Modulu:Infobox gene
Moduluaren dokumentazioa[ikusi] [] [] []
Hemen erakusten dena /dok azpiorrialdeko dokumentazioa da. [kodearen kutxara saltatu]
Used by Txantiloi:Gene infotaula automatikoa.
You must translate Modulu:Infobox gene/eu.
Dokumentazio hau Modulu:Infobox gene/dok orrialdetik txertatua dago.
Mesedez, sar itzazu kategoriak dokumentazio azpiorrialdean eta interwiki loturak Wikidatan. Modulu honen azpiorrialdeak.
Mesedez, sar itzazu kategoriak dokumentazio azpiorrialdean eta interwiki loturak Wikidatan. Modulu honen azpiorrialdeak.
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, "P863", CFG.NotApplicableStr})
local ensembl_mm = check_values(p.getValue, {entity_mouse, "P863", 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 AND '
..'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, ",", "% or% ") --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 = RS.Orth_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