Convert quadrinomials to infrasubspecies script #819
Comments
Batch 1: Quadrinomials where the target subspecies exists
Scriptjonkerz = User.find 60
Activity.execute_script_activity jonkerz, "Convert quadrinomials to infrasubspecies [batch 1], see %github819"
# For PaperTrail
antcat_bot = User.find 62
PaperTrail.request.whodunnit = antcat_bot.id
def quadrinomials
Subspecies.joins(:name).where("(LENGTH(names.name) - LENGTH(REPLACE(names.name, ' ', '')) >= 3) ")
end
def puts_stats
"Quadrinomials count: #{quadrinomials.count}"
end
def fix! soon_infrasubspecies, antcat_bot
name_string = soon_infrasubspecies.name_cache
raise "#{soon_infrasubspecies.id}: has soft-validation issues" if soon_infrasubspecies.soft_validation_warnings.size.positive?
raise "#{soon_infrasubspecies.id}: #{name_string} contains weird characters" unless name_string =~ /^[[:alpha:][:blank:]-]+$/
target_subspecies_name_string = name_string.split[0..2].join(' ')
target_subspecies = Subspecies.where(name_cache: target_subspecies_name_string)
target_subspecies_count = target_subspecies.count
if target_subspecies_count == 0
puts "#{soon_infrasubspecies.id}: found no subspecies".blue
return
end
if target_subspecies_count > 1
raise "#{soon_infrasubspecies.id}: found too many subspecies"
end
the_target_subspecies = target_subspecies.first
Taxon.transaction do
soon_infrasubspecies.name.update!(type: 'InfrasubspeciesName')
soon_infrasubspecies.update_columns(type: 'Infrasubspecies')
infrasubspecies = Infrasubspecies.find(soon_infrasubspecies.id)
infrasubspecies.update!(subspecies: the_target_subspecies)
puts "#{soon_infrasubspecies.id}: fixed!".green
if infrasubspecies.soft_validation_warnings.size.positive?
puts "#{soon_infrasubspecies.id}: but it has soft-validation issues...".red
end
infrasubspecies.create_activity :update, antcat_bot, edit_summary: "Convert subspecies quadrinomial to infrasubspecies quadrinomial, see %github819"
end
end
puts_stats
quadrinomials.each do |taxon|
fix! taxon, antcat_bot
end; nil
puts_stats
puts "Done"ResultsQuadrinomials count: 763 430274: found no subspecies Quadrinomials count: 474 |
Step 2: Re-create missing subspecies
Scriptjonkerz = User.find(60)
Activity.execute_script_activity jonkerz, "Reified missing subspecies for quadrinomial, see %github819"
# For PaperTrail
def antcat_bot
@antcat_bot ||= User.find(62)
end
PaperTrail.request.whodunnit = antcat_bot.id
$reified_with_issues = []
$reified_without_issues = []
def quadrinomials
Subspecies.joins(:name).where("(LENGTH(names.name) - LENGTH(REPLACE(names.name, ' ', '')) >= 3) ")
end
def reify_subspecies subspecies_version
puts "reify_subspecies.... version #{subspecies_version.id}".blue
if (taxon = Taxon.where(id: subspecies_version.item_id).exists?)
puts "taxon exists now".green
return taxon
end
reified = subspecies_version.reify
unless reified.is_a?(Subspecies)
raise "reified subspecies is not a subspecies".red
end
unless reified.species
puts "reified subspecies has no species".red
return
end
if reified.status == Status::UNAVAILABLE_UNCATEGORIZED && reified.current_valid_taxon.nil?
puts "#{subspecies_version.id}: reified subspecies has current_valid_taxon".red
return
end
raise "Name #{reified.name_id} already exists" if Name.where(id: reified.name_id).exists?
reified_name = PaperTrail::Version.where(item_type: "Name", item_id: reified.name_id).last&.reify
raise "found no name to reify" unless reified_name
Taxon.transaction do
if reified_name && reified_name.save!
