Class: Queries::BiologicalAssociation::Filter

Inherits:
Query::Filter show all
Includes:
Concerns::Citations, Concerns::Confidences, Concerns::DataAttributes, Concerns::Depictions, Concerns::Geo, Concerns::Notes, Concerns::Tags
Defined in:
lib/queries/biological_association/filter.rb

Constant Summary collapse

PARAMS = 
[
  :anatomical_part_id,
  :biological_association_id,
  :biological_associations_graph_id,
  :biological_relationship_id,
  :collecting_event_id,
  :collection_object_as_subject_or_as_object,
  :collection_object_id,
  :descendants,
  :exclude_taxon_name_relationship,
  :field_occurrence_id,
  :geo_json,
  :geo_mode,
  :geo_shape_id,
  :geo_shape_type,
  :geo_collecting_event_geographic_area,
  :object_biological_property_id,
  :object_object_global_id,
  :object_taxon_name_id,
  :object_type,
  :otu_id,
  :radius,
  :subject_biological_property_id,
  :subject_object_global_id,
  :subject_taxon_name_id,
  :subject_type,
  :taxon_name_id,
  :taxon_name_id_mode,
  :wkt,
  :biological_association_object_id,
  :biological_association_object_type,
  :biological_association_subject_id,
  :biological_association_subject_type,

  anatomical_part_id: [],
  any_global_id: [],
  biological_association_id: [],
  biological_associations_graph_id: [],
  biological_relationship_id: [],
  collecting_event_id: [],
  collection_object_id: [],
  field_occurrence_id: [],
  geo_shape_id: [],
  geo_shape_type: [],
  object_biological_property_id: [],
  object_object_global_id: [],
  object_taxon_name_id: [],
  otu_id: [],
  subject_biological_property_id: [],
  subject_object_global_id: [],
  subject_taxon_name_id: [],
  taxon_name_id: [],
  biological_association_object_id: [],
  biological_association_object_type: [],
  biological_association_subject_id: [],
  biological_association_subject_type: []
].freeze
API_PARAM_EXCLUSIONS = 
[
  :any_global_id
]

Constants inherited from Query::Filter

Query::Filter::FILTER_QUERIES, Query::Filter::SUBQUERIES

Instance Attribute Summary collapse

Attributes inherited from Query::Filter

#anatomical_part_query, #api, #asserted_distribution_query, #biological_association_query, #biological_associations_graph_query, #collecting_event_query, #collection_object_query, #content_query, #controlled_vocabulary_term_query, #conveyance_query, #data_attribute_query, #depiction_query, #descriptor_query, #document_query, #dwc_occurrence_query, #extract_query, #field_occurrence_query, #image_query, #loan_query, #object_global_id, #observation_query, #order_by, #otu_query, #page, #paginate, #params, #per, #person_query, #project_id, #recent, #recent_target, #roll_call, #sound_query, #taxon_name_query, #taxon_name_relationship_query, #venn, #venn_ignore_pagination, #venn_mode

Attributes inherited from Query

#query_string, #terms

Instance Method Summary collapse

Methods inherited from Query::Filter

#all, #all_and_clauses, #all_merge_clauses, #annotator_and_clauses, #annotator_merge_clauses, annotator_params, api_except_params, api_excluded_params, #apply_venn, #attribute_exact_facet, base_filter, base_query_name, base_query_to_h, #deep_permit, #disable_paging, included_annotator_facets, instantiated_base_filter, inverted_subqueries, #model_id_facet, #object_global_id_facet, #only_project?, #only_project_or_less?, #paging_state, params, #permitted_params, #process_url_into_params, #project_id_facet, query_name, #set_nested_queries, #set_paging, set_paging, #shared_and_clauses, #subquery_vector, #target_and_clauses, #venn_query

Methods inherited from Query

#alphabetic_strings, #alphanumeric_strings, base_name, #base_name, #base_query, #build_terms, #cached_facet, #end_wildcard, #levenshtein_distance, #match_ordered_wildcard_pieces_in_cached, #no_terms?, referenced_klass, #referenced_klass, #referenced_klass_except, #referenced_klass_intersection, #referenced_klass_union, #start_and_end_wildcard, #start_wildcard, #table, #wildcard_pieces

Constructor Details

#initialize(query_params) ⇒ Filter

Returns a new instance of Filter.



