Class: Queries::TaxonName::Autocomplete

Inherits:
Query::Autocomplete show all
Defined in:
lib/queries/taxon_name/autocomplete.rb

Constant Summary collapse

CACHED_NAME_WEIGHT =

Weights. Theory (using this loosely) is that this will proportionally increase the importance in the list of the corresponding element. The tradeoff is subtle, but seems to work at first try.

8.0
CACHED_AUTHOR_YEAR_WEIGHT = 
6.0
CACHED_WEIGHT = 
4.0
CACHED_ORIGINAL_COMBINATION_WEIGHT = 
2.0

Instance Attribute Summary collapse

Attributes inherited from Query::Autocomplete

#dynamic_limit, #project_id, #query_string

Attributes inherited from Query

#query_string, #terms

Instance Method Summary collapse

Methods inherited from Query::Autocomplete

#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, #cached_facet, #combine_or_clauses, #common_name_name, #common_name_table, #common_name_wild_pieces, #exactly_named, #fragments, #integers, #least_levenshtein, #match_wildcard_end_in_cached, #match_wildcard_in_cached, #named, #only_ids, #only_integers?, #parent, #parent_child_join, #parent_child_where, #pieces, #safe_integers, #scope, #string_fragments, #wildcard_wrapped_integers, #wildcard_wrapped_years, #with_cached, #with_cached_like, #with_id, #with_project_id, #year_letter, #years

Methods inherited from Query

#alphabetic_strings, #alphanumeric_strings, base_name, #base_name, #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(string, **params) ⇒ Autocomplete

Returns a new instance of Autocomplete.

Parameters:

  • args (Hash) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 42

def initialize(string, **params)
  @nomenclature_group = params[:nomenclature_group]
  @valid = boolean_param(params, :valid)
  @type = params[:type]
  @parent_id = params[:parent_id]
  @no_leaves = boolean_param(params, :no_leaves)

  # TODO: move to mode
  @exact = boolean_param(params, :exact)
  super
end

Instance Attribute Details

#authorship ⇒ String

Returns (including empty).

Returns:

  • (String) —

    (including empty)



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

def authorship
  @authorship
end

#exact ⇒ Boolean

Returns &exact=<“true”|“false”> if ‘true’ then only #name = query_string results are returned (no fuzzy matching).

Returns:

  • (Boolean) —

    &exact=<“true”|“false”> if ‘true’ then only #name = query_string results are returned (no fuzzy matching)



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# File 'lib/queries/taxon_name/autocomplete.rb', line 31

def exact
  @exact
end

#no_leaves ⇒ Boolean

Returns &no_leaves=<“true”|“false”>

if 'true' then only names with descendents will be returned.

Returns:

  • (Boolean) —

    &no_leaves=<“true”|“false”>

    if 'true' then only names with descendents will be returned



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# File 'lib/queries/taxon_name/autocomplete.rb', line 36

def no_leaves
  @no_leaves
end

#nomenclature_group ⇒ Array

Returns &nomenclature_group[]=<<Iczn|Icnp|Icn>::<Higher|Family|Genus|Species>>.

Returns:

  • (Array) —

    &nomenclature_group[]=<<Iczn|Icnp|Icn>::<Higher|Family|Genus|Species>>



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# File 'lib/queries/taxon_name/autocomplete.rb', line 8

def nomenclature_group
  @nomenclature_group
end

#parent_id ⇒ Array

Returns &parent_id[]=<int>&parent_id=<other_int> etc.

Returns:



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# File 'lib/queries/taxon_name/autocomplete.rb', line 24

def parent_id
  @parent_id
end

#type ⇒ Array

Returns &type[]=<Protonym, Combination, Hybrid, etc.>&type[]=<other type> etc.

Returns:

  • (Array) —

    &type[]=<Protonym, Combination, Hybrid, etc.>&type[]=<other type> etc.



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# File 'lib/queries/taxon_name/autocomplete.rb', line 20

def type
  @type
end

#valid ⇒ Boolean?

