Class: Queries::TaxonName::Filter

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

Constant Summary collapse

PARAMS = 
[
  :ancestors,
  :ancestrify,
  :author,
  :author_exact,
  :authors,
  :collecting_event_id,
  :collection_object_id,
  :combinations,
  :combinationify,
  :descendants,
  :descendants_max_depth,
  :epithet_only,
  :etymology,
  :leaves,
  :name,
  :name_exact,
  :nomenclature_code,
  :nomenclature_date,
  :nomenclature_group, # !! different than autocomplete
  :not_specified,
  :original_combination,
  :otu_id,
  :otus,
  :rank,
  :synonymify,
  :taxon_name_author_id_or,
  :taxon_name_id,
  :taxon_name_type,
  :type_metadata,
  :validify,
  :validity,
  :verbatim_name,
  :year,
  :year_end,
  :year_start,

  collection_object_id: [],
  collecting_event_id: [],
  combination_taxon_name_id: [],
  name: [],
  otu_id: [],
  parent_id: [],
  rank: [],
  taxon_name_author_id: [],
  taxon_name_classification: [],
  taxon_name_id: [],
  taxon_name_relationship: [
    :subject_taxon_name_id,
    :object_taxon_name_id,
    :type,
  ],
  taxon_name_relationship_type: [],
  type: [],
].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, #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, #taxon_name_query, #venn, #venn_mode

Attributes inherited from Query

#query_string, #terms

Instance Method Summary collapse

Methods included from Helpers

#boolean_param, #integer_param

Methods inherited from Query::Filter

#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, included_annotator_facets, instantiated_base_filter, inverted_subqueries, #object_global_id_facet, #only_project?, params, #permitted_params, #process_url_into_params, #project_id_facet, query_name, #query_name, #set_nested_queries, #shared_and_clauses, #subquery_vector, #target_and_clauses, #venn_query

Methods inherited from Query

#alphabetic_strings, #alphanumeric_strings, base_name, #base_name, #base_query, #build_terms, #cached_facet, #end_wildcard, #levenshtein_distance, #match_ordered_wildcard_pieces_in_cached, #no_terms?, referenced_klass, #referenced_klass, #referenced_klass_except, #referenced_klass_intersection, #referenced_klass_union, #start_and_end_wildcard, #start_wildcard, #table, #wildcard_pieces

Constructor Details

#initialize(query_params) ⇒ Filter

Returns a new instance of Filter.

Parameters:

  • params (Params) —

    as permitted via controller



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# File 'lib/queries/taxon_name/filter.rb', line 300

def initialize(query_params)
  super

  @ancestors = boolean_param(params, :ancestors)
  @ancestrify = boolean_param(params, :ancestrify)
  @author = params[:author]
  @author_exact = boolean_param(params, :author_exact)
  @authors = boolean_param(params, :authors)
  @collecting_event_id = params[:collecting_event_id]
  @collection_object_id = params[:collection_object_id]
  @combination_taxon_name_id = params[:combination_taxon_name_id]
  @combinations = boolean_param(params, :combinations)
  @combinationify = boolean_param(params, :combinationify)
  @descendants = boolean_param(params, :descendants)
  @descendants_max_depth = params[:descendants_max_depth]
  @etymology = boolean_param(params, :etymology)
  @epithet_only = params[:epithet_only]
  @geo_json = params[:geo_json]
  @leaves = boolean_param(params, :leaves)
  @name = params[:name]
  @name_exact = boolean_param(params, :name_exact)
  @nomenclature_date = boolean_param(params, :nomenclature_date)
  @nomenclature_code = params[:nomenclature_code] if params[:nomenclature_code].present?
  @nomenclature_group = params[:nomenclature_group] if params[:nomenclature_group].present?
  @not_specified = boolean_param(params, :not_specified)
  @otu_id = params[:otu_id]
  @otus = boolean_param(params, :otus)
  @original_combination = boolean_param(params, :original_combination)
  @parent_id = params[:parent_id]
  @rank = params[:rank]
  @sort = params[:sort]
  @synonymify = boolean_param(params, :synonymify)
  @taxon_name_author_id = params[:taxon_name_author_id]
  @taxon_name_author_id_or = boolean_param(params, :taxon_name_author_id_or)
  @taxon_name_classification = params[:taxon_name_classification] || []
  @taxon_name_id = params[:taxon_name_id]
  @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)
  @validify = boolean_param(params, :validify)
  @validity = boolean_param(params, :validity)
  @verbatim_name = boolean_param(params, :verbatim_name)

