Module: Protonym::SoftValidationExtensions::Instance

Included in:
Protonym
Defined in:
app/models/protonym/soft_validation_extensions.rb

Instance Method Summary collapse

Instance Method Details

#sv_author_is_not_required ⇒ Object 



1563
1564
1565
1566
1567
1568
1569
1570
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1563

def sv_author_is_not_required
  if self.verbatim_author && (!self.taxon_name_author_roles.empty? || (self.source && self.verbatim_author == self.source.authority_name))
    soft_validations.add(
      :verbatim_author, 'Verbatim author is not required, it is derived from the source and taxon name author roles',
      success_message: 'Verbatim author was deleted',
      failure_message:  'Failed to delete verbatim author')
  end
end

#sv_extant_children ⇒ Object 



1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1504

def sv_extant_children
  unless self.parent_id.blank?
    if self.is_fossil?
      taxa = Protonym.where(parent_id: self.id)
      z = 0
      unless taxa.empty?
        taxa.each do |t|
          soft_validations.add(:base, "Extinct taxon #{self.cached_html} has extant children") if !t.is_fossil? && t.id == t.cached_valid_taxon_name_id && z == 0
          z = 1
        end
      end
    end
  end
end

#sv_family_is_invalid ⇒ Object 



1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1370

def sv_family_is_invalid
  if persisted? && is_family_rank? && is_available?
    tg = type_genus
    if tg && (!TaxonNameRelationship.where_subject_is_taxon_name(tg).homonym_or_suppressed.empty? ||
        !TaxonNameClassification.where_taxon_name(tg).with_type_string('TaxonNameClassification::Iczn::Available::Invalid::Homonym').empty? )
      if self.id == self.lowest_rank_coordinated_taxon.id
        if TaxonNameClassification.where_taxon_name(self).with_type_base('TaxonNameClassification::Iczn::Available::Invalid').empty?
          soft_validations.add(:base, "Missing relationship: #{self.cached_html_name_and_author_year} is invalid due to the homonymy or suppression of its type genus")
        end
      end
    end
  end
end

#sv_family_is_invalid_no_substitute ⇒ Object 



1384
1385
1386
1387
1388
1389
1390
1391
1392
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1384

def sv_family_is_invalid_no_substitute
  if persisted? && is_family_rank? && self.id == self.lowest_rank_coordinated_taxon.id
    if !TaxonNameClassification.where_taxon_name(self).with_type_base('TaxonNameClassification::Iczn::Available::Invalid').empty?
      if self.iczn_set_as_synonym_of.nil?
        soft_validations.add(:base, 'Missing relationship: The name is invalid, but a substitute name is not selected')
      end
    end
  end
end

#sv_fix_add_nominotypical_sub ⇒ Object 



1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1273

def sv_fix_add_nominotypical_sub
  return false if list_of_coordinated_names.collect{|r| r.id}.include?(parent_id)
  rank  = rank_string
  p     = self.parent
  prank = p.rank_string
  if (rank =~ /Family/ && prank =~ /Family/) || (rank =~ /Genus/ && prank =~ /Genus/) || (rank =~ /Species/ && prank =~ /Species/)
    begin
      Protonym.transaction do
        if rank =~ /Family/ && prank =~ /Family/
          name = Protonym.family_group_base(self.parent.name)
          case self.rank_class.rank_name
          when 'subfamily'
            name += 'inae'
          when 'tribe'
            name += 'ini'
          when 'subtribe'
            name += 'ina'
          end
        else
          name = p.name
        end

        t = Protonym.new(name: name, rank_class: rank, verbatim_author: p.verbatim_author, year_of_publication: p.year_of_publication, source: p.source, parent: p)
        t.save
        t.soft_validate
        t.fix_soft_validations
      end
    rescue ActiveRecord::RecordInvalid # naked rescue is very bad
      return false
    end
    return true
  end
end

#sv_fix_author_is_not_required ⇒ Object 



1572
1573
1574
1575
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1572

def sv_fix_author_is_not_required
  self.update_column(:verbatim_author, nil)
  return true
end

#sv_fix_coordinated_names_author ⇒ Object 



646
647
648
649
650
651
652
653
654
655
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 646

def sv_fix_coordinated_names_author
  return false if !self.verbatim_author.nil? || !self.taxon_name_author_roles.empty?
  list_of_coordinated_names.each do |t|
    if self.verbatim_author.nil? && !t.verbatim_author.nil?
      self.update_column(:verbatim_author, t.verbatim_author)
      return true
    end
  end
  return false
end

#sv_fix_coordinated_names_etymology ⇒ Object 



939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 939

def sv_fix_coordinated_names_etymology
  fixed = false
  return false unless self.etymology.blank?
  list_of_coordinated_names.each do |t|
    if !t.etymology.blank?
      self.etymology = t.etymology
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_gender ⇒ Object 



686
687
688
689
690
691
692
693
694
695
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 686

def sv_fix_coordinated_names_gender
  return false unless self.gender_class.nil?
  list_of_coordinated_names.each do |t|
    unless t.gender_class.nil?
      c = self.taxon_name_classifications.create(type: t.gender_class.to_s)
      return true if c.id
    end
  end
  return false
end

#sv_fix_coordinated_names_original_form ⇒ Object 



877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 877

def sv_fix_coordinated_names_original_form
  fixed = false
  return false unless self.original_form.nil?
  list_of_coordinated_names.each do |t|
    if !t.original_form.nil?
      self.original_form = t.original_form
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_original_genus ⇒ Object 



727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 727

def sv_fix_coordinated_names_original_genus
  fixed = false
  return false unless self.original_genus.nil?
  list_of_coordinated_names.each do |t|
    if !t.original_genus.nil?
      self.original_genus = t.original_genus
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_original_species ⇒ Object 



787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 787

def sv_fix_coordinated_names_original_species
  fixed = false
  return false unless self.original_species.nil?
  list_of_coordinated_names.each do |t|
    if !t.original_species.nil?
      self.original_species = t.original_species
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_original_subgenus ⇒ Object 



757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 757

def sv_fix_coordinated_names_original_subgenus
  fixed = false
  return false unless self.original_subgenus.nil?
  list_of_coordinated_names.each do |t|
    if !t.original_subgenus.nil?
      self.original_subgenus = t.original_subgenus
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_original_subspecies ⇒ Object 



817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 817

def sv_fix_coordinated_names_original_subspecies
  fixed = false
  return false unless self.original_subspecies.nil?
  list_of_coordinated_names.each do |t|
    if !t.original_subspecies.nil?
      self.original_subspecies = t.original_subspecies
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_original_variety ⇒ Object 



847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 847

def sv_fix_coordinated_names_original_variety
  fixed = false
  return false unless self.original_variety.nil?
  list_of_coordinated_names.each do |t|
    if !t.original_variety.nil?
      self.original_variety = t.original_variety
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_page ⇒ Object 



