Module:Signature
From BugSigDB
Documentation for this module may be created at Module:Signature/doc
local p = {}
local titleParts, getEntry
local sigReview = require( 'Module:Signature review' )
function p.reviewButton( frame, currentfullpagename )
local invertedState = 'Reviewed'
local invertedStateText = 'Mark reviewed'
if mw.title.makeTitle( 'Review', currentfullpagename ).exists then
if frame:expandTemplate{ title = 'getReviewValues', args = {'Review state'} } == 'Reviewed' then
invertedState = 'Incorrect'
invertedStateText = 'Flag for review'
end
end
return '<span class="with-pholder text-nowrap d-user-inline reviewer">' ..
frame:callParserFunction(
'#autoedit',
'form=Review',
'target=Review:' .. currentfullpagename,
'link text=' .. invertedStateText,
'link type=link',
'Review[Subject]=' .. currentfullpagename,
-- Important use current user over myvariables magic word due to caching.
'Review[Reviewer]=current user',
'Review[Review date]=now',
'Review[Review state]=' .. invertedState
) .. '<span class="pholder plainlinks" title="Reload the page to see the new status">' ..
'[[' .. mw.title.getCurrentTitle().fullText .. '|' .. 'Your review change was submitted]]</span></span>'
end
function titleParts( text, count, first )
local out = ""
for i in mw.text.gsplit( text, '/', true ) do
if count < 1 then
return out
end
if first > 1 then
first = first - 1
else
if out == '' then
out = i
else
out = out .. '/' .. i
end
count = count - 1
end
end
return out
end
function getEntry( name )
if type( name ) == 'table' then
return table.concat( name, ', ')
end
if name == nil then
return ''
end
return name
end
function p.signature( frame )
-- Unclear why this div is here since it would be empty anyways.
local out = '<div class="d-none">'
local t = mw.title.getCurrentTitle()
local basePage = t.basePageTitle.prefixedText
local currentfullpagename = mw.ext.VariablesLua.var( 'CURRENTFULLPAGENAME', t.fullText )
local pargs = frame:getParent().args
local basePageData = (mw.smw.ask{
'[[' .. basePage .. ']]',
'?Body site',
'?Condition',
'?Modification date'
} or {{}})[1]
-- The +sep= args don't work properly with named parameters.
out = out .. frame:callParserFunction( '#set', { '',
'Base page=' .. basePage,
'Semantic Dependency=' .. basePage,
'State=' .. ( frame:getParent().args['State'] or "Incomplete" ),
'Related experiment=' .. titleParts( basePage, 1, 2 ),
'Related study=' .. titleParts( basePage, 1, 1 ),
'Original page name=' .. titleParts( currentfullpagename, 1, 3 ),
'Page sort number=' .. frame:preprocess( "{{#replace:{{#titleparts:{{CURRENTFULLPAGENAME}}||-1}}|Signature |}}" ),
'Related directly=' .. ( frame:getParent().args['NCBI'] or '' ),
'+sep=,',
'Body site=' .. getEntry( basePageData['Body site'] ),
'+sep=,',
'Condition=' .. getEntry( basePageData['Condition'] )
} )
if
basePageData['Modification date'] == nil or
(mw.smw.ask{ '[[' .. t.rootPageTitle.prefixedText .. ']]', '?Modification date' } or {{}})[1]['Modification date'] == nil
then
out = out .. '[[Category:Orphaned signatures]]'
end
if mw.ext.VariablesLua.var( 'inside_embed_loop' ) ~= 'yes' then
out = out .. frame:preprocess( '{{DISPLAYTITLE:{{#getdisplaytitle:{{#titleparts:{{CURRENTFULLPAGENAME}}|1|1}}}}/{{#titleparts:{{CURRENTFULLPAGENAME}}|2|2}}}}' )
end
out = out .. '</div><div class="bg-light btn-group mt-3 study-btn study-btn-group">'
out = out .. frame:callParserFunction(
'#formlink',
'form=Signature',
'link text=Edit',
'target=' .. currentfullpagename,
'reload',
'returnto=' .. t.fullText
) .. '[' .. tostring( mw.uri.fullUrl( currentfullpagename, { action = 'history' } ) ) .. ' History]' ..
'[' .. tostring( mw.uri.fullUrl( currentfullpagename, { action = 'delete' } ) ) .. ' Delete]'
if frame:getParent().args['State'] == 'Complete' then
out = out .. p.reviewButton( frame, currentfullpagename )
end
out = out .. '</div><div class="mb-2 p-3 alert bg-light signature">'
out = out .. '<div class="float-right">' .. frame:expandTemplate{ title = 'Display state', args = { pargs['State'] or '' } } .. '</div>'
-- FIXME underscore or no underscore
out = out .. '<div>' .. frame:expandTemplate{ title = 'Curation', args = { Curator = pargs['Curator'] or '', Curated_date = pargs['Curated_date]'] or '' } } .. '</div></div>\n'
-- Future todo might be to bring FieldTooltip into lua to batch the SMW queries.
out = out .. '\'\'\'Source:\'\'\' ' .. frame:expandTemplate{ title = 'FieldTooltip', args = { 'Source' } } .. ' [[Source data::' .. ( pargs['Source'] or '' ) .. ']]\n\n'
out = out .. '\'\'\'Description:\'\'\' ' .. frame:expandTemplate{ title = 'FieldTooltip', args = { 'Description' } }
frame:callParserFunction( '#set', 'Description=' .. ( pargs['Description'] or '' ) )
out = out .. ( pargs['Description'] or '' ) .. '\n\n'
out = out .. '\'\'\'Abundance in Group 1:\'\'\' ' .. frame:expandTemplate{ title = 'FieldTooltip', args = { 'Abundance in Group 1' } }
if pargs['Abundance in Group 1'] then
frame:callParserFunction( '#set', 'Abundance in Group 1=' .. pargs['Abundance in Group 1'] )
out = out .. pargs['Abundance in Group 1'] .. ' abundance' .. frame:preprocess( '{{#show:{{#titleparts:{{CURRENTFULLPAGENAME}}|2}}|?Group 1 name|intro= in }}\n\n' )
end
out = out .. '<table class="datatable display sortable mb-4"><tr><th>\'\'\'NCBI\'\'\' ' ..
frame:expandTemplate{ title = 'FieldTooltip', args = { 'NCBI' } } ..