Returns &valid=<“true”|“false”>

if 'true'  then id == cached_valid_taxon_name_id
if 'false' then id != cached_valid_taxon_name
if nil   then no check made, i.e. all names

string is converted to Boolean here.

Returns:

  • (Boolean, nil) —

    &valid=<“true”|“false”>

    if 'true'  then id == cached_valid_taxon_name_id
if 'false' then id != cached_valid_taxon_name
if nil   then no check made, i.e. all names

    string is converted to Boolean here



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# File 'lib/queries/taxon_name/autocomplete.rb', line 16

def valid
  @valid
end

Instance Method Details

#and_clauses ⇒ Arel:Nodes?

Returns:

  • (Arel:Nodes, nil) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 67

def and_clauses
  clauses = [
    valid_state,
    is_type,
    with_parent_id,
    with_nomenclature_group,
  ].compact

  return nil if clauses.nil?

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

#autocomplete ⇒ Array

Returns:

  • (Array) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 367

def autocomplete
  # exact, unified, comprehensive

  queries = (exact ? exact_autocomplete : comprehensive_autocomplete )
  queries.compact!

  result = []

  queries.each_with_index do |q,i|
    a = q
    a = q.where(project_id:) if project_id.present?

    a = a.where(and_clauses.to_sql) if and_clauses

    if !parent_id.empty?
      a = a.descendants_of(::TaxonName.where(id: parent_id))
    end

    a = a.not_leaves if no_leaves

    result += a.limit(20).to_a
    break if result.count > 19
  end

  result.uniq!
  # result[0..19]
  result
end

#autocomplete_cached ⇒ Object

—- gin methods Consider word_similarity()



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# File 'lib/queries/taxon_name/autocomplete.rb', line 245

def autocomplete_cached
  ::TaxonName.where(project_id:).select(ApplicationRecord.sanitize_sql(['taxon_names.*, similarity(?, taxon_names.cached) AS sml', query_string]))
    .where('taxon_names.cached % ?', query_string) # `%` in where means nothing < 0.3 (internal PG similarity value)
    .where(ApplicationRecord.sanitize_sql_array(["similarity('%s', taxon_names.cached) > 0.6", query_string]))
    .order('sml DESC, taxon_names.cached')
end

#autocomplete_cached_author_year ⇒ Object 



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# File 'lib/queries/taxon_name/autocomplete.rb', line 259

def autocomplete_cached_author_year
  ::TaxonName.select(ApplicationRecord.sanitize_sql(['taxon_names.*, similarity(?, taxon_names.cached_author_year) AS sml', query_string]))
    .where('taxon_names.cached_author_year % ?', query_string)
    .where(ApplicationRecord.sanitize_sql(["similarity('%s', taxon_names.cached_author_year) > 0.6", query_string]))
    .order('sml DESC, taxon_names.cached_author_year')
end

#autocomplete_cached_end_wildcard ⇒ Scope

Returns:

  • (Scope) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 156

def autocomplete_cached_end_wildcard
  s = query_string.delete('\\')
  a = table[:cached].matches("#{s}%")
  base_query.where(a.to_sql).limit(20)
end

#autocomplete_cached_name_end_wildcard ⇒ Scope

Returns:

  • (Scope) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 185

def autocomplete_cached_name_end_wildcard
  a = table[:name].matches("#{query_string}%")
  base_query.where(a.to_sql).limit(20)
end

#autocomplete_cached_original_combination_wildcard_whitespace_with_space ⇒ Object 



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# File 'lib/queries/taxon_name/autocomplete.rb', line 195

def autocomplete_cached_original_combination_wildcard_whitespace_with_space
  a = table[:cached_original_combination].matches("#{query_string.gsub('. ', ' ').gsub(/[\s\\]/, '% ')}%")
  base_query.where(a.to_sql).limit(20)
end

#autocomplete_cached_wildcard_whitespace ⇒ Scope

Returns:

