「モジュール:Infobox gene」の版間の差分
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2016年4月22日 (金) 23:07時点における版
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| ファイル:Green check.svg | This module is rated as ready for general use. It has reached a mature form and is thought to be bug-free and ready for use wherever appropriate. It is ready to mention on help pages and other Wikipedia resources as an option for new users to learn. To reduce server load and bad output, it should be improved by sandbox testing rather than repeated trial-and-error editing. |
| ファイル:Full-protection-shackle.svg | This module is subject to page protection. It is a highly visible module in use by a very large number of pages, or is substituted very frequently. Because vandalism or mistakes would affect many pages, and even trivial editing might cause substantial load on the servers, it is protected from editing. |
This module provides content of Template:Infobox gene.
Usage
{{#invoke:Infobox gene|getTemplateData}}
{{#invoke:Infobox gene|getTemplateData|QID=Q414043}}
local p = { }
local navbar = require('Module:Navbar')._navbar
local infobox = require('Module:Infobox3cols').infobox
local infoboxImage = require('Module:InfoboxImage').InfoboxImage
--on a page {{#invoke:Sandbox/genewiki/alllua|getTemplateData|QID=Q14865053}}
--in debug window
--frame = mw.getCurrentFrame()
--frame.args = {QID="Q14865053"} Q18031325
--print(p.getTemplateData(frame))
p.getTemplateData = function(frame)
--make some guesses about whether the provided QID is a good one
--could expand here if we had some kind of error handling framework
--did we get it from the page
local root_qid = mw.text.trim(frame.args['QID'] or "") --try to get it from the args
local mm_qid = ""
--pull all the entity objects that we will need
local entity = {}
local entity_protein = {}
local entity_mouse = {}
local entity_mouse_protein = {}
local checkOrtholog = "" --flag used to see if mouse data avaliable
local mouse_propertyID = "P684"
local protein_propertyID = "P688"
--get root gene entity
if root_qid == "" then
entity = mw.wikibase.getEntityObject()
if entity then root_qid = entity.id else root_qid = "" end
else
--assuming we think its good make one call to retrieve and store its wikidata representation
entity = mw.wikibase.getEntity(root_qid)
end
--need to figure out if it is protein or gene here
local subclass = p.getValue(entity, "P279") or ""
if string.find(subclass, 'protein') then --if protein switch entity to gene
if entity.claims then
claims = entity.claims["P702"] --encoded by
end
if claims then
--go through each index and reassign entity
entity = {}
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do --this would be problematic if multiple genes for the protein
local itemID = "Q" .. claims[#entity + 1].mainsnak.datavalue.value["numeric-id"]
entity[#entity + 1] = mw.wikibase.getEntity(itemID)
root_qid = itemID
end
end --will return nothing if no claims are found
end
entity = mw.wikibase.getEntity(root_qid)
end
--get the other related entities
if entity then
local claims = ""
--get protein entity object
if entity.claims then
claims = entity.claims[protein_propertyID]
end
if claims then
--go through each index and then make entity_protein indexed
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do
local protein_itemID = "Q" .. claims[#entity_protein + 1].mainsnak.datavalue.value["numeric-id"]
entity_protein[#entity_protein + 1] = mw.wikibase.getEntity(protein_itemID)
end
end --will return nothing if no claims are found
end
--get mouse entity object
if entity.claims then
claims = entity.claims[mouse_propertyID]
end
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
local mouse_itemID = "Q" .. claims[1].mainsnak.datavalue.value["numeric-id"]
mm_qid = mouse_itemID
entity_mouse = mw.wikibase.getEntity(mouse_itemID)
checkOrtholog = 1
end --will return nothing if no claims are found
else
checkOrtholog = 0
end
--get mouse protein entity object
if entity_mouse and entity_mouse.claims then
claims = entity_mouse.claims[protein_propertyID]
end
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do
local protein_itemID = "Q" .. claims[#entity_mouse_protein + 1].mainsnak.datavalue.value["numeric-id"]
entity_mouse_protein[#entity_mouse_protein + 1] = mw.wikibase.getEntity(protein_itemID)
end
end --will return nothing if no claims are found
end
end
if entity then --only require the main gene entity
--a list variables of all the data in the info box
local name = p.getLabel(entity)
local entrez_gene = p.getValue(entity, "P351")
local entrez_gene_mm = p.getValue(entity_mouse, "P351", "n/a")
local image = p.getImage(entity, "P18", " ", "250px") --need to set size
local uniprotID_hs = p.getValueProtein(entity_protein, "P352", "n/a")
local uniprotID_mm = p.getValueProtein(entity_mouse_protein, "P352", "n/a")
local pdbIDs = p.getPDB(entity_protein) --makes a list with links to RCSB
local aliases = p.getAliases(entity)
local gene_symbol = p.getValue(entity, "P353")
local hgnc_id = p.getValue(entity, "P354")
local homologene_id = p.getValue(entity, "P593")
local omim_id = p.getValue(entity, "P492")
local mgi_id = p.getValue(entity_mouse, "P671")
local ChEMBL_id = p.getValue(entity_protein, "P592")
local IUPHAR_id = p.getValue(entity_protein, "P595")
local ec_no = p.getValueProtein(entity_protein, "P591")
local mol_funct = p.getGO(entity_protein, "P680")
local cell_comp = p.getGO(entity_protein, "P681")
local bio_process = p.getGO(entity_protein, "P682")
local expression_images = p.getImage(entity,"P692","<br><br>","250px")
local ensembl = p.getValue(entity, "P594", "n/a")
local ensembl_mm = p.getValue(entity_mouse, "P594", "n/a")
local refseq_mRNA = p.getRefseq_mRNA(entity, "P639", "n/a")
local refseq_mRNA_mm = p.getRefseq_mRNA(entity_mouse, "P639", "n/a")
local refseq_prot = p.getRefseq_protein(entity_protein, "P637", "n/a")
local refseq_prot_mm = p.getRefseq_protein(entity_mouse_protein, "P637", "n/a")
local gstart = p.getChromosomeLoc(entity, "P644", "hg")
local gend = p.getChromosomeLoc(entity, "P645", "hg")
local chr = p.trimChromosome(entity)
local db = p.getAliasFromGenomeAssembly(entity,"hg")
local gstart_mm = p.getChromosomeLoc(entity_mouse, "P644", "mm")
local gend_mm = p.getChromosomeLoc(entity_mouse, "P645", "mm")
local db_mm = p.getAliasFromGenomeAssembly(entity_mouse,"mm")
local chr_mm = p.trimChromosome(entity_mouse)
local disease, dis_ref = p.getDisease(entity, "P2293")
local drug = p.getDrug(entity_protein, "P129")
--define Global Color Scheme
rowBGcolor = '#eee'
titleBGcolor = '#ddd'
sideTitleBGcolor = '#c3fdb8'
p.createTable()
p.renderUpperTitle(name)
--p.renderCaption()
p.renderImage(image)
p.renderAvailableStructures(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs) --PDB info
p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene)
if (disease ~= "" and dis_ref ~= "") then --removes section from those items without disease info
p.renderDiseases(disease, dis_ref)
end
if (drug ~= "" ) then --removes section from those items without drug info
p.renderDrug(drug)
end
if (mol_funct ~= "" and cell_comp ~= "" and bio_process ~= "") then
p.renderGeneOntology(mol_funct, cell_comp, bio_process, uniprotID_hs)
end
if expression_images ~= "" then
p.renderRNAexpression(expression_images, entrez_gene)
end
p.renderOrthologs(entrez_gene, entrez_gene_mm, ensembl, ensembl_mm, uniprotID_hs, uniprotID_mm, refseq_mRNA, refseq_mRNA_mm, refseq_prot, refseq_prot_mm, db, chr, gstart, gend, db_mm, chr_mm, gstart_mm, gend_mm)
p.renderFooter(root_qid, mm_qid)
return tostring(root)
else return "An Error has occured retrieving Wikidata item for infobox"
end
end
p.createTable = function(subbox)
if subbox == 'sub' then --doesn't work
root
