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Module:Sandbox/genewiki/alllua

local p = { }

local navbar = require('Module:Navbar')._navbar

local infobox = require('Module:Infobox3cols').infobox

local infoboxImage = require('Module:InfoboxImage').InfoboxImage

-- wrapaped "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**

--on a page {{#invoke:Sandbox/genewiki/alllua|getTemplateData|QID=Q14865053}}

--in debug window

--frame = mw.getCurrentFrame()

--frame.args = {QID="Q14865053"} Q18031325

--print(p.getTemplateData(frame))

p.getTemplateData = function(frame)

--make some guesses about whether the provided QID is a good one

--could expand here if we had some kind of error handling framework

--did we get it from the page

local root_qid = mw.text.trim(frame.args['QID'] or "") --try to get it from the args

local mm_qid = ""

--pull all the entity objects that we will need

local entity = {}

local entity_protein = {}

local entity_mouse = {}

local entity_mouse_protein = {}

local checkOrtholog = "" --flag used to see if mouse data avaliable

local mouse_propertyID = "P684" --actually ortholog property additional orthologs can exist

local protein_propertyID = "P688"

--get root gene entity

if root_qid == "" then

entity = mw.wikibase.getEntityObject()

if entity then root_qid = entity.id else root_qid = "" end

else

--assuming we think its good make one call to retrieve and store its wikidata representation

entity = mw.wikibase.getEntity(root_qid)

end

--need to figure out if it is protein or gene here

local subclass = p.getValue(entity, "P279") or ""

if string.find(subclass, 'protein') then --if protein switch entity to gene

if entity.claims then

claims = entity.claims["P702"] --encoded by

end

if claims then

--go through each index and reassign entity

entity = {}

if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then

for k, v in pairs(claims) do --this would be problematic if multiple genes for the protein

local itemID = "Q" .. claims[#entity + 1].mainsnak.datavalue.value["numeric-id"]

entity[#entity + 1] = mw.wikibase.getEntity(itemID)

root_qid = itemID

end

end --will return nothing if no claims are found

end

entity = mw.wikibase.getEntity(root_qid)

end

--get the other related entities

if entity then

local claims = ""

--get protein entity object

if entity.claims then

claims = entity.claims[protein_propertyID]

end

if claims then

--go through each index and then make entity_protein indexed

if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then

for k, v in pairs(claims) do

local protein_itemID = "Q" .. claims[#entity_protein + 1].mainsnak.datavalue.value["numeric-id"]

entity_protein[#entity_protein + 1] = mw.wikibase.getEntity(protein_itemID)

end

end --will return nothing if no claims are found

end

--get mouse entity object

if entity.claims then

claims = entity.claims[mouse_propertyID]

end

local qualifierID = "P703" --found in taxon

local mouse_tax = "Mus musculus"

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 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 name in qualifier

local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]

mw.wikibase.label(qual_obj_id)

local qual_obj = mw.wikibase.label(qual_obj_id)

if string.match(qual_obj, mouse_tax) then --check if this is mouse or other

mm_qid = mouse_itemID

entity_mouse = mw.wikibase.getEntity(mouse_itemID)

checkOrtholog = 1

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 entrez_gene = check_values(p.getValue, {entity, "P351", "n/a"} )

local entrez_gene_mm = check_values(p.getValue, {entity_mouse, "P351", "n/a"})

local image = check_values( p.getImage, {entity, "P18", " ", "250px"}) --need to set size

local uniprotID_hs = check_values(p.getValueProtein, {entity_protein, "P352", "n/a"})

local uniprotID_mm = check_values(p.getValueProtein, {entity_mouse_protein, "P352", "n/a"})

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","

","250px"})

local ensembl = check_values(p.getValue, {entity, "P594", "n/a"})

local ensembl_mm = check_values(p.getValue, {entity_mouse, "P594", "n/a"})

local refseq_mRNA = check_values(p.getRefseq_mRNA, {entity, "P639", "n/a"})

local refseq_mRNA_mm = check_values(p.getRefseq_mRNA, {entity_mouse, "P639", "n/a"})

local refseq_prot = check_values(p.getRefseq_protein, {entity_protein, "P637", "n/a"})

local refseq_prot_mm = check_values(p.getRefseq_protein, {entity_mouse_protein, "P637", "n/a"})

