link_list) < 5 then
entrez_mm_collapse = "none"
if entrez_mm_default == nil and table.getn(entrez_mm_link_list) == 0 then entrez_mm_link = localNotApplicableStr 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 = "앙상블"
ensembl = string.gsub(ensembl, "%s", "")
local ensembl_link = localNotApplicableStr
local ensembl_collapse
local ensembl_default = ""
local split_ensembl = mw.text.split(ensembl, localSeparatorStr)
local ensembl_link_list = {}
for k,v in ipairs(split_ensembl) do
if string.match(v, '%w+') and v ~= localNotApplicableStr then
ensembl_link_list[#ensembl_link_list+1] = ""..v..";db=core".." "..v..""
end
end
--if less than 5 don't create collapsible list
if table.getn(ensembl_link_list) < 5 then
ensembl_collapse = "none"
if ensembl_default == nil and table.getn(ensembl_link_list) == 0 then ensembl_link = localNotApplicableStr 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
ensembl_mm = string.gsub(ensembl_mm, "%s", "")
local ensembl_mm_link = localNotApplicableStr
local ensembl_mm_collapse
local ensembl_mm_default = ""
local split_ensembl_mm = mw.text.split(ensembl_mm, localSeparatorStr)
local ensembl_mm_link_list = {}
for k,v in ipairs(split_ensembl_mm) do
if string.match(v, '%w+') and v ~= localNotApplicableStr then
ensembl_mm_link_list[#ensembl_mm_link_list+1] = ""..v..";db=core".." "..v..""
end
end
--if less than 5 don't create collapsible list
if table.getn(ensembl_mm_link_list) < 5 then
ensembl_mm_collapse = "none"
if ensembl_mm_default == nil and table.getn(ensembl_mm_link_list) == 0 then ensembl_mm_link = localNotApplicableStr 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 = "유니프롯"
local uniprot_url = "https://www.uniprot.org/uniprot/"
local uniprot_link = localNotApplicableStr
local uniprot_collapse
local uniprot_default = ""
--split string and loop through concatenate by
local split_uniprot = mw.text.split(uniprot, '%p') -- the separator may be different sometimes, see note on zhwiki. This is unlikely to have punctuation, prayer.
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 ~= localNotApplicableStr 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 = localNotApplicableStr 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 = localNotApplicableStr
local uniprot_mm_collapse
local uniprot_mm_default = ""
--split string and loop through concatenate by
local split_uniprot_mm = mw.text.split(uniprot_mm, localSeparatorStr)
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 ~= localNotApplicableStr 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 = localNotApplicableStr 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 = localNotApplicableStr
local refseq_mRNA_collapse
local refseq_mRNA_default = ""
--split string and loop through concatenate by
local split_refseq_mRNA = mw.text.split(refseq_mRNA, localSeparatorStr)
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 ~= localNotApplicableStr 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 = localNotApplicableStr 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 = localNotApplicableStr
local refseq_mRNA_mm_collapse
local refseq_mRNA_mm_default = ""
local split_refseq_mRNA_mm = mw.text.split(refseq_mRNA_mm, localSeparatorStr)
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 ~= localNotApplicableStr 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 = localNotApplicableStr 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(단백질)"
--create list of links for human refseq protein
local refseq_prot_link = localNotApplicableStr
local refseq_prot_collapse
local refseq_prot_default = ""
local split_refseq_prot = mw.text.split(refseq_prot, localSeparatorStr)
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 ~= localNotApplicableStr 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 = localNotApplicableStr 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 = localNotApplicableStr
local refseq_prot_mm_collapse
local refseq_prot_mm_default = ""
local split_refseq_prot_mm = mw.text.split(refseq_prot_mm, localSeparatorStr)
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 ~= localNotApplicableStr 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 = localNotApplicableStr 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 = "위치(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 = ""..db.."&position=chr"..chr_ucsc..":"..gstart.."-"..gend.." ".."Chr "..chr_ucsc..": "..gstart_mb.." – "..gend_mb.." Mb"
else
chr_loc_link = localNotApplicableStr
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 = ""..db_mm.."&position=chr"..chr_mm_ucsc..":"..gstart_mm.."-"..gend_mm.." ".."Chr "..chr_mm_ucsc..": "..gstart_mm_mb.." – "..gend_mm_mb.." Mb"
else
chr_loc_mm_link = localNotApplicableStr
end
local pubmedTitle = "PubMed 검색" -- *lclz*
local pubmed_link = entrez_gene
if string.match(entrez_gene, '%w+') and entrez_gene ~= localNotApplicableStr then
pubmed_link = frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title ="Human PubMed Reference:" , url = "https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene, website = "National Center for Biotechnology Information, U.S. National Library of Medicine" } } )--expandTemplate creates cite web template [ref_link..ect “value”] |url= 값 확인 필요 (도움말).