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', 'auto')
:css('min-width', '100%')
:css('font-size', '100%')
:css('clear', 'none')
:css('float', 'none')
:css('background-color', 'transparent')
else
root = mw.html.create('table')
root
:addClass('infobox')
:css('width', '26.4em')
:newline()
end
end
--Title above image
p.renderUpperTitle = function(name)
local title = name
if not title then return "error: failed to get label"; end
root
:tag('tr')
:tag('th')
:attr('colspan', 4)
:css('text-align', 'center')
:css('font-size', '125%')
:css('font-weight', 'bold')
:wikitext(title)
:newline()
end
--This is a place holder for the image caption, which is stored in wikicommons comments unsure how to access
p.renderCaption = function(entity)
--caption
end
--gets default image
p.renderImage = function(image)
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:wikitext(image)
:done()
:newline()
end
p.renderAvailableStructures = function(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs)
local title = 'Available structures'
local pdb_link = "[[Protein_Data_Bank|PDB]]"
local searchTitle = ""
local listTitle = "List of PDB id codes"
local PDBe_base = 'http://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
else
searchTitle = 'Human UniProt search: '
url_uniprot = uniprotID_hs
end
local PDBe_list = " " --create a list with " or " if there is more than one uniprot
--get first uniprot in a list
if url_uniprot:match("([^,]+),") then--first check if there is a list if not just assume one value
PDBe_list = string.gsub(url_uniprot, ",", "%%20or%%20") --add or's inststead of commas
else
PDBe_list = url_uniprot
end
local PDBe = "["..PDBe_base..PDBe_list.." PDBe] "
local RCSB = "["..RCSB_base..url_uniprot.." RCSB] "
if string.match(pdbIDs, '%w+') then --if there aren't any PDB_ID don't display this part of the infobox
--p.formatRow(title)---how to not close the tags is a mystery and I could condense code once I figure out
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:newline()
--p.createTable('sub')
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:newline()
:tag('tr') --create title header
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color',titleBGcolor)
:wikitext(title)
:done()
:newline()
--p.rowLabel(pdb_link)
:tag('tr')
:tag('th')
:attr('rowspan', '2')
:css('background-color', sideTitleBGcolor)
:css('width', '43px')
:wikitext(pdb_link)
:done()
:tag('td')
:attr('colspan', '2')
:css('background-color', rowBGcolor)
:wikitext(searchTitle)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(PDBe)
:wikitext(RCSB)
:done()
:done()
:done() --this may not be needed
:newline()
--new row for collapsible list of PDB codes
:tag('tr')
:tag('td')
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:newline()
:tag('tr')
:css('background-color',titleBGcolor)
:css('text-align', 'center')
:newline()
:tag('th')
:attr('colspan', '2')
:wikitext(listTitle)
:done()
:newline()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '2')
:css('background-color', rowBGcolor)
:newline()
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(pdbIDs)
:done()
:newline()
else
return ""
end
end
p.renderIdentifiers = function(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene)
local title = "Identifiers"
local label_aliases = "[https://en.wikipedia.org/wiki/Human_Genome_Organisation Aliases]"
local symbol_url
if gene_symbol == "" or gene_symbol == nil then
symbol_url = ""
else
if hgnc_id == "" or hgnc_id == nil then
symbol_url = gene_symbol
else
symbol_url = "[http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id="..hgnc_id.." "..gene_symbol.."], "
end
end
aliases = string.gsub(aliases, gene_symbol, "") --get rid of gene name if in aliases list
aliases = string.gsub(aliases, ", ,", ",") --remove comma from middle
aliases = string.gsub(aliases, ", $", "") --remove comma from end
aliases = string.gsub(aliases, "^,", "") --remove comma from start
local label_ext_id = "External IDs"
omim_id = string.gsub(omim_id, "%s", "")
local omim_list = mw.text.split(omim_id, ",")
local omim = ""
if (omim_id ~= nil and omim_id ~= "") then
omim = "[[Mendelian_Inheritance_in_Man|OMIM:]]".." "
end
for i, v in ipairs(omim_list) do
if string.match(v, '%w+') then
omim = omim.."[https://omim.org/entry/"..v.." "..v.."], "
end
end
omim = string.gsub(omim, ", $"," ") --remove comma from end
homologene_id = string.gsub(homologene_id, "%s", "")
local homolo_list = mw.text.split(homologene_id, ",")
local homolo =""
if (homologene_id ~= nil and homologene_id ~= "") then
homolo = "[[HomoloGene|HomoloGene:]]".." "
end
for i, v in ipairs(homolo_list) do
if string.match(v, '%w+') then
homolo = homolo.."[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=homologene&dopt=HomoloGene&list_uids="..v.." "..v.."] "
end
end
homolo = string.gsub(homolo, ", $"," ") --remove comma from end
entrez_gene = string.gsub(entrez_gene, "%s", "")
local entrez_list = mw.text.split(entrez_gene, ",")
local genecards = ""
if (entrez_list ~= nil and entrez_list ~= "") then
genecards = "[[GeneCards|GeneCards:]]".." "
end
for i, v in ipairs(entrez_list) do
if string.match(v, '%w+') then
genecards = genecards.."[http://www.genecards.org/cgi-bin/carddisp.pl?id_type=entrezgene&id="..v.." "..v.."] "
end
end
genecards = string.gsub(genecards, ", $"," ") --remove comma from end
mgi_id = string.gsub(mgi_id, "%s", "")
local mgi_list = mw.text.split(mgi_id, ",")
local mgi = ""
if (mgi_id ~= nil and mgi_id ~= "") then
mgi = "[[Mouse_Genome_Informatics|MGI:]]".." "
end
for i, v in ipairs(mgi_list) do
if string.match(v, '%w+') then
local mgi_number = string.sub(mgi_id, 5)
mgi = mgi.."[http://www.informatics.jax.org/marker/"..mgi_id.." "..mgi_number.."] "
end
end
mgi = string.gsub(mgi, ", $"," ")--remove comma from end
local ChEMBL = ""
if string.match(ChEMBL_id, '%w+') then
ChEMBL = "[[ChEMBL|ChEMBL:]]".." ".."[https://www.ebi.ac.uk/chembldb/index.php/target/inspect/CHEMBL"..ChEMBL_id.." "..ChEMBL_id.."] "
end
local IUPHAR = ""
if string.match(IUPHAR_id, '%w+') then
IUPHAR = "[[International_Union_of_Basic_and_Clinical_Pharmacology|IUPHAR:]]".." ".."[http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId="..IUPHAR_id.." "..IUPHAR_id.."] "
end
local label_EC = "[[Enzyme_Commission_number|EC number]]"
ec_no = string.gsub(ec_no, "%d%.%d+%.%d+%.%-,", "")--remove those with"-" in list
ec_no = string.gsub(ec_no, "%d%.%d+%.%d+%.%-", "")--remove those with"-" not in list
local link_ec_no = string.gsub(ec_no, "," ,"+") --create format for link
local EC = "[http://www.genome.jp/dbget-bin/www_bget?enzyme+" .. link_ec_no .. " " .. ec_no .. "]"
root
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:newline()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(label_aliases)
:done()
:newline()
:tag('td')
:attr('colspan','3')
:css('background', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(symbol_url)
:done()
:wikitext(aliases)
:done()
:newline()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(label_ext_id)
:done()
:newline()
:tag('td')
:attr('colspan', '3')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(omim)
:wikitext(mgi)
:wikitext(homolo)
:wikitext(ChEMBL)
:wikitext(IUPHAR)
:wikitext(genecards)
:done()
:newline()
:done()
if ec_no ~= "" then
root
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(label_EC)
:done()
:newline()
:tag('td')
:attr('colspan', '3')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(EC)
:done()
:newline()
:done()
end
end
p.renderDiseases = function(disease, dis_ref)
local title = "Genetically Related Diseases"
local disease_title = "Disease Name"
local source_title = "'''References'''"
--check first to see if any of the diseases have references
local ref_flag = {} --check each disease for a reference