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# File 'lib/queries/biological_association/filter.rb', line 200

def initialize(query_params)
  super

  @any_global_id = params[:any_global_id]
  @biological_association_id = params[:biological_association_id]
  @biological_associations_graph_id = params[:biological_associations_graph_id]
  @biological_relationship_id = params[:biological_relationship_id]
  @collecting_event_id = params[:collecting_event_id]
  @collection_object_as_subject_or_as_object = params[:collection_object_as_subject_or_as_object]
  @collection_object_id = params[:collection_object_id]
  @field_occurrence_id = params[:field_occurrence_id]
  @anatomical_part_id = params[:anatomical_part_id]
  @descendants = boolean_param(params, :descendants)
  @exclude_taxon_name_relationship = boolean_param(params, :exclude_taxon_name_relationship)
  @geo_shape_type = params[:geo_shape_type]
  @geo_shape_id = integer_param(params, :geo_shape_id)
  @geo_mode = boolean_param(params, :geo_mode)
  @geo_collecting_event_geographic_area = boolean_param(params, :geo_collecting_event_geographic_area)
  @geo_json = params[:geo_json]
  @object_biological_property_id = params[:object_biological_property_id]
  @object_object_global_id = params[:object_object_global_id]
  @object_taxon_name_id = params[:object_taxon_name_id]
  @object_type = params[:object_type]
  @otu_id = params[:otu_id]
  @radius = params[:radius].presence || 100.0
  @subject_biological_property_id = params[:subject_biological_property_id]
  @subject_object_global_id = params[:subject_object_global_id]
  @subject_taxon_name_id = params[:subject_taxon_name_id]
  @subject_type = params[:subject_type]
  @taxon_name_id = params[:taxon_name_id]
  @taxon_name_id_mode = boolean_param(params, :taxon_name_id_mode)
  @wkt = params[:wkt]
  @biological_association_object_id = params[:biological_association_object_id]
  @biological_association_object_type = params[:biological_association_object_type]
  @biological_association_subject_id = params[:biological_association_subject_id]
  @biological_association_subject_type = params[:biological_association_subject_type]

  set_confidences_params(params)
  set_notes_params(params)
  set_tags_params(params)
  set_citations_params(params)
  set_depiction_params(params)
  set_data_attributes_params(params)
  set_geo_params(params)
end

Instance Attribute Details

#anatomical_part_id ⇒ Array

matching subject OR object

Parameters:

  • anatomical_part_id

Returns:

  • (Array) —

    All biological relationships with AnatomicalPart (only)



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# File 'lib/queries/biological_association/filter.rb', line 108

def anatomical_part_id
  @anatomical_part_id
end

#any_global_id ⇒ Array

Returns:

  • (Array) 


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# File 'lib/queries/biological_association/filter.rb', line 174

def any_global_id
  @any_global_id
end

#biological_association_id ⇒ Array

Returns one or more BiologicalAssociation#id.

Parameters:

  • biological_association_id (Array, Integer)

Returns:

  • (Array) —

    one or more BiologicalAssociation#id



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# File 'lib/queries/biological_association/filter.rb', line 154

def biological_association_id
  @biological_association_id
end

#biological_association_object_id ⇒ Object

Returns the value of attribute biological_association_object_id.



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# File 'lib/queries/biological_association/filter.rb', line 188

def biological_association_object_id
  @biological_association_object_id
end

#biological_association_object_type ⇒ Object

Returns the value of attribute biological_association_object_type.



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# File 'lib/queries/biological_association/filter.rb', line 190

def biological_association_object_type
  @biological_association_object_type
end

#biological_association_subject_id ⇒ Object

Returns the value of attribute biological_association_subject_id.



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# File 'lib/queries/biological_association/filter.rb', line 192

def biological_association_subject_id
  @biological_association_subject_id
end

#biological_association_subject_type ⇒ Object

Returns the value of attribute biological_association_subject_type.



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# File 'lib/queries/biological_association/filter.rb', line 194

def biological_association_subject_type
  @biological_association_subject_type
end

#biological_associations_graph_id ⇒ Array

Returns a biological relationship graph ID.

Parameters:

  • biological_associations_graph_id (Array, Integer)

Returns:

  • (Array) —

    a biological relationship graph ID



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# File 'lib/queries/biological_association/filter.rb', line 141

def biological_associations_graph_id
  @biological_associations_graph_id
end

#biological_relationship_id ⇒ Array

See also exclude_taxon_name_relationship

Parameters:

  • biological_relationship_id (Array, Integer)

Returns:

  • (Array) —

    one or more biological relationship ID



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# File 'lib/queries/biological_association/filter.rb', line 160

def biological_relationship_id
  @biological_relationship_id
end

#collecting_event_id ⇒ Object

linked to one or more CollectingEvent

Parameters:

  • collecting_event_id

Returns:

  • Integer All BiologicalAssociations with CollectionObjects



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# File 'lib/queries/biological_association/filter.rb', line 84

def collecting_event_id
  @collecting_event_id
end

#collection_object_as_subject_or_as_object ⇒ Object

object. !! Only used in tandem with collection_object_query!

Parameters:

  • collection_object_as_subject_or_as_object —

    Whether collection_object_query should be matched against subject or



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# File 'lib/queries/biological_association/filter.rb', line 114

def collection_object_as_subject_or_as_object
  @collection_object_as_subject_or_as_object
end

#collection_object_id ⇒ Array

matching subject OR object

Parameters:

  • collection_object_id

Returns:

  • (Array) —

    All biological relationships with CollectionObject (only)



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# File 'lib/queries/biological_association/filter.rb', line 96

def collection_object_id
  @collection_object_id
end

#descendants ⇒ Object

Returns the value of attribute descendants.