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 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 db_mm = check_values(p.getAliasFromGenomeAssembly, {entity_mouse,"mm"})

local chr_mm = check_values( p.trimChromosome, {entity_mouse})

local disease, dis_ref = ''

if p.getDisease(entity, "P2293") then disease, dis_ref = p.getDisease(entity, "P2293") else disease, dis_ref = {"VALUE_ERROR","VALUE_ERROR" } end

if p.getDrug(entity_protein, "P129") then drug, drug_ref, drug_pqid, drug_pname = p.getDrug(entity_protein, "P129") else drug, drug_ref, drug_pqid, drug_pname = {"VALUE_ERROR","VALUE_ERROR" } end

--local drug = check_values(p.getDrug, {entity_protein, "P129"})

--define Global Color Scheme

rowBGcolor = '#eee'

titleBGcolor = '#ddd'

sideTitleBGcolor = '#c3fdb8'

p.createTable()

p.renderUpperTitle(name)

--p.renderCaption()

p.renderImage(image)

p.renderAvailableStructures(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs) --PDB info

p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene)

if (disease ~= "" and dis_ref ~= "") then --removes section from those items without disease info

p.renderDiseases(frame, disease, dis_ref, name, root_qid)

end

if (drug ~= "" ) then --removes section from those items without drug info

p.renderDrug(frame,drug, drug_ref, drug_pqid, drug_pname)

end

if (mol_funct ~= "" and cell_comp ~= "" and bio_process ~= "") then

p.renderGeneOntology(mol_funct, cell_comp, bio_process, uniprotID_hs)

end

if expression_images ~= "" then

p.renderRNAexpression(expression_images, entrez_gene)

end

p.renderOrthologs(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

p.createTable = function(subbox)

if subbox == 'sub' then --doesn't work

root

:tag('table')

:css('padding', '0')

:css('border', 'none')

:css('margin', '0')

:css('width', 'auto')

:css('min-width', '100%')

:css('font-size', '100%')

:css('clear', 'none')

:css('float', 'none')

:css('background-color', 'transparent')

else

root = mw.html.create('table')

root

-- *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

p.renderUpperTitle = function(name)

local title = name

if not title then return "error: failed to get label"; end

root

:tag('tr')

:tag('th')

:attr('colspan', 4)

:css('text-align', 'center')

:css('font-size', '125%')

:css('font-weight', 'bold')

:wikitext(title)

: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

p.renderCaption = function(entity)

--caption

end

--gets default image

p.renderImage = function(image)

root

:tag('tr')

:tag('td')

:attr('colspan', 4)

:css('text-align', 'center')

:wikitext(image)

:done() --end td

:done() --end tr

end

p.renderAvailableStructures = function(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs)

local title = 'Available structures' --**lclz**

local pdb_link = "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 = 'http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=UpAccessionIdQuery&accessionIdList='

local url_uniprot = " "

if checkOrtholog == 1 and uniprotID_mm ~= 'n/a' then

searchTitle = 'Ortholog search: '

url_uniprot = uniprotID_mm..','..uniprotID_hs

else

searchTitle = 'Human UniProt search: '

url_uniprot = uniprotID_hs

end

local PDBe_list = " " --create a list with " or " if there is more than one uniprot

--get first uniprot in a list

if url_uniprot:match("([^,]+),") then--first check if there is a list if not just assume one value

PDBe_list = string.gsub(url_uniprot, ",", "%%20or%%20") --add or's inststead of commas

else

PDBe_list = url_uniprot

end

local PDBe = "["..PDBe_base..PDBe_list.." PDBe] "

local RCSB = "["..RCSB_base..url_uniprot.." RCSB] "

if string.match(pdbIDs, '%w+') then --if there aren't any PDB_ID don't display this part of the infobox

--p.formatRow(title)---how to not close the tags is a mystery and I could condense code once I figure out

root

:tag('tr')

:tag('td')

:attr('colspan', 4)

:css('text-align', 'center')

:css('background-color', rowBGcolor)

: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

p.renderIdentifiers = function(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene)

local title = "Identifiers" --**lclz**

local label_aliases = "[https://en.wikipedia.org/wiki/Human_Genome_Organisation 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 = "[http://www.genenames.org/cgi-bin/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, ",")

local omim = ""

if (omim_id ~= nil and omim_id ~= "") then

omim = "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, ",")

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, ",")

local mgi = ""

if (mgi_id ~= nil and mgi_id ~= "") then

mgi = "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 = "IUPHAR:".." ".."[http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId="..IUPHAR_id.." "..IUPHAR_id.."] " --**lclz**

end -- *lclz*

local label_EC = "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 = "[http://www.genome.jp/dbget-bin/www_bget?enzyme+" .. link_ec_no .. " " .. ec_no .. "]"

root

:tag('tr')

:tag('th')