local ref_flag_all = "" --check if any disease have references if not then don't render the headers
for index,value in ipairs(disease) do
if (dis_ref[index] ~= nil and dis_ref[index] ~= '') then
ref_flag[index] = "true"
ref_flag_all = "true"
end
end
if ref_flag_all == "true" then
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:newline()
:tag('tr') --create title bar
:tag('th')
:attr('colspan', '3')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:done()
:newline()
:tag('tr')
:tag('th')
:css('background-color', sideTitleBGcolor)
:attr('colspan', '2')
:wikitext(disease_title)
:done()
:newline()
:tag('td')
:css('background-color', sideTitleBGcolor)
:attr('colspan', '2')
:wikitext(source_title)
:done()
:newline()
:done()
end
for index,value in ipairs(disease) do
local i = 0
local ref_collapse = ""
local ref_default = ""
local ref_link = ""
local ref_link_list = ""
if ref_flag[index] == "true" then
if (dis_ref[index] ~= nil or dis_ref[index] ~= '') then
ref_link_list = mw.text.split(dis_ref[index], ",")
end
--if less than 4 don't create collapsible list
if table.getn(ref_link_list) < 5 then
ref_collapse = "none"
else
ref_collapse = "collapsible collapsed"
for i =1, 5 do --get at most 4 elements to display
ref_default = ref_default..table.remove(ref_link_list, 1) .. ' '
end
local br_count = 0
for i =1, table.getn(ref_link_list) do --get at most 4 elements to display
ref_link = ref_link..table.remove(ref_link_list, 1) .. ' '
if br_count < 5 then
br_count = br_count + 1
else
br_count = 0
ref_link = ref_link ..'<br>'
end
end
end
if ref_link_list[#ref_link_list] then
ref_link = table.concat(ref_link_list, " ")
end
root
:tag('tr')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:newline()
:tag('th')
:css('background-color', rowBGcolor)
:attr('scope', 'row')
:attr('colspan', '2')
:wikitext(value)
:done()
:newline()
:tag('td')
:tag('span')
:attr('colspan', '2')
:tag('table')
:attr('class', ref_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:newline()
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(ref_default)
:done()
:done()
:newline()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:newline()
:tag('p')
:attr('class', 'plainlinks')
:wikitext(ref_link)
:newline()
:done()
:done()
:done()
:done()
:newline()
end
end
end
--p.renderDrug = function(drug, drug_ref)
p.renderDrug = function(drug)
local title = "Targeted by Drug"
local drug_title = "Drug Name"
local source_title = "'''References'''"
--check first to see if any of the drugs have references
--local ref_flag = {} --check each drug for a reference
local ref_flag_all = "" --check if any drugs have references if not then don't render the headers
for k,v in pairs(drug) do
ref_flag_all = "true"
end
if ref_flag_all == "true" then
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:newline()
:tag('tr') --create title bar
:tag('th')
:attr('colspan', '3')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:done()
:newline()
:tag('tr')
:tag('th')
:css('background-color', sideTitleBGcolor)
:attr('colspan', '2')
:wikitext(drug_title)
:done()
:newline()
:tag('td')
:css('background-color', sideTitleBGcolor)
:attr('colspan', '2')
:wikitext(source_title)
:done()
:newline()
:done()
end
for key,value in pairs(drug) do
local i = 0
local ref_collapse = ""
local ref_default = ""
local ref_link = ""
local ref_link_list = {}
local ref_split = mw.text.split(value, ",")
local hash = {} --storage to look for duplicated values in case
for k,v in ipairs(ref_split) do
if not hash[v] then --only add if not found previously
ref_link_list[#ref_link_list+1] = v
hash[v] = true
end
end
--if less than 4 don't create collapsible list
if table.getn(ref_link_list) < 5 then
ref_collapse = "none"
else
ref_collapse = "collapsible collapsed"
for i =1, 5 do --get at most 4 elements to display
ref_default = ref_default..table.remove(ref_link_list, 1) .. ' '
end
local br_count = 0
for i =1, table.getn(ref_link_list) do --get at most 4 elements to display
ref_link = ref_link..table.remove(ref_link_list, 1) .. ' '
if br_count < 5 then
br_count = br_count + 1
else
br_count = 0
ref_link = ref_link ..'<br>'
end
end
end
if ref_link_list[#ref_link_list] then
ref_link = table.concat(ref_link_list, " ")
end
root
:tag('tr')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:newline()
:tag('th')
:css('background-color', rowBGcolor)
:attr('scope', 'row')
:attr('colspan', '2')
--:wikitext(value)
:wikitext(key)
:done()
:newline()
:tag('td')
:tag('span')
:attr('colspan', '2')
:tag('table')
:attr('class', ref_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:newline()
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(ref_default)
:done()
:done()
:newline()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:newline()
:tag('p')
:attr('class', 'plainlinks')
:wikitext(ref_link)
:newline()
:done()
:done()
:done()
:done()
:newline()
end
end
p.renderGeneOntology = function(mol_funct, cell_comp, bio_process, uniprotID)
local title = "[[Gene_ontology|Gene ontology]]"
local mol_funct_title = "Molecular function"
local cell_comp_title = "Cellular component"
local bio_process_title = "Biological process"
local amigo_link = "[http://amigo.geneontology.org/" .. " Amigo]"
local quickGO_link = "[http://www.ebi.ac.uk/QuickGO/" .. " QuickGO]"
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:newline()
--p.createTable('sub')
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:newline()
:tag('tr') --create title bar
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:done()
:newline()
:tag('tr')
:tag('th')
:css('background-color', sideTitleBGcolor)
:wikitext(mol_funct_title)
:done()
:tag('td')
:css('background-color', rowBGcolor)
:newline()
:tag('span')
:attr('class', 'plainlinks')
:wikitext(mol_funct)
:done()
:newline()
:done()
:tag('tr')
:tag('th')
:css('background-color', sideTitleBGcolor)
:wikitext(cell_comp_title)
:done()
:tag('td')
:css('background-color', rowBGcolor)
:newline()
:tag('span')
:attr('class', 'plainlinks')
:wikitext(cell_comp)
:done()
:newline()
:done()
:tag('tr')
:tag('th')
:css('background-color', sideTitleBGcolor)
:wikitext(bio_process_title)
:done()
:tag('td')
:css('background-color', rowBGcolor)
:newline()
:tag('span')
:attr('class', 'plainlinks')
:wikitext(bio_process)
:done()
:newline()
:done()
:tag('tr')
:tag('td')
:css('background-color', rowBGcolor)
:css('text-align', 'center')
:attr('colspan', '4')
:wikitext("Sources:")
:wikitext(amigo_link)
:wikitext(" / ")
:wikitext(quickGO_link)
:done()
:done()
end
p.renderRNAexpression = function(expression_images, entrez_gene)
local title = "RNA expression pattern"
local biogps_link = "[http://biogps.org/gene/"..entrez_gene.."/ More reference expression data]"
root
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:done()
:newline()
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:wikitext(expression_images)
:done()
:newline()
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(biogps_link)
:done()
:newline()
end
p.renderOrthologs = function(entrez_gene, entrez_gene_mm, ensembl, ensembl_mm, uniprot, uniprot_mm, refseq_mRNA, refseq_mRNA_mm, refseq_prot, refseq_prot_mm, db, chr, gstart, gend, db_mm, chr_mm,gstart_mm, gend_mm)
local title = "Orthologs"
--to do make the list creation a function
--create list for entrez ids
local entrezTitle = "[[Entrez|Entrez]]"
entrez_gene = string.gsub(entrez_gene, "%s", "")
local entrez_link = "n/a"
local entrez_collapse
local entrez_default = ""
local split_entrez = mw.text.split(entrez_gene, ",")
local entrez_link_list = {}
for k,v in ipairs(split_entrez) do
if string.match(v, '%w+') and v ~= "n/a" then
entrez_link_list[#entrez_link_list+1] = "[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=default&list_uids="..entrez_gene.."&rn=1 "..entrez_gene.."]"
