Class: Queries::FieldOccurrence::Filter

Inherits:
Query::Filter show all
Includes:
Concerns::Citations, Concerns::DataAttributes, Concerns::Depictions, Concerns::Notes, Concerns::Protocols, Concerns::Tags, Concerns::TaxonDetermination, Helpers
Defined in:
lib/queries/field_occurrence/filter.rb

Constant Summary collapse

PARAMS = 
[
  *::Queries::CollectingEvent::Filter::BASE_PARAMS,
  *Queries::Concerns::DateRanges.params, # Fead to CE query. Revisit possibly.

  :biocuration_class_id,
  :biological_association_id,
  :biological_associations,
  # :biological_relationship_id,
  :collecting_event_id,
  :determiner_id,
  :field_occurrence_id,
  # :collectors,
  :dates,
  # :determiner_id_all,
  # :determiner_name_regex,
  # :determiners,
  # :dwc_indexed,
  :georeferences,
  # :import_dataset_id,
  # :sled_image_id,
  :spatial_geographic_areas,
  # :taxon_determination_id,
  biocuration_class_id: [],
  biological_association_id: [],
  # biological_relationship_id: [],
  collecting_event_id: [],
  field_occurrence_id: [],
  determiner_id: [],
  # import_dataset_id: [],
  # is_type: [],
].inject([{}]) { |ary, k| k.is_a?(Hash) ? ary.last.merge!(k) : ary.unshift(k); ary }.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, #asserted_environment_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 included from Helpers

#boolean_param, #integer_param, #negate_facet, #split_pairs, #split_repeated_pairs, #tri_value_array

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

rubocop:disable Metric/MethodLength



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

def initialize(query_params)
  super

  # Only CollectingEvent fields are permitted, for advanced nesting (e.g. tags on CEs), use collecting_event_query
  collecting_event_params = ::Queries::CollectingEvent::Filter.base_params + Queries::Concerns::DateRanges.params

  # project_id is handled during use
  @base_collecting_event_query = ::Queries::CollectingEvent::Filter.new(
    params.select{ |a, b| collecting_event_params.include?(a) } # maintain this to avoid sub query initialization for now
  )

  @biological_association_id = params[:biological_association_id]
  @biocuration_class_id = params[:biocuration_class_id]
  @biological_relationship_id = params[:biological_relationship_id] # TODO: no reference?
  @biological_associations = boolean_param(params, :biological_associations)
  @collectors = boolean_param(params, :collectors)
  @collecting_event_id = params[:collecting_event_id]
  @field_occurrence_id = params[:field_occurrence_id]
  @dates = boolean_param(params, :dates)
  @determiners = boolean_param(params, :determiners)
  @determiner_id = params[:determiner_id]
  @determiner_id_all = boolean_param(params, :determiner_id_all)
  @determiner_name_regex = params[:determiner_name_regex]
  @dwc_indexed = boolean_param(params, :dwc_indexed)
  @import_dataset_id = params[:import_dataset_id]
  @is_type = params[:is_type] || []
  @otu_descendants = boolean_param(params, :otu_descendants)
  @sled_image_id = (params[:sled_image_id].presence)

  set_citations_params(params)
  set_data_attributes_params(params)
  set_depiction_params(params)
  set_notes_params(params)
  set_protocols_params(params)
  set_tags_params(params)
  set_taxon_determination_params(params)
end

Instance Attribute Details

#base_collecting_event_query ⇒ Object

All params managed by CollectingEvent filter are available here as well



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# File 'lib/queries/field_occurrence/filter.rb', line 69

def base_collecting_event_query
  @base_collecting_event_query
end

#biocuration_class_id ⇒ Array

Returns of biocuration_class ids.

Returns:

  • (Array) —

    of biocuration_class ids



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

def biocuration_class_id
  @biocuration_class_id
end

#biological_association_id ⇒ Object

Returns Array Matching records in this BiologicalAssociation.

Returns:

  • Array Matching records in this BiologicalAssociation



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

def biological_association_id
  @biological_association_id
end

#biological_associations ⇒ True, ...

Returns true - is used in a bilogical association false - is not used in a biological association nil - not applied.

