Class: Queries::FieldOccurrence::Filter

Inherits:
Query::Filter show all
Includes:
Concerns::Citations, Concerns::DataAttributes, Concerns::Depictions, Concerns::Notes, Concerns::Protocols, Concerns::Tags, 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.

# :biological_association_id,
# :biological_associations,
# :biological_relationship_id,
# :collecting_event,
 :field_occurrence_id,
# :collection_object_type,
# :collectors,
# :current_determinations,
# :current_repository,
# :current_repository_id,
# :dates,
# :deaccessioned,
# :descendants,
# :determiner_id_or,
# :determiner_name_regex,
# :determiners,
# :dwc_indexed,
# :extract_id,
# :georeferences,
# :import_dataset_id,
# :repository,
# :repository_id,
# :sled_image_id,
# :spatial_geographic_areas,
# :taxon_determination_id,
# :taxon_determinations,
# :taxon_name_id,
# :validity,
# biocuration_class_id: [],
# biological_association_id: [],
# biological_relationship_id: [],
# collecting_event_id: [],
# field_occurrence_id: [],
# determiner_id: [],
# extract_id: [],
# geographic_area_id: [],
# import_dataset_id: [],
# is_type: [],
# otu_id: [],
# taxon_name_id: [],
].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

#api, #asserted_distribution_query, #biological_association_query, #biological_associations_graph_query, #collecting_event_query, #collection_object_query, #content_query, #controlled_vocabulary_term_query, #data_attribute_query, #descriptor_query, #document_query, #dwc_occurrence_query, #extract_query, #field_occurrence_query, #image_query, #loan_query, #object_global_id, #observation_query, #otu_query, #page, #paginate, #params, #per, #person_query, #project_id, #recent, #taxon_name_query, #venn, #venn_mode

Attributes inherited from Query

#query_string, #terms

Instance Method Summary collapse

Methods included from Helpers

#boolean_param

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, #deep_permit, included_annotator_facets, instatiated_base_filter, inverted_subqueries, #model_id_facet, #object_global_id_facet, params, #permitted_params, #process_url_into_params, #project_id_facet, query_name, #query_name, #set_nested_queries, #shared_and_clauses, #subquery_vector, #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 230

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)
  @collecting_event = boolean_param(params, :collecting_event)
  @collectors = boolean_param(params, :collectors)
  @collecting_event_id = params[:collecting_event_id]
  @field_occurrence_id = params[:field_occurrence_id]
  @collection_object_type = params[:collection_object_type].presence
  @current_determinations = boolean_param(params, :current_determinations)
  @current_repository = boolean_param(params, :current_repository)
  @current_repository_id = params[:current_repository_id].presence
  @dates = boolean_param(params, :dates)
  @descendants = boolean_param(params, :descendants)
  @deaccessioned = boolean_param(params, :deaccessioned)
  @determiners = boolean_param(params, :determiners)
  @determiner_id = params[:determiner_id]
  @determiner_id_or = boolean_param(params, :determiner_id_or)
  @determiner_name_regex = params[:determiner_name_regex]
  @dwc_indexed = boolean_param(params, :dwc_indexed)
  @extract_id = params[:extract_id]
  @geographic_area = boolean_param(params, :geographic_area)
  @georeferences = boolean_param(params, :georeferences)
  @import_dataset_id = params[:import_dataset_id]
  @is_type = params[:is_type] || []
  @otu_descendants = boolean_param(params, :otu_descendants)
  @otu_id = params[:otu_id]
  @repository = boolean_param(params, :repository)
  @repository_id = params[:repository_id]
  @sled_image_id = (params[:sled_image_id].presence)
  @taxon_determinations = boolean_param(params, :taxon_determinations)
  @taxon_name_id = params[:taxon_name_id]
  @validity = boolean_param(params, :validity)

  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)
end

Instance Attribute Details

#base_collecting_event_queryObject

All params managed by CollectingEvent filter are available here as well



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# File 'lib/queries/field_occurrence/filter.rb', line 87

def base_collecting_event_query
  @base_collecting_event_query
end

#biocuration_class_idArray

Returns of biocuration_class ids.

Returns:

  • (Array)

    of biocuration_class ids



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# File 'lib/queries/field_occurrence/filter.rb', line 133

def biocuration_class_id
  @biocuration_class_id
end

#biological_association_idObject

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 72

def biological_association_id
  @biological_association_id
end

#biological_associationsTrue, ...

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 68

def biological_associations
  @biological_associations
end

#biological_relationship_idArray

Returns of biological_relationship#id.

Returns:

  • (Array)

    of biological_relationship#id



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

def biological_relationship_id
  @biological_relationship_id
end

#collecting_eventTrue, ...