end
end
--if less than 5 don't create collapsible list
if table.getn(entrez_link_list) < 5 then
entrez_collapse = "none"
if entrez_default == nil and table.getn(entrez_link_list) == 0 then entrez_link = "n/a" end
else
entrez_collapse = "collapsible collapsed"
entrez_default = table.remove(entrez_link_list, 1) .. '<br>' .. table.remove(entrez_link_list, 1) .. '<br>' ..table.remove(entrez_link_list, 1) .. '<br>' .. table.remove(entrez_link_list, 1) .. '<br>' .. table.remove(entrez_link_list, 1) .. '<br>'--get first 5 elements in table and use for display
end
if entrez_link_list[#entrez_link_list] then
entrez_link = table.concat(entrez_link_list, "<br>")
end
--create list for mouse Entrez id
entrez_gene_mm = string.gsub(entrez_gene_mm, "%s", "")
local entrez_mm_link = "n/a"
local entrez_mm_collapse
local entrez_mm_default = ""
local split_entrez_mm = mw.text.split(entrez_gene_mm, ",")
local entrez_mm_link_list = {}
for k,v in ipairs(split_entrez_mm) do
if string.match(v, '%w+') and v ~= "n/a" then
entrez_mm_link_list[#entrez_mm_link_list+1] = "[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=default&list_uids="..v.."&rn=1 "..v.."]"
end
end
--if less than 5 don't create collapsible list
if table.getn(entrez_mm_link_list) < 5 then
entrez_mm_collapse = "none"
if entrez_mm_default == nil and table.getn(entrez_mm_link_list) == 0 then entrez_mm_link = "n/a" end
else
entrez_mm_collapse = "collapsible collapsed"
entrez_mm_default = table.remove(entrez_mm_link_list, 1) .. '<br>' .. table.remove(entrez_mm_link_list, 1) .. '<br>' ..table.remove(entrez_mm_link_list, 1) .. '<br>' .. table.remove(entrez_mm_link_list, 1) .. '<br>' .. table.remove(entrez_mm_link_list, 1) .. '<br>'--get first 5 elements in table and use for display
end
if entrez_mm_link_list[#entrez_mm_link_list] then
entrez_mm_link = table.concat(entrez_mm_link_list, "<br>")
end
--create list of ensembl id
local ensemblTitle = "[[Ensembl|Ensembl]]"
ensembl = string.gsub(ensembl, "%s", "")
local ensembl_link = "n/a"
local ensembl_collapse
local ensembl_default = ""
local split_ensembl = mw.text.split(ensembl, ",")
local ensembl_link_list = {}
for k,v in ipairs(split_ensembl) do
if string.match(v, '%w+') and v ~= "n/a" then
ensembl_link_list[#ensembl_link_list+1] = "[http://www.ensembl.org/Homo_sapiens/geneview?gene="..v..";db=core".." "..v.."]"
end
end
--if less than 5 don't create collapsible list
if table.getn(ensembl_link_list) < 5 then
ensembl_collapse = "none"
if ensembl_default == nil and table.getn(ensembl_link_list) == 0 then ensembl_link = "n/a" end
else
ensembl_collapse = "collapsible collapsed"
ensembl_default = table.remove(ensembl_link_list, 1) .. '<br>' .. table.remove(ensembl_link_list, 1) .. '<br>' ..table.remove(ensembl_link_list, 1) .. '<br>' .. table.remove(ensembl_link_list, 1) .. '<br>' .. table.remove(ensembl_link_list, 1) .. '<br>'--get first 5 elements in table and use for display
end
if ensembl_link_list[#ensembl_link_list] then
ensembl_link = table.concat(ensembl_link_list, "<br>")
end
--create list of mouse ensembl id
local ensemblTitle = "[[Ensembl|Ensembl]]"
ensembl_mm = string.gsub(ensembl_mm, "%s", "")
local ensembl_mm_link = "n/a"
local ensembl_mm_collapse
local ensembl_mm_default = ""
local split_ensembl_mm = mw.text.split(ensembl_mm, ",")
local ensembl_mm_link_list = {}
for k,v in ipairs(split_ensembl_mm) do
if string.match(v, '%w+') and v ~= "n/a" then
ensembl_mm_link_list[#ensembl_mm_link_list+1] = "[http://www.ensembl.org/Homo_sapiens/geneview?gene="..v..";db=core".." "..v.."]"
