local p = { }
--To translate visual items of this module, you do not modify this module !!.
--You must to copy and save the file "en:Module:Infobox gene/sandbox/en" in your wiki,
--changing the name of the Module (as needed) and the "en" with your language international code
local root
--CHANGED, BEGIN--
--local SD = require "Module:SimpleDebug"
local local_lang = mw.getContentLanguage().code
local LOC = require (mw.getCurrentFrame():getTitle().."/"..local_lang) --the translated module
local CFG = LOC.CFG
local RS = LOC.RS
local MkExtLnk = LOC.MkExtLnk
local LToRWriting = CFG.LeftToRigthWriting
local ColTextAlign_MarginToModi = ''
if LToRWriting then
ColTextAlign_MarginToModi = 'left'
else
ColTextAlign_MarginToModi = 'right'
end
--CHANGED, END
local function title_without_disambig () --CHANGED, NEW, from Global infobox tools
-- returns the current page name without text between "()"
local s = mw.title.getCurrentTitle().baseText
s = mw.ustring.gsub(s,'%s%(.*%)','')
return s
end
local function GetParam (args, NameValues) --CHANGED, NEW
local value = nil
for k, v in pairs(NameValues) do
if args[v] ~= nil then
value = args[v]
break
end
end
return value
end --GetParam
local function MkIntLnk (S) --CHANGED, NEW
return "[["..S.."]]"
end
local function getInYourLang (ident) --CHANGED, NEW
local function lnk ()
return "https://www.wikidata.org/wiki/" .. ident .. "?uselang="..local_lang
end
local label = mw.wikibase.getLabelByLang(ident, local_lang)
local addEnd = ''
local Article = nil
if label == nil then
label = mw.wikibase.getLabelByLang(ident,'en')
if CFG.WDLnk_Transl then
local Inv = ''
if not LToRWriting then
Inv = '-inv'
end
addEnd = ' [[File:OOjs UI icon Wikidata Echo lightcolors en'..Inv..'.svg|17px|text-bottom|'..RS.youCanTranslateIt
.. "|link="..lnk().."]]"
end
else
if CFG.ArticleLnk then
Article = mw.wikibase.getSitelink (ident)
end
if (Article == nil) and CFG.WDLnk_CorrectTransl then
addEnd = ' [[File:OOjs UI icon Wikidata Echo lightcolors.svg|10px|baseline|'..RS.youCanModifyIt
.. "|link="..lnk().."]]"
end
end
return label, addEnd, Article
end --getInYourLang
local function getInYourLang1 (ident) --CHANGED, NEW. Used for p.getDisease and p.getDrug
label, addEnd, Article = getInYourLang (ident)
if Article then
label = MkIntLnk (Article..'|'..label)
end
return label..addEnd
end
-- wrapped "protected call", return "value error" with error info on error
local function check_values(f,args)
--local u= table.upack(args)
local exist, val = pcall(f, unpack(args))
if exist and val ~= nil then
return(val)
else
-- Leaking some debugging info won't hurt....
return("'''VALUE_ERROR''' (" .. tostring(val) .. ")")
end
end --check_values
local function trim(s)
return (s:gsub("^%s*(.-)%s*$", "%1"))
end
function p.GetArgs (frame) --CHANGED, NEW
local origArgs
if frame == mw.getCurrentFrame() then
-- We're being called via #invoke. If the invoking template passed any parameters,
-- use them. Otherwise, use the parameters that were passed into the template.
origArgs = frame:getParent().args
for _, v in pairs( frame.args ) do
origArgs = frame.args
break
end
else
-- We're being called from another module or from the debug console, so assume
-- the parameters are passed in directly.
origArgs = frame
end
return origArgs
end --GetArgs
--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))
function p.getTemplateData(frame)
if (local_lang == 'en') or (local_lang == 'simple') then --CHANGED, NEW
CFG.WDLnk_Transl = false
CFG.WDLnk_CorrectTransl = false
end
--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 args = p.GetArgs (frame)
local root_qid = mw.text.trim(args['QID'] or "") --try to get it from the args
local mm_qid = ""
--pull all the entity objects that we will need
local entity = {}
local entity_protein = {}
local entity_mouse = {}
local entity_mouse_protein = {}
local checkOrtholog = "" --flag used to see if mouse data avaliable
local mouse_propertyID = "P684" --actually ortholog property additional orthologs can exist
local protein_propertyID = "P688"
--get root gene entity
if root_qid == "" then
entity = mw.wikibase.getEntity()
if entity then root_qid = entity.id else root_qid = "" end
else
--assuming we think its good make one call to retrieve and store its wikidata representation
entity = mw.wikibase.getEntity(root_qid)
end
--need to figure out if it is protein or gene here
local subclass = p.getValue(entity, "P31") or ""
if string.find(subclass, RS.proteinL) then --if protein switch entity to gene
local claims
if entity.claims then
claims = entity.claims["P702"] --encoded bychrLength_mm
end
if claims then
--go through each index and reassign entity
entity = {}
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do --this would be problematic if multiple genes for the protein
local itemID = "Q" .. claims[#entity + 1].mainsnak.datavalue.value["numeric-id"]
entity[#entity + 1] = mw.wikibase.getEntity(itemID)
root_qid = itemID
end
end --will return nothing if no claims are found
end
entity = mw.wikibase.getEntity(root_qid)
end
--get the other related entities
if entity then
local claims
--get protein entity object
if entity.claims then
claims = entity.claims[protein_propertyID]
end
if claims then
--go through each index and then make entity_protein indexed
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do
local protein_itemID = "Q" .. claims[#entity_protein + 1].mainsnak.datavalue.value["numeric-id"]
entity_protein[#entity_protein + 1] = mw.wikibase.getEntity(protein_itemID)
end
end --will return nothing if no claims are found
end
--get mouse entity object
if entity.claims then
claims = entity.claims[mouse_propertyID]
end
local qualifierID = "P703" --found in taxon
local mouse_qual = "Q83310"
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do
if checkOrtholog == 1 then -- Don't have to go on if we already got it
break
end
local mouse_itemID = "Q" .. v.mainsnak.datavalue.value["numeric-id"]
local quals
if v.qualifiers then
quals = v.qualifiers.P703
end
if quals then
for qk, qv in pairs(quals) do
--get the taxon qualifier id
local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]
if qual_obj_id == mouse_qual then --check if this is mouse or other
mm_qid = mouse_itemID
entity_mouse = mw.wikibase.getEntity(mouse_itemID)
checkOrtholog = 1
break
end
end
end
end
end --will return nothing if no claims are found
else
checkOrtholog = 0
end
--get mouse protein entity object
if entity_mouse and entity_mouse.claims then
claims = entity_mouse.claims[protein_propertyID]
end
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do
local protein_itemID = "Q" .. claims[#entity_mouse_protein + 1].mainsnak.datavalue.value["numeric-id"]
entity_mouse_protein[#entity_mouse_protein + 1] = mw.wikibase.getEntity(protein_itemID)
end
end --will return nothing if no claims are found
end
end
if entity then --only require the main gene entity
--a list variables of all the data in the info box
local name = check_values(p.getLabel,{entity})
local bgee_wikidata_id = 'Q54985720'
local expressed_in_tissues = check_values(p.getValue, {entity, "P5572", CFG.NotApplicableStr, CFG.SeparatorStr, bgee_wikidata_id, CFG.ArticleLnk}) --P5572: expressed in --CHANGED: add CFG.ArticleLnk
local expressed_in_mouse_tissues = check_values(p.getValue, {entity_mouse, "P5572", CFG.NotApplicableStr, CFG.SeparatorStr, bgee_wikidata_id, false}) --P5572: expressed in --CHANGED: add false
local entrez_gene = check_values(p.getValue, {entity, "P351", CFG.NotApplicableStr} )
local entrez_gene_mm = check_values(p.getValue, {entity_mouse, "P351", CFG.NotApplicableStr})
local image = GetParam (args, RS.imageNames) --CHANGED, image from args
local caption = nil --CHANGED, NEW
if image == nil then
--image = check_values( p.getImage, {entity, "P18", " ", "250px"}) --need to set size
image, caption = p.getImage (entity, "P18", " ", "250px", true) --CHANGED, need to set size
else
image = "[[File:" .. image .. "|250px]]"
caption = GetParam (args, RS.captionNames) --CHANGED, NEW
end
local uniprotID_hs = check_values(p.getValueProtein, {entity_protein, "P352", CFG.NotApplicableStr})
local uniprotID_mm = check_values(p.getValueProtein, {entity_mouse_protein, "P352", CFG.NotApplicableStr})
local pdbIDs = check_values(p.getPDB, {entity_protein}) --makes a list with links to RCSB
