Module:Infobox gene: Difference between revisions
From Vigyanwiki
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m (1 revision imported from alpha:Module:Infobox_gene) |
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Latest revision as of 17:34, 29 July 2023
Documentation for this module may be created at Module:Infobox gene/doc
local p = {}
local localSeparatorStr = "," -- **lclz** Correct it if your wiki has different setting, like zhwiki uses "、" for now
local localNotApplicableStr = "n/a" -- **lclz**
local root
--define Global Color Scheme
local rowBGcolor = '#eee'
local titleBGcolor = '#ddd'
local sideTitleBGcolor = '#c3fdb8'
-- 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
--texts relevant to localization are tagged with --**lclz** and/or *lclz*
--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)
--make some guesses about whether the provided QID is a good one
--could expand here if we had some kind of error handling framework
--did we get it from the page
local root_qid = mw.text.trim(frame.args['QID'] or "") --try to get it from the args
local mm_qid = ""
--pull all the entity objects that we will need
local entity = {}
local entity_protein = {}
local entity_mouse = {}
local entity_mouse_protein = {}
local checkOrtholog = "" --flag used to see if mouse data avaliable
local mouse_propertyID = "P684" --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, 'protein') then --if protein switch entity to gene **lclz**
local claims
if entity.claims then
claims = entity.claims["P702"] --encoded by
end
if claims then
--go through each index and reassign entity
entity = {}
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do --this would be problematic if multiple genes for the protein
local itemID = "Q" .. claims[#entity + 1].mainsnak.datavalue.value["numeric-id"]
entity[#entity + 1] = mw.wikibase.getEntity(itemID)
root_qid = itemID
end
end --will return nothing if no claims are found
end
entity = mw.wikibase.getEntity(root_qid)
end
--get the other related entities
if entity then
local claims
--get protein entity object
if entity.claims then
claims = entity.claims[protein_propertyID]
end
if claims then
--go through each index and then make entity_protein indexed
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do
local protein_itemID = "Q" .. claims[#entity_protein + 1].mainsnak.datavalue.value["numeric-id"]
entity_protein[#entity_protein + 1] = mw.wikibase.getEntity(protein_itemID)
end
end --will return nothing if no claims are found
end
--get mouse entity object
if entity.claims then
claims = entity.claims[mouse_propertyID]
end
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", localNotApplicableStr, localSeparatorStr, bgee_wikidata_id}) --P5572: expressed in
local expressed_in_mouse_tissues = check_values(p.getValue, {entity_mouse, "P5572", localNotApplicableStr, localSeparatorStr, bgee_wikidata_id}) --P5572: expressed in
local entrez_gene = check_values(p.getValue, {entity, "P351", localNotApplicableStr} )
local entrez_gene_mm = check_values(p.getValue, {entity_mouse, "P351", localNotApplicableStr})
local image = check_values( p.getImage, {entity, "P18", " ", "250px"}) --need to set size
local uniprotID_hs = check_values(p.getValueProtein, {entity_protein, "P352", localNotApplicableStr})
local uniprotID_mm = check_values(p.getValueProtein, {entity_mouse_protein, "P352", localNotApplicableStr})
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", localNotApplicableStr})
local ensembl_mm = check_values(p.getValue, {entity_mouse, "P594", localNotApplicableStr})
local refseq_mRNA = check_values(p.getRefseq_mRNA, {entity, "P639", localNotApplicableStr})
local refseq_mRNA_mm = check_values(p.getRefseq_mRNA, {entity_mouse, "P639", localNotApplicableStr})
local refseq_prot = check_values(p.getRefseq_protein, {entity_protein, "P637", localNotApplicableStr})
local refseq_prot_mm = check_values(p.getRefseq_protein, {entity_mouse_protein, "P637", localNotApplicableStr})
local gstart = check_values(p.getChromosomeLoc, {entity, "P644", "hg"})
local gend = check_values(p.getChromosomeLoc, {entity, "P645", "hg"})
local chr = check_values(p.trimChromosome, {entity})
local cytoband = check_values(p.getValue, {entity, "P4196", localNotApplicableStr})
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 = check_values( p.trimChromosome, {entity_mouse})
local db_mm = check_values(p.getAliasFromGenomeAssembly, {entity_mouse,"mm"})
local cytoband_mm = check_values(p.getValue, {entity_mouse, "P4196", localNotApplicableStr})
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)
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)
--uncomment here to add a section of the infobox about genetically related diseases, with references
--if (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 (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 ~= localNotApplicableStr 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
-- *lclz*: Some projects, like zhwiki (again), use inline styles on
-- infobox modules in addition to the class. Be sure to check them out.
:addClass('infobox')
:css('width', '26.4em')
end
end
--Title above image
function p.renderUpperTitle(name)
local title = name
if not title then return "error: failed to get label"; end
root
:tag('tr')
:tag('th')
:attr('colspan', 4)
:css('text-align', 'center')
:css('font-size', '125%')
:css('font-weight', 'bold')
:wikitext(title)
:done() --end th
:done() --end tr
end
--This is a place holder for the image caption, which is stored in wikicommons comments unsure how to access
function p.renderCaption(entity)
--caption
end
--gets default image
function p.renderImage(image)
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 = 'Available structures' --**lclz**
local pdb_link = "[[Protein_Data_Bank|PDB]]" --**lclz**
local searchTitle = ""
local listTitle = "List of PDB id codes" --**lclz**
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 = 'Ortholog search: ' --**lclz**
url_uniprot = uniprotID_mm..','..uniprotID_hs
else
searchTitle = 'Human UniProt search: ' --**lclz**
url_uniprot = uniprotID_hs
end
local PDBe_list = " " --create a list with " or " if there is more than one uniprot
--get first uniprot in a list
if url_uniprot:match("([^,]+),") then--first check if there is a list if not just assume one value
PDBe_list = string.gsub(url_uniprot, ",", "%%20or%%20") --add or's inststead of commas
else
PDBe_list = url_uniprot
end
local PDBe = "["..PDBe_base..PDBe_list.." PDBe] "
local RCSB = "["..RCSB_base..url_uniprot.." RCSB] "
if string.match(pdbIDs, '%w+') then --if there aren't any PDB_ID don't display this part of the infobox
--p.formatRow(title)---how to not close the tags is a mystery and I could condense code once I figure out
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr') --create title header
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:tag('tr')
:tag('th')
:attr('rowspan', '2')
:css('background-color', sideTitleBGcolor)
:css('width', '43px')
:wikitext(pdb_link)
:done() --end th
:tag('td')
:attr('colspan', '2')
:css('background-color', rowBGcolor)
:wikitext(searchTitle)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(PDBe)
:wikitext(RCSB)
:done() --end span
:done() --end td
:done() --end tr
:tag('tr') --new row for collapsible list of PDB codes
:tag('td')
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:css('background-color', titleBGcolor)
:css('text-align', 'center')
:tag('th')
:attr('colspan', '2')
:wikitext(listTitle)
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '2')
:css('background-color', rowBGcolor)
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(pdbIDs)
:done() --end span
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
else
return ""
end
end
function p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene)
local title = "Identifiers" --**lclz**
local label_aliases = "[[Gene nomenclature|Aliases]]" --**lclz**
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.."]"
end
end
-- *lclz*: see getAliases. You can, say, use another punctuation for your language.
