Module: Shared::IsIndexedBiologicalAssociation

Extended by:
ActiveSupport::Concern
Included in:
BiologicalAssociation
Defined in:
app/models/concerns/shared/is_indexed_biological_association.rb

Overview

Shared code for BiologicalAssociation to maintain the biological_association_index table.

Constant Summary collapse

DWC_TYPES =

Types that have dwc_recorded_by method.

%w{CollectionObject FieldOccurrence}.freeze
SOURCE_TYPES =

Types that don’t have dwc_recorded_by - use citation sources instead.

%w{Otu AnatomicalPart}.freeze

Instance Method Summary collapse

Instance Method Details

#biological_association_citation_year ⇒ Object (private) 



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# File 'app/models/concerns/shared/is_indexed_biological_association.rb', line 147

def biological_association_citation_year
  ApplicationController.helpers.short_sources_year_tag(sources)
end

#biological_association_citations ⇒ Object (private)

TODO: Should reference DOIs, Identifiers, or identifiers in lieu of short citations. Could be collectors (ORCID or …) Could be citation providers



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# File 'app/models/concerns/shared/is_indexed_biological_association.rb', line 166

def biological_association_citations
  subject_type = biological_association_subject_type
  object_type = biological_association_object_type

  subject_is_dwc = DWC_TYPES.include?(subject_type)
  object_is_dwc = DWC_TYPES.include?(object_type)

  if !subject_is_dwc && !object_is_dwc
    # Both are source-based types, like OTU.
    ApplicationController.helpers.short_sources_tag(sources)
  elsif subject_is_dwc && !object_is_dwc
    # Subject is specimen-like, object is OTU-like.
    biological_association_subject.dwc_recorded_by || ApplicationController.helpers.short_sources_tag(sources)
  elsif !subject_is_dwc && object_is_dwc
    # Subject is OTU-like, object is specimen-like.
    biological_association_object.dwc_recorded_by || ApplicationController.helpers.short_sources_tag(sources)
  else
    # Both are specimen-like.
    # Lots of assumptions behind this. What if specimens were marked as
    # collected in 2 different events, that would be odd but perhaps not
    # impossible.
    biological_association_subject.dwc_recorded_by || biological_association_object.dwc_recorded_by
  end
end

#biological_association_established_date ⇒ Object (private) 



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# File 'app/models/concerns/shared/is_indexed_biological_association.rb', line 191

def biological_association_established_date
  subject_type = biological_association_subject_type
  object_type = biological_association_object_type

  subject_is_dwc = DWC_TYPES.include?(subject_type)
  object_is_dwc = DWC_TYPES.include?(object_type)

  if !subject_is_dwc && !object_is_dwc
    # Both are source-based types, like OTU.
    ApplicationController.helpers.short_sources_year_tag(sources)
  elsif subject_is_dwc && !object_is_dwc
    # Subject is specimen-like, object is OTU-like.
    biological_association_subject.dwc_event_date || ApplicationController.helpers.short_sources_year_tag(sources)
  elsif !subject_is_dwc && object_is_dwc
    # Subject is OTU-like, object is specimen-like.
    biological_association_object.dwc_event_date || ApplicationController.helpers.short_sources_year_tag(sources)
  else
    # Both are specimen-like.
    # Lots of assumptions behind this. What if specimens were marked as
    # collected in 2 different events, that would be odd but perhaps not
    # impossible.
    biological_association_subject.dwc_event_date || biological_association_object.dwc_event_date
  end
end

#biological_association_index_attributes ⇒ Object

!! This is expensive, it recomputes values for every field.

Returns:

  • Hash of field: value



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# File 'app/models/concerns/shared/is_indexed_biological_association.rb', line 51

def biological_association_index_attributes
  {
    biological_association_id: id,
    biological_association_uuid: uuid,
    biological_relationship_id: biological_relationship_id,
    project_id: project_id,
    created_by_id: created_by_id,
    updated_by_id: updated_by_id,

    # Subject fields
    subject_id: biological_association_subject_id,
    subject_type: biological_association_subject_type,
    subject_uuid: biological_association_subject_uuid,
    subject_label: biological_association_subject_label,
    subject_order: biological_association_subject_taxonomy_field('order'),
    subject_family: biological_association_subject_taxonomy_field('family'),
    subject_genus: biological_association_subject_taxonomy_field('genus'),
    subject_properties: biological_association_subject_properties,

    # Relationship fields
    biological_relationship_uri: biological_relationship_uri,
    relationship_name: biological_relationship.name,
    relationship_inverted_name: biological_relationship.inverted_name,

