Class: TaxonNameRelationship

Inherits:
ApplicationRecord show all
Includes:
Housekeeping, Shared::Citations, Shared::IsData, Shared::Notes, SoftValidation
Defined in:
app/models/taxon_name_relationship.rb

Overview

TODO:

SourceClassifiedAs is not really Combination in the other sense

TODO:

validate, that all the relationships in the table could be linked to relationships in classes (if those had changed)

TODO:

Check if more than one species associated with the genus in the original paper

A NOMEN github.com/SpeciesFileGroup/nomen relationship between two Protonyms.

Unless otherwise noted relationships read left to right, and can be interpreted by inserting “of” after the class name.

For example the triple:

Subject: Aus aus - TaxonNameRelationship::Iczn::Invalidating::Synonym - Object: Bus bus

Can be read as:

  aus synonym OF bus

Note that not all relationships are reflective.  We can't say, for the example above we can't say

  bus valid_name OF aus

Note that we can not say that all names that are subjects are valid, this is determined on a case by case basis.

TaxonNameRelationships have a domain (attributes on the subject) and range (attributes on the object). So if you use a relationship you may be asserting a TaxonNameClassification also exists for the subject or object.

Defined Under Namespace

Classes: Combination, Hybrid, Icn, Icnp, Icvcn, Iczn, OriginalCombination, SourceClassifiedAs, Typification

Constant Summary

Constants included from SoftValidation

SoftValidation::ANCESTORS_WITH_SOFT_VALIDATIONS

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from SoftValidation

#clear_soft_validations, #fix_soft_validations, #soft_fixed?, #soft_valid?, #soft_validate, #soft_validated?, #soft_validations

Methods included from Shared::IsData

#errors_excepting, #full_error_messages_excepting, #identical, #is_community?, #is_destroyable?, #is_editable?, #is_in_use?, #is_in_users_projects?, #metamorphosize, #similar

Methods included from Shared::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::Citations

#cited?, #mark_citations_for_destruction, #origin_citation_source_id, #reject_citations, #requires_citation?, #sources_by_topic_id

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Attribute Details

#no_cachedBoolean?

Returns When true, cached values are not built.

Returns:

  • (Boolean, nil)

    When true, cached values are not built


53
54
55
# File 'app/models/taxon_name_relationship.rb', line 53

def no_cached
  @no_cached
end

#object_taxon_name_idInteger

Returns the object taxon name.

Returns:

  • (Integer)

    the object taxon name


44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
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
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
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
481
482
483
484
485
486
487
488
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
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
# File 'app/models/taxon_name_relationship.rb', line 44

class TaxonNameRelationship < ApplicationRecord
  include Housekeeping
  include Shared::Citations
  include Shared::Notes
  include Shared::IsData
  include SoftValidation

  # @return [Boolean, nil]
  #   When true, cached values are not built
  attr_accessor :no_cached

  belongs_to :subject_taxon_name, class_name: 'TaxonName', foreign_key: :subject_taxon_name_id, inverse_of: :taxon_name_relationships # left side
  belongs_to :object_taxon_name, class_name: 'TaxonName', foreign_key: :object_taxon_name_id, inverse_of: :related_taxon_name_relationships # right side

  after_save :set_cached_names_for_taxon_names, unless: -> {self.no_cached}
  after_destroy :set_cached_names_for_taxon_names, unless: -> {self.no_cached}

  validates_presence_of :type, message: 'Relationship type should be specified'
  validates_presence_of :subject_taxon_name, message: 'Missing taxon name on the left side'
  validates_presence_of :object_taxon_name, message: 'Missing taxon name on the right side'

  validates_uniqueness_of :object_taxon_name_id, scope: :type, if: :is_combination?
  validates_uniqueness_of :object_taxon_name_id, scope: [:type, :subject_taxon_name_id], unless: :is_combination?

  validate :validate_type, :validate_subject_and_object_are_not_identical

  validate :subject_and_object_in_same_project

  with_options unless: -> {!subject_taxon_name || !object_taxon_name} do |v|
    v.validate :validate_subject_and_object_share_code,
      :validate_uniqueness_of_typification_object,
      #:validate_uniqueness_of_synonym_subject,
      :validate_object_and_subject_both_protonyms,
      :validate_object_must_equal_subject_for_uncertain_placement,
      :validate_subject_and_object_ranks,
      :validate_rank_group
  end

  soft_validate(:sv_validate_required_relationships, set: :validate_required_relationships, has_fix: false)
  soft_validate(:sv_validate_disjoint_relationships, set: :validate_disjoint_relationships, has_fix: false)
  soft_validate(:sv_validate_disjoint_object, set: :validate_disjoint_object, has_fix: false)
  soft_validate(:sv_validate_disjoint_subject, set: :validate_disjoint_subject, has_fix: false)
  soft_validate(:sv_specific_relationship, set: :specific_relationship, has_fix: false) # some do, some don't
  soft_validate(:sv_objective_synonym_relationship, set: :objective_synonym_relationship, has_fix: false)
  soft_validate(:sv_synonym_relationship, set: :synonym_relationship, has_fix: false)
  soft_validate(:sv_not_specific_relationship, set: :not_specific_relationship, has_fix: true)
  soft_validate(:sv_synonym_linked_to_valid_name, set: :synonym_linked_to_valid_name, has_fix: true)
  soft_validate(:sv_validate_priority, set: :validate_priority, has_fix: false)
  soft_validate(:sv_coordinated_taxa, set: :coordinated_taxa, has_fix: true)
  soft_validate(:sv_coordinated_taxa_object, set: :coordinated_taxa, has_fix: true)

  scope :where_subject_is_taxon_name, -> (taxon_name) {where(subject_taxon_name_id: taxon_name)}
  scope :where_object_is_taxon_name, -> (taxon_name) {where(object_taxon_name_id: taxon_name)}
  scope :where_object_in_taxon_names, -> (taxon_name_array) {where('"taxon_name_relationships"."object_taxon_name_id" IN (?)', taxon_name_array)}

  scope :with_type_string, -> (type_string) { where(sanitize_sql_array(["taxon_name_relationships.type = '%s'", type_string])) }

  scope :with_type_base, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "#{base_string}%")}
  scope :with_type_contains, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "%#{base_string}%")}

  scope :with_two_type_bases, -> (base_string1, base_string2) {
    where("taxon_name_relationships.type LIKE ? OR taxon_name_relationships.type LIKE ?", "#{base_string1}%", "#{base_string2}%") }

  scope :homonym_or_suppressed, -> {where("taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Homonym%' OR taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Suppression::Total'") }
  scope :with_type_array, -> (base_array) {where('taxon_name_relationships.type IN (?)', base_array ) }

  # @return [Array of TaxonNameClassification]
  #  the inferable TaxonNameClassification(s) added to the subject when this relationship is used
  #  !! Not implemented
  def subject_properties
    []
  end

  # @return [Array of TaxonNameClassification]
  #  the inferable TaxonNameClassification(s) added to the subject when this relationship is used
  #  !! Not implmented
  def object_properties
    []
  end

  # @return class
  #   this method calls Module#module_parent
  def self.parent
    self.module_parent
  end

  # @return [Array of NomenclatureRank]
  #   the valid ranks to which the subject name can belong, set in subclasses. (left side)
  def self.valid_subject_ranks
    []
  end

  # @return [Array of NomenclatureRank]
  #   the valid ranks to which the object name can belong, set in subclasses. (right side)
  def self.valid_object_ranks
    []
  end

  # @return [Array of TaxonNameRelationships]
  #   if this relationships is set for the subject, then others in this array should not be used for that subject
  def self.disjoint_taxon_name_relationships
    []
  end

  # TODO: why isn't this disjoint?
  # disjoint relationships for the taxon as a object
  def self.required_taxon_name_relationships
    []
  end

  def self.disjoint_subject_classes
    []
  end

  def self.disjoint_object_classes
    []
  end

  def self.gbif_status_of_subject
    nil
  end

  def self.gbif_status_of_object
    nil
  end

  def self.assignable
    false
  end

  # @return [Symbol]
  #   determine the relative age of subject and object
  #   :direct - subject is younger than object
  #   :reverse - object is younger than subject
  def self.nomenclatural_priority
    nil
  end

  # @return [String]
  #    the status inferred by the relationship to the object name
  def object_status
    self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
  end

  # @return [String]
  #    the status inferred by the relationship to the subject name
  def subject_status
    self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
  end

  # @return [String]
  #    the connecting word in the relationship from the subject name to object name
  def subject_status_connector_to_object
    ' of'
  end

  # @return [String]
  #    the connecting word in the relationship from the object name to subject name
  def object_status_connector_to_subject
    ' of'
  end

  # @return [String]
  #   a readable fragement combining status and connector
  def subject_status_tag
    subject_status + subject_status_connector_to_object
  end

  # @return [String]
  #   a readable fragement combining status and connector
  def object_status_tag
    object_status + object_status_connector_to_subject
  end

  # @return [String, nil]
  #   the type of this relationship, IF the type is a valid name, else nil
  def type_name
    r = self.type
    TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r : nil
  end

  def type_class=(value)
    write_attribute(:type, value.to_s)
  end

  # @return [TaxonNameRelationship, String]
  #    the type as a class, if legal, else a string  ! Strangeish
  def type_class
    r = read_attribute(:type).to_s
    TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r.safe_constantize : r
  end

  # @return [String, nil]
  #   the NOMEN uri for this type
  def self.nomen_uri
    const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil
  end

  # @return [Time]
  #   effective date of publication, used to determine nomenclatural priorities
  def nomenclature_date
    self.source ? (self.source.cached_nomenclature_date ? self.source.cached_nomenclature_date.to_time : Time.now) : Time.now
  end

  # @TODO SourceClassifiedAs is not really Combination in the other sense
  def is_combination?
    !!/TaxonNameRelationship::(OriginalCombination|Combination)/.match(self.type.to_s)
  end

  protected

  def subject_and_object_in_same_project
    if subject_taxon_name && object_taxon_name
      errors.add(:base, 'one name is not in the same project as the other') if subject_taxon_name.project_id != object_taxon_name.project_id
    end
  end

  def validate_type
    unless TAXON_NAME_RELATIONSHIP_NAMES.include?(type)
      errors.add(:type, "'#{type}' is not a valid taxon name relationship")
    end

    if object_taxon_name.class.to_s == 'Protonym' || object_taxon_name.class.to_s == 'Hybrid'
      errors.add(:type, "'#{type}' is not a valid taxon name relationship") if /TaxonNameRelationship::Combination::/.match(self.type)
    end

    if object_taxon_name.class.to_s == 'Combination'
      errors.add(:type, "'#{type}' is not a valid taxon name relationship") unless /TaxonNameRelationship::Combination::/.match(self.type)
    end
  end

  # @todo validate, that all the relationships in the table could be linked to relationships in classes (if those had changed)

  def validate_subject_and_object_share_code
    if object_taxon_name.type  == 'Protonym' && subject_taxon_name.type == 'Protonym'
      errors.add(:object_taxon_name_id, 'The related taxon is not in the same monenclatural group (ICZN, ICN, ICNP, ICTV') if subject_taxon_name.rank_class.try(:nomenclatural_code) != object_taxon_name.rank_class.try(:nomenclatural_code)
    end
  end

  def validate_subject_and_object_are_not_identical
    if !self.object_taxon_name_id.nil? && self.object_taxon_name == self.subject_taxon_name
      errors.add(:object_taxon_name_id, "#{self.object_taxon_name.try(:cached_html).to_s} should not refer to itself") unless self.type =~ /OriginalCombination/
    end
  end

  def validate_object_must_equal_subject_for_uncertain_placement
    if self.object_taxon_name_id != self.subject_taxon_name.parent_id && self.type_name == 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      errors.add(:object_taxon_name_id, "The parent #{self.subject_taxon_name.parent.cached_html} and the Incertae Sedis placement (#{self.object_taxon_name.cached_html}) should match")
    end
  end

  def validate_subject_and_object_ranks
    tname = self.type_name

    if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      rank_group = self.subject_taxon_name.rank_class.try(:parent)
      unless rank_group == self.object_taxon_name.rank_class.try(:parent)
        errors.add(:object_taxon_name_id, "Rank of related taxon should be in the #{rank_group.try(:rank_name)} rank group, not #{self.object_taxon_name.rank_class.try(:rank_name)}")
      end
    end

    unless self.type_class.blank? # only validate if it is set
      if object_taxon_name
        if object_taxon_name.type == 'Protonym' || object_taxon_name.type == 'Hybrid'
          unless self.type_class.valid_object_ranks.include?(self.object_taxon_name.rank_string)
            errors.add(:object_taxon_name_id, "#{self.object_taxon_name.rank_class.rank_name.capitalize} rank of #{self.object_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
            errors.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.object_taxon_name.rank_class.rank_name} rank of #{self.object_taxon_name.cached_html}")
          end
        end
      end

      if subject_taxon_name
        if subject_taxon_name.type == 'Protonym' || subject_taxon_name.type == 'Hybrid'
          unless self.type_class.valid_subject_ranks.include?(self.subject_taxon_name.parent.rank_string)
            soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
            soft_validations.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.subject_taxon_name.rank_class.rank_name} rank of #{self.subject_taxon_name.cached_html}")
          end
        end
      end
    end
  end

  ##### Protonym historically could be listed as a synonym to different taxa
  #def validate_uniqueness_of_synonym_subject 
  #  if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains('Synonym').not_self(self).empty?
  #    errors.add(:subject_taxon_name_id, 'Only one synonym relationship is allowed')
  #  end
  #end

  def validate_uniqueness_of_typification_object
    if /Typification/.match(self.type_name) && !TaxonNameRelationship.where(object_taxon_name_id: self.object_taxon_name_id).with_type_contains('Typification').not_self(self).empty?
      errors.add(:object_taxon_name_id, 'Only one Type designation relationship is allowed')
    end
  end

  def validate_rank_group
    if self.type =~ /Hybrid/ && self.subject_taxon_name && self.object_taxon_name
      if self.subject_taxon_name.rank_class.parent != self.object_taxon_name.rank_class.parent
        errors.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the rank of hybrid (#{self.object_taxon_name.rank_class.rank_name})")
      end
    end
  end

  def validate_object_and_subject_both_protonyms
    if /TaxonNameRelationship::Combination::/.match(self.type)
      errors.add(:object_taxon_name_id, 'Not a Combination') if object_taxon_name.type != 'Combination'
    else
      errors.add(:object_taxon_name_id, 'Not a Protonym') if object_taxon_name.type == 'Combination'
    end
    errors.add(:subject_taxon_name_id, 'Not a Protonym') if subject_taxon_name.type == 'Combination'
  end

  # TODO: Isolate to individual classes per type
  def set_cached_names_for_taxon_names
    begin
      TaxonName.transaction do
        if is_combination?
          t = object_taxon_name

          t.send(:set_cached)

          if type_name =~/OriginalCombination/ 
            t.update_columns(
              cached_original_combination: t.get_original_combination,
              cached_original_combination_html: t.get_original_combination_html,
            )
          end

        elsif type_name =~/TaxonNameRelationship::Hybrid/ # TODO: move to Hybrid
          t = object_taxon_name
          t.update_columns(
            cached: t.get_full_name,
            cached_html: t.get_full_name_html
          )

        elsif type_name =~/SourceClassifiedAs/
          t = subject_taxon_name
          t.set_cached_classified_as
          # t.update_column(:cached_classified_as, t.get_cached_classified_as)

        elsif is_invalidating?
          t = subject_taxon_name
          
          if type_name =~/Misspelling/
            t.update_column(:cached_misspelling, t.get_cached_misspelling)
            t.update_columns(
                cached_author_year: t.get_author_and_year,
                cached_original_combination: t.get_original_combination,
                cached_original_combination_html: t.get_original_combination_html
            )
          end

          if type_name =~/Misapplication/
            t.update_column( :cached_author_year, t.get_author_and_year)
          end

          vn = t.get_valid_taxon_name

          t.update_columns(
            cached: t.get_full_name,
            cached_html: t.get_full_name_html, # OK to force reload here, otherwise we need an exception in #set_cached 
            cached_valid_taxon_name_id: vn.id)
          t.combination_list_self.each do |c|
            c.update_column(:cached_valid_taxon_name_id, vn.id)
          end

          vn.list_of_invalid_taxon_names.each do |s|
            s.update_column(:cached_valid_taxon_name_id, vn.id)
            s.combination_list_self.each do |c|
              c.update_column(:cached_valid_taxon_name_id, vn.id)
            end
          end
        end

      end

    # no point in rescuing and not returning somthing
    rescue ActiveRecord::RecordInvalid
      raise
    end
    false
  end

  def is_invalidating?
    TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(type_name)
  end

  def sv_validate_required_relationships
    object_relationships = TaxonNameRelationship.where_object_is_taxon_name(self.object_taxon_name).not_self(self).collect{|r| r.type}
    required = self.type_class.required_taxon_name_relationships - object_relationships
    required.each do |r|
      soft_validations.add(:type, " Presence of #{self.subject_status} requires selection of #{r.demodulize.underscore.humanize.downcase}")
    end
  end

  def sv_validate_disjoint_relationships
    tname = self.type_name
    if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      subject_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).not_self(self)
      subject_relationships.each  do |i|
        if self.type_class.disjoint_taxon_name_relationships.include?(i.type_name)
          soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with another relationship: '#{i.subject_status}'")
        end
      end
    end
  end

  def sv_validate_disjoint_object
    classifications = self.object_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
    disjoint_object_classes = self.type_class.disjoint_object_classes
    compare = disjoint_object_classes & classifications
    compare.each do |i|
      c = i.demodulize.underscore.humanize.downcase
      soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with the taxon status: '#{c}'")
      soft_validations.add(:object_taxon_name_id, "#{self.object_taxon_name.cached_html} has a conflicting status: '#{c}'")
    end
  end

  def sv_validate_disjoint_subject
    classifications = self.subject_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
    disjoint_subject_classes = self.type_class.disjoint_subject_classes
    compare = disjoint_subject_classes & classifications
    compare.each do |i|
      c = i.demodulize.underscore.humanize.downcase
      soft_validations.add(:type, "#{self.subject_status.capitalize} conflicting with the status: '#{c}'")
      soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.cached_html} has a conflicting status: '#{c}'")
    end
  end

  def sv_specific_relationship
    true # all validations moved to subclasses

#    s = subject_taxon_name
#    o = object_taxon_name
#    case type
#      when 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Subjective' || 'TaxonNameRelationship::Icn::Unaccepting::Synonym::Heterotypic'
#        if (s.type_taxon_name == o.type_taxon_name && !s.type_taxon_name.nil? ) || (!s.get_primary_type.empty? && s.has_same_primary_type(o) )
#          soft_validations.add(:type, "Subjective synonyms #{s.cached_html} and #{o.cached_html} should not have the same type")
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym'
#        # primary names don't match
#        if (s.cached_primary_homonym_alternative_spelling != o.cached_primary_homonym_alternative_spelling)
#          # there is a secondary name ... and it doesn't match either
#          if (s.cached_secondary_homonym_alternative_spelling.blank? && o.cached_secondary_homonym_alternative_spelling.blank?) || (s.cached_secondary_homonym_alternative_spelling != o.cached_secondary_homonym_alternative_spelling)
#            soft_validations.add(:type, "#{subject_taxon_name.cached_html_name_and_author_year} and #{object_taxon_name.cached_html_name_and_author_year} are not similar enough to be homonyms")
#          end
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary' || 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary::Forgotten' || 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary::Suppressed'
#        if s.original_genus != o.original_genus
#          soft_validations.add(:type, "Primary homonyms #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} should have the same original genus")
#        elsif s.cached_primary_homonym_alternative_spelling != o.cached_primary_homonym_alternative_spelling
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} are not similar enough to be homonyms")
#        end
#        if type == 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary::Forgotten' && s.year_of_publication > 1899
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} was not described after 1899")
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Secondary'
#        if s.original_genus == o.original_genus && !s.original_genus.nil?
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} species described in the same original genus #{s.original_genus}, they are primary homonyms")
#        elsif s.get_valid_taxon_name.ancestor_at_rank('genus') != o.get_valid_taxon_name.ancestor_at_rank('genus')
#          soft_validations.add(:type, "Secondary homonyms #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} should be placed in the same parent genus, the homonymy should be deleted or changed to 'secondary homonym replaced before 1961'")
#        elsif s.cached_secondary_homonym_alternative_spelling != o.cached_secondary_homonym_alternative_spelling
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} are not similar enough to be homonyms")
#        end