reified.ichnotaxon ||= false
reified.nomen_nudum ||= false
reified.collective_group_name ||= false
reified.update!(name: reified_name)
puts "reified #{reified.id}".green
end
end
if reified.persisted?
if reified.soft_validation_warnings.present?
puts "#{reified.id}: reified has soft-validation issues...".red
$reified_with_issues << reified.id
reified.create_activity :create, antcat_bot, edit_summary: "Reified missing subspecies for quadrinomial (taxon has soft-validation issues), see %github819"
else
$reified_without_issues << reified.id
reified.create_activity :create, antcat_bot, edit_summary: "Reified missing subspecies for quadrinomial, see %github819"
end
return reified
else
raise "could not persist subspecies version #{subspecies_version.id}"
end
end
quadrinomials.each do |taxon|
name_string = taxon.name_cache
raise "#{taxon.id}: has soft-validation issues" if taxon.soft_validation_warnings.size.positive?
raise "#{taxon.id}: #{name_string} contains weird characters" unless name_string =~ /^[[:alpha:][:blank:]-]+$/
target_subspecies_name_string = name_string.split[0..2].join(' ')
subspecies_version = PaperTrail::Version.where(item_type: "Taxon").where("object LIKE ?", "%name_cache: #{target_subspecies_name_string}\n%").last
if subspecies_version
reify_subspecies subspecies_version
else
puts "no subspecies version".red
end
end; nil
puts "reified_with_issues = #{$reified_with_issues}"
puts "reified_without_issues = #{$reified_without_issues}"
puts "all_reified = #{$reified_with_issues + $reified_without_issues}"
puts "Done"Resultsreified_with_issues = [497287, 505104, 504885, 491154, 505448, 491526, 490467, 503153, 464741, 490044, 490574, 465957, 491372, 491120, 490618, 490074, 468634, 505895, 503332, 506856, 493406, 474883, 489783, 479474, 504415]
reified_without_issues = [495560, 462941, 462965, 463175, 463496, 463950, 464622, 465638, 466281, 464310, 464240, 484921, 465222, 466309, 465243, 490480, 466590, 466785, 502707, 490110, 484327, 495209, 466360, 484067, 484544, 466679, 464484, 485279, 466965, 467194, 485524, 467899, 467839, 467768, 468269, 492242, 468586, 468180, 467863, 485569, 485547, 468912, 469146, 469078, 503579, 469088, 469835, 470938, 470915, 470764, 470233, 486559, 471473, 471524, 471512, 471780, 472253, 506348, 472871, 473260, 473004, 474014, 473690, 474020, 473799, 473844, 473985, 474100, 487479, 474205, 475486, 475633, 475542, 477616, 476479, 476610, 476616, 477908, 477856, 487997, 488218, 488179, 477886, 488255, 488112, 478282, 478521, 488143, 488261, 488100, 478098, 477876, 488161, 488205, 479026, 488823, 488707, 479605, 479793, 488826, 488811, 488936, 480053, 488954, 480405, 480867, 481533, 481701, 481039, 481857, 489463, 482134, 482352, 466921, 471750, 472177, 480387, 483108, 466001, 465681]
all_reified = [497287, 505104, 504885, 491154, 505448, 491526, 490467, 503153, 464741, 490044, 490574, 465957, 491372, 491120, 490618, 490074, 468634, 505895, 503332, 506856, 493406, 474883, 489783, 479474, 504415, 495560, 462941, 462965, 463175, 463496, 463950, 464622, 465638, 466281, 464310, 464240, 484921, 465222, 466309, 465243, 490480, 466590, 466785, 502707, 490110, 484327, 495209, 466360, 484067, 484544, 466679, 464484, 485279, 466965, 467194, 485524, 467899, 467839, 467768, 468269, 492242, 468586, 468180, 467863, 485569, 485547, 468912, 469146, 469078, 503579, 469088, 469835, 470938, 470915, 470764, 470233, 486559, 471473, 471524, 471512, 471780, 472253, 506348, 472871, 473260, 473004, 474014, 473690, 474020, 473799, 473844, 473985, 474100, 487479, 474205, 475486, 475633, 475542, 477616, 476479, 476610, 476616, 477908, 477856, 487997, 488218, 488179, 477886, 488255, 488112, 478282, 478521, 488143, 488261, 488100, 478098, 477876, 488161, 488205, 479026, 488823, 488707, 479605, 479793, 488826, 488811, 488936, 480053, 488954, 480405, 480867, 481533, 481701, 481039, 481857, 489463, 482134, 482352, 466921, 471750, 472177, 480387, 483108, 466001, 465681] |
Batch 2: Quadrinomials where a
|
Batch 3/4/5
Script
EDIT_SUMMARY = 'Convert quadrinomials to infrasubspecies [batch 5], see %github819'
ANTCATBOT = User.find_by!(name: 'AntCatBot')