local aliases = check_values(p.getAliases, {entity})
local gene_symbol = check_values(p.getValue, {entity, "P353"})
local hgnc_id = check_values(p.getValue, {entity, "P354"})
local homologene_id = check_values(p.getValue, {entity, "P593"})
local omim_id = check_values(p.getValue, {entity, "P492"})
local mgi_id = check_values(p.getValue, {entity_mouse, "P671"})
local ChEMBL_id = check_values(p.getValue, {entity_protein, "P592"})
local IUPHAR_id = check_values(p.getValue, {entity_protein, "P595"})
local ec_no = check_values(p.getValueProtein, {entity_protein, "P591"})
local mol_funct = check_values(p.getGO, {entity_protein, "P680"})
local cell_comp = check_values(p.getGO, {entity_protein, "P681"})
local bio_process = check_values(p.getGO, {entity_protein, "P682"})
local expression_images = check_values(p.getImage, {entity,"P692","<br><br>","250px"})
local ensembl = check_values(p.getValue, {entity, "P594", CFG.NotApplicableStr})
local ensembl_mm = check_values(p.getValue, {entity_mouse, "P594", CFG.NotApplicableStr})
local refseq_mRNA = check_values(p.getRefseq_mRNA, {entity, "P639", CFG.NotApplicableStr})
local refseq_mRNA_mm = check_values(p.getRefseq_mRNA, {entity_mouse, "P639", CFG.NotApplicableStr})
local refseq_prot = check_values(p.getRefseq_protein, {entity_protein, "P637", CFG.NotApplicableStr})
local refseq_prot_mm = check_values(p.getRefseq_protein, {entity_mouse_protein, "P637", CFG.NotApplicableStr})
local gstart = check_values(p.getChromosomeLoc, {entity, "P644", "hg"})
local gend = check_values(p.getChromosomeLoc, {entity, "P645", "hg"})
local chr = p.trimChromosome (entity)
local cytoband = check_values(p.getValue, {entity, "P4196", CFG.NotApplicableStr})
local db = check_values(p.getAliasFromGenomeAssembly, {entity,"hg"})
local gstart_mm = check_values(p.getChromosomeLoc, {entity_mouse, "P644", "mm"})
local gend_mm = check_values(p.getChromosomeLoc, {entity_mouse, "P645", "mm"})
local chr_mm = p.trimChromosome (entity_mouse)
local db_mm = check_values(p.getAliasFromGenomeAssembly, {entity_mouse,"mm"})
local cytoband_mm = check_values(p.getValue, {entity_mouse, "P4196", CFG.NotApplicableStr})
local disease, dis_ref = p.getDisease(entity, "P2293")
local drug, drug_ref, drug_pqid, drug_pname = p.getDrug(entity_protein, "P129")
--local drug = check_values(p.getDrug, {entity_protein, "P129"})
p.createTable()
p.renderUpperTitle(name)
--p.renderCaption()
p.renderImage(image, caption) --CHANGED, Added caption
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, ensembl)
--uncomment here to add a section of the infobox about genetically related diseases, with references
if (CFG.ShowDiseases and disease ~= "" and dis_ref ~= "") then --removes section from those items without disease info
p.renderDiseases(frame, disease, dis_ref, name, root_qid)
end
--uncomment here to add a section of the infobox about drugs that target the protein product of this gene, with references
if (CFG.ShowDrugs and drug ~= "" ) then --removes section from those items without drug info
p.renderDrug(frame,drug, drug_ref, drug_pqid, drug_pname)
end
if (chr ~= "" and gstart ~= "" and gend ~= "") or (chr_mm ~= "" and gstart_mm ~= "" and gend_mm ~= "") then
p.renderGeneLocation(frame, chr, gstart, gend, db, cytoband, ensembl, chr_mm, gstart_mm, gend_mm, db_mm, cytoband_mm, ensembl_mm, name)
end
if expression_images ~= "" or expressed_in_tissues ~= CFG.NotApplicableStr then
p.renderRNAexpression(expression_images, entrez_gene, ensembl, expressed_in_tissues, ensembl_mm, expressed_in_mouse_tissues)
end
if (mol_funct ~= "" and cell_comp ~= "" and bio_process ~= "") then
p.renderGeneOntology(mol_funct, cell_comp, bio_process, uniprotID_hs)
end
p.renderOrthologs(frame, entrez_gene, entrez_gene_mm, ensembl, ensembl_mm, uniprotID_hs, uniprotID_mm, refseq_mRNA, refseq_mRNA_mm, refseq_prot, refseq_prot_mm, db, chr, gstart, gend, db_mm, chr_mm, gstart_mm, gend_mm)
p.renderFooter(root_qid, mm_qid)
return tostring(root)
--return table.concat(drug_pqid)
else
return "An Error has occurred retrieving Wikidata item for infobox"
end
end
function p.createTable(subbox)
if subbox == 'sub' then --doesn't work
root
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', 'auto')
:css('min-width', '100%')
:css('font-size', '100%')
:css('clear', 'none')
:css('float', 'none')
:css('background-color', 'transparent')
else
root = mw.html.create('table')
root
:addClass('infobox')
:css('font-size', CFG.InfoboxFontSize) --NEW
:css('width', CFG.InfoboxWidth) --NEW
end
end
--Title above image
function p.renderUpperTitle(name)
local title = name
if not title then return "error: failed to get label"; end
if CFG.TitleIcon ~= '' and CFG.TitleIcon ~= nil then
title = '<span style="float:left; margin-left: 3px;">[[File:'..CFG.TitleIcon..'|8px|Infotaula de gen|link=]]</span>'
..' '..title --CHANGED, NEW
end
root
:tag('tr')
:tag('th')
:attr('colspan', 4)
:css('text-align', 'center')
:css('font-size', '125%')
:css('font-weight', 'bold')
:css('background-color', CFG.topTitleBGcolor) --CHANGED, NEW
:wikitext(title)
:done() --end th
:done() --end tr
end
--This is a place holder for the image caption, which is stored in wikicommons comments unsure how to access
function p.renderCaption(entity)
--caption
end
--gets default image
--function p.renderImage(image)
function p.renderImage(image, caption) --CHANGED, New
if caption ~= nil then
image = image.."<br />"..caption
end
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:wikitext(image)
:done() --end td
:done() --end tr
end
function p.renderAvailableStructures(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs)
local title = RS.AvailableStructures
local pdb_link = MkIntLnk (RS.PDB_lnk)
local searchTitle = ""
local listTitle = RS.PDBListTitle
local PDBe_base = 'https://www.ebi.ac.uk/pdbe/searchResults.html?display=both&term='
local RCSB_base = 'https://www.rcsb.org/search?q='
..'rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_name:UniProt%20AND%20'
..'rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_accession:'
local url_uniprot = " "
if checkOrtholog == 1 and uniprotID_mm ~= 'n/a' then
searchTitle = RS.checkOrtholog
url_uniprot = uniprotID_mm..','..uniprotID_hs
else
searchTitle = RS.checkOrthologH
url_uniprot = uniprotID_hs
end
searchTitle = searchTitle ..': ' --CHANGED, New
local PDBe_list = " " --create a list with " or " if there is more than one uniprot
--get LinkList_first uniprot in a list
if url_uniprot:match("([^,]+),") then--LinkList_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', CFG.rowBGcolor)
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, for the different directions in writing
:tag('tr') --create title header
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', CFG.titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:tag('tr')
:tag('th')
:attr('rowspan', '2')
:css('background-color', CFG.sideTitleBGcolor)
:css('width', CFG.PDB_bar_width) --CHANGED
:wikitext(pdb_link)
:done() --end th
:tag('td')
:attr('colspan', '2')
:css('background-color', CFG.rowBGcolor)
:wikitext(searchTitle)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(PDBe)
:wikitext(RCSB)
:done() --end span
:done() --end td
:done() --end tr
:tag('tr') --new row for collapsible list of PDB codes
:tag('td')
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, for the different directions in writing
:tag('tr')
:css('background-color', CFG.titleBGcolor)
:css('text-align', 'center')
:tag('th')
:attr('colspan', '2')
:wikitext(listTitle)
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '2')
:css('background-color', CFG.rowBGcolor)
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(pdbIDs)
:done() --end span
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
else
return ""
end
end
function p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene, ensembl)
local title = RS.IdentifiersU
local label_aliases = MkIntLnk (RS.aliases_lnk)
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 = "[https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"..hgnc_id.." "..gene_symbol.."]"
.." ("..MkIntLnk(RS.HUGO_lnk)..")" --CHANGED, New
end
end
-- *lclz*: see getAliases. You can, say, use another punctuation for your language.