:attr('colspan', '4')

:css('text-align', 'center')

:css('background-color', titleBGcolor)

:wikitext(title)

: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(aliases)

: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

p.renderDiseases = function(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"

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

p.renderDrug = function(frame,drug, drug_ref, drug_pqid, drug_pname)

local title = "Targeted by Drug" --**lzlc**

--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

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

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"

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

p.renderGeneOntology = function(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('th')

:css('background-color', sideTitleBGcolor)

:wikitext(mol_funct_title)

:done() --end th

:tag('td')

:css('background-color', rowBGcolor)

:tag('span')

:attr('class', 'plainlinks')

:wikitext(mol_funct)

:done() --end span

:done() --end td

:done() --end tr

:tag('tr')

:tag('th')

:css('background-color', sideTitleBGcolor)

:wikitext(cell_comp_title)

:done() --end th

:tag('td')

:css('background-color', rowBGcolor)

:tag('span')

:attr('class', 'plainlinks')

:wikitext(cell_comp)

:done() --end span

:done() --end td

:done() --end tr

:tag('tr')

:tag('th')

:css('background-color', sideTitleBGcolor)

:wikitext(bio_process_title)

:done() --end th

:tag('td')

:css('background-color', rowBGcolor)

:tag('span')

:attr('class', 'plainlinks')

:wikitext(bio_process)

:done() --end span

:done() --end td

:done() --end tr

:tag('tr')

:tag('td')

:css('background-color', rowBGcolor)

:css('text-align', 'center')

:attr('colspan', '4')

:wikitext("Sources:")

:wikitext(amigo_link)

:wikitext(" / ")

:wikitext(quickGO_link)

:done() --end td

:done() --end tr

:done() --end table

:done() --end td

:done() --end tr

end

p.renderRNAexpression = function(expression_images, entrez_gene)

local title = "RNA expression pattern" --**lclz**

local biogps_link = "[http://biogps.org/gene/"..entrez_gene.."/ More reference expression data]" --**lclz**

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('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

end

p.renderOrthologs = function(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

-- *lclz*: Category name

local category_chromosome = 'Category:Genes on human chromosome '..chr..''

if mw.title.getCurrentTitle().namespace ~= 0 then

category_chromosome = ""

end

local entrezTitle = "Entrez"

entrez_gene = string.gsub(entrez_gene, "%s", "")

local entrez_link = "n/a"

local entrez_collapse

local entrez_default = ""

local split_entrez = mw.text.split(entrez_gene, ",")

local entrez_link_list = {}

for k,v in ipairs(split_entrez) do

if string.match(v, '%w+') and v ~= "n/a" then

entrez_link_list[#entrez_link_list+1] = "[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 = "n/a" end

else

entrez_collapse = "collapsible collapsed"

entrez_default = table.remove(entrez_link_list, 1) .. '
' .. table.remove(entrez_link_list, 1) .. '
' ..table.remove(entrez_link_list, 1) .. '
' .. table.remove(entrez_link_list, 1) .. '
' .. table.remove(entrez_link_list, 1) .. '
'--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, "
")

end

--create list for mouse Entrez id

entrez_gene_mm = string.gsub(entrez_gene_mm, "%s", "")

local entrez_mm_link = "n/a"

local entrez_mm_collapse

local entrez_mm_default = ""

local split_entrez_mm = mw.text.split(entrez_gene_mm, ",")

local entrez_mm_link_list = {}

for k,v in ipairs(split_entrez_mm) do

if string.match(v, '%w+') and v ~= "n/a" then

entrez_mm_link_list[#entrez_mm_link_list+1] = "[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 = "n/a" end

else

entrez_mm_collapse = "collapsible collapsed"

entrez_mm_default = table.remove(entrez_mm_link_list, 1) .. '
' .. table.remove(entrez_mm_link_list, 1) .. '
' ..table.remove(entrez_mm_link_list, 1) .. '
' .. table.remove(entrez_mm_link_list, 1) .. '
' .. table.remove(entrez_mm_link_list, 1) .. '
'--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, "
")

end

--create list of ensembl id

local ensemblTitle = "Ensembl"

ensembl = string.gsub(ensembl, "%s", "")

local ensembl_link = "n/a"

local ensembl_collapse

local ensembl_default = ""

local split_ensembl = mw.text.split(ensembl, ",")

local ensembl_link_list = {}

for k,v in ipairs(split_ensembl) do

if string.match(v, '%w+') and v ~= "n/a" then

ensembl_link_list[#ensembl_link_list+1] = "[http://www.ensembl.org/Homo_sapiens/geneview?gene="..v..";db=core".." "..v.."]"