#        if (s.all_generic_placements & o.all_generic_placements).empty?
#          soft_validations.add(:base, "No combination available showing #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} placed in the same genus")
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Secondary::Secondary1961'
#        soft_validations.add(:type, "#{s.cached_html_name_and_author_year} was not described before 1961") if s.year_of_publication > 1960
#        soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} described in the same original genus #{s.original_genus}, they are primary homonyms") if s.original_genus == o.original_genus && !s.original_genus.nil?
#        soft_validations.add(:base, 'The original publication is not selected') unless source

#        soft_validations.add(:base, "#{s.cached_html_name_and_author_year} should not be treated as a homonym established before 1961") if self.source && self.source.year > 1960

#        if (s.all_generic_placements & o.all_generic_placements).empty?
#          soft_validations.add(:base, "No combination available showing #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} placed in the same genus")
#        end
#      when 'TaxonNameRelationship::Iczn::PotentiallyValidating::FamilyBefore1961'
#        soft_validations.add(:type, "#{s.cached_html_name_and_author_year} was not described before 1961") if s.year_of_publication > 1960
#        soft_validations.add(:base, "#{s.cached_html_name_and_author_year} should be accepted as a replacement name before 1961") if self.source && self.source.year > 1960
#      when 'TaxonNameRelationship::Typification::Genus::Subsequent::SubsequentDesignation'
#        soft_validations.add(:type, "Genus #{o.cached_html_name_and_author_year} described after 1930 is nomen nudum, if type was not designated in the original publication") if o.year_of_publication && o.year_of_publication > 1930
#      when 'TaxonNameRelationship::Iczn::PotentiallyValidating::ReplacementName'
#        r1 = TaxonNameRelationship.where(type: 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Objective::ReplacedHomonym', subject_taxon_name_id: o.id, object_taxon_name_id: s.id).first
#        r2 = TaxonNameRelationship.where(type: 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Objective::UnnecessaryReplacementName', subject_taxon_name_id: s.id, object_taxon_name_id: o.id).first
#        soft_validations.add(:base, "Missing relationship: #{s.cached_html_name_and_author_year} is a replacement name for #{o.cached_html_name_and_author_year}. Please add an objective synonym relationship (either 'replaced homonym' or 'unnecessary replacement name')") if r1.nil? && r2.nil?
#      when 'TaxonNameRelationship::Typification::Genus::Original::OriginalMonotypy'
#        # @todo Check if more than one species associated with the genus in the original paper
#    end
  end

  def sv_objective_synonym_relationship
    true # all validations moved to subclasses
#    if self.type_name =~ /TaxonNameRelationship::(Iczn::Invalidating::Synonym::Objective|Icn::Unaccepting::Synonym::Homotypic|Icnp::Unaccepting::Synonym::Homotypic)/
#      s = self.subject_taxon_name
#      o = self.object_taxon_name
#      if (s.type_taxon_name != o.type_taxon_name ) || !s.has_same_primary_type(o)
#        soft_validations.add(:type, "Objective synonyms #{s.cached_html} and #{o.cached_html} should have the same type")
#      end
#    end
  end

  def sv_synonym_relationship
    true # all validations moved to subclasses
#    relationships = TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM +
#      TaxonNameRelationship.collect_to_s(TaxonNameRelationship::Typification::Genus::Subsequent::SubsequentDesignation,
#                                         TaxonNameRelationship::Typification::Genus::Subsequent::RulingByCommission)
#    if relationships.include?(self.type_name)
#      if self.source
#        date1 = self.source.cached_nomenclature_date.to_time
#        date2 = self.subject_taxon_name.nomenclature_date
#        if !!date1 && !!date2
#          soft_validations.add(:base, "#{self.subject_taxon_name.cached_html_name_and_author_year} was not described at the time of citation (#{date1}") if date2 > date1
#        end
#      elsif TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING.include?(self.type_name)
#        # misspelling does not requere original publication
#      else
#        soft_validations.add(:base, 'The original publication is not selected')
#      end
#    end
  end

  def sv_not_specific_relationship
    true # all validations moved to subclasses

#    case self.type_name
#      when 'TaxonNameRelationship::Typification::Genus'
#        soft_validations.add(:type, 'Please specify if the type designation is original or subsequent')
#      when 'TaxonNameRelationship::Typification::Genus::Original'
#        soft_validations.add(:type, 'Please specify if this is Original Designation or Original Monotypy')
#      when 'TaxonNameRelationship::Typification::Genus::Subsequent'
#        soft_validations.add(:type, 'Please specify if this is Subsequent Designation or Subsequent Monotypy')
#      when 'TaxonNameRelationship::Typification::Genus::Tautonomy'
#        soft_validations.add(:type, 'Please specify if the tautonomy is absolute or Linnaean')
#      when 'TaxonNameRelationship::Icn::Unaccepting'
#        soft_validations.add(:type, 'Please specify the reasons for the name being Unaccepted')
#      when 'TaxonNameRelationship::Icn::Unaccepting::Synonym'
#        soft_validations.add(:type, 'Please specify if this is a homotypic or heterotypic synonym',
#          fix: :sv_fix_specify_synonymy_type, success_message: 'Synonym updated to being homotypic or heterotypic')
#      when 'TaxonNameRelationship::Icnp::Unaccepting::Synonym'
#        soft_validations.add(:type, 'Please specify if this is a objective or subjective synonym',
#          fix: :sv_fix_specify_synonymy_type, success_message: 'Synonym updated to being objective or subjective')
#      when 'TaxonNameRelationship::Iczn::Invalidating'
#        soft_validations.add(:type, 'Please specify the reason for the name being Invalid') unless self.subject_taxon_name.classification_invalid_or_unavailable?
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym'
#        if NomenclaturalRank::Iczn::SpeciesGroup.descendants.collect{|t| t.to_s}.include?(self.subject_taxon_name.rank_string)
#          soft_validations.add(:type, 'Please specify if this is a primary or secondary homonym',
#              fix: :sv_fix_specify_homonymy_type, success_message: 'Homonym updated to being primary or secondary')
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Synonym'
#        soft_validations.add(:type, 'Please specify if this is a objective or subjective synonym',
#            fix: :sv_fix_specify_synonymy_type, success_message: 'Synonym updated to being objective or subjective')
#      when 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Suppression'
#        soft_validations.add(:type, 'Please specify if this is a total, partial, or conditional suppression')
#    end
  end

  def sv_synonym_linked_to_valid_name
    #synonyms and misspellings should be linked to valid names
    if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
      obj = self.object_taxon_name
      subj = self.subject_taxon_name
        if subj.rank_class.try(:nomenclatural_code) == :iczn && obj.parent_id != subj.parent_id &&  subj.cached_valid_taxon_name_id == obj.cached_valid_taxon_name_id
        soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize}  #{subj.cached_html_name_and_author_year} should have the same parent with  #{obj.cached_html_name_and_author_year}",
                             fix: :sv_fix_subject_parent_update, success_message: 'The parent was updated')
      end
    end
  end

  #  def sv_fix_synonym_linked_to_valid_name
  #    if TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(self.type_name)
  #      obj = self.object_taxon_name
  #      unless obj.get_valid_taxon_name == obj
  #        self.object_taxon_name = obj.get_valid_taxon_name
  #        begin
  #          TaxonName.transaction do
  #            self.save
  #            return true
  #          end
  #        rescue
  #        end
  #      end
  #    end
  #    false
  #  end

  def sv_fix_subject_parent_update
    if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
      obj = self.object_taxon_name
      subj = self.subject_taxon_name
      unless obj.parent_id == subj.parent_id
        subj.parent_id = obj.parent_id
        begin
          TaxonName.transaction do
            subj.save
            return true
          end
        rescue
        end
      end
    end
    false
  end

  def subject_invalid_statuses
    TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID & self.subject_taxon_name.taxon_name_classifications.collect{|c| c.type_class.to_s}
  end

  def sv_validate_priority
    true # all validations moved to subclasses

#    unless self.type_class.nomenclatural_priority.nil?
#      date1 = self.subject_taxon_name.nomenclature_date
#      date2 = self.object_taxon_name.nomenclature_date
#      if !!date1 and !!date2
#        case self.type_class.nomenclatural_priority
#        when :direct
#          if date2 > date1 && subject_invalid_statuses.empty?
#            if self.type_name =~ /TaxonNameRelationship::Iczn::Invalidating::Homonym/
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be older than #{self.object_status} #{self.object_taxon_name.cached_html_name_and_author_year}")
#            elsif self.type_name =~ /::Iczn::/ && TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).with_two_type_bases('TaxonNameRelationship::Iczn::Invalidating::Homonym', 'TaxonNameRelationship::Iczn::Validating').not_self(self).empty?
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be older than #{self.object_status} #{self.object_taxon_name.cached_html_name_and_author_year}, unless it is also a homonym or conserved name")
#            elsif self.type_name =~ /::Icn::/ && TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).with_two_type_bases('TaxonNameRelationship::Icn::Accepting::Conserved', 'TaxonNameRelationship::Icn::Accepting::Sanctioned').not_self(self).empty?
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be older than #{self.object_status} #{self.object_taxon_name.cached_html_name_and_author_year}, unless it is also conserved or sanctioned name")
#            end
#          end
#        when :reverse
#          if date1 > date2 && subject_invalid_statuses.empty?
#            if self.type_name =~ /TaxonNameRelationship::(Typification|Combination|OriginalCombination)/
#              if self.type_name != 'TaxonNameRelationship::Typification::Genus::Subsequent::RulingByCommission' || (self.type_name =~ /TaxonNameRelationship::Typification::Genus::(Monotypy::SubsequentMonotypy|SubsequentDesignation)/ && date2 > '1930-12-31'.to_time)
#                soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be younger than #{self.object_taxon_name.cached_html_name_and_author_year}")
#              end
#            else
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be younger than #{self.object_taxon_name.cached_html_name_and_author_year}")
#            end
#          end
#        end
#      end
#    end
  end

  def sv_coordinated_taxa
    s = subject_taxon_name
    o = object_taxon_name
    s_new = s.lowest_rank_coordinated_taxon
    if s != s_new
      soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s.cached_html}",
                           fix: :sv_fix_coordinated_subject_taxa, success_message: "Relationship moved to  #{s_new.rank_class.rank_name}")
    end
  end

  def sv_coordinated_taxa_object
    s = subject_taxon_name
    o = object_taxon_name
    o_new = o.lowest_rank_coordinated_taxon
    if o != o_new && type_name != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o.cached_html}",
                           fix: :sv_fix_coordinated_object_taxa, success_message: "Relationship moved to  #{o_new.rank_class.rank_name}")
    end
  end

  def sv_fix_coordinated_subject_taxa
    s = subject_taxon_name
    s_new = s.lowest_rank_coordinated_taxon
    if s != s_new
      self.subject_taxon_name = s_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_fix_coordinated_object_taxa
    o = self.object_taxon_name
    o_new = o.lowest_rank_coordinated_taxon
    if o != o_new
      self.object_taxon_name = o_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_fix_combination_relationship
    s = self.subject_taxon_name
    list = s.list_of_coordinated_names + [s]
    if s.rank_string =~ /Species/
      s_new = list.detect{|t| t.rank_class.rank_name == 'species'}
    elsif s.rank_string =~ /Genus/
      s_new = list.detect{|t| t.rank_class.rank_name == 'genus'}
    else
      s_new = s
    end
    if s != s_new && !s.nil?
      self.subject_taxon_name = s_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def self.collect_to_s(*args)
    args.collect{|arg| arg.to_s}
  end

  def self.collect_descendants_to_s(*classes)
    ans = []
    classes.each do |klass|
      ans += klass.descendants.collect{|k| k.to_s}
    end
    ans
  end

  def self.collect_descendants_and_itself_to_s(*classes)
    classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes)
  end
end

#project_idInteger

the project ID

Returns:

  • (Integer)

44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
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
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
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
481
482
483
484
485
486
487
488
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
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
# File 'app/models/taxon_name_relationship.rb', line 44

class TaxonNameRelationship < ApplicationRecord
  include Housekeeping
  include Shared::Citations
  include Shared::Notes
  include Shared::IsData
  include SoftValidation

  # @return [Boolean, nil]
  #   When true, cached values are not built
  attr_accessor :no_cached

  belongs_to :subject_taxon_name, class_name: 'TaxonName', foreign_key: :subject_taxon_name_id, inverse_of: :taxon_name_relationships # left side
  belongs_to :object_taxon_name, class_name: 'TaxonName', foreign_key: :object_taxon_name_id, inverse_of: :related_taxon_name_relationships # right side

  after_save :set_cached_names_for_taxon_names, unless: -> {self.no_cached}
  after_destroy :set_cached_names_for_taxon_names, unless: -> {self.no_cached}

  validates_presence_of :type, message: 'Relationship type should be specified'
  validates_presence_of :subject_taxon_name, message: 'Missing taxon name on the left side'
  validates_presence_of :object_taxon_name, message: 'Missing taxon name on the right side'

  validates_uniqueness_of :object_taxon_name_id, scope: :type, if: :is_combination?
  validates_uniqueness_of :object_taxon_name_id, scope: [:type, :subject_taxon_name_id], unless: :is_combination?

  validate :validate_type, :validate_subject_and_object_are_not_identical

  validate :subject_and_object_in_same_project

  with_options unless: -> {!subject_taxon_name || !object_taxon_name} do |v|
    v.validate :validate_subject_and_object_share_code,
      :validate_uniqueness_of_typification_object,
      #:validate_uniqueness_of_synonym_subject,
      :validate_object_and_subject_both_protonyms,
      :validate_object_must_equal_subject_for_uncertain_placement,
      :validate_subject_and_object_ranks,
      :validate_rank_group
  end

  soft_validate(:sv_validate_required_relationships, set: :validate_required_relationships, has_fix: false)
  soft_validate(:sv_validate_disjoint_relationships, set: :validate_disjoint_relationships, has_fix: false)
  soft_validate(:sv_validate_disjoint_object, set: :validate_disjoint_object, has_fix: false)
  soft_validate(:sv_validate_disjoint_subject, set: :validate_disjoint_subject, has_fix: false)
  soft_validate(:sv_specific_relationship, set: :specific_relationship, has_fix: false) # some do, some don't
  soft_validate(:sv_objective_synonym_relationship, set: :objective_synonym_relationship, has_fix: false)
  soft_validate(:sv_synonym_relationship, set: :synonym_relationship, has_fix: false)
  soft_validate(:sv_not_specific_relationship, set: :not_specific_relationship, has_fix: true)
  soft_validate(:sv_synonym_linked_to_valid_name, set: :synonym_linked_to_valid_name, has_fix: true)
  soft_validate(:sv_validate_priority, set: :validate_priority, has_fix: false)
  soft_validate(:sv_coordinated_taxa, set: :coordinated_taxa, has_fix: true)
  soft_validate(:sv_coordinated_taxa_object, set: :coordinated_taxa, has_fix: true)

  scope :where_subject_is_taxon_name, -> (taxon_name) {where(subject_taxon_name_id: taxon_name)}
  scope :where_object_is_taxon_name, -> (taxon_name) {where(object_taxon_name_id: taxon_name)}
  scope :where_object_in_taxon_names, -> (taxon_name_array) {where('"taxon_name_relationships"."object_taxon_name_id" IN (?)', taxon_name_array)}

  scope :with_type_string, -> (type_string) { where(sanitize_sql_array(["taxon_name_relationships.type = '%s'", type_string])) }

  scope :with_type_base, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "#{base_string}%")}
  scope :with_type_contains, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "%#{base_string}%")}

  scope :with_two_type_bases, -> (base_string1, base_string2) {
    where("taxon_name_relationships.type LIKE ? OR taxon_name_relationships.type LIKE ?", "#{base_string1}%", "#{base_string2}%") }

  scope :homonym_or_suppressed, -> {where("taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Homonym%' OR taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Suppression::Total'") }
  scope :with_type_array, -> (base_array) {where('taxon_name_relationships.type IN (?)', base_array ) }

  # @return [Array of TaxonNameClassification]
  #  the inferable TaxonNameClassification(s) added to the subject when this relationship is used
  #  !! Not implemented
  def subject_properties
    []
  end

  # @return [Array of TaxonNameClassification]
  #  the inferable TaxonNameClassification(s) added to the subject when this relationship is used
  #  !! Not implmented
  def object_properties
    []
  end

  # @return class
  #   this method calls Module#module_parent
  def self.parent
    self.module_parent
  end

  # @return [Array of NomenclatureRank]
  #   the valid ranks to which the subject name can belong, set in subclasses. (left side)
  def self.valid_subject_ranks
    []
  end

  # @return [Array of NomenclatureRank]
  #   the valid ranks to which the object name can belong, set in subclasses. (right side)
  def self.valid_object_ranks
    []
  end

  # @return [Array of TaxonNameRelationships]
  #   if this relationships is set for the subject, then others in this array should not be used for that subject
  def self.disjoint_taxon_name_relationships
    []
  end

  # TODO: why isn't this disjoint?
  # disjoint relationships for the taxon as a object
  def self.required_taxon_name_relationships
    []
  end

  def self.disjoint_subject_classes
    []
  end

  def self.disjoint_object_classes
    []
  end

  def self.gbif_status_of_subject
    nil
  end

  def self.gbif_status_of_object
    nil
  end

  def self.assignable
    false
  end

  # @return [Symbol]
  #   determine the relative age of subject and object
  #   :direct - subject is younger than object
  #   :reverse - object is younger than subject
  def self.nomenclatural_priority
    nil
  end

  # @return [String]
  #    the status inferred by the relationship to the object name
  def object_status
    self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
  end

  # @return [String]
  #    the status inferred by the relationship to the subject name
  def subject_status
    self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
  end

  # @return [String]
  #    the connecting word in the relationship from the subject name to object name
  def subject_status_connector_to_object
    ' of'
  end

  # @return [String]
  #    the connecting word in the relationship from the object name to subject name
  def object_status_connector_to_subject
    ' of'
  end

  # @return [String]
  #   a readable fragement combining status and connector
  def subject_status_tag
    subject_status + subject_status_connector_to_object
  end

  # @return [String]
  #   a readable fragement combining status and connector
  def object_status_tag
    object_status + object_status_connector_to_subject
  end

  # @return [String, nil]
  #   the type of this relationship, IF the type is a valid name, else nil
  def type_name
    r = self.type
    TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r : nil
  end

  def type_class=(value)
    write_attribute(:type, value.to_s)
  end

  # @return [TaxonNameRelationship, String]
  #    the type as a class, if legal, else a string  ! Strangeish
  def type_class
    r = read_attribute(:type).to_s
    TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r.safe_constantize : r
  end

  # @return [String, nil]
  #   the NOMEN uri for this type
  def self.nomen_uri
    const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil
  end

  # @return [Time]
  #   effective date of publication, used to determine nomenclatural priorities
  def nomenclature_date
    self.source ? (self.source.cached_nomenclature_date ? self.source.cached_nomenclature_date.to_time : Time.now) : Time.now
  end

