Module: Shared::BiologicalExtensions

Extended by:
ActiveSupport::Concern
Included in:
CollectionObject, FieldOccurrence
Defined in:
app/models/concerns/shared/biological_extensions.rb

Overview

Shared code that references things with TaxonDeterminations and Biocuration classes

Current FieldOccurence
        CollectionObject (should be CollectionObject::BiologicalCollectionObject)

Instance Method Summary collapse

Instance Method Details

#descendant_anatomical_part_ids ⇒ Array<Integer> (private)

Returns:

  • (Array<Integer>) 


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
 
# File 'app/models/concerns/shared/biological_extensions.rb', line 120

def descendant_anatomical_part_ids
  project = project_id
  seen_ids = Set.new
  result = []
  frontier = [id]
  old_type = self.class.base_class.name

  while frontier.any?
    old_frontier = frontier
    frontier = []
    old_old_type = old_type
    old_type = 'AnatomicalPart'

    old_frontier.each do |old_id|
      rels = OriginRelationship
        .where(
          project_id: project,
          old_object_type: old_old_type,
          old_object_id: old_id,
          new_object_type: 'AnatomicalPart')
        .pluck(:new_object_id)

      rels.each do |anatomical_part_id|
        next if seen_ids.include?(anatomical_part_id)
        seen_ids << anatomical_part_id
        result << anatomical_part_id
        frontier << anatomical_part_id
      end
    end
  end

  result
end

#missing_determination ⇒ Object

see BiologicalCollectionObject



72
73
 
# File 'app/models/concerns/shared/biological_extensions.rb', line 72

def missing_determination
end

#name_at_rank_string(rank) ⇒ String

Ugh: TODO: deprecate! no utility gained here, and it’s HTML!!!

Parameters:

  • rank (String)

Returns:

  • (String) —

    if a determination exists, and the Otu in the determination has a taxon name then return the taxon name at the rank supplied



82
83
84
 
# File 'app/models/concerns/shared/biological_extensions.rb', line 82

def name_at_rank_string(rank)
  current_taxon_name.try(:ancestor_at_rank, rank).try(:cached_html)
end

#propagate_current_otu_change!(from_id:, to_id:) ⇒ Object

Propagate a change in the accepted OTU (top/position 1 TaxonDetermination) down to descendant AnatomicalParts.



99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
 
# File 'app/models/concerns/shared/biological_extensions.rb', line 99

def propagate_current_otu_change!(from_id:, to_id:)
  return true if from_id == to_id # includes nil == nil
  return true if !AnatomicalPart.valid_old_object_classes.include?(self.class.name)

  anatomical_part_ids = descendant_anatomical_part_ids
  return true if anatomical_part_ids.empty?

  scope = AnatomicalPart
    .where(project_id: project_id, id: anatomical_part_ids)
    .where(cached_otu_id: from_id)

  scope.update_all(cached_otu_id: to_id)
  true
rescue => e
  Rails.logger.warn("#{self.class}##{id} propagation failed: #{e.class}: #{e.message}")
  false
end

#reject_otus(attributed) ⇒ Object 



91
92
93
94
95
 
# File 'app/models/concerns/shared/biological_extensions.rb', line 91

def reject_otus(attributed)
  a = attributed['taxon_name_id']
  b = attributed['name']
  a.blank? && b.blank?
end

#reject_taxon_determinations(attributed) ⇒ Boolean

Returns:

  • (Boolean) 


87
88
89
 
# File 'app/models/concerns/shared/biological_extensions.rb', line 87

def reject_taxon_determinations(attributed)
  attributed['otu_id'].blank? && attributed[:otu]&.id.blank?
end

#requires_taxon_determination? ⇒ Boolean

Returns:

  • (Boolean) 


75
76
77
 
# File 'app/models/concerns/shared/biological_extensions.rb', line 75

def requires_taxon_determination?
  false
end