User:Kaguya-Taketori/SB2
local p = { }
local navbar = require('Module:Navbar')._navbar local infobox = require('Module:Infobox3cols').infobox local infoboxImage = require('Module:InfoboxImage').InfoboxImage
local wbr = '' -- U+200B 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 return("VALUE_ERROR (" .. tostring(val) .. ")") end end --texts relevant to localization are tagged with -- localization required! or ";10n" --on a page 脚本错误：没有“Sandbox/genewiki/alllua”这个模块。 --in debug window --frame = mw.getCurrentFrame() --frame.args = {QID="Q14865053"} Q18031325 --print(p.getTemplateData(frame)) p.getTemplateData = function(frame)
--make some guesses about whether the provided QID is a good one --could expand here if we had some kind of error handling framework --did we get it from the page local root_qid = mw.text.trim(frame.args['QID'] or "") --try to get it from the args local mm_qid = "" --pull all the entity objects that we will need local entity = {} local entity_protein = {} local entity_mouse = {} local entity_mouse_protein = {} local checkOrtholog = "" --flag used to see if mouse data avaliable
local mouse_propertyID = "P684" local protein_propertyID = "P688"
--get root gene entity if root_qid == "" then entity = mw.wikibase.getEntityObject() if entity then root_qid = entity.id else root_qid = "" end
else --assuming we think its good make one call to retrieve and store its wikidata representation entity = mw.wikibase.getEntity(root_qid) end
--need to figure out if it is protein or gene here
local subclass = p.getValue(entity, "P279") or "" if string.find(subclass, 'protein') then --if protein switch entity to gene if entity.claims then claims = entity.claims["P702"] --encoded by end if claims then --go through each index and reassign entity entity = {} if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then for k, v in pairs(claims) do --this would be problematic if multiple genes for the protein local itemID = "Q" .. claims[#entity + 1].mainsnak.datavalue.value["numeric-id"] entity[#entity + 1] = mw.wikibase.getEntity(itemID) root_qid = itemID end
end --will return nothing if no claims are found end entity = mw.wikibase.getEntity(root_qid) end
--get the other related entities
if entity then
local claims = ""
--get protein entity object
if entity.claims then
claims = entity.claims[protein_propertyID]
end
if claims then
--go through each index and then make entity_protein indexed
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do
local protein_itemID = "Q" .. claims[#entity_protein + 1].mainsnak.datavalue.value["numeric-id"]
entity_protein[#entity_protein + 1] = mw.wikibase.getEntity(protein_itemID)
end
end --will return nothing if no claims are found end
--get mouse entity object if entity.claims then claims = entity.claims[mouse_propertyID] end if claims then if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then local mouse_itemID = "Q" .. claims[1].mainsnak.datavalue.value["numeric-id"] mm_qid = mouse_itemID entity_mouse = mw.wikibase.getEntity(mouse_itemID) checkOrtholog = 1 end --will return nothing if no claims are found else checkOrtholog = 0 end
--get mouse protein entity object if entity_mouse and entity_mouse.claims then claims = entity_mouse.claims[protein_propertyID] end if claims then if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then for k, v in pairs(claims) do local protein_itemID = "Q" .. claims[#entity_mouse_protein + 1].mainsnak.datavalue.value["numeric-id"] entity_mouse_protein[#entity_mouse_protein + 1] = mw.wikibase.getEntity(protein_itemID) end end --will return nothing if no claims are found end
end
if entity then --only require the main gene entity
--a list variables of all the data in the info box
local name = check_values(p.getLabel,{entity})
local entrez_gene = check_values(p.getValue, {entity, "P351", "n/a"} )
local entrez_gene_mm = check_values(p.getValue, {entity_mouse, "P351", "n/a"})
local image = check_values( p.getImage, {entity, "P18", " ", "250px"}) --need to set size
local uniprotID_hs = check_values(p.getValueProtein, {entity_protein, "P352", "n/a"})
local uniprotID_mm = check_values(p.getValueProtein, {entity_mouse_protein, "P352", "n/a"})
local pdbIDs = check_values(p.getPDB, {entity_protein}) --makes a list with links to RCSB; wikitext (l10n)
local gene_symbol = check_values(p.getValue, {entity, "P353"})
local aliases = check_values(p.getAliases, {entity, gene_symbol}) -- l10nmod: eliminate early
local hgnc_id = check_values(p.getValue, {entity, "P354"})
local homologene_id = check_values(p.getValue, {entity, "P593"})
local omim_id = check_values(p.getValue, {entity, "P492"})
local mgi_id = check_values(p.getValue, {entity_mouse, "P671"})
local ChEMBL_id = check_values(p.getValue, {entity_protein, "P592"})
local IUPHAR_id = check_values(p.getValue, {entity_protein, "P595"})
local ec_no = check_values(p.getValueProtein, {entity_protein, "P591"})
local mol_funct = check_values(p.getGO, {entity_protein, "P680"})
local cell_comp = check_values(p.getGO, {entity_protein, "P681"})
local bio_process = check_values(p.getGO, {entity_protein, "P682"})
local expression_images = check_values(p.getImage, {entity,"P692","
","250px"})
local ensembl = check_values(p.getValue, {entity, "P594", "n/a"})
local ensembl_mm = check_values(p.getValue, {entity_mouse, "P594", "n/a"})
local refseq_mRNA = check_values(p.getRefseq_mRNA, {entity, "P639", "n/a"})
local refseq_mRNA_mm = check_values(p.getRefseq_mRNA, {entity_mouse, "P639", "n/a"})
local refseq_prot = check_values(p.getRefseq_protein, {entity_protein, "P637", "n/a"})
local refseq_prot_mm = check_values(p.getRefseq_protein, {entity_mouse_protein, "P637", "n/a"})
local gstart = check_values(p.getChromosomeLoc, {entity, "P644", "hg"})
local gend = check_values(p.getChromosomeLoc, {entity, "P645", "hg"})
local chr = check_values(p.trimChromosome, {entity})
local db = check_values(p.getAliasFromGenomeAssembly, {entity,"hg"})
local gstart_mm = check_values(p.getChromosomeLoc, {entity_mouse, "P644", "mm"})
local gend_mm = check_values(p.getChromosomeLoc, {entity_mouse, "P645", "mm"})
local db_mm = check_values(p.getAliasFromGenomeAssembly, {entity_mouse,"mm"})
local chr_mm = check_values( p.trimChromosome, {entity_mouse})
local disease, dis_ref =
if p.getDisease(entity, "P2293") then disease, dis_ref = p.getDisease(entity, "P2293") else disease, dis_ref = {"VALUE_ERROR","VALUE_ERROR" } end
if p.getDrug(entity_protein, "P129") then drug, drug_ref, drug_pqid, drug_pname = p.getDrug(entity_protein, "P129") else drug, drug_ref, drug_pqid, drug_pname = {"VALUE_ERROR","VALUE_ERROR" } end
--local drug = check_values(p.getDrug, {entity_protein, "P129"})
--define Global Color Scheme rowBGcolor = '#eee' titleBGcolor = '#ddd' sideTitleBGcolor = '#c3fdb8'
p.createTable()
