Class: Queries::TaxonName::Filter

Inherits:
Query
  • Object
show all
Includes:
Concerns::Tags, Concerns::Users, Helpers
Defined in:
lib/queries/taxon_name/filter.rb

Overview

api.taxonworks.org/#/taxon_names

Instance Attribute Summary collapse

Attributes inherited from Query

#dynamic_limit, #options, #query_string, #terms

Instance Method Summary collapse

Methods included from Helpers

#boolean_param

Methods inherited from Query

#alphabetic_strings, #attribute_exact_facet, #autocomplete, #autocomplete_cached, #autocomplete_cached_wildcard_anywhere, #autocomplete_common_name_exact, #autocomplete_common_name_like, #autocomplete_exact_id, #autocomplete_exactly_named, #autocomplete_named, #autocomplete_ordered_wildcard_pieces_in_cached, #build_terms, #cached, #combine_or_clauses, #common_name_name, #common_name_table, #common_name_wild_pieces, #end_wildcard, #exactly_named, #fragments, #integers, #levenshtein_distance, #match_ordered_wildcard_pieces_in_cached, #match_wildcard_end_in_cached, #match_wildcard_in_cached, #named, #no_terms?, #only_ids, #only_integers?, #parent, #parent_child_join, #parent_child_where, #pieces, #result, #scope, #start_and_end_wildcard, #start_wildcard, #wildcard_pieces, #wildcard_wrapped_integers, #wildcard_wrapped_years, #with_cached, #with_cached_like, #with_id, #with_project_id, #year_letter, #years

Constructor Details

#initialize(params) ⇒ Filter

Returns a new instance of Filter.

Parameters:

  • params (Params) —

    as permitted via controller



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

def initialize(params)
  @author = params[:author]
  @authors = boolean_param(params, :authors )
  @citations = params[:citations]
  @descendants = boolean_param(params,:descendants )
  @descendants_max_depth = params[:descendants_max_depth]
  @ancestors = boolean_param(params,:ancestors )
  @exact = boolean_param(params, :exact)
  @leaves = boolean_param(params, :leves)
  @name = params[:name]
  @not_specified = boolean_param(params, :not_specified)
  @nomenclature_code = params[:nomenclature_code]  if !params[:nomenclature_code].nil?
  @nomenclature_group = params[:nomenclature_group]  if !params[:nomenclature_group].nil?
  @otus = boolean_param(params, :otus)
  @etymology = boolean_param(params, :etymology)
  @project_id = params[:project_id]
  @taxon_name_classification = params[:taxon_name_classification] || []
  @taxon_name_id = params[:taxon_name_id] || []
  @parent_id = params[:parent_id] || []
  @sort = params[:sort]
  @taxon_name_relationship = params[:taxon_name_relationship] || []
  @taxon_name_relationship_type = params[:taxon_name_relationship_type] || []
  @taxon_name_type = params[:taxon_name_type]
  @type_metadata = boolean_param(params, :type_metadata)
  @updated_since = params[:updated_since].to_s
  @validity = boolean_param(params, :validity)
  @year = params[:year].to_s

  @taxon_name_author_ids = params[:taxon_name_author_ids].blank? ? [] : params[:taxon_name_author_ids]
  @taxon_name_author_ids_or = boolean_param(params, :taxon_name_author_ids_or)

  set_tags_params(params)
  set_user_dates(params)
end

Instance Attribute Details

#ancestors ⇒ Object

'true' or 'false'

on initialize

Ignored when taxon_name_id[].empty?  Works as AND clause with descendants :(

Parameters:

  • ancestors (Boolean) 


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

def ancestors
  @ancestors
end

#author ⇒ Object

Parameters:

  • author (String) —

    Use “&” for “and”. Matches against cached_author_year.



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# File 'lib/queries/taxon_name/filter.rb', line 18

def author
  @author
end

#authors ⇒ Object

'true' or 'false'

on initialize

whether the name has an author string, from any source, provided

Parameters:

  • authors (Boolean, nil) 


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

def authors
  @authors
end

#citations ⇒ Object

Returns the value of attribute citations.



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# File 'lib/queries/taxon_name/filter.rb', line 93

def citations
  @citations
end

#descendants ⇒ Object

'true' or 'false'

on initialize

Ignored when taxon_name_id[].empty? Return descendants of parents as well.

Parameters:

  • descendants (Boolean) 


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# File 'lib/queries/taxon_name/filter.rb', line 56

def descendants
  @descendants
end

#descendants_max_depth ⇒ Object

A positive integer indicating how many levels deep of descenants to retrieve.