if (gene_symbol ~= "") and (gene_symbol ~= nil) then --CHANGED with checking gene_symbol
aliases = string.gsub(aliases, ', '..gene_symbol..'$', '') --get rid of gene name if last in alias list
aliases = string.gsub(aliases, gene_symbol..', ', '') --get rid of gene name if LinkList_first in aliases list
aliases = string.gsub(aliases, ', '..gene_symbol..',', ',') --get rid of gene name if in aliases list
end
aliases = string.gsub(aliases, ", ,", ",") --remove comma from middle
aliases = string.gsub(aliases, ", $", "") --remove comma from end
local label_ext_id = RS.ext_id
omim_id = string.gsub(omim_id, "%s", "")
local omim_list = mw.text.split(omim_id, CFG.SeparatorStr)
local omim = ""
if (omim_id ~= nil and omim_id ~= "") then
omim = MkIntLnk (RS.OMIM_lnk)..": "
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, CFG.SeparatorStr)
local homolo =""
if (homologene_id ~= nil and homologene_id ~= "") then
homolo = MkIntLnk (RS.Homolo_lnk)..": "
end
for i, v in ipairs(homolo_list) do
if string.match(v, '%w+') then
homolo = homolo.."[https://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
local genecards = MkIntLnk (RS.GeneCards_lnk)..": "
genecards = genecards.."[https://www.genecards.org/cgi-bin/carddisp.pl?gene="..gene_symbol.." "..gene_symbol.."] "
mgi_id = string.gsub(mgi_id, "%s", "")
local mgi_list = mw.text.split(mgi_id, CFG.SeparatorStr)
local mgi = ""
if (mgi_id ~= nil and mgi_id ~= "") then
mgi = MkIntLnk (RS.MGI_lnk)..": "
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 = MkIntLnk (RS.ChEMBL_lnk)..": ".."[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 = MkIntLnk (RS.IUPHAR_lnk)..": ".."[http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId="..IUPHAR_id.." "..IUPHAR_id.."] "
end
local label_EC = MkIntLnk (RS.EC_lnk)
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 = "[https://www.genome.jp/dbget-bin/www_bget?enzyme+" .. link_ec_no .. " " .. ec_no .. "]"
local oma = MkIntLnk (RS.OMA_lnk)..": "
oma = oma.."[https://omabrowser.org/oma/vps/"..mw.text.split(ensembl,",")[1].." "..gene_symbol.." - orthologs]"
external_id_table = {omim, mgi, homolo, ChEMBL, IUPHAR, genecards, oma}
external_id_processed_table = {}
for i, v in ipairs(external_id_table) do
if (v ~= "") then
external_id_processed_table[#external_id_processed_table + 1] = v
end
end
external_ids = tostring(table.concat(external_id_processed_table, " "))
root
:tag('tr')
:tag('th')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', CFG.titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', CFG.sideTitleBGcolor)
:css('width', CFG.id_bar_width) --CHANGED, New
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, New for the different directions in writing
:tag('span')
:attr('class', 'plainlinks')
:wikitext(label_aliases)
:done() --end span
:done() --end th
:tag('td')
:attr('colspan','3')
:css('background', CFG.rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(symbol_url)
:done() --end span
:wikitext(mw.text.nowiki(aliases)) -- escape raw text so it cannot be wikitext markup
:done() --end td
:done() --end tr
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', CFG.sideTitleBGcolor)
:css('width', CFG.id_bar_width) --CHANGED, New
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, New for the different directions in writing
:wikitext(label_ext_id)
:done() --end th
:tag('td')
:attr('colspan', '3')
:css('background-color', CFG.rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(external_ids)
:done() --end span
:done() --end td
:done() --end tr
if ec_no ~= "" then
root
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', CFG.sideTitleBGcolor)
:wikitext(label_EC)
:done() --end th
:tag('td')
:attr('colspan', '3')
:css('background-color', CFG.rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(EC)
:done() --end span
:done() --end td
:done() --end tr
end
end
function p.renderDiseases(frame, disease, dis_ref, name, qid)
local title = RS.RelDiseases
--check LinkList_first to see if any of the diseases have references
local ref_flag_all = false --check if any disease have references if not then don't render the headers
local disease_name = '' --local disease_name = table.concat(disease, ", ")
for index,value in ipairs(disease) do
if (dis_ref[index] ~= nil and dis_ref[index] ~= '') then
if disease_name == '' then
disease_name = value
else
disease_name = disease_name..CFG.SeparatorStr.." "..value --CHANGED
end
ref_flag_all = true
end
end
if ref_flag_all then
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', CFG.rowBGcolor)
:tag('tr') --create title bar
:tag('th')
:attr('colspan', '3')
:css('text-align', 'center')
:css('background-color', CFG.titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:done() --end td
:done() --end tr
local ref_url = "https://www.wikidata.org/wiki/"..qid.."#P2293" --direct page to property genetically associated disease
local title = RS.AssocDiseases..name..RS.SeeEditWDRef
local ref_link = disease_name..' '..frame:extensionTag("ref", MkExtLnk (frame, title, ref_url)) --CHANGED
root
:tag('tr')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', CFG.rowBGcolor)
:tag('td')
:css('background-color', CFG.rowBGcolor)
:attr('scope', 'row')
:attr('colspan', '3')
:wikitext(ref_link)
:done() --end td
:done() --end tr
end
end
function p.renderDrug(frame,drug, drug_ref, drug_pqid, drug_pname)
local title = RS.TargDrug
--check LinkList_first to see if any of the drugs have references
local ref_flag_all = false --check if any drugs have references if not then don't render the headers
local drug_list_per_protein = {} -- a list of lists of drugs to put in reference string each protein will have a list
--for i,v in ipairs(drug_pqid) do -- set all lists keys to empty so can append without key errors
--end
for index,value in ipairs(drug) do
if (drug_ref[index] ~= nil and drug_ref[index] ~= '') then
local protein_qid = drug_pqid[index]
if drug_list_per_protein[protein_qid] == '' or drug_list_per_protein[protein_qid] == nil then
drug_list_per_protein[protein_qid] = value
else
drug_list_per_protein[protein_qid] = drug_list_per_protein[protein_qid]..CFG.SeparatorStr.." "..value --CHANGED, each list of drugs keyed on protein qid
end
ref_flag_all = true
end
end
if ref_flag_all then
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', CFG.rowBGcolor)
:tag('tr') --create title bar
:tag('th')
:attr('colspan', '3')
:css('text-align', 'center')
:css('background-color', CFG.titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:done() --end td
:done() --end tr
--loop to create reference links from drug lists
for k,v in pairs(drug_list_per_protein) do
local drug_name = v
local ref_url = "https://www.wikidata.org/wiki/"..k.."#P129" --direct page to property genetically associated disease
local title = RS.InterDrug..drug_pname[k]..RS.SeeEditWDRef
local ref_link = drug_name..' '..frame:extensionTag("ref", MkExtLnk (frame, title, ref_url)) --CHANGED
root
:tag('tr')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', CFG.rowBGcolor)
:tag('td')
:css('background-color', CFG.rowBGcolor)
:attr('scope', 'row')
:attr('colspan', '3')
:wikitext(ref_link)
:done() --end td
:done() --end tr
end
end
end
function p.renderGeneLocation(frame, chr, gstart, gend, db, cytoband, ensembl, chr_mm, gstart_mm, gend_mm, db_mm, cytoband_mm, ensembl_mm, name)
local function MkChrLabels (chr, specie, isHuman) --CHANGED, NEW
local val, val2
if chr == "MT" then
val = string.format (RS.ChromosomeMit, specie)
val2 = val
elseif (chr == 'X') or (chr == 'Y') then
local chr_lab
if chr == 'X' then
chr_lab = RS.XForChromosome
else
chr_lab = RS.YForChromosome
end
val = string.format (RS.ChromosomeAutoSex_abbr, chr_lab, specie)
val2 = string.format (RS.ChromosomeSex_lnk, chr_lab, specie)
if isHuman then
val = val2..'|'..val
end
else
val = string.format (RS.ChromosomeAutoSex_abbr, chr, specie)
val2 = string.format (RS.ChromosomeAuto_lnk, chr, specie)
if isHuman then
val = val2..'|'..val
end
end
return val, val2
end --MkChrLabels
local function rootItems (specie_lnk, ideogramChromo, LabelLnkChromo, wikitext_for_ideogram, cytob,
pair_start, link_start, pair_end, link_end) --CHANGED, NEW
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', CFG.rowBGcolor)
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, for the different directions in writing
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', CFG.titleBGcolor)
:wikitext(RS.GL_GeneLoc..' ('..MkIntLnk(specie_lnk)..')')
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', CFG.rowBGcolor)
:wikitext(ideogramChromo)
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('background-color', CFG.titleBGcolor)
:done() --end td
:done() --end tr
:tag('tr')
:tag('td') --CHANGED, BEGIN
:attr('colspan', '4')
:css('text-align', 'center')
:wikitext(LabelLnkChromo)
:done() --end td --CHANGED, END
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', CFG.rowBGcolor)
:wikitext(wikitext_for_ideogram)
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:attr('rowspan', '2')
:css('width', CFG.label_locus_width) --CHANGED
:css('background-color', CFG.sideTitleBGcolor)
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, New for the different directions in writing
:wikitext(MkIntLnk (RS.GL_locus_lnk))
:done() --end th
:tag('td')
:attr('rowspan', '2')
:css('background-color', CFG.rowBGcolor)
:css('width', CFG.cytoband_width) --CHANGED
:tag('span')
:attr('class', 'plainlinks')
:wikitext(cytob)
:done() --end span
:done() --end td
:tag('th')
:attr('scope', 'row')
:css('background-color', CFG.sideTitleBGcolor)
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, New for the different directions in writing
:css('width', CFG.label_StartEnd_width) --CHANGED, NEW!!!!
:wikitext(RS.GL_gstart)
:done() --end th
:tag('td')
:css('background-color', CFG.rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(p.FormatNaturalNumber(pair_start).." "
..MkIntLnk(RS.BasePair_only_lnk..'|'..RS.BasePair)..link_start)
:done() --end span
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', CFG.sideTitleBGcolor)
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, New for the different directions in writing
:css('width', CFG.label_StartEnd_width) --CHANGED, NEW!!!!
:wikitext(RS.GL_gend)
:done() --end th
:tag('td')
:css('background-color', CFG.rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(p.FormatNaturalNumber(pair_end).." "
..RS.BasePair..link_end)
:done() --end span
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
end --rootItems
local function MkWikitextForChrIdeoImg (Filename, chr, chrText2,
gend, gstart, chrLength) --CHANGED, NEW
--about the calculation below, see https://en.wikipedia.org/wiki/User:Was_a_bee/Gene#3._Calculation_detail
local arrowSign_width = 14
local markerWidth = ((gend - gstart) * 294.133 )/ chrLength
if markerWidth < 2 then
markerWidth = 2
else
markerWidth = math.ceil(markerWidth)
end
local markerLocation = (147.0666 * (gstart + gend) / chrLength ) + 1.6 - (markerWidth / 2)
local arrowSignLocation = markerLocation + (markerWidth / 2) - (arrowSign_width / 2)
markerLocation = math.floor( markerLocation * 10 + 0.5 ) / 10
local tooltip_arrowSign = RS.GL_tooltip..name
local wtfii --wikitext used for showing gene location
if chr == "MT" then -- wikitext for mitochondrial DNA
--wtfii =
--"<div align=\"center\">"
--.."<div style=\"position: relative; width: 300px;\">"
--.."[[File:Map of the human mitochondrial genome.svg|300px|"..chrText.."]]"
--.."</div>"
--.."</div>"
else -- wikitext for autosome and sex chromosome
wtfii =
"<div align=\"center\">"
.."<div style=\"position: relative; width: 300px;\">"
.."[[File:"..string.format (Filename, chr)..".svg|300px|"..chrText2.."]]"