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 first in aliases list
aliases = string.gsub(aliases, ', '..gene_symbol..',', ',') --get rid of gene name if in aliases list
aliases = string.gsub(aliases, ", ,", ",") --remove comma from middle
aliases = string.gsub(aliases, ", $", "") --remove comma from end
local label_ext_id = "External IDs" --**lclz**
omim_id = string.gsub(omim_id, "%s", "")
local omim_list = mw.text.split(omim_id, localSeparatorStr)
local omim = ""
if (omim_id ~= nil and omim_id ~= "") then
omim = "[[Mendelian_Inheritance_in_Man|OMIM]]"..": " --**lclz**
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, localSeparatorStr)
local homolo =""
if (homologene_id ~= nil and homologene_id ~= "") then
homolo = "[[HomoloGene]]"..": "
end
for i, v in ipairs(homolo_list) do
if string.match(v, '%w+') then
homolo = homolo.."[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 = "[[GeneCards]]"..": "
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, localSeparatorStr)
local mgi = ""
if (mgi_id ~= nil and mgi_id ~= "") then
mgi = "[[Mouse_Genome_Informatics|MGI]]"..": " --**lclz**
end
for i, v in ipairs(mgi_list) do
if string.match(v, '%w+') then
local mgi_number = string.sub(mgi_id, 5)
mgi = mgi.."[http://www.informatics.jax.org/marker/"..mgi_id.." "..mgi_number.."] "
end
end
mgi = string.gsub(mgi, ", $"," ")--remove comma from end
local ChEMBL = ""
if string.match(ChEMBL_id, '%w+') then
ChEMBL = "[[ChEMBL]]"..": ".."[https://www.ebi.ac.uk/chembldb/index.php/target/inspect/CHEMBL"..ChEMBL_id.." "..ChEMBL_id.."] "
end
local IUPHAR = ""
if string.match(IUPHAR_id, '%w+') then
IUPHAR = "[[International_Union_of_Basic_and_Clinical_Pharmacology|IUPHAR]]"..": ".."[http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId="..IUPHAR_id.." "..IUPHAR_id.."] " --**lclz**
end -- *lclz*
local label_EC = "[[Enzyme_Commission_number|EC number]]" --**lclz**
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 .. "]"
root
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(label_aliases)
:done() --end span
:done() --end th
:tag('td')
:attr('colspan','3')
:css('background', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(symbol_url)
:done() --end span
:wikitext(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', sideTitleBGcolor)
:wikitext(label_ext_id)
:done() --end th
:tag('td')
:attr('colspan', '3')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(omim)
:wikitext(mgi)
:wikitext(homolo)
:wikitext(ChEMBL)
:wikitext(IUPHAR)
:wikitext(genecards)
:done() --end span
:done() --end td
:done() --end tr
if ec_no ~= "" then
root
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(label_EC)
:done() --end th
:tag('td')
:attr('colspan', '3')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(EC)
:done() --end span
:done() --end td
:done() --end tr
end
end
function p.renderDiseases(frame, disease, dis_ref, name, qid)
local title = "Genetically Related Diseases" --**lclz**
--check first to see if any of the diseases have references
local ref_flag_all = false --check if any disease have references if not then don't render the headers
local disease_name = '' --local disease_name = table.concat(disease, ", ")
for index,value in ipairs(disease) do
if (dis_ref[index] ~= nil and dis_ref[index] ~= '') then
if disease_name == '' then
disease_name = value
else
disease_name = disease_name..", "..value -- *lclz*: punctuation
end
ref_flag_all = true
end
end
if ref_flag_all then
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('tr') --create title bar
:tag('th')
:attr('colspan', '3')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:done() --end td
:done() --end tr
local ref_url = "https://www.wikidata.org/wiki/"..qid.."#P2293" --direct page to property genetically associated disease
local title = "Diseases that are genetically associated with "..name.." view/edit references on wikidata" --**lclz**
local ref_link = disease_name..frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title = title, url = ref_url} })
root
:tag('tr')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('td')
:css('background-color', rowBGcolor)
:attr('scope', 'row')
:attr('colspan', '3')
:wikitext(ref_link)
:done() --end td
:done() --end tr
end
end
function p.renderDrug(frame,drug, drug_ref, drug_pqid, drug_pname)
local title = "Targeted by Drug" --**lclz**
--check first to see if any of the drugs have references
local ref_flag_all = false --check if any drugs have references if not then don't render the headers
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
-- *lclz*: comma
drug_list_per_protein[protein_qid] = drug_list_per_protein[protein_qid]..', '..value --each list of drugs keyed on protein qid
end
ref_flag_all = true
end
end
if ref_flag_all then
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('tr') --create title bar
:tag('th')
:attr('colspan', '3')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:done() --end td
:done() --end tr
--loop to create reference links from drug lists
for k,v in pairs(drug_list_per_protein) do
local drug_name = v
local ref_url = "https://www.wikidata.org/wiki/"..k.."#P129" --direct page to property genetically associated disease
local title = "Drugs that physically interact with "..drug_pname[k].." view/edit references on wikidata" --**lclz**
local ref_link = drug_name..frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title = title, url = ref_url} })
root
:tag('tr')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('td')
:css('background-color', rowBGcolor)
:attr('scope', 'row')
:attr('colspan', '3')
:wikitext(ref_link)
:done() --end td
:done() --end tr
end
end
end
function p.renderGeneLocation(frame, chr, gstart, gend, db, cytoband, ensembl, chr_mm, gstart_mm, gend_mm, db_mm, cytoband_mm, ensembl_mm, name)
local titleHuman = "Gene location ([[Human genome|Human]])" --**lclz**
local titleMouse = "Gene location ([[Laboratory mouse|Mouse]])" --**lclz**
local label_chr = "[[Chromosome|Chr.]]" --**lclz**
local label_locus = "[[Locus (genetics)|Band]]" --**lclz**
local label_gstart = "Start" --**lclz**
local label_gend = "End" --**lclz**
local tooltip_arrowSign = "Genomic location for "..name --**lclz**
local arrowSign_width = 14
if chr ~= "" 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 = {}
chrLengthTable["1"] = 248956422
chrLengthTable["2"] = 242193529
chrLengthTable["3"] = 198295559
chrLengthTable["4"] = 190214555
chrLengthTable["5"] = 181538259
chrLengthTable["6"] = 170805979
chrLengthTable["7"] = 159345973
chrLengthTable["8"] = 145138636
chrLengthTable["9"] = 138394717
chrLengthTable["10"] = 133797422
chrLengthTable["11"] = 135086622
chrLengthTable["12"] = 133275309
chrLengthTable["13"] = 114364328
chrLengthTable["14"] = 107043718
chrLengthTable["15"] = 101991189
chrLengthTable["16"] = 90338345
chrLengthTable["17"] = 83257441
chrLengthTable["18"] = 80373285
chrLengthTable["19"] = 58617616
chrLengthTable["20"] = 64444167
chrLengthTable["21"] = 46709983
chrLengthTable["22"] = 50818468
chrLengthTable["X"] = 156040895
chrLengthTable["Y"] = 57227415
chrLengthTable["MT"] = 16569
local chrLength = chrLengthTable[chr]
--Different languages have different word order.
