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Combination refactoring with related model consequences.
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@mjy
mjy committed Jan 14, 2015
1 parent 79b559e commit de803f7
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Showing 6 changed files with 182 additions and 153 deletions.
229 changes: 120 additions & 109 deletions app/models/protonym.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -102,17 +102,17 @@ class Protonym < TaxonName
where("taxon_names.id NOT IN (SELECT subject_taxon_name_id FROM taxon_name_relationships WHERE type LIKE 'TaxonNameRelationship::Iczn::Invalidating%' OR type LIKE 'TaxonNameRelationship::Icn::Unaccepting%')")
}

soft_validate(:sv_validate_parent_rank, set: :validate_parent_rank)
soft_validate(:sv_missing_relationships, set: :missing_relationships)
soft_validate(:sv_missing_classifications, set: :missing_classifications)
soft_validate(:sv_species_gender_agreement, set: :species_gender_agreement)
soft_validate(:sv_type_placement, set: :type_placement)
soft_validate(:sv_primary_types, set: :primary_types)
soft_validate(:sv_validate_coordinated_names, set: :validate_coordinated_names)
soft_validate(:sv_single_sub_taxon, set: :single_sub_taxon)
soft_validate(:sv_parent_priority, set: :parent_priority)
soft_validate(:sv_homotypic_synonyms, set: :homotypic_synonyms)
soft_validate(:sv_potential_homonyms, set: :potential_homonyms)
soft_validate(:sv_validate_parent_rank, set: :validate_parent_rank)
soft_validate(:sv_missing_relationships, set: :missing_relationships)
soft_validate(:sv_missing_classifications, set: :missing_classifications)
soft_validate(:sv_species_gender_agreement, set: :species_gender_agreement)
soft_validate(:sv_type_placement, set: :type_placement)
soft_validate(:sv_primary_types, set: :primary_types)
soft_validate(:sv_validate_coordinated_names, set: :validate_coordinated_names)
soft_validate(:sv_single_sub_taxon, set: :single_sub_taxon)
soft_validate(:sv_parent_priority, set: :parent_priority)
soft_validate(:sv_homotypic_synonyms, set: :homotypic_synonyms)
soft_validate(:sv_potential_homonyms, set: :potential_homonyms)

before_validation :check_format_of_name,
:validate_rank_class_class,
Expand All @@ -122,39 +122,42 @@ class Protonym < TaxonName
:validate_source_type,
:new_parent_taxon_name

def family_group_endigns
def family_group_endings
%w{ini ina inae idae oidae odd ad oidea}
end

def list_of_coordinated_names
if self.incorrect_original_spelling.nil?
search_rank = NomenclaturalRank::Iczn.group_base(self.rank_string)
if !!search_rank
if search_rank =~ /Family/
z = Protonym.family_group_base(self.name)
search_name = z.nil? ? nil : family_group_endigns.collect{|i| z+i}
#search_name = z.nil? ? nil : "#{z}(ini|ina|inae|idae|oidae|odd|ad|oidea)"
list = []
if self.rank_string
if self.incorrect_original_spelling.nil?
search_rank = NomenclaturalRank::Iczn.group_base(self.rank_string)
if !!search_rank
if search_rank =~ /Family/
z = Protonym.family_group_base(self.name)
search_name = z.nil? ? nil : family_group_endings.collect{|i| z+i}
#search_name = z.nil? ? nil : "#{z}(ini|ina|inae|idae|oidae|odd|ad|oidea)"
else
search_name = self.name
end
else
search_name = self.name
search_name = nil
end
else
search_name = nil
end