Ignored when descentants is false/unspecified

Parameters:

  • descendants_max_depth (Integer) 


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# File 'lib/queries/taxon_name/filter.rb', line 61

def descendants_max_depth
  @descendants_max_depth
end

#etymology ⇒ Object

'true' or 'false'

on initialize

whether the name has etymology

Parameters:

  • etymology (Boolean, nil) 


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

def etymology
  @etymology
end

#exact ⇒ Object

Parameters:

  • exact (Boolean) —

    true if matching must be exact, false if partial matches are allowed.



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# File 'lib/queries/taxon_name/filter.rb', line 27

def exact
  @exact
end

#leaves ⇒ Boolean?

TODO: inverse is duplicated in autocomplete

Returns:

  • (Boolean, nil) —

    &leaves=<“true”|“false”> if 'true' then return only names without descendents if 'false' then return only names with descendents



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# File 'lib/queries/taxon_name/filter.rb', line 136

def leaves
  @leaves
end

#name ⇒ Object

Parameters:

  • name (String) —

    Matches against cached. See also exact.



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# File 'lib/queries/taxon_name/filter.rb', line 14

def name
  @name
end

#nomenclature_code ⇒ String?

Returns accessor for attr :nomenclature_code, wrap with needed wildcards.

Returns:

  • (String, nil) —

    accessor for attr :nomenclature_code, wrap with needed wildcards



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# File 'lib/queries/taxon_name/filter.rb', line 129

def nomenclature_code
  @nomenclature_code
end

#nomenclature_group ⇒ String?

Returns accessor for attr :nomenclature_group, wrap with needed wildcards.

Returns:

  • (String, nil) —

    accessor for attr :nomenclature_group, wrap with needed wildcards



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# File 'lib/queries/taxon_name/filter.rb', line 125

def nomenclature_group
  @nomenclature_group
end

#not_specified ⇒ Object

Returns the value of attribute not_specified.



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

def not_specified
  @not_specified
end

#otus ⇒ Object

'true' or 'false'

on initialize

whether the name has an Otu

Parameters:

  • otus (Boolean, nil) 


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# File 'lib/queries/taxon_name/filter.rb', line 98

def otus
  @otus
end

#parent_id ⇒ Object

Return the taxon names with this/these parent_ids

Returns:

  • Return the taxon names with this/these parent_ids



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# File 'lib/queries/taxon_name/filter.rb', line 51

def parent_id
  @parent_id
end

#project_id ⇒ Object

TODO: probably should be an array for API purposes. TODO: unify globally as to whether param belongs here, or at controller level.

Parameters:

  • project_id (String) —

    The project scope.



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# File 'lib/queries/taxon_name/filter.rb', line 88

def project_id
  @project_id
end

#sort ⇒ String?

Parameters:

  • sort (String, nil) —

    one of :classification, :alphabetical

Returns:

  • (String, nil) 


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# File 'lib/queries/taxon_name/filter.rb', line 153

def sort
  @sort
end

#taxon_name_author_ids ⇒ Array

Returns:

  • (Array) 


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# File 'lib/queries/taxon_name/filter.rb', line 143

def taxon_name_author_ids
  @taxon_name_author_ids
end

#taxon_name_author_ids_or ⇒ Boolean

Parameters:

  • 'true' (String)

Returns:

  • (Boolean) 


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# File 'lib/queries/taxon_name/filter.rb', line 148

def taxon_name_author_ids_or
  @taxon_name_author_ids_or
end

#taxon_name_classification ⇒ Object

Parameters:

  • taxon_name_classification (Array) —

    Class names of TaxonNameClassification, as strings.



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# File 'lib/queries/taxon_name/filter.rb', line 82

def taxon_name_classification
  @taxon_name_classification
end

#taxon_name_id ⇒ Object

Return the taxon name(s) with this/these ids

Returns:

  • Return the taxon name(s) with this/these ids



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# File 'lib/queries/taxon_name/filter.rb', line 45

def taxon_name_id
  @taxon_name_id
end

#taxon_name_relationship ⇒ Object

Each entry must have a 'type' Each entry must have one (and only one) of 'subject_taxon_name_id' or 'object_taxon_name_id'

Return all taxon names in a relationship of a given type and in relation to a another name. For example, return all synonyms of Aus bus.

