local p =
local navbar = require('Module:Navbar')._navbarlocal infobox = require('Module:Infobox3cols').infoboxlocal infoboxImage = require('Module:InfoboxImage').InfoboxImage
--on a page --in debug window --frame = mw.getCurrentFrame--frame.args = 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 entity_genasscn = "" local mouse_propertyID = "P684" local protein_propertyID = "P688" local genasscn_propertyID = "P2293" --get root gene entity if root_qid
"value" and claims[1].mainsnak.datavalue.type
"value" and claims[1].mainsnak.datavalue.type
"value" and claims[1].mainsnak.datavalue.type
"value" and claims[1].mainsnak.datavalue.type
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, ec_no, entrez_gene) p.renderDiseases(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, disease, disomim_id) 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(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)
else return "root entity not set" end end
p.createTable = function(subbox)
if subbox
end
--Title above imagep.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) :newlineend
--This is a place holder for the image caption, which is stored in wikicommons comments unsure how to access p.renderCaption = function(entity) --captionend
--gets default imagep.renderImage = function(image)
root :tag('tr') :tag('td') :attr('colspan', 4) :css('text-align', 'center') :wikitext(image) :done :newlineend
p.renderAvailableStructures = function(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs)
local title = 'Available structures' local pdb_link = "PDB" local searchTitle = "" local listTitle = "List of PDB id codes" local PDBe_base = 'http://www.ebi.ac.uk/pdbe/searchResults.html?display=both&term=' local RCSB_base = 'http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=UpAccessionIdQuery&accessionIdList=' local url_uniprot = " " if checkOrtholog
:tag('tr') --create title header :tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color',titleBGcolor) :wikitext(title) :done :newline --p.rowLabel(pdb_link) :tag('tr') :tag('th') :attr('rowspan', '2') :css('background-color', sideTitleBGcolor) :css('width', '43px') :wikitext(pdb_link) :done :tag('td') :attr('colspan', '2') :css('background-color', rowBGcolor) :wikitext(searchTitle) :tag('span') :attr('class', 'plainlinks') :wikitext(PDBe) :wikitext(RCSB) :done :done :done --this may not be needed :newline --new row for collapsible list of PDB codes :tag('tr') :tag('td') :tag('table') :attr('class', 'collapsible collapsed') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'left') :newline :tag('tr') :css('background-color',titleBGcolor) :css('text-align', 'center') :newline :tag('th') :attr('colspan', '2') :wikitext(listTitle) :done :newline :done :tag('tr') :tag('td') :attr('colspan', '2') :css('background-color', rowBGcolor) :newline :tag('p') :tag('span') :attr('class', 'plainlinks') :wikitext(pdbIDs) :done :newline else return "" end
end
p.renderIdentifiers = function(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, ec_no, entrez_gene) local title = "Identifiers" local label_aliases = "Aliases" local symbol_url if gene_symbol
nil then symbol_url = "" else if hgnc_id
nil then symbol_url = gene_symbol else symbol_url = ""..gene_symbol..", " end end 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 aliases = string.gsub(aliases, "^,", "") --remove comma from start local label_ext_id = "External IDs" local omim = "" if string.match(omim_id, '%w+') then omim = "OMIM:".." "..""..omim_id.." " end local homolo ="" if string.match(homologene_id, '%w+') then homolo = "HomoloGene:".." "..""..homologene_id.." " end local genecards = "" if string.match(entrez_gene, '%w+') then genecards = "GeneCards:".." "..""..entrez_gene.." " end local mgi = "" if string.match(mgi_id, '%w+') then mgi = "MGI:".." "..""..mgi_id.." " end local ChEMBL = "" if string.match(ChEMBL_id, '%w+') then ChEMBL = "ChEMBL:".." "..""..ChEMBL_id.." " end root :tag('tr') :tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :newline
:tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(label_aliases) :done :newline :tag('td') :attr('colspan','3') :css('background', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(symbol_url) :done :wikitext(aliases) :done :newline
:tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(label_ext_id) :done :newline :tag('td') :attr('colspan', '3') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(omim) :wikitext(mgi) :wikitext(homolo) :wikitext(ChEMBL) :wikitext(genecards) :done :newline :doneend