    # Object fields
    object_id: biological_association_object_id,
    object_type: biological_association_object_type,
    object_uuid: biological_association_object_uuid,
    object_label: biological_association_object_label,
    object_order: biological_association_object_taxonomy_field('order'),
    object_family: biological_association_object_taxonomy_field('family'),
    object_genus: biological_association_object_taxonomy_field('genus'),
    object_properties: biological_association_object_properties,

    # Citations and metadata
    citations: biological_association_citations,
    citation_year: biological_association_citation_year,
    established_date: biological_association_established_date,
    remarks: biological_association_remarks
  }
end

#biological_association_object_label ⇒ Object (private) 



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# File 'app/models/concerns/shared/is_indexed_biological_association.rb', line 123

def biological_association_object_label
  ApplicationController.helpers.label_for(biological_association_object)
end

#biological_association_object_properties ⇒ Object (private) 



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# File 'app/models/concerns/shared/is_indexed_biological_association.rb', line 139

def biological_association_object_properties
  object_biological_properties.pluck(:name).join(Shared::IsDwcOccurrence::DWC_DELIMITER).presence
end

#biological_association_object_taxonomy_field(rank) ⇒ Object (private) 



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# File 'app/models/concerns/shared/is_indexed_biological_association.rb', line 131

def biological_association_object_taxonomy_field(rank)
  [biological_association_object.taxonomy[rank]].flatten.compact.join(' ').presence
end

#biological_association_object_uuid ⇒ Object (private) 



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# File 'app/models/concerns/shared/is_indexed_biological_association.rb', line 112

def biological_association_object_uuid
  case biological_association_object.class.base_class.name
  when 'Otu', 'CollectionObject', 'FieldOccurrence', 'AnatomicalPart'
    biological_association_object.uuid
  end
end

#biological_association_remarks ⇒ Object (private)

TODO: Generic helper



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# File 'app/models/concerns/shared/is_indexed_biological_association.rb', line 152

def biological_association_remarks
  Utilities::Strings.sanitize_for_csv(notes.collect { |n| n.text }.join(Shared::IsDwcOccurrence::DWC_DELIMITER)).presence
end

#biological_association_subject_label ⇒ Object (private) 



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# File 'app/models/concerns/shared/is_indexed_biological_association.rb', line 119

def biological_association_subject_label
  ApplicationController.helpers.label_for(biological_association_subject)
end

#biological_association_subject_properties ⇒ Object (private) 



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# File 'app/models/concerns/shared/is_indexed_biological_association.rb', line 135

def biological_association_subject_properties
  subject_biological_properties.pluck(:name).join(Shared::IsDwcOccurrence::DWC_DELIMITER).presence
end

#biological_association_subject_taxonomy_field(rank) ⇒ Object (private) 



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# File 'app/models/concerns/shared/is_indexed_biological_association.rb', line 127

def biological_association_subject_taxonomy_field(rank)
  [biological_association_subject.taxonomy[rank]].flatten.compact.join(' ').presence
end

#biological_association_subject_uuid ⇒ Object (private) 



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# File 'app/models/concerns/shared/is_indexed_biological_association.rb', line 105

def biological_association_subject_uuid
  case biological_association_subject.class.base_class.name
  when 'Otu', 'CollectionObject', 'FieldOccurrence', 'AnatomicalPart'
    biological_association_subject.uuid
  end
end

#biological_relationship_uri ⇒ Object (private) 



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# File 'app/models/concerns/shared/is_indexed_biological_association.rb', line 143

def biological_relationship_uri
  biological_relationship.uris.first&.cached
end

#get_biological_association_index ⇒ BiologicalAssociationIndex

Returns does not rebuild if already built.

Returns:



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# File 'app/models/concerns/shared/is_indexed_biological_association.rb', line 95

def get_biological_association_index
  if biological_association_index_persisted?
    biological_association_index
  else
    set_biological_association_index
  end
end

#set_biological_association_index ⇒ BiologicalAssociationIndex

Returns !! always touches the database.

Returns:



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# File 'app/models/concerns/shared/is_indexed_biological_association.rb', line 23

def set_biological_association_index
  retried = false
  begin
    if biological_association_index_persisted?
      biological_association_index.update_columns(
        biological_association_index_attributes.merge(
          rebuild_set: nil,
          updated_at: Time.zone.now)
      )
    else
      create_biological_association_index!(biological_association_index_attributes)
    end
  rescue ActiveRecord::ActiveRecordError
    unless retried
      retried = true
      biological_association_index&.reload
      retry
    else
      raise
    end
  end
  biological_association_index
end