 |
This module is rated as ready for general use. It has reached a mature form and is thought to be relatively bug-free and ready for use wherever appropriate. It is ready to mention on help pages and other Wikipedia resources as an option for new users to learn. To reduce server load and bad output, it should be improved by sandbox testing rather than repeated trial-and-error editing. |
This module provides content of Template:Infobox gene.
{{#invoke:Infobox gene|getTemplateData}}
{{#invoke:Infobox gene|getTemplateData|QID=Q414043}}
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
