Module:Infobox gene: Difference between revisions

Revision as of 22:03, 15 July 2016

Revision as of 22:29, 1 August 2016

Line 171:

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)

end

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

p.renderDrug(frame,drug)

end

Line 184:

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)

Line 532:

end

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

local title = "Genetically Related Diseases"

local disease_title = "Disease Name"

Line 581:

for index,value in ipairs(disease) do

local i = 0

--local ref_collapse = ""

local ref_default = ""

local ref_link = ""

Line 589:

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

end

local br_count = 0

--if less than 4 don't create collapsible list

iffor i =1, table.getn(ref_link_list) < 5do then

ref_linkref_url = ref_link..table.remove(ref_link_list, 1) .. ' '

ref_collapse = "none"

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

else

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

ref_collapse = "collapsible collapsed"

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

for i =1, 5 do --get at most 4 elements to display

else

ref_default = ref_default..table.remove(ref_link_list, 1) .. ' '

br_count = br_count + -1

end

local br_count = 0

if br_count < 53 then

for i =1, table.getn(ref_link_list) do --get at most 4 elements to display

ref_linkbr_count = ref_link..table.remove(ref_link_list,br_count + 1) .. ' '

else

if br_count < 5= then0

br_countref_link = br_countref_link + 1..'<br>'

elseend

br_count = 0

ref_link = ref_link ..'<br>'

end

end

end

if ref_link_list[#ref_link_list] then

ref_link = table.concat(ref_link_list, " ")

end

root

:tag('tr')

Line 634 ⟶ 626:

:tag('table')

:attr('class', ref_collapse)

:css('padding', '0')

:css('border', 'none')

Line 640 ⟶ 631:

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

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

:tag('tr')

:newline()

:tag('th')

:attr('colspan', '1')

:tag('span')

:attr('class', 'plainlinks')

:wikitext(ref_default)

:done()

:done()

:newline()

:done()

:tag('tr')

:tag('td')

Line 670 ⟶ 650:

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

p.renderDrug = function(frame,drug)

local title = "Targeted by Drug"

local drug_title = "Drug Name"

Line 717 ⟶ 697:

for key,value in pairs(drug) do

local i = 0

--local ref_collapse = ""

local ref_default = ""

local ref_link = ""

Line 730 ⟶ 710:

end

end

local br_count = 0

for i =1, table.getn(ref_link_list) do --get at most 4 elements to display

ref_defaultref_url = ref_default..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

endelse

br_count = 0

ref_link = ref_link ..'<br>'

end

end

root

--if less than 4 don't create collapsible list

if table.getn(ref_link_list) < 5 then

ref_collapse = "none"

else

ref_collapse = "collapsible collapsed"

for i =1, 5 do --get at most 4 elements to display

ref_default = ref_default..table.remove(ref_link_list, 1) .. ' '

end

local br_count = 0

for i =1, table.getn(ref_link_list) do --get at most 4 elements to display

ref_link = ref_link..table.remove(ref_link_list, 1) .. ' '

if br_count < 5 then

br_count = br_count + 1

else

br_count = 0

ref_link = ref_link ..'<br>'

end

end

end

if ref_link_list[#ref_link_list] then

ref_link = table.concat(ref_link_list, " ")

end

root

:tag('tr')

:attr('colspan', 4)

Line 783 ⟶ 754:

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

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

:tag('tr')

:newline()

:tag('th')

:attr('colspan', '1')

:tag('span')

:attr('class', 'plainlinks')

:wikitext(ref_default)

:done()

:done()

:newline()

:done()

:tag('tr')

:tag('td')

Line 933 ⟶ 893:

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"

--to do make the list creation a function

Line 1,313 ⟶ 1,273:

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 = "[http://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 ="[http://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

Line 2,424 ⟶ 2,384:

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

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

refLink = refLink..",["..ref.."]"

end

end

Line 2,474 ⟶ 2,434:

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

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

refLink = refLink..",["..ref.."]"

end

end