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# File 'lib/queries/biological_association/filter.rb', line 137

def descendants
  @descendants
end

#exclude_taxon_name_relationship ⇒ Object

those listed in biological_relationship_id

Returns:

  • Boolean, nil if true then return relationships excluding



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# File 'lib/queries/biological_association/filter.rb', line 78

def exclude_taxon_name_relationship
  @exclude_taxon_name_relationship
end

#field_occurrence_id ⇒ Array

matching subject OR object

Parameters:

  • field_occurrence_id

Returns:

  • (Array) —

    All biological relationships with FieldOccurrence (only)



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# File 'lib/queries/biological_association/filter.rb', line 102

def field_occurrence_id
  @field_occurrence_id
end

#geo_json ⇒ Object

Returns the value of attribute geo_json.



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# File 'lib/queries/biological_association/filter.rb', line 178

def geo_json
  @geo_json
end

#object_biological_property_id ⇒ Array

Returns All BiologicalAssociations with object having this property.

Returns:

  • (Array) —

    All BiologicalAssociations with object having this property



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# File 'lib/queries/biological_association/filter.rb', line 149

def object_biological_property_id
  @object_biological_property_id
end

#object_object_global_id ⇒ Array

Returns:

  • (Array) 


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# File 'lib/queries/biological_association/filter.rb', line 171

def object_object_global_id
  @object_object_global_id
end

#object_taxon_name_id ⇒ Object

its children !! TaxonName must be valid!

Parameters:

  • object_taxon_name_id —

    All BiologicalAssociations matching this name or



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# File 'lib/queries/biological_association/filter.rb', line 126

def object_taxon_name_id
  @object_taxon_name_id
end

#object_type ⇒ nil, ...

Returns limit object to a type.

Returns:



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# File 'lib/queries/biological_association/filter.rb', line 186

def object_type
  @object_type
end

#otu_id ⇒ Array

matching subject OR object

Parameters:

  • otu_id

Returns:

  • (Array) —

    All BiologicalAssociations with OTU (only)



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# File 'lib/queries/biological_association/filter.rb', line 90

def otu_id
  @otu_id
end

#radius ⇒ Object

Integer in Meters

!! defaults to 100m



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# File 'lib/queries/biological_association/filter.rb', line 198

def radius
  @radius
end

#subject_biological_property_id ⇒ Array

Returns All BiologicalAssociations with subject having this property.

Returns:

  • (Array) —

    All BiologicalAssociations with subject having this property



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# File 'lib/queries/biological_association/filter.rb', line 145

def subject_biological_property_id
  @subject_biological_property_id
end

#subject_object_global_id ⇒ Array

Returns:

  • (Array) 


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# File 'lib/queries/biological_association/filter.rb', line 168

def subject_object_global_id
  @subject_object_global_id
end

#subject_taxon_name_id ⇒ Object

its children. !! TaxonName must be valid!

Parameters:

  • subject_taxon_name_id —

    All BiologicalAssociations matching this name or



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# File 'lib/queries/biological_association/filter.rb', line 120

def subject_taxon_name_id
  @subject_taxon_name_id
end

#subject_type ⇒ nil, ...

Returns limit subject to a type.

Returns:



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# File 'lib/queries/biological_association/filter.rb', line 182

def subject_type
  @subject_type
end

#taxon_name_id ⇒ Array

their children

Parameters:

  • taxon_name_id

Returns:

  • (Array) —

    All BiologicalAssociations matching these names or



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# File 'lib/queries/biological_association/filter.rb', line 132

def taxon_name_id
  @taxon_name_id
end

#taxon_name_id_mode ⇒ Boolean?

Returns:

  • (Boolean, nil) 


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# File 'lib/queries/biological_association/filter.rb', line 135

def taxon_name_id_mode
  @taxon_name_id_mode
end

#wkt ⇒ Object

See lib/queries/otu/filter.rb



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# File 'lib/queries/biological_association/filter.rb', line 177

def wkt
  @wkt
end

Instance Method Details

#anatomical_part_params ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 502

def anatomical_part_params
  h = {}
  [ # TODO??
    :anatomical_part_id
    # :geo_json,
    # :geo_mode,
    # :geo_shape_id,
    # :geo_shape_type,
    # :wkt,
  ].each do |p|
    v = send(p)
    h[p] = v if v.present?
  end
  h
end