end
local pubmed_mm_link = entrez_gene_mm
if string.match(entrez_gene_mm, '%w+') and entrez_gene_mm ~= localNotApplicableStr then
pubmed_mm_link = frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title ="Mouse PubMed Reference:" , url ="https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene_mm, website = "National Center for Biotechnology Information, U.S. National Library of Medicine" } } )--expandTemplate creates cite web template [ref_link..ect “value”] |url= 값 확인 필요 (도움말).
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(title)
:done() --end th
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext("종") --**lclz**
:done() --end th
:tag('td')
:wikitext("인간") --**lclz**
:done() --end td
:tag('td')
:wikitext("쥐") --**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
:done() --end table
:done() --end td
:done() --end tr
end
function p.formatRow(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
function p.renderFooter(Qid, Qid_mm)
local text = "위키데이터" --**lclz**
local hs_link = "인간 보기/편집" --**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 = "쥐 보기/편집" --**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
function p.rowLabel(label)
root
:tag('tr')
:tag('th')
:attr('rowspan', '2')
:css('background-color', sideTitleBGcolor)
:css('width', '43px')
:wikitext(label)
--:done()
end
-- look into entity object
function p.getLabel(entity)
local data = entity
local f = {'labels','ko','value'} --**lclz**
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
-- Get property values formatted as a string of a given instance/entity.
-- 'entity' parameter denfines the instance from which we want to get some property values.
-- 'propertyID' parameter defines from which property the values are gotten.
-- 'rertun_val' parameter, if no result is returned, the value assigned to this parameter is returned, the default value is an empty string.
-- 'sep' parameter is the separation caracter used to separate returned values (e.g. ','), default is a space caracter, e.g. ' '.
-- Assign to 'stated_in' a wikidata entry id, if getValue() should only return values containing a reference statement 'stated in' (e.g. database, project, catalog). Note that the 'stated_in' parameter is only considered, if the assigned value to 'propertyID' is a wikidata entry.
function p.getValue(entity, propertyID, return_val, sep, stated_in)
local claims
if return_val == nil then return_val = "" end
if sep == nil then sep = " " 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 = {}
for k, v in pairs(claims) do
local datav = mw.wikibase.label(v.mainsnak.datavalue.value["id"])
if datav == nil then datav = " " end
--Filter statements with the specified stated_in reference value, if none (stated_in = nil) all statements are considered.
local is_from_given_source = true
if stated_in ~= nil then
is_from_given_source = false
if v.references then
for rk, rv in pairs(v.references) do
local ref_val = rv.snaks.P248
if ref_val then
for stated_k, stated_v in pairs(ref_val) do
if (stated_v and stated_v.snaktype == "value" and stated_v.datavalue.type == "wikibase-entityid") then
local ref_stated_in_val = stated_v.datavalue.value["id"]
if ref_stated_in_val == stated_in then is_from_given_source = true end
end
end
end
end
end
end
if is_from_given_source then
out[#out + 1] = datav
end
end
return table.concat(out, sep)
else
-- just return best values
return entity:formatPropertyValues(propertyID).value
end
else
return return_val
end
end
function p.getValueProtein(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.getLabel("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
function p.getQid(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.