local chrTextTable = {} --**lclz** linked articles
chrTextTable["1"] = "Chromosome 1 (human)"
chrTextTable["2"] = "Chromosome 2 (human)"
chrTextTable["3"] = "Chromosome 3 (human)"
chrTextTable["4"] = "Chromosome 4 (human)"
chrTextTable["5"] = "Chromosome 5 (human)"
chrTextTable["6"] = "Chromosome 6 (human)"
chrTextTable["7"] = "Chromosome 7 (human)"
chrTextTable["8"] = "Chromosome 8 (human)"
chrTextTable["9"] = "Chromosome 9 (human)"
chrTextTable["10"] = "Chromosome 10 (human)"
chrTextTable["11"] = "Chromosome 11 (human)"
chrTextTable["12"] = "Chromosome 12 (human)"
chrTextTable["13"] = "Chromosome 13 (human)"
chrTextTable["14"] = "Chromosome 14 (human)"
chrTextTable["15"] = "Chromosome 15 (human)"
chrTextTable["16"] = "Chromosome 16 (human)"
chrTextTable["17"] = "Chromosome 17 (human)"
chrTextTable["18"] = "Chromosome 18 (human)"
chrTextTable["19"] = "Chromosome 19 (human)"
chrTextTable["20"] = "Chromosome 20 (human)"
chrTextTable["21"] = "Chromosome 21 (human)"
chrTextTable["22"] = "Chromosome 22 (human)"
chrTextTable["X"] = "X chromosome (human)"
chrTextTable["Y"] = "Y chromosome (human)"
chrTextTable["MT"] = "Mitochondrial DNA (human)"
local chrText = chrTextTable[chr]
--about the calculation below, see https://en.wikipedia.org/wiki/User:Was_a_bee/Gene#3._Calculation_detail
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 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.."] - [[Ensembl genome database project|Ensembl]], May 2017", {name = "refGRCh38Ensembl"}) --**lclz**
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.."] - [[Ensembl genome database project|Ensembl]], May 2017", {name = "refGRCh37Ensembl"}) --**lclz**
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 = "" --wikitext used for showing gene location
if chr == "MT" then -- wikitext for mitochondrial DNA
--wikitext_for_ideogram_image = wikitext_for_ideogram_image.."<div align=\"center\">"
--wikitext_for_ideogram_image = wikitext_for_ideogram_image.."<div style=\"position\: relative\; width\: 300px\;\">"
--wikitext_for_ideogram_image = wikitext_for_ideogram_image.."[[File:Map of the human mitochondrial genome.svg|300px|"..chrText.."]]"
--wikitext_for_ideogram_image = wikitext_for_ideogram_image.."</div>"
--wikitext_for_ideogram_image = wikitext_for_ideogram_image.."</div>"
else -- wikitext for autosome and sex chromosome
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."<div align=\"center\">"
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."<div style=\"position\: relative\; width\: 300px\;\">"
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."[[File:Human chromosome "..chr.." ideogram.svg|300px|"..chrText.."]]"
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."<div style=\"position\: absolute\; left\: "..arrowSignLocation.."px\; top\: 2px\; padding\: 0\;\">"
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."[[File:HSR 1996 II 3.5e.svg|"..arrowSign_width.."px|"..tooltip_arrowSign.."]]</div>"
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."<div style=\"position\: absolute\; left\: "..markerLocation.."px\; top\: 19px\; padding\: 0\;\">[[File:Red rectangle "..markerWidth.."x18.png|"..markerWidth.."px|"..tooltip_arrowSign.."]]</div>"
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."</div>"
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."</div>"
end
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(titleHuman)
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:wikitext("[[File:Ideogram human chromosome "..chr..".svg|300px|"..chrText.."]]")
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:attr('width', '15%')
:css('background-color', sideTitleBGcolor)
:wikitext(label_chr)
:done() --end th
:tag('td')
:attr('colspan', '3')
:attr('width', '85%')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext("[["..chrText.."]]"..source_link_chr)
:done() --end span
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:wikitext(wikitext_for_ideogram_image)
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:attr('rowspan', '2')
:attr('width', '15%')
:css('background-color', sideTitleBGcolor)
:wikitext(label_locus)
:done() --end th
:tag('td')
:attr('rowspan', '2')
:attr('width', '35%')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(cytoband)
:done() --end span
:done() --end td
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(label_gstart)
:done() --end th
:tag('td')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(p.separateWithComma(gstart).." [[Base pair|bp]]"..source_link_gstart) -- **lclz** Change it if it is inappropriate
:done() --end span
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(label_gend)
:done() --end th
:tag('td')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(p.separateWithComma(gend).." [[Base pair|bp]]"..source_link_gend) -- **lclz** Change it if it is inappropriate
:done() --end span
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
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 = {}
chrLengthTable_mm["1"] = 195471971
chrLengthTable_mm["2"] = 182113224
chrLengthTable_mm["3"] = 160039680
chrLengthTable_mm["4"] = 156508116
chrLengthTable_mm["5"] = 151834684
chrLengthTable_mm["6"] = 149736546
chrLengthTable_mm["7"] = 145441459
chrLengthTable_mm["8"] = 129401213
chrLengthTable_mm["9"] = 124595110
chrLengthTable_mm["10"] = 130694993
chrLengthTable_mm["11"] = 122082543
chrLengthTable_mm["12"] = 120129022
chrLengthTable_mm["13"] = 120421639
chrLengthTable_mm["14"] = 124902244
chrLengthTable_mm["15"] = 104043685
chrLengthTable_mm["16"] = 98207768
chrLengthTable_mm["17"] = 94987271
chrLengthTable_mm["18"] = 90702639
chrLengthTable_mm["19"] = 61431566
chrLengthTable_mm["X"] = 171031299
chrLengthTable_mm["Y"] = 91744698
chrLengthTable_mm["MT"] = 16299
local chrLength_mm = chrLengthTable_mm[chr_mm]
--Different languages have different word order.
local chrTextTable_mm = {}--**lclz** Articles not yet created
chrTextTable_mm["1"] = "Chromosome 1 (mouse)"
chrTextTable_mm["2"] = "Chromosome 2 (mouse)"
chrTextTable_mm["3"] = "Chromosome 3 (mouse)"
chrTextTable_mm["4"] = "Chromosome 4 (mouse)"
chrTextTable_mm["5"] = "Chromosome 5 (mouse)"
chrTextTable_mm["6"] = "Chromosome 6 (mouse)"
chrTextTable_mm["7"] = "Chromosome 7 (mouse)"
chrTextTable_mm["8"] = "Chromosome 8 (mouse)"
chrTextTable_mm["9"] = "Chromosome 9 (mouse)"
chrTextTable_mm["10"] = "Chromosome 10 (mouse)"
chrTextTable_mm["11"] = "Chromosome 11 (mouse)"
chrTextTable_mm["12"] = "Chromosome 12 (mouse)"
chrTextTable_mm["13"] = "Chromosome 13 (mouse)"
chrTextTable_mm["14"] = "Chromosome 14 (mouse)"
chrTextTable_mm["15"] = "Chromosome 15 (mouse)"
chrTextTable_mm["16"] = "Chromosome 16 (mouse)"
chrTextTable_mm["17"] = "Chromosome 17 (mouse)"
chrTextTable_mm["18"] = "Chromosome 18 (mouse)"
chrTextTable_mm["19"] = "Chromosome 19 (mouse)"
chrTextTable_mm["X"] = "X chromosome (mouse)"
chrTextTable_mm["Y"] = "Y chromosome (mouse)"
chrTextTable_mm["MT"] = "Mitochondrial DNA (mouse)"
local chrText_mm = chrTextTable_mm[chr_mm]
--about the calculation below, see https://en.wikipedia.org/wiki/User:Was_a_bee/Gene#3._Calculation_detail
local markerWidth_mm = ((gend_mm - gstart_mm) * 294.133 )/ chrLength_mm
if markerWidth_mm < 2 then
markerWidth_mm = 2
else
markerWidth_mm = math.ceil(markerWidth_mm)
end
local markerLocation_mm = (147.0666 * (gstart_mm + gend_mm) / chrLength_mm ) + 1.6 - (markerWidth_mm / 2)
local arrowSignLocation_mm = markerLocation_mm + (markerWidth_mm / 2) - (arrowSign_width / 2)
markerLocation_mm = math.floor( markerLocation_mm * 10 + 0.5 ) / 10
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.."] - [[Ensembl genome database project|Ensembl]], May 2017", {name = "refGRCm38Ensembl"}) --**lclz**
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 = "" --wikitext used for showing gene location
if chr_mm == "MT" then -- wikitext for mitochondrial DNA
--wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."<div align=\"center\">"
--wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."<div style=\"position\: relative\; width\: 300px\;\">"
--wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."[[File:Map of the human mitochondrial genome.svg|300px|"..chrText_mm.."]]"
--wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."</div>"
--wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."</div>"
else -- wikitext for autosome and sex chromosome
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."<div align=\"center\">"
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."<div style=\"position\: relative\; width\: 300px\;\">"
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."[[File:Ideogram of house mouse chromosome "..chr_mm..".svg|300px|"..chrText_mm.."]]"
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."<div style=\"position\: absolute\; left\: "..arrowSignLocation_mm.."px\; top\: 2px\; padding\: 0\;\">"
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."[[File:HSR 1996 II 3.5e.svg|"..arrowSign_width.."px|"..tooltip_arrowSign.."]]</div>"
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."<div style=\"position\: absolute\; left\: "..markerLocation_mm.."px\; top\: 19px\; padding\: 0\;\">[[File:Red rectangle "..markerWidth_mm.."x18.png|"..markerWidth_mm.."px|"..tooltip_arrowSign.."]]</div>"
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."</div>"
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."</div>"
end
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(titleMouse)
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:wikitext("[[File:Ideogram house mouse chromosome "..chr_mm..".svg|260px|"..chrText_mm.."]]")
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:attr('width', '15%')
:css('background-color', sideTitleBGcolor)
:wikitext(label_chr)
:done() --end th
:tag('td')
:attr('colspan', '3')
:attr('width', '85%')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(chrText_mm..source_link_chr_mm)
:done() --end span
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:wikitext(wikitext_for_ideogram_image_mm)
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:attr('rowspan', '2')
:attr('width', '15%')
:css('background-color', sideTitleBGcolor)
:wikitext(label_locus)
:done() --end th
:tag('td')
:attr('rowspan', '2')
:attr('width', '35%')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(cytoband_mm)
:done() --end span
:done() --end td
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(label_gstart)
:done() --end th
:tag('td')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(p.separateWithComma(gstart_mm).." [[Base pair|bp]]"..source_link_gstart_mm) -- **lclz** Change it if it is inappropriate
:done() --end span
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(label_gend)
:done() --end th
:tag('td')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(p.separateWithComma(gend_mm).." [[Base pair|bp]]"..source_link_gend_mm) -- **lclz** Change it if it is inappropriate
:done() --end span
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
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 = localNotApplicableStr
local collapse = "none"
local split_values = mw.text.split(expressed_in_tissues, localSeparatorStr)
local anatomic_entity_list = {}
local anatomic_entities = {}
local results
for k,v in ipairs(split_values) do
if string.match(v, '%w+') and v ~= localNotApplicableStr 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 = localNotApplicableStr
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 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 = "[[Gene expression|RNA expression]] pattern" --**lclz**
local biogps_link = ""
local biogps_title = "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.."/ More reference expression data]" --**lclz**
else
expression_images = localNotApplicableStr
end
local ensembl_id = string.match(ensembl,"%a+%d+") or ""
local ensembl_id_mouse = string.match(ensembl_mouse,"%a+%d+") or ""
local bgee_title = "Bgee"
bgee_title = "[https://bgee.org/ " .. bgee_title .. "]"
local bgee_default = "["..bgee_gene_page..ensembl_id.." Top expressed in]"
bgee_expression = p.renderExpressionList(bgee_expression, bgee_default)
local bgee_collapse = bgee_expression[1]
bgee_default = bgee_expression[2]
local bgee_tissues = bgee_expression[3]
local bgee_default_mm = "["..bgee_gene_page..ensembl_id_mouse.." Top expressed in]"
bgee_expression_mouse = p.renderExpressionList(bgee_expression_mouse, bgee_default_mm)
local bgee_collapse_mm = bgee_expression_mouse[1]
bgee_default_mm = bgee_expression_mouse[2]
local bgee_tissues_mm = bgee_expression_mouse[3]
local bgee_more_link = ""
if bgee_tissues ~= localNotApplicableStr then
bgee_more_link = "["..bgee_gene_page..ensembl_id.." More reference expression data]"
end
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(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', 'left')
:tag('tr')
:tag('th')
:wikitext("'''[[Human genome|Human]]'''")
:done() --end th
:tag('th')
:wikitext("'''[[Laboratory mouse|Mouse]] (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', 'center')
: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', 'center')
: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', 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', sideTitleBGcolor)
: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', 'left')
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:wikitext(expression_images)
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(biogps_link)
:done() --end span
:done() --end td
:done() --end tr
: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 = "[[Gene ontology]]" --**lclz**
local mol_funct_title = "Molecular function" --**lclz**
local cell_comp_title = "Cellular component" --**lclz**
local bio_process_title = "Biological process" --**lclz**
local amigo_link = "[http://amigo.geneontology.org/" .. " Amigo]"
local quickGO_link = "[https://www.ebi.ac.uk/QuickGO/" .. " QuickGO]"
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr') --create title bar
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:css('background-color', sideTitleBGcolor)
:css('font-weight', 'bold')
:wikitext(mol_funct_title)
:done() --end td
:tag('td')
:css('background-color', rowBGcolor)
:tag('div')
:attr('class', 'plainlinks')
:wikitext(mol_funct)
:wikitext( '\n' ) -- newline before ending div tag, to ensure next section formats properly
:done() --end div
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:css('background-color', sideTitleBGcolor)
:css('font-weight', 'bold')
:wikitext(cell_comp_title)
:done() --end td
:tag('td')
:css('background-color', rowBGcolor)
:tag('div')
:attr('class', 'plainlinks')
:wikitext(cell_comp)
:wikitext( '\n' ) -- newline before ending div tag, to ensure next section formats properly
:done() --end div
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:css('background-color', sideTitleBGcolor)
:css('font-weight', 'bold')
:wikitext(bio_process_title)
:done() --end td
:tag('td')
:css('background-color', rowBGcolor)
:tag('div')
:attr('class', 'plainlinks')
:wikitext(bio_process)
:wikitext( '\n' ) -- newline before ending div tag, to ensure next section formats properly
:done() --end div
:done() --end td
:done() --end tr
:tag('tr')
:tag('td')
:css('background-color', rowBGcolor)
:css('text-align', 'center')
:attr('colspan', '4')
:wikitext("Sources:") -- **lclz**
:wikitext(amigo_link)
:wikitext(" / ")
:wikitext(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 = "[[Orthologs]]" --**lclz**
--to do make the list creation a function
--create list for entrez ids
local category_chromosome = '[[Category:Genes on human chromosome '..chr..']]'-- *lclz*: Category name
if chr == "MT" then
category_chromosome = '[[Category:Human mitochondrial genes]]'-- *lclz*: Category name for mtDNA genes
end
if mw.title.getCurrentTitle().namespace ~= 0 then
category_chromosome = ""
end
local entrezTitle = "[[Entrez]]"
entrez_gene = string.gsub(entrez_gene, "%s", "")
local entrez_link = localNotApplicableStr
local entrez_collapse
local entrez_default = ""
local split_entrez = mw.text.split(entrez_gene, localSeparatorStr)
local entrez_link_list = {}
for k,v in ipairs(split_entrez) do
if string.match(v, '%w+') and v ~= localNotApplicableStr then
entrez_link_list[#entrez_link_list+1] = "[https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=default&list_uids="..entrez_gene.."&rn=1 "..entrez_gene.."]"
