Class: Queries::AssertedDistribution::Filter

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

Constant Summary collapse

PARAMS = 
[
  :asserted_distribution_id,
  :asserted_distribution_object_id,
  :asserted_distribution_object_type,
  :asserted_distribution_shape_type,
  :biological_association_id,
  :geo_shape_id,
  :geo_mode,
  :geo_shape_type,
  :descendants,
  :geo_json,
  :geographic_area_id,
  :geographic_item_id,
  :geographic_area_mode,
  :otu_id,
  :presence,
  :radius,
  :source_id,
  :shape_type,
  :taxon_name_id,
  :wkt,
  asserted_distribution_id: [],
  asserted_distribution_object_id: [],
  asserted_distribution_object_type: [],
  asserted_distribution_shape_type: [],
  biological_association_id: [],
  geo_shape_id: [],
  geo_shape_type: [],
  geographic_area_id: [],
  geographic_item_id: [],
  otu_id: [],
  source_id: [],
  taxon_name_id: []
].freeze

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

Class Method Summary collapse

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/asserted_distribution/filter.rb', line 114

def initialize(query_params)
  super
  @asserted_distribution_id =
    integer_param(params, :asserted_distribution_id)
  @asserted_distribution_object_id =
    integer_param(params, :asserted_distribution_object_id)
  @asserted_distribution_object_type =
    params[:asserted_distribution_object_type]
  @biological_association_id =
    integer_param(params, :biological_association_id)
  @descendants = boolean_param(params, :descendants)
  @geo_json = params[:geo_json]
  @geographic_area_id = integer_param(params,:geographic_area_id)
  @geographic_item_id = integer_param(params, :geographic_item_id)
  @geographic_area_mode = boolean_param(params, :geographic_area_mode)
  @otu_id = integer_param(params, :otu_id)
  @presence = boolean_param(params, :presence)
  @radius = params[:radius].presence || 100.0
  @asserted_distribution_shape_type =
    params[:asserted_distribution_shape_type]
  @source_id = integer_param(params, :source_id)
  @taxon_name_id = integer_param(params, :taxon_name_id)
  @wkt = params[:wkt]

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

Instance Attribute Details

#asserted_distribution_id ⇒ Array

Parameters:

  • asserted_distribution_id (Array, Integer, String)

Returns:

  • (Array) 


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# File 'lib/queries/asserted_distribution/filter.rb', line 50

def asserted_distribution_id
  @asserted_distribution_id
end

#asserted_distribution_object_id ⇒ Array

Parameters:

  • asserted_distribution_object_id (Array, Integer, String)

Returns:

  • (Array) 


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# File 'lib/queries/asserted_distribution/filter.rb', line 54

def asserted_distribution_object_id
  @asserted_distribution_object_id
end

#asserted_distribution_object_type ⇒ Array

Parameters:

  • asserted_distribution_object_type (Array, Integer, String)

Returns:

  • (Array) 


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# File 'lib/queries/asserted_distribution/filter.rb', line 58

def asserted_distribution_object_type
  @asserted_distribution_object_type
end

#asserted_distribution_shape_type ⇒ Array

Returns:

  • (Array) 


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# File 'lib/queries/asserted_distribution/filter.rb', line 112

def asserted_distribution_shape_type
  @asserted_distribution_shape_type
end

#biological_association_id ⇒ Array

Parameters:

  • biological_association_id (Array, Integer, String)

Returns:

  • (Array) 


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# File 'lib/queries/asserted_distribution/filter.rb', line 62

def biological_association_id
  @biological_association_id
end

#descendants ⇒ Boolean?

Returns true - include descendants of taxon_name_id in scope false, nil - only exact matches.

Returns:

  • (Boolean, nil) —

    true - include descendants of taxon_name_id in scope false, nil - only exact matches



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# File 'lib/queries/asserted_distribution/filter.rb', line 105

def descendants
  @descendants
end

#geo_json ⇒ Object

Returns the value of attribute geo_json.