#anatomical_part_query_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 868

def anatomical_part_query_facet
  return nil if anatomical_part_query.nil?
  s = 'WITH query_ap_ba AS (' + anatomical_part_query.all.to_sql + ') '

  a = ::BiologicalAssociation
    .joins("JOIN query_ap_ba as query_ap_ba1 on biological_associations.biological_association_subject_id = query_ap_ba1.id AND biological_associations.biological_association_subject_type = 'AnatomicalPart'")

  b = ::BiologicalAssociation
    .joins("JOIN query_ap_ba as query_ap_ba2 on biological_associations.biological_association_object_id = query_ap_ba2.id AND biological_associations.biological_association_object_type = 'AnatomicalPart'")

  s << referenced_klass_union([a,b]).to_sql

  ::BiologicalAssociation.from('(' + s + ') as biological_associations')
end

#and_clauses ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 938

def and_clauses
  [
    any_global_id_facet,
    biological_association_id_facet,
    biological_relationship_id_facet,
    object_object_global_id_facet,
    object_type_facet,
    subject_object_global_id_facet,
    subject_type_facet,
    biological_association_object_id_facet,
    biological_association_object_type_facet,
    biological_association_subject_id_facet,
    biological_association_subject_id_facet
  ]
end

#any_global_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 758

def any_global_id_facet
  return nil if any_global_id.empty?
  a = matching_global_id(:subject, any_global_id)
  b = matching_global_id(:object, any_global_id)
  if a && b
    return a.or(b)
  else
    return a ? a : b
  end
end

#asserted_distribution_query_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 825

def asserted_distribution_query_facet
  return nil if asserted_distribution_query.nil?

  ::BiologicalAssociation
    .with(ad: asserted_distribution_query.all)
    .joins("JOIN asserted_distributions ON asserted_distributions.asserted_distribution_object_id = biological_associations.id AND asserted_distributions.asserted_distribution_object_type = 'BiologicalAssociation'").distinct
end

#base_anatomical_part_query(opts) ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 547

def base_anatomical_part_query(opts)
  ::Queries::AnatomicalPart::Filter.new(opts)
end

#base_collection_object_query(opts) ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 539

def base_collection_object_query(opts)
  ::Queries::CollectionObject::Filter.new(opts)
end

#base_field_occurrence_query(opts) ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 543

def base_field_occurrence_query(opts)
  ::Queries::FieldOccurrence::Filter.new(opts)
end

#base_otu_query(opts) ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 535

def base_otu_query(opts)
  ::Queries::Otu::Filter.new(opts)
end

#base_queries_to_subject_object(otu_query, collection_object_query, field_occurrence_query, anatomical_part_query, target) ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 721

def base_queries_to_subject_object(
  otu_query, collection_object_query, field_occurrence_query,
  anatomical_part_query, target
)
  o = otu_query.nil? ? ::BiologicalAssociation.none :
    ::BiologicalAssociation
      .with(a: otu_query)
      .joins("JOIN a ON a.id = biological_associations.biological_association_#{target}_id AND biological_associations.biological_association_#{target}_type = 'Otu'")

  co = collection_object_query.nil? ? ::BiologicalAssociation.none :
    ::BiologicalAssociation
      .with(b: collection_object_query)
      .joins("JOIN b ON b.id = biological_associations.biological_association_#{target}_id AND biological_associations.biological_association_#{target}_type = 'CollectionObject'")

  fo = field_occurrence_query.nil? ? ::BiologicalAssociation.none :
    ::BiologicalAssociation
      .with(c: field_occurrence_query)
      .joins("JOIN c ON c.id = biological_associations.biological_association_#{target}_id AND biological_associations.biological_association_#{target}_type = 'FieldOccurrence'")

  ap = anatomical_part_query.nil? ? ::BiologicalAssociation.none :
    ::BiologicalAssociation
      .with(d: anatomical_part_query)
      .joins("JOIN d ON d.id = biological_associations.biological_association_#{target}_id AND biological_associations.biological_association_#{target}_type = 'AnatomicalPart'")

  referenced_klass_union([o,co,fo,ap])
end

#biological_association_and_subject_object_facet ⇒ Object

Combines facets that apply to both BA itself and to subject/object.



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# File 'lib/queries/biological_association/filter.rb', line 917

def biological_association_and_subject_object_facet
  # These are facets that need to be (individually) *unioned* with the
  # subject_object_facet and biological_associations_graph_geo_facet, not
  # intersected.
  # The final result, modulo nils, is just intersection(a) union b.
  a = [wkt_facet, geo_json_facet, biological_association_geo_facet].compact
  b = if biological_associations_graph_geo_facet.nil? &&
         subject_object_facet.nil?
        nil
      else
        referenced_klass_union(
          [biological_associations_graph_geo_facet, subject_object_facet]
        )
      end

  return b if a.empty?

  i = referenced_klass_intersection(a)
  referenced_klass_union([i, b])
end

#biological_association_geo_facet ⇒ Object

Results are also returned from the otu and CO queries on subject/object.