p.renderUpperTitle(name) --p.renderCaption() p.renderImage(image) p.renderAvailableStructures(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs) --PDB info
p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene) if (disease ~= "" and dis_ref ~= "") then --removes section from those items without disease info p.renderDiseases(frame, disease, dis_ref, name, root_qid) end
if (drug ~= "" ) then --removes section from those items without drug info p.renderDrug(frame,drug, drug_ref, drug_pqid, drug_pname)
end
if (mol_funct ~= "" and cell_comp ~= "" and bio_process ~= "") then p.renderGeneOntology(mol_funct, cell_comp, bio_process, uniprotID_hs) end if expression_images ~= "" then p.renderRNAexpression(expression_images, entrez_gene) end p.renderOrthologs(frame, entrez_gene, entrez_gene_mm, ensembl, ensembl_mm, uniprotID_hs, uniprotID_mm, refseq_mRNA, refseq_mRNA_mm, refseq_prot, refseq_prot_mm, db, chr, gstart, gend, db_mm, chr_mm, gstart_mm, gend_mm) p.renderFooter(root_qid, mm_qid)
return tostring(root)
--return table.concat(drug_pqid)
else return "An Error has occurred retrieving Wikidata item for infobox" end end
p.createTable = function(subbox)
if subbox == 'sub' then --doesn't work
root
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', 'auto')
:css('min-width', '100%')
:css('font-size', '100%')
:css('clear', 'none')
:css('float', 'none')
:css('background-color', 'transparent')
else
root = mw.html.create('table')
root
:addClass('infobox')
-- :css('width', '26.4em')
-- l10n: zh Module:Infobox
:css('width', '22em')
:css('text-align', 'left')
:css('font-size', 'small')
:css('line-height', '1.5em')
end
end
--Title above image p.renderUpperTitle = function(name) local title = name
if not title then return "error: failed to get label"; end
root
:tag('tr')
:tag('th')
:attr('colspan', 4)
:css('text-align', 'center')
:css('font-size', '125%')
:css('font-weight', 'bold')
:wikitext(title)
:done() --end th
:done() --end tr
end
--This is a place holder for the image caption, which is stored in wikicommons comments unsure how to access p.renderCaption = function(entity) --caption end
--gets default image p.renderImage = function(image)
root :tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:wikitext(image)
:done() --end td
:done() --end tr
end
p.renderAvailableStructures = function(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs)
local title = '已知的結構' -- localization required! local pdb_link = "PDB" -- localization required! local searchTitle = "" local listTitle = "PDBID列表" -- localization required! local PDBe_base = 'https://www.ebi.ac.uk/pdbe/searchResults.html?display=both&term=' local RCSB_base = 'http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=UpAccessionIdQuery&accessionIdList=' local url_uniprot = " " if checkOrtholog == 1 and uniprotID_mm ~= 'n/a' then searchTitle = 'Ortholog search: ' url_uniprot = uniprotID_mm..','..uniprotID_hs else searchTitle = 'Human UniProt search: ' url_uniprot = uniprotID_hs end local PDBe_list = " " --create a list with " or " if there is more than one uniprot --get first uniprot in a list
if url_uniprot:match("([^,]+),") then--first check if there is a list if not just assume one value PDBe_list = string.gsub(url_uniprot, ",", "%%20or%%20") --add or's inststead of commas else PDBe_list = url_uniprot end
local PDBe = "["..PDBe_base..PDBe_list.." PDBe] " local RCSB = "["..RCSB_base..url_uniprot.." RCSB] " if string.match(pdbIDs, '%w+') then --if there aren't any PDB_ID don't display this part of the infobox --p.formatRow(title)---how to not close the tags is a mystery and I could condense code once I figure out root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr') --create title header
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color',titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:tag('tr')
:tag('th')
:attr('rowspan', '2')
:css('background-color', sideTitleBGcolor)
:css('width', '43px')
:wikitext(pdb_link)
:done() --end th
:tag('td')
:attr('colspan', '2')
:css('background-color', rowBGcolor)
:wikitext(searchTitle)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(PDBe)
:wikitext(RCSB)
:done() --end span
:done() --end td
:done() --end tr
:tag('tr') --new row for collapsible list of PDB codes
:tag('td')
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:css('background-color',titleBGcolor)
:css('text-align', 'center')
:tag('th')
:attr('colspan', '2')
:wikitext(listTitle)
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '2')
:css('background-color', rowBGcolor)
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(pdbIDs)
:done() --end span
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
else
return ""
end
end
p.renderIdentifiers = function(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene) local title = "識別號" -- localization required! local label_aliases = "别名" -- localization required! 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
-- l10n: alias filter removed (pre-done) local label_ext_id = "外部ID" -- localization required!
omim_id = string.gsub(omim_id, "%s", "") local omim_list = mw.text.split(omim_id, ",") local omim = "" if (omim_id ~= nil and omim_id ~= "") then omim = "OMIM".."：" -- localization required! 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, ",") 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, ",") local mgi = "" if (mgi_id ~= nil and mgi_id ~= "") then mgi = "MGI".."：" -- localization required! 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.." " -- localization required! end local label_EC = "EC number" -- localization required! ec_no = string.gsub(ec_no, "%d%.%d+%.%d+%.%-,", "")--remove those with"-" in list ec_no = string.gsub(ec_no, "%d%.%d+%.%d+%.%-", "")--remove those with"-" not in list local link_ec_no = string.gsub(ec_no, "," ,"+") --create format for link
local EC = "" .. link_ec_no .. " " .. ec_no .. ""
root :tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(label_aliases)
:done() --end span
:done() --end th
:tag('td')
:attr('colspan','3')
:css('background', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(symbol_url)
:done() --end span
:wikitext('；' .. aliases)
:done() --end td
:done() --end tr
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(label_ext_id)
:done() --end th
:tag('td')
:attr('colspan', '3')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(omim)
:wikitext(mgi)
:wikitext(homolo)
:wikitext(ChEMBL)
:wikitext(IUPHAR)
:wikitext(genecards)
:done() --end span
:done() --end td
:done() --end tr
if ec_no ~= "" then root
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(label_EC)
:done() --end th
:tag('td')
:attr('colspan', '3')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(EC)
:done() --end span
:done() --end td :done() --end tr
end
end
p.renderDiseases = function(frame, disease, dis_ref, name, qid) local title = "相關疾病" -- localization required!