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# File 'lib/queries/asserted_distribution/filter.rb', line 85

def geo_json
  @geo_json
end

#geographic_area_id ⇒ Array

Parameters:

  • geographic_area_id (Array, Integer, String)

Returns:

  • (Array) 


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# File 'lib/queries/asserted_distribution/filter.rb', line 70

def geographic_area_id
  @geographic_area_id
end

#geographic_area_mode ⇒ Boolean?

Returns How to treat GeographicAreas

nil - non-spatial match by only those records matching the geographic_area_id exactly
true - spatial match
false - non-spatial match (descendants).

Returns:

  • (Boolean, nil) —

    How to treat GeographicAreas

    nil - non-spatial match by only those records matching the geographic_area_id exactly
true - spatial match
false - non-spatial match (descendants)



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# File 'lib/queries/asserted_distribution/filter.rb', line 81

def geographic_area_mode
  @geographic_area_mode
end

#geographic_item_id ⇒ Array

Parameters:

  • geographic_item_id (Array, Integer, String)

Returns:

  • (Array) 


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# File 'lib/queries/asserted_distribution/filter.rb', line 74

def geographic_item_id
  @geographic_item_id
end

#otu_id ⇒ Array

Parameters:

  • otu_id (Array, Integer, String)

Returns:

  • (Array) 


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# File 'lib/queries/asserted_distribution/filter.rb', line 66

def otu_id
  @otu_id
end

#presence ⇒ Boolean?

Returns true - Return AssertedDistributions where the OTU is asserted as present according to the Source false - Return AssertedDistributions where the OTU is asserted as absent according to the Source nil - both.

Returns:

  • (Boolean, nil) —

    true - Return AssertedDistributions where the OTU is asserted as present according to the Source false - Return AssertedDistributions where the OTU is asserted as absent according to the Source nil - both



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# File 'lib/queries/asserted_distribution/filter.rb', line 91

def presence
  @presence
end

#radius ⇒ Object

Integer in Meters

!! defaults to 100m



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# File 'lib/queries/asserted_distribution/filter.rb', line 109

def radius
  @radius
end

#source_id ⇒ Array

Parameters:

  • source_id (Array, Integer, String)

Returns:

  • (Array) 


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# File 'lib/queries/asserted_distribution/filter.rb', line 100

def source_id
  @source_id
end

#taxon_name_id ⇒ Array

Parameters:

  • all (taxon name ids, nil) —

    Otus matching these taxon names

Returns:

  • (Array) 


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

def taxon_name_id
  @taxon_name_id
end

#wkt ⇒ Object

Returns the value of attribute wkt.



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# File 'lib/queries/asserted_distribution/filter.rb', line 83

def wkt
  @wkt
end

Class Method Details

.from_geographic_items(geographic_items_sql) ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 211

def self.from_geographic_items(geographic_items_sql)
  # TODO: can we combine GAs and GAZs *before* joining with
  # geographic_items_sql? That would save a spatial contains query.
  a = self.geographic_areas_for_geographic_items(geographic_items_sql)
  b = self.gazetteers_for_geographic_items(geographic_items_sql)

  ::Queries.union(::AssertedDistribution, [a,b])
end

.gazetteers_for_geographic_items(geographic_items_sql) ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 241

def self.gazetteers_for_geographic_items(geographic_items_sql)
  i = ::GeographicItem.joins(:gazetteers).where(geographic_items_sql)

  gazetteer_ids = ::Gazetteer
    .joins(:geographic_item).merge(i).pluck(:id)

  if gazetteer_ids.empty?
    return ::AssertedDistribution.none
  end

  ::AssertedDistribution
    .where(asserted_distribution_shape_id: gazetteer_ids,
      asserted_distribution_shape_type: 'Gazetteer')
end