# For activities and PaperTrail.
RequestStore.store[:current_request_uuid] = SecureRandom.uuid
PaperTrail.request.whodunnit = ANTCATBOT.id
def quadrinomials
Subspecies.joins(:name).where("(LENGTH(names.name) - LENGTH(REPLACE(names.name, ' ', '')) >= 3) ")
end
def puts_stats
puts <<~STATS
Quadrinomials count: #{quadrinomials.count}
Infrasubspecies count: #{Infrasubspecies.count}
STATS
end
def fix! soon_infrasubspecies, antcat_bot, edit_summary
name_string = soon_infrasubspecies.name_cache
raise "#{soon_infrasubspecies.id}: has soft-validation issues" if soon_infrasubspecies.soft_validations.failed?
raise "#{soon_infrasubspecies.id}: #{name_string} contains weird characters" unless name_string =~ /^[[:alpha:][:blank:]-]+$/
target_subspecies_name_string = name_string.split[0..2].join(' ')
target_subspecies = Subspecies.where(name_cache: target_subspecies_name_string)
target_subspecies_count = target_subspecies.count
if target_subspecies_count == 0
puts "#{soon_infrasubspecies.id}: found no subspecies".blue
return
end
if target_subspecies_count > 1
raise "#{soon_infrasubspecies.id}: found too many subspecies"
end
the_target_subspecies = target_subspecies.first
the_target_subspecies_validation_issues = the_target_subspecies.soft_validations.failed.reject do |validation|
validation.database_script.is_a?(DatabaseScripts::NonValidTaxaWithACurrentTaxonThatIsNotValid)
end
if the_target_subspecies_validation_issues.present?
puts "target subspecies #{the_target_subspecies.id} has soft-validation issues"
return
end
Taxon.transaction do
soon_infrasubspecies.name.update!(type: 'InfrasubspeciesName')
soon_infrasubspecies.update_columns(type: 'Infrasubspecies')
infrasubspecies = Infrasubspecies.find(soon_infrasubspecies.id)
infrasubspecies.update!(subspecies: the_target_subspecies)
puts "#{soon_infrasubspecies.id}: fixed!".green
if infrasubspecies.soft_validations.failed.present?
puts "#{soon_infrasubspecies.id}: but it has soft-validation issues...".red
end
infrasubspecies.create_activity :update, antcat_bot, edit_summary: edit_summary
end
end
puts_stats
quadrinomials.each do |taxon|
fix! taxon, ANTCATBOT, EDIT_SUMMARY
end; nil
Activity.execute_script_activity User.find_by!(name: 'Fredrik Palmkron'), EDIT_SUMMARY
puts_stats
puts "Done"
Output 3
Quadrinomials count: 248
Infrasubspecies count: 491
430288: fixed!
430355: fixed!
430770: fixed!
430771: fixed!
431244: fixed!
431284: fixed!
431285: fixed!
431426: found no subspecies
431824: fixed!
431825: fixed!
431902: found no subspecies
431925: fixed!
431949: found no subspecies
431955: found no subspecies
432115: found no subspecies
432243: fixed!