  # @TODO SourceClassifiedAs is not really Combination in the other sense
  def is_combination?
    !!/TaxonNameRelationship::(OriginalCombination|Combination)/.match(self.type.to_s)
  end

  protected

  def subject_and_object_in_same_project
    if subject_taxon_name && object_taxon_name
      errors.add(:base, 'one name is not in the same project as the other') if subject_taxon_name.project_id != object_taxon_name.project_id
    end
  end

  def validate_type
    unless TAXON_NAME_RELATIONSHIP_NAMES.include?(type)
      errors.add(:type, "'#{type}' is not a valid taxon name relationship")
    end

    if object_taxon_name.class.to_s == 'Protonym' || object_taxon_name.class.to_s == 'Hybrid'
      errors.add(:type, "'#{type}' is not a valid taxon name relationship") if /TaxonNameRelationship::Combination::/.match(self.type)
    end

    if object_taxon_name.class.to_s == 'Combination'
      errors.add(:type, "'#{type}' is not a valid taxon name relationship") unless /TaxonNameRelationship::Combination::/.match(self.type)
    end
  end

  # @todo validate, that all the relationships in the table could be linked to relationships in classes (if those had changed)

  def validate_subject_and_object_share_code
    if object_taxon_name.type  == 'Protonym' && subject_taxon_name.type == 'Protonym'
      errors.add(:object_taxon_name_id, 'The related taxon is not in the same monenclatural group (ICZN, ICN, ICNP, ICTV') if subject_taxon_name.rank_class.try(:nomenclatural_code) != object_taxon_name.rank_class.try(:nomenclatural_code)
    end
  end

  def validate_subject_and_object_are_not_identical
    if !self.object_taxon_name_id.nil? && self.object_taxon_name == self.subject_taxon_name
      errors.add(:object_taxon_name_id, "#{self.object_taxon_name.try(:cached_html).to_s} should not refer to itself") unless self.type =~ /OriginalCombination/
    end
  end

  def validate_object_must_equal_subject_for_uncertain_placement
    if self.object_taxon_name_id != self.subject_taxon_name.parent_id && self.type_name == 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      errors.add(:object_taxon_name_id, "The parent #{self.subject_taxon_name.parent.cached_html} and the Incertae Sedis placement (#{self.object_taxon_name.cached_html}) should match")
    end
  end

  def validate_subject_and_object_ranks
    tname = self.type_name

    if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      rank_group = self.subject_taxon_name.rank_class.try(:parent)
      unless rank_group == self.object_taxon_name.rank_class.try(:parent)
        errors.add(:object_taxon_name_id, "Rank of related taxon should be in the #{rank_group.try(:rank_name)} rank group, not #{self.object_taxon_name.rank_class.try(:rank_name)}")
      end
    end

    unless self.type_class.blank? # only validate if it is set
      if object_taxon_name
        if object_taxon_name.type == 'Protonym' || object_taxon_name.type == 'Hybrid'
          unless self.type_class.valid_object_ranks.include?(self.object_taxon_name.rank_string)
            errors.add(:object_taxon_name_id, "#{self.object_taxon_name.rank_class.rank_name.capitalize} rank of #{self.object_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
            errors.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.object_taxon_name.rank_class.rank_name} rank of #{self.object_taxon_name.cached_html}")
          end
        end
      end

      if subject_taxon_name
        if subject_taxon_name.type == 'Protonym' || subject_taxon_name.type == 'Hybrid'
          unless self.type_class.valid_subject_ranks.include?(self.subject_taxon_name.parent.rank_string)
            soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
            soft_validations.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.subject_taxon_name.rank_class.rank_name} rank of #{self.subject_taxon_name.cached_html}")
          end
        end
      end
    end
  end

  ##### Protonym historically could be listed as a synonym to different taxa
  #def validate_uniqueness_of_synonym_subject 
  #  if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains('Synonym').not_self(self).empty?
  #    errors.add(:subject_taxon_name_id, 'Only one synonym relationship is allowed')
  #  end
  #end

  def validate_uniqueness_of_typification_object
    if /Typification/.match(self.type_name) && !TaxonNameRelationship.where(object_taxon_name_id: self.object_taxon_name_id).with_type_contains('Typification').not_self(self).empty?
      errors.add(:object_taxon_name_id, 'Only one Type designation relationship is allowed')
    end
  end

  def validate_rank_group
    if self.type =~ /Hybrid/ && self.subject_taxon_name && self.object_taxon_name
      if self.subject_taxon_name.rank_class.parent != self.object_taxon_name.rank_class.parent
        errors.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the rank of hybrid (#{self.object_taxon_name.rank_class.rank_name})")
      end
    end
  end

  def validate_object_and_subject_both_protonyms
    if /TaxonNameRelationship::Combination::/.match(self.type)
      errors.add(:object_taxon_name_id, 'Not a Combination') if object_taxon_name.type != 'Combination'
    else
      errors.add(:object_taxon_name_id, 'Not a Protonym') if object_taxon_name.type == 'Combination'
    end
    errors.add(:subject_taxon_name_id, 'Not a Protonym') if subject_taxon_name.type == 'Combination'
  end

  # TODO: Isolate to individual classes per type
  def set_cached_names_for_taxon_names
    begin
      TaxonName.transaction do
        if is_combination?
          t = object_taxon_name

          t.send(:set_cached)

          if type_name =~/OriginalCombination/ 
            t.update_columns(
              cached_original_combination: t.get_original_combination,
              cached_original_combination_html: t.get_original_combination_html,
            )
          end

        elsif type_name =~/TaxonNameRelationship::Hybrid/ # TODO: move to Hybrid
          t = object_taxon_name
          t.update_columns(
            cached: t.get_full_name,
            cached_html: t.get_full_name_html
          )

        elsif type_name =~/SourceClassifiedAs/
          t = subject_taxon_name
          t.set_cached_classified_as
          # t.update_column(:cached_classified_as, t.get_cached_classified_as)

        elsif is_invalidating?
          t = subject_taxon_name
          
          if type_name =~/Misspelling/
            t.update_column(:cached_misspelling, t.get_cached_misspelling)
            t.update_columns(
                cached_author_year: t.get_author_and_year,
                cached_original_combination: t.get_original_combination,
                cached_original_combination_html: t.get_original_combination_html
            )
          end

          if type_name =~/Misapplication/
            t.update_column( :cached_author_year, t.get_author_and_year)
          end

          vn = t.get_valid_taxon_name

          t.update_columns(
            cached: t.get_full_name,
            cached_html: t.get_full_name_html, # OK to force reload here, otherwise we need an exception in #set_cached 
            cached_valid_taxon_name_id: vn.id)
          t.combination_list_self.each do |c|
            c.update_column(:cached_valid_taxon_name_id, vn.id)
          end

          vn.list_of_invalid_taxon_names.each do |s|
            s.update_column(:cached_valid_taxon_name_id, vn.id)
            s.combination_list_self.each do |c|
              c.update_column(:cached_valid_taxon_name_id, vn.id)
            end
          end
        end

      end

    # no point in rescuing and not returning somthing
    rescue ActiveRecord::RecordInvalid
      raise
    end
    false
  end

  def is_invalidating?
    TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(type_name)
  end

  def sv_validate_required_relationships
    object_relationships = TaxonNameRelationship.where_object_is_taxon_name(self.object_taxon_name).not_self(self).collect{|r| r.type}
    required = self.type_class.required_taxon_name_relationships - object_relationships
    required.each do |r|
      soft_validations.add(:type, " Presence of #{self.subject_status} requires selection of #{r.demodulize.underscore.humanize.downcase}")
    end
  end

  def sv_validate_disjoint_relationships
    tname = self.type_name
    if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      subject_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).not_self(self)
      subject_relationships.each  do |i|
        if self.type_class.disjoint_taxon_name_relationships.include?(i.type_name)
          soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with another relationship: '#{i.subject_status}'")
        end
      end
    end
  end

  def sv_validate_disjoint_object
    classifications = self.object_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
    disjoint_object_classes = self.type_class.disjoint_object_classes
    compare = disjoint_object_classes & classifications
    compare.each do |i|
      c = i.demodulize.underscore.humanize.downcase
      soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with the taxon status: '#{c}'")
      soft_validations.add(:object_taxon_name_id, "#{self.object_taxon_name.cached_html} has a conflicting status: '#{c}'")
    end
  end

  def sv_validate_disjoint_subject
    classifications = self.subject_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
    disjoint_subject_classes = self.type_class.disjoint_subject_classes
    compare = disjoint_subject_classes & classifications
    compare.each do |i|
      c = i.demodulize.underscore.humanize.downcase
      soft_validations.add(:type, "#{self.subject_status.capitalize} conflicting with the status: '#{c}'")
      soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.cached_html} has a conflicting status: '#{c}'")
    end
  end

  def sv_specific_relationship
    true # all validations moved to subclasses

#    s = subject_taxon_name
#    o = object_taxon_name
#    case type
#      when 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Subjective' || 'TaxonNameRelationship::Icn::Unaccepting::Synonym::Heterotypic'
#        if (s.type_taxon_name == o.type_taxon_name && !s.type_taxon_name.nil? ) || (!s.get_primary_type.empty? && s.has_same_primary_type(o) )
#          soft_validations.add(:type, "Subjective synonyms #{s.cached_html} and #{o.cached_html} should not have the same type")
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym'
#        # primary names don't match
#        if (s.cached_primary_homonym_alternative_spelling != o.cached_primary_homonym_alternative_spelling)
#          # there is a secondary name ... and it doesn't match either
#          if (s.cached_secondary_homonym_alternative_spelling.blank? && o.cached_secondary_homonym_alternative_spelling.blank?) || (s.cached_secondary_homonym_alternative_spelling != o.cached_secondary_homonym_alternative_spelling)
#            soft_validations.add(:type, "#{subject_taxon_name.cached_html_name_and_author_year} and #{object_taxon_name.cached_html_name_and_author_year} are not similar enough to be homonyms")
#          end
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary' || 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary::Forgotten' || 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary::Suppressed'
#        if s.original_genus != o.original_genus
#          soft_validations.add(:type, "Primary homonyms #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} should have the same original genus")
#        elsif s.cached_primary_homonym_alternative_spelling != o.cached_primary_homonym_alternative_spelling
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} are not similar enough to be homonyms")
#        end
#        if type == 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary::Forgotten' && s.year_of_publication > 1899
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} was not described after 1899")
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Secondary'
#        if s.original_genus == o.original_genus && !s.original_genus.nil?
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} species described in the same original genus #{s.original_genus}, they are primary homonyms")
#        elsif s.get_valid_taxon_name.ancestor_at_rank('genus') != o.get_valid_taxon_name.ancestor_at_rank('genus')
#          soft_validations.add(:type, "Secondary homonyms #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} should be placed in the same parent genus, the homonymy should be deleted or changed to 'secondary homonym replaced before 1961'")
#        elsif s.cached_secondary_homonym_alternative_spelling != o.cached_secondary_homonym_alternative_spelling
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} are not similar enough to be homonyms")
#        end

#        if (s.all_generic_placements & o.all_generic_placements).empty?
#          soft_validations.add(:base, "No combination available showing #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} placed in the same genus")
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Secondary::Secondary1961'
#        soft_validations.add(:type, "#{s.cached_html_name_and_author_year} was not described before 1961") if s.year_of_publication > 1960
#        soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} described in the same original genus #{s.original_genus}, they are primary homonyms") if s.original_genus == o.original_genus && !s.original_genus.nil?
#        soft_validations.add(:base, 'The original publication is not selected') unless source

#        soft_validations.add(:base, "#{s.cached_html_name_and_author_year} should not be treated as a homonym established before 1961") if self.source && self.source.year > 1960

#        if (s.all_generic_placements & o.all_generic_placements).empty?
#          soft_validations.add(:base, "No combination available showing #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} placed in the same genus")
#        end
#      when 'TaxonNameRelationship::Iczn::PotentiallyValidating::FamilyBefore1961'
#        soft_validations.add(:type, "#{s.cached_html_name_and_author_year} was not described before 1961") if s.year_of_publication > 1960
#        soft_validations.add(:base, "#{s.cached_html_name_and_author_year} should be accepted as a replacement name before 1961") if self.source && self.source.year > 1960
#      when 'TaxonNameRelationship::Typification::Genus::Subsequent::SubsequentDesignation'
#        soft_validations.add(:type, "Genus #{o.cached_html_name_and_author_year} described after 1930 is nomen nudum, if type was not designated in the original publication") if o.year_of_publication && o.year_of_publication > 1930
#      when 'TaxonNameRelationship::Iczn::PotentiallyValidating::ReplacementName'
#        r1 = TaxonNameRelationship.where(type: 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Objective::ReplacedHomonym', subject_taxon_name_id: o.id, object_taxon_name_id: s.id).first
#        r2 = TaxonNameRelationship.where(type: 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Objective::UnnecessaryReplacementName', subject_taxon_name_id: s.id, object_taxon_name_id: o.id).first
#        soft_validations.add(:base, "Missing relationship: #{s.cached_html_name_and_author_year} is a replacement name for #{o.cached_html_name_and_author_year}. Please add an objective synonym relationship (either 'replaced homonym' or 'unnecessary replacement name')") if r1.nil? && r2.nil?
#      when 'TaxonNameRelationship::Typification::Genus::Original::OriginalMonotypy'
#        # @todo Check if more than one species associated with the genus in the original paper
#    end
  end

  def sv_objective_synonym_relationship
    true # all validations moved to subclasses
#    if self.type_name =~ /TaxonNameRelationship::(Iczn::Invalidating::Synonym::Objective|Icn::Unaccepting::Synonym::Homotypic|Icnp::Unaccepting::Synonym::Homotypic)/
#      s = self.subject_taxon_name
#      o = self.object_taxon_name
#      if (s.type_taxon_name != o.type_taxon_name ) || !s.has_same_primary_type(o)
#        soft_validations.add(:type, "Objective synonyms #{s.cached_html} and #{o.cached_html} should have the same type")
#      end
#    end
  end

  def sv_synonym_relationship
    true # all validations moved to subclasses
#    relationships = TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM +
#      TaxonNameRelationship.collect_to_s(TaxonNameRelationship::Typification::Genus::Subsequent::SubsequentDesignation,
#                                         TaxonNameRelationship::Typification::Genus::Subsequent::RulingByCommission)
#    if relationships.include?(self.type_name)
#      if self.source
#        date1 = self.source.cached_nomenclature_date.to_time
#        date2 = self.subject_taxon_name.nomenclature_date
#        if !!date1 && !!date2
#          soft_validations.add(:base, "#{self.subject_taxon_name.cached_html_name_and_author_year} was not described at the time of citation (#{date1}") if date2 > date1
#        end
#      elsif TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING.include?(self.type_name)
#        # misspelling does not requere original publication
#      else
#        soft_validations.add(:base, 'The original publication is not selected')
#      end
#    end
  end

  def sv_not_specific_relationship
    true # all validations moved to subclasses

#    case self.type_name
#      when 'TaxonNameRelationship::Typification::Genus'
#        soft_validations.add(:type, 'Please specify if the type designation is original or subsequent')
#      when 'TaxonNameRelationship::Typification::Genus::Original'
#        soft_validations.add(:type, 'Please specify if this is Original Designation or Original Monotypy')
#      when 'TaxonNameRelationship::Typification::Genus::Subsequent'
#        soft_validations.add(:type, 'Please specify if this is Subsequent Designation or Subsequent Monotypy')
#      when 'TaxonNameRelationship::Typification::Genus::Tautonomy'
#        soft_validations.add(:type, 'Please specify if the tautonomy is absolute or Linnaean')
#      when 'TaxonNameRelationship::Icn::Unaccepting'
#        soft_validations.add(:type, 'Please specify the reasons for the name being Unaccepted')
#      when 'TaxonNameRelationship::Icn::Unaccepting::Synonym'
#        soft_validations.add(:type, 'Please specify if this is a homotypic or heterotypic synonym',
#          fix: :sv_fix_specify_synonymy_type, success_message: 'Synonym updated to being homotypic or heterotypic')
#      when 'TaxonNameRelationship::Icnp::Unaccepting::Synonym'
#        soft_validations.add(:type, 'Please specify if this is a objective or subjective synonym',
#          fix: :sv_fix_specify_synonymy_type, success_message: 'Synonym updated to being objective or subjective')
#      when 'TaxonNameRelationship::Iczn::Invalidating'
#        soft_validations.add(:type, 'Please specify the reason for the name being Invalid') unless self.subject_taxon_name.classification_invalid_or_unavailable?
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym'
#        if NomenclaturalRank::Iczn::SpeciesGroup.descendants.collect{|t| t.to_s}.include?(self.subject_taxon_name.rank_string)
#          soft_validations.add(:type, 'Please specify if this is a primary or secondary homonym',
#              fix: :sv_fix_specify_homonymy_type, success_message: 'Homonym updated to being primary or secondary')
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Synonym'
#        soft_validations.add(:type, 'Please specify if this is a objective or subjective synonym',
#            fix: :sv_fix_specify_synonymy_type, success_message: 'Synonym updated to being objective or subjective')
#      when 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Suppression'
#        soft_validations.add(:type, 'Please specify if this is a total, partial, or conditional suppression')
#    end
  end

  def sv_synonym_linked_to_valid_name
    #synonyms and misspellings should be linked to valid names
    if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
      obj = self.object_taxon_name
      subj = self.subject_taxon_name
        if subj.rank_class.try(:nomenclatural_code) == :iczn && obj.parent_id != subj.parent_id &&  subj.cached_valid_taxon_name_id == obj.cached_valid_taxon_name_id
        soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize}  #{subj.cached_html_name_and_author_year} should have the same parent with  #{obj.cached_html_name_and_author_year}",
                             fix: :sv_fix_subject_parent_update, success_message: 'The parent was updated')
      end
    end
  end