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# File 'lib/queries/biological_association/filter.rb', line 359

def biological_association_geo_facet
  return nil if geo_shape_id.empty? || geo_shape_type.empty? ||
    # TODO: this should raise an error(?)
    geo_shape_id.length != geo_shape_type.length
  return ::BiologicalAssociation.none if roll_call

  geographic_area_shapes, gazetteer_shapes = shapes_for_geo_mode

  a = biological_association_geo_facet_by_type(
    'GeographicArea', geographic_area_shapes
  )

  b = biological_association_geo_facet_by_type(
    'Gazetteer', gazetteer_shapes
  )

  if geo_mode == true # spatial
    i = ::Queries.union(::GeographicItem, [a,b])
    u = ::Queries::GeographicItem.st_union_text(i).to_a.first

    return from_wkt(u['st_astext'])
  end

  referenced_klass_union([a,b])
end

#biological_association_geo_facet_by_type(shape_string, shape_ids) ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 385

def biological_association_geo_facet_by_type(shape_string, shape_ids)
  case geo_mode
  when nil, false # exact, descendants
    ::BiologicalAssociation
      .joins("JOIN asserted_distributions ON asserted_distributions.asserted_distribution_object_id = biological_associations.id AND asserted_distributions.asserted_distribution_object_type = 'BiologicalAssociation'")
      .where(asserted_distributions: {
        asserted_distribution_shape: shape_ids
     })
  when true # spatial
    m = shape_string.tableize
    b = ::GeographicItem.joins(m.to_sym).where(m => shape_ids)
  end
end

#biological_association_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 778

def biological_association_id_facet
  return nil if biological_association_id.empty?
  table[:id].in(biological_association_id)
end

#biological_association_object_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 435

def biological_association_object_id_facet
  return nil if biological_association_object_id.empty?
  table[:biological_association_object_id].in(biological_association_object_id)
end

#biological_association_object_type_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 430

def biological_association_object_type_facet
  return nil if biological_association_object_type.empty?
  table[:biological_association_object_type].in(biological_association_object_type)
end

#biological_association_subject_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 445

def biological_association_subject_id_facet
  return nil if biological_association_subject_id.empty?
  table[:biological_association_subject_id].in(biological_association_subject_id)
end

#biological_association_subject_type_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 440

def biological_association_subject_type_facet
  return nil if biological_association_subject_type.empty?
  table[:biological_association_subject_type].in(biological_association_subject_type)
end

#biological_associations_graph_geo_facet ⇒ Object

Results are also returned from the otu and CO queries on subject/object.



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# File 'lib/queries/biological_association/filter.rb', line 400

def biological_associations_graph_geo_facet
  bag_query = ::Queries::BiologicalAssociationsGraph::Filter.new({
    geo_json:,
    geo_shape_id:,
    geo_shape_type:,
    geo_mode:,
    radius:,
    wkt:
  })

  bag_scope = bag_query.all
  return nil if bag_query.only_project_or_less?() || bag_scope.nil?

  ::BiologicalAssociation
    .joins(:biological_associations_graphs)
    .where(biological_associations_graphs: {id: bag_scope.select(:id)})
end

#biological_associations_graph_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 462

def biological_associations_graph_id_facet
  return nil if biological_associations_graph_id.empty?
  ::BiologicalAssociation.joins(:biological_associations_graphs).where(biological_associations_graphs: {id: biological_associations_graph_id})
end

#biological_relationship_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 769

def biological_relationship_id_facet
  return nil if biological_relationship_id.empty?
  if exclude_taxon_name_relationship
    table[:biological_relationship_id].not_in(biological_relationship_id)
  else
    table[:biological_relationship_id].in(biological_relationship_id)
  end
end

#collecting_event_query_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 793

def collecting_event_query_facet
  return nil if collecting_event_query.nil?

  s = 'WITH query_ce_ba AS (' + collecting_event_query.all.to_sql + ') '

  a = ::BiologicalAssociation
    .joins("JOIN collection_objects co1 on co1.id = biological_associations.biological_association_subject_id AND biological_associations.biological_association_subject_type = 'CollectionObject'")
    .joins('JOIN query_ce_ba as query_ce_ba1 on co1.collecting_event_id = query_ce_ba1.id')

  b = ::BiologicalAssociation
    .joins("JOIN collection_objects co2 on co2.id = biological_associations.biological_association_object_id AND biological_associations.biological_association_object_type = 'CollectionObject'")
    .joins('JOIN query_ce_ba as query_ce_ba2 on co2.collecting_event_id = query_ce_ba2.id')

  s << referenced_klass_union([a,b]).to_sql

  ::BiologicalAssociation.from('(' + s + ') as biological_associations')
end

#collection_object_params ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 467

def collection_object_params
  h = {}
  [
    :collecting_event_id,
    :collection_object_id,
    :geo_json,
    :geo_mode,
    :geo_shape_id,
    :geo_shape_type,
    :geo_collecting_event_geographic_area,
    :wkt,
  ].each do |p|
    v = send(p)
    h[p] = v if v.present?
  end
  h
end

#collection_object_query_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 833

def collection_object_query_facet
  return nil if collection_object_query.nil?