Parameters:

  • collecting_event ('true', 'false')

    true - has collecting_event_id false - does not have collecting_event_id nil - not applied

Returns:

  • (True, False, nil)


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

def collecting_event
  @collecting_event
end

#collecting_event_idObject

Array

only return objects with these collecting event ID



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

def collecting_event_id
  @collecting_event_id
end

#collection_object_typeObject

Parameters:

  • one (String, nil)

    of ‘Specimen’, ‘Lot’, or ‘RangedLot’



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# File 'lib/queries/field_occurrence/filter.rb', line 80

def collection_object_type
  @collection_object_type
end

#collectorsBoolean?

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 129

def collectors
  @collectors
end

#current_determinationsBoolean?

Returns nil = TaxonDeterminations match regardless of current or historical true = TaxonDetermination must be .current false = TaxonDetermination must be .historical.

Returns:

  • (Boolean, nil)

    nil = TaxonDeterminations match regardless of current or historical true = TaxonDetermination must be .current false = TaxonDetermination must be .historical



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# File 'lib/queries/field_occurrence/filter.rb', line 117

def current_determinations
  @current_determinations
end

#current_repositoryTrue, ...

Returns true - has current_repository_id false - does not have current_repository_id nil - not applied.

Returns:

  • (True, False, nil)

    true - has current_repository_id false - does not have current_repository_id nil - not applied



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# File 'lib/queries/field_occurrence/filter.rb', line 187

def current_repository
  @current_repository
end

#current_repository_idCurrentRepository#id?

Returns:

  • (CurrentRepository#id, nil)


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

def current_repository_id
  @current_repository_id
end

#datesObject

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 227

def dates
  @dates
end

#deaccessionedBoolean?

Returns nil = Ignored true = FieldOccurrence with deaccessioned_at OR deaccessioned_reason populated or deaccession_recipient.present? false = without true.

Returns:

  • (Boolean, nil)

    nil = Ignored true = FieldOccurrence with deaccessioned_at OR deaccessioned_reason populated or deaccession_recipient.present? false = without true



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

def deaccessioned
  @deaccessioned
end

#descendantsObject

Returns the value of attribute descendants.



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# File 'lib/queries/field_occurrence/filter.rb', line 99

def descendants
  @descendants
end

#determiner_idArray

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 205

def determiner_id
  @determiner_id
end

#determiner_id_orBoolean

Parameters:

  • determiner_id_or (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 211

def determiner_id_or
  @determiner_id_or
end

#determiner_name_regexObject

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 217

def determiner_name_regex
  @determiner_name_regex
end

#determinersBoolean?

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 123

def determiners
  @determiners
end

#dwc_indexedTrue, ...

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 143

def dwc_indexed
  @dwc_indexed
end

#extract_idObject

Returns Array match all FieldOccurrences that are the origin of these Extracts.

Returns:

  • Array match all FieldOccurrences that are the origin of these Extracts



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# File 'lib/queries/field_occurrence/filter.rb', line 221

def extract_id
  @extract_id
end

#field_occurrence_idObject

Parameters:

  • Array (String, nil)

    or Integer of FieldOccurrence ids



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# File 'lib/queries/field_occurrence/filter.rb', line 76

def field_occurrence_id
  @field_occurrence_id
end

#geographic_areaTrue, ...

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 200

def geographic_area
  @geographic_area
end

#georeferencesTrue, ...

Returns true - has one ore more georeferences false - does not have any georeferences nil - not applied.

Returns:

  • (True, False, nil)

    true - has one ore more georeferences false - does not have any georeferences nil - not applied



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# File 'lib/queries/field_occurrence/filter.rb', line 175

def georeferences
  @georeferences
end

#import_dataset_idArray

Returns of ImportDataset ids.

Returns:

  • (Array)

    of ImportDataset ids



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

def import_dataset_id
  @import_dataset_id
end

#is_typeArray?

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 154

def is_type
  @is_type
end

#otu_idArray?

Returns Otu ids, matches on the TaxonDetermination, see also current_determinations.

Parameters:

  • (Array)

Returns:

  • (Array, nil)

    Otu ids, matches on the TaxonDetermination, see also current_determinations



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# File 'lib/queries/field_occurrence/filter.rb', line 92

def otu_id
  @otu_id
end

#repositoryTrue, ...

Returns true - has repository_id false - does not have repository_id nil - not applied.

Returns:

  • (True, False, nil)

    true - has repository_id false - does not have repository_id nil - not applied



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# File 'lib/queries/field_occurrence/filter.rb', line 181

def repository
  @repository
end

#repository_idRepository#id?

Returns:



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# File 'lib/queries/field_occurrence/filter.rb', line 146

def repository_id
  @repository_id
end

#sled_image_idSledImage#id?

Returns:



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# File 'lib/queries/field_occurrence/filter.rb', line 157

def sled_image_id
  @sled_image_id
end

#taxon_determinationsTrue, ...