function p.getRefseq_mRNA(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.getSitelink("Q" .. v.mainsnak.datavalue.value["numeric-id"])
local label = mw.wikibase.getLabel("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, localSeparatorStr)
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
function p.getRefseq_protein(protein_entities, propertyID, return_val)
local sep = localSeparatorStr
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[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.getLabel("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, 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
function p.getImage(entity, propertyID, sep, imgsize)
local claims
if entity and entity.claims then
claims = entity.claims[propertyID]
end
if claims then
if (claims[1] and claims[1].mainsnak.datatype == "commonsMedia") then
local out = {}
for k, v in pairs(claims) do
local filename = v.mainsnak.datavalue.value
out[#out + 1] = "" .. imgsize .. ""
end
return table.concat(out, sep)
else
return ""
end
else
return ""
end
end
function p.getPDB(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.getLabel(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(pdb_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)
if entity['aliases'] ~= nil then
-- *lclz*: You will need a different language here.
-- If you are aiming for an "en" fallback, consider a set data structure.
-- zhwp went a bit further here: they moved this call after "gene_symbol",
-- so that this function can perform the deduplication here instead of
-- in renderIdentifiers. That way they skip messing with commas and spaces.
local test = entity['aliases']['en']
if test then
local a =
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
function p.getChromosomeLoc(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.getEntity(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.getEntity(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
function p.getAliasFromGenomeAssembly(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 location = -- TODO what should this be? defining location is required for 'output = location' below
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.getEntity(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.
function p.trimChromosome(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, 'chromosome') then --**lclz** Add your local label, otherwise it may break
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
function p.locToMb(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
function p.isempty(s)
return s == nil or s ==
end
function p.getGO(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.getEntity(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.getLabel("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 = "\n* [" .. sitelink .. result_GOID .. " " .. label .."]"
else
wiki_link = "\n* [[:d:Q" .. v.mainsnak.datavalue.value["numeric-id"] .. "|" .. label .. "]]"
end
overall_results[#overall_results+1] = wiki_link
end
else
results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value
end
end
--overall_results[#overall_results+1] = results --each protein GO terms stored in this index, so table contains all the GO terms with duplicates
end
local hash = {} --temp check
local res = {} --no dups
for _,v in ipairs(overall_results) do
if (not hash[v]) then
res[#res+1] = v
hash[v] = true
end
end
return table.concat(res, "")
end
local function getReference(qID, entity, property_id, ref_index)
local f = {"claims",property_id, ref_index, "references"}
local id = qID
--if id and (#id == 0) then
-- id = nil
--end
local data = entity
if not data then
return nil
end
local i = 1
while true do
local index = f[i]
if not index then
if type(data) == "table" then
return mw.text.jsonEncode(data, mw.text.JSON_PRESERVE_KEYS + mw.text.JSON_PRETTY)
else
return tostring(data)
end
end
data = data[index] or data[tonumber(index)]
if not data then
return ""
end
i = i + 1
end
end
function p.getDisease(entity, propertyID)
local claims
local return_val = "" -- define variable; this line was 'if return_val == nil then return_val = "" end' which looks like a copy/paste
if entity and entity.claims then
claims = entity.claims[propertyID]
end
if claims then
-- if wiki-linked value output as link if possible
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
local out = {}
local datasource = {}
--https://omim.org/entry/131244
--maybe there is a more direct way to find this than looping through the json object
for k, v in pairs(claims) do
local datav = mw.wikibase.getLabel("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.getSitelink(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
function p.getDrug(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.getLabel("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.getSitelink(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
function p.separateWithComma(bp)
--Separate number with comma. For example when this function gets "12345678", returns "12,345,678"
local commaSeparated = bp
while true do
local k
commaSeparated, k = string.gsub(commaSeparated, "^(-?%d+)(%d%d%d)", '%1,%2')
if k == 0 then
break
end
end
return commaSeparated
end
return p