unless search_name.nil?
list = Protonym.ancestors_and_descendants_of(self).
unless search_name.nil?
list = Protonym.ancestors_and_descendants_of(self).
with_rank_class_including(search_rank).
with_name_in_array(search_name).
as_subject_without_taxon_name_relationship_base('TaxonNameRelationship::Iczn::Invalidating::Synonym') # <- use this
#list1 = self.ancestors_and_descendants # scope with parens
#list1 = list1.select{|i| /#{search_rank}.*/.match(i.rank_class.to_s)} # scope on rank_class
#list1 = list1.select{|i| /#{search_name}/.match(i.name)} # scope on named
#list1 = list1.reject{|i| i.unavailable_or_invalid?} # scope with join on taxon_name_relationships and where > 1 on them
#list1 = self.ancestors_and_descendants # scope with parens
#list1 = list1.select{|i| /#{search_rank}.*/.match(i.rank_class.to_s)} # scope on rank_class
#list1 = list1.select{|i| /#{search_name}/.match(i.name)} # scope on named
#list1 = list1.reject{|i| i.unavailable_or_invalid?} # scope with join on taxon_name_relationships and where > 1 on them
else
list = []
end
else
list = []
list = [self.incorrect_original_spelling.object_taxon_name]
end
else
list = [self.incorrect_original_spelling.object_taxon_name]
end
return list
end
Expand Down Expand Up @@ -266,13 +269,13 @@ def sv_source_older_then_description
end
end



def sv_validate_parent_rank
if self.rank_class.to_s == 'NomenclaturalRank' || self.parent.rank_class.to_s == 'NomenclaturalRank' || !!self.incertae_sedis
true
elsif !self.rank_class.valid_parents.include?(self.parent.rank_class.to_s)
soft_validations.add(:rank_class, "The rank #{self.rank_class.rank_name} is not compatible with the rank of parent (#{self.parent.rank_class.rank_name})")
if self.rank_class
if self.rank_class.to_s == 'NomenclaturalRank' || self.parent.rank_class.to_s == 'NomenclaturalRank' || !!self.incertae_sedis
true
elsif !self.rank_class.valid_parents.include?(self.parent.rank_class.to_s)
soft_validations.add(:rank_class, "The rank #{self.rank_class.rank_name} is not compatible with the rank of parent (#{self.parent.rank_class.rank_name})")
end
end
end

Expand Down Expand Up @@ -505,33 +508,37 @@ def sv_type_placement
end

def sv_primary_types
if self.rank_class.parent.to_s =~ /Species/
if self.type_materials.primary.empty? && self.type_materials.syntypes.empty?
soft_validations.add(:base, 'Primary type is not selected')
elsif self.type_materials.primary.count > 1 || (!self.type_materials.primary.empty? && !self.type_materials.syntypes.empty?)
soft_validations.add(:base, 'More than one primary type are selected')
if self.rank_class
if self.rank_class.parent.to_s =~ /Species/
if self.type_materials.primary.empty? && self.type_materials.syntypes.empty?
soft_validations.add(:base, 'Primary type is not selected')
elsif self.type_materials.primary.count > 1 || (!self.type_materials.primary.empty? && !self.type_materials.syntypes.empty?)
soft_validations.add(:base, 'More than one primary type are selected')
end
end
end
end