end
end
--if less than 5 don't create collapsible list
if table.getn(entrez_link_list) < 5 then
entrez_collapse = "none"
if entrez_default == nil and table.getn(entrez_link_list) == 0 then entrez_link = localNotApplicableStr end
else
entrez_collapse = "collapsible collapsed"
entrez_default = table.remove(entrez_link_list, 1) .. '<br>' .. table.remove(entrez_link_list, 1) .. '<br>' ..table.remove(entrez_link_list, 1) .. '<br>' .. table.remove(entrez_link_list, 1) .. '<br>' .. table.remove(entrez_link_list, 1) .. '<br>'--get first 5 elements in table and use for display
end
if entrez_link_list[#entrez_link_list] then
entrez_link = table.concat(entrez_link_list, "<br>")
end
--create list for mouse Entrez id
entrez_gene_mm = string.gsub(entrez_gene_mm, "%s", "")
local entrez_mm_link = localNotApplicableStr
local entrez_mm_collapse
local entrez_mm_default = ""
local split_entrez_mm = mw.text.split(entrez_gene_mm, localSeparatorStr)
local entrez_mm_link_list = {}
for k,v in ipairs(split_entrez_mm) do
if string.match(v, '%w+') and v ~= localNotApplicableStr then
entrez_mm_link_list[#entrez_mm_link_list+1] = "[https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=default&list_uids="..v.."&rn=1 "..v.."]"
end
end
--if less than 5 don't create collapsible list
if table.getn(entrez_mm_link_list) < 5 then
entrez_mm_collapse = "none"
if entrez_mm_default == nil and table.getn(entrez_mm_link_list) == 0 then entrez_mm_link = localNotApplicableStr end
else
entrez_mm_collapse = "collapsible collapsed"
entrez_mm_default = table.remove(entrez_mm_link_list, 1) .. '<br>' .. table.remove(entrez_mm_link_list, 1) .. '<br>' ..table.remove(entrez_mm_link_list, 1) .. '<br>' .. table.remove(entrez_mm_link_list, 1) .. '<br>' .. table.remove(entrez_mm_link_list, 1) .. '<br>'--get first 5 elements in table and use for display
end
if entrez_mm_link_list[#entrez_mm_link_list] then
entrez_mm_link = table.concat(entrez_mm_link_list, "<br>")
end
--create list of ensembl id
local ensemblTitle = "[[Ensembl]]"
ensembl = string.gsub(ensembl, "%s", "")
local ensembl_link = localNotApplicableStr
local ensembl_collapse
local ensembl_default = ""
local split_ensembl = mw.text.split(ensembl, localSeparatorStr)
local ensembl_link_list = {}
for k,v in ipairs(split_ensembl) do
if string.match(v, '%w+') and v ~= localNotApplicableStr then
ensembl_link_list[#ensembl_link_list+1] = "[http://www.ensembl.org/Homo_sapiens/geneview?gene="..v..";db=core".." "..v.."]"
end
end
--if less than 5 don't create collapsible list
if table.getn(ensembl_link_list) < 5 then
ensembl_collapse = "none"
if ensembl_default == nil and table.getn(ensembl_link_list) == 0 then ensembl_link = localNotApplicableStr end
else
ensembl_collapse = "collapsible collapsed"
ensembl_default = table.remove(ensembl_link_list, 1) .. '<br>' .. table.remove(ensembl_link_list, 1) .. '<br>' ..table.remove(ensembl_link_list, 1) .. '<br>' .. table.remove(ensembl_link_list, 1) .. '<br>' .. table.remove(ensembl_link_list, 1) .. '<br>'--get first 5 elements in table and use for display
end
if ensembl_link_list[#ensembl_link_list] then
ensembl_link = table.concat(ensembl_link_list, "<br>")
end
--create list of mouse ensembl id
ensembl_mm = string.gsub(ensembl_mm, "%s", "")
local ensembl_mm_link = localNotApplicableStr
local ensembl_mm_collapse
local ensembl_mm_default = ""
local split_ensembl_mm = mw.text.split(ensembl_mm, localSeparatorStr)
local ensembl_mm_link_list = {}
for k,v in ipairs(split_ensembl_mm) do
if string.match(v, '%w+') and v ~= localNotApplicableStr then
ensembl_mm_link_list[#ensembl_mm_link_list+1] = "[http://www.ensembl.org/Mus_musculus/geneview?gene="..v..";db=core".." "..v.."]"
end
end
--if less than 5 don't create collapsible list
if table.getn(ensembl_mm_link_list) < 5 then
ensembl_mm_collapse = "none"
if ensembl_mm_default == nil and table.getn(ensembl_mm_link_list) == 0 then ensembl_mm_link = localNotApplicableStr end
else
ensembl_mm_collapse = "collapsible collapsed"
ensembl_mm_default = table.remove(ensembl_mm_link_list, 1) .. '<br>' .. table.remove(ensembl_mm_link_list, 1) .. '<br>' ..table.remove(ensembl_mm_link_list, 1) .. '<br>' .. table.remove(ensembl_mm_link_list, 1) .. '<br>' .. table.remove(ensembl_mm_link_list, 1) .. '<br>'--get first 5 elements in table and use for display
end
if ensembl_mm_link_list[#ensembl_mm_link_list] then
ensembl_mm_link = table.concat(ensembl_mm_link_list, "<br>")
end
--create lists of uniprot ID
local uniprotTitle = "[[UniProt]]"
local uniprot_url = "https://www.uniprot.org/uniprot/"
local uniprot_link = localNotApplicableStr
local uniprot_collapse
local uniprot_default = ""
--split string and loop through concatenate by <br>
local split_uniprot = mw.text.split(uniprot, '%p') -- the separator may be different sometimes, see note on zhwiki. This is unlikely to have punctuation, prayer.