--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..'、'.. wbr..value --l10n 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 = "與"..name.."相關的疾病；在維基數據上查看/編輯參考" local ref_link = disease_name..frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title = title, url = ref_url} })
root :tag('tr') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor) :tag('td') :css('background-color', rowBGcolor) :attr('scope', 'row') :attr('colspan', '3') :wikitext(ref_link) :done() --end td :done() --end tr
end
end
p.renderDrug = function(frame,drug, drug_ref, drug_pqid, drug_pname)
local title = "為以下藥物的標靶" --**lzlc**
--check first to see if any of the drugs have references
local ref_flag_all = false --check if any drugs have references if not then don't render the headers drug_list_per_protein = {} -- a list of lists of drugs to put in reference string each protein will have a list --for i,v in ipairs(drug_pqid) do -- set all lists keys to empty so can append without key errors
--end for index,value in ipairs(drug) do if (drug_ref[index] ~= nil and drug_ref[index] ~= ) then protein_qid = drug_pqid[index] if drug_list_per_protein[protein_qid] == or drug_list_per_protein[protein_qid] == nil then drug_list_per_protein[protein_qid] = value else -- localization required! (punct) drug_list_per_protein[protein_qid] = drug_list_per_protein[protein_qid]..'、'.. wbr ..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 = "對"..drug_pname[k].."起作用的藥物；在維基數據上查看/編輯參考"
local ref_link = drug_name..frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title = title, url = ref_url} })
root :tag('tr')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('td') :css('background-color', rowBGcolor) :attr('scope', 'row') :attr('colspan', '3') :wikitext(ref_link) :done() --end td :done() --end tr
end end
end
p.renderGeneOntology = function(mol_funct, cell_comp, bio_process, uniprotID) local title = "基因本體" -- localization required! local mol_funct_title = "分子功能" -- localization required! local cell_comp_title = "細胞組分" -- localization required! local bio_process_title = "生物學過程" -- localization required! local amigo_link = "" .. " Amigo" local quickGO_link = "" .. " QuickGO"
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr') --create title bar
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:tag('tr')
:tag('th')
:css('background-color', sideTitleBGcolor)
:wikitext(mol_funct_title)
:done() --end th
:tag('td')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(mol_funct)
:done() --end span
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:css('background-color', sideTitleBGcolor)
:wikitext(cell_comp_title)
:done() --end th
:tag('td')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(cell_comp)
:done() --end span
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:css('background-color', sideTitleBGcolor)
:wikitext(bio_process_title)
:done() --end th
:tag('td')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(bio_process)
:done() --end span
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:css('background-color', rowBGcolor)
:css('text-align', 'center')
:attr('colspan', '4')
:wikitext("Sources:")
:wikitext(amigo_link)
:wikitext(" / ")
:wikitext(quickGO_link)
:done() --end td
:done() --end tr
:done() --end table :done() --end td :done() --end tr end
p.renderRNAexpression = function(expression_images, entrez_gene) local title = "RNA表达模式" -- localization required! -- ^^^ zhnote: one-way NoteTA local biogps_link = ""..entrez_gene.."/ 更多參考（基因）表达數據" -- localization required! root :tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:wikitext(expression_images)
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(biogps_link)
:done() --end span
:done() --end td
:done() --end tr
end
p.renderOrthologs = function(frame, entrez_gene, entrez_gene_mm, ensembl, ensembl_mm, uniprot, uniprot_mm, refseq_mRNA, refseq_mRNA_mm, refseq_prot, refseq_prot_mm, db, chr, gstart, gend, db_mm, chr_mm,gstart_mm, gend_mm) local title = "直系同源" -- localization required! --to do make the list creation a function --create list for entrez ids
-- Special Cases for zh
local category_chromosome_special = {
['X']=,
['Y']=,
['M']=, -- 不知道有沒有用
}
local category_chromosome = category_chromosome_special[chr] or
if mw.title.getCurrentTitle().namespace ~= 0 then
category_chromosome = ""
end
local entrezTitle = "Entrez"
entrez_gene = string.gsub(entrez_gene, "%s", "")
local entrez_link = "n/a"
local entrez_collapse
local entrez_default = ""
local split_entrez = mw.text.split(entrez_gene, ",")
local entrez_link_list = {}
for k,v in ipairs(split_entrez) do
if string.match(v, '%w+') and v ~= "n/a" then
entrez_link_list[#entrez_link_list+1] = ""..entrez_gene.."&rn=1 "..entrez_gene..""
end
end
--if less than 5 don't create collapsible list
if table.getn(entrez_link_list) < 5 then
entrez_collapse = "none"
if entrez_default == nil and table.getn(entrez_link_list) == 0 then entrez_link = "n/a" end
else
entrez_collapse = "collapsible collapsed"
entrez_default = table.remove(entrez_link_list, 1) .. '
' .. table.remove(entrez_link_list, 1) .. '
' ..table.remove(entrez_link_list, 1) .. '
' .. table.remove(entrez_link_list, 1) .. '
' .. table.remove(entrez_link_list, 1) .. '
'--get first 5 elements in table and use for display
end
if entrez_link_list[#entrez_link_list] then
entrez_link = table.concat(entrez_link_list, "
")
end
--create list for mouse Entrez id
entrez_gene_mm = string.gsub(entrez_gene_mm, "%s", "")
local entrez_mm_link = "n/a"
local entrez_mm_collapse
local entrez_mm_default = ""
local split_entrez_mm = mw.text.split(entrez_gene_mm, ",")
local entrez_mm_link_list = {}
for k,v in ipairs(split_entrez_mm) do
if string.match(v, '%w+') and v ~= "n/a" then
entrez_mm_link_list[#entrez_mm_link_list+1] = ""..v.."&rn=1 "..v..""
end
end
--if less than 5 don't create collapsible list
if table.getn(entrez_mm_link_list) < 5 then
entrez_mm_collapse = "none"
if entrez_mm_default == nil and table.getn(entrez_mm_link_list) == 0 then entrez_mm_link = "n/a" end
else
entrez_mm_collapse = "collapsible collapsed"
entrez_mm_default = table.remove(entrez_mm_link_list, 1) .. '
' .. table.remove(entrez_mm_link_list, 1) .. '
' ..table.remove(entrez_mm_link_list, 1) .. '
' .. table.remove(entrez_mm_link_list, 1) .. '
' .. table.remove(entrez_mm_link_list, 1) .. '
'--get first 5 elements in table and use for display
end
if entrez_mm_link_list[#entrez_mm_link_list] then
entrez_mm_link = table.concat(entrez_mm_link_list, "
")
end
--create list of ensembl id
local ensemblTitle = "Ensembl"
ensembl = string.gsub(ensembl, "%s", "")
local ensembl_link = "n/a"
local ensembl_collapse
local ensembl_default = ""
local split_ensembl = mw.text.split(ensembl, ",")
local ensembl_link_list = {}
for k,v in ipairs(split_ensembl) do
if string.match(v, '%w+') and v ~= "n/a" then
ensembl_link_list[#ensembl_link_list+1] = ""..v..";db=core".." "..v..""