end
end
--if less than 5 don't create collapsible list
if table.getn(ensembl_mm_link_list) < 5 then
ensembl_mm_collapse = "none"
if ensembl_mm_default == nil and table.getn(ensembl_mm_link_list) == 0 then ensembl_mm_link = "n/a" end
else
ensembl_mm_collapse = "collapsible collapsed"
ensembl_mm_default = table.remove(ensembl_mm_link_list, 1) .. '<br>' .. table.remove(ensembl_mm_link_list, 1) .. '<br>' ..table.remove(ensembl_mm_link_list, 1) .. '<br>' .. table.remove(ensembl_mm_link_list, 1) .. '<br>' .. table.remove(ensembl_mm_link_list, 1) .. '<br>'--get first 5 elements in table and use for display
end
if ensembl_mm_link_list[#ensembl_mm_link_list] then
ensembl_mm_link = table.concat(ensembl_mm_link_list, "<br>")
end
--create lists of uniprot ID
local uniprotTitle = "[[UniProt|UniProt]]"
local uniprot_url = "http://www.uniprot.org/uniprot/"
local uniprot_link = "n/a"
local uniprot_collapse
local uniprot_default = ""
--split string and loop through concatenate by <br>
local split_uniprot = mw.text.split(uniprot, ",")
local uniprot_link_list = {}
local 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
uniprot_link_list[#uniprot_link_list+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"
end
hash[v] = true
end
end
--if less than 5 don't create collapsible list
if table.getn(uniprot_link_list) < 5 then
uniprot_collapse = "none"
if uniprot_default == nil and table.getn(uniprot_link_list) == 0 then uniprot_link = "n/a" end
else
uniprot_collapse = "collapsible collapsed"
uniprot_default = table.remove(uniprot_link_list, 1) .. '<br>' .. table.remove(uniprot_link_list, 1) .. '<br>' ..table.remove(uniprot_link_list, 1) .. '<br>' .. table.remove(uniprot_link_list, 1) .. '<br>' .. table.remove(uniprot_link_list, 1) .. '<br>'--get first 5 elements in table and use for display
end
if uniprot_link_list[#uniprot_link_list] then
uniprot_link = table.concat(uniprot_link_list, "<br>")
end
--mouse uniprot lists
local uniprot_mm_link = "n/a"
local uniprot_mm_collapse
local uniprot_mm_default = ""
--split string and loop through concatenate by <br>
local split_uniprot_mm = mw.text.split(uniprot_mm, ",")
local uniprot_mm_link_list = {}
for k,v in ipairs(split_uniprot_mm) do
local label = mw.text.trim(v)
local concat_uniprot_link = uniprot_url .. label
if string.match(v, '%w+') and v ~= "n/a" then
uniprot_mm_link_list[#uniprot_mm_link_list+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"
end
end
--if less than 5 don't create collapsible list
if table.getn(uniprot_mm_link_list) < 5 then
uniprot__mm_collapse = "none"
if uniprot_mm_default == nil and table.getn(uniprot_mm_link_list) == 0 then uniprot_mm_link = "n/a" end
else
uniprot_mm_collapse = "collapsible collapsed"
uniprot_mm_default = table.remove(uniprot_link_mm_list, 1) .. '<br>' .. table.remove(uniprot_link_mm_list, 1) .. '<br>' ..table.remove(uniprot_link_mm_list, 1) .. '<br>' .. table.remove(uniprot_link_mm_list, 1) .. '<br>' .. table.remove(uniprot_link_mm_list, 1) .. '<br>'--get first 5 elements in table and use for display
end
if uniprot_mm_link_list[#uniprot_mm_link_list] then
uniprot_mm_link = table.concat(uniprot_mm_link_list, "<br>")
end
local ncbi_link = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="
local refseq_mRNATitle = "RefSeq (mRNA)"
--create list of links for refSeq mRNA
local refseq_mRNA_link = "n/a"
local refseq_mRNA_collapse
local refseq_mRNA_default = ""
--split string and loop through concatenate by <br>
local split_refseq_mRNA = mw.text.split(refseq_mRNA, ",")
local link_list = {}
for k,v in ipairs(split_refseq_mRNA) do
local label = mw.text.trim(v)
local concat_ncbi_link = ncbi_link .. label
if string.match(v, '%w+') and v ~= "n/a" then
link_list[#link_list+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
end
end
--if less than 5 don't create collapsible list
if table.getn(link_list) < 6 then
refseq_mRNA_collapse = "none"
if refseq_mRNA_default == nil and table.getn(link_list) == 0 then refseq_mRNA_link = "n/a" end
else
refseq_mRNA_collapse = "collapsible collapsed"
refseq_mRNA_default = table.remove(link_list, 1) .. '<br>' .. table.remove(link_list, 1) .. '<br>' ..table.remove(link_list, 1) .. '<br>' .. table.remove(link_list, 1) .. '<br>' .. table.remove(link_list, 1) .. '<br>'--get first 5 elements in table and use for display
end
if link_list[#link_list] then
refseq_mRNA_link = table.concat(link_list, "<br>")
end
--create list of links for refSeq mRNA for mouse
local refseq_mRNA_mm_link = "n/a"
local refseq_mRNA_mm_collapse
local refseq_mRNA_mm_default = ""
local split_refseq_mRNA_mm = mw.text.split(refseq_mRNA_mm, ",")
local link_list_mm = {}
for k,v in ipairs(split_refseq_mRNA_mm) do
if string.match(v, '%w+') and v ~= "n/a" then
local label = mw.text.trim(v)
local concat_ncbi_link = ncbi_link .. label
if string.match(v, '%w+') and v ~= "n/a" then
link_list_mm[#link_list_mm+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
end
end
end
--if less than 5 don't create collapsible list
if table.getn(link_list_mm) < 6 then
refseq_mRNA_mm_collapse = "none"
if refseq_mRNA_mm_default == nil and table.getn(link_list_mm) == 0 then refseq_mRNA_mm_link = "n/a" end
else
refseq_mRNA_mm_collapse = "collapsible collapsed"
refseq_mRNA_mm_default = table.remove(link_list_mm, 1) .. '<br>' .. table.remove(link_list_mm, 1) .. '<br>' ..table.remove(link_list_mm, 1) .. '<br>' .. table.remove(link_list_mm, 1) .. '<br>' .. table.remove(link_list_mm, 1) .. '<br>'--get first 5 elements in table and use for display
end
if link_list_mm[#link_list_mm] then
refseq_mRNA_mm_link = table.concat(link_list_mm, "<br>")
end
local refseq_protTitle = "RefSeq (protein)"
--create list of links for human refseq protein
local refseq_prot_link = "n/a"
local refseq_prot_collapse
local refseq_prot_default = ""
local split_refseq_prot = mw.text.split(refseq_prot, ",")
local link_list_prot = {}
for k,v in ipairs(split_refseq_prot) do
if string.match(v, '%w+') and v ~= "n/a" then
local label = mw.text.trim(v)
local concat_ncbi_link = ncbi_link .. label
if string.match(v, '%w+') and v ~= "n/a" then
link_list_prot[#link_list_prot+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
end
end
end
--if less than 5 don't create collapsible list
if table.getn(link_list_prot) < 6 then
refseq_prot_collapse = "none"
if refseq_prot_default == nil and table.getn(link_list_prot) == 0 then refseq_prot_link = "n/a" end
else
refseq_prot_collapse = "collapsible collapsed"
refseq_prot_default = table.remove(link_list_prot, 1) --get first element in table and use for display
end
if link_list_prot[#link_list_prot] then
refseq_prot_link = table.concat(link_list_prot, "<br>")
end
--create list of links for mouse refseq protein
local refseq_prot_mm_link = "n/a"
local refseq_prot_mm_collapse
local refseq_prot_mm_default = ""
local split_refseq_prot_mm = mw.text.split(refseq_prot_mm, ",")
local link_list_mm = {}
for k,v in ipairs(split_refseq_prot_mm) do
if string.match(v, '%w+') and v ~= "n/a" then
local label = mw.text.trim(v)
local concat_ncbi_link = ncbi_link .. label
if string.match(v, '%w+') and v ~= "n/a" then
link_list_mm[#link_list_mm+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
end
end
end
--if less than 5 don't create collapsible list
if table.getn(link_list_mm) < 6 then
refseq_prot_mm_collapse = "none"
if refseq_prot_mm_default == nil and table.getn(link_list_mm) == 0 then refseq_prot_mm_link = "n/a" end
else
refseq_prot_mm_collapse = "collapsible collapsed"
refseq_prot_mm_default = table.remove(link_list_mm, 1) --get first element in table and use for display
end
if link_list_mm[#link_list_mm] then
refseq_prot_mm_link = table.concat(link_list_mm, "<br>")
end
local locTitle = "Location (UCSC)"
local gstart_mb = p.locToMb(gstart, 2)
local gend_mb = p.locToMb(gend, 2)
local chr_loc_link = ""
if (string.match(db, '%w+') and string.match(chr, '%w+') and string.match(gstart, '%w+') and string.match(gend, '%w+') )then
chr_loc_link = "[http://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db="..db.."&position=chr"..chr..":"..gstart.."-"..gend.." ".."Chr "..chr..": "..gstart_mb.." – "..gend_mb.." Mb]"
else
chr_loc_link = "n/a"
end
local gstart_mm_mb = p.locToMb(gstart_mm, 2)
local gend_mm_mb = p.locToMb(gend_mm, 2)
local chr_loc_mm_link = ""
if (string.match(db_mm, '%w+') and string.match(chr_mm, '%w+') and string.match(gstart_mm, '%w+') and string.match(gend_mm, '%w+') )then
chr_loc_mm_link = "[http://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db="..db_mm.."&position=chr"..chr_mm..":"..gstart_mm.."-"..gend_mm.." ".."Chr "..chr_mm..": "..gstart_mm_mb.." – "..gend_mm_mb.." Mb]"
else
chr_loc_link = "n/a"
end
local pubmedTitle = "[[PubMed|PubMed]] search"
local pubmed_link = entrez_gene
if string.match(entrez_gene, '%w+') and entrez_gene ~= "n/a" then
pubmed_link = "[http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene.."]"