  a = ::BiologicalAssociation
    .with(query_co_ba1: collection_object_query.all)
    .joins("JOIN query_co_ba1 ON biological_associations.biological_association_subject_id = query_co_ba1.id AND biological_associations.biological_association_subject_type = 'CollectionObject'")

  b = ::BiologicalAssociation
    .with(query_co_ba2: collection_object_query.all)
    .joins("JOIN query_co_ba2 ON biological_associations.biological_association_object_id = query_co_ba2.id AND biological_associations.biological_association_object_type = 'CollectionObject'")

  if collection_object_as_subject_or_as_object&.to_sym == :subject
    return a
  elsif collection_object_as_subject_or_as_object&.to_sym == :object
    return b
  else
    return referenced_klass_union([a,b])
  end
end

#field_occurrence_params ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 485

def field_occurrence_params
  h = {}
  [
    :collecting_event_id,
    :field_occurrence_id,
    :geo_json,
    :geo_mode,
    :geo_shape_id,
    :geo_shape_type,
    :wkt,
  ].each do |p|
    v = send(p)
    h[p] = v if v.present?
  end
  h
end

#field_occurrence_query_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 853

def field_occurrence_query_facet
  return nil if field_occurrence_query.nil?
  s = 'WITH query_fo_ba AS (' + field_occurrence_query.all.to_sql + ') '

  a = ::BiologicalAssociation
    .joins("JOIN query_fo_ba as query_fo_ba1 on biological_associations.biological_association_subject_id = query_fo_ba1.id AND biological_associations.biological_association_subject_type = 'FieldOccurrence'")

  b = ::BiologicalAssociation
    .joins("JOIN query_fo_ba as query_fo_ba2 on biological_associations.biological_association_object_id = query_fo_ba2.id AND biological_associations.biological_association_object_type = 'FieldOccurrence'")

  s << referenced_klass_union([a,b]).to_sql

  ::BiologicalAssociation.from('(' + s + ') as biological_associations')
end

#from_wkt(wkt_shape) ⇒ Object

Results are also returned from the otu and CO queries on subject/object.



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# File 'lib/queries/biological_association/filter.rb', line 332

def from_wkt(wkt_shape)
  a = ::Queries::AssertedDistribution::Filter.new(
    wkt: wkt_shape, project_id:,
    asserted_distribution_object_type: 'BiologicalAssociation'
  )

  ::BiologicalAssociation
    .with(ad: a.all)
    .joins('JOIN ad ON ad.asserted_distribution_object_id = biological_associations.id')
end

#geo_json_facet ⇒ Object

Results are also returned from the otu and CO queries on subject/object.



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# File 'lib/queries/biological_association/filter.rb', line 344

def geo_json_facet
  return nil if geo_json.blank?
  return ::BiologicalAssociation.none if roll_call

  a = ::Queries::AssertedDistribution::Filter.new(
    geo_json:, project_id:, radius:,
    asserted_distribution_object_type: 'BiologicalAssociation'
  )

  ::BiologicalAssociation
    .with(ad: a.all)
    .joins('JOIN ad ON ad.asserted_distribution_object_id = biological_associations.id')
end

#matching_global_id(target = :subject, global_id = []) ⇒ Object (private) 



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# File 'lib/queries/biological_association/filter.rb', line 983

def matching_global_id(target = :subject, global_id = [])
  a = global_id
  b = "#{target}_matches".to_sym

  q = send(b, object_for(a[0]))
  a[1..a.length].each do |i|
    q = q.or( send(b, object_for(i) ))
  end
  q
end

#merge_clauses ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 954

def merge_clauses
  [
    anatomical_part_query_facet,
    asserted_distribution_query_facet,
    collecting_event_query_facet,
    collection_object_query_facet,
    field_occurrence_query_facet,
    otu_query_facet,
    taxon_name_query_facet,

    taxon_name_id_facet,
    biological_associations_graph_id_facet,
    object_biological_property_id_facet,
    subject_biological_property_id_facet,
    # This handles all Otu/CollectionObject attributes
    biological_association_and_subject_object_facet,
  ]
end

#object_biological_property_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 450

def object_biological_property_id_facet
  return nil if object_biological_property_id.empty?
  ::BiologicalAssociation.joins(:object_biological_relationship_types)
    .where(biological_relationship_types: {biological_property_id: object_biological_property_id })
end

#object_collection_object_query ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 565

def object_collection_object_query
  p = {}
  s = object_taxon_name_ids

  if s.empty?
    return nil
  elsif s.present?
    p[:taxon_name_id] = s
    p[:descendants] = descendants
  end

  q = base_collection_object_query(p)
end

#object_field_occurrence_query ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 593

def object_field_occurrence_query
  p = {}
  s = object_taxon_name_ids

  if s.empty?
    return nil
  elsif s.present?
    p[:taxon_name_id] = s
    p[:descendants] = descendants
  end

  q = base_field_occurrence_query(p)
end

#object_for(global_id) ⇒ Object (private) 