def sv_single_sub_taxon
rank = self.rank_class.to_s
if rank != 'potentially_validating rank' && self.rank_class.nomenclatural_code == :iczn && %w(subspecies subgenus subtribe tribe subfamily).include?(self.rank_class.rank_name)
sisters = self.parent.descendants.with_rank_class(rank)
if rank =~ /Family/
z = Protonym.family_group_base(self.name)
search_name = z.nil? ? nil : family_group_endigns.collect{|i| z+i}
a = sisters.collect{|i| Protonym.family_group_base(i.name) }
sister_names = a.collect{|z| family_group_endigns.collect{|i| z+i} }.flatten
else
search_name = [self.name]
sister_names = sisters.collect{|i| i.name }
end
if search_name.include?(self.parent.name) && sisters.count == 1
soft_validations.add(:base, "This taxon is a single #{self.rank_class.rank_name} in the nominal #{self.parent.rank_class.rank_name}")
elsif !sister_names.include?(self.parent.name)
soft_validations.add(:base, "The parent #{self.parent.rank_class.rank_name} of this #{self.rank_class.rank_name} does not contain nominotypical #{self.rank_class.rank_name}",
fix: :sv_fix_add_nominotypical_sub, success_message: "Nominotypical #{self.rank_class.rank_name} was added to nominal #{self.parent.rank_class.rank_name}")
if self.rank_class
rank = self.rank_class.to_s
if rank != 'potentially_validating rank' && self.rank_class.nomenclatural_code == :iczn && %w(subspecies subgenus subtribe tribe subfamily).include?(self.rank_class.rank_name)
sisters = self.parent.descendants.with_rank_class(rank)
if rank =~ /Family/
z = Protonym.family_group_base(self.name)
search_name = z.nil? ? nil : family_group_endings.collect{|i| z+i}
a = sisters.collect{|i| Protonym.family_group_base(i.name) }
sister_names = a.collect{|z| family_group_endings.collect{|i| z+i} }.flatten
else
search_name = [self.name]
sister_names = sisters.collect{|i| i.name }
end
if search_name.include?(self.parent.name) && sisters.count == 1
soft_validations.add(:base, "This taxon is a single #{self.rank_class.rank_name} in the nominal #{self.parent.rank_class.rank_name}")
elsif !sister_names.include?(self.parent.name)
soft_validations.add(:base, "The parent #{self.parent.rank_class.rank_name} of this #{self.rank_class.rank_name} does not contain nominotypical #{self.rank_class.rank_name}",
fix: :sv_fix_add_nominotypical_sub, success_message: "Nominotypical #{self.rank_class.rank_name} was added to nominal #{self.parent.rank_class.rank_name}")
end
end
end
end
Expand Down Expand Up @@ -567,16 +574,18 @@ def sv_fix_add_nominotypical_sub
end

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

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

if parent && rank_group == parent.rank_class.parent
unless self.unavailable_or_invalid?
date1 = self.nomenclature_date
date2 = parent.nomenclature_date
unless date1.nil? || date2.nil?
if date1 < date2
soft_validations.add(:base, "#{self.rank_class.rank_name.capitalize} should not be older than parent #{parent.rank_class.rank_name}")
end
end
end
end
Expand Down Expand Up @@ -620,50 +629,52 @@ def reduce_list_of_synonyms(list)
end