p.renderDiseases = function(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, disease, disomim_id) local title = "Disease" local entrezTitle = "Entrez" --check all values to see if exists so don't create nonsense links in infobox must have some alphanumberic character local entrez_link = "" if string.match(entrez_gene, '%w+') and entrez_gene ~= "n/a" then entrez_link = ""..entrez_gene.."" end local entrez_mm_link = entrez_gene_mm if string.match(entrez_gene_mm, '%w+') and entrez_gene_mm ~= "n/a" then entrez_mm_link = ""..entrez_gene_mm.."" end local shipType = "" if disease ~= "" then shipType = "genetic" end --local split_omim = mw.text.split(disomim_id,"%s*,%s*") local split_omim = mw.text.split(disomim_id,",") -- INCORRECT: entrez_gene = "https://omim.org/entry/"..split_omim[1.. "|" .. "OMIM entry" .."] " entrez_gene = "https://omim.org/entry/"..split_omim[1.." ".."OMIM entry".."] " disease = ""..disease.."" --entrez_gene = split_omim[1] -- result[0] will give "cat", result[1] will give "dog"
root :tag('tr') :tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :done :newline :tag('tr') :tag('th') :wikitext("Disease Name") :done :newline :tag('td') :wikitext("Relationship Type") :done :newline :tag('td') :wikitext("Data Source") :done :newline :done ---this section would be nice to do in a loop if the tag closures were figured out :tag('tr') :tag('th') :attr('scope', 'row') :wikitext(disease) :done :newline :tag('td') :tag('span') :wikitext(shipType) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(entrez_gene)--disomim_id[0]) :done :newline end
p.renderGeneOntology = function(mol_funct, cell_comp, bio_process, uniprotID) local title = "Gene ontology" local mol_funct_title = "Molecular function" local cell_comp_title = "Cellular component" local bio_process_title = "Biological process" local amigo_link = ".. " Amigo" local quickGO_link = ".. " QuickGO"
root :tag('tr') :tag('td') :attr('colspan', 4) :css('text-align', 'center') :css('background-color', rowBGcolor) :newline --p.createTable('sub') :tag('table') :attr('class', 'collapsible collapsed') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'left') :newline :tag('tr') --create title bar :tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :done :newline :tag('tr') :tag('th') :css('background-color', sideTitleBGcolor) :wikitext(mol_funct_title) :done :tag('td') :css('background-color', rowBGcolor) :newline :tag('span') :attr('class', 'plainlinks') :wikitext(mol_funct) :done :newline :done :tag('tr') :tag('th') :css('background-color', sideTitleBGcolor) :wikitext(cell_comp_title) :done :tag('td') :css('background-color', rowBGcolor) :newline :tag('span') :attr('class', 'plainlinks') :wikitext(cell_comp) :done :newline :done :tag('tr') :tag('th') :css('background-color', sideTitleBGcolor) :wikitext(bio_process_title) :done :tag('td') :css('background-color', rowBGcolor) :newline :tag('span') :attr('class', 'plainlinks') :wikitext(bio_process) :done :newline :done :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 :done end
p.renderRNAexpression = function(expression_images, entrez_gene) local title = "RNA expression pattern" local biogps_link = "More reference expression data" root :tag('tr') :tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :done :newline :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', rowBGcolor) :wikitext(expression_images) :done :newline :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', rowBGcolor) :tag('span') :attr('class', 'plainlinks') :wikitext(biogps_link) :done :newlineend
p.renderOrthologs = function(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" local entrezTitle = "Entrez" --check all values to see if exists so don't create nonsense links in infobox must have some alphanumberic character local entrez_link = "" if string.match(entrez_gene, '%w+') and entrez_gene ~= "n/a" then entrez_link = ""..entrez_gene.."" end local entrez_mm_link = entrez_gene_mm if string.match(entrez_gene_mm, '%w+') and entrez_gene_mm ~= "n/a" then entrez_mm_link = ""..entrez_gene_mm.."" end local ensemblTitle = "Ensembl" local ensembl_link = ensembl --default to result so n/a defined if string.match(ensembl, '%w+') and ensembl ~= "n/a" then ensembl_link = ""..ensembl.."" end local ensembl_mm_link = ensembl_mm if string.match(ensembl_mm, '%w+') and ensembl_mm ~= "n/a" then ensembl_mm_link = ""..ensembl_mm.."" end
--create lists of uniprot ID local uniprotTitle = "UniProt" local uniprot_url = "http://www.uniprot.org/uniprot/" local uniprot_link = "n/a" local uniprot_collapse local uniprot_default = "" --split string and loop through concatenate by
local split_uniprot = mw.text.split(uniprot, ",") local uniprot_link_list = local 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(uniprot, '%w+') and uniprot ~= "n/a" then uniprot_link_list[#uniprot_link_list+1] = "[" .. concat_uniprot_link .. " " ..label .. "]" end hash[v] = true end end