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# File 'lib/queries/biological_association/filter.rb', line 975

def object_for(global_id)
  if o = GlobalID::Locator.locate(global_id)
    o
  else
    nil
  end
end

#object_matches(object) ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 424

def object_matches(object)
  table['biological_association_object_id'].eq(object.id).and(
    table['biological_association_object_type'].eq(object.class.base_class.name)
  )
end

#object_object_global_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 753

def object_object_global_id_facet
  return nil if object_object_global_id.empty?
  matching_global_id(:object, object_object_global_id)
end

#object_otu_query ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 621

def object_otu_query
  p = {}
  s = object_taxon_name_ids

  if s.empty?
    return nil
  elsif s.present?
    p[:taxon_name_id] = s
    p[:descendants] = descendants
  end

  base_otu_query(p)
end

#object_scope ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 639

def object_scope
  target_scope('object')
end

#object_taxon_name_ids ⇒ Object (private)

!! Plural is correct



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# File 'lib/queries/biological_association/filter.rb', line 995

def object_taxon_name_ids
  return taxon_name_id if !taxon_name_id.empty?
  return object_taxon_name_id if !object_taxon_name_id.empty?
  return []
end

#object_type_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 783

def object_type_facet
  return nil if object_type.nil?
  table[:biological_association_object_type].eq(object_type)
end

#otu_params ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 518

def otu_params
  h = {}
  [
    :geo_json,
    :geo_mode,
    :geo_shape_id,
    :geo_shape_type,
    :geo_collecting_event_geographic_area,
    :otu_id,
    :wkt,
  ].each do |p|
    v = send(p)
    h[p] = v if v.present?
  end
  h
end

#otu_query_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 811

def otu_query_facet
  return nil if otu_query.nil?
  s = 'WITH query_otu_ba AS (' + otu_query.all.to_sql + ') '

  a = ::BiologicalAssociation
    .joins("JOIN query_otu_ba as query_otu_ba1 on biological_associations.biological_association_subject_id = query_otu_ba1.id AND biological_associations.biological_association_subject_type = 'Otu'")

  b = ::BiologicalAssociation
    .joins("JOIN query_otu_ba as query_otu_ba2 on biological_associations.biological_association_object_id = query_otu_ba2.id AND biological_associations.biological_association_object_type = 'Otu'")

  s << referenced_klass_union([a,b]).to_sql
  ::BiologicalAssociation.from('(' + s + ') as biological_associations')
end

#subject_biological_property_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 456

def subject_biological_property_id_facet
  return nil if subject_biological_property_id.empty?
  ::BiologicalAssociation.joins(:subject_biological_relationship_types)
    .where(biological_relationship_types: {biological_property_id: subject_biological_property_id })
end

#subject_collection_object_query ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 551

def subject_collection_object_query
  p = {}
  s = subject_taxon_name_ids

  if s.empty?
    return nil
  elsif s.present?
    p[:taxon_name_id] = s
    p[:descendants] = descendants
  end

  q = base_collection_object_query(p)
end

#subject_field_occurrence_query ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 579

def subject_field_occurrence_query
  p = {}
  s = subject_taxon_name_ids

  if s.empty?
    return nil
  elsif s.present?
    p[:taxon_name_id] = s
    p[:descendants] = descendants
  end

  q = base_field_occurrence_query(p)
end

#subject_matches(object) ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 418

def subject_matches(object)
  table['biological_association_subject_id'].eq(object.id).and(
    table['biological_association_subject_type'].eq(object.class.base_class.name)
  )
end

#subject_object_facet ⇒ Object

Merges results from Otu and CollectionObject filters as the basis for the query



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# File 'lib/queries/biological_association/filter.rb', line 689

def subject_object_facet
  o_params = otu_params
  co_params = collection_object_params
  fo_params = field_occurrence_params
  ap_params = anatomical_part_params
  return nil if o_params.empty? && co_params.empty? && fo_params.empty? && ap_params.empty?

  a = o_params.empty? ? nil : base_otu_query(o_params).all
  b = co_params.empty? ? nil : base_collection_object_query(co_params).all
  c = fo_params.empty? ? nil : base_field_occurrence_query(fo_params).all
  d = ap_params.empty? ? nil : base_anatomical_part_query(ap_params).all

  subjects = base_queries_to_subject_object(a, b, c, d, 'subject')
  objects = base_queries_to_subject_object(a, b, c, d, 'object')

  referenced_klass_union([subjects,objects])
end

#subject_object_global_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 748

def subject_object_global_id_facet
  return nil if subject_object_global_id.empty?
  matching_global_id(:subject, subject_object_global_id)
end