Parameters:

  • taxon_name_relationship (Array) —
    { 'type' => 'TaxonNameRelationship::<>', 'subject|object_taxon_name_id' => '123' } … {} 


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

def taxon_name_relationship
  @taxon_name_relationship
end

#taxon_name_relationship_type ⇒ Object

Parameters:

  • taxon_name_relationship (Array) —

    All names involved in any of these relationship



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

def taxon_name_relationship_type
  @taxon_name_relationship_type
end

#taxon_name_type ⇒ String?

Returns &taxon_name_type=<Protonym|Combination|Hybrid>.

Returns:

  • (String, nil) —

    &taxon_name_type=<Protonym|Combination|Hybrid>



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# File 'lib/queries/taxon_name/filter.rb', line 140

def taxon_name_type
  @taxon_name_type
end

#type_metadata ⇒ Object

'true' or 'false'

on initialize

whether the name has TypeMaterial



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# File 'lib/queries/taxon_name/filter.rb', line 113

def type_metadata
  @type_metadata
end

#updated_since ⇒ Object

TODO: deprecate for Queries::Concerns::User

Parameters:

  • updated_since (String) —

    in format yyyy-mm-dd Names updated (.modified_at) since this date.



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# File 'lib/queries/taxon_name/filter.rb', line 34

def updated_since
  @updated_since
end

#validity ⇒ Object

'true' or 'false'

on initialize

true if only valid, false if only invalid, nil if both



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# File 'lib/queries/taxon_name/filter.rb', line 39

def validity
  @validity
end

#year ⇒ Object

Matches against cached_author_year.

Parameters:

  • year (String) —

    “yyyy”



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# File 'lib/queries/taxon_name/filter.rb', line 23

def year
  @year
end

Instance Method Details

#all ⇒ ActiveRecord::Relation

Returns:

  • (ActiveRecord::Relation) 


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

def all
  a = and_clauses
  b = merge_clauses

  q = nil
  if a && b
    q = b.where(a)
  elsif a
    q = ::TaxonName.where(a)
  elsif b
    q = b
  else
    q = ::TaxonName.all
  end

  q = q.where(project_id: project_id) if project_id
  q = order_clause(q) if sort

  q
end

#ancestor_facet ⇒ Object

A merge facet.

Returns:

  • Scope match only names that are a ancestor of some taxon_name_id



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# File 'lib/queries/taxon_name/filter.rb', line 251

def ancestor_facet
  return nil if taxon_name_id.empty? || !(ancestors == true)

  ancestors_subquery = ::TaxonNameHierarchy.where(
    ::TaxonNameHierarchy.arel_table[:ancestor_id].eq(::TaxonName.arel_table[:id]).and(
      ::TaxonNameHierarchy.arel_table[:descendant_id].in(taxon_name_id))
  )

  ::TaxonName.where(ancestors_subquery.arel.exists)
end

#and_clauses ⇒ ActiveRecord::Relation

Returns:

  • (ActiveRecord::Relation) 


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# File 'lib/queries/taxon_name/filter.rb', line 448

def and_clauses
  clauses = []

  clauses += [
    parent_id_facet,
    author_facet,
    cached_name,
    year_facet,
    updated_since_facet,
    validity_facet,
    taxon_name_id_facet,
    with_nomenclature_group,
    with_nomenclature_code,
    taxon_name_type_facet
  ].compact

  return nil if clauses.empty?

  a = clauses.shift
  clauses.each do |b|
    a = a.and(b)
  end
  a
end

#author_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 414

def author_facet
  return nil if author.blank?
  if exact
    table[:cached_author_year].eq(author.strip)
  else
    table[:cached_author_year].matches('%' + author.strip.gsub(/\s/, '%') + '%')
  end
end

#authors_facet ⇒ Object

Returns Scope.

Returns:

  • Scope



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

def authors_facet
  return nil if authors.nil?
  authors ?
    ::TaxonName.where.not(cached_author_year: nil) :
    ::TaxonName.where(cached_author_year: nil)
end

#base_query ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 197

def base_query
  ::TaxonName.select('taxon_names.*')
end

#cached_name ⇒ Object 



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

def cached_name
  return nil if name.blank?
  if exact
    table[:cached].eq(name.strip)
  else
    table[:cached].matches('%' + name.strip.gsub(/\s+/, '%') + '%')
  end
end

#citations_facet ⇒ Object

Returns Scope.

