Class: Catalog::Otu::InventoryEntry

Inherits:
Entry
  • Object
show all
Defined in:
lib/catalog/otu/inventory_entry.rb

Overview

A Catalog::Entry that contains the biological history of an otu via citations on the otu and its coordinate otus, and on their associated data (images, asserted distributions, observations, etc.).

Instance Attribute Summary collapse

Attributes inherited from Entry

#dates, #item_index, #items, #object, #sort_order, #sources, #topics

Instance Method Summary collapse

Methods inherited from Entry

#all_citations, #all_dates, #all_sources, #all_topics, #citations, #coordinate_entry_items, #date_range, #first_item?, #index_items, #is_subsequent_entry_item?, #items_by_object, #last_item?, #ordered_by_nomenclature_date, #original_citation_present?, #to_json, #topics_for_source, #year_hash

Constructor Details

#initialize(otu, include_belongs_to: false) ⇒ InventoryEntry

nomenclature catalog typically handles citations on taxon_name, so by default we don't process belongs_to relations on otu.



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# File 'lib/catalog/otu/inventory_entry.rb', line 10

def initialize(otu, include_belongs_to: false)
  @include_belongs_to = include_belongs_to
  super(otu)
  true
end

Instance Attribute Details

#include_belongs_to ⇒ Object

Returns the value of attribute include_belongs_to.



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# File 'lib/catalog/otu/inventory_entry.rb', line 6

def include_belongs_to
  @include_belongs_to
end

Instance Method Details

#add_rendering_includes(citation_query, relation_klass) ⇒ Object (private)

Eager load citation associations and the cited object for views. (We're unfortunately tied to views since catalog is essentially a rendering tool.)



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# File 'lib/catalog/otu/inventory_entry.rb', line 201

def add_rendering_includes(citation_query, relation_klass)
  if relation_klass.name == 'BiologicalAssociation'
    citation_query = citation_query
      .includes(
        :source,
        :notes,
        :topics,
        {
          citation_object: [
            { biological_association_subject: { taxon_name: [:taxon_name_classifications, :taxon_name_relationships] } },
            { biological_association_object: { taxon_name: [:taxon_name_classifications, :taxon_name_relationships] } }
          ]
        }
      )
  else
    citation_query = citation_query
      .includes(:source, :notes, :topics, :citation_object)
  end

  citation_query
end

#build ⇒ Object 



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# File 'lib/catalog/otu/inventory_entry.rb', line 16

def build
  from_self
  true
end

#entry_item_matches_target?(item_object, reference_object) ⇒ Boolean (private)

Returns:

  • (Boolean) 


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# File 'lib/catalog/otu/inventory_entry.rb', line 224

def entry_item_matches_target?(item_object, reference_object)
  item_object.taxon_name_id == reference_object.taxon_name_id
end

#from_self ⇒ Object 



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# File 'lib/catalog/otu/inventory_entry.rb', line 25

def from_self
  coordinate_otu_ids = ::Otu.coordinate_otus(object.id).pluck(:id)
  relation_names = ApplicationEnumeration.citable_relations(Otu).values.flatten(1)
  reflections = ApplicationEnumeration.filter_sti_relations(Otu, relation_names)

  # Include taxon_name with nested associations to avoid N+1 queries when
  # rendering.
  coordinate_otus = ::Otu
    .where(id: coordinate_otu_ids)
    .includes(
      taxon_name: [:taxon_name_classifications, :taxon_name_relationships]
    )
    .index_by(&:id)

  belongs_to_relations = []
  has_one_relations = []
  has_many_relations = []
  through_relations = []

  reflections.each do |relation_name, reflection|
    if reflection.through_reflection
      through_relations << relation_name
    elsif reflection.macro == :belongs_to
      belongs_to_relations << relation_name
    elsif reflection.macro == :has_one
      has_one_relations << relation_name
    elsif reflection.macro == :has_many
      has_many_relations << relation_name
    end
  end

  process_otu_citations(coordinate_otu_ids, coordinate_otus)

  if include_belongs_to
    process_belongs_to_relations(belongs_to_relations, coordinate_otus)
  end

  # has_one and has_many use the same foreign key logic.
  process_has_relations(has_one_relations + has_many_relations, coordinate_otus)

  process_through_relations(through_relations, coordinate_otu_ids)

  @items.uniq! { |item| [item.citation.id, item.object.class.name, item.object.id] }
end

#process_belongs_to_relations(belongs_to_relations, coordinate_otus) ⇒ Object (private) 



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# File 'lib/catalog/otu/inventory_entry.rb', line 72

def process_belongs_to_relations(belongs_to_relations, coordinate_otus)
  belongs_to_relations.each do |relation_name|
    reflection = Otu.reflect_on_association(relation_name)
    relation_klass = reflection.klass
    foreign_key = reflection.foreign_key

    target_ids = coordinate_otus.values.map { |otu| otu.send(foreign_key) }.compact.uniq
    next if target_ids.empty?