  • (Scope) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 201

def autocomplete_cached_wildcard_whitespace
  a = table[:cached].matches("#{query_string.gsub('. ', ' ').gsub(/[\s\\]/, '%')}")
  base_query.where(a.to_sql).limit(20)
end

#autocomplete_cached_wildcard_whitespace_with_space ⇒ Object 



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# File 'lib/queries/taxon_name/autocomplete.rb', line 190

def autocomplete_cached_wildcard_whitespace_with_space
  a = table[:cached].matches("#{query_string.gsub('. ', ' ').gsub(/[\s\\]/, '% ')}%")
  base_query.where(a.to_sql).limit(20)
end

#autocomplete_combined_gin ⇒ Object

Used in /otus/api/v1/autocomplete



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# File 'lib/queries/taxon_name/autocomplete.rb', line 275

def autocomplete_combined_gin
  a = ::TaxonName.select(ApplicationRecord.sanitize_sql(
    ['taxon_names.*, similarity(?, name) AS sml_n, similarity(?, taxon_names.cached_author_year) AS sml_cay, similarity(?, cached) AS sml_c, similarity(?, taxon_names.cached_original_combination) AS sml_coc',
     query_string, authorship, query_string, query_string])
                        ).where('taxon_names.cached_author_year % ? OR taxon_names.cached_original_combination % ? OR cached % ?', query_string, query_string, query_string)

  s = 'WITH tns AS (' + a.to_sql + ') ' +
    ::TaxonName
    .select(Arel.sql("taxon_names.*, (( COALESCE(tns1.sml_n,0) * #{CACHED_NAME_WEIGHT} + \
                                            COALESCE(tns1.sml_cay,0) * #{CACHED_AUTHOR_YEAR_WEIGHT} + \
                                            COALESCE(tns1.sml_c,0) * #{CACHED_WEIGHT} + \
                                            COALESCE(tns1.sml_coc,0) * #{CACHED_ORIGINAL_COMBINATION_WEIGHT} \
                                          )) sml_tn"))
    .joins('JOIN tns as tns1  on tns1.id = taxon_names.id')
    .to_sql

  ::TaxonName.select('taxon_names.*, sml_tn as sml_t').from('(' + s + ') as taxon_names').order('sml_tn DESC').distinct
end

#autocomplete_exact_cached ⇒ Scope

Returns:

  • (Scope) 


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

def autocomplete_exact_cached
  a = table[:cached].eq(query_string)
  base_query.where(a.to_sql).order('cached_author_year ASC').limit(20)
end

#autocomplete_exact_cached_original_combination ⇒ Scope

Returns:

  • (Scope) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 119

def autocomplete_exact_cached_original_combination
  a = table[:cached_original_combination].eq(query_string)
  base_query.where(a.to_sql).order('cached_author_year ASC').limit(20)
end

#autocomplete_exact_name ⇒ Scope

Returns:

  • (Scope) 


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

def autocomplete_exact_name
  a = table[:name].eq(query_string)
  base_query.where(a.to_sql).order('cached_author_year ASC').limit(20)
end

#autocomplete_exact_name_and_year ⇒ Scope

Returns:

  • (Scope) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 131

def autocomplete_exact_name_and_year
  a = alphabetic_strings.select { |b| !(b =~ /\d/) }
  b = years
  if a.size == 1 && !b.empty?
    a = table[:name].eq(a.first).and(table[:cached_author_year].matches_any(wildcard_wrapped_years))
    base_query.where(a.to_sql).limit(10)
  else
    nil
  end
end

#autocomplete_genus_species1(result) ⇒ Scope

Parameters:

  • result (String)

Returns:

  • (Scope) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 170

def autocomplete_genus_species1(result)
  return nil if result.nil?
  a = table[:cached].matches(result)
  base_query.where(a.to_sql).order('type DESC, cached ASC').limit(8)
end

#autocomplete_genus_species2(result) ⇒ Scope

Parameters:

  • result (String)

Returns:

  • (Scope) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 178

def autocomplete_genus_species2(result)
  return nil if result.nil?
  a = table[:cached].matches(result + '%')
  base_query.where(a.to_sql).order('type DESC, cached ASC').limit(8)
end

#autocomplete_name_author_year_fragment ⇒ Scope?