Returns:

  • (True, False, nil) —

    true - is used in a bilogical association false - is not used in a biological association nil - not applied



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

def biological_associations
  @biological_associations
end

#biological_relationship_id ⇒ Array

Returns of biological_relationship#id.

Returns:

  • (Array) —

    of biological_relationship#id



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# File 'lib/queries/field_occurrence/filter.rb', line 89

def biological_relationship_id
  @biological_relationship_id
end

#collecting_event_id ⇒ Object

[Array] only return objects with these collecting event ID



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

def collecting_event_id
  @collecting_event_id
end

#collectors ⇒ Boolean?

Returns true - A collector role exists false - A collector role exists nil - not applied.

Returns:

  • (Boolean, nil) —

    true - A collector role exists false - A collector role exists nil - not applied



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

def collectors
  @collectors
end

#dates ⇒ Object

Returns Boolean true - any of start/end date or verbatim date are populated false - none of start/end date or verbatim date are populated nil - ignored.

Returns:

  • Boolean true - any of start/end date or verbatim date are populated false - none of start/end date or verbatim date are populated nil - ignored



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# File 'lib/queries/field_occurrence/filter.rb', line 138

def dates
  @dates
end

#determiner_id ⇒ Array

Parameters:

  • determiner (Array or Person#id) —

    one ore more people id

Returns:

  • (Array) 


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

def determiner_id
  @determiner_id
end

#determiner_id_all ⇒ Boolean

Parameters:

  • determiner_id_all (String, nil) —

    false, nil - treat the ids in determiner_id as "or" 'true' - treat the ids in determiner_id as "and" (only collection objects with all and only all will match)

Returns:

  • (Boolean) 


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

def determiner_id_all
  @determiner_id_all
end

#determiner_name_regex ⇒ Object

A PostgreSQL valid regular expression. Note that simple strings evaluate as wildcard matches. !! Probably shouldn't expose to external API.

Returns:

  • String



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

def determiner_name_regex
  @determiner_name_regex
end

#determiners ⇒ Boolean?

Returns true - A determiner role exists false - No determiner role exists nil - not applied.

Returns:

  • (Boolean, nil) —

    true - A determiner role exists false - No determiner role exists nil - not applied



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# File 'lib/queries/field_occurrence/filter.rb', line 75

def determiners
  @determiners
end

#dwc_indexed ⇒ True, ...

Returns true - index is built false - index is not built nil - not applied.

Returns:

  • (True, False, nil) —

    true - index is built false - index is not built nil - not applied



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# File 'lib/queries/field_occurrence/filter.rb', line 95

def dwc_indexed
  @dwc_indexed
end

#field_occurrence_id ⇒ Object

Parameters:

  • Array (String, nil) —

    or Integer of FieldOccurrence ids



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

def field_occurrence_id
  @field_occurrence_id
end

#geographic_area ⇒ True, ...

Returns true - has collecting event that has geographic_area false - does not have collecting event that has geographic area nil - not applied.

Returns:

  • (True, False, nil) —

    true - has collecting event that has geographic_area false - does not have collecting event that has geographic area nil - not applied



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# File 'lib/queries/field_occurrence/filter.rb', line 115

def geographic_area
  @geographic_area
end

#import_dataset_id ⇒ Array

Returns of ImportDataset ids.

Returns:

  • (Array) —

    of ImportDataset ids



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# File 'lib/queries/field_occurrence/filter.rb', line 48

def import_dataset_id
  @import_dataset_id
end

#is_type ⇒ Array?

Returns one of holotype, lectotype etc. nil - not applied.

Returns:

  • (Array, nil) —

    one of holotype, lectotype etc. nil - not applied



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

def is_type
  @is_type
end

#sled_image_id ⇒ SledImage#id?

Returns:



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# File 'lib/queries/field_occurrence/filter.rb', line 103

def sled_image_id
  @sled_image_id
end

#taxon_name ⇒ True, ...

Returns true - Otu has taxon name false - Otu without taxon name nil - not applied.