618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 618

def sv_fix_coordinated_names_page
  fixed = false
  return false if self.origin_citation.nil? || !self.origin_citation.pages.nil?
  list_of_coordinated_names.each do |t|
    if !t.origin_citation.nil? && !t.origin_citation.pages.nil? && self.origin_citation.source_id == t.origin_citation.source_id
      self.origin_citation.pages = t.origin_citation.pages
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.origin_citation.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_part_of_speech ⇒ Object 



707
708
709
710
711
712
713
714
715
716
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 707

def sv_fix_coordinated_names_part_of_speech
  return false unless self.part_of_speech_class.nil?
  list_of_coordinated_names.each do |t|
    unless t.part_of_speech_class.nil?
      c = self.taxon_name_classifications.create(type: t.part_of_speech_class.to_s)
      return true if c.id
    end
  end
  return false
end

#sv_fix_coordinated_names_roles ⇒ Object 



969
970
971
972
973
974
975
976
977
978
979
980
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 969

def sv_fix_coordinated_names_roles
  return false unless self.taxon_name_author_roles.empty?
  list_of_coordinated_names.each do |t|
    if !t.taxon_name_author_roles.empty?
      t.taxon_name_author_roles.each do |r|
        TaxonNameAuthor.create(person_id: r.person_id, role_object: self, position: r.position)
      end
      return true
    end
  end
  return false
end

#sv_fix_coordinated_names_source ⇒ Object 



583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 583

def sv_fix_coordinated_names_source
  fixed = false
  pg = nil
  return false unless self.source.nil?
    list_of_coordinated_names.each do |t|
      if !t.source.nil?
        self.source = t.source
        pg = t.origin_citation.pages
        fixed = true
      end
    end
    if fixed
    begin
      Protonym.transaction do
        self.source.save
        self.origin_citation.update_column(:pages, pg)
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_type_genus ⇒ Object 



1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1027

def sv_fix_coordinated_names_type_genus
  fixed = false
  return false unless self.type_genus.nil?
  list_of_coordinated_names.each do |t|
    if !t.type_genus.nil?
      self.type_genus = t.type_genus
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.type_genus.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_type_species ⇒ Object 



908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 908

def sv_fix_coordinated_names_type_species
  fixed = false
  tr = nil
  return false unless self.type_species.nil?
  list_of_coordinated_names.each do |t|
    if !t.type_species.nil? && fixed == false
      tr = TaxonNameRelationship.new(type: t.type_species_relationship.type, subject_taxon_name_id: t.type_species_relationship.subject_taxon_name_id, object_taxon_name_id: self.id)
      fixed = true
    end
  end
  if fixed
    begin
      TaxonNameRelationship.transaction do
        tr.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_type_species_type ⇒ Object 



994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 994

def sv_fix_coordinated_names_type_species_type
  sttnr = self.type_taxon_name_relationship
  return false if sttnr.nil?
  fixed = false
  list_of_coordinated_names.each do |t|
    tttnr = t.type_taxon_name_relationship
    if !tttnr.nil? && sttnr.type != tttnr.type && sttnr.type.safe_constantize.descendants.collect{|i| i.to_s}.include?(tttnr.type.to_s)
      self.type_taxon_name_relationship.type = t.type_taxon_name_relationship.type
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.type_taxon_name_relationship.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_type_specimen ⇒ Object 



1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1057

def sv_fix_coordinated_names_type_specimen
  fixed = false
  return false unless self.get_primary_type.empty?
  list_of_coordinated_names.each do |t1|
    types2 = t1.get_primary_type
    if !types2.empty?
      new_type_material = []
      types2.each do |t|
        new_type_material.push({type_type: t.type_type, protonym_id: self.id, collection_object_id: t.collection_object_id, source: t.source})
      end
      self.type_materials.build(new_type_material)
      fixed = true
    end
  end
  if fixed
    begin
      Protonym.transaction do
        self.save
      end
      return true
    rescue
      return false
    end
  end
end

#sv_fix_coordinated_names_year ⇒ Object 



664
665
666
667
668
669
670
671
672
673
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 664

def sv_fix_coordinated_names_year
  return false if !self.year_of_publication.nil? || !self.source.try(:year).nil?
  list_of_coordinated_names.each do |t|
    if self.year_of_publication.nil? && !t.year_of_publication.nil?
      self.update_column(:year_of_publication, t.year_of_publication)
      return true
    end
  end
  return false
end

#sv_fix_missing_otu ⇒ Object 



1632
1633
1634
1635
1636
1637
1638
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1632

def sv_fix_missing_otu
  if is_available? && otus.empty?
    otus.create(taxon_name_id: id)
    return true
  end
  return false
end

#sv_fix_misspelling_author_is_not_required ⇒ Object 



1604
1605
1606
1607
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1604

def sv_fix_misspelling_author_is_not_required
  self.update_column(:verbatim_author, nil)
  return true
end

#sv_fix_misspelling_roles_are_not_required ⇒ Object 



1588
1589
1590
1591
1592
1593
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1588

def sv_fix_misspelling_roles_are_not_required
  self.taxon_name_author_roles.each do |r|
    r.destroy
  end
  return true
end

#sv_fix_misspelling_year_is_not_required ⇒ Object 



1618
1619
1620
1621
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1618

def sv_fix_misspelling_year_is_not_required
  self.update_column(:year_of_publication, nil)
  return true
end

#sv_fix_presence_of_combination ⇒ Object 



1660
1661
1662
1663
1664
1665
1666
1667
1668
1669
1670
1671
1672
1673
1674
1675
1676
1677
1678
1679
1680
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1660

def sv_fix_presence_of_combination
  begin
    TaxonName.transaction do
      c = Combination.new
      safe_self_and_ancestors.each do |i|
        case i.rank
          when 'genus'
            c.genus = i
          when 'subgenus'
            c.subgenus = i
          when 'species'
            c.species = i
          when 'subspecies'
            c.subspecies = i
        end
      end
      c.save
    end
  rescue
  end
end

#sv_fix_type_placement1 ⇒ Object 



1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1205

def sv_fix_type_placement1
  self.type_of_taxon_names.each do |t|
    coordinated = t.lowest_rank_coordinated_taxon
    if self.parent_id != coordinated.id
      #          if t.id != coordinated.id && self.parent_id != coordinated.id
      begin
        Protonym.transaction do
          self.parent_id = coordinated.id
          self.save
        end
        return true
      rescue
        return false
      end
    end
  end
end

#sv_fix_year_is_not_required ⇒ Object 



1558
1559
1560
1561
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1558

def sv_fix_year_is_not_required
  self.update_column(:year_of_publication, nil)
  return true
end