end
end
--if less than 5 don't create collapsible list
if table.getn(ensembl_link_list) < 5 then
ensembl_collapse = "none"
if ensembl_default == nil and table.getn(ensembl_link_list) == 0 then ensembl_link = "n/a" end
else
ensembl_collapse = "collapsible collapsed"
ensembl_default = table.remove(ensembl_link_list, 1) .. '
' .. table.remove(ensembl_link_list, 1) .. '
' ..table.remove(ensembl_link_list, 1) .. '
' .. table.remove(ensembl_link_list, 1) .. '
' .. table.remove(ensembl_link_list, 1) .. '
'--get first 5 elements in table and use for display
end
if ensembl_link_list[#ensembl_link_list] then
ensembl_link = table.concat(ensembl_link_list, "
")
end
--create list of mouse ensembl id
local ensemblTitle = "Ensembl"
ensembl_mm = string.gsub(ensembl_mm, "%s", "")
local ensembl_mm_link = "n/a"
local ensembl_mm_collapse
local ensembl_mm_default = ""
local split_ensembl_mm = mw.text.split(ensembl_mm, ",")
local ensembl_mm_link_list = {}
for k,v in ipairs(split_ensembl_mm) do
if string.match(v, '%w+') and v ~= "n/a" then
ensembl_mm_link_list[#ensembl_mm_link_list+1] = ""..v..";db=core".." "..v..""
end
end
--if less than 5 don't create collapsible list
if table.getn(ensembl_mm_link_list) < 5 then
ensembl_mm_collapse = "none"
if ensembl_mm_default == nil and table.getn(ensembl_mm_link_list) == 0 then ensembl_mm_link = "n/a" end
else
ensembl_mm_collapse = "collapsible collapsed"
ensembl_mm_default = table.remove(ensembl_mm_link_list, 1) .. '
' .. table.remove(ensembl_mm_link_list, 1) .. '
' ..table.remove(ensembl_mm_link_list, 1) .. '
' .. table.remove(ensembl_mm_link_list, 1) .. '
' .. table.remove(ensembl_mm_link_list, 1) .. '
'--get first 5 elements in table and use for display
end
if ensembl_mm_link_list[#ensembl_mm_link_list] then
ensembl_mm_link = table.concat(ensembl_mm_link_list, "
")
end
--create lists of uniprot ID
local uniprotTitle = "UniProt"
local uniprot_url = "http://www.uniprot.org/uniprot/"
local uniprot_link = "n/a"
local uniprot_collapse
local uniprot_default = ""
--split string and loop through concatenate by
local split_uniprot = mw.text.split(uniprot, ",")
local uniprot_link_list = {}
local uniprot_first = {} --preferred values only display [O,P,Q] prefixed entries if they exist
local uniprot_alternate = {} --[A-N,R-Z] entries
local hash = {} --storage to look for duplicated values
for k,v in ipairs(split_uniprot) do
if not hash[v] then --only add if not found previously..some encodes uniprotID dup in different encodes
local label = mw.text.trim(v)
local concat_uniprot_link = uniprot_url .. label
if string.match(v, '%w+') and v ~= "n/a" then
if string.match(v, '^O') or string.match(v,'^P') or string.match(v, '^Q') then
uniprot_first[#uniprot_first+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"
else
uniprot_alternate[#uniprot_alternate+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"
end
end
hash[v] = true
end
end
if table.getn(uniprot_first)>0 then --if there is something in the preferred values display else display anything else
uniprot_link_list = uniprot_first else uniprot_link_list = uniprot_alternate end
--if less than 5 don't create collapsible list
if table.getn(uniprot_link_list) < 5 then
uniprot_collapse = "none"
if uniprot_default == nil and table.getn(uniprot_link_list) == 0 then uniprot_link = "n/a" end
else
uniprot_collapse = "collapsible collapsed"
uniprot_default = table.remove(uniprot_link_list, 1) .. '
' .. table.remove(uniprot_link_list, 1) .. '
' ..table.remove(uniprot_link_list, 1) .. '
' .. table.remove(uniprot_link_list, 1) .. '
' .. table.remove(uniprot_link_list, 1) .. '
'--get first 5 elements in table and use for display
end
if uniprot_link_list[#uniprot_link_list] then
uniprot_link = table.concat(uniprot_link_list, "
")
end
--mouse uniprot lists
local uniprot_mm_link = "n/a"
local uniprot_mm_collapse
local uniprot_mm_default = ""
--split string and loop through concatenate by
local split_uniprot_mm = mw.text.split(uniprot_mm, ",")
local uniprot_mm_link_list = {}
local uniprot_mm_first = {} --preferred values only display [O,P,Q] prefixed entries if they exist
local uniprot_mm_alternate = {} --[A-N,R-Z] entries
local hash = {} --storage to look for duplicated values
for k,v in ipairs(split_uniprot_mm) do if not hash[v] then --only add if not found previously..some encodes uniprotID dup in different encodes local label = mw.text.trim(v) local concat_uniprot_link = uniprot_url .. label if string.match(v, '%w+') and v ~= "n/a" then if string.match(v, '^O') or string.match(v,'^P') or string.match(v, '^Q') then uniprot_mm_first[#uniprot_mm_first+1] = "[" .. concat_uniprot_link .. " " ..label .. "]" else uniprot_mm_alternate[#uniprot_mm_alternate+1] = "[" .. concat_uniprot_link .. " " ..label .. "]" end end hash[v] = true end end if table.getn(uniprot_mm_first)>0 then --if there is something in the preferred values display else display anything else uniprot_mm_link_list = uniprot_mm_first else uniprot_mm_link_list = uniprot_mm_alternate end
--if less than 5 don't create collapsible list
if table.getn(uniprot_mm_link_list) < 5 then
uniprot__mm_collapse = "none"
if uniprot_mm_default == nil and table.getn(uniprot_mm_link_list) == 0 then uniprot_mm_link = "n/a" end
else
uniprot_mm_collapse = "collapsible collapsed"
uniprot_mm_default = table.remove(uniprot_mm_link_list, 1) .. '
' .. table.remove(uniprot_mm_link_list, 1) .. '
' ..table.remove(uniprot_mm_link_list, 1) .. '
' .. table.remove(uniprot_mm_link_list, 1) .. '
' .. table.remove(uniprot_mm_link_list, 1) .. '
'--get first 5 elements in table and use for display
end
if uniprot_mm_link_list[#uniprot_mm_link_list] then
uniprot_mm_link = table.concat(uniprot_mm_link_list, "
")
end
-- l10n: tentative:PBB old title
local ncbi_link = "https://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="
local refseq_mRNATitle = "mRNA" .. wbr .. "序列"
--create list of links for refSeq mRNA
local refseq_mRNA_link = "n/a"
local refseq_mRNA_collapse
local refseq_mRNA_default = ""
--split string and loop through concatenate by
local split_refseq_mRNA = mw.text.split(refseq_mRNA, ",")
local link_list_first = {} --hold those the have NM or NP values
local link_list_alternate = {} --hold those that are XM or XP values
local link_list = {} --if NM,NP display if not display XM, XP values
for k,v in ipairs(split_refseq_mRNA) do
local label = mw.text.trim(v)
local concat_ncbi_link = ncbi_link .. label
if string.match(v, '%w+') and v ~= "n/a" then
if string.match(v, 'NM') or string.match(v, 'NP') then
link_list_first[#link_list_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
elseif string.match(v, 'XM') or string.match(v, 'XP') then
link_list_alternate[#link_list_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
end
end
end if table.getn(link_list_first)>0 then
link_list = link_list_first else link_list = link_list_alternate end