.geographic_areas_for_geographic_items(geographic_items_sql) ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 220

def self.geographic_areas_for_geographic_items(geographic_items_sql)
  i = ::GeographicItem
    .joins(:geographic_areas)
    .where(geographic_items_sql)

  j = ::GeographicArea.joins(:geographic_items).merge(i).pluck(:id)

  # TODO: There are only 58 GAs with shape that have a descendant without
  # shape: could this be a lookup table instead?
  k = ::GeographicArea.descendants_of(j).pluck(:id) # Add children that might not be caught because they don't have shapes

  geographic_area_ids = (j + k).uniq
  if geographic_area_ids.empty?
    return ::AssertedDistribution.none
  end

  ::AssertedDistribution
    .where(asserted_distribution_shape_id: geographic_area_ids,
      asserted_distribution_shape_type: 'GeographicArea')
end

Instance Method Details

#and_clauses ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 496

def and_clauses
  [
    biological_association_id_facet,
    otu_id_facet,
    presence_facet,
    asserted_distribution_shape_type_facet,
    asserted_distribution_object_type_facet,
    asserted_distribution_object_facet,
  ]
end

#asserted_distribution_geo_facet ⇒ Object 



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

def asserted_distribution_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 ::AssertedDistribution.none if roll_call

  geographic_area_shapes, gazetteer_shapes = shapes_for_geo_mode

  a = asserted_distribution_geo_facet_by_type(
    'GeographicArea', geographic_area_shapes
  )

  b = asserted_distribution_geo_facet_by_type(
    'Gazetteer', gazetteer_shapes
  )

  if geo_mode != true # exact or descendants
    return referenced_klass_union([a,b])
  end

  # Spatial.
  i = ::Queries.union(::GeographicItem, [a,b])
  self.class.from_geographic_items(
    ::GeographicItem.covered_by_geographic_items_sql(i)
  )
end

#asserted_distribution_geo_facet_by_type(shape_string, shape_ids) ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 371

def asserted_distribution_geo_facet_by_type(shape_string, shape_ids)
  b = nil

  case geo_mode
  when nil, false # exact, descendants
    b = ::AssertedDistribution
      .where(asserted_distribution_shape: shape_ids)
  when true # spatial
    m = shape_string.tableize
    b = ::GeographicItem.joins(m.to_sym).where(m => shape_ids)
  end

  b
end

#asserted_distribution_object_facet ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 319

def asserted_distribution_object_facet
  return nil if asserted_distribution_object_type.length != 1 ||
    asserted_distribution_object_id.empty?

  table[:asserted_distribution_object_id]
    .in(asserted_distribution_object_id).and(
      table[:asserted_distribution_object_type]
        .eq(asserted_distribution_object_type.first)
    )
end

#asserted_distribution_object_type_facet ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 330

def asserted_distribution_object_type_facet
  return nil if asserted_distribution_object_type.empty?

  table[:asserted_distribution_object_type]
    .in(asserted_distribution_object_type)
end

#asserted_distribution_shape_type_facet ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 337

def asserted_distribution_shape_type_facet
  return nil if asserted_distribution_shape_type.empty?

  table[:asserted_distribution_shape_type]
    .in(asserted_distribution_shape_type)
end

#biological_association_id_facet ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 393

def biological_association_id_facet
  return nil if biological_association_id.empty?
  table[:asserted_distribution_object_type].eq('BiologicalAssociation')
    .and(table[:asserted_distribution_object_id]
      .in(biological_association_id)
    )
end

#biological_association_query_facet ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 459

def biological_association_query_facet
  return nil if biological_association_query.nil?
  # On the BA itself.
  a = ::AssertedDistribution
    .with(ba: biological_association_query.all)
    .joins("JOIN ba ON ba.id = asserted_distributions.asserted_distribution_object_id AND asserted_distributions.asserted_distribution_object_type = 'BiologicalAssociation'")