  #  def sv_fix_synonym_linked_to_valid_name
  #    if TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(self.type_name)
  #      obj = self.object_taxon_name
  #      unless obj.get_valid_taxon_name == obj
  #        self.object_taxon_name = obj.get_valid_taxon_name
  #        begin
  #          TaxonName.transaction do
  #            self.save
  #            return true
  #          end
  #        rescue
  #        end
  #      end
  #    end
  #    false
  #  end

  def sv_fix_subject_parent_update
    if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
      obj = self.object_taxon_name
      subj = self.subject_taxon_name
      unless obj.parent_id == subj.parent_id
        subj.parent_id = obj.parent_id
        begin
          TaxonName.transaction do
            subj.save
            return true
          end
        rescue
        end
      end
    end
    false
  end

  def subject_invalid_statuses
    TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID & self.subject_taxon_name.taxon_name_classifications.collect{|c| c.type_class.to_s}
  end

  def sv_validate_priority
    true # all validations moved to subclasses

#    unless self.type_class.nomenclatural_priority.nil?
#      date1 = self.subject_taxon_name.nomenclature_date
#      date2 = self.object_taxon_name.nomenclature_date
#      if !!date1 and !!date2
#        case self.type_class.nomenclatural_priority
#        when :direct
#          if date2 > date1 && subject_invalid_statuses.empty?
#            if self.type_name =~ /TaxonNameRelationship::Iczn::Invalidating::Homonym/
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be older than #{self.object_status} #{self.object_taxon_name.cached_html_name_and_author_year}")
#            elsif self.type_name =~ /::Iczn::/ && TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).with_two_type_bases('TaxonNameRelationship::Iczn::Invalidating::Homonym', 'TaxonNameRelationship::Iczn::Validating').not_self(self).empty?
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be older than #{self.object_status} #{self.object_taxon_name.cached_html_name_and_author_year}, unless it is also a homonym or conserved name")
#            elsif self.type_name =~ /::Icn::/ && TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).with_two_type_bases('TaxonNameRelationship::Icn::Accepting::Conserved', 'TaxonNameRelationship::Icn::Accepting::Sanctioned').not_self(self).empty?
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be older than #{self.object_status} #{self.object_taxon_name.cached_html_name_and_author_year}, unless it is also conserved or sanctioned name")
#            end
#          end
#        when :reverse
#          if date1 > date2 && subject_invalid_statuses.empty?
#            if self.type_name =~ /TaxonNameRelationship::(Typification|Combination|OriginalCombination)/
#              if self.type_name != 'TaxonNameRelationship::Typification::Genus::Subsequent::RulingByCommission' || (self.type_name =~ /TaxonNameRelationship::Typification::Genus::(Monotypy::SubsequentMonotypy|SubsequentDesignation)/ && date2 > '1930-12-31'.to_time)
#                soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be younger than #{self.object_taxon_name.cached_html_name_and_author_year}")
#              end
#            else
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be younger than #{self.object_taxon_name.cached_html_name_and_author_year}")
#            end
#          end
#        end
#      end
#    end
  end

  def sv_coordinated_taxa
    s = subject_taxon_name
    o = object_taxon_name
    s_new = s.lowest_rank_coordinated_taxon
    if s != s_new
      soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s.cached_html}",
                           fix: :sv_fix_coordinated_subject_taxa, success_message: "Relationship moved to  #{s_new.rank_class.rank_name}")
    end
  end

  def sv_coordinated_taxa_object
    s = subject_taxon_name
    o = object_taxon_name
    o_new = o.lowest_rank_coordinated_taxon
    if o != o_new && type_name != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o.cached_html}",
                           fix: :sv_fix_coordinated_object_taxa, success_message: "Relationship moved to  #{o_new.rank_class.rank_name}")
    end
  end

  def sv_fix_coordinated_subject_taxa
    s = subject_taxon_name
    s_new = s.lowest_rank_coordinated_taxon
    if s != s_new
      self.subject_taxon_name = s_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_fix_coordinated_object_taxa
    o = self.object_taxon_name
    o_new = o.lowest_rank_coordinated_taxon
    if o != o_new
      self.object_taxon_name = o_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_fix_combination_relationship
    s = self.subject_taxon_name
    list = s.list_of_coordinated_names + [s]
    if s.rank_string =~ /Species/
      s_new = list.detect{|t| t.rank_class.rank_name == 'species'}
    elsif s.rank_string =~ /Genus/
      s_new = list.detect{|t| t.rank_class.rank_name == 'genus'}
    else
      s_new = s
    end
    if s != s_new && !s.nil?
      self.subject_taxon_name = s_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def self.collect_to_s(*args)
    args.collect{|arg| arg.to_s}
  end

  def self.collect_descendants_to_s(*classes)
    ans = []
    classes.each do |klass|
      ans += klass.descendants.collect{|k| k.to_s}
    end
    ans
  end

  def self.collect_descendants_and_itself_to_s(*classes)
    classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes)
  end
end

#subject_taxon_name_idInteger

Returns the subject taxon name.

Returns:

  • (Integer)

    the subject taxon name


44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
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
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
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
481
482
483
484
485
486
487
488
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
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
# File 'app/models/taxon_name_relationship.rb', line 44

class TaxonNameRelationship < ApplicationRecord
  include Housekeeping
  include Shared::Citations
  include Shared::Notes
  include Shared::IsData
  include SoftValidation

  # @return [Boolean, nil]
  #   When true, cached values are not built
  attr_accessor :no_cached

  belongs_to :subject_taxon_name, class_name: 'TaxonName', foreign_key: :subject_taxon_name_id, inverse_of: :taxon_name_relationships # left side
  belongs_to :object_taxon_name, class_name: 'TaxonName', foreign_key: :object_taxon_name_id, inverse_of: :related_taxon_name_relationships # right side

  after_save :set_cached_names_for_taxon_names, unless: -> {self.no_cached}
  after_destroy :set_cached_names_for_taxon_names, unless: -> {self.no_cached}

  validates_presence_of :type, message: 'Relationship type should be specified'
  validates_presence_of :subject_taxon_name, message: 'Missing taxon name on the left side'
  validates_presence_of :object_taxon_name, message: 'Missing taxon name on the right side'

  validates_uniqueness_of :object_taxon_name_id, scope: :type, if: :is_combination?
  validates_uniqueness_of :object_taxon_name_id, scope: [:type, :subject_taxon_name_id], unless: :is_combination?

  validate :validate_type, :validate_subject_and_object_are_not_identical

  validate :subject_and_object_in_same_project

  with_options unless: -> {!subject_taxon_name || !object_taxon_name} do |v|
    v.validate :validate_subject_and_object_share_code,
      :validate_uniqueness_of_typification_object,
      #:validate_uniqueness_of_synonym_subject,
      :validate_object_and_subject_both_protonyms,
      :validate_object_must_equal_subject_for_uncertain_placement,
      :validate_subject_and_object_ranks,
      :validate_rank_group
  end

  soft_validate(:sv_validate_required_relationships, set: :validate_required_relationships, has_fix: false)
  soft_validate(:sv_validate_disjoint_relationships, set: :validate_disjoint_relationships, has_fix: false)
  soft_validate(:sv_validate_disjoint_object, set: :validate_disjoint_object, has_fix: false)
  soft_validate(:sv_validate_disjoint_subject, set: :validate_disjoint_subject, has_fix: false)
  soft_validate(:sv_specific_relationship, set: :specific_relationship, has_fix: false) # some do, some don't
  soft_validate(:sv_objective_synonym_relationship, set: :objective_synonym_relationship, has_fix: false)
  soft_validate(:sv_synonym_relationship, set: :synonym_relationship, has_fix: false)
  soft_validate(:sv_not_specific_relationship, set: :not_specific_relationship, has_fix: true)
  soft_validate(:sv_synonym_linked_to_valid_name, set: :synonym_linked_to_valid_name, has_fix: true)
  soft_validate(:sv_validate_priority, set: :validate_priority, has_fix: false)
  soft_validate(:sv_coordinated_taxa, set: :coordinated_taxa, has_fix: true)
  soft_validate(:sv_coordinated_taxa_object, set: :coordinated_taxa, has_fix: true)

  scope :where_subject_is_taxon_name, -> (taxon_name) {where(subject_taxon_name_id: taxon_name)}
  scope :where_object_is_taxon_name, -> (taxon_name) {where(object_taxon_name_id: taxon_name)}
  scope :where_object_in_taxon_names, -> (taxon_name_array) {where('"taxon_name_relationships"."object_taxon_name_id" IN (?)', taxon_name_array)}

  scope :with_type_string, -> (type_string) { where(sanitize_sql_array(["taxon_name_relationships.type = '%s'", type_string])) }

  scope :with_type_base, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "#{base_string}%")}
  scope :with_type_contains, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "%#{base_string}%")}

  scope :with_two_type_bases, -> (base_string1, base_string2) {
    where("taxon_name_relationships.type LIKE ? OR taxon_name_relationships.type LIKE ?", "#{base_string1}%", "#{base_string2}%") }

  scope :homonym_or_suppressed, -> {where("taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Homonym%' OR taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Suppression::Total'") }
  scope :with_type_array, -> (base_array) {where('taxon_name_relationships.type IN (?)', base_array ) }

  # @return [Array of TaxonNameClassification]
  #  the inferable TaxonNameClassification(s) added to the subject when this relationship is used
  #  !! Not implemented
  def subject_properties
    []
  end

  # @return [Array of TaxonNameClassification]
  #  the inferable TaxonNameClassification(s) added to the subject when this relationship is used
  #  !! Not implmented
  def object_properties
    []
  end

  # @return class
  #   this method calls Module#module_parent
  def self.parent
    self.module_parent
  end

  # @return [Array of NomenclatureRank]
  #   the valid ranks to which the subject name can belong, set in subclasses. (left side)
  def self.valid_subject_ranks
    []
  end

  # @return [Array of NomenclatureRank]
  #   the valid ranks to which the object name can belong, set in subclasses. (right side)
  def self.valid_object_ranks
    []
  end

  # @return [Array of TaxonNameRelationships]
  #   if this relationships is set for the subject, then others in this array should not be used for that subject
  def self.disjoint_taxon_name_relationships
    []
  end

  # TODO: why isn't this disjoint?
  # disjoint relationships for the taxon as a object
  def self.required_taxon_name_relationships
    []
  end

  def self.disjoint_subject_classes
    []
  end

  def self.disjoint_object_classes
    []
  end

  def self.gbif_status_of_subject
    nil
  end

  def self.gbif_status_of_object
    nil
  end

  def self.assignable
    false
  end

  # @return [Symbol]
  #   determine the relative age of subject and object
  #   :direct - subject is younger than object
  #   :reverse - object is younger than subject
  def self.nomenclatural_priority
    nil
  end

  # @return [String]
  #    the status inferred by the relationship to the object name
  def object_status
    self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
  end

  # @return [String]
  #    the status inferred by the relationship to the subject name
  def subject_status
    self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
  end

  # @return [String]
  #    the connecting word in the relationship from the subject name to object name
  def subject_status_connector_to_object
    ' of'
  end

  # @return [String]
  #    the connecting word in the relationship from the object name to subject name
  def object_status_connector_to_subject
    ' of'
  end

  # @return [String]
  #   a readable fragement combining status and connector
  def subject_status_tag
    subject_status + subject_status_connector_to_object
  end

  # @return [String]
  #   a readable fragement combining status and connector
  def object_status_tag
    object_status + object_status_connector_to_subject
  end

  # @return [String, nil]
  #   the type of this relationship, IF the type is a valid name, else nil
  def type_name
    r = self.type
    TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r : nil
  end

  def type_class=(value)
    write_attribute(:type, value.to_s)
  end

  # @return [TaxonNameRelationship, String]
  #    the type as a class, if legal, else a string  ! Strangeish
  def type_class
    r = read_attribute(:type).to_s
    TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r.safe_constantize : r
  end

  # @return [String, nil]
  #   the NOMEN uri for this type
  def self.nomen_uri
    const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil
  end

  # @return [Time]
  #   effective date of publication, used to determine nomenclatural priorities
  def nomenclature_date
    self.source ? (self.source.cached_nomenclature_date ? self.source.cached_nomenclature_date.to_time : Time.now) : Time.now
  end

  # @TODO SourceClassifiedAs is not really Combination in the other sense
  def is_combination?
    !!/TaxonNameRelationship::(OriginalCombination|Combination)/.match(self.type.to_s)
  end

  protected

  def subject_and_object_in_same_project
    if subject_taxon_name && object_taxon_name
      errors.add(:base, 'one name is not in the same project as the other') if subject_taxon_name.project_id != object_taxon_name.project_id
    end
  end

  def validate_type
    unless TAXON_NAME_RELATIONSHIP_NAMES.include?(type)
      errors.add(:type, "'#{type}' is not a valid taxon name relationship")
    end

    if object_taxon_name.class.to_s == 'Protonym' || object_taxon_name.class.to_s == 'Hybrid'
      errors.add(:type, "'#{type}' is not a valid taxon name relationship") if /TaxonNameRelationship::Combination::/.match(self.type)
    end

    if object_taxon_name.class.to_s == 'Combination'
      errors.add(:type, "'#{type}' is not a valid taxon name relationship") unless /TaxonNameRelationship::Combination::/.match(self.type)
    end
  end

  # @todo validate, that all the relationships in the table could be linked to relationships in classes (if those had changed)

  def validate_subject_and_object_share_code
    if object_taxon_name.type  == 'Protonym' && subject_taxon_name.type == 'Protonym'
      errors.add(:object_taxon_name_id, 'The related taxon is not in the same monenclatural group (ICZN, ICN, ICNP, ICTV') if subject_taxon_name.rank_class.try(:nomenclatural_code) != object_taxon_name.rank_class.try(:nomenclatural_code)
    end
  end

  def validate_subject_and_object_are_not_identical
    if !self.object_taxon_name_id.nil? && self.object_taxon_name == self.subject_taxon_name
      errors.add(:object_taxon_name_id, "#{self.object_taxon_name.try(:cached_html).to_s} should not refer to itself") unless self.type =~ /OriginalCombination/
    end
  end

  def validate_object_must_equal_subject_for_uncertain_placement
    if self.object_taxon_name_id != self.subject_taxon_name.parent_id && self.type_name == 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      errors.add(:object_taxon_name_id, "The parent #{self.subject_taxon_name.parent.cached_html} and the Incertae Sedis placement (#{self.object_taxon_name.cached_html}) should match")
    end
  end

  def validate_subject_and_object_ranks
    tname = self.type_name

    if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      rank_group = self.subject_taxon_name.rank_class.try(:parent)
      unless rank_group == self.object_taxon_name.rank_class.try(:parent)
        errors.add(:object_taxon_name_id, "Rank of related taxon should be in the #{rank_group.try(:rank_name)} rank group, not #{self.object_taxon_name.rank_class.try(:rank_name)}")
      end
    end

    unless self.type_class.blank? # only validate if it is set
      if object_taxon_name
        if object_taxon_name.type == 'Protonym' || object_taxon_name.type == 'Hybrid'
          unless self.type_class.valid_object_ranks.include?(self.object_taxon_name.rank_string)
            errors.add(:object_taxon_name_id, "#{self.object_taxon_name.rank_class.rank_name.capitalize} rank of #{self.object_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
            errors.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.object_taxon_name.rank_class.rank_name} rank of #{self.object_taxon_name.cached_html}")
          end
        end
      end

      if subject_taxon_name
        if subject_taxon_name.type == 'Protonym' || subject_taxon_name.type == 'Hybrid'
          unless self.type_class.valid_subject_ranks.include?(self.subject_taxon_name.parent.rank_string)
            soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
            soft_validations.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.subject_taxon_name.rank_class.rank_name} rank of #{self.subject_taxon_name.cached_html}")
          end
        end
      end
    end
  end

  ##### Protonym historically could be listed as a synonym to different taxa
  #def validate_uniqueness_of_synonym_subject 
  #  if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains('Synonym').not_self(self).empty?
  #    errors.add(:subject_taxon_name_id, 'Only one synonym relationship is allowed')
  #  end
  #end

  def validate_uniqueness_of_typification_object
    if /Typification/.match(self.type_name) && !TaxonNameRelationship.where(object_taxon_name_id: self.object_taxon_name_id).with_type_contains('Typification').not_self(self).empty?
      errors.add(:object_taxon_name_id, 'Only one Type designation relationship is allowed')
    end
  end

  def validate_rank_group
    if self.type =~ /Hybrid/ && self.subject_taxon_name && self.object_taxon_name
      if self.subject_taxon_name.rank_class.parent != self.object_taxon_name.rank_class.parent
        errors.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the rank of hybrid (#{self.object_taxon_name.rank_class.rank_name})")
      end
    end
  end

  def validate_object_and_subject_both_protonyms
    if /TaxonNameRelationship::Combination::/.match(self.type)
      errors.add(:object_taxon_name_id, 'Not a Combination') if object_taxon_name.type != 'Combination'
    else
      errors.add(:object_taxon_name_id, 'Not a Protonym') if object_taxon_name.type == 'Combination'
    end
    errors.add(:subject_taxon_name_id, 'Not a Protonym') if subject_taxon_name.type == 'Combination'
  end

  # TODO: Isolate to individual classes per type
  def set_cached_names_for_taxon_names
    begin
      TaxonName.transaction do
        if is_combination?
          t = object_taxon_name

          t.send(:set_cached)

          if type_name =~/OriginalCombination/ 
            t.update_columns(
              cached_original_combination: t.get_original_combination,
              cached_original_combination_html: t.get_original_combination_html,
            )
          end

        elsif type_name =~/TaxonNameRelationship::Hybrid/ # TODO: move to Hybrid
          t = object_taxon_name
          t.update_columns(
            cached: t.get_full_name,
            cached_html: t.get_full_name_html
          )

        elsif type_name =~/SourceClassifiedAs/
          t = subject_taxon_name
          t.set_cached_classified_as
          # t.update_column(:cached_classified_as, t.get_cached_classified_as)

        elsif is_invalidating?
          t = subject_taxon_name
          
          if type_name =~/Misspelling/
            t.update_column(:cached_misspelling, t.get_cached_misspelling)
            t.update_columns(
                cached_author_year: t.get_author_and_year,
                cached_original_combination: t.get_original_combination,
                cached_original_combination_html: t.get_original_combination_html
            )
          end

          if type_name =~/Misapplication/
            t.update_column( :cached_author_year, t.get_author_and_year)
          end

          vn = t.get_valid_taxon_name

          t.update_columns(
            cached: t.get_full_name,
            cached_html: t.get_full_name_html, # OK to force reload here, otherwise we need an exception in #set_cached 
            cached_valid_taxon_name_id: vn.id)
          t.combination_list_self.each do |c|
            c.update_column(:cached_valid_taxon_name_id, vn.id)
          end

          vn.list_of_invalid_taxon_names.each do |s|
            s.update_column(:cached_valid_taxon_name_id, vn.id)
            s.combination_list_self.each do |c|
              c.update_column(:cached_valid_taxon_name_id, vn.id)
            end
          end
        end

      end

    # no point in rescuing and not returning somthing
    rescue ActiveRecord::RecordInvalid
      raise
    end
    false
  end

  def is_invalidating?
    TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(type_name)
  end

  def sv_validate_required_relationships
    object_relationships = TaxonNameRelationship.where_object_is_taxon_name(self.object_taxon_name).not_self(self).collect{|r| r.type}
    required = self.type_class.required_taxon_name_relationships - object_relationships
    required.each do |r|
      soft_validations.add(:type, " Presence of #{self.subject_status} requires selection of #{r.demodulize.underscore.humanize.downcase}")
    end
  end

  def sv_validate_disjoint_relationships
    tname = self.type_name
    if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      subject_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).not_self(self)
      subject_relationships.each  do |i|
        if self.type_class.disjoint_taxon_name_relationships.include?(i.type_name)
          soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with another relationship: '#{i.subject_status}'")
        end
      end
    end
  end

  def sv_validate_disjoint_object
    classifications = self.object_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
    disjoint_object_classes = self.type_class.disjoint_object_classes
    compare = disjoint_object_classes & classifications
    compare.each do |i|
      c = i.demodulize.underscore.humanize.downcase
      soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with the taxon status: '#{c}'")
      soft_validations.add(:object_taxon_name_id, "#{self.object_taxon_name.cached_html} has a conflicting status: '#{c}'")
    end
  end

  def sv_validate_disjoint_subject
    classifications = self.subject_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
    disjoint_subject_classes = self.type_class.disjoint_subject_classes
    compare = disjoint_subject_classes & classifications
    compare.each do |i|
      c = i.demodulize.underscore.humanize.downcase
      soft_validations.add(:type, "#{self.subject_status.capitalize} conflicting with the status: '#{c}'")
      soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.cached_html} has a conflicting status: '#{c}'")
    end
  end

  def sv_specific_relationship
    true # all validations moved to subclasses

#    s = subject_taxon_name
#    o = object_taxon_name
#    case type
#      when 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Subjective' || 'TaxonNameRelationship::Icn::Unaccepting::Synonym::Heterotypic'
#        if (s.type_taxon_name == o.type_taxon_name && !s.type_taxon_name.nil? ) || (!s.get_primary_type.empty? && s.has_same_primary_type(o) )
#          soft_validations.add(:type, "Subjective synonyms #{s.cached_html} and #{o.cached_html} should not have the same type")
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym'
#        # primary names don't match
#        if (s.cached_primary_homonym_alternative_spelling != o.cached_primary_homonym_alternative_spelling)
#          # there is a secondary name ... and it doesn't match either
#          if (s.cached_secondary_homonym_alternative_spelling.blank? && o.cached_secondary_homonym_alternative_spelling.blank?) || (s.cached_secondary_homonym_alternative_spelling != o.cached_secondary_homonym_alternative_spelling)
#            soft_validations.add(:type, "#{subject_taxon_name.cached_html_name_and_author_year} and #{object_taxon_name.cached_html_name_and_author_year} are not similar enough to be homonyms")
#          end
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary' || 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary::Forgotten' || 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary::Suppressed'
#        if s.original_genus != o.original_genus
#          soft_validations.add(:type, "Primary homonyms #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} should have the same original genus")
#        elsif s.cached_primary_homonym_alternative_spelling != o.cached_primary_homonym_alternative_spelling
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} are not similar enough to be homonyms")
#        end
#        if type == 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary::Forgotten' && s.year_of_publication > 1899
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} was not described after 1899")
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Secondary'
#        if s.original_genus == o.original_genus && !s.original_genus.nil?
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} species described in the same original genus #{s.original_genus}, they are primary homonyms")
#        elsif s.get_valid_taxon_name.ancestor_at_rank('genus') != o.get_valid_taxon_name.ancestor_at_rank('genus')
#          soft_validations.add(:type, "Secondary homonyms #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} should be placed in the same parent genus, the homonymy should be deleted or changed to 'secondary homonym replaced before 1961'")
#        elsif s.cached_secondary_homonym_alternative_spelling != o.cached_secondary_homonym_alternative_spelling
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} are not similar enough to be homonyms")
#        end