--if less than 5 don't create collapsible list if table.getn(uniprot_link_list) < 5 then uniprot_collapse = "none" if uniprot_default
0 then uniprot_link = "n/a" end else uniprot_collapse = "collapsible collapsed" uniprot_default = table.remove(uniprot_link_list, 1) .. '
' .. table.remove(uniprot_link_list, 1) .. '
' ..table.remove(uniprot_link_list, 1) .. '
' .. table.remove(uniprot_link_list, 1) .. '
' .. table.remove(uniprot_link_list, 1) .. '
'--get first 5 elements in table and use for display end if uniprot_link_list[#uniprot_link_list] then uniprot_link = table.concat(uniprot_link_list, "
") end --mouse uniprot lists local uniprot_mm_link = "n/a" local uniprot_mm_collapse local uniprot_mm_default = "" --split string and loop through concatenate by
local split_uniprot_mm = mw.text.split(uniprot_mm, ",") local uniprot_mm_link_list = for k,v in ipairs(split_uniprot_mm) do local label = mw.text.trim(v) local concat_uniprot_link = uniprot_url .. label if string.match(uniprot_mm, '%w+') and uniprot_mm ~= "n/a" then uniprot_mm_link_list[#uniprot_mm_link_list+1] = "[" .. concat_uniprot_link .. " " ..label .. "]" end 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
0 then uniprot_mm_link = "n/a" end else uniprot_mm_collapse = "collapsible collapsed" uniprot_mm_default = table.remove(uniprot_link_mm_list, 1) .. '
' .. table.remove(uniprot_link_mm_list, 1) .. '
' ..table.remove(uniprot_link_mm_list, 1) .. '
' .. table.remove(uniprot_link_mm_list, 1) .. '
' .. table.remove(uniprot_link_mm_list, 1) .. '
'--get first 5 elements in table and use for display end if uniprot_mm_link_list[#uniprot_mm_link_list] then uniprot_mm_link = table.concat(uniprot_mm_link_list, "
") end local ncbi_link = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=" local refseq_mRNATitle = "RefSeq (mRNA)" --create list of links for refSeq mRNA local refseq_mRNA_link = "n/a" local refseq_mRNA_collapse local refseq_mRNA_default = "" --split string and loop through concatenate by
local split_refseq_mRNA = mw.text.split(refseq_mRNA, ",") local link_list = 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 link_list[#link_list+1] = "[" .. concat_ncbi_link .. " " ..label .. "]" end 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
0 then refseq_mRNA_link = "n/a" end else refseq_mRNA_collapse = "collapsible collapsed" refseq_mRNA_default = table.remove(link_list, 1) .. '
' .. table.remove(link_list, 1) .. '
' ..table.remove(link_list, 1) .. '
' .. table.remove(link_list, 1) .. '
' .. table.remove(link_list, 1) .. '
'--get first 5 elements in table and use for display end if link_list[#link_list] then refseq_mRNA_link = table.concat(link_list, "
") end --create list of links for refSeq mRNA for mouse local refseq_mRNA_mm_link = "n/a" local refseq_mRNA_mm_collapse local refseq_mRNA_mm_default = "" local split_refseq_mRNA_mm = mw.text.split(refseq_mRNA_mm, ",") local link_list_mm = for k,v in ipairs(split_refseq_mRNA_mm) do if string.match(v, '%w+') and v ~= "n/a" then local label = mw.text.trim(v) local concat_ncbi_link = ncbi_link .. label if string.match(v, '%w+') and v ~= "n/a" then link_list_mm[#link_list_mm+1] = "[" .. concat_ncbi_link .. " " ..label .. "]" end end 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
0 then refseq_mRNA_mm_link = "n/a" end else refseq_mRNA_mm_collapse = "collapsible collapsed" refseq_mRNA_mm_default = table.remove(link_list_mm, 1) .. '
' .. table.remove(link_list_mm, 1) .. '
' ..table.remove(link_list_mm, 1) .. '
' .. table.remove(link_list_mm, 1) .. '
' .. table.remove(link_list_mm, 1) .. '
'--get first 5 elements in table and use for display end
if link_list_mm[#link_list_mm] then refseq_mRNA_mm_link = table.concat(link_list_mm, "
") end
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 = for k,v in ipairs(split_refseq_prot) do if string.match(v, '%w+') and v ~= "n/a" then local label = mw.text.trim(v) local concat_ncbi_link = ncbi_link .. label if string.match(v, '%w+') and v ~= "n/a" then link_list_prot[#link_list_prot+1] = "[" .. concat_ncbi_link .. " " ..label .. "]" end end 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
0 then refseq_prot_link = "n/a" end else refseq_prot_collapse = "collapsible collapsed" refseq_prot_default = table.remove(link_list_prot, 1) --get first element in table and use for display end
if link_list_prot[#link_list_prot] then refseq_prot_link = table.concat(link_list_prot, "