  # On subject/object of the BA.
  b = ::AssertedDistribution
    .with(ba: biological_association_query.all)
    .joins("JOIN ba ON asserted_distributions.asserted_distribution_object_id = ba.biological_association_subject_id AND ba.biological_association_subject_type = 'Otu'")

  c = ::AssertedDistribution
    .with(ba: biological_association_query.all)
    .joins("JOIN ba ON asserted_distributions.asserted_distribution_object_id = ba.biological_association_object_id AND ba.biological_association_object_type = 'Otu'")

  # On a graph containing the BA.
  d = ::AssertedDistribution
    .with(ba: biological_association_query.all)
    .joins("JOIN biological_associations_graphs ON biological_associations_graphs.id = asserted_distributions.asserted_distribution_object_id AND asserted_distributions.asserted_distribution_object_type = 'BiologicalAssociationsGraph' " \
    "JOIN biological_associations_biological_associations_graphs ON biological_associations_biological_associations_graphs.biological_associations_graph_id = biological_associations_graphs.id JOIN ba ON ba.id = biological_associations_biological_associations_graphs.biological_association_id")

    referenced_klass_union([a,b,c,d])
end

#dwc_occurrence_query_facet ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 484

def dwc_occurrence_query_facet
  return nil if dwc_occurrence_query.nil?

   s = ::AssertedDistribution
    .with(query_dwc_ad: dwc_occurrence_query.all.select(:dwc_occurrence_object_id, :dwc_occurrence_object_type, :id))
    .joins(:dwc_occurrence)
    .joins('JOIN query_dwc_ad as query_dwc_ad1 on query_dwc_ad1.id = dwc_occurrences.id')
    .to_sql

  ::AssertedDistribution.from('(' + s + ') as asserted_distributions').distinct
end

#from_wkt(wkt_shape) ⇒ Object 



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

def from_wkt(wkt_shape)
  a = self.class.geographic_areas_for_geographic_items(
    ::GeographicItem.covered_by_wkt_sql(wkt_shape)
  )
  b = self.class.gazetteers_for_geographic_items(
    ::GeographicItem.covered_by_wkt_sql(wkt_shape)
  )

  ::Queries.union(::AssertedDistribution, [a, b])
end

#geo_json_facet ⇒ Object

Shape is a Hash in GeoJSON format



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# File 'lib/queries/asserted_distribution/filter.rb', line 257

def geo_json_facet
  return nil if geo_json.nil?
  return ::AssertedDistribution.none if roll_call

  i = spatial_query
  return nil if i.nil?

  j = ::GeographicArea.joins(:geographic_items).where(geographic_items: i)

  # Expand to include all descendants of any spatial match!
  # We only care about areas actually used here.
  k = ::GeographicArea.joins(:asserted_distributions).descendants_of(j)

  ga_ids = ::GeographicArea.from("((#{j.to_sql}) UNION (#{k.to_sql})) as geographic_areas").distinct

  gz_ids = ::Gazetteer.joins(:geographic_item).where(geographic_item: i)

  return ::AssertedDistribution
    .where( asserted_distribution_shape: ga_ids )
    .where( asserted_distribution_shape_type: 'GeographicArea')
    .or(
      ::AssertedDistribution
        .where( asserted_distribution_shape: gz_ids )
        .where( asserted_distribution_shape_type: 'Gazetteer')
    )

end

#geographic_item_id_facet ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 401

def geographic_item_id_facet
  return nil if geographic_item_id.empty?
  ::GeographicArea.joins(:geographic_areas_geographic_items).where(
    geographic_areas_geographic_items: {geographic_item_id:}
  )
end

#merge_clauses ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 507

def merge_clauses
  [
    dwc_occurrence_query_facet,
    biological_association_query_facet,
    geo_json_facet,
    otu_query_facet,
    taxon_name_query_facet,
    source_id_facet,

    asserted_distribution_geo_facet,
    geographic_item_id_facet,
    taxon_name_id_facet,
    observation_query_facet,
    wkt_facet,
  ]
end