--if less than 5 don't create collapsible list
if table.getn(link_list) < 6 then
refseq_mRNA_collapse = "none"
if refseq_mRNA_default == nil and table.getn(link_list) == 0 then refseq_mRNA_link = "n/a" end
else
refseq_mRNA_collapse = "collapsible collapsed"
refseq_mRNA_default = table.remove(link_list, 1) .. '
' .. table.remove(link_list, 1) .. '
' ..table.remove(link_list, 1) .. '
' .. table.remove(link_list, 1) .. '
' .. table.remove(link_list, 1) .. '
'--get first 5 elements in table and use for display
end
if link_list[#link_list] then
refseq_mRNA_link = table.concat(link_list, "
")
end
--create list of links for refSeq mRNA for mouse
local refseq_mRNA_mm_link = "n/a"
local refseq_mRNA_mm_collapse
local refseq_mRNA_mm_default = ""
local split_refseq_mRNA_mm = mw.text.split(refseq_mRNA_mm, ",")
local link_list_mm = {} --if NM,NP display if not display XM, XP values
local link_list_first = {} --hold those the have NM or NP values
local link_list_alternate = {} --hold those that are XM or XP values
for k,v in ipairs(split_refseq_mRNA_mm) do local label = mw.text.trim(v) local concat_ncbi_link = ncbi_link .. label if string.match(v, '%w+') and v ~= "n/a" then if string.match(v, 'NM') or string.match(v, 'NP') then link_list_first[#link_list_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]" elseif string.match(v, 'XM') or string.match(v, 'XP') then link_list_alternate[#link_list_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]" end end
end
if table.getn(link_list_first)>0 then
link_list_mm = link_list_first
else
link_list_mm = link_list_alternate
end
--if less than 5 don't create collapsible list
if table.getn(link_list_mm) < 6 then
refseq_mRNA_mm_collapse = "none"
if refseq_mRNA_mm_default == nil and table.getn(link_list_mm) == 0 then refseq_mRNA_mm_link = "n/a" end
else
refseq_mRNA_mm_collapse = "collapsible collapsed"
refseq_mRNA_mm_default = table.remove(link_list_mm, 1) .. '
' .. table.remove(link_list_mm, 1) .. '
' ..table.remove(link_list_mm, 1) .. '
' .. table.remove(link_list_mm, 1) .. '
' .. table.remove(link_list_mm, 1) .. '
'--get first 5 elements in table and use for display
end
if link_list_mm[#link_list_mm] then
refseq_mRNA_mm_link = table.concat(link_list_mm, "
")
end
-- l10n: tentative; old box local refseq_protTitle = "蛋白序列" --create list of links for human refseq protein local refseq_prot_link = "n/a" local refseq_prot_collapse local refseq_prot_default = "" local split_refseq_prot = mw.text.split(refseq_prot, ",") local link_list_prot = {}
local link_list_first = {} --hold those the have NM or NP values
local link_list_alternate = {} --hold those that are XM or XP values
for k,v in ipairs(split_refseq_prot) do
local label = mw.text.trim(v)
local concat_ncbi_link = ncbi_link .. label
if string.match(v, '%w+') and v ~= "n/a" then
if string.match(v, 'NM') or string.match(v, 'NP') then
link_list_first[#link_list_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
elseif string.match(v, 'XM') or string.match(v, 'XP') then
link_list_alternate[#link_list_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
end
end
end
if table.getn(link_list_first)>0 then
link_list_prot = link_list_first
else
link_list_prot = link_list_alternate
end
--if less than 5 don't create collapsible list
if table.getn(link_list_prot) < 6 then
refseq_prot_collapse = "none"
if refseq_prot_default == nil and table.getn(link_list_prot) == 0 then refseq_prot_link = "n/a" end
else
refseq_prot_collapse = "collapsible collapsed"
refseq_prot_default = table.remove(link_list_prot, 1) .. '
' .. table.remove(link_list_prot, 1) .. '
' ..table.remove(link_list_prot, 1) .. '
' .. table.remove(link_list_prot, 1) .. '
' .. table.remove(link_list_prot, 1) .. '
'--get first 5 elements in table and use for display
end
if link_list_prot[#link_list_prot] then
refseq_prot_link = table.concat(link_list_prot, "
")
end
--create list of links for mouse refseq protein
local refseq_prot_mm_link = "n/a"
local refseq_prot_mm_collapse
local refseq_prot_mm_default = ""
local split_refseq_prot_mm = mw.text.split(refseq_prot_mm, ",")
local link_list_prot_mm = {}
local link_list_first = {} --hold those the have NM or NP values
local link_list_alternate = {} --hold those that are XM or XP values
for k,v in ipairs(split_refseq_prot_mm) do
local label = mw.text.trim(v)
local concat_ncbi_link = ncbi_link .. label
if string.match(v, '%w+') and v ~= "n/a" then
if string.match(v, 'NM') or string.match(v, 'NP') then
link_list_first[#link_list_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
elseif string.match(v, 'XM') or string.match(v, 'XP') then
link_list_alternate[#link_list_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
end
end
end
if table.getn(link_list_first)>0 then
link_list_prot_mm = link_list_first
else
link_list_prot_mm = link_list_alternate
end
--if less than 5 don't create collapsible list
if table.getn(link_list_prot_mm) < 6 then
refseq_prot_mm_collapse = "none"
if refseq_prot_mm_default == nil and table.getn(link_list_prot_mm) == 0 then refseq_prot_mm_link = "n/a" end
else
refseq_prot_mm_collapse = "collapsible collapsed"
refseq_prot_mm_default = table.remove(link_list_prot_mm, 1) .. '
' .. table.remove(link_list_prot_mm, 1) .. '
' ..table.remove(link_list_prot_mm, 1) .. '
' .. table.remove(link_list_prot_mm, 1) .. '
' .. table.remove(link_list_prot_mm, 1) .. '
'--get first 5 elements in table and use for display
end
if link_list_prot_mm[#link_list_prot_mm] then
refseq_prot_mm_link = table.concat(link_list_prot_mm, "
")
end
-- l10n: tentative
local locTitle = "基因位置" .. wbr .. "(UCSC)" local gstart_mb = p.locToMb(gstart, 2) local gend_mb = p.locToMb(gend, 2) local chr_loc_link = "" if (string.match(db, '%w+') and string.match(chr, '%w+') and string.match(gstart, '%w+') and string.match(gend, '%w+') )then chr_loc_link = ""..db.."&position=chr"..chr..":"..gstart.."-"..gend.." ".."Chr "..chr..": "..gstart_mb.." – "..gend_mb.." Mb" else chr_loc_link = "n/a" end local gstart_mm_mb = p.locToMb(gstart_mm, 2) local gend_mm_mb = p.locToMb(gend_mm, 2) local chr_loc_mm_link = "" if (string.match(db_mm, '%w+') and string.match(chr_mm, '%w+') and string.match(gstart_mm, '%w+') and string.match(gend_mm, '%w+') )then chr_loc_mm_link = ""..db_mm.."&position=chr"..chr_mm..":"..gstart_mm.."-"..gend_mm.." ".."Chr "..chr_mm..": "..gstart_mm_mb.." – "..gend_mm_mb.." Mb" else chr_loc_mm_link = "n/a" end
-- l10n
local pubmedTitle = "PubMed" .. wbr .. "查找"
local pubmed_link = entrez_gene
if string.match(entrez_gene, '%w+') and entrez_gene ~= "n/a" then
pubmed_link = frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title ="Human PubMed Reference:" , url = "https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene } } )--expandTemplate creates cite web template [ref_link..ect value] 请检查|url=值 (帮助).