  @year = params[:year]
  @year_end = params[:year_end]
  @year_start = params[:year_start]

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

Instance Attribute Details

#ancestors ⇒ Object

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

Parameters:

  • ancestors (Boolean, 'true', 'false', nil)

Returns:

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



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# File 'lib/queries/taxon_name/filter.rb', line 72

def ancestors
  @ancestors
end

#ancestrify ⇒ Object

!! This parameter is not like the others, it is applied POST result, see also synonymify and validify, etc.

Parameters:

  • ancestrify (Boolean) —

    true - extend result to include all ancestors of names in the result along with the result false/nil - ignore



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

def ancestrify
  @ancestrify
end

#author ⇒ Object

Parameters:

  • author (String) —

    Use “&” for “and”. Matches against cached_author_year. See also author_exact.



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

def author
  @author
end

#author_exact ⇒ Object

Returns Boolean.

Returns:

  • Boolean



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# File 'lib/queries/taxon_name/filter.rb', line 123

def author_exact
  @author_exact
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 237

def authors
  @authors
end

#collecting_event_id ⇒ Object

Returns Array.

Parameters:

  • collecting_event_id (String, Array)

Returns:

  • Array



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

def collecting_event_id
  @collecting_event_id
end

#collection_object_id ⇒ Object

Returns Array.

Parameters:

  • collection_object_id (String, Array)

Returns:

  • Array



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

def collection_object_id
  @collection_object_id
end

#combination_taxon_name_id ⇒ Array

Returns taxon_name_ids for which all Combinations will be returned.

Returns:

  • (Array) —

    taxon_name_ids for which all Combinations will be returned



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# File 'lib/queries/taxon_name/filter.rb', line 287

def combination_taxon_name_id
  @combination_taxon_name_id
end

#combinationify ⇒ Object

!! This parameter is not like the others, it is applied POST result, see also synonymify and validify

Parameters:

  • combinationify (Boolean) —

    true - extend result to include all Combinations in which the finest name is a member of the result false/nil - ignore



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

def combinationify
  @combinationify
end

#combinations ⇒ Object

This parameter should be used along side species or genus group limits.

Parameters:

  • combinations (Boolean) —

    true - only return names that have (subsequent) Combinations false - only return names without (subequent) Combinations nil - ignore



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# File 'lib/queries/taxon_name/filter.rb', line 94

def combinations
  @combinations
end

#descendants ⇒ Boolean

Returns true - only descendants NOT SELF false - self AND descendants nil - ignored Ignored when taxon_name_id[].empty?.

Parameters:

  • descendants (Boolean, 'true', 'false', nil) —

    Read carefully! descendants = false is NOT no descendants, it’s descendants and self

Returns:

  • (Boolean) —

    true - only descendants NOT SELF false - self AND descendants nil - ignored Ignored when taxon_name_id[].empty?



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

def descendants
  @descendants
end

#descendants_max_depth ⇒ Integer?

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

Ignored when descentants is false/unspecified.
Defaults to nil

Parameters:

  • descendants_max_depth (Integer)

Returns:

  • (Integer, nil) 


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# File 'lib/queries/taxon_name/filter.rb', line 188

def descendants_max_depth
  @descendants_max_depth
end

#epithet_only ⇒ Object

Parameters:

  • epithet_only (Boolean) —

    true - use name property instead of cached to find taxon name false/nil - ignore



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

def epithet_only
  @epithet_only
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 232

def etymology
  @etymology
end

#geo_json ⇒ Object

Returns the value of attribute geo_json.



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

def geo_json
  @geo_json
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 265

def leaves
  @leaves
end

#name ⇒ Array

Returns Matches against cached. See also name_exact.

Parameters:

  • name (String, Array)

Returns:

  • (Array) —

    Matches against cached. See also name_exact.



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

def name
  @name
end

#name_exact ⇒ Object

Returns Boolean.