#observation_query_facet ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 441

def observation_query_facet
  return nil if observation_query.nil?
  ::AssertedDistribution
    .with(obs: observation_query.all)
    .joins("JOIN obs ON obs.id = asserted_distributions.asserted_distribution_object_id AND asserted_distributions.asserted_distribution_object_type = 'Observation'")
    .distinct
end

#otu_id_facet ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 386

def otu_id_facet
  return nil if otu_id.empty?
  table[:asserted_distribution_object_type].eq('Otu').and(
    table[:asserted_distribution_object_id].in(otu_id)
  )
end

#otu_query_facet ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 432

def otu_query_facet
  return nil if otu_query.nil?
  s = 'WITH query_otu_ad AS (' + otu_query.all.to_sql + ') ' +
    ::AssertedDistribution
    .joins("JOIN query_otu_ad AS query_otu_ad1 ON query_otu_ad1.id = asserted_distributions.asserted_distribution_object_id AND asserted_distributions.asserted_distribution_object_type = 'Otu'")
    .to_sql
  ::AssertedDistribution.from('(' + s + ') as asserted_distributions')
end

#presence_facet ⇒ Object 



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

def presence_facet
  return nil if presence.nil?
  if presence
    table[:is_absent].eq_any(['f', nil]) # !! not eq_any()
  else
    table[:is_absent].eq('t')
  end
end

#source_id_facet ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 423

def source_id_facet
  return nil if source_id.empty?

  ::AssertedDistribution
    .joins(:citations)
    .where(citations: { source_id: })
    .distinct
end

#spatial_query ⇒ GeographicItem scope

Returns:



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# File 'lib/queries/asserted_distribution/filter.rb', line 286

def spatial_query
  if geometry = RGeo::GeoJSON.decode(geo_json)
    case geometry.geometry_type.to_s
    when 'Point'
      a = ::GeographicItem
        .joins(:geographic_areas)
        .where(
          ::GeographicItem.within_radius_of_wkt_sql(geometry.to_s, radius)
        )
      b = ::GeographicItem
        .joins(:gazetteers)
        .where(
          ::GeographicItem.within_radius_of_wkt_sql(geometry.to_s, radius)
        )

      ::Queries.union(::GeographicItem, [a, b])
    when 'Polygon', 'MultiPolygon'
      a = ::GeographicItem
        .joins(:geographic_areas)
        .where(::GeographicItem.covered_by_wkt_sql(geometry.to_s))
      b = ::GeographicItem
        .joins(:gazetteers)
        .where(::GeographicItem.covered_by_wkt_sql(geometry.to_s))

      ::Queries.union(::GeographicItem, [a, b])
    else
      nil
    end
  else
    nil
  end
end

#taxon_name_id_facet ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 408

def taxon_name_id_facet
  return nil if taxon_name_id.empty?
  if descendants
    h = Arel::Table.new(:taxon_name_hierarchies)
    o = Arel::Table.new(:otus)

    j = o.join(h, Arel::Nodes::InnerJoin).on(o[:taxon_name_id].eq(h[:descendant_id]))
    z = h[:ancestor_id].in(taxon_name_id)

    ::AssertedDistribution.with_otus.joins(j.join_sources).where(z)
  else
    ::AssertedDistribution.with_otus.where(otus: {taxon_name_id:})
  end
end

#taxon_name_query_facet ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 449

def taxon_name_query_facet
  return nil if taxon_name_query.nil?
  s = 'WITH query_tn_ad AS (' + taxon_name_query.all.to_sql + ') ' +
    ::AssertedDistribution
    .with_otus
    .joins('JOIN query_tn_ad as query_tn_ad1 on query_tn_ad1.id = otus.taxon_name_id')
    .to_sql
  ::AssertedDistribution.from('(' + s + ') as asserted_distributions').distinct
end

#wkt_facet ⇒ Object 



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# File 'lib/queries/asserted_distribution/filter.rb', line 195

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