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Modul:Infobox gene

Ti Wikipédia Sunda, énsiklopédi bébas

This module provides content of Template:Infobox gene.

Pamakéan

[édit sumber]
{{#invoke:Infobox gene|getTemplateData}}
{{#invoke:Infobox gene|getTemplateData|QID=Q414043}}

local p = { }

local navbar = require('Module:Navbar')._navbar
local infobox = require('Module:Infobox3cols').infobox
local infoboxImage = require('Module:InfoboxImage').InfoboxImage

-- 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**
--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, "P31") 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","<br><br>","250px"})
        local ensembl = check_values(p.getValue, {entity, "P863", "n/a"})
        local ensembl_mm = check_values(p.getValue, {entity_mouse, "P863", "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)
        --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 (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 = "[[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&amp;term='
    local RCSB_base = 'http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=UpAccessionIdQuery&amp;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, ",", "% or% ") --add or's inststead of commas
    else
        PDBe_list = url_uniprot
    end
    
    local PDBe = "["..PDBe_base..PDBe_list.." PDBe] "
    local RCSB = "["..RCSB_base..url_uniprot.." RCSB] "
    
    if string.match(pdbIDs, '%w ') then --if there aren't any PDB_ID don't display this part of the infobox
        --p.formatRow(title)---how to not close the tags is a mystery and I could condense code once I figure out
        root
             :tag('tr')
                :tag('td')
                       :attr('colspan', 4)
                    :css('text-align', 'center')
                    :css('background-color', 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 = "[[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, ",")
    local homolo =""
    if (homologene_id ~= nil and homologene_id ~= "") then
        homolo = "[[HomoloGene|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 = 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 = "[[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|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 = "[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|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 = "[[Gene expression|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]]"
    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&amp;cmd=retrieve&amp;dopt=default&amp;list_uids="..entrez_gene.."&amp;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) .. '<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 = "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&amp;cmd=retrieve&amp;dopt=default&amp;list_uids="..v.."&amp;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) .. '<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]]"
    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) .. '<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
    local ensemblTitle = "[[Ensembl|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) .. '<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|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 <br>
    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) .. '<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 = "n/a"
    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, ",")
    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) .. '<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 = "n/a"
    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, ",")
    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) .. '<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 = "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) .. '<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 = "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) .. '<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 = "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) .. '<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
        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|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|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
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] = "[[" .. 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, ",")
            
            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] = "[[File:" .. filename .. "|" .. 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] = "[[:d:Q" .. v.mainsnak.datavalue.value .. "|" .. 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 = "<big>•</big> [" .. sitelink .. result_GOID .. " " .. label .."]<br>"
                    else
                        wiki_link = "<big>•</big> [[:d:Q" .. v.mainsnak.datavalue.value["numeric-id"] .. "|" .. label .. "]]<br>"
                    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] = "[["..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

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] = "[["..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

return p