Returns:

  • Boolean



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# File 'lib/queries/taxon_name/filter.rb', line 116

def name_exact
  @name_exact
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 258

def nomenclature_code
  @nomenclature_code
end

#nomenclature_date ⇒ Object

Returns Boolean with/out cached nomenclature date set.

Parameters:

  • ancestors (Boolean, 'true', 'false', nil)

Returns:

  • Boolean with/out cached nomenclature date set



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

def nomenclature_date
  @nomenclature_date
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 254

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 249

def not_specified
  @not_specified
end

#original_combination ⇒ Boolean?

Returns true - name has at least one element of original combination false - name has no element of original combination nil - ignored.

Parameters:

  • original_combination (Boolean)

Returns:

  • (Boolean, nil) —

    true - name has at least one element of original combination false - name has no element of original combination nil - ignored



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

def original_combination
  @original_combination
end

#otu_id ⇒ Array?

Returns one or more OTU ids.

Parameters:

  • otu_id (Array, nil)

Returns:

  • (Array, nil) —

    one or more OTU ids



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# File 'lib/queries/taxon_name/filter.rb', line 222

def otu_id
  @otu_id
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 227

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 172

def parent_id
  @parent_id
end

#rank ⇒ Array

Returns:

  • (Array) 


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

def rank
  @rank
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 283

def sort
  @sort
end

#synonymify ⇒ Object

!! This parameter is not like the others, it is applied POST result, see also combinationify and validify

Parameters:

  • synonymify (Boolean) —

    true - extend result to include all Synonyms of any member of the list false/nil - ignore



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

def synonymify
  @synonymify
end

#taxon_name_author_id ⇒ Array

Returns:

  • (Array) 


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# File 'lib/queries/taxon_name/filter.rb', line 272

def taxon_name_author_id
  @taxon_name_author_id
end

#taxon_name_author_id_or ⇒ Boolean

Parameters:

  • `false`, (String) —

    nil - treat the ids in taxon_name_author_id as “or” (match any TaxonName with any of these authors) ‘true’ - treat the ids in taxon_name_author_id as “and” (only TaxonNames with all and only all will match)

Returns:

  • (Boolean) 


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

def taxon_name_author_id_or
  @taxon_name_author_id_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 210

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 166

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 202

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 206

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 269

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 242

def type_metadata
  @type_metadata
end

#validify ⇒ Object

name is returned !! This param is not like the others. !!

Returns:

  • Boolean if true then for each name in the result its valid



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# File 'lib/queries/taxon_name/filter.rb', line 155

def validify
  @validify
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 148

def validity
  @validity
end

#verbatim_name ⇒ Object

Returns Boolean if true then ‘verbatim_name` is populated.

Returns:

  • Boolean if true then ‘verbatim_name` is populated



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# File 'lib/queries/taxon_name/filter.rb', line 160

def verbatim_name
  @verbatim_name
end

#year ⇒ Object

Matches against cached_author_year.

Parameters:

  • year (String) —

    “yyyy”



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# File 'lib/queries/taxon_name/filter.rb', line 128

def year
  @year
end

#year_end ⇒ Object

Matches against cached_nomenclature_date

Parameters:

  • year_end (String) —

    “yyyy”



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

def year_end
  @year_end
end

#year_start ⇒ Object

Matches against cached_nomenclature_date

Parameters:

  • year_start (String) —

    “yyyy”



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

def year_start
  @year_start
end

Instance Method Details

#all(nil_empty = false) ⇒ ActiveRecord::Relation

Returns:

  • (ActiveRecord::Relation) 


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# File 'lib/queries/taxon_name/filter.rb', line 936

def all(nil_empty = false)
  q = super

  # Order matters, use this first to go up
  q = ancestrify_result(q) if ancestrify

  # Then out in various ways
  q = validify_result(q) if validify
  q = combinationify_result(q) if combinationify
  q = synonimify_result(q) if synonymify

  # Then sort
  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 508

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

#ancestrify_result(q) ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 905

def ancestrify_result(q)
  s = 'WITH tn_result_query_anc AS (' + q.to_sql + ') ' +
      ::TaxonName
        .joins('JOIN taxon_name_hierarchies tnh on tnh.ancestor_id = taxon_names.id')
        .joins('JOIN tn_result_query_anc as tn_result_query_anc1 on tn_result_query_anc1.id = tnh.descendant_id')
        .distinct
        .to_sql