end

end

--if less than 5 don't create collapsible list

if table.getn(ensembl_link_list) < 5 then

ensembl_collapse = "none"

if ensembl_default == nil and table.getn(ensembl_link_list) == 0 then ensembl_link = "n/a" end

else

ensembl_collapse = "collapsible collapsed"

ensembl_default = table.remove(ensembl_link_list, 1) .. '
' .. table.remove(ensembl_link_list, 1) .. '
' ..table.remove(ensembl_link_list, 1) .. '
' .. table.remove(ensembl_link_list, 1) .. '
' .. table.remove(ensembl_link_list, 1) .. '
'--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, "
")

end

--create list of mouse ensembl id

local ensemblTitle = "Ensembl"

ensembl_mm = string.gsub(ensembl_mm, "%s", "")

local ensembl_mm_link = "n/a"

local ensembl_mm_collapse

local ensembl_mm_default = ""

local split_ensembl_mm = mw.text.split(ensembl_mm, ",")

local ensembl_mm_link_list = {}

for k,v in ipairs(split_ensembl_mm) do

if string.match(v, '%w+') and v ~= "n/a" then

ensembl_mm_link_list[#ensembl_mm_link_list+1] = "[http://www.ensembl.org/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 = "n/a" end

else

ensembl_mm_collapse = "collapsible collapsed"

ensembl_mm_default = table.remove(ensembl_mm_link_list, 1) .. '
' .. table.remove(ensembl_mm_link_list, 1) .. '
' ..table.remove(ensembl_mm_link_list, 1) .. '
' .. table.remove(ensembl_mm_link_list, 1) .. '
' .. table.remove(ensembl_mm_link_list, 1) .. '
'--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, "
")

end

--create lists of uniprot ID

local uniprotTitle = "UniProt"

local uniprot_url = "http://www.uniprot.org/uniprot/"

local uniprot_link = "n/a"

local uniprot_collapse

local uniprot_default = ""

--split string and loop through concatenate by

local split_uniprot = mw.text.split(uniprot, ",")

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 ~= "n/a" 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 = "n/a" end

else

uniprot_collapse = "collapsible collapsed"

uniprot_default = table.remove(uniprot_link_list, 1) .. '
' .. table.remove(uniprot_link_list, 1) .. '
' ..table.remove(uniprot_link_list, 1) .. '
' .. table.remove(uniprot_link_list, 1) .. '
' .. table.remove(uniprot_link_list, 1) .. '
'--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, "
")

end

--mouse uniprot lists

local uniprot_mm_link = "n/a"

local uniprot_mm_collapse

local uniprot_mm_default = ""

--split string and loop through concatenate by

local split_uniprot_mm = mw.text.split(uniprot_mm, ",")

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 ~= "n/a" 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 = "n/a" end

else

uniprot_mm_collapse = "collapsible collapsed"

uniprot_mm_default = table.remove(uniprot_mm_link_list, 1) .. '
' .. table.remove(uniprot_mm_link_list, 1) .. '
' ..table.remove(uniprot_mm_link_list, 1) .. '
' .. table.remove(uniprot_mm_link_list, 1) .. '
' .. table.remove(uniprot_mm_link_list, 1) .. '
'--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, "
")

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 = "n/a"

local refseq_mRNA_collapse

local refseq_mRNA_default = ""

--split string and loop through concatenate by

local split_refseq_mRNA = mw.text.split(refseq_mRNA, ",")

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 ~= "n/a" 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 = "n/a" end

else

refseq_mRNA_collapse = "collapsible collapsed"

refseq_mRNA_default = table.remove(link_list, 1) .. '
' .. table.remove(link_list, 1) .. '
' ..table.remove(link_list, 1) .. '
' .. table.remove(link_list, 1) .. '
' .. table.remove(link_list, 1) .. '
'--get first 5 elements in table and use for display

end

if link_list[#link_list] then

refseq_mRNA_link = table.concat(link_list, "
")

end

--create list of links for refSeq mRNA for mouse

local refseq_mRNA_mm_link = "n/a"

local refseq_mRNA_mm_collapse

local refseq_mRNA_mm_default = ""

local split_refseq_mRNA_mm = mw.text.split(refseq_mRNA_mm, ",")

local link_list_mm = {} --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 ~= "n/a" 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 = "n/a" end

else

refseq_mRNA_mm_collapse = "collapsible collapsed"

refseq_mRNA_mm_default = table.remove(link_list_mm, 1) .. '
' .. table.remove(link_list_mm, 1) .. '
' ..table.remove(link_list_mm, 1) .. '
' .. table.remove(link_list_mm, 1) .. '
' .. table.remove(link_list_mm, 1) .. '
'--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, "
")

end

-- *lclz*: sometimes

local refseq_protTitle = "RefSeq (protein)"