Returns:

  • Scope



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# File 'lib/queries/taxon_name/filter.rb', line 368

def citations_facet
  return nil if citations.nil?

  citation_conditions = ::Citation.arel_table[:citation_object_id].eq(::TaxonName.arel_table[:id]).and(
    ::Citation.arel_table[:citation_object_type].eq('TaxonName'))

  if citations == 'without_origin_citation'
    citation_conditions = citation_conditions.and(::Citation.arel_table[:is_original].eq(true))
  end

  ::TaxonName.where.not(::Citation.where(citation_conditions).arel.exists)
end

#descendant_facet ⇒ Object

A merge facet.

Returns:

  • Scope match only names that are a descendant of some taxon_name_id



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# File 'lib/queries/taxon_name/filter.rb', line 233

def descendant_facet
  return nil if taxon_name_id.empty? || !(descendants == true)

  descendants_subquery = ::TaxonNameHierarchy.where(
    ::TaxonNameHierarchy.arel_table[:descendant_id].eq(::TaxonName.arel_table[:id]).and(
      ::TaxonNameHierarchy.arel_table[:ancestor_id].in(taxon_name_id))
  )

  unless descendants_max_depth.nil? || descendants_max_depth.to_i < 0
    descendants_subquery = descendants_subquery.where(TaxonNameHierarchy.arel_table[:generations].lteq(descendants_max_depth.to_i))
  end

  ::TaxonName.where(descendants_subquery.arel.exists)
end

#leaves_facet ⇒ Object

Returns Scope.

Returns:

  • Scope



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# File 'lib/queries/taxon_name/filter.rb', line 292

def leaves_facet
  return nil if leaves.nil?
  leaves ? ::TaxonName.leaves : ::TaxonName.not_leaves
end

#matching_taxon_name_author_ids ⇒ Object

TODO: dry with Source, CollectingEvent , etc.



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# File 'lib/queries/taxon_name/filter.rb', line 325

def matching_taxon_name_author_ids
  return nil if taxon_name_author_ids.empty?
  o = table
  r = ::Role.arel_table

  a = o.alias("a_")
  b = o.project(a[Arel.star]).from(a)

  c = r.alias('r1')

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

  e = c[:id].not_eq(nil)
  f = c[:person_id].eq_any(taxon_name_author_ids)

  b = b.where(e.and(f))
  b = b.group(a['id'])
  b = b.having(a['id'].count.eq(taxon_name_author_ids.length)) unless taxon_name_author_ids_or
  b = b.as('tn_z1_')

  ::TaxonName.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(o['id']))))
end

#merge_clauses ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 473

def merge_clauses
  clauses = [
    ancestor_facet,
    authors_facet,
    citations_facet,
    created_updated_facet,
    descendant_facet,
    keyword_id_facet,
    leaves_facet,
    matching_taxon_name_author_ids,
    not_specified_facet,
    otus_facet,
    taxon_name_classification_facet,
    taxon_name_relationship_type_facet,
    type_metadata_facet,
    with_etymology_facet
  ].compact

  taxon_name_relationship.each do |hsh|
    clauses << taxon_name_relationship_facet(hsh)
  end

  return nil if clauses.empty?

  a = clauses.shift
  clauses.each do |b|
    a = a.merge(b)
  end
  a
end

#not_specified_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 219

def not_specified_facet
  return nil if not_specified.nil?
  if not_specified
    ::TaxonName.where(table[:cached].matches("%NOT SPECIFIED%").or(
      table[:cached_original_combination].matches("%NOT SPECIFIED%")))
  else
    ::TaxonName.where(table[:cached].does_not_match("%NOT SPECIFIED%").and(
      table[:cached_original_combination].does_not_match("%NOT SPECIFIED%")))
  end
end

#order_clause(query) ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 526

def order_clause(query)
  case sort
  when 'alphabetical'
    ::TaxonName.select('*').from(
      query.order('taxon_names.cached'), :inner_query
    )
  when 'classification'
    ::TaxonName.select('*').from(
      query
      .joins('INNER JOIN taxon_name_hierarchies ON taxon_names.id = taxon_name_hierarchies.descendant_id')
      .order('taxon_name_hierarchies.generations, taxon_name_hierarchies.ancestor_id, taxon_names.cached'),
    :inner_query
    )
  else
    query
  end
end

#otus_facet ⇒ Object

Returns Scope.

