Module:Infobox gene: Difference between revisions

Revision as of 20:45, 15 August 2016

Revision as of 21:18, 10 October 2016

Line 157:

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"})

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

--define Global Color Scheme

Line 171 ⟶ 172:

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

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

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

end

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

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

end

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

Line 188 ⟶ 189:

return tostring(root)

--return table.concat(drug_pqid)

else return "An Error has occurred retrieving Wikidata item for infobox"

end

Line 532 ⟶ 533:

end

p.renderDiseases = function(frame, disease, dis_ref, name, qid)

local title = "Genetically Related Diseases"

local disease_title = "Disease Name"

local source_title = "'''References'''"

--check first to see if any of the diseases have references

local ref_flagref_flag_all = {}false --check eachif any disease forhave references if not then don't render athe referenceheaders

local disease_name = ''

local ref_flag_all = "" --check if any disease have references if not then don't render the headers

for index,value in ipairs(disease) do

if (dis_ref[index] ~= nil and dis_ref[index] ~= '') then

ref_flag[index]if disease_name == '' truethen

disease_name = value

else

disease_name = disease_name..","..value

end

ref_flag_all = true

end

Line 564 ⟶ 566:

:done()

:newline()

:tag('tr')

:tag('th')

:css('background-color', sideTitleBGcolor)

:attr('colspan', '2')

:wikitext(disease_title)

:done()

:newline()

:tag('td')

:css('background-color', sideTitleBGcolor)

:attr('colspan', '2')

:wikitext(source_title)

:done()

:newline()

:done()

end

for index,value in ipairs(disease) do

local i = 0

--local ref_collapse = ""

local ref_default = ""

local ref_link = ""

local ref_link_list = ""

if ref_flag[index] then

if (dis_ref[index] ~= nil or dis_ref[index] ~= '') then

ref_link_list = mw.text.split(dis_ref[index], ",")

end

local br_count = 0

for i =1, table.getn(ref_link_list) do

ref_url = table.remove(ref_link_list, 1)

abbr_url = string.gsub(ref_url, "http://", '')

if i > 1 then --not sure why indexing off, but renders empty value if don't do this

ref_link = ref_link..frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title = abbr_url, url = ref_url} })

else

br_count = br_count -1

end

if br_count < 3 then

br_count = br_count + 1

else

br_count = 0

ref_link = ref_link ..'<br>'

end

end

--local disease_name = table.concat(disease, ", ")

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')

Line 617 ⟶ 584:

:css('background-color', rowBGcolor)

:attr('scope', 'row')

:attr('colspan', '23')

:wikitext(valueref_link)

:done()

:newline()

:tag('td')

:tag('span')

:attr('colspan', '2')

:tag('table')

:css('padding', '0')

:css('border', 'none')

:css('margin', '0')

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

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

:tag('tr')

:tag('td')

:attr('colspan', '1')

:newline()

:tag('p')

:attr('class', 'plainlinks')

:wikitext(ref_link)

:newline()

:done()

:done()

:done()

:done()

:newline()

end end

end

end

--p.renderDrug = function(drug, drug_ref)

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

local title = "Targeted by Drug"

local drug_title = "Drug Name"

local source_title = "'''References'''"

--check first to see if any of the drugs have references

--check first to see if any of the drugs have references

--local ref_flag = {} --check each drug for a reference

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

for k,v in pairs(drug) do

ref_flag_all = true

--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

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

Line 680 ⟶ 634:

:done()

:newline()

:tag('tr')

:tag('th')

:css('background-color', sideTitleBGcolor)

:attr('colspan', '2')

:wikitext(drug_title)

:done()

:newline()

:tag('td')

:css('background-color', sideTitleBGcolor)

:attr('colspan', '2')

:wikitext(source_title)

:done()

:newline()