--create list of links for human refseq protein

local refseq_prot_link = "n/a"

local refseq_prot_collapse

local refseq_prot_default = ""

local split_refseq_prot = mw.text.split(refseq_prot, ",")

local link_list_prot = {}

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 ~= "n/a" 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 = "n/a" end

else

refseq_prot_collapse = "collapsible collapsed"

refseq_prot_default = table.remove(link_list_prot, 1) .. '
' .. table.remove(link_list_prot, 1) .. '
' ..table.remove(link_list_prot, 1) .. '
' .. table.remove(link_list_prot, 1) .. '
' .. table.remove(link_list_prot, 1) .. '
'--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, "
")

end

--create list of links for mouse refseq protein

local refseq_prot_mm_link = "n/a"

local refseq_prot_mm_collapse

local refseq_prot_mm_default = ""

local split_refseq_prot_mm = mw.text.split(refseq_prot_mm, ",")

local link_list_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 ~= "n/a" 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 = "n/a" end

else

refseq_prot_mm_collapse = "collapsible collapsed"

refseq_prot_mm_default = table.remove(link_list_prot_mm, 1) .. '
' .. table.remove(link_list_prot_mm, 1) .. '
' ..table.remove(link_list_prot_mm, 1) .. '
' .. table.remove(link_list_prot_mm, 1) .. '
' .. table.remove(link_list_prot_mm, 1) .. '
'--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, "
")

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

chr_loc_link = "[https://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db="..db.."&position=chr"..chr..":"..gstart.."-"..gend.." ".."Chr "..chr..": "..gstart_mb.." – "..gend_mb.." Mb]"

else

chr_loc_link = "n/a"

end

local gstart_mm_mb = p.locToMb(gstart_mm, 2)

local gend_mm_mb = p.locToMb(gend_mm, 2)

local chr_loc_mm_link = ""

if (string.match(db_mm, '%w+') and string.match(chr_mm, '%w+') and string.match(gstart_mm, '%w+') and string.match(gend_mm, '%w+') )then

chr_loc_mm_link = "[https://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db="..db_mm.."&position=chr"..chr_mm..":"..gstart_mm.."-"..gend_mm.." ".."Chr "..chr_mm..": "..gstart_mm_mb.." – "..gend_mm_mb.." Mb]"

else

chr_loc_mm_link = "n/a"

end

local pubmedTitle = "PubMed search" -- *lclz*

local pubmed_link = entrez_gene

if string.match(entrez_gene, '%w+') and entrez_gene ~= "n/a" 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 } } )--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 ~= "n/a" 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 } } )--expandTemplate creates cite web template {{cite web|title=value|url=ref_link..ect}}

end

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)

: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

end

p.formatRow = function(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

p.renderFooter = function(Qid, Qid_mm)

local text = "Wikidata" --**lclz**

local hs_link = "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 = "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

--Julia

: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

p.rowLabel=function(label)

root

:tag('tr')

:tag('th')

:attr('rowspan', '2')

:css('background-color', sideTitleBGcolor)

:css('width', '43px')

:wikitext(label)

--:done()

end

-- look into entity object

p.getLabel = function(entity)

local data = entity

local f = {'labels','en','value'}

local i = 1

while true do

local index = f[i]

if not index then

if type(data) == "table" then

return mw.text.jsonEncode(data, mw.text.JSON_PRESERVE_KEYS + mw.text.JSON_PRETTY)

else

return tostring(data)

end

end

data = data[index] or data[tonumber(index)]

if not data then

return

end

i = i + 1

end

end

--general function to get value given an entity and property

p.getValue = function(entity, propertyID, return_val)

local claims

if return_val == nil then return_val = "" end

local sep = " " --could ad as input parameter if need be

if entity and entity.claims then

claims = entity.claims[propertyID]

end

if claims then

-- if wiki-linked value output as link if possible

if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then

local out = {}

for k, v in pairs(claims) do

local datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])

if datav == nil then datav = " " end

out[#out + 1] = datav

end

return table.concat(out, sep)

else

-- just return best values

return entity:formatPropertyValues(propertyID).value

end

else

return return_val

end

end

p.getValueProtein = function(protein_entities, propertyID, return_val)

if return_val == nil then return_val = "" end

local sep = ","