") end --create list of links for mouse refseq protein local refseq_prot_mm_link = "n/a" local refseq_prot_mm_collapse local refseq_prot_mm_default = "" local split_refseq_prot_mm = mw.text.split(refseq_prot_mm, ",") local link_list_mm = for k,v in ipairs(split_refseq_prot_mm) do if string.match(v, '%w+') and v ~= "n/a" then local label = mw.text.trim(v) local concat_ncbi_link = ncbi_link .. label if string.match(v, '%w+') and v ~= "n/a" then link_list_mm[#link_list_mm+1] = "[" .. concat_ncbi_link .. " " ..label .. "]" end end end --if less than 5 don't create collapsible list if table.getn(link_list_mm) < 6 then refseq_prot_mm_collapse = "none" if refseq_prot_mm_default
0 then refseq_prot_mm_link = "n/a" end else refseq_prot_mm_collapse = "collapsible collapsed" refseq_prot_mm_default = table.remove(link_list_mm, 1) --get first element in table and use for display end if link_list_mm[#link_list_mm] then refseq_prot_mm_link = table.concat(link_list_mm, "
") end
local locTitle = "Location (UCSC)" 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 = "".."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 = "".."Chr "..chr_mm..": "..gstart_mm_mb.." – "..gend_mm_mb.." Mb" else chr_loc_link = "n/a" end local pubmedTitle = "PubMed search" local pubmed_link = entrez_gene if string.match(entrez_gene, '%w+') and entrez_gene ~= "n/a" then pubmed_link = "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene.."" 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 = "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene_mm.."" end root :tag('tr') :tag('th') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', titleBGcolor) :wikitext(title) :done :newline :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext("Species") :done :newline :tag('td') :wikitext("Human") :done :newline :tag('td') :wikitext("Mouse") :done :newline :done ---this section would be nice to do in a loop if the tag closures were figured out :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(entrezTitle) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(entrez_link) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(entrez_mm_link) :done :newline :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(ensemblTitle) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(ensembl_link) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(ensembl_mm_link) :done :newline :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(uniprotTitle) :done :newline :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') :newline :tag('th') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(uniprot_default) :done :done :newline :done :tag('tr') :tag('td') :attr('colspan', '1') :newline :tag('p') :attr('class', 'plainlinks') :wikitext(uniprot_link) :newline :done :done :done :done :newline :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') :newline :tag('th') :attr('colspan', '1') :tag('span') :attr('class', 'plainlinks') :wikitext(uniprot_mm_default) :done :done :newline :done :tag('tr') :tag('td') :attr('colspan', '1') :newline :tag('p') :attr('class', 'plainlinks') :wikitext(uniprot_mm_link) :newline :done :done :done :done :newline :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(refseq_mRNATitle) :done :newline :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') :newline :tag('th') :attr('colspan', '1') :attr('class', 'plainlinks') :wikitext(refseq_mRNA_default) :done :newline :done :tag('tr') :tag('td') :attr('colspan', '1') :newline :tag('p') :tag('span') :attr('class', 'plainlinks') :wikitext(refseq_mRNA_link) :done :newline :done :done :done :done :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') :newline :tag('th') :attr('colspan', '1') :attr('class', 'plainlinks') :wikitext(refseq_mRNA_mm_default) :done :newline :done :tag('tr') :tag('td') :attr('colspan', '1') :newline :tag('p') :tag('span') :attr('class', 'plainlinks') :wikitext(refseq_mRNA_mm_link) :done :newline :done :done :done :done :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(refseq_protTitle) :done :newline :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') :newline :tag('th') :attr('colspan', '1') :attr('class', 'plainlinks') :wikitext(refseq_prot_default) :done :newline :done :tag('tr') :tag('td') :attr('colspan', '1') :newline :tag('p') :tag('span') :attr('class', 'plainlinks') :wikitext(refseq_prot_link) :done :newline :done :done :done :done :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') :newline :tag('th') :attr('colspan', '1') :attr('class', 'plainlinks') :wikitext(refseq_prot_mm_default) :done :done :tag('tr') :tag('td') :attr('colspan', '1') :newline :tag('p') :tag('span') :attr('class', 'plainlinks') :wikitext(refseq_prot_mm_link) :done :newline :done :done :done :done :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(locTitle) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(chr_loc_link) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(chr_loc_mm_link) :done :newline :tag('tr') :tag('th') :attr('scope', 'row') :css('background-color', sideTitleBGcolor) :wikitext(pubmedTitle) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(pubmed_link) :done :newline :tag('td') :tag('span') :attr('class', 'plainlinks') :wikitext(pubmed_mm_link) :done :newlineend