.."<div style=\"position: absolute; left: "..arrowSignLocation.."px; top: 2px; padding: 0;\">"
.."[[File:HSR 1996 II 3.5e.svg|"..arrowSign_width.."px|"..tooltip_arrowSign.."]]"
.."</div>"
.."<div style=\"position: absolute; left: "..markerLocation.."px; top: 19px; padding: 0;\">"
.."[[File:Red rectangle "..markerWidth.."x18.png|"..markerWidth.."px|"..tooltip_arrowSign.."]]"
.."</div>"
.."</div>"
.."</div>"
end
return wtfii
end --MkWikitextForChrIdeoImg
local label_chr = MkIntLnk (RS.GL_chr_lnk)
if chr ~= "" and chr ~= nil and gstart ~= "" and gend ~= "" then
--Chromosome lengths are from GRCh38.p10 https://www.ncbi.nlm.nih.gov/grc/human/data?asm=GRCh38.p10
--This table is used only for calculating "Where should red-rectangle put?"
--Curretly, Aug 2017, it seems all gene data, which are stored in Wikidata, have start/end positions based on GRCh38.
local chrLengthTable = {
["1"] = 248956422,
["2"] = 242193529,
["3"] = 198295559,
["4"] = 190214555,
["5"] = 181538259,
["6"] = 170805979,
["7"] = 159345973,
["8"] = 145138636,
["9"] = 138394717,
["10"] = 133797422,
["11"] = 135086622,
["12"] = 133275309,
["13"] = 114364328,
["14"] = 107043718,
["15"] = 101991189,
["16"] = 90338345,
["17"] = 83257441,
["18"] = 80373285,
["19"] = 58617616,
["20"] = 64444167,
["21"] = 46709983,
["22"] = 50818468,
["X"] = 156040895,
["Y"] = 57227415,
["MT"] = 16569}
local chrLength = chrLengthTable[chr]
--Different languages have different word order.
local chrText, chrText2 = MkChrLabels (chr, RS.HumanL, true) --CHANGED, NEW
local source_link_chr, source_link_gstart, source_link_gend
if( db == "hg38" ) then
source_link_chr = frame:extensionTag("ref", "[http://May2017.archive.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g="..ensembl.." GRCh38: Ensembl release 89: "..ensembl.."] - "..MkIntLnk(RS.Ensembl_lnk)..", May 2017", {name = "refGRCh38Ensembl"})
source_link_gstart = frame:extensionTag("ref", "", {name = "refGRCh38Ensembl"})
source_link_gend = frame:extensionTag("ref", "", {name = "refGRCh38Ensembl"})
elseif( db == "hg37") then
source_link_chr = frame:extensionTag("ref", "[http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;&g="..ensembl.." GRCh37: Ensembl release 89: "..ensembl.."] - "..MkIntLnk(RS.Ensembl_lnk)..", May 2017", {name = "refGRCh37Ensembl"})
source_link_gstart = frame:extensionTag("ref", "", {name = "refGRCh37Ensembl"})
source_link_gend = frame:extensionTag("ref", "", {name = "refGRCh37Ensembl"})
else
source_link_chr = ""
source_link_gstart = ""
source_link_gend = ""
end
local wikitext_for_ideogram_image =
MkWikitextForChrIdeoImg ("Human chromosome %s ideogram", chr, chrText2,
gend, gstart, chrLength)
rootItems (
RS.GL_Human_lnk,
"[[File:Ideogram human chromosome "..chr..".svg|300px|"..string.format (RS.HumanChromosomeIdeogr,chr).."]]",
"'''"..label_chr..": '''[["..chrText.."]]"..source_link_chr,
wikitext_for_ideogram_image,
cytoband,
gstart, source_link_gstart,
gend, source_link_gend)
end
if chr_mm ~= "" and gstart_mm ~= "" and gend_mm ~= "" then
--Chromosome lengths are from GRCm38.p5 https://www.ncbi.nlm.nih.gov/grc/mouse/data?asm=GRCm38.p5
local chrLengthTable_mm = {
["1"] = 195471971,
["2"] = 182113224,
["3"] = 160039680,
["4"] = 156508116,
["5"] = 151834684,
["6"] = 149736546,
["7"] = 145441459,
["8"] = 129401213,
["9"] = 124595110,
["10"] = 130694993,
["11"] = 122082543,
["12"] = 120129022,
["13"] = 120421639,
["14"] = 124902244,
["15"] = 104043685,
["16"] = 98207768,
["17"] = 94987271,
["18"] = 90702639,
["19"] = 61431566,
["X"] = 171031299,
["Y"] = 91744698,
["MT"] = 16299}
local chrLength_mm = chrLengthTable_mm[chr_mm]
--Different languages have different word order.
local chrText_mm, chrText_mm2 = MkChrLabels (chr_mm, RS.MouseL, false) --CHANGED, NEW
local source_link_chr_mm = ""
local source_link_gstart_mm = ""
local source_link_gend_mm = ""
if( db_mm == "mm10" or db_mm == "mm0") then
--"mm0" happens because of function "getAliasFromGenomeAssembly()" is not prepared for mouse data.
--But as of now, Aug. 2017, it seems that all data which is stored in Wikidata are based on GRCm38/mm10.
--So treating mouse genomic data as GRCm38/mm10 if not specified.
source_link_chr_mm = frame:extensionTag("ref", "[http://May2017.archive.ensembl.org/Mus_musculus/Gene/Summary?db=core;g="..ensembl_mm.." GRCm38: Ensembl release 89: "..ensembl_mm.."] – "..MkIntLnk(RS.Ensembl_lnk)..", May 2017", {name = "refGRCm38Ensembl"})
source_link_gstart_mm = frame:extensionTag("ref", "", {name = "refGRCm38Ensembl"})
source_link_gend_mm = frame:extensionTag("ref", "", {name = "refGRCm38Ensembl"})
else
source_link_chr_mm = ""
source_link_gstart_mm = ""
source_link_gend_mm = ""
end
local wikitext_for_ideogram_image_mm =
MkWikitextForChrIdeoImg ("Ideogram of house mouse chromosome %s", chr_mm, chrText_mm2,
gend_mm, gstart_mm, chrLength_mm)
rootItems (
RS.GL_Mouse_lnk,
"[[File:Ideogram house mouse chromosome "..chr_mm..".svg|260px|"..string.format (RS.MouseChromosomeIdeogr,chr_mm).."]]",
"'''"..label_chr..": '''"..chrText_mm..source_link_chr_mm,
wikitext_for_ideogram_image_mm,
cytoband_mm,
gstart_mm, source_link_gstart_mm,
gend_mm, source_link_gend_mm)
end
end
--Get the render elements collapse option, collapsed anatomic entities (defaut text),
--and anatomic entity list for the gene expression list rendering.
function p.renderExpressionList(expressed_in_tissues, default_text)
--create list of expressed in anatomic entities
if default_text == nil then default_text = "" end
local anatomic_entity_labels = CFG.NotApplicableStr
local collapse = "none"
local split_values = mw.text.split(expressed_in_tissues, CFG.SeparatorStr)
local anatomic_entity_list = {}
local anatomic_entities = {}
local results
for k,v in ipairs(split_values) do
if string.match(v, '%w+') and v ~= CFG.NotApplicableStr then
anatomic_entity_list[#anatomic_entity_list+1] = "<li style='line-height: 137%;'>"..v.."</li>"
anatomic_entities[#anatomic_entities+1] = v
end
end
--if less than 11 don't create collapsible list
if table.getn(anatomic_entity_list) < 11 then
if table.getn(anatomic_entity_list) == 0 then
anatomic_entity_labels = CFG.NotApplicableStr
default_text = ""
end
else
collapse = "collapsible collapsed"
default_text = default_text .. '<br>' .. table.remove(anatomic_entities, 1) .. '<br>' .. table.remove(anatomic_entities, 1) .. '<br>' ..table.remove(anatomic_entities, 1) .. '<br>' .. table.remove(anatomic_entities, 1) .. '<br>' .. table.remove(anatomic_entities, 1) .. '<br>'--get LinkList_first 5 elements in table and use for display
end
if anatomic_entity_list[#anatomic_entity_list] then
anatomic_entity_labels = table.concat(anatomic_entity_list, "<br>")
end
results = {collapse, default_text, anatomic_entity_labels}
return results
end
function p.renderRNAexpression(expression_images, entrez_gene,
ensembl, bgee_expression, ensembl_mouse, bgee_expression_mouse)
local bgee_gene_page = "https://bgee.org/gene/"
local title = RS.RNAexpres
local biogps_link = ""
local biogps_title = RS.BioGPS
biogps_title = "[http://biogps.org/ " .. biogps_title .. "]"
-- If no expression image exist in BioGPS, the N/A is displayed
if expression_images ~= "" then
biogps_link = "[http://biogps.org/gene/"..entrez_gene.."/ "..RS.RNAexpres_more_exprdata.."]"
else
expression_images = CFG.NotApplicableStr
end
local bgee_title = RS.Bgee
bgee_title = "[https://bgee.org/ " .. bgee_title .. "]"
local function EnsemblBgee (ensembl0, bgee_expression0) --CHANGED, New
local ensembl_id = string.match(ensembl0,"%a+%d+") or ""
local bgee_default = "["..bgee_gene_page..ensembl_id.." "..RS.RNAexpres_more_expl.."]"
bgee_expression0 = p.renderExpressionList(bgee_expression0, bgee_default)
local bgee_collapse = bgee_expression0[1]
bgee_default = bgee_expression0[2]
local bgee_tissues = bgee_expression0[3]
return ensembl_id, bgee_default, bgee_collapse, bgee_tissues
end
local ensembl_id, bgee_default, bgee_collapse, bgee_tissues = EnsemblBgee (ensembl, bgee_expression) --CHANGED, New
local ensembl_id_mouse, bgee_default_mm, bgee_collapse_mm, bgee_tissues_mm = EnsemblBgee (ensembl_mouse, bgee_expression_mouse) --CHANGED, New
local bgee_more_link = ""
if bgee_tissues ~= CFG.NotApplicableStr then
bgee_more_link = "["..bgee_gene_page..ensembl_id.." "..RS.RNAexpres_more_exprdata.."]"
end
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', CFG.rowBGcolor)
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', CFG.titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', CFG.sideTitleBGcolor)
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, for the different directions in writing
:css('width', CFG.BgeeBioGPS_width)
:wikitext(bgee_title)
:done() --end th
:tag('td')
:tag('table')
:attr('class', 'none')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, for the different directions in writing
:tag('tr')
:tag('th')
:wikitext("'''"..MkIntLnk(RS.GL_Human_lnk).."'''")