432298: fixed!
432303: fixed!
432304: fixed!
432306: fixed!
432326: fixed!
432337: found no subspecies
432435: fixed!
432495: fixed!
432650: fixed!
432663: found no subspecies
432683: fixed!
432723: fixed!
432747: fixed!
432758: found no subspecies
432770: fixed!
432837: fixed!
432926: found no subspecies
433012: fixed!
433082: fixed!
433083: fixed!
433085: fixed!
433149: fixed!
433167: found no subspecies
433209: fixed!
433261: fixed!
433293: found no subspecies
433336: fixed!
433338: fixed!
433385: fixed!
433396: fixed!
433522: fixed!
433622: fixed!
433644: fixed!
433776: fixed!
433841: fixed!
433858: fixed!
433930: found no subspecies
433946: fixed!
433968: fixed!
433992: fixed!
434372: fixed!
434373: fixed!
434378: fixed!
434379: fixed!
434384: fixed!
434394: fixed!
434398: fixed!
434413: found no subspecies
434415: fixed!
434442: fixed!
434492: fixed!
434504: fixed!
434511: fixed!
434621: fixed!
434740: fixed!
434857: found no subspecies
435181: fixed!
435246: fixed!
435373: fixed!
435378: fixed!
435396: found no subspecies
435431: fixed!
435450: found no subspecies
435470: fixed!
435481: fixed!
435512: fixed!
435530: fixed!
435555: found no subspecies
435753: fixed!
435773: fixed!
435801: fixed!
435856: fixed!
435875: fixed!
435962: fixed!
436060: fixed!
436066: fixed!
436092: fixed!
436104: fixed!
436324: found no subspecies
436329: found no subspecies
436341: found no subspecies
436358: fixed!
436359: found no subspecies
436768: fixed!
436916: fixed!
436923: fixed!
436925: fixed!
436942: fixed!
437006: fixed!
437108: fixed!
437266: fixed!
437293: fixed!
437354: fixed!
437382: fixed!
437384: fixed!
437455: fixed!
437575: fixed!
437579: fixed!
437627: fixed!
437753: fixed!
437827: fixed!
437830: fixed!
437841: found no subspecies
437846: fixed!
438026: found no subspecies
438160: fixed!
438169: fixed!
438172: found no subspecies
438492: fixed!
438500: fixed!
438524: fixed!
438542: fixed!
438571: fixed!
438647: fixed!
438936: fixed!
438974: fixed!
439015: found no subspecies
439365: fixed!
439546: fixed!
439558: fixed!
439569: found no subspecies
439583: fixed!
439602: fixed!
439603: found no subspecies
439604: found no subspecies
439649: found no subspecies
439654: found no subspecies
439843: fixed!
439891: fixed!
440011: fixed!
440051: fixed!
440066: fixed!
440079: fixed!
440108: fixed!
440134: fixed!
440151: fixed!
440176: found no subspecies
440177: found no subspecies
440185: fixed!
440196: fixed!
440230: fixed!
440237: fixed!
440251: fixed!
440342: found no subspecies
440354: fixed!
440356: fixed!
440486: fixed!
440523: fixed!
440551: fixed!
440570: fixed!
440716: found no subspecies
440720: fixed!
440728: fixed!
440778: fixed!
440795: fixed!
440830: found no subspecies
440863: fixed!
440888: found no subspecies
441392: fixed!
441425: found no subspecies
441484: fixed!
441666: fixed!
442478: fixed!
442494: fixed!
442516: fixed!
442539: fixed!
442586: fixed!
442589: fixed!
442600: fixed!
443125: fixed!
443340: fixed!
443659: found no subspecies
443752: fixed!
443828: fixed!
443954: fixed!
444639: found no subspecies
444871: found no subspecies
444876: found no subspecies
444886: found no subspecies
444888: found no subspecies
444941: found no subspecies
445123: fixed!
445189: fixed!
445249: fixed!
445627: fixed!
446125: fixed!