Returns:

  • (True, False, nil) —

    true - Otu has taxon name false - Otu without taxon name nil - not applied



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

def taxon_name
  @taxon_name
end

Instance Method Details

#anatomical_part_query_facet ⇒ Object 



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# File 'lib/queries/field_occurrence/filter.rb', line 442

def anatomical_part_query_facet
  return nil if anatomical_part_query.nil?

  ::FieldOccurrence
    .joins(:origin_relationships)
    .where(origin_relationships: { new_object_type: 'AnatomicalPart' })
    .where("origin_relationships.new_object_id IN (#{ anatomical_part_query.all.select(:id).to_sql })")
    .distinct
end

#and_clauses ⇒ Object 



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# File 'lib/queries/field_occurrence/filter.rb', line 452

def and_clauses
  [
    collecting_event_id_facet,
    field_occurrence_id_facet,
  ]
end

#base_collecting_event_query_facet ⇒ Object 



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

def base_collecting_event_query_facet
  return nil if base_collecting_event_query.only_project?

  s = 'WITH query_ce_base_co AS (' + base_collecting_event_query.all.to_sql + ') ' +
    ::FieldOccurrence
    .joins('JOIN query_ce_base_co as query_ce_base_co1 on query_ce_base_co1.id = field_occurrences.collecting_event_id')
    .to_sql

  ::FieldOccurrence.from('(' + s + ') as field_occurrences').distinct
end

#biocuration_facet ⇒ Object 



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# File 'lib/queries/field_occurrence/filter.rb', line 270

def biocuration_facet
  return nil if biocuration_class_id.empty?
  ::FieldOccurrence::BiologicalFieldOccurrence.joins(:biocuration_classifications)
    .where(biocuration_classifications: { biocuration_class_id: })
end

#biological_association_id_facet ⇒ Object

TODO: turn into UNION!



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# File 'lib/queries/field_occurrence/filter.rb', line 370

def biological_association_id_facet
  return nil if biological_association_id.empty?
  b = ::BiologicalAssociation.where(id: biological_association_id)
  s = 'WITH query_ba_id_co AS (' + b.all.to_sql + ') ' +
    ::FieldOccurrence
    .joins("LEFT JOIN query_ba_id_co as query_ba_id_co1 on field_occurrences.id = query_ba_id_co1.biological_association_subject_id AND query_ba_id_co1.biological_association_subject_type = 'FieldOccurrence'")
    .joins("LEFT JOIN query_ba_id_co as query_ba_id_co2 on field_occurrences.id = query_ba_id_co2.biological_association_object_id AND query_ba_id_co2.biological_association_object_type = 'FieldOccurrence'")
    .where('(query_ba_id_co1.id) IS NOT NULL OR (query_ba_id_co2.id IS NOT NULL)')
    .to_sql

  ::FieldOccurrence.from('(' + s + ') as field_occurrences').distinct
end

#biological_association_query_facet ⇒ Object

TODO: turn into UNION!



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# File 'lib/queries/field_occurrence/filter.rb', line 384

def biological_association_query_facet
  return nil if biological_association_query.nil?
  s = 'WITH query_ba_co AS (' + biological_association_query.all.to_sql + ') ' +
    ::FieldOccurrence
    .joins("LEFT JOIN query_ba_co as query_ba_co1 on field_occurrences.id = query_ba_co1.biological_association_subject_id AND query_ba_co1.biological_association_subject_type = 'FieldOccurrence'")
    .joins("LEFT JOIN query_ba_co as query_ba_co2 on field_occurrences.id = query_ba_co2.biological_association_object_id AND query_ba_co2.biological_association_object_type = 'FieldOccurrence'")
    .where('(query_ba_co1.id) IS NOT NULL OR (query_ba_co2.id IS NOT NULL)')
    .to_sql

  ::FieldOccurrence.from('(' + s + ') as field_occurrences').distinct
end

#biological_associations_facet ⇒ Object 



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# File 'lib/queries/field_occurrence/filter.rb', line 361

def biological_associations_facet
  return nil if biological_associations.nil?
  a = ::FieldOccurrence.joins(:biological_associations)
  b = ::FieldOccurrence.joins(:related_biological_associations)

  referenced_klass_union([a, b])
end

#biological_relationship_id_facet ⇒ Object 



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# File 'lib/queries/field_occurrence/filter.rb', line 281

def biological_relationship_id_facet
  return nil if biological_relationship_id.empty?
  ::FieldOccurrence.with_biological_relationship_id(biological_relationship_id)
end