:done() --end th
:tag('th')
:wikitext("'''"..MkIntLnk(RS.GL_Mouse_lnk).."''' "..RS.GL_ortholog)
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:tag('table')
:attr('class', bgee_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, for the different directions in writing
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:css('margin', '-3px')
:wikitext(bgee_default)
:done() --end span
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('div')
:css('margin', '-12px 0px -10px 0px')
:attr('class', 'plainlinks')
:tag('ul')
:css('line-height', '15%')
:css('margin', '9px')
:wikitext(bgee_tissues)
:done() --end ul
:done() --end div
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:tag('td')
:tag('table')
:attr('class', bgee_collapse_mm)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, for the different directions in writing
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:css('margin', '-3px')
:wikitext(bgee_default_mm)
:done() --end span
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('div')
:css('margin', '-12px 0px -10px 0px')
:attr('class', 'plainlinks')
:tag('ul')
:css('line-height', '15%')
:css('margin', '9px')
:wikitext(bgee_tissues_mm)
:done() --end ul
:done() --end div
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', CFG.rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(bgee_more_link)
:done() --end span
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', CFG.sideTitleBGcolor)
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, for the different directions in writing
:css('width', CFG.BgeeBioGPS_width)
:wikitext(biogps_title)
:done() --end th
:tag('td')
:tag('table')
:attr('class', bgee_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, for the different directions in writing
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', CFG.rowBGcolor)
:wikitext(expression_images)
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', CFG.rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(biogps_link)
:done() --end span
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
end
function p.renderGeneOntology(mol_funct, cell_comp, bio_process, uniprotID)
local title = MkIntLnk (RS.GO_title_lnk)
--local mol_funct_title = RS.GO_mol_funct
--local cell_comp_title = RS.GO_cell_comp
--local bio_process_title = RS.GO_bio_process
local amigo_link = "[http://amigo.geneontology.org/" .. " Amigo]"
local quickGO_link = "[https://www.ebi.ac.uk/QuickGO/" .. " QuickGO]"
local tab1 --CHANGED, NEW
local function GOMkRow (title, items) --NEW
tab1
:tag('tr')
:tag('td')
:css('width', CFG.GO_bar_width) --CHANGED. New
:css('background-color', CFG.sideTitleBGcolor)
:css('font-weight', 'bold')
:wikitext(title)
:done() --end td
:tag('td')
:css('background-color', CFG.rowBGcolor)
:tag('div')
:attr('class', 'plainlinks')
:css('margin-'..ColTextAlign_MarginToModi, '-0.5em')
:wikitext(items)
:wikitext( '\n' ) -- newline before ending div tag, to ensure next section formats properly
:done() --end div
:done() --end td
:done() --end tr
return tab1
end --GOMkRow
local tr1 = root:tag('tr') --CHANGED
local td1 = tr1:tag('td') --CHANGED
td1 --CHANGED
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', CFG.rowBGcolor)
tab1 = td1:tag('table') --CHANGED
tab1 --CHANGED
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, for the different directions in writing
:tag('tr') --create title bar
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', CFG.titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
--BEGIN NEW
GOMkRow (RS.GO_mol_funct, mol_funct)
GOMkRow (RS.GO_cell_comp, cell_comp)
GOMkRow (RS.GO_bio_process, bio_process)
--END NEW
:tag('tr')
:tag('td')
:css('background-color', CFG.rowBGcolor)
:css('text-align', 'center') --CHANGED
:attr('colspan', '4')
:wikitext(RS.SourcesTP..': '..amigo_link.." / "..quickGO_link)
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
end
function p.renderOrthologs(frame, entrez_gene, entrez_gene_mm, ensembl, ensembl_mm, uniprot, uniprot_mm, refseq_mRNA, refseq_mRNA_mm, refseq_prot, refseq_prot_mm, db, chr, gstart, gend, db_mm, chr_mm,gstart_mm, gend_mm)
local title = RS.Orth_Orthologs
--to do make the list creation a function
local category_chromosome
if (chr == 'X') or (chr == 'Y') then
category_chromosome = MkIntLnk (RS.Orth_Categ..string.format (RS.Orth_C_Sex, chr))
elseif chr == "MT" then
category_chromosome = MkIntLnk (RS.Orth_Categ..RS.Orth_C_Mit) --Category name for mtDNA genes
elseif chr ~= "" then
category_chromosome = MkIntLnk (RS.Orth_Categ..string.format (RS.Orth_C_Num, chr)) --Category name
elseif chr == "" then
category_chromosome = MkIntLnk (RS.Orth_Categ..RS.Orth_HumanGens) -- Per [[Wikipedia:Categories for discussion/Log/2023 August 15]]
end
if mw.title.getCurrentTitle().namespace ~= 0 then
category_chromosome = ""
end
local function ArrangeCollap (link_list, collapse, default, link, num) --CHANGED New
--if less than num don't create collapsible list
if CFG.OrthologsCollapsed or (table.getn(link_list) < num) then --CHANGED, added OrthologsCollapsed
collapse = "none"
if default == nil and table.getn(link_list) == 0 then link = CFG.NotApplicableStr end
else
collapse = "collapsible collapsed"
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 LinkList_first 5 elements in table and use for display
end
if link_list[#link_list] then
link = table.concat(link_list, "<br>")
end
return collapse, default, link
end
local function Entrez0 (VV, isHuman)
VV = string.gsub(VV, "%s", "")
local link = CFG.NotApplicableStr
local collapse
local default = ""
local Split = mw.text.split(VV, CFG.SeparatorStr)
local LinkList = {}
for k,v in ipairs(Split) do
if string.match(v, '%w+') and v ~= CFG.NotApplicableStr then
local p
if isHuman then
p = VV
else
p = v
end
LinkList[#LinkList+1] = "[https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=default&list_uids="..p.."&rn=1 "..p.."]"
end
end
return ArrangeCollap (LinkList, collapse, default, link, 5)
end --Entrez0
--create lists of Entrez
local entrezTitle = MkIntLnk (RS.Orth_Entrez_lnk)
local entrez_collapse, entrez_default, entrez_link =
Entrez0 (entrez_gene, true)
local entrez_mm_collapse, entrez_mm_default, entrez_mm_link =
Entrez0 (entrez_gene_mm, false)
local function Ensemble0 (VV, genderName)
VV = string.gsub(VV, "%s", "")
local link = CFG.NotApplicableStr
local collapse
local default = ""
local Split = mw.text.split(VV, CFG.SeparatorStr)
local LinkList = {}
for k,v in ipairs(Split) do
if string.match(v, '%w+') and v ~= CFG.NotApplicableStr then
LinkList[#LinkList+1] = "[http://www.ensembl.org/"..genderName.."/geneview?gene="..v..";db=core".." "..v.."]"
end
end
return ArrangeCollap (LinkList, collapse, default, link, 5)
end --Ensemble0
--create lists of Ensembl
local ensemblTitle = MkIntLnk (RS.Orth_Ensembl_lnk)
ensembl_collapse, ensembl_default, ensembl_link =
Ensemble0 (ensembl, "Homo_sapiens")
ensembl_mm_collapse, ensembl_mm_default, ensembl_mm_link =
Ensemble0 (ensembl_mm, "Mus_musculus")
local function UniProt0 (VV)
local uniprot_url = "https://www.uniprot.org/uniprot/"
local link = CFG.NotApplicableStr
local collapse
local default = ""
--split string and loop through concatenate by <br>
local Split = mw.text.split(VV, '%p') -- the separator may be different sometimes, see note on zhwiki. This is unlikely to have punctuation, prayer.