:done()

end

for key,value in pairs(drug) do

local i = 0

--local ref_collapse = ""

local ref_default = ""

local ref_link = ""

local ref_link_list = {}

local ref_split = mw.text.split(value, ",")

local hash = {} --storage to look for duplicated values in case

--loop to create reference links from drug lists

for k,v in ipairs(ref_split) do

for k,v in pairs(drug_list_per_protein) do

if not hash[v] then --only add if not found previously

local drug_name = v

ref_link_list[#ref_link_list+1] = v

local ref_url = "https://www.wikidata.org/wiki/"..k.."#P129" --direct page to property genetically associated disease

hash[v] = true

local title = "Drugs that physically interact with "..drug_pname[k].." view/edit references on wikidata"

end

local ref_link = drug_name..frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title = title, url = ref_url} })

end

local br_count = 0

for i =1, table.getn(ref_link_list) do

ref_url = table.remove(ref_link_list, 1)

abbr_url = string.gsub(ref_url, "http://", '')

if i > 1 then --not sure why indexing off, but renders empty value if don't do this

ref_link = ref_link..frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title = abbr_url, url = ref_url} })

else

br_count = br_count -1

end

if br_count < 3 then

br_count = br_count + 1

else

br_count = 0

ref_link = ref_link ..'<br>'

end

end

root

Line 738 ⟶ 655:

:css('background-color', rowBGcolor)

:attr('scope', 'row')

:attr('colspan', '23')

--:wikitext(valueref_link)

:wikitext(key)

:done()

:newline()

:tag('td')

:tag('span')

:attr('colspan', '2')

:tag('table')

:attr('class', ref_collapse)

:css('padding', '0')

:css('border', 'none')

:css('margin', '0')

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

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

:tag('tr')

:tag('td')

:attr('colspan', '1')

:newline()

:tag('p')

:attr('class', 'plainlinks')

:wikitext(ref_link)

:newline()

:done()

:done()

:done()

:done()

:newline()

end

end

end

Line 2,324 ⟶ 2,219:

end

local function getReference(qID, index, entity, property_id, ref_index)

local f = {"claims",property_id,index ref_index, "references",ref_index,"snaks","P854",1,"datavalue","value"}

local id = qID

--if id and (#id == 0) then

Line 2,379 ⟶ 2,274:

local linkTarget = mw.wikibase.sitelink(id)

local refLink = ""

local iref = ""

ref = getReference("", entity, "P2293", k)

for i=1,100 do --limits to 100 references displayed

if (ref local~= nil and ref ~= ""'') then

--refLink = refLink..","..ref

ref = getReference("", k, entity, "P2293", i)

if (ref ~= nilrefLink and= ref ~= '') then

refLink = refLink..","..ref

end

end

--if refLink = "" then --skip if there isn't a reference found

datasource[#out + 1] = refLink

if linkTarget then

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

Line 2,394 ⟶ 2,288:

out[#out + 1] = "[[:d:" .. id .. "|" .. datav .. "]]"

end

datasource[#out] = refLink

--end

end

Line 2,411 ⟶ 2,306:

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

Line 2,429 ⟶ 2,328:

local linkTarget = mw.wikibase.sitelink(id)

local refLink = ""

local ref = getReference(protein_id, entity, "P129",k) --just check if anything returned

local i

forif i(ref ~=1,100 donil --limitsand toref 100~= references'') displayedthen

local ref refLink = ""ref

end

ref = getReference(protein_id, k, entity, "P129", i)

if (ref ~= nil and ref ~= '')linkTarget then

refLink out[#out + 1] = refLink"[["..datav..",|"..refdatav.."]]"

end else

out[#out + 1] = "[[:d:" .. id .. "|" .. datav .. "]]"

end

end

pname[protein_id] = name

local wikiLink = "[["..datav.."|"..datav.."]]"

pqid[#out] = protein_id

local wikidataLink = "[[:d:" .. id .. "|" .. datav .. "]]"

ifdatasource[#out] (refLink ~= nil and refLink ~= '') then

if linkTarget then

if out[wikiLink] then

out[wikiLink] = out[wikiLink]..","..refLink

else

out[wikiLink] = refLink

end

else

if out[wikidataLink] then

out[wikidataLink] = out[wikidataLink]..","..refLink

else

out[wikidataLink] = refLink

end

end--end if linkTarget

end -- end if 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