end
local pubmed_mm_link = entrez_gene_mm
if string.match(entrez_gene_mm, '%w+') and entrez_gene_mm ~= "n/a" then
pubmed_mm_link = frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title ="Mouse PubMed Reference:" , url ="https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene_mm } } )--expandTemplate creates cite web template [ref_link..ect value] 请检查|url=值 (帮助).
end
root :tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext("物種") -- localization required!
:done() --end th
:tag('td')
:wikitext("人類") -- localization required!
:done() --end td
:tag('td')
:wikitext("小鼠") -- localization required!
-- note: Mus musculus
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(entrezTitle)
:done() --end th
:tag('td')
:tag('table')
:attr('class', entrez_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(entrez_default)
:done() --end span
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(entrez_link)
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:tag('td')
:tag('table')
:attr('class', entrez_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(entrez_mm_default)
:done() --end span
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(entrez_mm_link)
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(ensemblTitle)
:done() --end th
:tag('td')
:tag('table')
:attr('class', ensembl_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(ensembl_default)
:done() --end span
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(ensembl_link)
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:tag('td')
:tag('table')
:attr('class', ensembl_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(ensembl_mm_default)
:done() --end span
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(ensembl_mm_link)
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(uniprotTitle)
:done() --end th
:tag('td')
:tag('table')
:attr('class', uniprot_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(uniprot_default)
:done() --end span
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(uniprot_link)
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:tag('td')
:tag('table')
:attr('class', uniprot_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(uniprot_mm_default)
:done() --end span
:done() --end th
:done() --end th
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(uniprot_mm_link)
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(refseq_mRNATitle)
:done() --end th
:tag('td') --RNASeq mRNA collapsible table
:tag('table')
:attr('class', refseq_mRNA_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:attr('class', 'plainlinks')
:wikitext(refseq_mRNA_default)
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(refseq_mRNA_link)
:done() --end span
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:tag('td') --RNASeq mRNA collapsible table for mouse
:tag('table')
:attr('class', refseq_mRNA_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:attr('class', 'plainlinks')
:wikitext(refseq_mRNA_mm_default)
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(refseq_mRNA_mm_link)
:done() --end span
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(refseq_protTitle)
:done() --end th
:tag('td') --RNASeq protein collapsible table
:tag('table')
:attr('class', refseq_prot_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:attr('class', 'plainlinks')
:wikitext(refseq_prot_default)
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(refseq_prot_link)
:done() --end span
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:tag('td') --RNASeq protein collapsible table for mouse
:tag('table')
:attr('class', refseq_prot_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:attr('class', 'plainlinks')
:wikitext(refseq_prot_mm_default)
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(refseq_prot_mm_link)
:done() --end span
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(locTitle)
:done() --end th
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(chr_loc_link)
:done() --end span
:done() --end td
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(chr_loc_mm_link)
:done() --end span
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(pubmedTitle)
:done() --end th
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(pubmed_link)
:done() --end span
:done() --end td
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(pubmed_mm_link)
:done() --end span
:wikitext(category_chromosome)
:done() --end td
:done() --end tr
end
p.formatRow = function(title) root :tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr') --create title header
:css('background-color',titleBGcolor)
:css('text-align', 'center')
:tag('th')
:attr('colspan',"2")
:wikitext(title)
:done() --end th
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
end
p.renderFooter = function(Qid, Qid_mm)
local text = "維基數據" -- localization required! local hs_link = "檢視/編輯 人類" -- localization required! 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 = "檢視/編輯 小鼠" -- localization required! 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('table') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'center') :tag('tr') :tag('td') :attr('colspan', link_no_hs) :css('background-color', rowBGcolor) :css('text-align', 'center')
:css('font-size','x-small') :wikitext(hs_link) :done() --end td :tag('td')
:attr('colspan', link_no_mm)
:css('background-color', rowBGcolor)
:css('text-align', 'center')
:css('font-size','x-small') :wikitext(mm_link) :done() --end td :done() --end tr :done() --end table :done() --end tr root:done() --end root table end
--this code isn't used was hoping could do some generalization of rows p.rowLabel=function(label) root :tag('tr')
:tag('th')
:attr('rowspan', '2')
:css('background-color', sideTitleBGcolor)
:css('width', '43px')
:wikitext(label)
--:done()
end
-- look into entity object p.getLabel = function(entity) local data = entity
local f = {'labels','en','value'}
local i = 1 while true do local index = f[i] if not index then if type(data) == "table" then return mw.text.jsonEncode(data, mw.text.JSON_PRESERVE_KEYS + mw.text.JSON_PRETTY) else return tostring(data) end end
data = data[index] or data[tonumber(index)] if not data then return end
i = i + 1 end end
--general function to get value given an entity and property p.getValue = function(entity, propertyID, return_val)
local claims if return_val == nil then return_val = "" end
local sep = " " --could ad as input parameter if need be
if entity and entity.claims then claims = entity.claims[propertyID] end if claims then -- if wiki-linked value output as link if possible if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then local out = {} for k, v in pairs(claims) do local datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"]) if datav == nil then datav = " " end out[#out + 1] = datav end return table.concat(out, sep) else -- just return best values return entity:formatPropertyValues(propertyID).value end else return return_val end end
p.getValueProtein = function(protein_entities, propertyID, return_val) if return_val == nil then return_val = "" end local sep = ","
local overall_results = {} --should return empty if nothing assigned
for key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a whole local claims local entity = val --each protein in encodes if entity and entity.claims then claims = entity.claims[propertyID] end if claims then local results -- if wiki-linked value output as link if possible if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then local out = {} for k, v in pairs(claims) do local datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"]) if datav == nil then datav = " " end out[#out + 1] = datav end results = table.concat(out, sep) else results = entity:formatPropertyValues(propertyID).value end overall_results[#overall_results+1] = results --individual propertyID value stored in this index end end