local LinkList = {}
local LinkList_first = {} --preferred values only display [O,P,Q] prefixed entries if they exist
local LinkList_alternate = {} --[A-N,R-Z] entries
local hash = {} --storage to look for duplicated values
for k,v in ipairs(Split) 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_link = uniprot_url .. label
if string.match(v, '%w+') and v ~= CFG.NotApplicableStr then
if string.match(v, '^O') or string.match(v,'^P') or string.match(v, '^Q') then
LinkList_first[#LinkList_first+1] = "[" .. concat_link .. " " ..label .. "]"
else
LinkList_alternate[#LinkList_alternate+1] = "[" .. concat_link .. " " ..label .. "]"
end
end
hash[v] = true
end
end
if table.getn(LinkList_first)>0 then --if there is something in the preferred values display else display anything else
LinkList = LinkList_first
else
LinkList = LinkList_alternate
end
return ArrangeCollap (LinkList, collapse, default, link, 6)
end --UniProt0
--create lists of links of UniProt
local uniprotTitle = MkIntLnk (RS.Orth_UniProt_lnk)
local uniprot_collapse, uniprot_default, uniprot_link =
UniProt0 (uniprot)
local uniprot_mm_collapse, uniprot_mm_default, uniprot_mm_link =
UniProt0 (uniprot_mm)
local function RefSeq0 (VV)
local ncbi_link = "https://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="
local link = CFG.NotApplicableStr
local collapse
local default = ""
local Split = mw.text.split(VV, CFG.SeparatorStr)
local LinkList = {} --if NM,NP display if not display XM, XP values
local LinkList_LinkList_first = {} --hold those the have NM or NP values
local LinkList_alternate = {} --hold those that are XM or XP values
for k,v in ipairs(Split) do
local label = mw.text.trim(v)
local concat_ncbi_link = ncbi_link .. label
if string.match(v, '%w+') and v ~= CFG.NotApplicableStr then
if string.match(v, 'NM') or string.match(v, 'NP') then
LinkList_LinkList_first[#LinkList_LinkList_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
elseif string.match(v, 'XM') or string.match(v, 'XP') then
LinkList_alternate[#LinkList_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
end
end
end
if table.getn(LinkList_LinkList_first)>0 then
LinkList = LinkList_LinkList_first
else
LinkList = LinkList_alternate
end
return ArrangeCollap (LinkList, collapse, default, link, 6)
end --RefSeq0
--create lists of links for RefSeq mRNA
local refseq_mRNATitle = MkIntLnk (RS.Orth_RefSeq_lnk).." "..RS.refseq_RNAm
local refseq_mRNA_collapse, refseq_mRNA_default, refseq_mRNA_link =
RefSeq0 (refseq_mRNA)
local refseq_mRNA_mm_collapse, refseq_mRNA_mm_default, refseq_mRNA_mm_link =
RefSeq0 (refseq_mRNA_mm)
--create lists of links for RefSeq protein
local refseq_protTitle = "RefSeq "..RS.refseq_protein
local refseq_prot_default, refseq_prot_default, refseq_prot_link =
RefSeq0 (refseq_prot)
local refseq_prot_mm_collapse, refseq_prot_mm_default, refseq_prot_mm_link =
RefSeq0 (refseq_prot_mm)
local function UCSC0 (GStart, GEnd, Db, Chr, specie)
local gstart_mb = p.locToMb(GStart, 2)
local gend_mb = p.locToMb(GEnd, 2)
local link = ""
if (string.match(Db, '%w+') and string.match(Chr, '%w+') and string.match(GStart, '%w+') and string.match(GEnd, '%w+') )then
local chr_ucsc
if Chr == "MT" then
chr_ucsc = "M" --UCSC uses "M" (not "MT") in URL for mitochondrial DNA
else
chr_ucsc = Chr
end
link = "[https://genome.ucsc.edu/cgi-bin/hgTracks?org="..specie.."&Db="..Db.."&position=Chr"..chr_ucsc..":"..GStart.."-"..GEnd.." ".."Chr "..chr_ucsc..": "..gstart_mb.." – "..gend_mb.." Mb]"
else
link = CFG.NotApplicableStr
end
return link
end --UCSC0
local locTitle = string.format (RS.Orth_UCSC, MkIntLnk(RS.Orth_UCSC_lnk))
local chr_loc_link = UCSC0 (gstart, gend, db, chr, 'Human')
local chr_loc_mm_link = UCSC0 (gstart_mm, gend_mm, db_mm, chr_mm, 'Mouse')
local function PubMed (VV, specie)
local link = "" --CHANGED: Added
if string.match(VV, '%w+') and VV ~= CFG.NotApplicableStr then
link = frame:extensionTag("ref", MkExtLnk (frame, specie.." PubMed Reference:" , --CHANGED
"https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..VV,
"National Center for Biotechnology Information, U.S. National Library of Medicine") )--expandTemplate creates cite web template {{cite web|title=value|url=ref_link..ect}}
end
return link
end --PubMed
local pubmedTitle = string.format (RS.PubMed_Search, MkIntLnk(RS.PubMed_lnk))
local pubmed_link = PubMed (entrez_gene, "Human")
local pubmed_mm_link = PubMed (entrez_gene_mm, "Mouse")
local OrthologsClass = 'collapsible'
if CFG.OrthologsCollapsed then --CHANGED, NEW
OrthologsClass = 'collapsible collapsed'
end
local tab1 --CHANGED, NEW for OMkRow and OM2kRow
-- For Entrez, Ensembl, UniProt and RefSeq (RNAm and protein):
local function OMkRow (title, collapse_h, default_h, link_h, collapse_mm, default_mm, link_mm) --NEW
tab1
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', CFG.sideTitleBGcolor)
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, New for the different directions in writing
:wikitext(title)
:done() --end th
:tag('td')
:tag('table')
:attr('class', collapse_h)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, for the different directions in writing
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(default_h)
:done() --end span
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(link_h)
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:tag('td')
:tag('table')
:attr('class', collapse_mm)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, for the different directions in writing
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(default_mm)
:done() --end span
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(link_mm)
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
return tab1
end --OMkRow
-- For Location and PubMed:
local function OM2kRow (title, link_h, link_mm, AtEnd) --CHANGED, NEW
tab1
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', CFG.sideTitleBGcolor)
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, New for the different directions in writing
:wikitext(title)
:done() --end th
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(link_h)
:done() --end span
:done() --end td
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(link_mm)
:done() --end span
:wikitext(AtEnd)
:done() --end td
:done() --end tr
return tab1
end
local tr1 = root:tag('tr') --CHANGED
local td1 = tr1:tag('td') --CHANGED
td1 --CHANGED
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', CFG.rowBGcolor)
tab1 = td1:tag('table') --CHANGED
tab1 --CHANGED
:attr('class', OrthologsClass) --CHANGED, NEW
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, for the different directions in writing
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', CFG.titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', CFG.sideTitleBGcolor)
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, New for the different directions in writing
:wikitext(RS.SpeciesU)
:done() --end th
:tag('td')
:wikitext("'''"..RS.HumanU.."'''")
:done() --end td
:tag('td')
:wikitext("'''"..RS.MouseU.."'''")
:done() --end td
:done() --end tr
--BEGIN NEW
OMkRow (entrezTitle, entrez_collapse, entrez_default, entrez_link,
entrez_mm_collapse, entrez_mm_default, entrez_mm_link)
OMkRow (ensemblTitle, ensembl_collapse, ensembl_default, ensembl_link,
ensembl_mm_collapse, ensembl_mm_default, ensembl_mm_link)
OMkRow (uniprotTitle, uniprot_collapse, uniprot_default, uniprot_link,
uniprot_mm_collapse, uniprot_mm_default, uniprot_mm_link)
OMkRow (refseq_mRNATitle, refseq_mRNA_collapse, refseq_mRNA_default, refseq_mRNA_link,
refseq_mRNA_mm_collapse, refseq_mRNA_mm_default, refseq_mRNA_mm_link)
OMkRow (refseq_protTitle, refseq_prot_default, refseq_prot_default, refseq_prot_link,
refseq_prot_mm_collapse, refseq_prot_mm_default, refseq_prot_mm_link)
OM2kRow (locTitle, chr_loc_link, chr_loc_mm_link, '')
OM2kRow (pubmedTitle, pubmed_link, pubmed_mm_link, category_chromosome)
--END NEW
:done() --end table
:done() --end td
:done() --end tr
end
function p.formatRow(title)
root
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', CFG.rowBGcolor)
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', ColTextAlign_MarginToModi) --CHANGED, for the different directions in writing
:tag('tr') --create title header
:css('background-color', CFG.titleBGcolor)
:css('text-align', 'center')
:tag('th')
:attr('colspan',"2")
:wikitext(title)
:done() --end th
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
end
function p.renderFooter(Qid, Qid_mm)
local text = MkIntLnk (RS.Wikidata_lnk)
local hs_link = MkIntLnk ("d:"..Qid.."|"..RS.SeeEditHuman)
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 = MkIntLnk ("d:"..Qid_mm.."|"..RS.SeeEditMouse)
end
root
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('font-size','x-small')
:css('background-color', CFG.rowBGcolor)
:wikitext(text)
:done() --end td
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('font-size','x-small')
:css('background-color', CFG.rowBGcolor)
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'center')
:tag('tr')
:tag('td')
:attr('colspan', link_no_hs)
:css('background-color', CFG.rowBGcolor)
:css('text-align', 'center')
:css('font-size','x-small')
:wikitext(hs_link)
:done() --end td
:tag('td')
:attr('colspan', link_no_mm)
:css('background-color', CFG.rowBGcolor)
:css('text-align', 'center')
:css('font-size','x-small')
:wikitext(mm_link)
:done() --end td
:done() --end tr
:done() --end table
:done() --end tr
root:done() --end root table
end
-- look into entity object
function p.getLabel(entity)
local data = entity
local f = {'labels', local_lang, 'value'} --CHANGED: use of local_lang
local i = 1
while true do
local index = f[i]
if not index then
if type(data) == "table" then
return mw.text.jsonEncode(data, mw.text.JSON_PRESERVE_KEYS + mw.text.JSON_PRETTY)
else
return tostring(data)
end
end
data = data[index] or data[tonumber(index)]
if not data then
return
end
i = i + 1
end
end
-- Get property values formatted as a string of a given instance/entity.
-- 'entity' parameter denfines the instance from which we want to get some property values.
-- 'propertyID' parameter defines from which property the values are gotten.
-- 'rertun_val' parameter, if no result is returned, the value assigned to this parameter is returned, the default value is an empty string.
-- 'sep' parameter is the separation caracter used to separate returned values (e.g. ','), default is a space caracter, e.g. ' '.