local uniprot_link_list = {}
local uniprot_first = {} --preferred values only display [O,P,Q] prefixed entries if they exist
local uniprot_alternate = {} --[A-N,R-Z] entries
local hash = {} --storage to look for duplicated values
for k,v in ipairs(split_uniprot) do
if not hash[v] then --only add if not found previously..some encodes uniprotID dup in different encodes
local label = mw.text.trim(v)
local concat_uniprot_link = uniprot_url .. label
if string.match(v, '%w+') and v ~= localNotApplicableStr then
if string.match(v, '^O') or string.match(v,'^P') or string.match(v, '^Q') then
uniprot_first[#uniprot_first+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"
else
uniprot_alternate[#uniprot_alternate+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"
end
end
hash[v] = true
end
end
if table.getn(uniprot_first)>0 then --if there is something in the preferred values display else display anything else
uniprot_link_list = uniprot_first
else
uniprot_link_list = uniprot_alternate
end
--if less than 5 don't create collapsible list
if table.getn(uniprot_link_list) < 5 then
uniprot_collapse = "none"
if uniprot_default == nil and table.getn(uniprot_link_list) == 0 then uniprot_link = localNotApplicableStr end
else
uniprot_collapse = "collapsible collapsed"
uniprot_default = table.remove(uniprot_link_list, 1) .. '<br>' .. table.remove(uniprot_link_list, 1) .. '<br>' ..table.remove(uniprot_link_list, 1) .. '<br>' .. table.remove(uniprot_link_list, 1) .. '<br>' .. table.remove(uniprot_link_list, 1) .. '<br>'--get first 5 elements in table and use for display
end
if uniprot_link_list[#uniprot_link_list] then
uniprot_link = table.concat(uniprot_link_list, "<br>")
end
--mouse uniprot lists
local uniprot_mm_link = localNotApplicableStr
local uniprot_mm_collapse
local uniprot_mm_default = ""
--split string and loop through concatenate by <br>
local split_uniprot_mm = mw.text.split(uniprot_mm, localSeparatorStr)
local uniprot_mm_link_list = {}
local uniprot_mm_first = {} --preferred values only display [O,P,Q] prefixed entries if they exist
local uniprot_mm_alternate = {} --[A-N,R-Z] entries
local hash = {} --storage to look for duplicated values
for k,v in ipairs(split_uniprot_mm) do
if not hash[v] then --only add if not found previously..some encodes uniprotID dup in different encodes
local label = mw.text.trim(v)
local concat_uniprot_link = uniprot_url .. label
if string.match(v, '%w+') and v ~= localNotApplicableStr then
if string.match(v, '^O') or string.match(v,'^P') or string.match(v, '^Q') then
uniprot_mm_first[#uniprot_mm_first+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"
else
uniprot_mm_alternate[#uniprot_mm_alternate+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"
end
end
hash[v] = true
end
end
if table.getn(uniprot_mm_first)>0 then --if there is something in the preferred values display else display anything else
uniprot_mm_link_list = uniprot_mm_first
else
uniprot_mm_link_list = uniprot_mm_alternate
end
--if less than 5 don't create collapsible list
if table.getn(uniprot_mm_link_list) < 5 then
uniprot_mm_collapse = "none"
if uniprot_mm_default == nil and table.getn(uniprot_mm_link_list) == 0 then uniprot_mm_link = localNotApplicableStr end
else
uniprot_mm_collapse = "collapsible collapsed"
uniprot_mm_default = table.remove(uniprot_mm_link_list, 1) .. '<br>' .. table.remove(uniprot_mm_link_list, 1) .. '<br>' ..table.remove(uniprot_mm_link_list, 1) .. '<br>' .. table.remove(uniprot_mm_link_list, 1) .. '<br>' .. table.remove(uniprot_mm_link_list, 1) .. '<br>'--get first 5 elements in table and use for display
end
if uniprot_mm_link_list[#uniprot_mm_link_list] then
uniprot_mm_link = table.concat(uniprot_mm_link_list, "<br>")
end
local ncbi_link = "https://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="
local refseq_mRNATitle = "RefSeq (mRNA)" -- *lclz*: sometimes
--create list of links for refSeq mRNA
local refseq_mRNA_link = localNotApplicableStr
local refseq_mRNA_collapse
local refseq_mRNA_default = ""
--split string and loop through concatenate by <br>
local split_refseq_mRNA = mw.text.split(refseq_mRNA, localSeparatorStr)
local link_list_first = {} --hold those the have NM or NP values
local link_list_alternate = {} --hold those that are XM or XP values
local link_list = {} --if NM,NP display if not display XM, XP values
for k,v in ipairs(split_refseq_mRNA) do
local label = mw.text.trim(v)
local concat_ncbi_link = ncbi_link .. label
if string.match(v, '%w+') and v ~= localNotApplicableStr then
if string.match(v, 'NM') or string.match(v, 'NP') then
link_list_first[#link_list_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
elseif string.match(v, 'XM') or string.match(v, 'XP') then
link_list_alternate[#link_list_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
end
end
end
if table.getn(link_list_first)>0 then
link_list = link_list_first
else
link_list = link_list_alternate
end
--if less than 5 don't create collapsible list
if table.getn(link_list) < 6 then
refseq_mRNA_collapse = "none"
if refseq_mRNA_default == nil and table.getn(link_list) == 0 then refseq_mRNA_link = localNotApplicableStr end
else
refseq_mRNA_collapse = "collapsible collapsed"
refseq_mRNA_default = table.remove(link_list, 1) .. '<br>' .. table.remove(link_list, 1) .. '<br>' ..table.remove(link_list, 1) .. '<br>' .. table.remove(link_list, 1) .. '<br>' .. table.remove(link_list, 1) .. '<br>'--get first 5 elements in table and use for display
end
if link_list[#link_list] then
refseq_mRNA_link = table.concat(link_list, "<br>")
end
--create list of links for refSeq mRNA for mouse
local refseq_mRNA_mm_link = localNotApplicableStr
local refseq_mRNA_mm_collapse
local refseq_mRNA_mm_default = ""
local split_refseq_mRNA_mm = mw.text.split(refseq_mRNA_mm, localSeparatorStr)
local link_list_mm = {} --if NM,NP display if not display XM, XP values
local link_list_first = {} --hold those the have NM or NP values
local link_list_alternate = {} --hold those that are XM or XP values
for k,v in ipairs(split_refseq_mRNA_mm) do
local label = mw.text.trim(v)
local concat_ncbi_link = ncbi_link .. label
if string.match(v, '%w+') and v ~= localNotApplicableStr then
if string.match(v, 'NM') or string.match(v, 'NP') then
link_list_first[#link_list_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
elseif string.match(v, 'XM') or string.match(v, 'XP') then
link_list_alternate[#link_list_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
end
end
end
if table.getn(link_list_first)>0 then
link_list_mm = link_list_first
else
link_list_mm = link_list_alternate
end
--if less than 5 don't create collapsible list
if table.getn(link_list_mm) < 6 then
refseq_mRNA_mm_collapse = "none"
if refseq_mRNA_mm_default == nil and table.getn(link_list_mm) == 0 then refseq_mRNA_mm_link = localNotApplicableStr end
else
refseq_mRNA_mm_collapse = "collapsible collapsed"
refseq_mRNA_mm_default = table.remove(link_list_mm, 1) .. '<br>' .. table.remove(link_list_mm, 1) .. '<br>' ..table.remove(link_list_mm, 1) .. '<br>' .. table.remove(link_list_mm, 1) .. '<br>' .. table.remove(link_list_mm, 1) .. '<br>'--get first 5 elements in table and use for display
end
if link_list_mm[#link_list_mm] then
refseq_mRNA_mm_link = table.concat(link_list_mm, "<br>")
end
-- *lclz*: sometimes
local refseq_protTitle = "RefSeq (protein)"
--create list of links for human refseq protein
local refseq_prot_link = localNotApplicableStr
local refseq_prot_collapse
local refseq_prot_default = ""
local split_refseq_prot = mw.text.split(refseq_prot, localSeparatorStr)
local link_list_prot = {}
local link_list_first = {} --hold those the have NM or NP values
local link_list_alternate = {} --hold those that are XM or XP values
for k,v in ipairs(split_refseq_prot) do
local label = mw.text.trim(v)
local concat_ncbi_link = ncbi_link .. label