#sv_homotypic_synonyms ⇒ Object 



1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1326

def sv_homotypic_synonyms
  unless !is_valid? # unavailable_or_invalid?
    if self.id == self.lowest_rank_coordinated_taxon.id
      possible_synonyms = []
      if rank_string =~ /Species/
        primary_types = self.get_primary_type
        unless primary_types.empty?
          p                 = primary_types.collect {|t| t.collection_object_id}
          possible_synonyms = Protonym.with_type_material_array(p).without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self).with_project(self.project_id)
        end
      elsif rank_string =~ /Family/ && self.name == Protonym.family_group_base(self.name)
        # do nothing
      else
        type = self.type_taxon_name
        unless type.nil?
          possible_synonyms = Protonym.with_type_of_taxon_names(type.id).not_self(self).with_project(self.project_id)
        end
      end

      possible_synonyms = reduce_list_of_synonyms(possible_synonyms)
      possible_synonyms.each do |s|
        soft_validations.add(:base, "Missing relationship: #{self.rank_class.rank_name} #{self.cached_html} should be a synonym of #{s.cached_html} #{s.cached_author_year} since they share the same type")
      end
    end
  end
end

#sv_missing_etymology ⇒ Object 



1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1480

def sv_missing_etymology
  if self.etymology.nil? && self.rank_string =~ /(Genus|Species)/ && is_available?
    z = TaxonName.
        where(name: name, project_id: project_id).where.not(etymology: nil).
        group(:etymology).
        count(:etymology)

    if z.empty?
      z = TaxonName.where(name: name).where.not(etymology: nil).group(:etymology).count(:etymology)
      other_project = ' in different projects'
    else
      other_project = ''
    end

    if z.empty?
      soft_validations.add(:etymology, 'Etymology is missing')
    else
      z1 = z.sort_by {|k, v| -v}
      t = z1[0][1] == 1 ? 'time' : 'times'
      soft_validations.add(:etymology, "Etymology is missing. Previously used etymology for similar name#{other_project}: '#{z1[0][0]}' (#{z1[0][1]} #{t})")
    end
  end
end

#sv_missing_gender ⇒ Object 



482
483
484
485
486
487
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 482

def sv_missing_gender
  if is_genus_rank? && self.gender_class.nil? && !self.cached_misspelling && is_available?
    g = genus_suggested_gender
    soft_validations.add(:base, "Gender is not specified#{ g.nil? ? '' : ' (possible gender is ' + g + ')'}")
  end
end

#sv_missing_original_genus ⇒ Object 



1459
1460
1461
1462
1463
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1459

def sv_missing_original_genus
  if is_genus_or_species_rank? && self.original_genus.nil? && !not_binominal?
    soft_validations.add(:base, 'Missing relationship: Original genus is not selected')
  end
end

#sv_missing_otu ⇒ Object 



1623
1624
1625
1626
1627
1628
1629
1630
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1623

def sv_missing_otu
  if is_available? && otus.empty? && rank_string != 'NomenclaturalRank'
    soft_validations.add(
      :year_of_publication, 'Missing OTU',
      success_message: 'OTU was created',
      failure_message:  'Failed to create OTU')
  end
end

#sv_missing_part_of_speech ⇒ Object 



448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 448

def sv_missing_part_of_speech
  if is_species_rank? && self.part_of_speech_class.nil? && !has_misspelling_relationship? && is_available?

    z = TaxonNameClassification.
        joins(:taxon_name).
        where(taxon_names: { name: name, project_id: project_id }).
        where("taxon_name_classifications.type LIKE 'TaxonNameClassification::Latinized::PartOfSpeech%'").
        group(:type).
        count(:type)

    if z.empty?
      z = TaxonNameClassification.
          joins(:taxon_name).
          where(taxon_names: { name: name}).
          where("taxon_name_classifications.type LIKE 'TaxonNameClassification::Latinized::PartOfSpeech%'").
          group(:type).
          count(:type)
      other_project = ' in different projects'
    else
      other_project = ''
    end

    if z.empty?
      soft_validations.add(:base, 'Part of speech is not specified. Please select if the name is a noun or an adjective.')
    else
      l = []
      z.each do |key, value|
        l << (value == 1 ? " as '#{key.constantize.label}' #{value.to_s} time" : " as '#{key.constantize.label}' #{value.to_s} times")
      end
      soft_validations.add(:base, "Part of speech is not specified. The name was previously used#{other_project}" + l.join('; '))
    end
  end
end

#sv_missing_roles ⇒ Object 



1527
1528
1529
1530
1531
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1527

def sv_missing_roles
  if self.taxon_name_author_roles.empty? && !has_misspelling_relationship? && !name_is_misapplied? && is_family_or_genus_or_species_rank?
    soft_validations.add(:base, 'Taxon name author role is not selected')
  end
end

#sv_missing_substitute_name ⇒ Object 



440
441
442
443
444
445
446
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 440

def sv_missing_substitute_name
  if !self.iczn_set_as_homonym_of.nil? || !TaxonNameClassification.where_taxon_name(self).with_type_string('TaxonNameClassification::Iczn::Available::Invalid::Homonym').empty?
    if self.iczn_set_as_synonym_of.nil? && is_available?
      soft_validations.add(:base, 'Missing relationship: The name is a homonym, but a substitute name is not selected')
    end
  end
end

#sv_missing_type_genus ⇒ Object 



434
435
436
437
438
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 434

def sv_missing_type_genus
  if is_family_rank? && self.type_genus.nil? && is_available?
    soft_validations.add(:base, 'Missing relationship: Type genus is not selected')
  end
end

#sv_missing_type_species ⇒ Object 



428
429
430
431
432
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 428

def sv_missing_type_species
  if is_genus_rank? && self.type_species.nil? && is_available?
    soft_validations.add(:base, 'Missing relationship: Type species is not selected')
  end
end

#sv_misspelling_author_is_not_required ⇒ Object 



1595
1596
1597
1598
1599
1600
1601
1602
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1595

def sv_misspelling_author_is_not_required
  if self.verbatim_author && self.source && (has_misspelling_relationship? || name_is_misapplied?)
    soft_validations.add(
      :verbatim_author, 'Verbatim author is not required for misspellings and misapplications',
      success_message: 'Verbatim author was deleted',
      failure_message:  'Failed to delete verbatim author')
  end
end

#sv_misspelling_roles_are_not_required ⇒ Object 



1577
1578
1579
1580
1581
1582
1583
1584
1585
1586
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1577

def sv_misspelling_roles_are_not_required
  #DD: do not use .has_misspelling_relationship?
  misspellings = taxon_name_relationships.with_type_array(TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING_AUTHOR_STRING).any?
  if !self.taxon_name_author_roles.empty? && self.source && misspellings
    soft_validations.add(
      :base, 'Taxon name author role is not required for misspellings and misapplications',
      success_message: 'Roles were deleted',
      failure_message:  'Fail to delete roles')
  end
end

#sv_misspelling_year_is_not_required ⇒ Object 



1609
1610
1611
1612
1613
1614
1615
1616
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1609

def sv_misspelling_year_is_not_required
  if self.year_of_publication && self.source && (has_misspelling_relationship? || name_is_misapplied?)
    soft_validations.add(
      :year_of_publication, 'Year is not required for misspellings and misapplications',
      success_message: 'Year was deleted',
      failure_message:  'Failed to delete year')
  end
end