446357: found no subspecies
446714: fixed!
446734: fixed!
446742: found no subspecies
446748: fixed!
447218: fixed!
447267: fixed!
447429: fixed!
447675: fixed!
449304: found no subspecies
450089: fixed!
450090: found no subspecies
450175: found no subspecies
450184: found no subspecies
450227: fixed!
450252: fixed!
450288: fixed!
450307: found no subspecies
450351: fixed!
450356: fixed!
450370: found no subspecies
450480: fixed!
450618: fixed!
450639: found no subspecies
450681: found no subspecies
450748: found no subspecies
450760: found no subspecies
450796: fixed!
450906: fixed!
451087: found no subspecies
451357: found no subspecies
451376: fixed!
451399: fixed!
451424: fixed!
456717: found no subspecies
457066: found no subspecies
457083: found no subspecies
457255: found no subspecies
457703: found no subspecies
457780: found no subspecies
458031: found no subspecies
458333: found no subspecies
458338: found no subspecies
459909: found no subspecies
461383: found no subspecies
508189: found no subspecies
Quadrinomials count: 70
Infrasubspecies count: 669Output 4
Quadrinomials count: 70
Infrasubspecies count: 670
431426: found no subspecies
431902: found no subspecies
431949: found no subspecies
431955: fixed!
432115: found no subspecies
432337: found no subspecies
432663: found no subspecies
432758: found no subspecies
432926: found no subspecies
433167: found no subspecies
433293: found no subspecies
433930: found no subspecies
434413: found no subspecies
434857: found no subspecies
435396: found no subspecies
435450: found no subspecies
435555: found no subspecies
436324: found no subspecies
436329: found no subspecies
436341: found no subspecies
436359: found no subspecies
437841: fixed!
438026: fixed!
438172: found no subspecies
439015: fixed!
439569: found no subspecies
439603: found no subspecies
439604: found no subspecies
439649: fixed!
439654: fixed!
440176: fixed!
440177: found no subspecies
440342: found no subspecies
440716: fixed!
440830: fixed!
440888: found no subspecies
441425: fixed!
443659: found no subspecies
444639: found no subspecies
444871: found no subspecies
444876: found no subspecies
444886: found no subspecies
444888: found no subspecies
444941: fixed!
446357: fixed!
446742: fixed!
449304: found no subspecies
450090: fixed!
450175: fixed!
450184: fixed!
450307: found no subspecies
450370: fixed!
450639: found no subspecies
450681: fixed!
450748: fixed!
450760: fixed!
451087: found no subspecies
451357: found no subspecies
456717: fixed!
457066: found no subspecies
457083: fixed!
457255: found no subspecies
457703: fixed!
457780: fixed!
458031: fixed!
458333: found no subspecies
458338: found no subspecies
459909: fixed!
461383: found no subspecies
508189: fixed!
Quadrinomials count: 43
Infrasubspecies count: 697
Output 4
Quadrinomials count: 43
Infrasubspecies count: 700
431426: fixed!
431902: fixed!
431949: fixed!
432115: fixed!
432337: fixed!
432663: fixed!
432758: fixed!
432926: fixed!
433167: fixed!
433293: fixed!
433930: fixed!
434413: fixed!
434857: fixed!
435396: fixed!
435450: fixed!
435555: fixed!
436324: fixed!
436329: fixed!
436341: fixed!
436359: fixed!
438172: fixed!
439569: fixed!
439603: fixed!
439604: fixed!
440177: fixed!
440342: fixed!
440888: fixed!
443659: fixed!
444639: fixed!
444871: fixed!
444876: fixed!
444886: fixed!
444888: fixed!
449304: fixed!
450307: fixed!
450639: fixed!
451087: fixed!
451357: fixed!
457066: fixed!
457255: fixed!
458333: fixed!
458338: fixed!
461383: fixed!
Quadrinomials count: 0
Infrasubspecies count: 743 |
See #714, AC issue: https://antcat.org/issues/41
TODO:
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