if string.match(v, '%w+') and v ~= localNotApplicableStr then
if string.match(v, 'NM') or string.match(v, 'NP') then
link_list_first[#link_list_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
elseif string.match(v, 'XM') or string.match(v, 'XP') then
link_list_alternate[#link_list_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
end
end
end
if table.getn(link_list_first)>0 then
link_list_prot = link_list_first
else
link_list_prot = link_list_alternate
end
--if less than 5 don't create collapsible list
if table.getn(link_list_prot) < 6 then
refseq_prot_collapse = "none"
if refseq_prot_default == nil and table.getn(link_list_prot) == 0 then refseq_prot_link = localNotApplicableStr end
else
refseq_prot_collapse = "collapsible collapsed"
refseq_prot_default = table.remove(link_list_prot, 1) .. '<br>' .. table.remove(link_list_prot, 1) .. '<br>' ..table.remove(link_list_prot, 1) .. '<br>' .. table.remove(link_list_prot, 1) .. '<br>' .. table.remove(link_list_prot, 1) .. '<br>'--get first 5 elements in table and use for display
end
if link_list_prot[#link_list_prot] then
refseq_prot_link = table.concat(link_list_prot, "<br>")
end
--create list of links for mouse refseq protein
local refseq_prot_mm_link = localNotApplicableStr
local refseq_prot_mm_collapse
local refseq_prot_mm_default = ""
local split_refseq_prot_mm = mw.text.split(refseq_prot_mm, localSeparatorStr)
local link_list_prot_mm = {}
local link_list_first = {} --hold those the have NM or NP values
local link_list_alternate = {} --hold those that are XM or XP values
for k,v in ipairs(split_refseq_prot_mm) do
local label = mw.text.trim(v)
local concat_ncbi_link = ncbi_link .. label
if string.match(v, '%w+') and v ~= localNotApplicableStr then
if string.match(v, 'NM') or string.match(v, 'NP') then
link_list_first[#link_list_first+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
elseif string.match(v, 'XM') or string.match(v, 'XP') then
link_list_alternate[#link_list_alternate+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
end
end
end
if table.getn(link_list_first)>0 then
link_list_prot_mm = link_list_first
else
link_list_prot_mm = link_list_alternate
end
--if less than 5 don't create collapsible list
if table.getn(link_list_prot_mm) < 6 then
refseq_prot_mm_collapse = "none"
if refseq_prot_mm_default == nil and table.getn(link_list_prot_mm) == 0 then refseq_prot_mm_link = localNotApplicableStr end
else
refseq_prot_mm_collapse = "collapsible collapsed"
refseq_prot_mm_default = table.remove(link_list_prot_mm, 1) .. '<br>' .. table.remove(link_list_prot_mm, 1) .. '<br>' ..table.remove(link_list_prot_mm, 1) .. '<br>' .. table.remove(link_list_prot_mm, 1) .. '<br>' .. table.remove(link_list_prot_mm, 1) .. '<br>'--get first 5 elements in table and use for display
end
if link_list_prot_mm[#link_list_prot_mm] then
refseq_prot_mm_link = table.concat(link_list_prot_mm, "<br>")
end
local locTitle = "Location (UCSC)" -- *lclz*
local gstart_mb = p.locToMb(gstart, 2)
local gend_mb = p.locToMb(gend, 2)
local chr_loc_link = ""
if (string.match(db, '%w+') and string.match(chr, '%w+') and string.match(gstart, '%w+') and string.match(gend, '%w+') )then
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
chr_loc_link = "[https://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db="..db.."&position=chr"..chr_ucsc..":"..gstart.."-"..gend.." ".."Chr "..chr_ucsc..": "..gstart_mb.." – "..gend_mb.." Mb]"
else
chr_loc_link = localNotApplicableStr
end
local gstart_mm_mb = p.locToMb(gstart_mm, 2)
local gend_mm_mb = p.locToMb(gend_mm, 2)
local chr_loc_mm_link = ""
if (string.match(db_mm, '%w+') and string.match(chr_mm, '%w+') and string.match(gstart_mm, '%w+') and string.match(gend_mm, '%w+') )then
local chr_mm_ucsc
if chr_mm == "MT" then
chr_mm_ucsc = "M" --UCSC uses "M" (not "MT") in URL for mitochondrial DNA
else
chr_mm_ucsc = chr_mm
end
chr_loc_mm_link = "[https://genome.ucsc.edu/cgi-bin/hgTracks?org=Mouse&db="..db_mm.."&position=chr"..chr_mm_ucsc..":"..gstart_mm.."-"..gend_mm.." ".."Chr "..chr_mm_ucsc..": "..gstart_mm_mb.." – "..gend_mm_mb.." Mb]"
else
chr_loc_mm_link = localNotApplicableStr
end
local pubmedTitle = "[[PubMed]] search" -- *lclz*
local pubmed_link = entrez_gene
if string.match(entrez_gene, '%w+') and entrez_gene ~= localNotApplicableStr then
pubmed_link = frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title ="Human PubMed Reference:" , url = "https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene, website = "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
local pubmed_mm_link = entrez_gene_mm
if string.match(entrez_gene_mm, '%w+') and entrez_gene_mm ~= localNotApplicableStr then
pubmed_mm_link = frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title ="Mouse PubMed Reference:" , url ="https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene_mm, website = "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
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:tag('table')
:attr('class', 'collapsible')
: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', titleBGcolor)
:wikitext(title)
:done() --end th
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext("Species") --**lclz**
:done() --end th
:tag('td')
:wikitext("'''Human'''") --**lclz**
:done() --end td
:tag('td')
:wikitext("'''Mouse'''") --**lclz**
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(entrezTitle)
:done() --end th
:tag('td')
:tag('table')
:attr('class', entrez_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(entrez_default)
:done() --end span
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(entrez_link)
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:tag('td')
:tag('table')
:attr('class', entrez_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(entrez_mm_default)
:done() --end span
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(entrez_mm_link)
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(ensemblTitle)
:done() --end th
:tag('td')
:tag('table')
:attr('class', ensembl_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(ensembl_default)
:done() --end span
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(ensembl_link)
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:tag('td')
:tag('table')
:attr('class', ensembl_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(ensembl_mm_default)
:done() --end span
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(ensembl_mm_link)
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(uniprotTitle)
:done() --end th
:tag('td')
:tag('table')
:attr('class', uniprot_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(uniprot_default)
:done() --end span
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(uniprot_link)
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:tag('td')
:tag('table')
:attr('class', uniprot_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(uniprot_mm_default)
:done() --end span
:done() --end th
:done() --end th
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(uniprot_mm_link)
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(refseq_mRNATitle)
:done() --end th
:tag('td') --RNASeq mRNA collapsible table
:tag('table')
:attr('class', refseq_mRNA_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:attr('class', 'plainlinks')
:wikitext(refseq_mRNA_default)
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(refseq_mRNA_link)
:done() --end span
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:tag('td') --RNASeq mRNA collapsible table for mouse
:tag('table')
:attr('class', refseq_mRNA_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:attr('class', 'plainlinks')
:wikitext(refseq_mRNA_mm_default)
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(refseq_mRNA_mm_link)
:done() --end span
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(refseq_protTitle)
:done() --end th