local str_overall_results = table.concat(overall_results, sep) --weirdness happens when add a sep = " " otherwise each value represented one time if string.match(str_overall_results, '%w+') then return str_overall_results else return return_val end end
--general function to get value given an entity and property
p.getQid = function(entity)
local Qid
if entity and entity.id then
Qid = entity.id
return Qid
else
return ""
end
end
--get random value that is preferred ranked p.getRefseq_mRNA = function(entity, propertyID, return_val) if return_val == nil then return_val = "" end local input_rank = "RANK_PREFERRED" ---this is mostly like won't do anything because ranking isn't maintained in wikidata local claims
if entity.claims then claims = entity.claims[propertyID] end if claims then -- if wiki-linked value output as link if possible if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid" ) then local out = {} for k, v in pairs(claims) do local sitelink = mw.wikibase.sitelink("Q" .. v.mainsnak.datavalue.value["numeric-id"]) local label = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"]) if label == nil then label = "Q" .. v.mainsnak.datavalue.value["numeric-id"] end
if sitelink then out[#out + 1] = "" .. label .. "" else out[#out + 1] = "[[:d:Q" .. v.mainsnak.datavalue.value["numeric-id"] .. "|" .. label .. "]]" end end return table.concat(out, ",") else local results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value
--loop through results until get a NP or NM or just return whatever is in first element --[[local results_split = mw.text.split(results, ",")
local preffered_results = " " if results_split[1] then preferred_result = mw.text.trim(results_split[1]) --return first element if desired prefix not found and remove whitespace end local id --refseq id in question for i, id in ipairs(results_split) do local trim_id = mw.text.trim(id)
if string.match( trim_id, '^NM_%d+') then preferred_result = trim_id --overwrite each time found only need one to display end
end if preferred_result then return preferred_result --return a id starting with NP or NM else return return_val --return first element because desired prefix not found and remove whitespaces end --]] return results:gsub("，", ",") -- l10n: I don't know how this happened but whatever end else return return_val end end
p.getRefseq_protein = function(protein_entities, propertyID, return_val) local sep = "," local overall_results = {} --should return empty if nothing assigned
for key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a whole
local claims local entity = val --each protein in encodes if entity.claims then claims = entity.claims["P637"] end if claims then local results -- if wiki-linked value output as link if possible if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid" ) then local out = {} for k, v in pairs(claims) do local datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"]) if datav == nil then datav = " " end out[#out + 1] = datav end results = table.concat(out, sep) else results = entity:formatPropertyValues("P637", mw.wikibase.entity.claimRanks).value results = results:gsub("，", ",") -- l10n: I don't know how this happened but whatever end overall_results[#overall_results+1] = results --a list is in each index end
end --why are there duplicate results here local str_overall_results = table.concat(overall_results, sep) return str_overall_results
end --[[ local results_split = mw.text.split(str_overall_results, sep) --split complete list so can loop through..probably a more direct way to do this --loop through results until get a NP or NM or just return whatever is in first element
local preffered_result = results_split[1] or ""
for i, id in ipairs(results_split) do local trim_id = mw.text.trim(id) --check of id starts with NP or NM if string.match( trim_id, '^NP_%d+') then preferred_result = trim_id --overwrite each time found only need one to display end end --check if something in preffered_result if not get first element in result_split if p.isempty(preffered_result) then return return_val else return preferred_result --return a id starting with NP or NM end
end --]]
--gets an image p.getImage = function(entity, propertyID, sep, imgsize)
local claims
if entity and entity.claims then
claims = entity.claims[propertyID]
end
if claims then
if (claims[1] and claims[1].mainsnak.datatype == "commonsMedia") then
local out = {}
for k, v in pairs(claims) do
local filename = v.mainsnak.datavalue.value
out[#out + 1] = "" .. imgsize .. ""
end
return table.concat(out, sep)
else
return ""
end
else
return "" end
end
p.getPDB = function(protein_entities) local pdb_propertyID = "P638" local overall_results = {} for key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a whole local claims local entity = val if entity and entity.claims then claims = entity.claims[pdb_propertyID] end local sitelink = "http://www.rcsb.org/pdb/explore/explore.do?pdbId=" if claims then local results if (claims[1] and claims[1].mainsnak.snaktype == "value") then
local out = {}
for k, v in pairs(claims) do
local label = mw.wikibase.label(v.mainsnak.datavalue.value)
if label == nil then label = v.mainsnak.datavalue.value end
if sitelink then out[#out + 1] = "[" .. sitelink .. label .. " " ..label .. "]" else out[#out + 1] = "" .. label .. "" end end results = table.concat(out, "、" .. wbr) -- l10n: punct else results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value end overall_results[#overall_results+1] = results --individual propertyID values stored in this index end end return table.concat(overall_results, ",%%s") end
function p.getAliases(entity, gene_symbol)
local aliasSet = {}
if entity['aliases'] ~= nil then
for _, lang in ipairs({'en', 'zh'}) do -- l10n: zh testing!
local aliases = entity['aliases'][lang]
if aliases then
for _, alias in ipairs(aliases) do
aliasSet[alias['value']] = true
end
end
end
end
local keys = {} for k, v in pairs(aliasSet) do if k ~= gene_symbol then table.insert(keys, k) -- "if v" omitted end end table.sort(keys) return table.concat(keys, '、' .. wbr) end
--get a geneome start P644 or end P645
p.getChromosomeLoc = function(entity, propertyID, prefix)
-- will contain the numeric value for the requested coordinate
local output = ""
local sep = " "
-- can only be P644 (genomic start) or P645 (genomic end) for this to work
-- should probably try to catch that. Might also increase legibility to use specific variable names when possible
-- local propertyID = mw.text.trim(frame.args[1] or "")
-- this can really only be P659 right now. I'm not sure of the value of including it as a parameter as other values will likely break this function
local qualifierID = "P659" --mw.text.trim(frame.args[2] or "")
-- Why do we include this here? What should happen if FETCH_WIKIDATA is not included?
--local input_parm = mw.text.trim(frame.args[3] or "")
-- this can needs to be fed to the function either by a call to or by setting it directly (e.g. if the function was applied on a page other than the targeted gene)
--alert if this id is not a valid thing in wikidata, a Lua error will occur that says
--The ID entered is unknown to the system. Please use a valid entity ID.