def sv_potential_homonyms
unless (self.unavailable? || !Protonym.with_taxon_name_relationships_as_subject.with_homonym_or_suppressed.empty?) # self.unavailable_or_invalid?
if self.id == self.lowest_rank_coordinated_taxon.id
rank_base = self.rank_class.parent.to_s
name1 = self.cached_primary_homonym ? self.cached_primary_homonym : nil
possible_primary_homonyms = name1 ? Protonym.with_primary_homonym(name1).without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).without_homonym_or_suppressed.not_self(self.id).with_base_of_rank_class(rank_base).with_project(self.project_id) : []
list1 = reduce_list_of_synonyms(possible_primary_homonyms)
if !list1.empty?
list1.each do |s|
if rank_base =~ /Species/
soft_validations.add(:base, "Taxon should be a primary homonym of #{s.cached_name_and_author_year}")
# fix: :sv_fix_add_relationship('iczn_set_as_primary_homonym_of'.to_sym, s.id),
# success_message: 'Primary homonym relationship was added',
# failure_message: 'Fail to add a relationship')
elsif
soft_validations.add(:base, "Taxon should be an homonym of #{s.cached_name_and_author_year}")
end
end
else
name2 = self.cached_primary_homonym_alternative_spelling ? self.cached_primary_homonym_alternative_spelling : nil
possible_primary_homonyms_alternative_spelling = name2 ? Protonym.with_primary_homonym_alternative_spelling(name2).without_homonym_or_suppressed.without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self.id).with_base_of_rank_class(rank_base).with_project(self.project_id) : []
list2 = reduce_list_of_synonyms(possible_primary_homonyms_alternative_spelling)
if !list2.empty?
list2.each do |s|
if self.parent
unless (self.unavailable? || !Protonym.with_taxon_name_relationships_as_subject.with_homonym_or_suppressed.empty?) # self.unavailable_or_invalid?
if self.id == self.lowest_rank_coordinated_taxon.id
rank_base = self.rank_class.parent.to_s
name1 = self.cached_primary_homonym ? self.cached_primary_homonym : nil
possible_primary_homonyms = name1 ? Protonym.with_primary_homonym(name1).without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).without_homonym_or_suppressed.not_self(self.id).with_base_of_rank_class(rank_base).with_project(self.project_id) : []
list1 = reduce_list_of_synonyms(possible_primary_homonyms)
if !list1.empty?
list1.each do |s|
if rank_base =~ /Species/
soft_validations.add(:base, "Taxon could be a primary homonym of #{s.cached_name_and_author_year} (alternative spelling)")
soft_validations.add(:base, "Taxon should be a primary homonym of #{s.cached_name_and_author_year}")
# fix: :sv_fix_add_relationship('iczn_set_as_primary_homonym_of'.to_sym, s.id),
# success_message: 'Primary homonym relationship was added',
# failure_message: 'Fail to add a relationship')
elsif
soft_validations.add(:base, "Taxon could be an homonym of #{s.cached_name_and_author_year} (alternative spelling)")
soft_validations.add(:base, "Taxon should be an homonym of #{s.cached_name_and_author_year}")
end
end
elsif rank_base =~ /Species/
name3 = self.cached_secondary_homonym ? self.cached_secondary_homonym : nil
possible_secondary_homonyms = name3 ? Protonym.with_secondary_homonym(name3).without_homonym_or_suppressed.without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self.id).with_base_of_rank_class(rank_base).with_project(self.project_id) : []
list3 = reduce_list_of_synonyms(possible_secondary_homonyms)
if !list3.empty?
list3.each do |s|
soft_validations.add(:base, "Taxon should be a secondary homonym of #{s.cached_name_and_author_year}")
else
name2 = self.cached_primary_homonym_alternative_spelling ? self.cached_primary_homonym_alternative_spelling : nil
possible_primary_homonyms_alternative_spelling = name2 ? Protonym.with_primary_homonym_alternative_spelling(name2).without_homonym_or_suppressed.without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self.id).with_base_of_rank_class(rank_base).with_project(self.project_id) : []
list2 = reduce_list_of_synonyms(possible_primary_homonyms_alternative_spelling)
if !list2.empty?
list2.each do |s|
if rank_base =~ /Species/
soft_validations.add(:base, "Taxon could be a primary homonym of #{s.cached_name_and_author_year} (alternative spelling)")
elsif
soft_validations.add(:base, "Taxon could be an homonym of #{s.cached_name_and_author_year} (alternative spelling)")
end
end
else
name4 = self.cached_secondary_homonym ? self.cached_secondary_homonym_alternative_spelling : nil
possible_secondary_homonyms_alternative_spelling = name4 ? Protonym.with_secondary_homonym_alternative_spelling(name4).without_homonym_or_suppressed.without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self.id).with_base_of_rank_class(rank_base).with_project(self.project_id) : []
list4 = reduce_list_of_synonyms(possible_secondary_homonyms_alternative_spelling)
if !list4.empty?
list4.each do |s|
soft_validations.add(:base, "Taxon could be a secondary homonym of #{s.cached_name_and_author_year} (alternative spelling)")
elsif rank_base =~ /Species/
name3 = self.cached_secondary_homonym ? self.cached_secondary_homonym : nil
possible_secondary_homonyms = name3 ? Protonym.with_secondary_homonym(name3).without_homonym_or_suppressed.without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self.id).with_base_of_rank_class(rank_base).with_project(self.project_id) : []
list3 = reduce_list_of_synonyms(possible_secondary_homonyms)
if !list3.empty?
list3.each do |s|
soft_validations.add(:base, "Taxon should be a secondary homonym of #{s.cached_name_and_author_year}")
end
else
name4 = self.cached_secondary_homonym ? self.cached_secondary_homonym_alternative_spelling : nil
possible_secondary_homonyms_alternative_spelling = name4 ? Protonym.with_secondary_homonym_alternative_spelling(name4).without_homonym_or_suppressed.without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self.id).with_base_of_rank_class(rank_base).with_project(self.project_id) : []
list4 = reduce_list_of_synonyms(possible_secondary_homonyms_alternative_spelling)
if !list4.empty?
list4.each do |s|
soft_validations.add(:base, "Taxon could be a secondary homonym of #{s.cached_name_and_author_year} (alternative spelling)")
end
end
end
end
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