#sv_original_combination_relationships ⇒ Object 



1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1465

def sv_original_combination_relationships
  relationships = self.original_combination_relationships
  unless relationships.empty?
    relationships = relationships.sort_by{|r| r.type_class.order_index }
    ids = relationships.collect{|r| r.subject_taxon_name_id}
    if !ids.include?(self.id)
      if (list_of_coordinated_names.collect{|r| r.id} & ids).empty?
        soft_validations.add(:base, "Missing relationship: The original rank of #{self.cached_html} is not specified in the original combination.")
      end
    elsif ids.last != self.id
      soft_validations.add(:base, "Invalid original combination relationship: #{self.cached_html} should be moved to the lowest rank")
    end
  end
end

#sv_parent_priority ⇒ Object 



1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1307

def sv_parent_priority
  if self.rank_class
    rank_group = self.rank_class.parent
    parent = self.parent

    if !is_higher_rank? && parent && rank_group == parent.rank_class.parent
      unless !is_valid? #  unavailable_or_invalid?
        date1 = self.cached_nomenclature_date
        date2 = parent.cached_nomenclature_date
        unless date1.nil? || date2.nil?
          if date1 < date2
            soft_validations.add(:base, "#{self.rank_class.rank_name.capitalize} #{self.cached_html_name_and_author_year} should not be older than parent #{parent.rank_class.rank_name} #{parent.cached_html_name_and_author_year}")
          end
        end
      end
    end
  end
end

#sv_person_vs_year_of_publication ⇒ Object 



1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
1547
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1533

def sv_person_vs_year_of_publication
  if self.cached_nomenclature_date
    year = self.cached_nomenclature_date&.year
    self.taxon_name_author_roles.each do |r|
      person = r.person
      if person.year_died && year > person.year_died + 2
        soft_validations.add(:base, "The year of description does not fit the years of #{person.last_name}'s life (#{person.year_born}–#{person.year_died})")
      elsif person.year_born && year > person.year_born + 105
        soft_validations.add(:base, "The year of description does not fit the years of #{person.last_name}'s life (#{person.year_born}–#{person.year_died})")
      elsif person.year_born && year < person.year_born + 10
        soft_validations.add(:base, "The year of description does not fit the years of #{person.last_name}'s life (#{person.year_born}–#{person.year_died})")
      end
    end
  end
end

#sv_potential_family_homonyms ⇒ Object 



1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1353

def sv_potential_family_homonyms
  if persisted? && is_family_rank? && is_available?
    if TaxonNameRelationship.where_subject_is_taxon_name(self).homonym_or_suppressed.empty?
      if self.id == self.lowest_rank_coordinated_taxon.id
        name2 = self.cached_primary_homonym_alternative_spelling ? self.cached_primary_homonym_alternative_spelling : nil
        possible_primary_homonyms_alternative_spelling = name2 ? Protonym.with_primary_homonym_alternative_spelling(name2).without_homonym_or_suppressed.without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self).with_base_of_rank_class('NomenclaturalRank::Iczn::FamilyGroup').with_project(self.project_id) : []
        list2 = reduce_list_of_synonyms(possible_primary_homonyms_alternative_spelling)
        if !list2.empty?
          list2.each do |s|
            soft_validations.add(:base, "Missing relationship: #{self.cached_html_name_and_author_year} should be a homonym or duplicate of #{s.cached_html_name_and_author_year}")
          end
        end
      end
    end
  end
end

#sv_potential_genus_homonyms ⇒ Object 



1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1394

def sv_potential_genus_homonyms
  if persisted? && is_genus_rank? && is_available?
    if TaxonNameRelationship.where_subject_is_taxon_name(self).homonym_or_suppressed.empty?
      if self.id == self.lowest_rank_coordinated_taxon.id
        name1 = self.cached_primary_homonym ? self.cached_primary_homonym : nil
        possible_primary_homonyms = name1 ? Protonym.with_primary_homonym(name1).without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).without_homonym_or_suppressed.not_self(self).with_base_of_rank_class('NomenclaturalRank::Iczn::GenusGroup').with_project(self.project_id) : []
        list1 = reduce_list_of_synonyms(possible_primary_homonyms)
        if !list1.empty?
          list1.each do |s|
            soft_validations.add(:base, "Missing relationship: #{self.cached_html_name_and_author_year} should be a homonym or duplicate of #{s.cached_html_name_and_author_year}") if s.nomenclatural_code == self.nomenclatural_code
          end
        end
      end
    end
  end
end

#sv_potential_species_homonyms ⇒ Object 



1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1411

def sv_potential_species_homonyms
  if persisted? && is_species_rank? && is_available?
    if TaxonNameRelationship.where_subject_is_taxon_name(self).homonym_or_suppressed.empty?
      if self.id == self.lowest_rank_coordinated_taxon.id
        name1 = self.cached_primary_homonym ? self.cached_primary_homonym : nil
        possible_primary_homonyms = name1 ? Protonym.with_primary_homonym(name1).without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).without_homonym_or_suppressed.not_self(self).with_base_of_rank_class('NomenclaturalRank::Iczn::SpeciesGroup').with_project(self.project_id) : []
        list1 = reduce_list_of_synonyms(possible_primary_homonyms)
        if !list1.empty?
          list1.each do |s|
            soft_validations.add(
              :base, "Missing relationship: #{self.cached_html_name_and_author_year} should be a primary homonym or duplicate of #{s.cached_html_name_and_author_year}")
            #  fix: :sv_fix_add_relationship('iczn_set_as_primary_homonym_of'.to_sym, s.id),
            #  success_message: 'Primary homonym relationship was added',
            #  failure_message: 'Fail to add a relationship')
          end
        else
          name2 = self.cached_primary_homonym_alternative_spelling ? self.cached_primary_homonym_alternative_spelling : nil
          possible_primary_homonyms_alternative_spelling = name2 ? Protonym.with_primary_homonym_alternative_spelling(name2).without_homonym_or_suppressed.without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self).with_base_of_rank_class('NomenclaturalRank::Iczn::SpeciesGroup').with_project(self.project_id) : []
          list2 = reduce_list_of_synonyms(possible_primary_homonyms_alternative_spelling)
          if !list2.empty?
            list2.each do |s|
              soft_validations.add(:base, "Missing relationship: #{self.cached_html_name_and_author_year} could be a primary homonym of #{s.cached_html_name_and_author_year} (alternative spelling)")
            end
          else
            name3 = self.cached_secondary_homonym ? self.cached_secondary_homonym : nil
            possible_secondary_homonyms = name3 ? Protonym.with_secondary_homonym(name3).without_homonym_or_suppressed.without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self).with_base_of_rank_class('NomenclaturalRank::Iczn::SpeciesGroup').with_project(self.project_id) : []
            list3 = reduce_list_of_synonyms(possible_secondary_homonyms)
            if !list3.empty?
              list3.each do |s|
                soft_validations.add(:base, "Missing relationship: #{self.cached_html_name_and_author_year} should be a secondary homonym or duplicate of #{s.cached_html_name_and_author_year}")
              end
            else
              name4 = self.cached_secondary_homonym ? self.cached_secondary_homonym_alternative_spelling : nil
              possible_secondary_homonyms_alternative_spelling = name4 ? Protonym.with_secondary_homonym_alternative_spelling(name4).without_homonym_or_suppressed.without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self).with_base_of_rank_class('NomenclaturalRank::Iczn::SpeciesGroup').with_project(self.project_id) : []
              list4 = reduce_list_of_synonyms(possible_secondary_homonyms_alternative_spelling)
              if !list4.empty?
                list4.each do |s|
                  soft_validations.add(:base, "Missing relationship: #{self.cached_html_name_and_author_year} could be a secondary homonym of #{s.cached_html_name_and_author_year} (alternative spelling)")
                end
              end
            end
          end
        end
      end
    end
  end
end