p.formatRow = function(title) root :tag('tr') :tag('td') :attr('colspan', '4') :css('text-align', 'center') :css('background-color', rowBGcolor) :newline --p.createTable('sub') :tag('table') :css('padding', '0') :css('border', 'none') :css('margin', '0') :css('width', '100%') :css('text-align', 'left') :newline :tag('tr') --create title header :css('background-color',titleBGcolor) :css('text-align', 'center') :tag('th') :attr('colspan',"2") :wikitext(title) :done :done :newlineend
p.renderFooter = function(Qid, Qid_mm) local text = "Wikidata" local hs_link = "View/Edit Human" local mm_link = "" local link_no_hs local link_no_mm if Qid_mm
: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 :tag('td') :attr('colspan', link_no_mm) :css('background-color', rowBGcolor) :css('text-align', 'center') :css('font-size','x-small') :wikitext(mm_link) :done :newline :done
end
--this code isn't used was hoping could do some generalization of rowsp.rowLabel=function(label) root :tag('tr') :tag('th') :attr('rowspan', '2') :css('background-color', sideTitleBGcolor) :css('width', '43px') :wikitext(label) --:doneend
-- look into entity objectp.getLabel = function(entity) local data = entity
local f =
local i = 1 while true do local index = f[i] if not index then if type(data)
--general function to get value given an entity and propertyp.getValue = function(entity, propertyID, return_val)
local claims if return_val
"value" and claims[1].mainsnak.datavalue.type
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 endend
p.getValueProtein = function(protein_entities, propertyID, return_val) if return_val
"value" and claims[1].mainsnak.datavalue.type
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 endend
--general function to get value given an entity and propertyp.getQid = function(entity) local Qid if entity and entity.id then Qid = entity.id return Qid else return "" endend
--get random value that is preferred ranked p.getRefseq_mRNA = function(entity, propertyID, return_val) if return_val
"value" and claims[1].mainsnak.datavalue.type
nil then label = "Q" .. v.mainsnak.datavalue.value["numeric-id"] end if sitelink then out[#out + 1] = "" .. label .. "" else out[#out + 1] = "" .. label .. "" end end return table.concat(out, ", ") else local results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value --loop through results until get a NP or NM or just return whatever is in first element --local results_split = mw.text.split(results, ",") local preffered_results = " " if results_split[1] then preferred_result = mw.text.trim(results_split[1]) --return first element if desired prefix not found and remove whitespace end local id --refseq id in question for i, id in ipairs(results_split) do local trim_id = mw.text.trim(id) if string.match(trim_id, '^NM_%d+') then preferred_result = trim_id --overwrite each time found only need one to display end end if preferred_result then return preferred_result --return a id starting with NP or NM else return return_val --return first element because desired prefix not found and remove whitespaces end -- return results end else return return_val endend
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
"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
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 imagep.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
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
nil then label = v.mainsnak.datavalue.value end if sitelink then out[#out + 1] = "[" .. sitelink .. label .. " " ..label .. "]" else out[#out + 1] = "" .. label .. "" end end results = table.concat(out, ", ") 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 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 P645p.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 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 endend
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 "" endend
p.trimChromosome = function(entity) local string_to_trim = p.getValue(entity, "P1057") local out = if string.find(string_to_trim, 'chromosome.') then out = string_to_trim:gsub("chromosome ", "") end if string.find(string_to_trim, 'mouse.chromosome.') then out = string_to_trim:gsub("mouse chromosome ", "") end return out end
p.locToMb = function(num, idp) num = tonumber(num) if num
p.isempty = function(s) return 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
"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
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
return p