Returns true - has one ore more taxon_determinations false - does not have any taxon_determinations nil - not applied.

Returns:

  • (True, False, nil)

    true - has one ore more taxon_determinations false - does not have any taxon_determinations nil - not applied



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# File 'lib/queries/field_occurrence/filter.rb', line 163

def taxon_determinations
  @taxon_determinations
end

#taxon_nameTrue, ...

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 169

def taxon_name
  @taxon_name
end

#taxon_name_idArray of Protonym.id?

Return all collection objects determined as an Otu that is self or descendant linked to this TaxonName

Returns:

  • (Array of Protonym.id, nil)

    return all collection objects determined as an Otu that is self or descendant linked to this TaxonName



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# File 'lib/queries/field_occurrence/filter.rb', line 97

def taxon_name_id
  @taxon_name_id
end

#validityBoolean?

Returns nil = Match against all ancestors, valid or invalid true = Match against only valid ancestors false = Match against only invalid ancestors.

Returns:

  • (Boolean, nil)

    nil = Match against all ancestors, valid or invalid true = Match against only valid ancestors false = Match against only invalid ancestors



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# File 'lib/queries/field_occurrence/filter.rb', line 111

def validity
  @validity
end

Instance Method Details

#and_clausesObject

::FieldOccurrence.from(‘(’ + s + ‘) as collection_objects’).distinct

end


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# File 'lib/queries/field_occurrence/filter.rb', line 731

def and_clauses
  [
    #collecting_event_id_facet,
    field_occurrence_id_facet,
  ]
end

#base_collecting_event_query_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 622

def base_collecting_event_query_facet
  # Turn project_id off and check for a truly empty query
  base_collecting_event_query.project_id = nil
  return nil if base_collecting_event_query.all(true).nil?

  # Turn project_id back on
  base_collecting_event_query.project_id = project_id

  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 = collection_objects.collecting_event_id')
        .to_sql

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

#biocuration_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 477

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

#biological_relationship_id_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 488

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

#collecting_event_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 455

def collecting_event_facet
  return nil if collecting_event.nil?
  if collecting_event
    ::FieldOccurrence.where.not(collecting_event_id: nil)
  else
    ::FieldOccurrence.where(collecting_event_id: nil)
  end
end

#collecting_event_id_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 500

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

#collecting_event_tableArel::Table

Returns:

  • (Arel::Table)


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# File 'lib/queries/field_occurrence/filter.rb', line 284

def collecting_event_table
  ::CollectingEvent.arel_table
end

#collectors_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 412

def collectors_facet
  return nil if collectors.nil?
  if collectors
    ::FieldOccurrence.joins(:collectors)
  else
    ::FieldOccurrence.where.missing(:collectors)
  end
end

#current_repository_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 446

def current_repository_facet
  return nil if current_repository.nil?
  if current_repository
    ::FieldOccurrence.where.not(current_repository_id: nil)
  else
    ::FieldOccurrence.where(current_repository_id: nil)
  end
end

#current_repository_id_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 510

def current_repository_id_facet
  return nil if current_repository_id.blank?
  table[:current_repository_id].eq(current_repository_id)
end

#dates_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 578

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

#deaccessioned_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 605

def deaccessioned_facet
  return nil if deaccessioned.nil?
  a = ::FieldOccurrence.where('(deaccession_reason IS NOT NULL) OR (deaccessioned_at IS NOT NULL)')
  b = ::FieldOccurrence.joins(:deaccession_recipient)

  c = referenced_klass_union([a, b])
  if deaccessioned
    c
  else
    s = 'WITH query_deac AS (' + c.all.to_sql + ') ' +
        ::FieldOccurrence
          .joins('LEFT JOIN query_deac as query_deac1 on query_deac1.id = collection_objects.id')
          .where('query_deac1.id IS NULL').to_sql
    ::FieldOccurrence.from('(' + s + ') as collection_objects').distinct
  end
end

#determiner_facetObject

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 372

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)) unless determiner_id_or

  b = b.as('det_z1_')

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

#determiner_name_regex_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 421

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

#determiners_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 403

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

#dwc_indexed_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 493

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

#extract_id_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 353

def extract_id_facet
  return nil if extract_id.empty?
  ::FieldOccurrence
    .joins(:origin_relationships)
    .where(origin_relationships: { new_object_id: extract_id, new_object_type: 'Extract' })
end

#field_occurrence_id_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 342

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

#geographic_area_facetObject

This is not spatial



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# File 'lib/queries/field_occurrence/filter.rb', line 465

def geographic_area_facet
  return nil if geographic_area.nil?

  if geographic_area
    ::FieldOccurrence.joins(:collecting_event).where.not(collecting_events: { geographic_area_id: nil }).distinct
  else
    ::FieldOccurrence.left_outer_joins(:collecting_event)
      .where(collecting_events: { geographic_area_id: nil })
      .distinct
  end
end