local overall_results = {} --should return empty if nothing assigned

for key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a whole

local claims

local entity = val --each protein in encodes

if entity and entity.claims then

claims = entity.claims[propertyID]

end

if claims then

local results

-- if wiki-linked value output as link if possible

if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then

local out = {}

for k, v in pairs(claims) do

local datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])

if datav == nil then datav = " " end

out[#out + 1] = datav

end

results = table.concat(out, sep)

else

results = entity:formatPropertyValues(propertyID).value

end

overall_results[#overall_results+1] = results --individual propertyID value stored in this index

end

end

local str_overall_results = table.concat(overall_results, sep) --weirdness happens when add a sep = " " otherwise each value represented one time

if string.match(str_overall_results, '%w+') then

return str_overall_results

else

return return_val

end

end

--general function to get value given an entity and property

p.getQid = function(entity)

local Qid

if entity and entity.id then

Qid = entity.id

return Qid

else

return ""

end

end

--get random value that is preferred ranked

-- *lclz*: Sometimes Wikibase returns punctuations other than "," depending on

-- your site's language. Consider adding a gsub here.

p.getRefseq_mRNA = function(entity, propertyID, return_val)

if return_val == nil then return_val = "" end

local input_rank = "RANK_PREFERRED" ---this is mostly like won't do anything because ranking isn't maintained in wikidata

local claims

if entity.claims then

claims = entity.claims[propertyID]

end

if claims then

-- if wiki-linked value output as link if possible

if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid" ) then

local out = {}

for k, v in pairs(claims) do

local sitelink = mw.wikibase.sitelink("Q" .. v.mainsnak.datavalue.value["numeric-id"])

local label = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])

if label == nil then label = "Q" .. v.mainsnak.datavalue.value["numeric-id"] end

if sitelink then

out[#out + 1] = "" .. label .. ""

else

out[#out + 1] = "" .. label .. ""

end

end

return table.concat(out, ", ")

else

local results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value

--loop through results until get a NP or NM or just return whatever is in first element

--[[local results_split = mw.text.split(results, ",")

local preffered_results = " "

if results_split[1] then

preferred_result = mw.text.trim(results_split[1]) --return first element if desired prefix not found and remove whitespace

end

local id --refseq id in question

for i, id in ipairs(results_split) do

local trim_id = mw.text.trim(id)

if string.match( trim_id, '^NM_%d+') then

preferred_result = trim_id --overwrite each time found only need one to display

end

end

if preferred_result then

return preferred_result --return a id starting with NP or NM

else

return return_val --return first element because desired prefix not found and remove whitespaces

end

--]]

return results

end

else

return return_val

end

end

-- *lclz*: same as getRefseq_mRNA

p.getRefseq_protein = function(protein_entities, propertyID, return_val)

local sep = ","

local overall_results = {} --should return empty if nothing assigned

for key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a whole

local claims

local entity = val --each protein in encodes

if entity.claims then

claims = entity.claims["P637"]

end

if claims then

local results

-- if wiki-linked value output as link if possible

if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid" ) then

local out = {}

for k, v in pairs(claims) do

local datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])

if datav == nil then datav = " " end

out[#out + 1] = datav

end

results = table.concat(out, sep)

else

results = entity:formatPropertyValues("P637", mw.wikibase.entity.claimRanks).value

end

overall_results[#overall_results+1] = results --a list is in each index

end

end

--why are there duplicate results here

local str_overall_results = table.concat(overall_results, sep)

return str_overall_results

end

--[[

local results_split = mw.text.split(str_overall_results, sep) --split complete list so can loop through..probably a more direct way to do this

--loop through results until get a NP or NM or just return whatever is in first element

local preffered_result = results_split[1] or ""

for i, id in ipairs(results_split) do

local trim_id = mw.text.trim(id)

--check of id starts with NP or NM

if string.match( trim_id, '^NP_%d+') then

preferred_result = trim_id --overwrite each time found only need one to display

end

end

--check if something in preffered_result if not get first element in result_split

if p.isempty(preffered_result) then

return return_val

else

return preferred_result --return a id starting with NP or NM

end

end --]]