Returns:

  • (Scope, nil) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 207

def autocomplete_name_author_year_fragment
  f = fragments
  if f.size == 2
    a = table[:name].matches(f[0]).and(table[:cached_author_year].matches(f[1]))
    base_query.where(a.to_sql).limit(20)
  else
    nil
  end
end

#autocomplete_original_combination ⇒ Object 



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# File 'lib/queries/taxon_name/autocomplete.rb', line 252

def autocomplete_original_combination
  ::TaxonName.select(ApplicationRecord.sanitize_sql(['taxon_names.*, similarity(?, taxon_names.cached_original_combination) AS sml', query_string]))
    .where('taxon_names.cached_original_combination % ?', query_string)
    .where(ApplicationRecord.sanitize_sql_array(["similarity('%s', taxon_names.cached_original_combination) > 0.6", query_string]))
    .order('sml DESC, taxon_names.cached_original_combination')
end

#autocomplete_taxon_name_author_year_matches ⇒ Arel::Nodes::Matches

Returns:

  • (Arel::Nodes::Matches) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 232

def autocomplete_taxon_name_author_year_matches
  a = authorship
  return nil if a.nil?
  base_query.where(table[:cached_author_year].matches(a).to_sql).limit(10)
end

#autocomplete_top_cached ⇒ Scope

Returns:

  • (Scope) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 149

def autocomplete_top_cached
  s = query_string
  a = table[:cached].matches("#{s}%")
  base_query.where(a.to_sql).limit(1)
end

#autocomplete_top_cached_subgenus ⇒ Scope

Returns:

  • (Scope) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 163

def autocomplete_top_cached_subgenus
  a = table[:cached].matches("%(#{query_string})")
  base_query.where(a.to_sql).limit(1)
end

#autocomplete_wildcard_author_year_joined_pieces ⇒ Scope?

Returns:

  • (Scope, nil) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 218

def autocomplete_wildcard_author_year_joined_pieces
  return nil if pieces.empty?
  a = table[:cached_author_year].matches("%#{pieces.join('%')}%")
  base_query.where(a.to_sql).order('cached ASC').limit(20)
end

#autocomplete_wildcard_cached_original_combination ⇒ Scope

Returns:

  • (Scope) 


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

def autocomplete_wildcard_cached_original_combination
  a = table[:cached_original_combination].matches(wildcard_pieces)
  base_query.where(a.to_sql).order('cached_author_year ASC').limit(20)
end

#autocomplete_wildcard_joined_strings ⇒ Scope?

Returns:

  • (Scope, nil) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 225

def autocomplete_wildcard_joined_strings
  return nil if alphabetic_strings.empty?
  a = table[:cached].matches("%#{alphabetic_strings.join('%')}%")
  base_query.where(a.to_sql).limit(10)
end

#base_query ⇒ Scope

TODO: this should deprecate for gin based approaches.

Returns:

  • (Scope) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 415

def base_query
  ::TaxonName.select('taxon_names.*, char_length(taxon_names.cached)')
    .includes(:ancestor_hierarchies)
    .order(Arel.sql('char_length(taxon_names.cached), taxon_names.cached ASC'))
end

#comprehensive_autocomplete ⇒ Object

TODO: Refactor to OTU approach?



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# File 'lib/queries/taxon_name/autocomplete.rb', line 320

def comprehensive_autocomplete
  z = genus_species
  queries = [
    autocomplete_exact_cached,
    autocomplete_exact_cached_original_combination,
    autocomplete_exact_name_and_year,
    autocomplete_exact_name,

    autocomplete_exact_id,
    autocomplete_identifier_cached_exact,
    autocomplete_identifier_identifier_exact,

    # All exact should be before these?
    #
    # There are left in, but the cutoff
    # is now 2x as high, i.e. more like wildcard matches we
    # were originally used to.
    autocomplete_cached, # sim
    autocomplete_original_combination, # sim
    autocomplete_cached_author_year, # sim