#        if (s.all_generic_placements & o.all_generic_placements).empty?
#          soft_validations.add(:base, "No combination available showing #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} placed in the same genus")
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Secondary::Secondary1961'
#        soft_validations.add(:type, "#{s.cached_html_name_and_author_year} was not described before 1961") if s.year_of_publication > 1960
#        soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} described in the same original genus #{s.original_genus}, they are primary homonyms") if s.original_genus == o.original_genus && !s.original_genus.nil?
#        soft_validations.add(:base, 'The original publication is not selected') unless source

#        soft_validations.add(:base, "#{s.cached_html_name_and_author_year} should not be treated as a homonym established before 1961") if self.source && self.source.year > 1960

#        if (s.all_generic_placements & o.all_generic_placements).empty?
#          soft_validations.add(:base, "No combination available showing #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} placed in the same genus")
#        end
#      when 'TaxonNameRelationship::Iczn::PotentiallyValidating::FamilyBefore1961'
#        soft_validations.add(:type, "#{s.cached_html_name_and_author_year} was not described before 1961") if s.year_of_publication > 1960
#        soft_validations.add(:base, "#{s.cached_html_name_and_author_year} should be accepted as a replacement name before 1961") if self.source && self.source.year > 1960
#      when 'TaxonNameRelationship::Typification::Genus::Subsequent::SubsequentDesignation'
#        soft_validations.add(:type, "Genus #{o.cached_html_name_and_author_year} described after 1930 is nomen nudum, if type was not designated in the original publication") if o.year_of_publication && o.year_of_publication > 1930
#      when 'TaxonNameRelationship::Iczn::PotentiallyValidating::ReplacementName'
#        r1 = TaxonNameRelationship.where(type: 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Objective::ReplacedHomonym', subject_taxon_name_id: o.id, object_taxon_name_id: s.id).first
#        r2 = TaxonNameRelationship.where(type: 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Objective::UnnecessaryReplacementName', subject_taxon_name_id: s.id, object_taxon_name_id: o.id).first
#        soft_validations.add(:base, "Missing relationship: #{s.cached_html_name_and_author_year} is a replacement name for #{o.cached_html_name_and_author_year}. Please add an objective synonym relationship (either 'replaced homonym' or 'unnecessary replacement name')") if r1.nil? && r2.nil?
#      when 'TaxonNameRelationship::Typification::Genus::Original::OriginalMonotypy'
#        # @todo Check if more than one species associated with the genus in the original paper
#    end
  end

  def sv_objective_synonym_relationship
    true # all validations moved to subclasses
#    if self.type_name =~ /TaxonNameRelationship::(Iczn::Invalidating::Synonym::Objective|Icn::Unaccepting::Synonym::Homotypic|Icnp::Unaccepting::Synonym::Homotypic)/
#      s = self.subject_taxon_name
#      o = self.object_taxon_name
#      if (s.type_taxon_name != o.type_taxon_name ) || !s.has_same_primary_type(o)
#        soft_validations.add(:type, "Objective synonyms #{s.cached_html} and #{o.cached_html} should have the same type")
#      end
#    end
  end

  def sv_synonym_relationship
    true # all validations moved to subclasses
#    relationships = TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM +
#      TaxonNameRelationship.collect_to_s(TaxonNameRelationship::Typification::Genus::Subsequent::SubsequentDesignation,
#                                         TaxonNameRelationship::Typification::Genus::Subsequent::RulingByCommission)
#    if relationships.include?(self.type_name)
#      if self.source
#        date1 = self.source.cached_nomenclature_date.to_time
#        date2 = self.subject_taxon_name.nomenclature_date
#        if !!date1 && !!date2
#          soft_validations.add(:base, "#{self.subject_taxon_name.cached_html_name_and_author_year} was not described at the time of citation (#{date1}") if date2 > date1
#        end
#      elsif TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING.include?(self.type_name)
#        # misspelling does not requere original publication
#      else
#        soft_validations.add(:base, 'The original publication is not selected')
#      end
#    end
  end

  def sv_not_specific_relationship
    true # all validations moved to subclasses

#    case self.type_name
#      when 'TaxonNameRelationship::Typification::Genus'
#        soft_validations.add(:type, 'Please specify if the type designation is original or subsequent')
#      when 'TaxonNameRelationship::Typification::Genus::Original'
#        soft_validations.add(:type, 'Please specify if this is Original Designation or Original Monotypy')
#      when 'TaxonNameRelationship::Typification::Genus::Subsequent'
#        soft_validations.add(:type, 'Please specify if this is Subsequent Designation or Subsequent Monotypy')
#      when 'TaxonNameRelationship::Typification::Genus::Tautonomy'
#        soft_validations.add(:type, 'Please specify if the tautonomy is absolute or Linnaean')
#      when 'TaxonNameRelationship::Icn::Unaccepting'
#        soft_validations.add(:type, 'Please specify the reasons for the name being Unaccepted')
#      when 'TaxonNameRelationship::Icn::Unaccepting::Synonym'
#        soft_validations.add(:type, 'Please specify if this is a homotypic or heterotypic synonym',
#          fix: :sv_fix_specify_synonymy_type, success_message: 'Synonym updated to being homotypic or heterotypic')
#      when 'TaxonNameRelationship::Icnp::Unaccepting::Synonym'
#        soft_validations.add(:type, 'Please specify if this is a objective or subjective synonym',
#          fix: :sv_fix_specify_synonymy_type, success_message: 'Synonym updated to being objective or subjective')
#      when 'TaxonNameRelationship::Iczn::Invalidating'
#        soft_validations.add(:type, 'Please specify the reason for the name being Invalid') unless self.subject_taxon_name.classification_invalid_or_unavailable?
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym'
#        if NomenclaturalRank::Iczn::SpeciesGroup.descendants.collect{|t| t.to_s}.include?(self.subject_taxon_name.rank_string)
#          soft_validations.add(:type, 'Please specify if this is a primary or secondary homonym',
#              fix: :sv_fix_specify_homonymy_type, success_message: 'Homonym updated to being primary or secondary')
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Synonym'
#        soft_validations.add(:type, 'Please specify if this is a objective or subjective synonym',
#            fix: :sv_fix_specify_synonymy_type, success_message: 'Synonym updated to being objective or subjective')
#      when 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Suppression'
#        soft_validations.add(:type, 'Please specify if this is a total, partial, or conditional suppression')
#    end
  end

  def sv_synonym_linked_to_valid_name
    #synonyms and misspellings should be linked to valid names
    if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
      obj = self.object_taxon_name
      subj = self.subject_taxon_name
        if subj.rank_class.try(:nomenclatural_code) == :iczn && obj.parent_id != subj.parent_id &&  subj.cached_valid_taxon_name_id == obj.cached_valid_taxon_name_id
        soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize}  #{subj.cached_html_name_and_author_year} should have the same parent with  #{obj.cached_html_name_and_author_year}",
                             fix: :sv_fix_subject_parent_update, success_message: 'The parent was updated')
      end
    end
  end

  #  def sv_fix_synonym_linked_to_valid_name
  #    if TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(self.type_name)
  #      obj = self.object_taxon_name
  #      unless obj.get_valid_taxon_name == obj
  #        self.object_taxon_name = obj.get_valid_taxon_name
  #        begin
  #          TaxonName.transaction do
  #            self.save
  #            return true
  #          end
  #        rescue
  #        end
  #      end
  #    end
  #    false
  #  end

  def sv_fix_subject_parent_update
    if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
      obj = self.object_taxon_name
      subj = self.subject_taxon_name
      unless obj.parent_id == subj.parent_id
        subj.parent_id = obj.parent_id
        begin
          TaxonName.transaction do
            subj.save
            return true
          end
        rescue
        end
      end
    end
    false
  end

  def subject_invalid_statuses
    TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID & self.subject_taxon_name.taxon_name_classifications.collect{|c| c.type_class.to_s}
  end

  def sv_validate_priority
    true # all validations moved to subclasses

#    unless self.type_class.nomenclatural_priority.nil?
#      date1 = self.subject_taxon_name.nomenclature_date
#      date2 = self.object_taxon_name.nomenclature_date
#      if !!date1 and !!date2
#        case self.type_class.nomenclatural_priority
#        when :direct
#          if date2 > date1 && subject_invalid_statuses.empty?
#            if self.type_name =~ /TaxonNameRelationship::Iczn::Invalidating::Homonym/
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be older than #{self.object_status} #{self.object_taxon_name.cached_html_name_and_author_year}")
#            elsif self.type_name =~ /::Iczn::/ && TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).with_two_type_bases('TaxonNameRelationship::Iczn::Invalidating::Homonym', 'TaxonNameRelationship::Iczn::Validating').not_self(self).empty?
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be older than #{self.object_status} #{self.object_taxon_name.cached_html_name_and_author_year}, unless it is also a homonym or conserved name")
#            elsif self.type_name =~ /::Icn::/ && TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).with_two_type_bases('TaxonNameRelationship::Icn::Accepting::Conserved', 'TaxonNameRelationship::Icn::Accepting::Sanctioned').not_self(self).empty?
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be older than #{self.object_status} #{self.object_taxon_name.cached_html_name_and_author_year}, unless it is also conserved or sanctioned name")
#            end
#          end
#        when :reverse
#          if date1 > date2 && subject_invalid_statuses.empty?
#            if self.type_name =~ /TaxonNameRelationship::(Typification|Combination|OriginalCombination)/
#              if self.type_name != 'TaxonNameRelationship::Typification::Genus::Subsequent::RulingByCommission' || (self.type_name =~ /TaxonNameRelationship::Typification::Genus::(Monotypy::SubsequentMonotypy|SubsequentDesignation)/ && date2 > '1930-12-31'.to_time)
#                soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be younger than #{self.object_taxon_name.cached_html_name_and_author_year}")
#              end
#            else
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be younger than #{self.object_taxon_name.cached_html_name_and_author_year}")
#            end
#          end
#        end
#      end
#    end
  end

  def sv_coordinated_taxa
    s = subject_taxon_name
    o = object_taxon_name
    s_new = s.lowest_rank_coordinated_taxon
    if s != s_new
      soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s.cached_html}",
                           fix: :sv_fix_coordinated_subject_taxa, success_message: "Relationship moved to  #{s_new.rank_class.rank_name}")
    end
  end

  def sv_coordinated_taxa_object
    s = subject_taxon_name
    o = object_taxon_name
    o_new = o.lowest_rank_coordinated_taxon
    if o != o_new && type_name != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o.cached_html}",
                           fix: :sv_fix_coordinated_object_taxa, success_message: "Relationship moved to  #{o_new.rank_class.rank_name}")
    end
  end

  def sv_fix_coordinated_subject_taxa
    s = subject_taxon_name
    s_new = s.lowest_rank_coordinated_taxon
    if s != s_new
      self.subject_taxon_name = s_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_fix_coordinated_object_taxa
    o = self.object_taxon_name
    o_new = o.lowest_rank_coordinated_taxon
    if o != o_new
      self.object_taxon_name = o_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_fix_combination_relationship
    s = self.subject_taxon_name
    list = s.list_of_coordinated_names + [s]
    if s.rank_string =~ /Species/
      s_new = list.detect{|t| t.rank_class.rank_name == 'species'}
    elsif s.rank_string =~ /Genus/
      s_new = list.detect{|t| t.rank_class.rank_name == 'genus'}
    else
      s_new = s
    end
    if s != s_new && !s.nil?
      self.subject_taxon_name = s_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def self.collect_to_s(*args)
    args.collect{|arg| arg.to_s}
  end

  def self.collect_descendants_to_s(*classes)
    ans = []
    classes.each do |klass|
      ans += klass.descendants.collect{|k| k.to_s}
    end
    ans
  end

  def self.collect_descendants_and_itself_to_s(*classes)
    classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes)
  end
end

#typeString

Returns the relationship/“predicate” between the subject and object taxon names.

Returns:

  • (String)

    the relationship/“predicate” between the subject and object taxon names


44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
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
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
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
481
482
483
484
485
486
487
488
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
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
# File 'app/models/taxon_name_relationship.rb', line 44

class TaxonNameRelationship < ApplicationRecord
  include Housekeeping
  include Shared::Citations
  include Shared::Notes
  include Shared::IsData
  include SoftValidation

  # @return [Boolean, nil]
  #   When true, cached values are not built
  attr_accessor :no_cached

  belongs_to :subject_taxon_name, class_name: 'TaxonName', foreign_key: :subject_taxon_name_id, inverse_of: :taxon_name_relationships # left side
  belongs_to :object_taxon_name, class_name: 'TaxonName', foreign_key: :object_taxon_name_id, inverse_of: :related_taxon_name_relationships # right side

  after_save :set_cached_names_for_taxon_names, unless: -> {self.no_cached}
  after_destroy :set_cached_names_for_taxon_names, unless: -> {self.no_cached}

  validates_presence_of :type, message: 'Relationship type should be specified'
  validates_presence_of :subject_taxon_name, message: 'Missing taxon name on the left side'
  validates_presence_of :object_taxon_name, message: 'Missing taxon name on the right side'

  validates_uniqueness_of :object_taxon_name_id, scope: :type, if: :is_combination?
  validates_uniqueness_of :object_taxon_name_id, scope: [:type, :subject_taxon_name_id], unless: :is_combination?

  validate :validate_type, :validate_subject_and_object_are_not_identical

  validate :subject_and_object_in_same_project

  with_options unless: -> {!subject_taxon_name || !object_taxon_name} do |v|
    v.validate :validate_subject_and_object_share_code,
      :validate_uniqueness_of_typification_object,
      #:validate_uniqueness_of_synonym_subject,
      :validate_object_and_subject_both_protonyms,
      :validate_object_must_equal_subject_for_uncertain_placement,
      :validate_subject_and_object_ranks,
      :validate_rank_group
  end

  soft_validate(:sv_validate_required_relationships, set: :validate_required_relationships, has_fix: false)
  soft_validate(:sv_validate_disjoint_relationships, set: :validate_disjoint_relationships, has_fix: false)
  soft_validate(:sv_validate_disjoint_object, set: :validate_disjoint_object, has_fix: false)
  soft_validate(:sv_validate_disjoint_subject, set: :validate_disjoint_subject, has_fix: false)
  soft_validate(:sv_specific_relationship, set: :specific_relationship, has_fix: false) # some do, some don't
  soft_validate(:sv_objective_synonym_relationship, set: :objective_synonym_relationship, has_fix: false)
  soft_validate(:sv_synonym_relationship, set: :synonym_relationship, has_fix: false)
  soft_validate(:sv_not_specific_relationship, set: :not_specific_relationship, has_fix: true)
  soft_validate(:sv_synonym_linked_to_valid_name, set: :synonym_linked_to_valid_name, has_fix: true)
  soft_validate(:sv_validate_priority, set: :validate_priority, has_fix: false)
  soft_validate(:sv_coordinated_taxa, set: :coordinated_taxa, has_fix: true)
  soft_validate(:sv_coordinated_taxa_object, set: :coordinated_taxa, has_fix: true)

  scope :where_subject_is_taxon_name, -> (taxon_name) {where(subject_taxon_name_id: taxon_name)}
  scope :where_object_is_taxon_name, -> (taxon_name) {where(object_taxon_name_id: taxon_name)}
  scope :where_object_in_taxon_names, -> (taxon_name_array) {where('"taxon_name_relationships"."object_taxon_name_id" IN (?)', taxon_name_array)}

  scope :with_type_string, -> (type_string) { where(sanitize_sql_array(["taxon_name_relationships.type = '%s'", type_string])) }

  scope :with_type_base, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "#{base_string}%")}
  scope :with_type_contains, -> (base_string) {where('"taxon_name_relationships"."type" LIKE ?', "%#{base_string}%")}

  scope :with_two_type_bases, -> (base_string1, base_string2) {
    where("taxon_name_relationships.type LIKE ? OR taxon_name_relationships.type LIKE ?", "#{base_string1}%", "#{base_string2}%") }

  scope :homonym_or_suppressed, -> {where("taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Homonym%' OR taxon_name_relationships.type LIKE 'TaxonNameRelationship::Iczn::Invalidating::Suppression::Total'") }
  scope :with_type_array, -> (base_array) {where('taxon_name_relationships.type IN (?)', base_array ) }

  # @return [Array of TaxonNameClassification]
  #  the inferable TaxonNameClassification(s) added to the subject when this relationship is used
  #  !! Not implemented
  def subject_properties
    []
  end

  # @return [Array of TaxonNameClassification]
  #  the inferable TaxonNameClassification(s) added to the subject when this relationship is used
  #  !! Not implmented
  def object_properties
    []
  end

  # @return class
  #   this method calls Module#module_parent
  def self.parent
    self.module_parent
  end

  # @return [Array of NomenclatureRank]
  #   the valid ranks to which the subject name can belong, set in subclasses. (left side)
  def self.valid_subject_ranks
    []
  end

  # @return [Array of NomenclatureRank]
  #   the valid ranks to which the object name can belong, set in subclasses. (right side)
  def self.valid_object_ranks
    []
  end

  # @return [Array of TaxonNameRelationships]
  #   if this relationships is set for the subject, then others in this array should not be used for that subject
  def self.disjoint_taxon_name_relationships
    []
  end

  # TODO: why isn't this disjoint?
  # disjoint relationships for the taxon as a object
  def self.required_taxon_name_relationships
    []
  end

  def self.disjoint_subject_classes
    []
  end

  def self.disjoint_object_classes
    []
  end

  def self.gbif_status_of_subject
    nil
  end

  def self.gbif_status_of_object
    nil
  end

  def self.assignable
    false
  end

  # @return [Symbol]
  #   determine the relative age of subject and object
  #   :direct - subject is younger than object
  #   :reverse - object is younger than subject
  def self.nomenclatural_priority
    nil
  end

  # @return [String]
  #    the status inferred by the relationship to the object name
  def object_status
    self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
  end

  # @return [String]
  #    the status inferred by the relationship to the subject name
  def subject_status
    self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
  end

  # @return [String]
  #    the connecting word in the relationship from the subject name to object name
  def subject_status_connector_to_object
    ' of'
  end

  # @return [String]
  #    the connecting word in the relationship from the object name to subject name
  def object_status_connector_to_subject
    ' of'
  end