--gets an image

p.getImage = function(entity, propertyID, sep, imgsize)

local claims

if entity and entity.claims then

claims = entity.claims[propertyID]

end

if claims then

if (claims[1] and claims[1].mainsnak.datatype == "commonsMedia") then

local out = {}

for k, v in pairs(claims) do

local filename = v.mainsnak.datavalue.value

out[#out + 1] = "" .. imgsize .. ""

end

return table.concat(out, sep)

else

return ""

end

else

return ""

end

end

p.getPDB = function(protein_entities)

local pdb_propertyID = "P638"

local overall_results = {}

for key, val in pairs(protein_entities) do --in cases where there are multiple encodes we loop through each and return concatenated data as a whole

local claims

local entity = val

if entity and entity.claims then

claims = entity.claims[pdb_propertyID]

end

local sitelink = "http://www.rcsb.org/pdb/explore/explore.do?pdbId="

if claims then

local results

if (claims[1] and claims[1].mainsnak.snaktype == "value") then

local out = {}

for k, v in pairs(claims) do

local label = mw.wikibase.label(v.mainsnak.datavalue.value)

if label == nil then label = v.mainsnak.datavalue.value end

if sitelink then

out[#out + 1] = "[" .. sitelink .. label .. " " ..label .. "]"

else

out[#out + 1] = "" .. label .. ""

end

end

results = table.concat(out, ", ") -- *lclz*: punctuation (CJK comma, etc.)

else

results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value

end

overall_results[#overall_results+1] = results --individual propertyID values stored in this index

end

end

return table.concat(overall_results, ",%%s")

end

function p.getAliases(entity)

a = ''

if entity['aliases'] ~= nil then

-- *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

for key, value in ipairs(test) do

a = a .. ', ' .. value['value']

end

return a

else

return ""

end

else

return ""

end

end

--get a geneome start P644 or end P645

p.getChromosomeLoc = function(entity, propertyID, prefix)

-- will contain the numeric value for the requested coordinate

local output = ""

local sep = " "

-- can only be P644 (genomic start) or P645 (genomic end) for this to work

-- should probably try to catch that. Might also increase legibility to use specific variable names when possible

-- local propertyID = mw.text.trim(frame.args[1] or "")

-- this can really only be P659 right now. I'm not sure of the value of including it as a parameter as other values will likely break this function

local qualifierID = "P659" --mw.text.trim(frame.args[2] or "")

-- Why do we include this here? What should happen if FETCH_WIKIDATA is not included?

--local input_parm = mw.text.trim(frame.args[3] or "")

-- this can needs to be fed to the function either by a call to {{#invoke:Wikidata|pageId}} or by setting it directly (e.g. if the function was applied on a page other than the targeted gene)

--alert if this id is not a valid thing in wikidata, a Lua error will occur that says

--The ID entered is unknown to the system. Please use a valid entity ID.

--local itemID = mw.text.trim(frame.args[4] or "")

-- will track the different builds pulled from the qualifiers

local newest_build = "0"

-- starts the process

--local entity = mw.wikibase.getEntityObject(itemID)

local claims

--gets a table of claims on the (genomic start or end) property Q19847637

if entity and entity.claims then

claims = entity.claims[propertyID]

end

--will return nothing if no claims are found

if claims then

--checking to be sure claims is populated, not sure it its needed

if (claims[1] ) then

--useful for debugging

--local out = {}

--pulls the genome location from the claim

for k, v in pairs(claims) do

local location = v.mainsnak.datavalue.value

--debugging

--out[#out + 1] = k.." location:" .. location.. " || "

--gets the qualifiers linked to the current claim

local quals

if v.qualifiers then

quals = v.qualifiers.P659

end

--if there are any

if quals then

for qk, qv in pairs(quals) do

local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]

--get to the entity targeted by the qualifier property. Genome builds are Items in wikidata

local qual_obj = mw.wikibase.getEntityObject(qual_obj_id)

local alias = ""

--this uses the aliases to pull out version numbers

--seems like there ought to be a better way to do this, but likely would need to change the data added by the bot

if qual_obj["aliases"] ~= nil then

local test = qual_obj["aliases"]["en"]

for key, value in ipairs(test) do

if string.match(value['value'], prefix) then

alias = value['value']

local build_no = alias:gsub(prefix,"")

--report only the most location associated with the most recent build

--if there is more than one location per build, just give one back as that is not our problem right now.

if build_no > newest_build then

output = location

newest_build = build_no

end

end

end

end

end

--in case there are no qualifiers, but there is a location, might as well return it

else output = location

end

end

return output

else

return ""

end

else

return ""

--debug

--"no claims for "..itemID.." prop "..propertyID

end

end

p.getAliasFromGenomeAssembly = function(entity, prefix)