    # Specialized results
    autocomplete_genus_species1(z),    # not tested
    autocomplete_genus_species2(z),    # not tested
    autocomplete_top_cached_subgenus,  # not tested

    # autocomplete_top_cached, # Wildcard end
    # autocomplete_cached_end_wildcard,
    # autocomplete_cached_name_end_wildcard,
    # autocomplete_cached_wildcard_whitespace,
    # autocomplete_name_author_year_fragment,
    # autocomplete_taxon_name_author_year_matches,
    autocomplete_wildcard_joined_strings,
    autocomplete_wildcard_author_year_joined_pieces,
    autocomplete_wildcard_cached_original_combination
  ]
end

#exact_autocomplete ⇒ Object

Used in New taxon name task, for example

TODO: what is intent?



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# File 'lib/queries/taxon_name/autocomplete.rb', line 296

def exact_autocomplete
  [
    autocomplete_exact_id,
    autocomplete_exact_cached,
    autocomplete_exact_cached_original_combination,
    autocomplete_identifier_cached_exact,
    autocomplete_identifier_identifier_exact,
    autocomplete_exact_name_and_year,

    autocomplete_cached_end_wildcard,
    autocomplete_cached_wildcard_whitespace_with_space,
    autocomplete_cached_original_combination_wildcard_whitespace_with_space,
    autocomplete_cached_wildcard_whitespace,
    autocomplete_name_author_year_fragment,
    autocomplete_taxon_name_author_year_matches,
    autocomplete_wildcard_joined_strings,
    autocomplete_wildcard_author_year_joined_pieces,
    autocomplete_wildcard_cached_original_combination,
    autocomplete_exact_name, # not exact enough, want the whole thing?
    # autocomplete_top_cached, # not exact at all
  ]
end

#genus_species ⇒ String?

Returns parse and only return what is assumed to be genus/species, with a wildcard in front.

Returns:

  • (String, nil) —

    parse and only return what is assumed to be genus/species, with a wildcard in front



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# File 'lib/queries/taxon_name/autocomplete.rb', line 398

def genus_species
  p = Vendor::Biodiversity::Result.new
  p.name = query_string
  r = p.parse

  a = p.genus
  b = p.species

  if a && b
    a + '%' + b
  else
    nil
  end
end

#is_type ⇒ Arel::Nodes::<>?

and clause

Returns:

  • (Arel::Nodes::<>, nil) 


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

def is_type
  return nil if type.empty?
  table[:type].in(type)
end

#taxon_name_hierarchies_table ⇒ Arel::Table

Returns:

  • (Arel::Table) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 422

def taxon_name_hierarchies_table
  Arel::Table.new('taxon_name_hierarchies')
end

#unified_autocomplete ⇒ Object 



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# File 'lib/queries/taxon_name/autocomplete.rb', line 358

def unified_autocomplete
  [
    autocomplete_exact_id,
    autocomplete_combined_gin,
    autocomplete_identifier_cached_exact,
  ]
end

#valid_state ⇒ Arel::Nodes::<>?

and clause

Returns:

  • (Arel::Nodes::<>, nil) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 86

def valid_state
  return nil if @valid.nil?
  valid ? table[:id].eq(table[:cached_valid_taxon_name_id]) : table[:id].not_eq(table[:cached_valid_taxon_name_id])
end

#with_cached_author_year ⇒ Arel::Nodes::Matches

Returns:

  • (Arel::Nodes::Matches) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 427

def with_cached_author_year
  table[:cached_author_year].matches_any(terms)
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/autocomplete.rb', line 107

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

#with_parent_id ⇒ Arel::Nodes::<>?

and clause, limit to ancestors or [ids]

Returns:

  • (Arel::Nodes::<>, nil) 


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# File 'lib/queries/taxon_name/autocomplete.rb', line 100

def with_parent_id
  return nil if parent_id.empty?
  taxon_name_hierarchies_table[:ancestor_id].in(parent_id)
end