#collecting_event_id_facet ⇒ Object 



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# File 'lib/queries/field_occurrence/filter.rb', line 293

def collecting_event_id_facet
  return nil if collecting_event_id.empty?
  table[:collecting_event_id].in(collecting_event_id)
end

#collecting_event_query_facet ⇒ Object 



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# File 'lib/queries/field_occurrence/filter.rb', line 396

def collecting_event_query_facet
  return nil if collecting_event_query.nil?
  s = 'WITH query_ce_co AS (' + collecting_event_query.all.select(:id).to_sql + ') ' +
    ::FieldOccurrence
    .joins('JOIN query_ce_co as query_ce_co1 on query_ce_co1.id = field_occurrences.collecting_event_id')
    .to_sql

  ::FieldOccurrence.from('(' + s + ') as field_occurrences').distinct
end

#collecting_event_table ⇒ Arel::Table

Returns:

  • (Arel::Table) 


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# File 'lib/queries/field_occurrence/filter.rb', line 180

def collecting_event_table
  ::CollectingEvent.arel_table
end

#dates_facet ⇒ Object

TODO: Probably just move to CE



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# File 'lib/queries/field_occurrence/filter.rb', line 299

def dates_facet
  return nil if dates.nil?
  if dates
    ::FieldOccurrence.left_joins(:collecting_event).where(
      'start_date_year IS NOT NULL OR ' \
      'start_date_month IS NOT NULL OR ' \
      'start_date_day IS NOT NULL OR ' \
      'end_date_year IS NOT NULL OR ' \
      'end_date_month IS NOT NULL OR ' \
      'end_date_day IS NOT NULL OR ' \
      'verbatim_date IS NOT NULL'
    )
  else
    ::FieldOccurrence.left_joins(:collecting_event).where(
      collecting_event: {
        start_date_year: nil,
        start_date_month: nil,
        start_date_day: nil,
        end_date_year: nil,
        end_date_month: nil,
        end_date_day: nil,
        verbatim_date: nil,
      },
    )
  end
end

#determiner_facet ⇒ Object

TODO: DRY with Source (author), TaxonName, etc. See Queries::ColletingEvent::Filter for other use



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# File 'lib/queries/field_occurrence/filter.rb', line 225

def determiner_facet
  return nil if determiner_id.empty?
  tt = table

  o = ::TaxonDetermination.arel_table
  r = ::Role.arel_table

  a = o.alias('a_det__')
  b = o.project(a[Arel.star]).from(a)

  c = r.alias('det_r1')

  b = b.join(c, Arel::Nodes::OuterJoin)
    .on(
      a[:id].eq(c[:role_object_id])
    .and(c[:role_object_type].eq('TaxonDetermination'))
    .and(c[:type].eq('Determiner'))
    )

  e = c[:id].not_eq(nil)
  f = c[:person_id].in(determiner_id)

  b = b.where(e.and(f))
  b = b.group(a['id'])
  b = b.having(a['id'].count.eq(determiner_id.length)) if determiner_id_all

  b = b.as('det_z1_')

  ::FieldOccurrence.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['taxon_determination_object_id'].eq(tt['id']))))
end

#determiner_name_regex_facet ⇒ Object 



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# File 'lib/queries/field_occurrence/filter.rb', line 265

def determiner_name_regex_facet
  return nil if determiner_name_regex.nil?
  ::FieldOccurrence.joins(:determiners).where('people.cached ~* ?', determiner_name_regex)
end

#determiners_facet ⇒ Object 



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# File 'lib/queries/field_occurrence/filter.rb', line 256

def determiners_facet
  return nil if determiners.nil?
  if determiners
    ::FieldOccurrence.joins(:determiners)
  else
    ::FieldOccurrence.where.missing(:determiners)
  end
end

#dwc_indexed_facet ⇒ Object 



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

def dwc_indexed_facet
  return nil if dwc_indexed.nil?
  dwc_indexed ?
    ::FieldOccurrence.dwc_indexed :
    ::FieldOccurrence.dwc_not_indexed
end