--local itemID = mw.text.trim(frame.args[4] or "")
-- will track the different builds pulled from the qualifiers
local newest_build = "0"
-- starts the process
--local entity = mw.wikibase.getEntityObject(itemID)
local claims
--gets a table of claims on the (genomic start or end) property Q19847637
if entity and entity.claims then
claims = entity.claims[propertyID]
end
--will return nothing if no claims are found
if claims then
--checking to be sure claims is populated, not sure it its needed
if (claims[1] ) then
--useful for debugging
--local out = {}
--pulls the genome location from the claim
for k, v in pairs(claims) do
local location = v.mainsnak.datavalue.value
--debugging
--out[#out + 1] = k.." location:" .. location.. " || "
--gets the qualifiers linked to the current claim
local quals
if v.qualifiers then
quals = v.qualifiers.P659
end
--if there are any
if quals then
for qk, qv in pairs(quals) do
local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]
--get to the entity targeted by the qualifier property. Genome builds are Items in wikidata
local qual_obj = mw.wikibase.getEntityObject(qual_obj_id)
local alias = ""
--this uses the aliases to pull out version numbers
--seems like there ought to be a better way to do this, but likely would need to change the data added by the bot
if qual_obj["aliases"] ~= nil then
local test = qual_obj["aliases"]["en"]
for key, value in ipairs(test) do
if string.match(value['value'], prefix) then
alias = value['value']
local build_no = alias:gsub(prefix,"")
--report only the most location associated with the most recent build
--if there is more than one location per build, just give one back as that is not our problem right now.
if build_no > newest_build then
output = location
newest_build = build_no
end
end
end
end
end
--in case there are no qualifiers, but there is a location, might as well return it
else output = location
end
end
return output
else
return ""
end
else
return ""
--debug
--"no claims for "..itemID.." prop "..propertyID
end
end
p.getAliasFromGenomeAssembly = function(entity, prefix) -- will contain the numeric value for the requested coordinate local output = "" local sep = " " local propertyID = "P644" --genomic start used local qualifierID = "P659"
local newest_build = "0" local claims if entity.claims then claims = entity.claims[propertyID] end --will return nothing if no claims are found if claims then --checking to be sure claims is populated, not sure it its needed if (claims[1] ) then --useful for debugging --local out = {} --pulls the genome location from the claim for k, v in pairs(claims) do local quals if v.qualifiers then quals = v.qualifiers.P659 end --if there are any if quals then for qk, qv in pairs(quals) do local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"] --get to the entity targeted by the qualifier property. Genome builds are Items in wikidata local qual_obj = mw.wikibase.getEntityObject(qual_obj_id) local alias = "" --this uses the aliases to pull out version numbers --seems like there ought to be a better way to do this, but likely would need to change the data added by the bot if qual_obj["aliases"] ~= nil then local test = qual_obj["aliases"]["en"] for key, value in ipairs(test) do if string.match(value['value'], prefix) then alias = value['value'] local build_no = alias:gsub(prefix,"") --report only the most location associated with the most recent build --if there is more than one location per build, just give one back as that is not our problem right now. if build_no > newest_build then newest_build = build_no end end end end end --in case there are no qualifiers, but there is a location, might as well return it else output = location end end return prefix..newest_build else return "" end else return "" end end
p.trimChromosome = function(entity) local string_to_trim = p.getValue(entity, "P1057") local out = -- localization required! if string.find(string_to_trim, '染色体') or string.find(string_to_trim, '染色體') then out = string.match(string_to_trim, "%d+")--extract number from string if out == nil then out = string.match(string_to_trim, "X") or string.match(string_to_trim, "Y") end end if string.find(string_to_trim, '线粒体') or string.find(string_to_trim, '線粒體') then out = "M" end return out end
p.locToMb = function(num, idp)
num = tonumber(num) if num == nil then return "" else local mb = num/1000000 local mult = 10^(idp or 0) return math.floor(mb * mult + 0.5) / mult end
end
p.isempty = function(s)
return s == nil or s ==
end
p.getGO = function(protein_entities, propertyID)
--propertyID ie molecular, cellular, function
local overall_results = {} local results = "" --string to return
for key, val in pairs(protein_entities) do
local claims local entity = val if entity.claims then claims = entity.claims[propertyID] -- ie molecular, cellular, function end local propertyID_child = "P686" -- Gene Ontology ID
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
--local out = {}
for k, v in pairs(claims) do
local itemID_child = "Q" .. v.mainsnak.datavalue.value["numeric-id"] --get Qid of property item so can get the GOid
local entity = mw.wikibase.getEntityObject(itemID_child)
local claims
local result_GOID =
if entity and entity.claims then claims = entity.claims[propertyID_child] end
if claims then
result_GOID = entity:formatPropertyValues(propertyID_child, mw.wikibase.entity.claimRanks).value
else
result_GOID = nil --no GO ID
end
local sitelink = "http://amigo.geneontology.org/amigo/term/"
local label = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if label == nil then label = "Q" .. v.mainsnak.datavalue.value["numeric-id"] end
local wiki_link = ""
if sitelink and result_GOID ~= nil then
wiki_link = "• [" .. sitelink .. result_GOID .. " " .. label .."]
"
else
wiki_link = "• [[: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
p.getDisease= function(entity, propertyID)
local claims
if return_val == nil then return_val = "" end if entity and entity.claims then claims = entity.claims[propertyID] end if claims then -- if wiki-linked value output as link if possible
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
local out = {} local datasource = {} --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.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if datav == nil then datav = " " end
local id = "Q" .. v.mainsnak.datavalue.value["numeric-id"] local linkTarget = mw.wikibase.sitelink(id) local refLink = "" local ref = "" ref = getReference("", entity, "P2293", k) if (ref ~= nil and ref ~= ) then --refLink = refLink..","..ref refLink = ref end
--if refLink = "" then --skip if there isn't a reference found
if linkTarget then out[#out + 1] = ""..datav.."" else out[#out + 1] = "" .. datav .. "" end datasource[#out] = refLink --end end return out, datasource else -- just return best values --return entity:formatPropertyValues(propertyID).value return return_val, return_val end else return return_val end
return return_val
end
p.getDrug= function(protein_entities, propertyID)
local out = {}
local datasource = {} local pname = {} local pqid = {}
for key, val in pairs(protein_entities) do
local claims
local entity = val
local name = check_values(p.getLabel,{entity})
if entity.claims then
claims = entity.claims[propertyID] -- ie physically interacts with
end
local protein_id
if entity then protein_id = entity.id else protein_id = "" end
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do
local datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if datav == nil then datav = "" end local id = "Q" .. v.mainsnak.datavalue.value["numeric-id"] local linkTarget = mw.wikibase.sitelink(id) local refLink = "" local ref = getReference(protein_id, entity, "P129",k) --just check if anything returned if (ref ~= nil and ref ~= ) then refLink = ref end if linkTarget then out[#out + 1] = ""..datav.."" else out[#out + 1] = "" .. datav .. "" end pname[protein_id] = name pqid[#out] = protein_id datasource[#out] = refLink end --end k,v claims loop end --end claims[1] end --if claims
end -- end protein_entities loop
return out, datasource, pqid, pname end
return p