-- will contain the numeric value for the requested coordinate

local output = ""

local sep = " "

local propertyID = "P644" --genomic start used

local qualifierID = "P659"

local newest_build = "0"

local claims

if entity.claims then

claims = entity.claims[propertyID]

end

--will return nothing if no claims are found

if claims then

--checking to be sure claims is populated, not sure it its needed

if (claims[1] ) then

--useful for debugging

--local out = {}

--pulls the genome location from the claim

for k, v in pairs(claims) do

local quals

if v.qualifiers then

quals = v.qualifiers.P659

end

--if there are any

if quals then

for qk, qv in pairs(quals) do

local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]

--get to the entity targeted by the qualifier property. Genome builds are Items in wikidata

local qual_obj = mw.wikibase.getEntityObject(qual_obj_id)

local alias = ""

--this uses the aliases to pull out version numbers

--seems like there ought to be a better way to do this, but likely would need to change the data added by the bot

if qual_obj["aliases"] ~= nil then

local test = qual_obj["aliases"]["en"]

for key, value in ipairs(test) do

if string.match(value['value'], prefix) then

alias = value['value']

local build_no = alias:gsub(prefix,"")

--report only the most location associated with the most recent build

--if there is more than one location per build, just give one back as that is not our problem right now.

if build_no > newest_build then

newest_build = build_no

end

end

end

end

end

--in case there are no qualifiers, but there is a location, might as well return it

else output = location

end

end

return prefix..newest_build

else

return ""

end

else

return ""

end

end

-- *lclz*: Your language's wikidata may have different nouns for chromosome and

-- mitochodria.

p.trimChromosome = function(entity)

local string_to_trim = p.getValue(entity, "P1057")

local out = ''

if string.find(string_to_trim, 'chromosome') then

out = string.match(string_to_trim, "%d+")--extract number from string

if out == nil then

out = string.match(string_to_trim, "X") or string.match(string_to_trim, "Y")

end

end

if string.find(string_to_trim, 'mitochondrial') then

out = "M"

end

return out

end

p.locToMb = function(num, idp)

num = tonumber(num)

if num == nil then

return ""

else

local mb = num/1000000

local mult = 10^(idp or 0)

return math.floor(mb * mult + 0.5) / mult

end

end

p.isempty = function(s)

return s == nil or s == ''

end

p.getGO = function(protein_entities, propertyID)

--propertyID ie molecular, cellular, function

local overall_results = {}

local results = "" --string to return

for key, val in pairs(protein_entities) do

local claims

local entity = val

if entity.claims then

claims = entity.claims[propertyID] -- ie molecular, cellular, function

end

local propertyID_child = "P686" -- Gene Ontology ID

if claims then

if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then

--local out = {}

for k, v in pairs(claims) do

local itemID_child = "Q" .. v.mainsnak.datavalue.value["numeric-id"] --get Qid of property item so can get the GOid

local entity = mw.wikibase.getEntityObject(itemID_child)

local claims

local result_GOID = ''

if entity and entity.claims then claims = entity.claims[propertyID_child] end

if claims then

result_GOID = entity:formatPropertyValues(propertyID_child, mw.wikibase.entity.claimRanks).value

else

result_GOID = nil --no GO ID

end

local sitelink = "http://amigo.geneontology.org/amigo/term/"

local label = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])

if label == nil then label = "Q" .. v.mainsnak.datavalue.value["numeric-id"] end

local wiki_link = ""

if sitelink and result_GOID ~= nil then

wiki_link = "• [" .. sitelink .. result_GOID .. " " .. label .."]
"

else

wiki_link = "• " .. 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

p.getDisease= function(entity, propertyID)

local claims

if return_val == nil then return_val = "" end

if entity and entity.claims then

claims = entity.claims[propertyID]

end

if claims then

-- if wiki-linked value output as link if possible

if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then

local out = {}

local datasource = {}

--{{#invoke:Wikidata |ViewSomething |id=Q18023174 |claims|P2293|1|references|1|snaks|P854|1|datavalue|value}}

--maybe there is a more direct way to find this than looping through the json object

for k, v in pairs(claims) do

local datav = mw.wikibase.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])

if datav == nil then datav = " " end

local id = "Q" .. v.mainsnak.datavalue.value["numeric-id"]

local linkTarget = mw.wikibase.sitelink(id)

local refLink = ""

local 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] = ""..datav..""

else

out[#out + 1] = "" .. 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

p.getDrug= function(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.label("Q" .. v.mainsnak.datavalue.value["numeric-id"])

if datav == nil then datav = "" end

local id = "Q" .. v.mainsnak.datavalue.value["numeric-id"]

local linkTarget = mw.wikibase.sitelink(id)

local refLink = ""

local 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] = ""..datav..""

else

out[#out + 1] = "" .. 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

return p