#sv_potential_usage_duplicates ⇒ Object 



1640
1641
1642
1643
1644
1645
1646
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1640

def sv_potential_usage_duplicates
  usage = TaxonNameRelationship::Iczn::Invalidating::Usage.where(subject_taxon_name_id: self.id).first
  return true if usage.nil?
  TaxonNameRelationship::Iczn::Invalidating::Usage.where(object_taxon_name_id: usage.object_taxon_name_id).not_self(usage).each do |tr|
    soft_validations.add(:base, "'#{name}' is a duplicate #{usage.subject_status + ' ' + usage.subject_status_connector_to_object} #{tr.object_taxon_name.cached_html}",) if usage.subject_taxon_name.name == tr.subject_taxon_name.name
  end
end

#sv_presence_of_combination ⇒ Object 



1649
1650
1651
1652
1653
1654
1655
1656
1657
1658
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1649

def sv_presence_of_combination
  if is_genus_or_species_rank? && is_valid? && self.id == self.lowest_rank_coordinated_taxon.id && !cached_original_combination.nil? && cached != cached_original_combination
    unless Combination.where("cached = ? AND cached_valid_taxon_name_id = ?", cached, cached_valid_taxon_name_id).any?
      soft_validations.add(
        :base, "Protonym #{self.cached_html} missing corresponding subsequent combination. Current classification of the taxon is different from original combination. (Fix will try to create a new combination if possible)",
        success_message: "Combination #{self.cached_html} was successfully create",
        failure_message:  'Failed to create a new combination')
    end
  end
end

#sv_primary_types ⇒ Object 



1223
1224
1225
1226
1227
1228
1229
1230
1231
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1223

def sv_primary_types
  if is_species_rank? && is_available?
    if self.type_materials.primary.empty? && self.type_materials.syntypes.empty?
      soft_validations.add(:base, 'Primary type is not selected')
    elsif self.type_materials.primary.count > 1 || (!self.type_materials.primary.empty? && !self.type_materials.syntypes.empty?)
      soft_validations.add(:base, 'More than one of primary types are selected. Uncheck the specimens which are not primary types for this taxon')
    end
  end
end

#sv_primary_types_repository ⇒ Object 



1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1233

def sv_primary_types_repository
  if is_species_rank?
    s = self.type_materials
    unless s.empty?
      s.primary.each do |t|
        soft_validations.add(:base, 'Primary type repository is not set') if t.collection_object.try(:repository).nil?
      end
      s.syntypes.each do |t|
        soft_validations.add(:base, 'Syntype repository is not set') if t.collection_object.try(:repository).nil?
      end
    end
  end
end

#sv_protonym_to_combination ⇒ Object 



1519
1520
1521
1522
1523
1524
1525
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1519

def sv_protonym_to_combination
  if convertable_to_combination?
    soft_validations.add(
      :base, "Unavailable or Invalid #{self.cached_original_combination_html} could potentially be converted into a combination (Fix will try to convert protonym into combination)",
      success_message: "Protonym #{self.cached_original_combination_html} was successfully converted into a combination", failure_message:  'Failed to convert protonym into combination')
  end
end

#sv_single_sub_taxon ⇒ Object 



1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1247

def sv_single_sub_taxon
  if self.rank_class
    rank = rank_string
    if rank != 'potentially_validating rank' && self.rank_class.nomenclatural_code == :iczn && %w(subspecies subgenus subtribe tribe subfamily).include?(self.rank_class.rank_name)
      sisters = self.parent.descendants.with_rank_class(rank).select{|t| t.id == t.cached_valid_taxon_name_id}
      if rank =~ /Family/
        z = Protonym.family_group_base(self.name)
        search_name = z.nil? ? nil : Protonym::FAMILY_GROUP_ENDINGS.collect{|i| z+i}
        a = sisters.collect{|i| Protonym.family_group_base(i.name) }
        sister_names = a.collect{|z| Protonym::FAMILY_GROUP_ENDINGS.collect{|i| z+i} }.flatten
      else
        search_name = [self.name]
        sister_names = sisters.collect{|i| i.name }
      end
      if search_name.include?(self.parent.name) && sisters.count == 1
        soft_validations.add(:base, "#{self.cached_html} is a single #{self.rank_class.rank_name} in the nominal #{self.parent.rank_class.rank_name} #{self.parent.cached_html}")
      elsif !sister_names.include?(self.parent.name) && !sisters.empty? && self.parent.name == Protonym.family_group_base(self.parent.name) && rank =~ /Family/
        # do nothing
      elsif !sister_names.include?(self.parent.name) && !sisters.empty?
        soft_validations.add(:base, "The parent #{self.parent.rank_class.rank_name} #{self.parent.cached_html} of this #{self.rank_class.rank_name} does not contain nominotypical #{self.rank_class.rank_name} #{Protonym.family_group_name_at_rank(self.parent.name, self.rank_class.rank_name)}",
                             success_message: "Nominotypical #{self.rank_class.rank_name} was added to nominal #{self.parent.rank_class.rank_name} #{self.parent.cached_html}", failure_message:  'Failed to create nomynotypical taxon')
      end
    end
  end
end

#sv_source_not_older_then_description ⇒ Object 



386
387
388
389
390
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 386

def sv_source_not_older_then_description
  if self.source && self.year_of_publication
    soft_validations.add(:base, 'The year of publication of the taxon and the year in the original reference do not match') if self.try(:source).try(:year) != self.year_of_publication
  end
end