end
local pubmed_mm_link = entrez_gene_mm
if string.match(entrez_gene_mm, '%w+') and entrez_gene_mm ~= "n/a" then
pubmed_mm_link = "[http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene_mm.."]"
end
root
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:done()
:newline()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext("Species")
:done()
:newline()
:tag('td')
:wikitext("'''Human'''")
:done()
:newline()
:tag('td')
:wikitext("'''Mouse'''")
:done()
:newline()
:done()
---this section would be nice to do in a loop if the tag closures were figured out
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(entrezTitle)
:done()
:newline()
:tag('td')
:tag('table')
:attr('class', entrez_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:newline()
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(entrez_default)
:done()
:done()
:newline()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:newline()
:tag('p')
:attr('class', 'plainlinks')
:wikitext(entrez_link)
:newline()
:done()
:done()
:done()
:done()
:newline()
:tag('td')
:tag('table')
:attr('class', entrez_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:newline()
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(entrez_mm_default)
:done()
:done()
:newline()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:newline()
:tag('p')
:attr('class', 'plainlinks')
:wikitext(entrez_mm_link)
:newline()
:done()
:done()
:done()
:done()
:newline()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(ensemblTitle)
:done()
:newline()
:tag('td')
:tag('table')
:attr('class', ensembl_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:newline()
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(ensembl_default)
:done()
:done()
:newline()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:newline()
:tag('p')
:attr('class', 'plainlinks')
:wikitext(ensembl_link)
:newline()
:done()
:done()
:done()
:done()
:newline()
:tag('td')
:tag('table')
:attr('class', ensembl_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:newline()
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(ensembl_mm_default)
:done()
:done()
:newline()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:newline()
:tag('p')
:attr('class', 'plainlinks')
:wikitext(ensembl_mm_link)
:newline()
:done()
:done()
:done()
:done()
:newline()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(uniprotTitle)
:done()
:newline()
:tag('td')
:tag('table')
:attr('class', uniprot_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:newline()
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(uniprot_default)
:done()
:done()
:newline()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:newline()
:tag('p')
:attr('class', 'plainlinks')
:wikitext(uniprot_link)
:newline()
:done()
:done()
:done()
:done()
:newline()
:tag('td')
:tag('table')
:attr('class', uniprot_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:newline()
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(uniprot_mm_default)
:done()
:done()
:newline()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:newline()
:tag('p')
:attr('class', 'plainlinks')
:wikitext(uniprot_mm_link)
:newline()
:done()
:done()
:done()
:done()
:newline()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(refseq_mRNATitle)
:done()
:newline()
:tag('td') --RNASeq mRNA collapsible table
:tag('table')
:attr('class', refseq_mRNA_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:newline()
:tag('th')
:attr('colspan', '1')
:attr('class', 'plainlinks')
:wikitext(refseq_mRNA_default)
:done()
:newline()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:newline()
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(refseq_mRNA_link)
:done()
:newline()
:done()
:done()
:done()
:done()
:tag('td') --RNASeq mRNA collapsible table for mouse
:tag('table')
:attr('class', refseq_mRNA_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:newline()
:tag('th')
:attr('colspan', '1')
:attr('class', 'plainlinks')
:wikitext(refseq_mRNA_mm_default)
:done()
:newline()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:newline()
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(refseq_mRNA_mm_link)
:done()
:newline()
:done()
:done()
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(refseq_protTitle)
:done()
:newline()
:tag('td') --RNASeq protein collapsible table
:tag('table')
:attr('class', refseq_prot_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:newline()
:tag('th')
:attr('colspan', '1')
:attr('class', 'plainlinks')
:wikitext(refseq_prot_default)
:done()
:newline()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:newline()
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(refseq_prot_link)
:done()
:newline()
:done()
:done()
:done()
:done()
:tag('td') --RNASeq protein collapsible table for mouse
:tag('table')
:attr('class', refseq_prot_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:newline()
:tag('th')
:attr('colspan', '1')
:attr('class', 'plainlinks')
:wikitext(refseq_prot_mm_default)
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:newline()
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(refseq_prot_mm_link)
:done()
:newline()
:done()
:done()
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(locTitle)
:done()
:newline()
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(chr_loc_link)
:done()
:newline()
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(chr_loc_mm_link)
:done()
:newline()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(pubmedTitle)
:done()
:newline()
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(pubmed_link)
:done()
:newline()
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(pubmed_mm_link)
:done()
:newline()
end
p.formatRow = function(title)
root
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:newline()
--p.createTable('sub')
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:newline()
:tag('tr') --create title header
:css('background-color',titleBGcolor)
:css('text-align', 'center')
:tag('th')
:attr('colspan',"2")
:wikitext(title)
:done()
:done()
:newline()
end
p.renderFooter = function(Qid, Qid_mm)
local text = "[[Wikidata|Wikidata]]"
local hs_link = "[[d:"..Qid.."|View/Edit Human]]"
local mm_link = ""
local link_no_hs
local link_no_mm
if Qid_mm == "" then
link_no_mm = 0
link_no_hs = 4
else
link_no_mm = 2
link_no_hs = 2
mm_link = "[[d:"..Qid_mm.."|View/Edit Mouse]]"
end
root
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('font-size','x-small')
:css('background-color', rowBGcolor)
:wikitext(text)
:done()
:newline()
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'center')
:tag('tr')
:tag('td')
:attr('colspan', link_no_hs)
:css('background-color', rowBGcolor)
:css('text-align', 'center')
:css('font-size','x-small')
:wikitext(hs_link)
:done()
:tag('td')
:attr('colspan', link_no_mm)
:css('background-color', rowBGcolor)
:css('text-align', 'center')
:css('font-size','x-small')
:wikitext(mm_link)
:done()
:newline()
:done()
end
--this code isn't used was hoping could do some generalization of rows
p.rowLabel=function(label)
root
:tag('tr')
:tag('th')
:attr('rowspan', '2')
:css('background-color', sideTitleBGcolor)
:css('width', '43px')
:wikitext(label)
--:done()
end