#dwc_occurrence_query_facet ⇒ Object 



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# File 'lib/queries/field_occurrence/filter.rb', line 406

def dwc_occurrence_query_facet
  return nil if dwc_occurrence_query.nil?

  s = ::FieldOccurrence
    .with(query_dwc_fo: dwc_occurrence_query.all.select(:dwc_occurrence_object_id, :dwc_occurrence_object_type, :id))
    .joins(:dwc_occurrence)
    .joins('JOIN query_dwc_fo as query_dwc_fo1 on query_dwc_fo1.id = dwc_occurrences.id')
    .to_sql

  ::FieldOccurrence.from('(' + s + ') as field_occurrences').distinct
end

#field_occurrence_id_facet ⇒ Object 



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# File 'lib/queries/field_occurrence/filter.rb', line 212

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

#image_query_facet ⇒ Object 



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

def image_query_facet
  return nil if image_query.nil?

  s = ::FieldOccurrence
    .with(query_image: image_query.all)
    .joins(:depictions)
    .joins('JOIN query_image ON query_image.id = depictions.image_id')
    .to_sql

  ::FieldOccurrence.from('(' + s + ') as field_occurrences').distinct
end

#import_dataset_id_facet ⇒ Object 



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# File 'lib/queries/field_occurrence/filter.rb', line 217

def import_dataset_id_facet
  return nil if import_dataset_id.blank?
  ::FieldOccurrence.joins(:related_origin_relationships)
    .where(origin_relationships: {old_object_id: import_dataset_id, old_object_type: 'ImportDataset'})
end

#merge_clauses ⇒ Object 



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

def merge_clauses
  [
    #  import_dataset_id_facet,
    anatomical_part_query_facet,
    biological_association_id_facet,
    base_collecting_event_query_facet,
    biological_association_query_facet,
    collecting_event_query_facet,
    dwc_occurrence_query_facet,
    image_query_facet,
    observation_query_facet,
    otu_query_facet,
    taxon_name_query_facet,
    biocuration_facet,
    biological_associations_facet,
    #  biological_relationship_id_facet,
    dates_facet,
    determiner_facet,
    # determiner_name_regex_facet,
    determiners_facet,
    # dwc_indexed_facet,
    # sled_image_facet,
  ]
end

#observation_query_facet ⇒ Object 



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

def observation_query_facet
  return nil if observation_query.nil?

  s = ::FieldOccurrence
    .with(obs_query_fo: observation_query.all)
    .joins(:observations)
    .joins('JOIN obs_query_fo on observations.id = obs_query_fo.id')
    .to_sql

  ::FieldOccurrence.from('(' + s + ') as field_occurrences').distinct
end

#otu_query_facet ⇒ Object 



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# File 'lib/queries/field_occurrence/filter.rb', line 349

def otu_query_facet
  return nil if otu_query.nil?
  s = 'WITH query_otu_co AS (' + otu_query.all.to_sql + ') ' +
    ::FieldOccurrence
    .joins(:taxon_determinations)
    .joins('JOIN query_otu_co as query_otu_co1 on query_otu_co1.id = taxon_determinations.otu_id')
    .where(taxon_determinations: { position: 1 })
    .to_sql

  ::FieldOccurrence.from('(' + s + ') as field_occurrences').distinct
end

#sled_image_facet ⇒ Object 



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# File 'lib/queries/field_occurrence/filter.rb', line 276

def sled_image_facet
  return nil if sled_image_id.nil?
  ::FieldOccurrence::BiologicalFieldOccurrence.joins(:depictions).where('depictions.sled_image_id = ?', sled_image_id)
end

#taxon_name_query_facet ⇒ Object 



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

def taxon_name_query_facet
  return nil if taxon_name_query.nil?

  s = ::FieldOccurrence
    .with(query_tn_fo: taxon_name_query.all.select(:id))
    .joins(:taxon_names)
    .joins('JOIN query_tn_fo on query_tn_fo.id = taxon_names.id')
    .to_sql

  ::FieldOccurrence.from('(' + s + ') as field_occurrences').distinct
end