#sv_species_gender_agreement ⇒ Object 



489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 489

def sv_species_gender_agreement
  if is_species_rank?
    s = part_of_speech_name
    if !s.nil? && is_available?
      if %w{adjective participle}.include?(s)
        if !feminine_name.blank? && !masculine_name.blank? && !neuter_name.blank? && name != masculine_name && name != feminine_name && name != neuter_name
          soft_validations.add(:base, 'Species name does not match with either of three alternative forms')
        else
          forms = predict_three_forms
          if feminine_name.blank?
            soft_validations.add(:feminine_name, "The species name is marked as #{part_of_speech_name}, but the name spelling in feminine is not provided")
          else
            # e = species_questionable_ending(TaxonNameClassification::Latinized::Gender::Feminine, feminine_name)
            # soft_validations.add(:feminine_name, "Name has a non feminine ending: -#{e}") unless e.nil?
            soft_validations.add(:feminine_name, "Feminine form does not match with predicted: #{forms[:feminine_name]}") if feminine_name != forms[:feminine_name]
          end

          if masculine_name.blank?
            soft_validations.add(:masculine_name, "The species name is marked as #{part_of_speech_name}, but the name spelling in masculine is not provided")
          else
            # e = species_questionable_ending(TaxonNameClassification::Latinized::Gender::Masculine, masculine_name)
            # soft_validations.add(:masculine_name, "Name has a non masculine ending: -#{e}") unless e.nil?
            soft_validations.add(:masculine_name, "Masculine form does not match with predicted: #{forms[:masculine_name]}") if masculine_name != forms[:masculine_name]
          end

          if neuter_name.blank?
            soft_validations.add(:neuter_name, "The species name is marked as #{part_of_speech_name}, but the name spelling in neuter is not provided")
          else
            # e = species_questionable_ending(TaxonNameClassification::Latinized::Gender::Neuter, neuter_name)
            # soft_validations.add(:neuter_name, "Name has a non neuter ending: -#{e}") unless e.nil?
            soft_validations.add(:neuter_name, "Neuter form does not match with predicted: #{forms[:neuter_name]}") if neuter_name != forms[:neuter_name]
          end
        end
      end
    end
  end
end

#sv_species_gender_agreement_not_required ⇒ Object 



527
528
529
530
531
532
533
534
535
536
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 527

def sv_species_gender_agreement_not_required
  if is_species_rank? && ((!feminine_name.blank? || !masculine_name.blank? || !neuter_name.blank?)) && is_available?
    s = part_of_speech_name
    if !s.nil? && !%w{adjective participle}.include?(s)
      soft_validations.add(:feminine_name, 'Alternative spelling is not required for the name which is not adjective or participle.') unless feminine_name.blank?
      soft_validations.add(:masculine_name, 'Alternative spelling is not required for the name which is not adjective or participle.')  unless masculine_name.blank?
      soft_validations.add(:neuter_name, 'Alternative spelling is not required for the name which is not adjective or participle.')  unless neuter_name.blank?
    end
  end
end

#sv_type_placement ⇒ Object

def sv_fix_coordinated_names

  fixed = false
  gender = self.gender_class
  speech = self.part_of_speech_class

  list_of_coordinated_names.each do |t|
    if t.source.nil? && !t.source.nil?
      self.source = t.source
      fixed = true
    end

    if self.verbatim_author.nil? && !t.verbatim_author.nil?
      self.verbatim_author = t.verbatim_author
      fixed = true
    end

    if self.year_of_publication.nil? && !t.year_of_publication.nil?
      self.year_of_publication = t.year_of_publication
      fixed = true
    end

    t_gender = t.gender_class

    if gender.nil? && !t_gender.nil?
      self.taxon_name_classifications.build(type: t_gender.to_s)
      fixed = true
    end

    t_speech = t.part_of_speech_class

    if speech.nil? && speech != t_speech
      self.taxon_name_classifications.build(type: t_speech.to_s)
      fixed = true
    end

    if self.gender_class.nil? && !t.gender_class.nil?
      self.taxon_name_classifications.build(type: t.gender_class.to_s)
      fixed = true
    end

    if self.original_genus.nil? && !t.original_genus.nil?
      self.original_genus = t.original_genus
      fixed = true
    end

    if self.original_subgenus.nil? && !t.original_subgenus.nil?
      self.original_subgenus = t.original_subgenus
      fixed = true
    end

    if self.original_species.nil? && !t.original_species.nil?
      self.original_species = t.original_species
      fixed = true
    end

    if self.original_subspecies.nil? && !t.original_subspecies.nil?
      self.original_subspecies = t.original_subspecies
      fixed = true
    end

    if self.type_species.nil? && !t.type_species.nil?
      self.type_species = t.type_species
      fixed = true
    end

    if self.type_genus.nil? && !t.type_genus.nil?
      self.type_genus = t.type_genus
      fixed = true
    end

    types1 = self.get_primary_type
    types2 = t.get_primary_type
    if types1.empty? && !types2.empty?
      new_type_material = []
      types2.each do |t|
        new_type_material.push({type_type: t.type_type, protonym_id: t.protonym_id, collection_object_id: t.collection_object_id, source: t.source})
      end
      self.type_materials.build(new_type_material)
      fixed = true
    end

    sttnr = self.type_taxon_name_relationship
    tttnr = t.type_taxon_name_relationship
    unless sttnr.nil? || tttnr.nil?
      if sttnr.type != tttnr.type && sttnr.type.safe_constantize.descendants.collect{|i| i.to_s}.include?(tttnr.type.to_s)
        self.type_taxon_name_relationship.type = t.type_taxon_name_relationship.type
        fixed = true
      end
    end
  end

  if fixed
    begin
      Protonym.transaction do
        self.save
      end
    rescue
      return false
    end
  end
  return fixed
end



1188
1189
1190
1191
1192
1193
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1188

def sv_type_placement
  # type of this taxon is not included in this taxon
  if !!self.type_taxon_name
    soft_validations.add(:base, "#{self.rank_class.rank_name} #{self.cached_html} has the type #{self.type_taxon_name.rank_class.rank_name} #{self.type_taxon_name.cached_html} classified outside of this taxon") unless self.type_taxon_name.get_valid_taxon_name.ancestors.include?(TaxonName.find(self.cached_valid_taxon_name_id))
  end
end

#sv_type_placement1 ⇒ Object 



1195
1196
1197
1198
1199
1200
1201
1202
1203
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1195

def sv_type_placement1
  # this taxon is a type, but not included in nominal taxon
  if !!self.type_of_taxon_names
    self.type_of_taxon_names.each do |t|
      soft_validations.add(:base, "#{self.rank_class.rank_name.capitalize} #{self.cached_html} is the type of #{t.rank_class.rank_name} #{t.cached_html} but it has a parent outside of #{t.cached_html}",
                           success_message: 'Parent for type species was updated', failure_message: 'Parent for type species was not updated') unless self.get_valid_taxon_name.ancestors.include?(TaxonName.find(t.cached_valid_taxon_name_id))
    end
  end
end

#sv_validate_coordinated_names_author ⇒ Object 



639
640
641
642
643
644
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 639

def sv_validate_coordinated_names_author
  s = self.verbatim_author
  list_of_coordinated_names.each do |t|
    soft_validations.add(:verbatim_author, "The author does not match with the author of the coordinate #{t.rank_class.rank_name}", success_message: 'Author was updated', failure_message:  'Failed to update author') unless s == t.verbatim_author
  end
end

#sv_validate_coordinated_names_etymology ⇒ Object 



930
931
932
933
934
935
936
937
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 930

def sv_validate_coordinated_names_etymology
  return true unless is_available?
  list_of_coordinated_names.each do |t|
    if self.etymology != t.etymology
      soft_validations.add(:etymology, "The etymology does not match with the etymology of the coordinate #{t.rank_class.rank_name}", success_message: 'Etymology was updated', failure_message:  'Etymology was not updated')
    end
  end
end