-- look into entity object
p.getLabel = function(entity)
local data = entity
local f = {'labels','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] = "[[" .. sitelink .. "|" .. label .. "]]"
else
out[#out + 1] = "[[:d:Q" .. v.mainsnak.datavalue.value["numeric-id"] .. "|" .. label .. "]]"
end
end
return table.concat(out, ", ")
else
local results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value
--loop through results until get a NP or NM or just return whatever is in first element
--[[local results_split = mw.text.split(results, ",")
local preffered_results = " "
if results_split[1] then
preferred_result = mw.text.trim(results_split[1]) --return first element if desired prefix not found and remove whitespace
end
local id --refseq id in question
for i, id in ipairs(results_split) do
local trim_id = mw.text.trim(id)
if string.match( trim_id, '^NM_%d+') then
preferred_result = trim_id --overwrite each time found only need one to display
end
end
if preferred_result then
return preferred_result --return a id starting with NP or NM
else
return return_val --return first element because desired prefix not found and remove whitespaces
end
--]]
return results
end
else
return return_val
end
end
p.getRefseq_protein = function(protein_entities, propertyID, return_val)
local sep = ","
local overall_results = {} --should return empty if nothing assigned
for key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a whole
local claims
local entity = val --each protein in encodes
if entity.claims then
claims = entity.claims["P637"]
end
if claims then
local results
-- if wiki-linked value output as link if possible
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid" ) then
local out = {}
for k, v in pairs(claims) do
local datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if datav == nil then datav = " " end
out[#out + 1] = datav
end
results = table.concat(out, sep)
else
results = entity:formatPropertyValues("P637", mw.wikibase.entity.claimRanks).value
end
overall_results[#overall_results+1] = results --a list is in each index
end
end
--why are there duplicate results here
local str_overall_results = table.concat(overall_results, sep)
return str_overall_results
end
--[[
local results_split = mw.text.split(str_overall_results, sep) --split complete list so can loop through..probably a more direct way to do this
--loop through results until get a NP or NM or just return whatever is in first element
local preffered_result = results_split[1] or ""
for i, id in ipairs(results_split) do
local trim_id = mw.text.trim(id)
--check of id starts with NP or NM
if string.match( trim_id, '^NP_%d+') then
preferred_result = trim_id --overwrite each time found only need one to display
end
end
--check if something in preffered_result if not get first element in result_split
if p.isempty(preffered_result) then
return return_val
else
return preferred_result --return a id starting with NP or NM
end
end --]]
--gets an image
p.getImage = function(entity, propertyID, sep, imgsize)
local claims
if entity and entity.claims then
claims = entity.claims[propertyID]
end
if claims then
if (claims[1] and claims[1].mainsnak.datatype == "commonsMedia") then
local out = {}
for k, v in pairs(claims) do
local filename = v.mainsnak.datavalue.value
out[#out + 1] = "[[File:" .. filename .. "|" .. imgsize .. "]]"
end
return table.concat(out, sep)
else
return ""
end
else
return ""
end
end
p.getPDB = function(protein_entities)
local pdb_propertyID = "P638"
local overall_results = {}
for key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a whole
local claims
local entity = val
if entity and entity.claims then
claims = entity.claims[pdb_propertyID]
end
local sitelink = "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] = "[[:d:Q" .. v.mainsnak.datavalue.value .. "|" .. label .. "]]"
end
end
results = table.concat(out, ", ")
else
results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value
end
overall_results[#overall_results+1] = results --individual propertyID values stored in this index
end
end
return table.concat(overall_results, ",%%s")
end
function p.getAliases(entity)
a = ''
if entity['aliases'] ~= nil then
local test = entity['aliases']['en']
if test then
for key, value in ipairs(test) do
a = a .. ', ' .. value['value']
end
return a
else
return ""
end
else
return ""
end
end
--get a geneome start P644 or end P645
p.getChromosomeLoc = function(entity, propertyID, prefix)
-- will contain the numeric value for the requested coordinate
local output = ""
local sep = " "
-- can only be P644 (genomic start) or P645 (genomic end) for this to work
-- should probably try to catch that. Might also increase legibility to use specific variable names when possible
-- local propertyID = mw.text.trim(frame.args[1] or "")
-- this can really only be P659 right now. I'm not sure of the value of including it as a parameter as other values will likely break this function
local qualifierID = "P659" --mw.text.trim(frame.args[2] or "")
-- Why do we include this here? What should happen if FETCH_WIKIDATA is not included?
--local input_parm = mw.text.trim(frame.args[3] or "")
-- this can needs to be fed to the function either by a call to {{#invoke:Wikidata|pageId}} or by setting it directly (e.g. if the function was applied on a page other than the targeted gene)
--alert if this id is not a valid thing in wikidata, a Lua error will occur that says
--The ID entered is unknown to the system. Please use a valid entity ID.
--local itemID = mw.text.trim(frame.args[4] or "")
-- will track the different builds pulled from the qualifiers
local newest_build = "0"
-- starts the process
--local entity = mw.wikibase.getEntityObject(itemID)
local claims
--gets a table of claims on the (genomic start or end) property Q19847637
if entity and entity.claims then
claims = entity.claims[propertyID]
end
--will return nothing if no claims are found
if claims then
--checking to be sure claims is populated, not sure it its needed
if (claims[1] ) then
--useful for debugging
--local out = {}
--pulls the genome location from the claim
for k, v in pairs(claims) do
local location = v.mainsnak.datavalue.value
--debugging
--out[#out + 1] = k.." location:" .. location.. " || "
--gets the qualifiers linked to the current claim
local quals
if v.qualifiers then
quals = v.qualifiers.P659
end
--if there are any
if quals then
for qk, qv in pairs(quals) do
local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]
--get to the entity targeted by the qualifier property. Genome builds are Items in wikidata
local qual_obj = mw.wikibase.getEntityObject(qual_obj_id)
local alias = ""
--this uses the aliases to pull out version numbers
--seems like there ought to be a better way to do this, but likely would need to change the data added by the bot
if qual_obj["aliases"] ~= nil then
local test = qual_obj["aliases"]["en"]
for key, value in ipairs(test) do
if string.match(value['value'], prefix) then
alias = value['value']
local build_no = alias:gsub(prefix,"")
--report only the most location associated with the most recent build
--if there is more than one location per build, just give one back as that is not our problem right now.