-- Assign to 'stated_in' a wikidata entry id, if getValue() should only return values containing a reference statement 'stated in' (e.g. database, project, catalog). Note that the 'stated_in' parameter is only considered, if the assigned value to 'propertyID' is a wikidata entry.
function p.getValue(entity, propertyID, return_val, sep, stated_in) --CHANGED, Add CFG.ArticleLnkH
local claims
if return_val == nil then return_val = "" end
if sep == nil then sep = " " end
if entity and entity.claims then
claims = entity.claims[propertyID]
end
if claims then
-- if wiki-linked value output as link if possible
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
local out = {}
for k, v in pairs(claims) do
--local datav = mw.wikibase.label(v.mainsnak.datavalue.value["id"]) --CHANGED, OLD
local datav, addEnd, Article = getInYourLang (v.mainsnak.datavalue.value["id"]) --CHANGED, BEGIN
if datav == nil then
datav = " "
else --CHANGED, BEGIN
if Article ~= nil then
datav = MkIntLnk (Article..'|'..datav)
end
if addEnd ~= '' then
datav = datav..addEnd
end
end --CHANGED, END
--Filter statements with the specified stated_in reference value, if none (stated_in = nil) all statements are considered.
local is_from_given_source = true
if stated_in ~= nil then
is_from_given_source = false
if v.references then
for rk, rv in pairs(v.references) do
local ref_val = rv.snaks.P248
if ref_val then
for stated_k, stated_v in pairs(ref_val) do
if (stated_v and stated_v.snaktype == "value" and stated_v.datavalue.type == "wikibase-entityid") then
local ref_stated_in_val = stated_v.datavalue.value["id"]
if ref_stated_in_val == stated_in then is_from_given_source = true end
end
end
end
end
end
end
if is_from_given_source then
out[#out + 1] = datav
end
end
return table.concat(out, sep)
else
-- just return best values
return entity:formatPropertyValues(propertyID).value
end
else
return return_val
end
end
function p.getValueProtein(protein_entities, propertyID, return_val)
if return_val == nil then return_val = "" end
local sep = ","
local overall_results = {} --should return empty if nothing assigned
for key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a whole
local claims
local entity = val --each protein in encodes
if entity and entity.claims then
claims = entity.claims[propertyID]
end
if claims then
local results
-- if wiki-linked value output as link if possible
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
local out = {}
for k, v in pairs(claims) do
local datav = mw.wikibase.getLabel("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if datav == nil then datav = " " end
out[#out + 1] = datav
end
results = table.concat(out, sep)
else
results = entity:formatPropertyValues(propertyID).value
end
overall_results[#overall_results+1] = results --individual propertyID value stored in this index
end
end
local str_overall_results = table.concat(overall_results, sep) --weirdness happens when add a sep = " " otherwise each value represented one time
if string.match(str_overall_results, '%w+') then
return str_overall_results
else
return return_val
end
end
--general function to get value given an entity and property
function p.getQid(entity)
local Qid
if entity and entity.id then
Qid = entity.id
return Qid
else
return ""
end
end
--get random value that is preferred ranked
-- *lclz*: Sometimes Wikibase returns punctuations other than "," depending on
-- your site's language. Consider adding a gsub here.
function p.getRefseq_mRNA(entity, propertyID, return_val)
if return_val == nil then return_val = "" end
local input_rank = "RANK_PREFERRED" ---this is mostly like won't do anything because ranking isn't maintained in wikidata
local claims
if entity.claims then
claims = entity.claims[propertyID]
end
if claims then
-- if wiki-linked value output as link if possible
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid" ) then
local out = {}
for k, v in pairs(claims) do
local sitelink = mw.wikibase.getSitelink("Q" .. v.mainsnak.datavalue.value["numeric-id"])
local label = mw.wikibase.getLabel("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if label == nil then label = "Q" .. v.mainsnak.datavalue.value["numeric-id"] end
if sitelink then
out[#out + 1] = "[[" .. 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 LinkList_first element
--[[local results_split = mw.text.split(results, CFG.SeparatorStr)
local preffered_results = " "
if results_split[1] then
preferred_result = mw.text.trim(results_split[1]) --return LinkList_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 LinkList_first element because desired prefix not found and remove whitespaces
end
--]]
return results
end
else
return return_val
end
end
-- *lclz*: same as getRefseq_mRNA
function p.getRefseq_protein(protein_entities, propertyID, return_val)
local sep = CFG.SeparatorStr
local overall_results = {} --should return empty if nothing assigned
for key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a whole
local claims
local entity = val --each protein in encodes
if entity.claims then
claims = entity.claims[propertyID]
end
if claims then
local results
-- if wiki-linked value output as link if possible
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid" ) then
local out = {}
for k, v in pairs(claims) do
local datav = mw.wikibase.getLabel("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if datav == nil then datav = " " end
out[#out + 1] = datav
end
results = table.concat(out, sep)
else
results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value
end
overall_results[#overall_results+1] = results --a list is in each index
end
end
--why are there duplicate results here
local str_overall_results = table.concat(overall_results, sep)
return str_overall_results
end
--[[
local results_split = mw.text.split(str_overall_results, sep) --split complete list so can loop through..probably a more direct way to do this
--loop through results until get a NP or NM or just return whatever is in LinkList_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 LinkList_first element in result_split
if p.isempty(preffered_result) then
return return_val
else
return preferred_result --return a id starting with NP or NM
end
end --]]
--gets an image
--function p.getImage(entity, propertyID, sep, imgsize)
function p.getImage(entity, propertyID, sep, imgsize, searchCaption) --CHANGED
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
if searchCaption and (claims[1].qualifiers ~= nil) then
local caption = nil
local vals = claims[1].qualifiers["P2096"][1].datavalue
if vals ~= nil then
for k, v in pairs(vals) do
if v.language == local_lang then
caption = v.text
break
end
end
end
return table.concat(out, sep), caption
else
return table.concat(out, sep)
end
else
return ""
end
else
return ""
end
end
function p.getPDB(protein_entities)
local pdb_propertyID = "P638"
local overall_results = {}
for key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a whole
local claims
local entity = val
if entity and entity.claims then
claims = entity.claims[pdb_propertyID]
end
local sitelink = "https://www.rcsb.org/structure/"
if claims then
local results
if (claims[1] and claims[1].mainsnak.snaktype == "value") then
local out = {}
for k, v in pairs(claims) do
local label = mw.wikibase.getLabel(v.mainsnak.datavalue.value)
if label == nil then label = v.mainsnak.datavalue.value end
if sitelink then
out[#out + 1] = "[" .. sitelink .. label .. " " ..label .. "]"
else
out[#out + 1] = "[[:d:Q" .. v.mainsnak.datavalue.value .. "|" .. label .. "]]"
end
end
results = table.concat(out, ", ") -- *lclz*: punctuation (CJK comma, etc.)
else
results = entity:formatPropertyValues(pdb_propertyID, mw.wikibase.entity.claimRanks).value
end
overall_results[#overall_results+1] = results --individual propertyID values stored in this index
end
end
return table.concat(overall_results, ",%%s")
end
function p.getAliases(entity)
if entity['aliases'] ~= nil then
-- *lclz*: You will need a different language here.
-- If you are aiming for an "en" fallback, consider a set data structure.
-- zhwp went a bit further here: they moved this call after "gene_symbol",
-- so that this function can perform the deduplication here instead of
-- in renderIdentifiers. That way they skip messing with commas and spaces.
local test = entity['aliases']['en']
if test then
local a = ''
for key, value in ipairs(test) do
a = a .. ', ' .. value['value']
end
return a
else
return ""
end
else
return ""
end
end
--get a geneome start P644 or end P645
function p.getChromosomeLoc(entity, propertyID, prefix)
-- will contain the numeric value for the requested coordinate
local output = ""
local sep = " "
-- can only be P644 (genomic start) or P645 (genomic end) for this to work
-- should probably try to catch that. Might also increase legibility to use specific variable names when possible
-- local propertyID = mw.text.trim(frame.args[1] or "")
-- this can really only be P659 right now. I'm not sure of the value of including it as a parameter as other values will likely break this function
local qualifierID = "P659" --mw.text.trim(frame.args[2] or "")
-- Why do we include this here? What should happen if FETCH_WIKIDATA is not included?
--local input_parm = mw.text.trim(frame.args[3] or "")
-- this can needs to be fed to the function either by a call to {{#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.getEntity(itemID)
local claims
--gets a table of claims on the (genomic start or end) property Q19847637
if entity and entity.claims then
claims = entity.claims[propertyID]
end
--will return nothing if no claims are found
if claims then
--checking to be sure claims is populated, not sure it its needed
if (claims[1] ) then
--useful for debugging
--local out = {}
--pulls the genome location from the claim
for k, v in pairs(claims) do
local location = v.mainsnak.datavalue.value
--debugging
--out[#out + 1] = k.." location:" .. location.. " || "
--gets the qualifiers linked to the current claim
local quals
if v.qualifiers then
quals = v.qualifiers.P659
end
--if there are any
if quals then
for qk, qv in pairs(quals) do
local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]
--get to the entity targeted by the qualifier property. Genome builds are Items in wikidata
local qual_obj = mw.wikibase.getEntity(qual_obj_id)
local alias = ""
--this uses the aliases to pull out version numbers
--seems like there ought to be a better way to do this, but likely would need to change the data added by the bot
if qual_obj["aliases"] ~= nil then
local test = qual_obj["aliases"]["en"]
for key, value in ipairs(test) do
if string.match(value['value'], prefix) then
alias = value['value']
local build_no = alias:gsub(prefix,"")
--report only the most location associated with the most recent build
--if there is more than one location per build, just give one back as that is not our problem right now.
if build_no > newest_build then
output = location
newest_build = build_no
end
end
end
end
end
--in case there are no qualifiers, but there is a location, might as well return it
else
output = location
end
end
return output
else
return ""
end
else
return ""
--debug
--"no claims for "..itemID.." prop "..propertyID
end
end
function p.getAliasFromGenomeAssembly(entity, prefix)
-- will contain the numeric value for the requested coordinate
local output = ""
local sep = " "
local propertyID = "P644" --genomic start used
local qualifierID = "P659" --genomic assembly
local newest_build = "0"
local claims
if entity.claims then
claims = entity.claims[propertyID]
end
--will return nothing if no claims are found
if claims then
--checking to be sure claims is populated, not sure it its needed
if (claims[1] ) then
--useful for debugging
--local out = {}
--pulls the genome location from the claim
for k, v in pairs(claims) do
local location = '' -- TODO what should this be? defining location is required for 'output = location' below
local quals
if v.qualifiers then
quals = v.qualifiers.P659
end
--if there are any
--as of Aug. 2017, P659-genomic assembly is stored only in human genomic data. GRCh38 (newer) or GRCh37(older).