  # @return [String]
  #   a readable fragement combining status and connector
  def subject_status_tag
    subject_status + subject_status_connector_to_object
  end

  # @return [String]
  #   a readable fragement combining status and connector
  def object_status_tag
    object_status + object_status_connector_to_subject
  end

  # @return [String, nil]
  #   the type of this relationship, IF the type is a valid name, else nil
  def type_name
    r = self.type
    TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r : nil
  end

  def type_class=(value)
    write_attribute(:type, value.to_s)
  end

  # @return [TaxonNameRelationship, String]
  #    the type as a class, if legal, else a string  ! Strangeish
  def type_class
    r = read_attribute(:type).to_s
    TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r.safe_constantize : r
  end

  # @return [String, nil]
  #   the NOMEN uri for this type
  def self.nomen_uri
    const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil
  end

  # @return [Time]
  #   effective date of publication, used to determine nomenclatural priorities
  def nomenclature_date
    self.source ? (self.source.cached_nomenclature_date ? self.source.cached_nomenclature_date.to_time : Time.now) : Time.now
  end

  # @TODO SourceClassifiedAs is not really Combination in the other sense
  def is_combination?
    !!/TaxonNameRelationship::(OriginalCombination|Combination)/.match(self.type.to_s)
  end

  protected

  def subject_and_object_in_same_project
    if subject_taxon_name && object_taxon_name
      errors.add(:base, 'one name is not in the same project as the other') if subject_taxon_name.project_id != object_taxon_name.project_id
    end
  end

  def validate_type
    unless TAXON_NAME_RELATIONSHIP_NAMES.include?(type)
      errors.add(:type, "'#{type}' is not a valid taxon name relationship")
    end

    if object_taxon_name.class.to_s == 'Protonym' || object_taxon_name.class.to_s == 'Hybrid'
      errors.add(:type, "'#{type}' is not a valid taxon name relationship") if /TaxonNameRelationship::Combination::/.match(self.type)
    end

    if object_taxon_name.class.to_s == 'Combination'
      errors.add(:type, "'#{type}' is not a valid taxon name relationship") unless /TaxonNameRelationship::Combination::/.match(self.type)
    end
  end

  # @todo validate, that all the relationships in the table could be linked to relationships in classes (if those had changed)

  def validate_subject_and_object_share_code
    if object_taxon_name.type  == 'Protonym' && subject_taxon_name.type == 'Protonym'
      errors.add(:object_taxon_name_id, 'The related taxon is not in the same monenclatural group (ICZN, ICN, ICNP, ICTV') if subject_taxon_name.rank_class.try(:nomenclatural_code) != object_taxon_name.rank_class.try(:nomenclatural_code)
    end
  end

  def validate_subject_and_object_are_not_identical
    if !self.object_taxon_name_id.nil? && self.object_taxon_name == self.subject_taxon_name
      errors.add(:object_taxon_name_id, "#{self.object_taxon_name.try(:cached_html).to_s} should not refer to itself") unless self.type =~ /OriginalCombination/
    end
  end

  def validate_object_must_equal_subject_for_uncertain_placement
    if self.object_taxon_name_id != self.subject_taxon_name.parent_id && self.type_name == 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      errors.add(:object_taxon_name_id, "The parent #{self.subject_taxon_name.parent.cached_html} and the Incertae Sedis placement (#{self.object_taxon_name.cached_html}) should match")
    end
  end

  def validate_subject_and_object_ranks
    tname = self.type_name

    if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      rank_group = self.subject_taxon_name.rank_class.try(:parent)
      unless rank_group == self.object_taxon_name.rank_class.try(:parent)
        errors.add(:object_taxon_name_id, "Rank of related taxon should be in the #{rank_group.try(:rank_name)} rank group, not #{self.object_taxon_name.rank_class.try(:rank_name)}")
      end
    end

    unless self.type_class.blank? # only validate if it is set
      if object_taxon_name
        if object_taxon_name.type == 'Protonym' || object_taxon_name.type == 'Hybrid'
          unless self.type_class.valid_object_ranks.include?(self.object_taxon_name.rank_string)
            errors.add(:object_taxon_name_id, "#{self.object_taxon_name.rank_class.rank_name.capitalize} rank of #{self.object_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
            errors.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.object_taxon_name.rank_class.rank_name} rank of #{self.object_taxon_name.cached_html}")
          end
        end
      end

      if subject_taxon_name
        if subject_taxon_name.type == 'Protonym' || subject_taxon_name.type == 'Hybrid'
          unless self.type_class.valid_subject_ranks.include?(self.subject_taxon_name.parent.rank_string)
            soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
            soft_validations.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.subject_taxon_name.rank_class.rank_name} rank of #{self.subject_taxon_name.cached_html}")
          end
        end
      end
    end
  end

  ##### Protonym historically could be listed as a synonym to different taxa
  #def validate_uniqueness_of_synonym_subject 
  #  if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains('Synonym').not_self(self).empty?
  #    errors.add(:subject_taxon_name_id, 'Only one synonym relationship is allowed')
  #  end
  #end

  def validate_uniqueness_of_typification_object
    if /Typification/.match(self.type_name) && !TaxonNameRelationship.where(object_taxon_name_id: self.object_taxon_name_id).with_type_contains('Typification').not_self(self).empty?
      errors.add(:object_taxon_name_id, 'Only one Type designation relationship is allowed')
    end
  end

  def validate_rank_group
    if self.type =~ /Hybrid/ && self.subject_taxon_name && self.object_taxon_name
      if self.subject_taxon_name.rank_class.parent != self.object_taxon_name.rank_class.parent
        errors.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the rank of hybrid (#{self.object_taxon_name.rank_class.rank_name})")
      end
    end
  end

  def validate_object_and_subject_both_protonyms
    if /TaxonNameRelationship::Combination::/.match(self.type)
      errors.add(:object_taxon_name_id, 'Not a Combination') if object_taxon_name.type != 'Combination'
    else
      errors.add(:object_taxon_name_id, 'Not a Protonym') if object_taxon_name.type == 'Combination'
    end
    errors.add(:subject_taxon_name_id, 'Not a Protonym') if subject_taxon_name.type == 'Combination'
  end

  # TODO: Isolate to individual classes per type
  def set_cached_names_for_taxon_names
    begin
      TaxonName.transaction do
        if is_combination?
          t = object_taxon_name

          t.send(:set_cached)

          if type_name =~/OriginalCombination/ 
            t.update_columns(
              cached_original_combination: t.get_original_combination,
              cached_original_combination_html: t.get_original_combination_html,
            )
          end

        elsif type_name =~/TaxonNameRelationship::Hybrid/ # TODO: move to Hybrid
          t = object_taxon_name
          t.update_columns(
            cached: t.get_full_name,
            cached_html: t.get_full_name_html
          )

        elsif type_name =~/SourceClassifiedAs/
          t = subject_taxon_name
          t.set_cached_classified_as
          # t.update_column(:cached_classified_as, t.get_cached_classified_as)

        elsif is_invalidating?
          t = subject_taxon_name
          
          if type_name =~/Misspelling/
            t.update_column(:cached_misspelling, t.get_cached_misspelling)
            t.update_columns(
                cached_author_year: t.get_author_and_year,
                cached_original_combination: t.get_original_combination,
                cached_original_combination_html: t.get_original_combination_html
            )
          end

          if type_name =~/Misapplication/
            t.update_column( :cached_author_year, t.get_author_and_year)
          end

          vn = t.get_valid_taxon_name

          t.update_columns(
            cached: t.get_full_name,
            cached_html: t.get_full_name_html, # OK to force reload here, otherwise we need an exception in #set_cached 
            cached_valid_taxon_name_id: vn.id)
          t.combination_list_self.each do |c|
            c.update_column(:cached_valid_taxon_name_id, vn.id)
          end

          vn.list_of_invalid_taxon_names.each do |s|
            s.update_column(:cached_valid_taxon_name_id, vn.id)
            s.combination_list_self.each do |c|
              c.update_column(:cached_valid_taxon_name_id, vn.id)
            end
          end
        end

      end

    # no point in rescuing and not returning somthing
    rescue ActiveRecord::RecordInvalid
      raise
    end
    false
  end

  def is_invalidating?
    TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(type_name)
  end

  def sv_validate_required_relationships
    object_relationships = TaxonNameRelationship.where_object_is_taxon_name(self.object_taxon_name).not_self(self).collect{|r| r.type}
    required = self.type_class.required_taxon_name_relationships - object_relationships
    required.each do |r|
      soft_validations.add(:type, " Presence of #{self.subject_status} requires selection of #{r.demodulize.underscore.humanize.downcase}")
    end
  end

  def sv_validate_disjoint_relationships
    tname = self.type_name
    if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      subject_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).not_self(self)
      subject_relationships.each  do |i|
        if self.type_class.disjoint_taxon_name_relationships.include?(i.type_name)
          soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with another relationship: '#{i.subject_status}'")
        end
      end
    end
  end

  def sv_validate_disjoint_object
    classifications = self.object_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
    disjoint_object_classes = self.type_class.disjoint_object_classes
    compare = disjoint_object_classes & classifications
    compare.each do |i|
      c = i.demodulize.underscore.humanize.downcase
      soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with the taxon status: '#{c}'")
      soft_validations.add(:object_taxon_name_id, "#{self.object_taxon_name.cached_html} has a conflicting status: '#{c}'")
    end
  end

  def sv_validate_disjoint_subject
    classifications = self.subject_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
    disjoint_subject_classes = self.type_class.disjoint_subject_classes
    compare = disjoint_subject_classes & classifications
    compare.each do |i|
      c = i.demodulize.underscore.humanize.downcase
      soft_validations.add(:type, "#{self.subject_status.capitalize} conflicting with the status: '#{c}'")
      soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.cached_html} has a conflicting status: '#{c}'")
    end
  end

  def sv_specific_relationship
    true # all validations moved to subclasses

#    s = subject_taxon_name
#    o = object_taxon_name
#    case type
#      when 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Subjective' || 'TaxonNameRelationship::Icn::Unaccepting::Synonym::Heterotypic'
#        if (s.type_taxon_name == o.type_taxon_name && !s.type_taxon_name.nil? ) || (!s.get_primary_type.empty? && s.has_same_primary_type(o) )
#          soft_validations.add(:type, "Subjective synonyms #{s.cached_html} and #{o.cached_html} should not have the same type")
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym'
#        # primary names don't match
#        if (s.cached_primary_homonym_alternative_spelling != o.cached_primary_homonym_alternative_spelling)
#          # there is a secondary name ... and it doesn't match either
#          if (s.cached_secondary_homonym_alternative_spelling.blank? && o.cached_secondary_homonym_alternative_spelling.blank?) || (s.cached_secondary_homonym_alternative_spelling != o.cached_secondary_homonym_alternative_spelling)
#            soft_validations.add(:type, "#{subject_taxon_name.cached_html_name_and_author_year} and #{object_taxon_name.cached_html_name_and_author_year} are not similar enough to be homonyms")
#          end
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary' || 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary::Forgotten' || 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary::Suppressed'
#        if s.original_genus != o.original_genus
#          soft_validations.add(:type, "Primary homonyms #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} should have the same original genus")
#        elsif s.cached_primary_homonym_alternative_spelling != o.cached_primary_homonym_alternative_spelling
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} are not similar enough to be homonyms")
#        end
#        if type == 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary::Forgotten' && s.year_of_publication > 1899
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} was not described after 1899")
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Secondary'
#        if s.original_genus == o.original_genus && !s.original_genus.nil?
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} species described in the same original genus #{s.original_genus}, they are primary homonyms")
#        elsif s.get_valid_taxon_name.ancestor_at_rank('genus') != o.get_valid_taxon_name.ancestor_at_rank('genus')
#          soft_validations.add(:type, "Secondary homonyms #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} should be placed in the same parent genus, the homonymy should be deleted or changed to 'secondary homonym replaced before 1961'")
#        elsif s.cached_secondary_homonym_alternative_spelling != o.cached_secondary_homonym_alternative_spelling
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} are not similar enough to be homonyms")
#        end

#        if (s.all_generic_placements & o.all_generic_placements).empty?
#          soft_validations.add(:base, "No combination available showing #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} placed in the same genus")
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Secondary::Secondary1961'
#        soft_validations.add(:type, "#{s.cached_html_name_and_author_year} was not described before 1961") if s.year_of_publication > 1960
#        soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} described in the same original genus #{s.original_genus}, they are primary homonyms") if s.original_genus == o.original_genus && !s.original_genus.nil?
#        soft_validations.add(:base, 'The original publication is not selected') unless source

#        soft_validations.add(:base, "#{s.cached_html_name_and_author_year} should not be treated as a homonym established before 1961") if self.source && self.source.year > 1960

#        if (s.all_generic_placements & o.all_generic_placements).empty?
#          soft_validations.add(:base, "No combination available showing #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} placed in the same genus")
#        end
#      when 'TaxonNameRelationship::Iczn::PotentiallyValidating::FamilyBefore1961'
#        soft_validations.add(:type, "#{s.cached_html_name_and_author_year} was not described before 1961") if s.year_of_publication > 1960
#        soft_validations.add(:base, "#{s.cached_html_name_and_author_year} should be accepted as a replacement name before 1961") if self.source && self.source.year > 1960
#      when 'TaxonNameRelationship::Typification::Genus::Subsequent::SubsequentDesignation'
#        soft_validations.add(:type, "Genus #{o.cached_html_name_and_author_year} described after 1930 is nomen nudum, if type was not designated in the original publication") if o.year_of_publication && o.year_of_publication > 1930
#      when 'TaxonNameRelationship::Iczn::PotentiallyValidating::ReplacementName'
#        r1 = TaxonNameRelationship.where(type: 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Objective::ReplacedHomonym', subject_taxon_name_id: o.id, object_taxon_name_id: s.id).first
#        r2 = TaxonNameRelationship.where(type: 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Objective::UnnecessaryReplacementName', subject_taxon_name_id: s.id, object_taxon_name_id: o.id).first
#        soft_validations.add(:base, "Missing relationship: #{s.cached_html_name_and_author_year} is a replacement name for #{o.cached_html_name_and_author_year}. Please add an objective synonym relationship (either 'replaced homonym' or 'unnecessary replacement name')") if r1.nil? && r2.nil?
#      when 'TaxonNameRelationship::Typification::Genus::Original::OriginalMonotypy'
#        # @todo Check if more than one species associated with the genus in the original paper
#    end
  end

  def sv_objective_synonym_relationship
    true # all validations moved to subclasses
#    if self.type_name =~ /TaxonNameRelationship::(Iczn::Invalidating::Synonym::Objective|Icn::Unaccepting::Synonym::Homotypic|Icnp::Unaccepting::Synonym::Homotypic)/
#      s = self.subject_taxon_name
#      o = self.object_taxon_name
#      if (s.type_taxon_name != o.type_taxon_name ) || !s.has_same_primary_type(o)
#        soft_validations.add(:type, "Objective synonyms #{s.cached_html} and #{o.cached_html} should have the same type")
#      end
#    end
  end

  def sv_synonym_relationship
    true # all validations moved to subclasses
#    relationships = TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM +
#      TaxonNameRelationship.collect_to_s(TaxonNameRelationship::Typification::Genus::Subsequent::SubsequentDesignation,
#                                         TaxonNameRelationship::Typification::Genus::Subsequent::RulingByCommission)
#    if relationships.include?(self.type_name)
#      if self.source
#        date1 = self.source.cached_nomenclature_date.to_time
#        date2 = self.subject_taxon_name.nomenclature_date
#        if !!date1 && !!date2
#          soft_validations.add(:base, "#{self.subject_taxon_name.cached_html_name_and_author_year} was not described at the time of citation (#{date1}") if date2 > date1
#        end
#      elsif TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING.include?(self.type_name)
#        # misspelling does not requere original publication
#      else
#        soft_validations.add(:base, 'The original publication is not selected')
#      end
#    end
  end

  def sv_not_specific_relationship
    true # all validations moved to subclasses

#    case self.type_name
#      when 'TaxonNameRelationship::Typification::Genus'
#        soft_validations.add(:type, 'Please specify if the type designation is original or subsequent')
#      when 'TaxonNameRelationship::Typification::Genus::Original'
#        soft_validations.add(:type, 'Please specify if this is Original Designation or Original Monotypy')
#      when 'TaxonNameRelationship::Typification::Genus::Subsequent'
#        soft_validations.add(:type, 'Please specify if this is Subsequent Designation or Subsequent Monotypy')
#      when 'TaxonNameRelationship::Typification::Genus::Tautonomy'
#        soft_validations.add(:type, 'Please specify if the tautonomy is absolute or Linnaean')
#      when 'TaxonNameRelationship::Icn::Unaccepting'
#        soft_validations.add(:type, 'Please specify the reasons for the name being Unaccepted')
#      when 'TaxonNameRelationship::Icn::Unaccepting::Synonym'
#        soft_validations.add(:type, 'Please specify if this is a homotypic or heterotypic synonym',
#          fix: :sv_fix_specify_synonymy_type, success_message: 'Synonym updated to being homotypic or heterotypic')
#      when 'TaxonNameRelationship::Icnp::Unaccepting::Synonym'
#        soft_validations.add(:type, 'Please specify if this is a objective or subjective synonym',
#          fix: :sv_fix_specify_synonymy_type, success_message: 'Synonym updated to being objective or subjective')
#      when 'TaxonNameRelationship::Iczn::Invalidating'
#        soft_validations.add(:type, 'Please specify the reason for the name being Invalid') unless self.subject_taxon_name.classification_invalid_or_unavailable?
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym'
#        if NomenclaturalRank::Iczn::SpeciesGroup.descendants.collect{|t| t.to_s}.include?(self.subject_taxon_name.rank_string)
#          soft_validations.add(:type, 'Please specify if this is a primary or secondary homonym',
#              fix: :sv_fix_specify_homonymy_type, success_message: 'Homonym updated to being primary or secondary')
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Synonym'
#        soft_validations.add(:type, 'Please specify if this is a objective or subjective synonym',
#            fix: :sv_fix_specify_synonymy_type, success_message: 'Synonym updated to being objective or subjective')
#      when 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Suppression'
#        soft_validations.add(:type, 'Please specify if this is a total, partial, or conditional suppression')
#    end
  end

  def sv_synonym_linked_to_valid_name
    #synonyms and misspellings should be linked to valid names
    if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
      obj = self.object_taxon_name
      subj = self.subject_taxon_name
        if subj.rank_class.try(:nomenclatural_code) == :iczn && obj.parent_id != subj.parent_id &&  subj.cached_valid_taxon_name_id == obj.cached_valid_taxon_name_id
        soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize}  #{subj.cached_html_name_and_author_year} should have the same parent with  #{obj.cached_html_name_and_author_year}",
                             fix: :sv_fix_subject_parent_update, success_message: 'The parent was updated')
      end
    end
  end