  # !! Do not use .distinct here
  ::TaxonName.from('(' + s + ') as taxon_names')
end

#and_clauses ⇒ ActiveRecord::Relation

Returns:

  • (ActiveRecord::Relation) 


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# File 'lib/queries/taxon_name/filter.rb', line 816

def and_clauses
  [
    nomenclature_date_facet,
    author_facet,
    name_facet,
    parent_id_facet,
    rank_facet,
    taxon_name_type_facet,
    validity_facet,
    verbatim_name_facet,
    with_nomenclature_code,
    with_nomenclature_group,
    year_facet,
  ]
end

#asserted_distribution_query_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 765

def asserted_distribution_query_facet
  return nil if asserted_distribution_query.nil?
  s = 'WITH query_ad_tn AS (' + asserted_distribution_query.all.to_sql + ') ' +
      ::TaxonName
        .joins(otus: [:asserted_distributions])
        .joins('JOIN query_ad_tn as query_ad_tn1 on query_ad_tn1.otu_id = asserted_distributions.otu_id')
        .to_sql

  ::TaxonName.from('(' + s + ') as taxon_names').distinct
end

#author_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 685

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

#authors_facet ⇒ Object

This is not true! It includes records that are year only.

Returns:

  • Scope



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# File 'lib/queries/taxon_name/filter.rb', line 538

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

#biological_association_query_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 798

def biological_association_query_facet
  return nil if biological_association_query.nil?
  s = 'WITH query_tn_ba AS (' + biological_association_query.all.to_sql + ') '

  a = ::TaxonName
    .joins(:otus)
    .joins("JOIN query_tn_ba as query_tn_ba1 on query_tn_ba1.biological_association_subject_id = otus.id AND query_tn_ba1.biological_association_subject_type = 'Otu'").to_sql

  b = ::TaxonName
    .joins(:otus)
    .joins("JOIN query_tn_ba as query_tn_ba2 on query_tn_ba2.biological_association_object_id = otus.id AND query_tn_ba2.biological_association_object_type = 'Otu'").to_sql

  s << ::TaxonName.from("((#{a}) UNION (#{b})) as taxon_names").to_sql

  ::TaxonName.from('(' + s + ') as taxon_names')
end

#collecting_event_id_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 737

def collecting_event_id_facet
  return nil if collecting_event_id.empty?
  ::TaxonName
    .joins(:collection_objects)
    .where(collection_objects: { collecting_event_id: })
end

#collecting_event_query_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 787

def collecting_event_query_facet
  return nil if collecting_event_query.nil?
  s = 'WITH query_ce_tns AS (' + collecting_event_query.all.to_sql + ') ' +
      ::TaxonName
        .joins(:collection_objects)
        .joins('JOIN query_ce_tns as query_ce_tns1 on collection_objects.collecting_event_id = query_ce_tns1.id')
        .to_sql

  ::TaxonName.from('(' + s + ') as taxon_names').distinct
end

#collection_object_id_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 520

def collection_object_id_facet
  return nil if collection_object_id.empty?
  ::TaxonName.joins(:collection_objects).where(collection_objects: { id: collection_object_id })
end

#collection_object_query_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 776

def collection_object_query_facet
  return nil if collection_object_query.nil?
  s = 'WITH query_collection_objects AS (' + collection_object_query.all.to_sql + ') ' +
      ::TaxonName
        .joins(:collection_objects)
        .joins('JOIN query_collection_objects as query_collection_objects1 on collection_objects.id = query_collection_objects1.id')
        .to_sql

  ::TaxonName.from('(' + s + ') as taxon_names').distinct
end

#combination_taxon_name_id_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 726

def combination_taxon_name_id_facet
  return nil if combination_taxon_name_id.empty?
  ::Combination.joins(:related_taxon_name_relationships)
    .where(
      taxon_name_relationships: {
        type: ::TAXON_NAME_RELATIONSHIP_COMBINATION_TYPES.values,
        subject_taxon_name_id: combination_taxon_name_id,
      },
    ).distinct
end

