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