#sv_validate_coordinated_names_gender ⇒ Object 



675
676
677
678
679
680
681
682
683
684
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 675

def sv_validate_coordinated_names_gender
  return true unless is_available?
  return true unless is_genus_rank?
  s = self.gender_class
  list_of_coordinated_names.each do |t|
    if s != t.gender_class
      soft_validations.add(:base, "The gender status does not match with that of the coordinate #{t.rank_class.rank_name}", success_message: 'Gender was updated', failure_message:  'Failed to update gender')
    end
  end
end

#sv_validate_coordinated_names_original_form ⇒ Object 



868
869
870
871
872
873
874
875
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 868

def sv_validate_coordinated_names_original_form
  return true if !is_species_rank? || has_misspelling_relationship?
  list_of_coordinated_names.each do |t|
    if self.original_form.try(:name) != t.original_form.try(:name)
      soft_validations.add(:base, "The original form does not match with the original form of coordinate #{t.rank_class.rank_name}", success_message: 'Original form was updated', failure_message:  'Failed to update original form')
    end
  end
end

#sv_validate_coordinated_names_original_genus ⇒ Object 



718
719
720
721
722
723
724
725
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 718

def sv_validate_coordinated_names_original_genus
  return true if !is_genus_or_species_rank? || !is_valid?
  list_of_coordinated_names.each do |t|
    if self.original_genus.try(:name) != t.original_genus.try(:name)
      soft_validations.add(:base, "The original genus does not match with the original genus of coordinate #{t.rank_class.rank_name}", success_message: 'Original genus was updated', failure_message:  'Failed to update original genus')
    end
  end
end

#sv_validate_coordinated_names_original_species ⇒ Object 



778
779
780
781
782
783
784
785
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 778

def sv_validate_coordinated_names_original_species
  return true if !is_species_rank? || has_misspelling_relationship?
  list_of_coordinated_names.each do |t|
    if self.original_species.try(:name) != t.original_species.try(:name)
      soft_validations.add(:base, "The original species does not match with the original species of coordinate #{t.rank_class.rank_name}", success_message: 'Original species was updated', failure_message:  'Failed to update original species')
    end
  end
end

#sv_validate_coordinated_names_original_subgenus ⇒ Object 



748
749
750
751
752
753
754
755
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 748

def sv_validate_coordinated_names_original_subgenus
  return true if !is_genus_or_species_rank? || has_misspelling_relationship?
  list_of_coordinated_names.each do |t|
    if self.original_subgenus.try(:name) != t.original_subgenus.try(:name)
      soft_validations.add(:base, "The original subgenus does not match with the original subgenus of coordinate #{t.rank_class.rank_name}", success_message: 'Original subgenus was updated', failure_message:  'Failed to update original subgenus')
    end
  end
end

#sv_validate_coordinated_names_original_subspecies ⇒ Object 



808
809
810
811
812
813
814
815
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 808

def sv_validate_coordinated_names_original_subspecies
  return true if !is_species_rank? || has_misspelling_relationship?
  list_of_coordinated_names.each do |t|
    if self.original_subspecies.try(:name) != t.original_subspecies.try(:name)
      soft_validations.add(:base, "The original subspecies does not match with the original subspecies of coordinate #{t.rank_class.rank_name}", success_message: 'Original subspecies was updated', failure_message:  'Failed to update original subspecies')
    end
  end
end

#sv_validate_coordinated_names_original_variety ⇒ Object 



838
839
840
841
842
843
844
845
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 838

def sv_validate_coordinated_names_original_variety
  return true if !is_species_rank? || has_misspelling_relationship?
  list_of_coordinated_names.each do |t|
    if self.original_variety.try(:name) != t.original_variety.try(:name)
      soft_validations.add(:base, "The original variety does not match with the original variety of coordinate #{t.rank_class.rank_name}", success_message: 'Original variety was updated', failure_message:  'Failed to update original variety')
    end
  end
end

#sv_validate_coordinated_names_page ⇒ Object 



607
608
609
610
611
612
613
614
615
616
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 607

def sv_validate_coordinated_names_page
  return true unless is_valid?
  s = self.origin_citation
  list_of_coordinated_names.each do |t|
    ts = t.origin_citation
    if s && ts && s.source_id == ts.source_id && (s.pages != ts.pages || (s.pages.nil? && !ts.pages.nil?))
      soft_validations.add(:base, "The original publication page does not match with the original publication page of the coordinate #{t.rank_class.rank_name}", success_message: 'Original publication pages were updated', failure_message: 'Original publication pages were not updated')
    end
  end
end

#sv_validate_coordinated_names_part_of_speech ⇒ Object 



697
698
699
700
701
702
703
704
705
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 697

def sv_validate_coordinated_names_part_of_speech
  return true unless is_available?
  return true unless is_species_rank?
  list_of_coordinated_names.each do |t|
    if self.part_of_speech_class != t.part_of_speech_class
      soft_validations.add(:base, "The part of speech status does not match with that of the coordinate #{t.rank_class.rank_name}", success_message: 'Part of speech was updated', failure_message:  'Failed to update part of speech')
    end
  end
end

#sv_validate_coordinated_names_roles ⇒ Object 



960
961
962
963
964
965
966
967
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 960

def sv_validate_coordinated_names_roles
  return true unless is_valid?
  list_of_coordinated_names.each do |t|
    if self.taxon_name_author_roles.collect{|i| i.person_id} != t.taxon_name_author_roles.collect{|i| i.person_id}
      soft_validations.add(:base, "The author roles do not match with the author roles of the coordinate #{t.rank_class.rank_name}", success_message: 'Author roles were updated', failure_message:  'Author roles were not updated')
    end
  end
end

#sv_validate_coordinated_names_source ⇒ Object

def sv_validate_coordinated_names

  return true unless is_available?
  r = self.iczn_set_as_incorrect_original_spelling_of_relationship
  list_of_coordinated_names.each do |t|
    soft_validations.add(:base, "The original publication does not match with the original publication of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Original publication was updated') if self.source && t.source && self.source.id != t.source.id
    soft_validations.add(:verbatim_author, "The author does not match with the author of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Author was updated') unless self.verbatim_author == t.verbatim_author
    soft_validations.add(:year_of_publication, "The year of publication does not match with the year of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Year was updated') unless self.year_of_publication == t.year_of_publication
    soft_validations.add(:base, "The gender status does not match with the gender of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Gender was updated') if rank_string =~ /Genus/ && self.gender_class != t.gender_class && !has_misspelling_relationship?
    soft_validations.add(:base, "The part of speech status does not match with the part of speech of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Gender was updated') if rank_string =~ /Species/ && self.part_of_speech_class != t.part_of_speech_class && !has_misspelling_relationship?
    soft_validations.add(:base, "The original genus does not match with the original genus of coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Original genus was updated') if self.original_genus != t.original_genus && r.blank?
    soft_validations.add(:base, "The original subgenus does not match with the original subgenus of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Original subgenus was updated') if self.original_subgenus != t.original_subgenus && r.blank?
    soft_validations.add(:base, "The original species does not match with the original species of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Original species was updated') if self.original_species != t.original_species && r.blank?
    soft_validations.add(:base, "The type species does not match with the type species of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Type species was updated') if self.type_species != t.type_species && !has_misspelling_relationship?
    soft_validations.add(:base, "The type genus does not match with the type genus of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Type genus was updated') if self.type_genus != t.type_genus && !has_misspelling_relationship?
    soft_validations.add(:base, "The type specimen does not match with the type specimen of the coordinated #{t.rank_class.rank_name}",
                         fix: :sv_fix_coordinated_names, success_message: 'Type specimen was updated') if !self.has_same_primary_type(t) && !has_misspelling_relationship?
    sttnr = self.type_taxon_name_relationship
    tttnr = t.type_taxon_name_relationship
    unless sttnr.nil? || tttnr.nil?
      soft_validations.add(:base, "The type species relationship does not match with the type species relationship of the coordinated #{t.rank_class.rank_name}",
                           fix: :sv_fix_coordinated_names, success_message: 'Type species relationship was updated') unless sttnr.type == tttnr.type
    end
  end
end