#combinationify_result(q) ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 893

def combinationify_result(q)
  s = 'WITH tn_result_query AS (' + q.to_sql + ') ' +
      ::TaxonName
        .joins('JOIN tn_result_query as tn_result_query3 on tn_result_query3.id = taxon_names.cached_valid_taxon_name_id')
        .where("taxon_names.type = 'Combination'")
        .to_sql

  a = ::TaxonName.from('(' + s + ') as taxon_names').distinct

  referenced_klass_union([q, a])
end

#combinations_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 744

def combinations_facet
  return nil if combinations.nil?
  a = ::Protonym.joins(:combination_relationships)
  if combinations
    a
  else
    referenced_klass_except(a)
  end
end

#descendant_facet ⇒ Object

Returns Scope match only names that are a descendant of some taxon_name_id.

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 478

def descendant_facet
  return nil if taxon_name_id.empty? || descendants.nil?

  h = ::TaxonNameHierarchy.arel_table

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

    if descendants_max_depth.present?
      descendants_subquery = descendants_subquery.where(::TaxonNameHierarchy.arel_table[:generations].lteq(descendants_max_depth.to_i))
    end

    ::TaxonName.where(descendants_subquery.arel.exists)
  else
    q = ::TaxonName.joins('JOIN taxon_name_hierarchies ON taxon_name_hierarchies.descendant_id = taxon_names.id')
      .where(taxon_name_hierarchies: {ancestor_id: taxon_name_id})
     if descendants_max_depth.present?
       q = q.where(::TaxonNameHierarchy.arel_table[:generations].lteq(descendants_max_depth.to_i))
     end
     q
  end
end

#geo_json_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 434

def geo_json_facet
  return nil if geo_json.nil?
  otus = ::Queries::Otu::Filter.new(geo_json:).all
  collection_objects = ::Queries::CollectionObject::Filter.new(geo_json:).all

  a = ::TaxonName.joins(:taxon_taxon_determinations).where(taxon_determinations: { taxon_determination_object: collection_objects })
  b = ::TaxonName.joins(:otus).where(otus:)

  ::TaxonName.from("((#{a.to_sql}) UNION (#{b.to_sql})) as taxon_names")
end

#leaves_facet ⇒ Object

Returns Scope.

Returns:

  • Scope



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# File 'lib/queries/taxon_name/filter.rb', line 560

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

#merge_clauses ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 832

def merge_clauses
  clauses = [
    asserted_distribution_query_facet,
    biological_association_query_facet,
    collecting_event_query_facet,
    collection_object_query_facet,
    otu_query_facet,

    ancestor_facet,
    authors_facet,
    collecting_event_id_facet,
    collection_object_id_facet,
    combination_taxon_name_id_facet,
    combinations_facet,
    descendant_facet,
    leaves_facet,
    not_specified_facet,
    original_combination_facet,
    otu_id_facet,
    taxon_name_author_id_facet,
    otus_facet,
    taxon_name_classification_facet,
    taxon_name_relationship_type_facet,
    type_metadata_facet,
    with_etymology_facet,
    year_range_facet,
  ]

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

  clauses.compact
end

#model_id_facet ⇒ Object

Overrides base class



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# File 'lib/queries/taxon_name/filter.rb', line 868

def model_id_facet
  return nil if taxon_name_id.empty? || !descendants.nil? || ancestors
  table[:id].in(taxon_name_id)
end

#name_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 662

def name_facet
  return nil if name.empty?
  if name_exact
    if (epithet_only)
      table[:name].in(name)
    else
      table[:cached].in(name).or(table[:cached_original_combination].in(name))
    end
    #  table[:cached].eq(name.strip).or(table[:cached_original_combination].eq(name.strip))
  else
    if (epithet_only)
      table[:name].matches_any(name.collect { |n| '%' + n.gsub(/\s+/, '%') + '%' })
    else
      table[:cached].matches_any(name.collect { |n| '%' + n.gsub(/\s+/, '%') + '%' }).or(table[:cached_original_combination].matches_any(name.collect { |n| '%' + n.gsub(/\s+/, '%') + '%' }))
    end
  end
end

#nomenclature_date_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 467

def nomenclature_date_facet
  return nil if nomenclature_date.nil?
  if nomenclature_date
    table[:cached_nomenclature_date].not_eq(nil)
  else
    table[:cached_nomenclature_date].eq(nil)
  end
end