--Mouse genomic data doesn't have P659-genomic assembly data. But mouse has only one version. GRCm38/mm10.
if quals then
for qk, qv in pairs(quals) do
local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]
--get to the entity targeted by the qualifier property. Genome builds are Items in wikidata
local qual_obj = mw.wikibase.getEntity(qual_obj_id)
local alias = ""
--this uses the aliases to pull out version numbers
--seems like there ought to be a better way to do this, but likely would need to change the data added by the bot
if qual_obj["aliases"] ~= nil then
local test = qual_obj["aliases"]["en"]
for key, value in ipairs(test) do
if string.match(value['value'], prefix) then
alias = value['value']
local build_no = alias:gsub(prefix,"")
--For example, prefix is "hg" (this is set when the function was called),
--alias is "hg38" (which is data stored in Wikidata). Then "build_no" becomes "38".
--report only the most location associated with the most recent build
--if there is more than one location per build, just give one back as that is not our problem right now.
if build_no > newest_build then
newest_build = build_no
end
end
end
end
end
--in case there are no qualifiers, but there is a location, might as well return it
else
output = location
end
end
return prefix .. newest_build
else
return ""
end
else
return ""
end
end
-- *lclz*: Your language's wikidata may have different nouns for chromosome and
-- mitochodria.
function p.trimChromosome(entity) --CHANGED, FULL CHANGED
local function getValue(entity, propertyID)
local claims
if entity and entity.claims then
claims = entity.claims[propertyID]
end
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
return mw.wikibase.getLabelByLang (claims[1].mainsnak.datavalue['value']['id'],'en')
end
else
return ''
end
end
local string_to_trim = getValue(entity, "P1057")
local out = ''
--"mitochondrion" and "chromosome MT" is used for mitochondrial DNA.
--See [[d:Special:WhatLinksHere/Q18694495]]
if string.find(string_to_trim, 'chromosome MT') or string.find(string_to_trim, 'mitochondri') then --match both 'mitochondrio'/'mitochondrial'
out = "MT"
elseif string.find(string_to_trim, 'chromosome') then
out = string.match(string_to_trim, "%d+")--extract number from string
if out == nil then
out = string.match(string_to_trim, "X") or string.match(string_to_trim, "Y")
end
end
return out
end
function p.locToMb(num, idp)
num = tonumber(num)
if num == nil then
return ""
else
local mb = num/1000000
local mult = 10^(idp or 0)
return math.floor(mb * mult + 0.5) / mult
end
end
function p.isempty(s)
return s == nil or s == ''
end
function p.getGO(protein_entities, propertyID)
--propertyID ie molecular, cellular, function
local overall_results = {}
local results = "" --string to return
for key, val in pairs(protein_entities) do
local claims
local entity = val
if entity.claims then
claims = entity.claims[propertyID] -- ie molecular, cellular, function
end
local propertyID_child = "P686" -- Gene Ontology ID
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
--local out = {}
for k, v in pairs(claims) do
local itemID_child = "Q" .. v.mainsnak.datavalue.value["numeric-id"] --get Qid of property item so can get the GOid
local entity = mw.wikibase.getEntity(itemID_child)
local claims
local result_GOID = ''
if entity and entity.claims then claims = entity.claims[propertyID_child] end
if claims then
result_GOID = entity:formatPropertyValues(propertyID_child, {mw.wikibase.entity.claimRanks.RANK_NORMAL}).value
else
result_GOID = nil --no GO ID
end
local sitelink = "http://amigo.geneontology.org/amigo/term/"
local identH = "Q" .. v.mainsnak.datavalue.value["numeric-id"]
--local label = mw.wikibase.getLabel(identH) --CHANGED
local label, addEnd, Article = getInYourLang (identH) --CHANGED
if label == nil then label = identH end
local wiki_link = ""
--CHANGED, BEGIN
if sitelink and result_GOID ~= nil then
wiki_link = "\n* [" .. sitelink .. result_GOID .. " " .. label .."]"
else
wiki_link = "\n* [[:d:Q" .. v.mainsnak.datavalue.value["numeric-id"] .. "|" .. label .. "]]"
end
local AtEnd = ''
if Article ~= nil then
Article = string.gsub (Article, ' ', '_')
AtEnd = ' [[File:Wiki article small light.svg|text-bottom|'
.. "|link=https://ca.wikipedia.org/wiki/"..Article.."]]"
elseif addEnd ~= '' then
AtEnd = addEnd
end
if AtEnd ~= '' then
wiki_link = wiki_link..AtEnd
end
--CHANGED, END
overall_results[#overall_results+1] = wiki_link
end
else
results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value
end
end
--overall_results[#overall_results+1] = results --each protein GO terms stored in this index, so table contains all the GO terms with duplicates
end
local hash = {} --temp check
local res = {} --no dups
for _,v in ipairs(overall_results) do
if (not hash[v]) then
res[#res+1] = v
hash[v] = true
end
end
return table.concat(res, "")
end
local function getReference(qID, entity, property_id, ref_index)
local f = {"claims",property_id, ref_index, "references"}
local id = qID
--if id and (#id == 0) then
-- id = nil
--end
local data = entity
if not data then
return nil
end
local i = 1
while true do
local index = f[i]
if not index then
if type(data) == "table" then
return mw.text.jsonEncode(data, mw.text.JSON_PRESERVE_KEYS + mw.text.JSON_PRETTY)
else
return tostring(data)
end
end
data = data[index] or data[tonumber(index)]
if not data then
return ""
end
i = i + 1
end
end
function getRefLink (id, entity, prop, k) --CHANGED, NEW. Used for p.getDisease and p.getDrug
local refLink = ""
local ref = ""
ref = getReference (id, entity, prop, k)
if (ref ~= nil and ref ~= '') then
refLink = ref
end
return refLink
end
function p.getDisease(entity, propertyID)
local claims
local return_val = "" -- define variable; this line was 'if return_val == nil then return_val = "" end' which looks like a copy/paste
if entity and entity.claims then
claims = entity.claims[propertyID]
end
if claims then
-- if wiki-linked value output as link if possible
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
local out = {}
local datasource = {}
--{{#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 --CHANGED
--local datav = mw.wikibase.getLabel("Q" .. v.mainsnak.datavalue.value["numeric-id"])
--if datav == nil then datav = " " end
--local id = "Q" .. v.mainsnak.datavalue.value["numeric-id"]
--local linkTarget = mw.wikibase.getSitelink(id)
--local refLink = ""
--local ref = ""
--ref = getReference("", entity, "P2293", k)
--if (ref ~= nil and ref ~= '') then
----refLink = refLink..","..ref
--refLink = ref
--end
--if refLink = "" then --skip if there isn't a reference found
--if linkTarget then
-- out[#out + 1] = "[["..linkTarget.."|"..datav.."]]"
--else
-- out[#out + 1] = "[[:d:" .. id .. "|" .. datav .. "]]"
--end
out[#out + 1] = getInYourLang1 ("Q" .. v.mainsnak.datavalue.value["numeric-id"]) --CHANGED, NEW
--datasource[#out] = refLink
datasource[#out] = getRefLink ("", entity, "P2293", k) --CHANGED, NEW
end
return out, datasource
else
-- just return best values
--return entity:formatPropertyValues(propertyID).value
return return_val, return_val
end
else
return return_val
end
return return_val
end
function p.getDrug(protein_entities, propertyID)
local out = {}
local datasource = {}
local pname = {}
local pqid = {}
for key, val in pairs(protein_entities) do
local claims
local entity = val
local name = check_values(p.getLabel,{entity})
if entity.claims then
claims = entity.claims[propertyID] -- ie physically interacts with
end
local protein_id
if entity then protein_id = entity.id else protein_id = "" end
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do --CHANGED
--local datav = mw.wikibase.getLabel("Q" .. v.mainsnak.datavalue.value["numeric-id"])
--if datav == nil then datav = "" end
--local id = "Q" .. v.mainsnak.datavalue.value["numeric-id"]
--local linkTarget = mw.wikibase.getSitelink(id)
--local refLink = ""
--local ref = getReference(protein_id, entity, "P129",k) --just check if anything returned
--if (ref ~= nil and ref ~= '') then
--refLink = ref
--end
--if linkTarget then
--out[#out + 1] = "[["..linkTarget.."|"..datav.."]]"
--else
--out[#out + 1] = "[[:d:" .. id .. "|" .. datav .. "]]"
--end
out[#out + 1] = getInYourLang1 ("Q" .. v.mainsnak.datavalue.value["numeric-id"]) --CHANGED, NEW
datasource[#out] = getRefLink (protein_id, entity, "P129",k) --CHANGED, NEW
pname[protein_id] = name
pqid[#out] = protein_id
end --end k,v claims loop
end --end claims[1]
end --if claims
end -- end protein_entities loop
return out, datasource, pqid, pname
end
function p.FormatNaturalNumber(bp) --CHANGED function name
--Separate number with comma. For example when this function gets "12345678", returns "12.345.678"
local FormatedNumber = bp
while true do
local k
FormatedNumber, k = string.gsub(FormatedNumber, "^(-?%d+)(%d%d%d)", '%1'..CFG.ThousandSeparator..'%2') --CHANGED, using CFG.ThousandSeparator
if k == 0 then
break
end
end
return FormatedNumber
end
return p