573
574
575
576
577
578
579
580
581
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 573

def sv_validate_coordinated_names_source
  return true unless is_valid?
  s = self.source
  list_of_coordinated_names.each do |t|
    if ((s && t.source && s.id != t.source.id) || (s.nil? && t.source))
      soft_validations.add(:base, "The original publication does not match with the original publication of the coordinate #{t.rank_class.rank_name}", success_message: 'Original publication was updated', failure_message:  'Failed to update original publication')
    end
  end
end

#sv_validate_coordinated_names_type_genus ⇒ Object 



1017
1018
1019
1020
1021
1022
1023
1024
1025
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1017

def sv_validate_coordinated_names_type_genus
  return true unless is_valid?
  return true unless is_family_rank?
  list_of_coordinated_names.each do |t|
    if self.type_genus != t.type_genus
      soft_validations.add(:base, "The type genus does not match with the type genus of the coordinate #{t.rank_class.rank_name}", success_message: 'Type genus was updated', failure_message:  'Failed to update type genus')
    end
  end
end

#sv_validate_coordinated_names_type_species ⇒ Object 



898
899
900
901
902
903
904
905
906
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 898

def sv_validate_coordinated_names_type_species
  return true unless is_valid?
  return true unless is_genus_rank?
  list_of_coordinated_names.each do |t|
    if self.type_species != t.type_species
      soft_validations.add(:base, "The type species does not match with the type species of the coordinate #{t.rank_class.rank_name}", success_message: 'Type species was updated', failure_message:  'Failed to update type species')
    end
  end
end

#sv_validate_coordinated_names_type_species_type ⇒ Object 



982
983
984
985
986
987
988
989
990
991
992
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 982

def sv_validate_coordinated_names_type_species_type
  return true unless is_genus_rank?
  sttnr = self.type_taxon_name_relationship
  return true if sttnr.nil?
  list_of_coordinated_names.each do |t|
    tttnr = t.type_taxon_name_relationship
    if !tttnr.nil? && sttnr.type != tttnr.type
      soft_validations.add(:base, "The type species relationship does not match with the type species relationship of the coordinate #{t.rank_class.rank_name}", success_message: 'Type species relationship was updated', failure_message:  'Failed to update type species relationship')
    end
  end
end

#sv_validate_coordinated_names_type_specimen ⇒ Object 



1048
1049
1050
1051
1052
1053
1054
1055
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1048

def sv_validate_coordinated_names_type_specimen
  return true if !is_species_rank? || !is_valid?
  list_of_coordinated_names.each do |t|
    if !self.has_same_primary_type(t)
      soft_validations.add(:base, "The type specimen does not match with the type specimen of the coordinate #{t.rank_class.rank_name}", success_message: 'Type specimen was updated', failure_message:  'Failed to update type specimen')
    end
  end
end

#sv_validate_coordinated_names_year ⇒ Object 



657
658
659
660
661
662
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 657

def sv_validate_coordinated_names_year
  s = self.year_of_publication
  list_of_coordinated_names.each do |t|
    soft_validations.add(:year_of_publication, "The year of publication does not match with the year of the coordinate #{t.rank_class.rank_name}", success_message: 'Year was updated', failure_message:  'Failed to update year') unless s == t.year_of_publication
  end
end

#sv_validate_name ⇒ Object 



392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 392

def sv_validate_name
  correct_name_format = false

  if rank_class
    # TODO: name these Regexp somewhere
    # TODO: move pertinent checks to base of nomenclature Classes to manage them there
    if (name =~ /^[a-zA-Z]*$/) || # !! should reference NOT_LATIN
        (nomenclatural_code == :iczn && name =~ /^[a-zA-Z]-[a-zA-Z]*$/) ||
        (nomenclatural_code == :icnp && name =~ /^[a-zA-Z]-[a-zA-Z]*$/) ||
        (nomenclatural_code == :icn && name =~  /^[a-zA-Z]*-[a-zA-Z]*$/) ||
        (nomenclatural_code == :icn && name =~  /^[a-zA-Z]*\s×\s[a-zA-Z]*$/) ||
        (nomenclatural_code == :icn && name =~  /^[a-zA-Z]*\s×[a-zA-Z]*$/) ||
        (nomenclatural_code == :icn && name =~  /^×[a-zA-Z]*$/) ||
        (nomenclatural_code == :icvcn)
      correct_name_format = true
    end

    unless correct_name_format
      icvcn_species = (nomenclatural_code == :icvcn && self.rank_string =~ /Species/) ? true : nil
      if is_available? && icvcn_species.nil?
        soft_validations.add(:name, 'Name should not have spaces or special characters, unless it has a status of misspelling or original misspelling')
      end
    end
  end
end

#sv_validate_parent_rank ⇒ Object 



418
419
420
421
422
423
424
425
426
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 418

def sv_validate_parent_rank
  if self.rank_class && self.id == self.cached_valid_taxon_name_id
    if rank_string == 'NomenclaturalRank' || self.parent&.rank_string == 'NomenclaturalRank' || !!self.iczn_uncertain_placement_relationship
      true
    elsif !self.rank_class&.valid_parents.include?(self.parent&.rank_string)
      soft_validations.add(:rank_class, "The rank #{self.rank_class&.rank_name} is not compatible with the rank of parent (#{self.parent&.rank_class&.rank_name}). The name should be marked as 'Incertae sedis'")
    end
  end
end

#sv_year_is_not_required ⇒ Object 



1549
1550
1551
1552
1553
1554
1555
1556
 
# File 'app/models/protonym/soft_validation_extensions.rb', line 1549

def sv_year_is_not_required
  if !self.year_of_publication.nil? && self.source && self.year_of_publication == self.source.year
    soft_validations.add(
      :year_of_publication, 'Year of publication is not required, it is derived from the source',
      success_message: 'Year was deleted',
      failure_message: 'Failed to delete year')
  end
end