    otu_to_target = coordinate_otus.transform_values { |otu| otu.send(foreign_key) }

    # Query citations directly on the target objects
    citations = Citation
      .where(citation_object_type: relation_klass.name, citation_object_id: target_ids)
      .includes(:source, :notes, :citation_object)
      .to_a

    citations.each do |citation|
      associated_object = citation.citation_object

      # Find which coordinate OTUs reference this object
      referencing_otu_ids = otu_to_target.select { |otu_id, target_id| target_id == associated_object.id }.keys

      referencing_otu_ids.each do |otu_id|
        base_otu = coordinate_otus[otu_id]
        @items << Catalog::Otu::InventoryEntryItem.new(
          object: associated_object,
          base_object: base_otu,
          citation: citation,
          nomenclature_date: citation.source&.cached_nomenclature_date,
          current_target: entry_item_matches_target?(base_otu, object)
        )
      end
    end
  end
end

#process_has_relations(has_relations, coordinate_otus) ⇒ Object (private)

Processes has_one and has_many relations (both use foreign key logic). !! Does not process :through relations.



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# File 'lib/catalog/otu/inventory_entry.rb', line 111

def process_has_relations(has_relations, coordinate_otus)
  coordinate_otu_ids = coordinate_otus.keys

  has_relations.each do |relation_name|
    reflection = Otu.reflect_on_association(relation_name)
    relation_klass = reflection.klass
    foreign_key = reflection.foreign_key

    citation_query = Citation
      .joins("INNER JOIN #{relation_klass.table_name} ON citations.citation_object_type = '#{relation_klass.name}' AND citations.citation_object_id = #{relation_klass.table_name}.id")
      .where("#{relation_klass.table_name}.#{foreign_key}" => coordinate_otu_ids)

    # Handle polymorphic associations (e.g., otu_id with otu_type = 'Otu')
    if reflection.type
      citation_query = citation_query.where("#{relation_klass.table_name}.#{reflection.type}" => 'Otu')
    end

    citations = add_rendering_includes(citation_query, relation_klass).to_a

    citations.each do |citation|
      associated_object = citation.citation_object
      base_otu_id = associated_object.send(foreign_key)
      base_otu = coordinate_otus[base_otu_id]

      @items << Catalog::Otu::InventoryEntryItem.new(
        object: associated_object,
        base_object: base_otu,
        citation: citation,
        nomenclature_date: citation.source&.cached_nomenclature_date,
        current_target: entry_item_matches_target?(base_otu, object)
      )
    end
  end
end

#process_otu_citations(coordinate_otu_ids, coordinate_otus) ⇒ Object (private) 



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# File 'lib/catalog/otu/inventory_entry.rb', line 181

def process_otu_citations(coordinate_otu_ids, coordinate_otus)
  citations = Citation
    .where(citation_object_type: 'Otu', citation_object_id: coordinate_otu_ids)
    .includes(:source, :notes, :topics)
    .sort_by { |c| c.citation_object_id == object.id ? 0 : 1 }

  citations.each do |citation|
    otu = coordinate_otus[citation.citation_object_id]
    @items << Catalog::Otu::InventoryEntryItem.new(
      object: otu,
      base_object: otu,
      citation: citation,
      nomenclature_date: citation.source&.cached_nomenclature_date,
      current_target: entry_item_matches_target?(otu, object)
    )
  end
end

#process_through_relations(through_relations, coordinate_otu_ids) ⇒ Object (private) 



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# File 'lib/catalog/otu/inventory_entry.rb', line 146

def process_through_relations(through_relations, coordinate_otu_ids)
  return if through_relations.empty?

  # Attempting to build custom joins for through relations a la
  # #process_has_relations is complex due to:
  # - STI tables (e.g., protonym → taxon_names table)
  # - Polymorphic sources
  # - Different join patterns for each through type
  # So here we just let rails handle everything.
  includes_hash = through_relations.each_with_object({}) do |rel, hash|
    hash[rel] = { citations: [:source, :notes, :topics] } # for views
  end

  coordinate_otus = ::Otu.where(id: coordinate_otu_ids).includes(includes_hash).to_a

  coordinate_otus.each do |otu|
    through_relations.each do |relation_name|
      association = otu.send(relation_name)
      association = [association] if !association.is_a?(Enumerable)

      association.compact.each do |associated_object|
        associated_object.citations.each do |citation|
          @items << Catalog::Otu::InventoryEntryItem.new(
            object: associated_object,
            base_object: otu,
            citation: citation,
            nomenclature_date: citation.source&.cached_nomenclature_date,
            current_target: entry_item_matches_target?(otu, object)
          )
        end
      end
    end
  end
end

#to_html_method ⇒ Object 



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# File 'lib/catalog/otu/inventory_entry.rb', line 21

def to_html_method
  :otu_catalog_entry_item_to_html
end