'</th><th class="unsortable text-center">Quality Control</th><th class="unsortable text-center">Links</th></tr>'
ncbiAlreadyDone = {}
ncbiExport = {}
ncbiExportIds = {}
for ncbi in mw.text.gsplit( pargs['NCBI'] or '', ',') do
ncbi = mw.text.trim( ncbi )
if ncbiAlreadyDone[ncbi] == nil then
if not string.match( ncbi, '%D' ) then
ncbiAlreadyDone[ncbi] = true
out = out .. '<tr><td>'
-- Taxon name. FIXME this could probably be optimized.
out = out .. frame:callParserFunction( '#tip-text', {
frame:callParserFunction( '#taxonomy', { ncbi, 'Taxon/ScientificName' } ),
frame:expandTemplate{ title = 'Get taxolist', args = { ncbi } }
} ) .. ' '
table.insert( ncbiExport, mw.ext.VariablesLua.var( 'NCBI_val' ) )
table.insert( ncbiExportIds, mw.ext.VariablesLua.var( 'NCBI_ids' ) )
out = out .. '</td><td class="px-4 text-nowrap">'
-- Taxon marks
out = out .. '<span class="mark-span contaminant">'
if mw.ext.VariablesLua.var( 'IsContaminant' ) == 'yes' then
out = out .. frame:callParserFunction( '#tip-text', { '', 'This taxon (' .. ncbi ..') is a potential contaminant.' } )
end
out = out .. '</span><span class="mark-span contaminant-not-host">'
if mw.ext.VariablesLua.var( 'IsContaminantNotHost' ) == 'yes' then
out = out .. frame:callParserFunction( '#tip-text', { '' , 'This taxon (' .. ncbi ..') is not host-associated.' } )
end
out = out .. '</span><span class="mark-span contaminant-prevalent">'
if mw.ext.VariablesLua.var( 'IsPrevalentContaminant' ) == 'yes' then
out = out .. frame:callParserFunction( '#tip-text', { '', 'This taxon (' .. ncbi ..') is prevalent in ' .. mw.ext.VariablesLua.var( 'IsPrevalentContaminantBodysite', '' ) .. '.' } )
end
out = out .. '</span></td><td class="px-4 text-nowrap">'
-- Taxon URL
out = out .. '[https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=' .. ncbi ..
' <span class="taxon-query-external"></span>]'
-- Taxon lookup link
out = out .. ' ' .. frame:callParserFunction(
'#queryformlink',
'form=Taxon',
'link text=<span class="taxon-query" title="' .. ncbi .. ' taxon lookup"></span>',
'Taxon[NCBI]=' .. ncbi,
'_run=1'
) .. ' '
out = out .. sigReview.getStatusReal( frame, currentfullpagename, ncbi )
out = out .. '</td></tr>'
else
-- Not numeric
out = out .. '[[Category:Pages with missing NCBI ID]]'
-- Original template called unique on subparts, but i don't think that is needed.
notnumeric = mw.text.split( ncbi, ';', true )
ncbiAlreadyDone[ncbi] = true
out = out .. '<tr><td class="text-warning">'
-- Taxon name
local taxonName = mw.text.encode( table.concat( notnumeric, ', ' ) )
out = out .. '<span class="text-warning notnumeric" title="' .. taxonName .. '">'
-- Lineage. FIXME, is this right, it seems like the Taxon would get repeated twice?
out = out .. '<span class="nn-lineage">' .. taxonName .. '</span>'
-- Taxon
out = out .. '<span class="nn-taxon">' .. notnumeric[#notnumeric] .. '</span>'
out = out .. '</span></td>'
out = out .. '<td></td><td style="padding-left: 81px !important;">'
-- Taxon sig review
out = out .. frame:expandTemplate{ title = 'Get_signature_review_status', args = { currentfullpagename, notnumeric[#notnumeric] } }
out = out .. '</td></tr>'
end
end
end
out = out .. '</table>'
local ncbiInherits = {}
local ncbiExportIdsIndiv = {}
for _, exportLin in ipairs( ncbiExportIds ) do
for indivExportLin in mw.text.gsplit( exportLin, '|' ) do
if not ncbiAlreadyDone[indivExportLin] then
table.insert( ncbiInherits, indivExportLin)
end
end
end
mw.smw.set{
-- Note, this is setting a single value with lots of commas, not multiple values
NCBI_export = table.concat( ncbiExport, ',' ),
NCBI_export_ids = table.concat( ncbiExportIds, ',' ),
NCBI_export_ids_sc = table.concat( ncbiExportIds, ';' ),
Inherits = ncbiInherits
}
out = out .. "\n\n\'\'\'Revision editor(s):\'\'\' " ..
frame:expandTemplate{ title = 'FieldTooltip', args = { 'Revision editor' } } .. ' ' ..
frame:expandTemplate{ title = 'DisplayRevisionEditors' }
out = out .. "[[Category:Signatures]]__NOTOC__ __NOEDITSECTION__"
return out
end
return p