#subject_otu_query ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 607

def subject_otu_query
  p = {}
  s = subject_taxon_name_ids

  if s.empty?
    return nil
  elsif s.present?
    p[:taxon_name_id] = s
    p[:descendants] = descendants
  end

  base_otu_query(p)
end

#subject_scope ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 635

def subject_scope
  target_scope('subject')
end

#subject_taxon_name_ids ⇒ Object (private)

!! Plural is correct



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# File 'lib/queries/biological_association/filter.rb', line 1002

def subject_taxon_name_ids
  return taxon_name_id if !taxon_name_id.empty? # only one or the other supposed to be sent
  return subject_taxon_name_id if !subject_taxon_name_id.empty?
  return []
end

#subject_type_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 788

def subject_type_facet
  return nil if subject_type.nil?
  table[:biological_association_subject_type].eq(subject_type)
end

#target_scope(target = 'subject') ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 643

def target_scope(target = 'subject')
  a = send((target + '_otu_query').to_sym)
  b = send((target + '_collection_object_query').to_sym)
  c = send((target + '_field_occurrence_query').to_sym)

  a_query, b_query, c_query = nil, nil, nil

  if !a.nil? && !a.only_project?
    a_query = a.all
  end

  if !b.nil? && !b.only_project?
    b_query = b.all
  end

  if !c.nil? && !c.only_project?
    c_query = c.all
  end

  return nil if a_query.nil? && b_query.nil? && c_query.nil?

  d, e, f = nil, nil, nil

  if a_query
    d = ::BiologicalAssociation
      .with(a: a_query)
      .joins("JOIN a ON a.id = biological_associations.biological_association_#{target}_id AND biological_associations.biological_association_#{target}_type = 'Otu'")
  end

  if b_query
    e = ::BiologicalAssociation
      .with(b: b_query)
      .joins("JOIN b ON b.id = biological_associations.biological_association_#{target}_id AND biological_associations.biological_association_#{target}_type = 'CollectionObject'")
  end

  if c_query
    f = ::BiologicalAssociation
      .with(c: c_query)
      .joins("JOIN c ON c.id = biological_associations.biological_association_#{target}_id AND biological_associations.biological_association_#{target}_type = 'FieldOccurrence'")
  end

  referenced_klass_union([d,e,f])
end

#taxon_name_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 707

def taxon_name_id_facet
  return nil if subject_taxon_name_ids.empty? && object_taxon_name_ids.empty?

  a = subject_scope
  b = object_scope

  case taxon_name_id_mode
  when true # and
    referenced_klass_intersection([a,b])
  when false, nil # or
    referenced_klass_union([a,b])
  end
end

#taxon_name_query_facet ⇒ Object

Brute-force style



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# File 'lib/queries/biological_association/filter.rb', line 884

def taxon_name_query_facet
  return nil if taxon_name_query.nil?

  s = 'WITH query_tn_ba AS (' + taxon_name_query.all.to_sql + ') '

  a = ::BiologicalAssociation
    .joins("JOIN otus on otus.id = biological_associations.biological_association_subject_id AND biological_associations.biological_association_subject_type = 'Otu'")
    .joins('JOIN query_tn_ba as query_tn_ba1 on otus.taxon_name_id = query_tn_ba1.id')

  b = ::BiologicalAssociation
    .joins("JOIN otus on otus.id = biological_associations.biological_association_object_id AND biological_associations.biological_association_object_type = 'Otu'")
    .joins('JOIN query_tn_ba as query_tn_ba2 on otus.taxon_name_id = query_tn_ba2.id')

  c = ::BiologicalAssociation
    .joins("JOIN collection_objects on collection_objects.id = biological_associations.biological_association_subject_id AND biological_associations.biological_association_subject_type = 'CollectionObject'")
    .joins("JOIN taxon_determinations on taxon_determinations.taxon_determination_object_id = collection_objects.id AND taxon_determinations.taxon_determination_object_type = 'CollectionObject'")
    .joins('JOIN otus on otus.id = taxon_determinations.otu_id')
    .joins('JOIN query_tn_ba as query_tn_ba3 on otus.taxon_name_id = query_tn_ba3.id')
    .where('taxon_determinations.position = 1')

  d = ::BiologicalAssociation
    .joins("JOIN collection_objects on collection_objects.id = biological_associations.biological_association_object_id AND biological_associations.biological_association_object_type = 'CollectionObject'")
    .joins("JOIN taxon_determinations on taxon_determinations.taxon_determination_object_id = collection_objects.id AND taxon_determinations.taxon_determination_object_type = 'CollectionObject'")
    .joins('JOIN otus on otus.id = taxon_determinations.otu_id')
    .joins('JOIN query_tn_ba as query_tn_ba4 on otus.taxon_name_id = query_tn_ba4.id')
    .where('taxon_determinations.position = 1')

  s << referenced_klass_union([a,b,c,d]).to_sql

  ::BiologicalAssociation.from('(' + s + ') as biological_associations')
end

#wkt_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 326

def wkt_facet
  return nil if wkt.nil?
  from_wkt(wkt)
end