:tag('td') --RNASeq protein collapsible table
:tag('table')
:attr('class', refseq_prot_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:attr('class', 'plainlinks')
:wikitext(refseq_prot_default)
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(refseq_prot_link)
:done() --end span
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:tag('td') --RNASeq protein collapsible table for mouse
:tag('table')
:attr('class', refseq_prot_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:attr('class', 'plainlinks')
:wikitext(refseq_prot_mm_default)
:done() --end th
:done() --end tr
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(refseq_prot_mm_link)
:done() --end span
:done() --end p
:done() --end td
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(locTitle)
:done() --end th
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(chr_loc_link)
:done() --end span
:done() --end td
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(chr_loc_mm_link)
:done() --end span
:done() --end td
:done() --end tr
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:wikitext(pubmedTitle)
:done() --end th
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(pubmed_link)
:done() --end span
:done() --end td
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(pubmed_mm_link)
:done() --end span
:wikitext(category_chromosome)
:done() --end td
:done() --end tr
: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', rowBGcolor)
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr') --create title header
:css('background-color', titleBGcolor)
:css('text-align', 'center')
:tag('th')
:attr('colspan',"2")
:wikitext(title)
:done() --end th
:done() --end tr
:done() --end table
:done() --end td
:done() --end tr
end
function p.renderFooter(Qid, Qid_mm)
local text = "[[Wikidata]]" --**lclz**
local hs_link = "[[d:"..Qid.."|View/Edit Human]]" --**lclz**
local mm_link = ""
local link_no_hs
local link_no_mm
if Qid_mm == "" then
link_no_mm = 0
link_no_hs = 4
else
link_no_mm = 2
link_no_hs = 2
mm_link = "[[d:"..Qid_mm.."|View/Edit Mouse]]" --**lclz**
end
root
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('font-size','x-small')
:css('background-color', rowBGcolor)
:wikitext(text)
:done() --end td
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('font-size','x-small')
:css('background-color', 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', rowBGcolor)
:css('text-align', 'center')
:css('font-size','x-small')
:wikitext(hs_link)
:done() --end td
:tag('td')
:attr('colspan', link_no_mm)
:css('background-color', rowBGcolor)
:css('text-align', 'center')
:css('font-size','x-small')
:wikitext(mm_link)
:done() --end td
:done() --end tr
:done() --end table
:done() --end tr
root:done() --end root table
end
--this code isn't used was hoping could do some generalization of rows
function p.rowLabel(label)
root
:tag('tr')
:tag('th')
:attr('rowspan', '2')
:css('background-color', sideTitleBGcolor)
:css('width', '43px')
:wikitext(label)
--:done()
end
-- look into entity object
function p.getLabel(entity)
local data = entity
local f = {'labels','en','value'} --**lclz**
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)
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"])
if datav == nil then datav = " " 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 first element
--[[local results_split = mw.text.split(results, localSeparatorStr)
local preffered_results = " "
if results_split[1] then
preferred_result = mw.text.trim(results_split[1]) --return first element if desired prefix not found and remove whitespace
end
local id --refseq id in question
for i, id in ipairs(results_split) do
local trim_id = mw.text.trim(id)
if string.match( trim_id, '^NM_%d+') then
preferred_result = trim_id --overwrite each time found only need one to display
end
end
if preferred_result then
return preferred_result --return a id starting with NP or NM
else
return return_val --return first element because desired prefix not found and remove whitespaces
end
--]]
return results
end
else
return return_val
end
end
-- *lclz*: same as getRefseq_mRNA
function p.getRefseq_protein(protein_entities, propertyID, return_val)
local sep = localSeparatorStr
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 first element
local preffered_result = results_split[1] or ""
for i, id in ipairs(results_split) do
local trim_id = mw.text.trim(id)
--check of id starts with NP or NM
if string.match( trim_id, '^NP_%d+') then
preferred_result = trim_id --overwrite each time found only need one to display
end
end
--check if something in preffered_result if not get first element in result_split
if p.isempty(preffered_result) then
return return_val
else
return preferred_result --return a id starting with NP or NM
end
end --]]
--gets an image
function p.getImage(entity, propertyID, sep, imgsize)
local claims
if entity and entity.claims then
claims = entity.claims[propertyID]
end
if claims then
if (claims[1] and claims[1].mainsnak.datatype == "commonsMedia") then
local out = {}
for k, v in pairs(claims) do
local filename = v.mainsnak.datavalue.value
out[#out + 1] = "[[File:" .. filename .. "|" .. imgsize .. "]]"
end
return table.concat(out, sep)
else
return ""
end
else
return ""
end
end
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)
local string_to_trim = p.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 --**lclz** Add your local label, otherwise it may break
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 label = mw.wikibase.getLabel("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if label == nil then label = "Q" .. v.mainsnak.datavalue.value["numeric-id"] end
local wiki_link = ""
if sitelink and result_GOID ~= nil then
wiki_link = "\n* [" .. sitelink .. result_GOID .. " " .. label .."]"
else
wiki_link = "\n* [[:d:Q" .. v.mainsnak.datavalue.value["numeric-id"] .. "|" .. label .. "]]"
end
overall_results[#overall_results+1] = wiki_link
end
else
results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value
end
end
--overall_results[#overall_results+1] = results --each protein GO terms stored in this index, so table contains all the GO terms with duplicates
end
local hash = {} --temp check
local res = {} --no dups
for _,v in ipairs(overall_results) do
if (not hash[v]) then
res[#res+1] = v
hash[v] = true
end
end
return table.concat(res, "")
end
local function getReference(qID, entity, property_id, ref_index)
local f = {"claims",property_id, ref_index, "references"}
local id = qID
--if id and (#id == 0) then
-- id = nil
--end
local data = entity
if not data then
return nil
end
local i = 1
while true do
local index = f[i]
if not index then
if type(data) == "table" then
return mw.text.jsonEncode(data, mw.text.JSON_PRESERVE_KEYS + mw.text.JSON_PRETTY)
else
return tostring(data)
end
end
data = data[index] or data[tonumber(index)]
if not data then
return ""
end
i = i + 1
end
end
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
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
datasource[#out] = refLink
--end
end
return out, datasource
else
-- just return best values
--return entity:formatPropertyValues(propertyID).value
return return_val, return_val
end
else
return return_val
end
return return_val
end
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
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
pname[protein_id] = name
pqid[#out] = protein_id
datasource[#out] = refLink
end --end k,v claims loop
end --end claims[1]
end --if claims
end -- end protein_entities loop
return out, datasource, pqid, pname
end
function p.separateWithComma(bp)
--Separate number with comma. For example when this function gets "12345678", returns "12,345,678"
local commaSeparated = bp
while true do
local k
commaSeparated, k = string.gsub(commaSeparated, "^(-?%d+)(%d%d%d)", '%1,%2')
if k == 0 then
break
end
end
return commaSeparated
end
return p