#georeferences_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 426

def georeferences_facet
  return nil if georeferences.nil?
  if georeferences
    ::FieldOccurrence.joins(:georeferences).distinct
  else
    ::FieldOccurrence.left_outer_joins(:georeferences)
      .where(georeferences: { id: nil })
      .distinct
  end
end

#import_dataset_id_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 347

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_clausesObject



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# File 'lib/queries/field_occurrence/filter.rb', line 738

def merge_clauses
  [

 #  import_dataset_id_facet,
 #  observation_query_facet,
 #  biological_association_id_facet,
 #  base_collecting_event_query_facet,
 #  biological_association_query_facet,
 #  collecting_event_query_facet,
 #  extract_query_facet,
 #  otu_query_facet,
 #  taxon_name_query_facet,

 #  biocuration_facet,
 #  biological_associations_facet,
 #  biological_relationship_id_facet,
 #  collecting_event_facet,
 #  collectors_facet,
 #  current_repository_facet,
 #  dates_facet,
 #  deaccessioned_facet,
 #  determiner_facet,
 #  determiner_name_regex_facet,
 #  determiners_facet,
 #  dwc_indexed_facet,
 #  extract_id_facet,
 #  geographic_area_facet,
 #  georeferences_facet,
 #  otu_id_facet,
 #  repository_facet,
 #  sled_image_facet,
 #  taxon_determinations_facet,
 #  taxon_name_id_facet,
  ]
end

#otu_id_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 515

def otu_id_facet
  return nil if otu_id.empty?

  w = taxon_determination_table[:biological_field_occurrence_id].eq(table[:id])
    .and(taxon_determination_table[:otu_id].in(otu_id))

  if current_determinations
    w = w.and(taxon_determination_table[:position].eq(1))
  elsif current_determinations == false
    w = w.and(taxon_determination_table[:position].gt(1))
  end

  ::FieldOccurrence.where(
    ::TaxonDetermination.where(w).arel.exists
  )
end

#otu_tableArel::Table

Returns:

  • (Arel::Table)


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# File 'lib/queries/field_occurrence/filter.rb', line 289

def otu_table
  ::Otu.arel_table
end

#repository_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 437

def repository_facet
  return nil if repository.nil?
  if repository
    ::FieldOccurrence.where.not(repository_id: nil)
  else
    ::FieldOccurrence.where(repository_id: nil)
  end
end

#repository_id_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 505

def repository_id_facet
  return nil if repository_id.blank?
  table[:repository_id].in(repository_id)
end

#sled_image_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 483

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_determination_tableArel::Table

Returns:

  • (Arel::Table)


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# File 'lib/queries/field_occurrence/filter.rb', line 294

def taxon_determination_table
  ::TaxonDetermination.arel_table
end

#taxon_determinations_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 360

def taxon_determinations_facet
  return nil if taxon_determinations.nil?

  if taxon_determinations
    ::FieldOccurrence.joins(:taxon_determinations).distinct
  else
    ::FieldOccurrence.where.missing(:taxon_determinations)
  end
end

#taxon_name_id_facetObject



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# File 'lib/queries/field_occurrence/filter.rb', line 532

def taxon_name_id_facet
  return nil if taxon_name_id.empty?

  q = nil
  z = nil

  if descendants
    h = Arel::Table.new(:taxon_name_hierarchies)
    t = ::TaxonName.arel_table

    q = table.join(taxon_determination_table, Arel::Nodes::InnerJoin).on(
      table[:id].eq(taxon_determination_table[:biological_field_occurrence_id])
    ).join(otu_table, Arel::Nodes::InnerJoin).on(
      taxon_determination_table[:otu_id].eq(otu_table[:id])
    ).join(t, Arel::Nodes::InnerJoin).on(
      otu_table[:taxon_name_id].eq(t[:id])
    ).join(h, Arel::Nodes::InnerJoin).on(
      t[:id].eq(h[:descendant_id])
    )
    z = h[:ancestor_id].in(taxon_name_id)

    if validity == true
      z = z.and(t[:cached_valid_taxon_name_id].eq(t[:id]))
    elsif validity == false
      z = z.and(t[:cached_valid_taxon_name_id].not_eq(t[:id]))
    end

    if current_determinations == true
      z = z.and(taxon_determination_table[:position].eq(1))
    elsif current_determinations == false
      z = z.and(taxon_determination_table[:position].gt(1))
    end
  else
    q = ::FieldOccurrence.joins(taxon_determinations: [:otu])
      .where(otus: { taxon_name_id: })

    if current_determinations
      q = q.where(taxon_determinations: { position: 1 })
    end

    return q
  end

  ::FieldOccurrence.joins(q.join_sources).where(z).distinct
end