Returns:

  • Scope



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# File 'lib/queries/taxon_name/filter.rb', line 263

def otus_facet
  return nil if otus.nil?
  subquery = ::Otu.where(::Otu.arel_table[:taxon_name_id].eq(::TaxonName.arel_table[:id])).arel.exists
  ::TaxonName.where(otus ? subquery : subquery.not)
end

#parent_id_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 409

def parent_id_facet
  return nil if parent_id.empty?
  table[:parent_id].eq_any(parent_id)
end

#table ⇒ Arel::Table

Returns:

  • (Arel::Table) 


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# File 'lib/queries/taxon_name/filter.rb', line 193

def table
  ::TaxonName.arel_table
end

#taxon_name_classification_facet ⇒ Object

Returns Scope.

Returns:

  • Scope



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# File 'lib/queries/taxon_name/filter.rb', line 313

def taxon_name_classification_facet
  return nil if taxon_name_classification.empty?

  ::TaxonName.where(
    ::TaxonNameClassification.where(
      ::TaxonNameClassification.arel_table[:taxon_name_id].eq(::TaxonName.arel_table[:id]).and(
        ::TaxonNameClassification.arel_table[:type].in(taxon_name_classification))
    ).arel.exists
  )
end

#taxon_name_id_facet ⇒ Object 



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

def taxon_name_id_facet
  return nil if taxon_name_id.empty? || descendants || ancestors
  table[:id].eq_any(taxon_name_id)
end

#taxon_name_relationship_facet(hsh) ⇒ Object

Returns Scope wrapped in descendant_facet!.

Returns:

  • Scope wrapped in descendant_facet!



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

def taxon_name_relationship_facet(hsh)
  param_key = hsh['subject_taxon_name_id'] ? 'subject_taxon_name_id' : 'object_taxon_name_id'
  join_key = hsh['subject_taxon_name_id'] ? 'object_taxon_name_id' : 'subject_taxon_name_id'

  ::TaxonName.where(
    ::TaxonNameRelationship.where(
      ::TaxonNameRelationship.arel_table[join_key].eq(::TaxonName.arel_table[:id]).and(
        ::TaxonNameRelationship.arel_table[param_key].eq(hsh[param_key])).and(
          ::TaxonNameRelationship.arel_table[:type].eq(hsh['type']))
    ).arel.exists
  )
end

#taxon_name_relationship_type_facet ⇒ Object

Returns Scope.

Returns:

  • Scope



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

def taxon_name_relationship_type_facet
  return nil if taxon_name_relationship_type.empty?
  ::TaxonName.with_taxon_name_relationship(taxon_name_relationship_type)
end

#taxon_name_type_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 395

def taxon_name_type_facet
  return nil if taxon_name_type.blank?
  table[:type].eq(taxon_name_type)
end

#type_metadata_facet ⇒ Object

Returns Scope.

Returns:

  • Scope



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# File 'lib/queries/taxon_name/filter.rb', line 354

def type_metadata_facet
  return nil if type_metadata.nil?
  subquery = ::TypeMaterial.where(::TypeMaterial.arel_table[:protonym_id].eq(::TaxonName.arel_table[:id])).arel.exists
  ::TaxonName.where(type_metadata ? subquery : subquery.not)
end

#updated_since_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 428

def updated_since_facet
  return nil if updated_since.blank?
  table[:updated_at].gt(Date.parse(updated_since))
end

#validity_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 433

def validity_facet
  return nil if validity.nil?
  if validity
    table[:id].eq(table[:cached_valid_taxon_name_id])
  else
    table[:id].not_eq(table[:cached_valid_taxon_name_id])
  end
end

#with_etymology_facet ⇒ Object

Returns Scope.

Returns:

  • Scope



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# File 'lib/queries/taxon_name/filter.rb', line 278

def with_etymology_facet
  return nil if etymology.nil?
  etymology ?
    ::TaxonName.where.not(etymology: nil) :
    ::TaxonName.where(etymology: nil)
end

#with_nomenclature_code ⇒ Arel::Nodes::Grouping?

Returns and clause.

Returns:

  • (Arel::Nodes::Grouping, nil) —

    and clause



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# File 'lib/queries/taxon_name/filter.rb', line 390

def with_nomenclature_code
  return nil if nomenclature_code.nil?
  table[:rank_class].matches(nomenclature_code)
end

#with_nomenclature_group ⇒ Arel::Nodes::Grouping?

Returns and clause.

Returns:

  • (Arel::Nodes::Grouping, nil) —

    and clause



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# File 'lib/queries/taxon_name/filter.rb', line 383

def with_nomenclature_group
  return nil if nomenclature_group.nil?
  table[:rank_class].matches(nomenclature_group)
end

#year_facet ⇒ Object 



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

def year_facet
  return nil if year.blank?
  table[:cached_author_year].matches('%' + year + '%')
end