#not_specified_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 445

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 917

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

#original_combination_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 458

def original_combination_facet
  return nil if original_combination.nil?
  if original_combination
    ::Protonym.joins(:original_combination_relationships).distinct
  else
    ::Protonym.left_joins(:original_combination_relationships).where(taxon_name_relationships: {id: nil})
  end
end

#otu_id_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 525

def otu_id_facet
  return nil if otu_id.empty?
  ::TaxonName.joins(:otus).where(otus: { id: otu_id })
end

#otu_query_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 754

def otu_query_facet
  return nil if otu_query.nil?
  s = 'WITH query_otu_tn AS (' + otu_query.all.to_sql + ') ' +
      ::TaxonName
        .joins(:otus)
        .joins('JOIN query_otu_tn as query_otu_tn1 on otus.id = query_otu_tn1.id') # Don't change, see `validify`
        .to_sql

  ::TaxonName.from('(' + s + ') as taxon_names').distinct
end

#otus_facet ⇒ Object

Returns Scope.

Returns:

  • Scope



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# File 'lib/queries/taxon_name/filter.rb', line 631

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 680

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

#rank_facet ⇒ Arel::Nodes::Grouping?

Returns:

  • (Arel::Nodes::Grouping, nil) 


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# File 'lib/queries/taxon_name/filter.rb', line 644

def rank_facet
  return nil if rank.blank?
  # We don't wildcard end so that we can isolate to specific ranks and below
  r = rank.collect { |i| "%#{i}" }
  table[:rank_class].matches_any(r)
end

#synonimify_result(q) ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 882

def synonimify_result(q)
  s = 'WITH tn_result_query AS (' + q.to_sql + ') ' +
      ::TaxonName
        .joins('JOIN tn_result_query as tn_result_query2 on tn_result_query2.id = taxon_names.cached_valid_taxon_name_id')
        .to_sql

  a = ::TaxonName.from('(' + s + ') as taxon_names').distinct

  referenced_klass_union([q, a])
end

#taxon_name_author_id_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 595

def taxon_name_author_id_facet
  return nil if taxon_name_author_id.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].in(taxon_name_author_id)

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

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

#taxon_name_classification_facet ⇒ Object

Returns Scope.

Returns:

  • Scope



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# File 'lib/queries/taxon_name/filter.rb', line 583

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_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 567

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 554

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 657

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 624

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

#validify_result(q) ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 873

def validify_result(q)
  s = 'WITH tn_result_query AS (' + q.to_sql + ') ' +
      ::TaxonName
        .joins('JOIN tn_result_query as tn_result_query1 on tn_result_query1.cached_valid_taxon_name_id = taxon_names.id')
        .to_sql

  ::TaxonName.from('(' + s + ') as taxon_names').distinct
end

#validity_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 708

def validity_facet
  return nil if validity.nil?
  if validity
    table[:cached_is_valid].eq(true)
  else
    table[:cached_is_valid].eq(false)
  end
end

#verbatim_name_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 717

def verbatim_name_facet
  return nil if verbatim_name.nil?
  if verbatim_name
    table[:verbatim_name].not_eq(nil)
  else
    table[:verbatim_name].eq(nil)
  end
end

#with_etymology_facet ⇒ Object

Returns Scope.

Returns:

  • Scope



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# File 'lib/queries/taxon_name/filter.rb', line 546

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:

  • (Arel::Nodes::Grouping, nil) 


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# File 'lib/queries/taxon_name/filter.rb', line 652

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

#with_nomenclature_group ⇒ Arel::Nodes::Grouping?

Returns:

  • (Arel::Nodes::Grouping, nil) 


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# File 'lib/queries/taxon_name/filter.rb', line 638

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

#year_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 694

def year_facet
  return nil if year.blank?

  s = Date.new(@year.to_i)
  e = Date.new(@year.to_i, 12, 31)
  table[:cached_nomenclature_date].between(s..e)
end

#year_range_facet ⇒ Object 



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# File 'lib/queries/taxon_name/filter.rb', line 702

def year_range_facet
  return nil if year_end.nil? && year_start.nil?
  s, e = [year_start, year_end].compact
  ::TaxonName.where(cached_nomenclature_date: (s..e))
end