if build_no > newest_build then
output = location
newest_build = build_no
end
end
end
end
end
--in case there are no qualifiers, but there is a location, might as well return it
else output = location
end
end
return output
else
return ""
end
else
return ""
--debug
--"no claims for "..itemID.." prop "..propertyID
end
end
p.getAliasFromGenomeAssembly = function(entity, prefix)
-- will contain the numeric value for the requested coordinate
local output = ""
local sep = " "
local propertyID = "P644" --genomic start used
local qualifierID = "P659"
local newest_build = "0"
local claims
if entity.claims then
claims = entity.claims[propertyID]
end
--will return nothing if no claims are found
if claims then
--checking to be sure claims is populated, not sure it its needed
if (claims[1] ) then
--useful for debugging
--local out = {}
--pulls the genome location from the claim
for k, v in pairs(claims) do
local quals
if v.qualifiers then
quals = v.qualifiers.P659
end
--if there are any
if quals then
for qk, qv in pairs(quals) do
local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]
--get to the entity targeted by the qualifier property. Genome builds are Items in wikidata
local qual_obj = mw.wikibase.getEntityObject(qual_obj_id)
local alias = ""
--this uses the aliases to pull out version numbers
--seems like there ought to be a better way to do this, but likely would need to change the data added by the bot
if qual_obj["aliases"] ~= nil then
local test = qual_obj["aliases"]["en"]
for key, value in ipairs(test) do
if string.match(value['value'], prefix) then
alias = value['value']
local build_no = alias:gsub(prefix,"")
--report only the most location associated with the most recent build
--if there is more than one location per build, just give one back as that is not our problem right now.
if build_no > newest_build then
newest_build = build_no
end
end
end
end
end
--in case there are no qualifiers, but there is a location, might as well return it
else output = location
end
end
return prefix..newest_build
else
return ""
end
else
return ""
end
end
p.trimChromosome = function(entity)
local string_to_trim = p.getValue(entity, "P1057")
local out = ''
if string.find(string_to_trim, 'chromosome.') then
out = string_to_trim:gsub("chromosome ", "")
end
if string.find(string_to_trim, 'mouse.chromosome.') then
out = string_to_trim:gsub("mouse chromosome ", "")
end
return out
end
p.locToMb = function(num, idp)
num = tonumber(num)
if num == nil then
return ""
else
local mb = num/1000000
local mult = 10^(idp or 0)
return math.floor(mb * mult + 0.5) / mult
end
end
p.isempty = function(s)
return s == nil or s == ''
end
p.getGO = function(protein_entities, propertyID)
--propertyID ie molecular, cellular, function
local overall_results = {}
local results = "" --string to return
for key, val in pairs(protein_entities) do
local claims
local entity = val
if entity.claims then
claims = entity.claims[propertyID] -- ie molecular, cellular, function
end
local propertyID_child = "P686" -- Gene Ontology ID
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
--local out = {}
for k, v in pairs(claims) do
local itemID_child = "Q" .. v.mainsnak.datavalue.value["numeric-id"] --get Qid of property item so can get the GOid
local entity = mw.wikibase.getEntityObject(itemID_child)
local claims
local result_GOID = ''
if entity and entity.claims then claims = entity.claims[propertyID_child] end
if claims then
result_GOID = entity:formatPropertyValues(propertyID_child, mw.wikibase.entity.claimRanks).value
else
result_GOID = nil --no GO ID
end
local sitelink = "http://amigo.geneontology.org/amigo/term/"
local label = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if label == nil then label = "Q" .. v.mainsnak.datavalue.value["numeric-id"] end
local wiki_link = ""
if sitelink and result_GOID ~= nil then
wiki_link = "<big>•</big> [" .. sitelink .. result_GOID .. " " .. label .."]<br>"
else
wiki_link = "<big>•</big> [[:d:Q" .. v.mainsnak.datavalue.value["numeric-id"] .. "|" .. label .. "]]<br>"
end
overall_results[#overall_results+1] = wiki_link
end
else
results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value
end
end
--overall_results[#overall_results+1] = results --each protein GO terms stored in this index, so table contains all the GO terms with duplicates
end
local hash = {} --temp check
local res = {} --no dups
for _,v in ipairs(overall_results) do
if (not hash[v]) then
res[#res+1] = v
hash[v] = true
end
end
return table.concat(res, "")
end
local function getReference(qID, index, entity, property_id, ref_index)
local f = {"claims",property_id,index,"references",ref_index,"snaks","P854",1,"datavalue","value"}
local id = qID
--if id and (#id == 0) then
-- id = nil
--end
local data = entity
if not data then
return nil
end
local i = 1
while true do
local index = f[i]
if not index then
if type(data) == "table" then
return mw.text.jsonEncode(data, mw.text.JSON_PRESERVE_KEYS + mw.text.JSON_PRETTY)
else
return tostring(data)
end
end
data = data[index] or data[tonumber(index)]
if not data then
return ""
end
i = i + 1
end
end
p.getDisease= function(entity, propertyID)
local claims
if return_val == nil then return_val = "" end
if entity and entity.claims then
claims = entity.claims[propertyID]
end
if claims then
-- if wiki-linked value output as link if possible
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
local out = {}
local datasource = {}
--{{#invoke:Wikidata |ViewSomething |id=Q18023174 |claims|P2293|1|references|1|snaks|P854|1|datavalue|value}}
--maybe there is a more direct way to find this than looping through the json object
for k, v in pairs(claims) do
local datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if datav == nil then datav = " " end
local id = "Q" .. v.mainsnak.datavalue.value["numeric-id"]
local linkTarget = mw.wikibase.sitelink(id)
local refLink = ""
local i
for i=1,100 do --limits to 100 references displayed
local ref = ""
ref = getReference("", 1, entity, "P2293", i)
if (ref ~= nil and ref ~= '') then
refLink = refLink..",["..ref.."]"
end
end
--if refLink = "" then --skip if there isn't a reference found
datasource[#out + 1] = refLink
if linkTarget then
out[#out + 1] = "[["..datav.."|"..datav.."]]"
else
out[#out + 1] = "[[:d:" .. id .. "|" .. datav .. "]]"
end
--end
end
return out, datasource
else
-- just return best values
--return entity:formatPropertyValues(propertyID).value
return return_val, return_val
end
else
return return_val
end
return return_val
end
p.getDrug= function(protein_entities, propertyID)
local out = {}
local datasource = {}
for key, val in pairs(protein_entities) do
local claims
local entity = val
if entity.claims then
claims = entity.claims[propertyID] -- ie physically interacts with
end
local protein_id
if entity then protein_id = entity.id else protein_id = "" end
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do
local datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if datav == nil then datav = "" end
local id = "Q" .. v.mainsnak.datavalue.value["numeric-id"]
local linkTarget = mw.wikibase.sitelink(id)
local refLink = ""
local i
for i=1,100 do --limits to 100 references displayed
local ref = ""
ref = getReference(protein_id, k, entity, "P129", i)
if (ref ~= nil and ref ~= '') then
refLink = refLink..",["..ref.."]"
end
end
local wikiLink = "[["..datav.."|"..datav.."]]"
local wikidataLink = "[[:d:" .. id .. "|" .. datav .. "]]"
if (refLink ~= nil and refLink ~= '') then
if linkTarget then
if out[wikiLink] then
out[wikiLink] = out[wikiLink]..","..refLink
else
out[wikiLink] = refLink
end
else
if out[wikidataLink] then
out[wikidataLink] = out[wikidataLink]..","..refLink
else
out[wikidataLink] = refLink
end
end--end if linkTarget
end -- end if refLink
end --end k,v claims loop
end --end claims[1]
end --if claims
end -- end protein_entities loop
return out
end
return p