  #  def sv_fix_synonym_linked_to_valid_name
  #    if TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(self.type_name)
  #      obj = self.object_taxon_name
  #      unless obj.get_valid_taxon_name == obj
  #        self.object_taxon_name = obj.get_valid_taxon_name
  #        begin
  #          TaxonName.transaction do
  #            self.save
  #            return true
  #          end
  #        rescue
  #        end
  #      end
  #    end
  #    false
  #  end

  def sv_fix_subject_parent_update
    if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
      obj = self.object_taxon_name
      subj = self.subject_taxon_name
      unless obj.parent_id == subj.parent_id
        subj.parent_id = obj.parent_id
        begin
          TaxonName.transaction do
            subj.save
            return true
          end
        rescue
        end
      end
    end
    false
  end

  def subject_invalid_statuses
    TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID & self.subject_taxon_name.taxon_name_classifications.collect{|c| c.type_class.to_s}
  end

  def sv_validate_priority
    true # all validations moved to subclasses

#    unless self.type_class.nomenclatural_priority.nil?
#      date1 = self.subject_taxon_name.nomenclature_date
#      date2 = self.object_taxon_name.nomenclature_date
#      if !!date1 and !!date2
#        case self.type_class.nomenclatural_priority
#        when :direct
#          if date2 > date1 && subject_invalid_statuses.empty?
#            if self.type_name =~ /TaxonNameRelationship::Iczn::Invalidating::Homonym/
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be older than #{self.object_status} #{self.object_taxon_name.cached_html_name_and_author_year}")
#            elsif self.type_name =~ /::Iczn::/ && TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).with_two_type_bases('TaxonNameRelationship::Iczn::Invalidating::Homonym', 'TaxonNameRelationship::Iczn::Validating').not_self(self).empty?
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be older than #{self.object_status} #{self.object_taxon_name.cached_html_name_and_author_year}, unless it is also a homonym or conserved name")
#            elsif self.type_name =~ /::Icn::/ && TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).with_two_type_bases('TaxonNameRelationship::Icn::Accepting::Conserved', 'TaxonNameRelationship::Icn::Accepting::Sanctioned').not_self(self).empty?
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be older than #{self.object_status} #{self.object_taxon_name.cached_html_name_and_author_year}, unless it is also conserved or sanctioned name")
#            end
#          end
#        when :reverse
#          if date1 > date2 && subject_invalid_statuses.empty?
#            if self.type_name =~ /TaxonNameRelationship::(Typification|Combination|OriginalCombination)/
#              if self.type_name != 'TaxonNameRelationship::Typification::Genus::Subsequent::RulingByCommission' || (self.type_name =~ /TaxonNameRelationship::Typification::Genus::(Monotypy::SubsequentMonotypy|SubsequentDesignation)/ && date2 > '1930-12-31'.to_time)
#                soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be younger than #{self.object_taxon_name.cached_html_name_and_author_year}")
#              end
#            else
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be younger than #{self.object_taxon_name.cached_html_name_and_author_year}")
#            end
#          end
#        end
#      end
#    end
  end

  def sv_coordinated_taxa
    s = subject_taxon_name
    o = object_taxon_name
    s_new = s.lowest_rank_coordinated_taxon
    if s != s_new
      soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s.cached_html}",
                           fix: :sv_fix_coordinated_subject_taxa, success_message: "Relationship moved to  #{s_new.rank_class.rank_name}")
    end
  end

  def sv_coordinated_taxa_object
    s = subject_taxon_name
    o = object_taxon_name
    o_new = o.lowest_rank_coordinated_taxon
    if o != o_new && type_name != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
      soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o.cached_html}",
                           fix: :sv_fix_coordinated_object_taxa, success_message: "Relationship moved to  #{o_new.rank_class.rank_name}")
    end
  end

  def sv_fix_coordinated_subject_taxa
    s = subject_taxon_name
    s_new = s.lowest_rank_coordinated_taxon
    if s != s_new
      self.subject_taxon_name = s_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_fix_coordinated_object_taxa
    o = self.object_taxon_name
    o_new = o.lowest_rank_coordinated_taxon
    if o != o_new
      self.object_taxon_name = o_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def sv_fix_combination_relationship
    s = self.subject_taxon_name
    list = s.list_of_coordinated_names + [s]
    if s.rank_string =~ /Species/
      s_new = list.detect{|t| t.rank_class.rank_name == 'species'}
    elsif s.rank_string =~ /Genus/
      s_new = list.detect{|t| t.rank_class.rank_name == 'genus'}
    else
      s_new = s
    end
    if s != s_new && !s.nil?
      self.subject_taxon_name = s_new
      begin
        TaxonNameRelationship.transaction do
          self.save
          return true
        end
      rescue
      end
    end
    false
  end

  def self.collect_to_s(*args)
    args.collect{|arg| arg.to_s}
  end

  def self.collect_descendants_to_s(*classes)
    ans = []
    classes.each do |klass|
      ans += klass.descendants.collect{|k| k.to_s}
    end
    ans
  end

  def self.collect_descendants_and_itself_to_s(*classes)
    classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes)
  end
end

Class Method Details

.assignableObject


170
171
172
# File 'app/models/taxon_name_relationship.rb', line 170

def self.assignable
  false
end

.collect_descendants_and_itself_to_s(*classes) ⇒ Object (protected)


773
774
775
# File 'app/models/taxon_name_relationship.rb', line 773

def self.collect_descendants_and_itself_to_s(*classes)
  classes.collect{|k| k.to_s} + self.collect_descendants_to_s(*classes)
end

.collect_descendants_to_s(*classes) ⇒ Object (protected)


765
766
767
768
769
770
771
# File 'app/models/taxon_name_relationship.rb', line 765

def self.collect_descendants_to_s(*classes)
  ans = []
  classes.each do |klass|
    ans += klass.descendants.collect{|k| k.to_s}
  end
  ans
end

.collect_to_s(*args) ⇒ Object (protected)


761
762
763
# File 'app/models/taxon_name_relationship.rb', line 761

def self.collect_to_s(*args)
  args.collect{|arg| arg.to_s}
end

.disjoint_object_classesObject


158
159
160
# File 'app/models/taxon_name_relationship.rb', line 158

def self.disjoint_object_classes
  []
end

.disjoint_subject_classesObject


154
155
156
# File 'app/models/taxon_name_relationship.rb', line 154

def self.disjoint_subject_classes
  []
end

.disjoint_taxon_name_relationshipsArray of TaxonNameRelationships

Returns if this relationships is set for the subject, then others in this array should not be used for that subject.

Returns:

  • (Array of TaxonNameRelationships)

    if this relationships is set for the subject, then others in this array should not be used for that subject


144
145
146
# File 'app/models/taxon_name_relationship.rb', line 144

def self.disjoint_taxon_name_relationships
  []
end

.gbif_status_of_objectObject


166
167
168
# File 'app/models/taxon_name_relationship.rb', line 166

def self.gbif_status_of_object
  nil
end

.gbif_status_of_subjectObject


162
163
164
# File 'app/models/taxon_name_relationship.rb', line 162

def self.gbif_status_of_subject
  nil
end

.nomen_uriString?

Returns the NOMEN uri for this type.

Returns:

  • (String, nil)

    the NOMEN uri for this type


238
239
240
# File 'app/models/taxon_name_relationship.rb', line 238

def self.nomen_uri
  const_defined?(:NOMEN_URI, false) ? self::NOMEN_URI : nil
end

.nomenclatural_prioritySymbol

Returns determine the relative age of subject and object :direct - subject is younger than object :reverse - object is younger than subject.

Returns:

  • (Symbol)

    determine the relative age of subject and object :direct - subject is younger than object :reverse - object is younger than subject


178
179
180
# File 'app/models/taxon_name_relationship.rb', line 178

def self.nomenclatural_priority
  nil
end

.parentObject

Returns class this method calls Module#module_parent.

Returns:

  • class this method calls Module#module_parent


126
127
128
# File 'app/models/taxon_name_relationship.rb', line 126

def self.parent
  self.module_parent
end

.required_taxon_name_relationshipsObject

TODO: why isn't this disjoint? disjoint relationships for the taxon as a object


150
151
152
# File 'app/models/taxon_name_relationship.rb', line 150

def self.required_taxon_name_relationships
  []
end

.valid_object_ranksArray of NomenclatureRank

Returns the valid ranks to which the object name can belong, set in subclasses. (right side).

Returns:

  • (Array of NomenclatureRank)

    the valid ranks to which the object name can belong, set in subclasses. (right side)


138
139
140
# File 'app/models/taxon_name_relationship.rb', line 138

def self.valid_object_ranks
  []
end

.valid_subject_ranksArray of NomenclatureRank

Returns the valid ranks to which the subject name can belong, set in subclasses. (left side).

Returns:

  • (Array of NomenclatureRank)

    the valid ranks to which the subject name can belong, set in subclasses. (left side)


132
133
134
# File 'app/models/taxon_name_relationship.rb', line 132

def self.valid_subject_ranks
  []
end

Instance Method Details

#is_combination?Boolean

Returns:

  • (Boolean)

249
250
251
# File 'app/models/taxon_name_relationship.rb', line 249

def is_combination?
  !!/TaxonNameRelationship::(OriginalCombination|Combination)/.match(self.type.to_s)
end

#is_invalidating?Boolean (protected)

Returns:

  • (Boolean)

427
428
429
# File 'app/models/taxon_name_relationship.rb', line 427

def is_invalidating?
  TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(type_name)
end

#nomenclature_dateTime

Returns effective date of publication, used to determine nomenclatural priorities.

Returns:

  • (Time)

    effective date of publication, used to determine nomenclatural priorities


244
245
246
# File 'app/models/taxon_name_relationship.rb', line 244

def nomenclature_date
  self.source ? (self.source.cached_nomenclature_date ? self.source.cached_nomenclature_date.to_time : Time.now) : Time.now
end

#object_propertiesArray of TaxonNameClassification

Returns the inferable TaxonNameClassification(s) added to the subject when this relationship is used !! Not implmented.

Returns:

  • (Array of TaxonNameClassification)

    the inferable TaxonNameClassification(s) added to the subject when this relationship is used !! Not implmented


120
121
122
# File 'app/models/taxon_name_relationship.rb', line 120

def object_properties
  []
end

#object_statusString

Returns the status inferred by the relationship to the object name.

Returns:

  • (String)

    the status inferred by the relationship to the object name


184
185
186
# File 'app/models/taxon_name_relationship.rb', line 184

def object_status
  self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
end

#object_status_connector_to_subjectString

Returns the connecting word in the relationship from the object name to subject name.

Returns:

  • (String)

    the connecting word in the relationship from the object name to subject name


202
203
204
# File 'app/models/taxon_name_relationship.rb', line 202

def object_status_connector_to_subject
  ' of'
end

#object_status_tagString

Returns a readable fragement combining status and connector.

Returns:

  • (String)

    a readable fragement combining status and connector


214
215
216
# File 'app/models/taxon_name_relationship.rb', line 214

def object_status_tag
  object_status + object_status_connector_to_subject
end

#set_cached_names_for_taxon_namesObject (protected)

TODO: Isolate to individual classes per type


357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
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
417
418
419
420
421
422
423
424
425
# File 'app/models/taxon_name_relationship.rb', line 357

def set_cached_names_for_taxon_names
  begin
    TaxonName.transaction do
      if is_combination?
        t = object_taxon_name

        t.send(:set_cached)

        if type_name =~/OriginalCombination/ 
          t.update_columns(
            cached_original_combination: t.get_original_combination,
            cached_original_combination_html: t.get_original_combination_html,
          )
        end

      elsif type_name =~/TaxonNameRelationship::Hybrid/ # TODO: move to Hybrid
        t = object_taxon_name
        t.update_columns(
          cached: t.get_full_name,
          cached_html: t.get_full_name_html
        )

      elsif type_name =~/SourceClassifiedAs/
        t = subject_taxon_name
        t.set_cached_classified_as
        # t.update_column(:cached_classified_as, t.get_cached_classified_as)

      elsif is_invalidating?
        t = subject_taxon_name
        
        if type_name =~/Misspelling/
          t.update_column(:cached_misspelling, t.get_cached_misspelling)
          t.update_columns(
              cached_author_year: t.get_author_and_year,
              cached_original_combination: t.get_original_combination,
              cached_original_combination_html: t.get_original_combination_html
          )
        end

        if type_name =~/Misapplication/
          t.update_column( :cached_author_year, t.get_author_and_year)
        end

        vn = t.get_valid_taxon_name

        t.update_columns(
          cached: t.get_full_name,
          cached_html: t.get_full_name_html, # OK to force reload here, otherwise we need an exception in #set_cached 
          cached_valid_taxon_name_id: vn.id)
        t.combination_list_self.each do |c|
          c.update_column(:cached_valid_taxon_name_id, vn.id)
        end

        vn.list_of_invalid_taxon_names.each do |s|
          s.update_column(:cached_valid_taxon_name_id, vn.id)
          s.combination_list_self.each do |c|
            c.update_column(:cached_valid_taxon_name_id, vn.id)
          end
        end
      end

    end

  # no point in rescuing and not returning somthing
  rescue ActiveRecord::RecordInvalid
    raise
  end
  false
end

#subject_and_object_in_same_projectObject (protected)


255
256
257
258
259
# File 'app/models/taxon_name_relationship.rb', line 255

def subject_and_object_in_same_project
  if subject_taxon_name && object_taxon_name
    errors.add(:base, 'one name is not in the same project as the other') if subject_taxon_name.project_id != object_taxon_name.project_id
  end
end

#subject_invalid_statusesObject (protected)


649
650
651
# File 'app/models/taxon_name_relationship.rb', line 649

def subject_invalid_statuses
  TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID & self.subject_taxon_name.taxon_name_classifications.collect{|c| c.type_class.to_s}
end

#subject_propertiesArray of TaxonNameClassification

Returns the inferable TaxonNameClassification(s) added to the subject when this relationship is used !! Not implemented.

Returns:

  • (Array of TaxonNameClassification)

    the inferable TaxonNameClassification(s) added to the subject when this relationship is used !! Not implemented


113
114
115
# File 'app/models/taxon_name_relationship.rb', line 113

def subject_properties
  []
end

#subject_statusString

Returns the status inferred by the relationship to the subject name.

Returns:

  • (String)

    the status inferred by the relationship to the subject name


190
191
192
# File 'app/models/taxon_name_relationship.rb', line 190

def subject_status
  self.type_name.demodulize.underscore.humanize.downcase.gsub(/\d+/, ' \0 ').squish
end

#subject_status_connector_to_objectString

Returns the connecting word in the relationship from the subject name to object name.

Returns:

  • (String)

    the connecting word in the relationship from the subject name to object name


196
197
198
# File 'app/models/taxon_name_relationship.rb', line 196

def subject_status_connector_to_object
  ' of'
end

#subject_status_tagString

Returns a readable fragement combining status and connector.

Returns:

  • (String)

    a readable fragement combining status and connector


208
209
210
# File 'app/models/taxon_name_relationship.rb', line 208

def subject_status_tag
  subject_status + subject_status_connector_to_object
end

#sv_coordinated_taxaObject (protected)


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

def sv_coordinated_taxa
  s = subject_taxon_name
  o = object_taxon_name
  s_new = s.lowest_rank_coordinated_taxon
  if s != s_new
    soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s.cached_html}",
                         fix: :sv_fix_coordinated_subject_taxa, success_message: "Relationship moved to  #{s_new.rank_class.rank_name}")
  end
end

#sv_coordinated_taxa_objectObject (protected)


696
697
698
699
700
701
702
703
704
# File 'app/models/taxon_name_relationship.rb', line 696

def sv_coordinated_taxa_object
  s = subject_taxon_name
  o = object_taxon_name
  o_new = o.lowest_rank_coordinated_taxon
  if o != o_new && type_name != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
    soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o.cached_html}",
                         fix: :sv_fix_coordinated_object_taxa, success_message: "Relationship moved to  #{o_new.rank_class.rank_name}")
  end
end

#sv_fix_combination_relationshipObject (protected)


738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
# File 'app/models/taxon_name_relationship.rb', line 738

def sv_fix_combination_relationship
  s = self.subject_taxon_name
  list = s.list_of_coordinated_names + [s]
  if s.rank_string =~ /Species/
    s_new = list.detect{|t| t.rank_class.rank_name == 'species'}
  elsif s.rank_string =~ /Genus/
    s_new = list.detect{|t| t.rank_class.rank_name == 'genus'}
  else
    s_new = s
  end
  if s != s_new && !s.nil?
    self.subject_taxon_name = s_new
    begin
      TaxonNameRelationship.transaction do
        self.save
        return true
      end
    rescue
    end
  end
  false
end

#sv_fix_coordinated_object_taxaObject (protected)


722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
# File 'app/models/taxon_name_relationship.rb', line 722

def sv_fix_coordinated_object_taxa
  o = self.object_taxon_name
  o_new = o.lowest_rank_coordinated_taxon
  if o != o_new
    self.object_taxon_name = o_new
    begin
      TaxonNameRelationship.transaction do
        self.save
        return true
      end
    rescue
    end
  end
  false
end

#sv_fix_coordinated_subject_taxaObject (protected)


706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
# File 'app/models/taxon_name_relationship.rb', line 706

def sv_fix_coordinated_subject_taxa
  s = subject_taxon_name
  s_new = s.lowest_rank_coordinated_taxon
  if s != s_new
    self.subject_taxon_name = s_new
    begin
      TaxonNameRelationship.transaction do
        self.save
        return true
      end
    rescue
    end
  end
  false
end

#sv_fix_subject_parent_updateObject (protected)

def sv_fix_synonym_linked_to_valid_name

  if TAXON_NAME_RELATIONSHIP_NAMES_INVALID.include?(self.type_name)
    obj = self.object_taxon_name
    unless obj.get_valid_taxon_name == obj
      self.object_taxon_name = obj.get_valid_taxon_name
      begin
        TaxonName.transaction do
          self.save
          return true
        end
      rescue
      end
    end
  end
  false
end

631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
# File 'app/models/taxon_name_relationship.rb', line 631

def sv_fix_subject_parent_update
  if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
    obj = self.object_taxon_name
    subj = self.subject_taxon_name
    unless obj.parent_id == subj.parent_id
      subj.parent_id = obj.parent_id
      begin
        TaxonName.transaction do
          subj.save
          return true
        end
      rescue
      end
    end
  end
  false
end

#sv_not_specific_relationshipObject (protected)


567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
# File 'app/models/taxon_name_relationship.rb', line 567

def sv_not_specific_relationship
  true # all validations moved to subclasses

#    case self.type_name
#      when 'TaxonNameRelationship::Typification::Genus'
#        soft_validations.add(:type, 'Please specify if the type designation is original or subsequent')
#      when 'TaxonNameRelationship::Typification::Genus::Original'
#        soft_validations.add(:type, 'Please specify if this is Original Designation or Original Monotypy')
#      when 'TaxonNameRelationship::Typification::Genus::Subsequent'
#        soft_validations.add(:type, 'Please specify if this is Subsequent Designation or Subsequent Monotypy')
#      when 'TaxonNameRelationship::Typification::Genus::Tautonomy'
#        soft_validations.add(:type, 'Please specify if the tautonomy is absolute or Linnaean')
#      when 'TaxonNameRelationship::Icn::Unaccepting'
#        soft_validations.add(:type, 'Please specify the reasons for the name being Unaccepted')
#      when 'TaxonNameRelationship::Icn::Unaccepting::Synonym'
#        soft_validations.add(:type, 'Please specify if this is a homotypic or heterotypic synonym',
#          fix: :sv_fix_specify_synonymy_type, success_message: 'Synonym updated to being homotypic or heterotypic')
#      when 'TaxonNameRelationship::Icnp::Unaccepting::Synonym'
#        soft_validations.add(:type, 'Please specify if this is a objective or subjective synonym',
#          fix: :sv_fix_specify_synonymy_type, success_message: 'Synonym updated to being objective or subjective')
#      when 'TaxonNameRelationship::Iczn::Invalidating'
#        soft_validations.add(:type, 'Please specify the reason for the name being Invalid') unless self.subject_taxon_name.classification_invalid_or_unavailable?
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym'
#        if NomenclaturalRank::Iczn::SpeciesGroup.descendants.collect{|t| t.to_s}.include?(self.subject_taxon_name.rank_string)
#          soft_validations.add(:type, 'Please specify if this is a primary or secondary homonym',
#              fix: :sv_fix_specify_homonymy_type, success_message: 'Homonym updated to being primary or secondary')
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Synonym'
#        soft_validations.add(:type, 'Please specify if this is a objective or subjective synonym',
#            fix: :sv_fix_specify_synonymy_type, success_message: 'Synonym updated to being objective or subjective')
#      when 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Suppression'
#        soft_validations.add(:type, 'Please specify if this is a total, partial, or conditional suppression')
#    end
end

#sv_objective_synonym_relationshipObject (protected)


536
537
538
539
540
541
542
543
544
545
# File 'app/models/taxon_name_relationship.rb', line 536

def sv_objective_synonym_relationship
  true # all validations moved to subclasses
#    if self.type_name =~ /TaxonNameRelationship::(Iczn::Invalidating::Synonym::Objective|Icn::Unaccepting::Synonym::Homotypic|Icnp::Unaccepting::Synonym::Homotypic)/
#      s = self.subject_taxon_name
#      o = self.object_taxon_name
#      if (s.type_taxon_name != o.type_taxon_name ) || !s.has_same_primary_type(o)
#        soft_validations.add(:type, "Objective synonyms #{s.cached_html} and #{o.cached_html} should have the same type")
#      end
#    end
end

#sv_specific_relationshipObject (protected)


473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
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
526
527
528
529
530
531
532
533
534
# File 'app/models/taxon_name_relationship.rb', line 473

def sv_specific_relationship
  true # all validations moved to subclasses

#    s = subject_taxon_name
#    o = object_taxon_name
#    case type
#      when 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Subjective' || 'TaxonNameRelationship::Icn::Unaccepting::Synonym::Heterotypic'
#        if (s.type_taxon_name == o.type_taxon_name && !s.type_taxon_name.nil? ) || (!s.get_primary_type.empty? && s.has_same_primary_type(o) )
#          soft_validations.add(:type, "Subjective synonyms #{s.cached_html} and #{o.cached_html} should not have the same type")
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym'
#        # primary names don't match
#        if (s.cached_primary_homonym_alternative_spelling != o.cached_primary_homonym_alternative_spelling)
#          # there is a secondary name ... and it doesn't match either
#          if (s.cached_secondary_homonym_alternative_spelling.blank? && o.cached_secondary_homonym_alternative_spelling.blank?) || (s.cached_secondary_homonym_alternative_spelling != o.cached_secondary_homonym_alternative_spelling)
#            soft_validations.add(:type, "#{subject_taxon_name.cached_html_name_and_author_year} and #{object_taxon_name.cached_html_name_and_author_year} are not similar enough to be homonyms")
#          end
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary' || 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary::Forgotten' || 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary::Suppressed'
#        if s.original_genus != o.original_genus
#          soft_validations.add(:type, "Primary homonyms #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} should have the same original genus")
#        elsif s.cached_primary_homonym_alternative_spelling != o.cached_primary_homonym_alternative_spelling
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} are not similar enough to be homonyms")
#        end
#        if type == 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Primary::Forgotten' && s.year_of_publication > 1899
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} was not described after 1899")
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Secondary'
#        if s.original_genus == o.original_genus && !s.original_genus.nil?
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} species described in the same original genus #{s.original_genus}, they are primary homonyms")
#        elsif s.get_valid_taxon_name.ancestor_at_rank('genus') != o.get_valid_taxon_name.ancestor_at_rank('genus')
#          soft_validations.add(:type, "Secondary homonyms #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} should be placed in the same parent genus, the homonymy should be deleted or changed to 'secondary homonym replaced before 1961'")
#        elsif s.cached_secondary_homonym_alternative_spelling != o.cached_secondary_homonym_alternative_spelling
#          soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} are not similar enough to be homonyms")
#        end

#        if (s.all_generic_placements & o.all_generic_placements).empty?
#          soft_validations.add(:base, "No combination available showing #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} placed in the same genus")
#        end
#      when 'TaxonNameRelationship::Iczn::Invalidating::Homonym::Secondary::Secondary1961'
#        soft_validations.add(:type, "#{s.cached_html_name_and_author_year} was not described before 1961") if s.year_of_publication > 1960
#        soft_validations.add(:type, "#{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} described in the same original genus #{s.original_genus}, they are primary homonyms") if s.original_genus == o.original_genus && !s.original_genus.nil?
#        soft_validations.add(:base, 'The original publication is not selected') unless source

#        soft_validations.add(:base, "#{s.cached_html_name_and_author_year} should not be treated as a homonym established before 1961") if self.source && self.source.year > 1960

#        if (s.all_generic_placements & o.all_generic_placements).empty?
#          soft_validations.add(:base, "No combination available showing #{s.cached_html_name_and_author_year} and #{o.cached_html_name_and_author_year} placed in the same genus")
#        end
#      when 'TaxonNameRelationship::Iczn::PotentiallyValidating::FamilyBefore1961'
#        soft_validations.add(:type, "#{s.cached_html_name_and_author_year} was not described before 1961") if s.year_of_publication > 1960
#        soft_validations.add(:base, "#{s.cached_html_name_and_author_year} should be accepted as a replacement name before 1961") if self.source && self.source.year > 1960
#      when 'TaxonNameRelationship::Typification::Genus::Subsequent::SubsequentDesignation'
#        soft_validations.add(:type, "Genus #{o.cached_html_name_and_author_year} described after 1930 is nomen nudum, if type was not designated in the original publication") if o.year_of_publication && o.year_of_publication > 1930
#      when 'TaxonNameRelationship::Iczn::PotentiallyValidating::ReplacementName'
#        r1 = TaxonNameRelationship.where(type: 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Objective::ReplacedHomonym', subject_taxon_name_id: o.id, object_taxon_name_id: s.id).first
#        r2 = TaxonNameRelationship.where(type: 'TaxonNameRelationship::Iczn::Invalidating::Synonym::Objective::UnnecessaryReplacementName', subject_taxon_name_id: s.id, object_taxon_name_id: o.id).first
#        soft_validations.add(:base, "Missing relationship: #{s.cached_html_name_and_author_year} is a replacement name for #{o.cached_html_name_and_author_year}. Please add an objective synonym relationship (either 'replaced homonym' or 'unnecessary replacement name')") if r1.nil? && r2.nil?
#      when 'TaxonNameRelationship::Typification::Genus::Original::OriginalMonotypy'
#        # @todo Check if more than one species associated with the genus in the original paper
#    end
end

#sv_synonym_linked_to_valid_nameObject (protected)


602
603
604
605
606
607
608
609
610
611
612
# File 'app/models/taxon_name_relationship.rb', line 602

def sv_synonym_linked_to_valid_name
  #synonyms and misspellings should be linked to valid names
  if TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM.include?(self.type_name)
    obj = self.object_taxon_name
    subj = self.subject_taxon_name
      if subj.rank_class.try(:nomenclatural_code) == :iczn && obj.parent_id != subj.parent_id &&  subj.cached_valid_taxon_name_id == obj.cached_valid_taxon_name_id
      soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize}  #{subj.cached_html_name_and_author_year} should have the same parent with  #{obj.cached_html_name_and_author_year}",
                           fix: :sv_fix_subject_parent_update, success_message: 'The parent was updated')
    end
  end
end

#sv_synonym_relationshipObject (protected)


547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
# File 'app/models/taxon_name_relationship.rb', line 547

def sv_synonym_relationship
  true # all validations moved to subclasses
#    relationships = TAXON_NAME_RELATIONSHIP_NAMES_SYNONYM +
#      TaxonNameRelationship.collect_to_s(TaxonNameRelationship::Typification::Genus::Subsequent::SubsequentDesignation,
#                                         TaxonNameRelationship::Typification::Genus::Subsequent::RulingByCommission)
#    if relationships.include?(self.type_name)
#      if self.source
#        date1 = self.source.cached_nomenclature_date.to_time
#        date2 = self.subject_taxon_name.nomenclature_date
#        if !!date1 && !!date2
#          soft_validations.add(:base, "#{self.subject_taxon_name.cached_html_name_and_author_year} was not described at the time of citation (#{date1}") if date2 > date1
#        end
#      elsif TAXON_NAME_RELATIONSHIP_NAMES_MISSPELLING.include?(self.type_name)
#        # misspelling does not requere original publication
#      else
#        soft_validations.add(:base, 'The original publication is not selected')
#      end
#    end
end

#sv_validate_disjoint_objectObject (protected)


451
452
453
454
455
456
457
458
459
460
# File 'app/models/taxon_name_relationship.rb', line 451

def sv_validate_disjoint_object
  classifications = self.object_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
  disjoint_object_classes = self.type_class.disjoint_object_classes
  compare = disjoint_object_classes & classifications
  compare.each do |i|
    c = i.demodulize.underscore.humanize.downcase
    soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with the taxon status: '#{c}'")
    soft_validations.add(:object_taxon_name_id, "#{self.object_taxon_name.cached_html} has a conflicting status: '#{c}'")
  end
end

#sv_validate_disjoint_relationshipsObject (protected)


439
440
441
442
443
444
445
446
447
448
449
# File 'app/models/taxon_name_relationship.rb', line 439

def sv_validate_disjoint_relationships
  tname = self.type_name
  if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
    subject_relationships = TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).not_self(self)
    subject_relationships.each  do |i|
      if self.type_class.disjoint_taxon_name_relationships.include?(i.type_name)
        soft_validations.add(:type, "#{self.subject_status.capitalize} relationship is conflicting with another relationship: '#{i.subject_status}'")
      end
    end
  end
end

#sv_validate_disjoint_subjectObject (protected)


462
463
464
465
466
467
468
469
470
471
# File 'app/models/taxon_name_relationship.rb', line 462

def sv_validate_disjoint_subject
  classifications = self.subject_taxon_name.taxon_name_classifications.reload.map {|i| i.type_name}
  disjoint_subject_classes = self.type_class.disjoint_subject_classes
  compare = disjoint_subject_classes & classifications
  compare.each do |i|
    c = i.demodulize.underscore.humanize.downcase
    soft_validations.add(:type, "#{self.subject_status.capitalize} conflicting with the status: '#{c}'")
    soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.cached_html} has a conflicting status: '#{c}'")
  end
end

#sv_validate_priorityObject (protected)


653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
# File 'app/models/taxon_name_relationship.rb', line 653

def sv_validate_priority
  true # all validations moved to subclasses

#    unless self.type_class.nomenclatural_priority.nil?
#      date1 = self.subject_taxon_name.nomenclature_date
#      date2 = self.object_taxon_name.nomenclature_date
#      if !!date1 and !!date2
#        case self.type_class.nomenclatural_priority
#        when :direct
#          if date2 > date1 && subject_invalid_statuses.empty?
#            if self.type_name =~ /TaxonNameRelationship::Iczn::Invalidating::Homonym/
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be older than #{self.object_status} #{self.object_taxon_name.cached_html_name_and_author_year}")
#            elsif self.type_name =~ /::Iczn::/ && TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).with_two_type_bases('TaxonNameRelationship::Iczn::Invalidating::Homonym', 'TaxonNameRelationship::Iczn::Validating').not_self(self).empty?
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be older than #{self.object_status} #{self.object_taxon_name.cached_html_name_and_author_year}, unless it is also a homonym or conserved name")
#            elsif self.type_name =~ /::Icn::/ && TaxonNameRelationship.where_subject_is_taxon_name(self.subject_taxon_name).with_two_type_bases('TaxonNameRelationship::Icn::Accepting::Conserved', 'TaxonNameRelationship::Icn::Accepting::Sanctioned').not_self(self).empty?
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be older than #{self.object_status} #{self.object_taxon_name.cached_html_name_and_author_year}, unless it is also conserved or sanctioned name")
#            end
#          end
#        when :reverse
#          if date1 > date2 && subject_invalid_statuses.empty?
#            if self.type_name =~ /TaxonNameRelationship::(Typification|Combination|OriginalCombination)/
#              if self.type_name != 'TaxonNameRelationship::Typification::Genus::Subsequent::RulingByCommission' || (self.type_name =~ /TaxonNameRelationship::Typification::Genus::(Monotypy::SubsequentMonotypy|SubsequentDesignation)/ && date2 > '1930-12-31'.to_time)
#                soft_validations.add(:subject_taxon_name_id, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be younger than #{self.object_taxon_name.cached_html_name_and_author_year}")
#              end
#            else
#              soft_validations.add(:type, "#{self.subject_status.capitalize} #{self.subject_taxon_name.cached_html_name_and_author_year} should not be younger than #{self.object_taxon_name.cached_html_name_and_author_year}")
#            end
#          end
#        end
#      end
#    end
end

#sv_validate_required_relationshipsObject (protected)


431
432
433
434
435
436
437
# File 'app/models/taxon_name_relationship.rb', line 431

def sv_validate_required_relationships
  object_relationships = TaxonNameRelationship.where_object_is_taxon_name(self.object_taxon_name).not_self(self).collect{|r| r.type}
  required = self.type_class.required_taxon_name_relationships - object_relationships
  required.each do |r|
    soft_validations.add(:type, " Presence of #{self.subject_status} requires selection of #{r.demodulize.underscore.humanize.downcase}")
  end
end

#type_classTaxonNameRelationship, String

Returns the type as a class, if legal, else a string ! Strangeish.

Returns:


231
232
233
234
# File 'app/models/taxon_name_relationship.rb', line 231

def type_class
  r = read_attribute(:type).to_s
  TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r.safe_constantize : r
end

#type_class=(value) ⇒ Object


225
226
227
# File 'app/models/taxon_name_relationship.rb', line 225

def type_class=(value)
  write_attribute(:type, value.to_s)
end

#type_nameString?

Returns the type of this relationship, IF the type is a valid name, else nil.

Returns:

  • (String, nil)

    the type of this relationship, IF the type is a valid name, else nil


220
221
222
223
# File 'app/models/taxon_name_relationship.rb', line 220

def type_name
  r = self.type
  TAXON_NAME_RELATIONSHIP_NAMES.include?(r) ? r : nil
end

#validate_object_and_subject_both_protonymsObject (protected)


347
348
349
350
351
352
353
354
# File 'app/models/taxon_name_relationship.rb', line 347

def validate_object_and_subject_both_protonyms
  if /TaxonNameRelationship::Combination::/.match(self.type)
    errors.add(:object_taxon_name_id, 'Not a Combination') if object_taxon_name.type != 'Combination'
  else
    errors.add(:object_taxon_name_id, 'Not a Protonym') if object_taxon_name.type == 'Combination'
  end
  errors.add(:subject_taxon_name_id, 'Not a Protonym') if subject_taxon_name.type == 'Combination'
end

#validate_object_must_equal_subject_for_uncertain_placementObject (protected)


289
290
291
292
293
# File 'app/models/taxon_name_relationship.rb', line 289

def validate_object_must_equal_subject_for_uncertain_placement
  if self.object_taxon_name_id != self.subject_taxon_name.parent_id && self.type_name == 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
    errors.add(:object_taxon_name_id, "The parent #{self.subject_taxon_name.parent.cached_html} and the Incertae Sedis placement (#{self.object_taxon_name.cached_html}) should match")
  end
end

#validate_rank_groupObject (protected)


339
340
341
342
343
344
345
# File 'app/models/taxon_name_relationship.rb', line 339

def validate_rank_group
  if self.type =~ /Hybrid/ && self.subject_taxon_name && self.object_taxon_name
    if self.subject_taxon_name.rank_class.parent != self.object_taxon_name.rank_class.parent
      errors.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the rank of hybrid (#{self.object_taxon_name.rank_class.rank_name})")
    end
  end
end

#validate_subject_and_object_are_not_identicalObject (protected)


283
284
285
286
287
# File 'app/models/taxon_name_relationship.rb', line 283

def validate_subject_and_object_are_not_identical
  if !self.object_taxon_name_id.nil? && self.object_taxon_name == self.subject_taxon_name
    errors.add(:object_taxon_name_id, "#{self.object_taxon_name.try(:cached_html).to_s} should not refer to itself") unless self.type =~ /OriginalCombination/
  end
end

#validate_subject_and_object_ranksObject (protected)


295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
# File 'app/models/taxon_name_relationship.rb', line 295

def validate_subject_and_object_ranks
  tname = self.type_name

  if tname =~ /TaxonNameRelationship::(Icnp|Icn|Iczn|Icvcn)/ && tname != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
    rank_group = self.subject_taxon_name.rank_class.try(:parent)
    unless rank_group == self.object_taxon_name.rank_class.try(:parent)
      errors.add(:object_taxon_name_id, "Rank of related taxon should be in the #{rank_group.try(:rank_name)} rank group, not #{self.object_taxon_name.rank_class.try(:rank_name)}")
    end
  end

  unless self.type_class.blank? # only validate if it is set
    if object_taxon_name
      if object_taxon_name.type == 'Protonym' || object_taxon_name.type == 'Hybrid'
        unless self.type_class.valid_object_ranks.include?(self.object_taxon_name.rank_string)
          errors.add(:object_taxon_name_id, "#{self.object_taxon_name.rank_class.rank_name.capitalize} rank of #{self.object_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
          errors.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.object_taxon_name.rank_class.rank_name} rank of #{self.object_taxon_name.cached_html}")
        end
      end
    end

    if subject_taxon_name
      if subject_taxon_name.type == 'Protonym' || subject_taxon_name.type == 'Hybrid'
        unless self.type_class.valid_subject_ranks.include?(self.subject_taxon_name.parent.rank_string)
          soft_validations.add(:subject_taxon_name_id, "#{self.subject_taxon_name.rank_class.rank_name.capitalize} rank of #{self.subject_taxon_name.cached_html} is not compatible with the #{self.subject_status} relationship")
          soft_validations.add(:type, "Relationship #{self.subject_status} is not compatible with the #{self.subject_taxon_name.rank_class.rank_name} rank of #{self.subject_taxon_name.cached_html}")
        end
      end
    end
  end
end

#validate_subject_and_object_share_codeObject (protected)

TODO:

validate, that all the relationships in the table could be linked to relationships in classes (if those had changed)


277
278
279
280
281
# File 'app/models/taxon_name_relationship.rb', line 277

def validate_subject_and_object_share_code
  if object_taxon_name.type  == 'Protonym' && subject_taxon_name.type == 'Protonym'
    errors.add(:object_taxon_name_id, 'The related taxon is not in the same monenclatural group (ICZN, ICN, ICNP, ICTV') if subject_taxon_name.rank_class.try(:nomenclatural_code) != object_taxon_name.rank_class.try(:nomenclatural_code)
  end
end

#validate_typeObject (protected)


261
262
263
264
265
266
267
268
269
270
271
272
273
# File 'app/models/taxon_name_relationship.rb', line 261

def validate_type
  unless TAXON_NAME_RELATIONSHIP_NAMES.include?(type)
    errors.add(:type, "'#{type}' is not a valid taxon name relationship")
  end

  if object_taxon_name.class.to_s == 'Protonym' || object_taxon_name.class.to_s == 'Hybrid'
    errors.add(:type, "'#{type}' is not a valid taxon name relationship") if /TaxonNameRelationship::Combination::/.match(self.type)
  end

  if object_taxon_name.class.to_s == 'Combination'
    errors.add(:type, "'#{type}' is not a valid taxon name relationship") unless /TaxonNameRelationship::Combination::/.match(self.type)
  end
end

#validate_uniqueness_of_typification_objectObject (protected)

Protonym historically could be listed as a synonym to different taxa def validate_uniqueness_of_synonym_subject

if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains('Synonym').not_self(self).empty?
  errors.add(:subject_taxon_name_id, 'Only one synonym relationship is allowed')
end

end


333
334
335
336
337
# File 'app/models/taxon_name_relationship.rb', line 333

def validate_uniqueness_of_typification_object
  if /Typification/.match(self.type_name) && !TaxonNameRelationship.where(object_taxon_name_id: self.object_taxon_name_id).with_type_contains('Typification').not_self(self).empty?
    errors.add(:object_taxon_name_id, 'Only one Type designation relationship is allowed')
  end
end